NSCC Concepts of Biology BIOL 1046 & 1047

NSCC Concepts of Biology BIOL 1046 & 1047

NSCC Edition

Charles Molnar, Jane Gair, Jung Choi, Mary Ann Clark, and Matthew Douglas

Contents

1

Preface to the original textbook, by OpenStax College

Charles Molnar and Jane Gair

Concepts of Biology is intended for the introductory biology course for non-science majors taught at most two- and four-year colleges. The scope, sequence, and level of the program are designed to match typical course syllabi. This text includes interesting features that make connections between scientific concepts and the everyday world of students. Concepts of Biology conveys the major themes of biology, such as a foundation in evolution, and features a rich and engaging art program.

Welcome to Concepts of Biology, an OpenStax College resource. This textbook has been created with several goals in mind: accessibility, customization, and student engagement—all while encouraging students toward high levels of academic scholarship. Instructors and students alike will find that this textbook offers a strong introduction to biology in an accessible format.

About OpenStax College

OpenStax College is a non-profit organization committed to improving student access to quality learning materials. Our free textbooks are developed and peer-reviewed by educators to ensure they are readable, accurate, and meet the scope and sequence requirements of today’s college courses. Unlike traditional textbooks, OpenStax College resources live online and are owned by the community of educators using them. Through our partnerships with companies and foundations committed to reducing costs for students, OpenStax College is working to improve access to higher education for all. OpenStax College is an initiative of Rice University and is made possible through the generous support of several philanthropic foundations.

About OpenStax College’s Resources

OpenStax College resources provide quality academic instruction. Three key features set our materials apart from others: they can be customized by instructors for each class, they are a “living” resource that grows online through contributions from science educators, and they are available free or for minimal cost.

Customization

OpenStax College learning resources are designed to be customized for each course. Our textbooks provide a solid foundation on which instructors can build, and our resources are conceived and written with flexibility in mind. Instructors can select the sections most relevant to their curricula and create a textbook that speaks directly to the needs of their classes and student body. Teachers are encouraged to expand on existing examples by adding unique context via geographically localized applications and topical connections.

Concepts of Biology can be easily customized using our online platform. Simply select the content most relevant to your syllabus and create a textbook that speaks directly to the needs of your class. Concepts of Biology is organized as a collection of sections that can be rearranged, modified, and enhanced through localized examples or to incorporate a specific theme of your course. This customization feature will help bring biology to life for your students and will ensure that your textbook truly reflects the goals of your course.

Curation

To broaden access and encourage community curation, Concepts of Biology is “open source” licensed under a Creative Commons Attribution (CC-BY) license. The scientific community is invited to submit examples, emerging research, and other feedback to enhance and strengthen the material and keep it current and relevant for today’s students. Submit your suggestions to info@openstaxcollege.org, and check in on edition status, alternate versions, errata, and news on the StaxDash at http://openstaxcollege.org.

Cost

Our textbooks are available for free online, and in low-cost print and e-book editions.

About Concepts of Biology

Concepts of Biology is designed for the single-semester introduction to biology course for non-science majors, which for many students is their only college-level science course. As such, this course represents an important opportunity for students to develop the necessary knowledge, tools, and skills to make informed decisions as they continue with their lives. Rather than being mired down with facts and vocabulary, the typical non-science major student needs information presented in a way that is easy to read and understand. Even more importantly, the content should be meaningful. Students do much better when they understand why biology is relevant to their everyday lives. For these reasons, Concepts of Biology is grounded on an evolutionary basis and includes exciting features that highlight careers in the biological sciences and everyday applications of the concepts at hand. We also strive to show the interconnectedness of topics within this extremely broad discipline. In order to meet the needs of today’s instructors and students, we maintain the overall organization and coverage found in most syllabi for this course. A strength of Concepts of Biology is that instructors can customize the book, adapting it to the approach that works best in their classroom. Concepts of Biology also includes an innovative art program that incorporates critical thinking and clicker questions to help students understand—and apply—key concepts.

Coverage and Scope

Our Concepts of Biology textbook adheres to the scope and sequence of most one-semester non-majors courses nationwide. We also strive to make biology, as a discipline, interesting and accessible to students. In addition to a comprehensive coverage of core concepts and foundational research, we have incorporated features that draw learners into the discipline in meaningful ways. Our scope of content was developed after surveying over a hundred biology professors and listening to their coverage needs. We provide a thorough treatment of biology’s fundamental concepts with a scope that is manageable for instructors and students alike.

  • Unit 1: The Cellular Foundation of Life. Our opening unit introduces students to the sciences, including the process of science and the underlying concepts from the physical sciences that provide a framework within which learners comprehend biological processes. Additionally, students will gain solid understanding of the structures, functions, and processes of the most basic unit of life: the cell.
  • Unit 2: Cell Division and Genetics. Our genetics unit takes learners from the foundations of cellular reproduction to the experiments that revealed the basis of genetics and laws of inheritance.
  • Unit 3: Molecular Biology and Biotechnology. Students will learn the intricacies of DNA, protein synthesis, and gene regulation and current applications of biotechnology and genomics.
  • Unit 4: Evolution and the Diversity of Life. The core concepts of evolution are discussed in this unit with examples illustrating evolutionary processes. Additionally, the evolutionary basis of biology reappears throughout the textbook in general discussion and is reinforced through special call-out features highlighting specific evolution-based topics. The diversity of life is explored with detailed study of various organisms and discussion of emerging phylogenetic relationships between and among bacteria, protist kingdoms, fungi, plants, and animals.
  • Unit 5: Animal Structure and Function. An introduction to the form and function of the animal body is followed by chapters on the immune system and animal development. This unit touches on the biology of all organisms while maintaining an engaging focus on human anatomy and physiology that helps students connect to the topics.
  • Unit 6: Ecology. Ecological concepts are broadly covered in this unit, with features highlighting localized, real-world issues of conservation and biodiversity.

Pedagogical Foundation and Features

Because of the impact science has on students and society, an important goal of science education is to achieve a scientifically literate population that consistently makes informed decisions. Scientific literacy transcends a basic understanding of scientific principles and processes to include the ability to make sense of the myriad instances where people encounter science in day-to-day life. Thus, a scientifically literate person is one who uses science content knowledge to make informed decisions, either personally or socially, about topics or issues that have a connection with science. Concepts of Biology is grounded on a solid scientific base and designed to promote scientific literacy. Throughout the text, you will find features that engage the students in scientific inquiry by taking selected topics a step further.

  • Evolution in Action features uphold the importance of evolution to all biological study through discussions like “Global Decline of Coral Reefs” and “The Red Queen Hypothesis.”
  • Career in Action features present information on a variety of careers in the biological sciences, introducing students to the educational requirements and day-to-day work life of a variety of professions, such as forensic scientists, registered dietitians, and biogeographers.
  • Biology in Action features tie biological concepts to emerging issues and discuss science in terms of everyday life. Topics include “Invasive Species” and “Photosynthesis at the Grocery Store.”

Art and Animations that Engage

Our art program takes a straightforward approach designed to help students learn the concepts of biology through simple, effective illustrations, photos, and micrographs. Concepts of Biology also incorporates links to relevant animations and interactive exercises that help bring biology to life for students.

  • Concepts in Action features direct students to online interactive exercises and animations to add a fuller context and examples to core content.

About Our Team

Concepts of Biology would not be possible if not for the tremendous contributions of the authors and community reviewing team

Senior Contributors

  • Samantha Fowler, Clayton State University
  • Rebecca Roush, Sandhills Community College
  • James Wise, Hampton University

Faculty Contributors and Reviewers

  • Mark Belk, Brigham Young University
  • Lisa Boggs, Southwestern Oklahoma State University
  • Sherryl Broverman, Duke University
  • David Byres, Florida State College at Jacksonville
  • Aaron Cassill, The University of Texas at San Antonio
  • Karen Champ, College of Central Florida
  • Sue Chaplin, University of St. Thomas
  • Diane Day, Clayton State University
  • Jean DeSaix, University of North Carolina at Chapel Hill
  • David Hunnicutt, St. Norbert College
  • Barbara Kuehner, Hawaii Community College
  • Brenda Leady, University of Toledo
  • Bernie Marcus, Genesee Community College
  • Flora Mhlanga, Lipscomb University
  • Madeline Mignone, Dominican College
  • Elizabeth Nash, Long Beach City College
  • Mark Newton, San Jose City College
  • Diana Oliveras, University of Colorado Boulder
  • Ann Paterson, Williams Baptist College
  • Joel Piperberg, Millersville University
  • Nick Reeves, Mt. San Jacinto College
  • Ann Reisenauer, San Jose State University
  • Lynn Rumfelt, Gordon College
  • Michael Rutledge, Middle Tennessee State University
  • Edward Saiff, Ramapo College of New Jersey
  • Brian Shmaefsky, Kingwood College
  • Gary Shultz, Marshall University
  • Donald Slish, SUNY Plattsburgh
  • Anh-Hue Tu, Georgia Southwestern State University
  • Elena Zoubina, Bridgewater State University

2

Preface to the 1st Canadian Edition

Charles Molnar and Jane Gair

Preface to the 1st Canadian Edition, by Charles Molnar and Jane Gair, adapters of Concepts of Biology

In this survey text, directed at those not majoring in biology, we dispel the assumption that a little learning is a dangerous thing. We hope that by skimming the surface of a very deep subject, biology, we may inspire you to drink more deeply and make more informed choices relating to your health, the environment, politics, and the greatest subject that all of us are entwined in, life itself.

In the adapted textbook, Concepts of Biology — 1st Canadian Edition, you will find the following units:

Adaptations to the original textbook Concepts of Biology by OpenStax College include:

Thanks to BCcampus and Camosun College for funding and support. We are most grateful to the Let’s Talk Science organization from their trove of science links.

I

Chapter 1: Introduction to Biology

""
Figure 1.1 This NASA image is a composite of several satellite-based views of Earth. To make the whole-Earth image, NASA scientists combine observations of different parts of the planet. (credit: modification of work by NASA)

Viewed from space, Earth offers few clues about the diversity of life forms that reside there. The first forms of life on Earth are thought to have been microorganisms that existed for billions of years before plants and animals appeared. The mammals, birds, and flowers so familiar to us are all relatively recent, originating 130 to 200 million years ago. Humans have inhabited this planet for only the last 2.5 million years, and only in the last 200,000 years have humans started looking like we do today.

Introduction to Interactive Learning

The goal of interactive learning is to promote engagement with and retention of the concepts and information being studied. The interactive learning activities in this open textbook support self directed practice and are not recorded assessments. Use the interactive learning activities to:

Watch an introduction to interactive videos

An interactive H5P element has been excluded from this version of the text. You can view it online here:
https://pressbooks.nscc.ca/conceptsofbiologynscc/?p=23#h5p-1

Search for Key Points in Chapter 1

Get to know your open textbook.

An interactive H5P element has been excluded from this version of the text. You can view it online here:
https://pressbooks.nscc.ca/conceptsofbiologynscc/?p=23#h5p-2

Media Attributions

1

1.1 Themes and Concepts of Biology

Charles Molnar and Jane Gair

Learning Objectives

By the end of this section, you will be able to:

  • Identify and describe the properties of life
  • Describe the levels of organization among living things
  • List examples of different sub disciplines in biology

Watch a video about Evolution by Natural Selection.

An interactive H5P element has been excluded from this version of the text. You can view it online here:
https://pressbooks.nscc.ca/conceptsofbiologynscc/?p=39#h5p-3

Biology is the science that studies life. What exactly is life? This may sound like a silly question with an obvious answer, but it is not easy to define life. For example, a branch of biology called virology studies viruses, which exhibit some of the characteristics of living entities but lack others. It turns out that although viruses can attack living organisms, cause diseases, and even reproduce, they do not meet the criteria that biologists use to define life.

From its earliest beginnings, biology has wrestled with four questions: What are the shared properties that make something “alive”? How do those various living things function? When faced with the remarkable diversity of life, how do we organize the different kinds of organisms so that we can better understand them? And, finally—what biologists ultimately seek to understand—how did this diversity arise and how is it continuing? As new organisms are discovered every day, biologists continue to seek answers to these and other questions.

Properties of Life

All groups of living organisms share multiple key characteristics or functions: order, sensitivity or response to stimuli, reproduction, adaptation, growth and development, regulation, homeostasis, and energy processing. When viewed together, these eight characteristics serve to define life.

Order

Organisms are highly organized structures that consist of one or more cells. Even very simple, single-celled organisms are remarkably complex. Inside each cell, atoms make up molecules. These in turn make up cell components or organelles. Multicellular organisms, which may consist of millions of individual cells, have an advantage over single-celled organisms in that their cells can be specialized to perform specific functions, and even sacrificed in certain situations for the good of the organism as a whole. How these specialized cells come together to form organs such as the heart, lung, or skin in organisms like the toad shown in Figure 1. 2 will be discussed later.

A photo shows a light-colored toad covered in bright green spots.
Figure 1.2 A toad represents a highly organized structure consisting of cells, tissues, organs, and organ systems.

Sensitivity or Response to Stimuli

Organisms respond to diverse stimuli. For example, plants can bend toward a source of light or respond to touch. Even tiny bacteria can move toward or away from chemicals (a process called chemotaxis) or light (phototaxis). Movement toward a stimulus is considered a positive response, while movement away from a stimulus is considered a negative response.

 
A photograph of the Mimosa pudica shows a plant with many tiny leaves.
Figure 1.3 The leaves of this sensitive plant (Mimosa pudica) will instantly droop and fold when touched. After a few minutes, the plant returns to its normal state.

Concept in Action


QR Code representing a URL

Watch this video to see how the sensitive plant responds to a touch stimulus.

Reproduction

Single-celled organisms reproduce by first duplicating their DNA, which is the genetic material, and then dividing it equally as the cell prepares to divide to form two new cells. Many multicellular organisms (those made up of more than one cell) produce specialized reproductive cells that will form new individuals. When reproduction occurs, DNA containing genes is passed along to an organism’s offspring. These genes are the reason that the offspring will belong to the same species and will have characteristics similar to the parent, such as fur color and blood type.

Adaptation

All living organisms exhibit a “fit” to their environment. Biologists refer to this fit as adaptation and it is a consequence of evolution by natural selection, which operates in every lineage of reproducing organisms. Examples of adaptations are diverse and unique, from heat-resistant Archaea that live in boiling hot springs to the tongue length of a nectar-feeding moth that matches the size of the flower from which it feeds. All adaptations enhance the reproductive potential of the individual exhibiting them, including their ability to survive to reproduce. Adaptations are not constant. As an environment changes, natural selection causes the characteristics of the individuals in a population to track those changes.

Growth and Development

Organisms grow and develop according to specific instructions coded for by their genes. These genes provide instructions that will direct cellular growth and development, ensuring that a species’ young will grow up to exhibit many of the same characteristics as its parents.

A photograph depicts four kittens: one has an orange and white tabby coat, another is entirely black, the third and fourth have a black, white and orange tabby coat but with different patterning.
Figure 1.4 Although no two look alike, these kittens have inherited genes from both parents and share many of the same characteristics.

Regulation

Even the smallest organisms are complex and require multiple regulatory mechanisms to coordinate internal functions, such as the transport of nutrients, response to stimuli, and coping with environmental stresses. For example, organ systems such as the digestive or circulatory systems perform specific functions like carrying oxygen throughout the body, removing wastes, delivering nutrients to every cell, and cooling the body.

Homeostasis

To function properly, cells require appropriate conditions such as proper temperature, pH, and concentrations of diverse chemicals. These conditions may, however, change from one moment to the next. Organisms are able to maintain internal conditions within a narrow range almost constantly, despite environmental changes, through a process called homeostasis or “steady state”—the ability of an organism to maintain constant internal conditions. For example, many organisms regulate their body temperature in a process known as thermoregulation. Organisms that live in cold climates, such as the polar bear, have body structures that help them withstand low temperatures and conserve body heat. In hot climates, organisms have methods (such as perspiration in humans or panting in dogs) that help them to shed excess body heat.

This photo shows a white, furry polar bear.
Figure 1.5 Polar bears and other mammals living in ice-covered regions maintain their body temperature by generating heat and reducing heat loss through thick fur and a dense layer of fat under their skin.

Energy Processing

All organisms (such as the California condor shown in Figure 1.6) use a source of energy for their metabolic activities. Some organisms capture energy from the sun and convert it into chemical energy in food; others use chemical energy from molecules they take in.

This photo shows a California condor in flight with a tag on its wing.
Figure 1.6 A lot of energy is required for a California condor to fly. Chemical energy derived from food is used to power flight. California condors are an endangered species; scientists have strived to place a wing tag on each bird to help them identify and locate each individual bird.

Levels of Organization of Living Things

Living things are highly organized and structured, following a hierarchy on a scale from small to large. The atom is the smallest and most fundamental unit of matter. It consists of a nucleus surrounded by electrons. Atoms form molecules. A molecule is a chemical structure consisting of at least two atoms held together by a chemical bond. Many molecules that are biologically important are macromolecules, large molecules that are typically formed by combining smaller units called monomers. An example of a macromolecule is deoxyribonucleic acid (DNA), which contains the instructions for the functioning of the organism that contains it.

Molecular model depicts a DNA molecule, showing its double helix structure.
Figure 1.7 A molecule, like this large DNA molecule, is composed of atoms.

Concept in Action


QR Code representing a URL

To see an animation of this DNA molecule, click here.

Some cells contain aggregates of macromolecules surrounded by membranes; these are called organelles. Organelles are small structures that exist within cells and perform specialized functions. All living things are made of cells; the cell itself is the smallest fundamental unit of structure and function in living organisms. (This requirement is why viruses are not considered living: they are not made of cells. To make new viruses, they have to invade and hijack a living cell; only then can they obtain the materials they need to reproduce.) Some organisms consist of a single cell and others are multicellular. Cells are classified as prokaryotic or eukaryotic. Prokaryotes are single-celled organisms that lack organelles surrounded by a membrane and do not have nuclei surrounded by nuclear membranes; in contrast, the cells of eukaryotes do have membrane-bound organelles and nuclei.

In most multicellular organisms, cells combine to make tissues, which are groups of similar cells carrying out the same function. Organs are collections of tissues grouped together based on a common function. Organs are present not only in animals but also in plants. An organ system is a higher level of organization that consists of functionally related organs. For example vertebrate animals have many organ systems, such as the circulatory system that transports blood throughout the body and to and from the lungs; it includes organs such as the heart and blood vessels. Organisms are individual living entities. For example, each tree in a forest is an organism. Single-celled prokaryotes and single-celled eukaryotes are also considered organisms and are typically referred to as microorganisms.

A flow chart shows the hierarchy of living organisms. From smallest to largest, this hierarchy includes: 1 An atom, with protons, neutrons and electrons. 2 Molecules such as the phospholipid shown, made up of atoms. 3 Organelles, such as Golgi apparatus and nuclei, that exist inside cells. 4 Cells, such as a red blood cell. 5 Tissues, such as human skin tissue. 6 Organs such as the stomach and intestine make up the human digestive system, an example of an organ system. 7 Organisms, populations and communities. In a park, each person is an organism. Together, all the people make up a population. All the plant and animal species in the park comprise a community. 8 Ecosystems: The ecosystem of Central Park in New York includes living organisms and the environment in which they live. 9 The biosphere: encompasses all the ecosystems on Earth.
Figure 1.8 From an atom to the entire Earth, biology examines all aspects of life.

Which of the following statements is false?

  1. Tissues exist within organs which exist within organ systems.
  2. Communities exist within populations which exist within ecosystems.
  3. Organelles exist within cells which exist within tissues.
  4. Communities exist within ecosystems which exist in the biosphere.

All the individuals of a species living within a specific area are collectively called a population. For example, a forest may include many white pine trees. All of these pine trees represent the population of white pine trees in this forest. Different populations may live in the same specific area. For example, the forest with the pine trees includes populations of flowering plants and also insects and microbial populations. A community is the set of populations inhabiting a particular area. For instance, all of the trees, flowers, insects, and other populations in a forest form the forest’s community. The forest itself is an ecosystem. An ecosystem consists of all the living things in a particular area together with the abiotic, or non-living, parts of that environment such as nitrogen in the soil or rainwater. At the highest level of organization, the biosphere is the collection of all ecosystems, and it represents the zones of life on Earth. It includes land, water, and portions of the atmosphere.

The Diversity of Life

The science of biology is very broad in scope because there is a tremendous diversity of life on Earth. The source of this diversity is evolution, the process of gradual change during which new species arise from older species. Evolutionary biologists study the evolution of living things in everything from the microscopic world to ecosystems.

In the 18th century, a scientist named Carl Linnaeus first proposed organizing the known species of organisms into a hierarchical taxonomy. In this system, species that are most similar to each other are put together within a grouping known as a genus. Furthermore, similar genera (the plural of genus) are put together within a family. This grouping continues until all organisms are collected together into groups at the highest level. The current taxonomic system now has eight levels in its hierarchy, from lowest to highest, they are: species, genus, family, order, class, phylum, kingdom, and domain. Thus species are grouped within genera, genera are grouped within families, families are grouped within orders, and so on.

A chart shows the eight levels of taxonomic hierarchy for the dog, Canis lupus.
Figure 1.9 This diagram shows the levels of taxonomic hierarchy for a dog, from the broadest category—domain—to the most specific—species.

The highest level, domain, is a relatively new addition to the system since the 1990s. Scientists now recognize three domains of life, the Eukarya, the Archaea, and the Bacteria. The domain Eukarya contains organisms that have cells with nuclei. It includes the kingdoms of fungi, plants, animals, and several kingdoms of protists. The Archaea, are single-celled organisms without nuclei and include many extremophiles that live in harsh environments like hot springs. The Bacteria are another quite different group of single-celled organisms without nuclei. Both the Archaea and the Bacteria are prokaryotes, an informal name for cells without nuclei. The recognition in the 1990s that certain “bacteria,” now known as the Archaea, were as different genetically and biochemically from other bacterial cells as they were from eukaryotes, motivated the recommendation to divide life into three domains. This dramatic change in our knowledge of the tree of life demonstrates that classifications are not permanent and will change when new information becomes available.

In addition to the hierarchical taxonomic system, Linnaeus was the first to name organisms using two unique names, now called the binomial naming system. Before Linnaeus, the use of common names to refer to organisms caused confusion because there were regional differences in these common names. Binomial names consist of the genus name (which is capitalized) and the species name (all lower-case). Both names are set in italics when they are printed. Every species is given a unique binomial which is recognized the world over, so that a scientist in any location can know which organism is being referred to. For example, the North American blue jay is known uniquely as Cyanocitta cristata. Our own species is Homo sapiens.

Photos depict: A: bacterial cells. B: a natural hot vent. C: a sunflower. D: a lion.
Figure 1.10 These images represent different domains. The scanning electron micrograph shows (a) bacterial cells belong to the domain Bacteria, while the (b) extremophiles, seen all together as colored mats in this hot spring, belong to domain Archaea. Both the (c) sunflower and (d) lion are part of domain Eukarya.

Evolution in Action

Carl Woese and the Phylogenetic Tree

The evolutionary relationships of various life forms on Earth can be summarized in a phylogenetic tree. A phylogenetic tree is a diagram showing the evolutionary relationships among biological species based on similarities and differences in genetic or physical traits or both. A phylogenetic tree is composed of branch points, or nodes, and branches. The internal nodes represent ancestors and are points in evolution when, based on scientific evidence, an ancestor is thought to have diverged to form two new species. The length of each branch can be considered as estimates of relative time.

In the past, biologists grouped living organisms into five kingdoms: animals, plants, fungi, protists, and bacteria. The pioneering work of American microbiologist Carl Woese in the early 1970s has shown, however, that life on Earth has evolved along three lineages, now called domains—Bacteria, Archaea, and Eukarya. Woese proposed the domain as a new taxonomic level and Archaea as a new domain, to reflect the new phylogenetic tree. Many organisms belonging to the Archaea domain live under extreme conditions and are called extremophiles. To construct his tree, Woese used genetic relationships rather than similarities based on morphology (shape). Various genes were used in phylogenetic studies. Woese’s tree was constructed from comparative sequencing of the genes that are universally distributed, found in some slightly altered form in every organism, conserved (meaning that these genes have remained only slightly changed throughout evolution), and of an appropriate length.

This phylogenetic tree shows that the three domains of life, bacteria, archaea and eukarya, all arose from a common ancestor.
Figure 1.11 This phylogenetic tree was constructed by microbiologist Carl Woese using genetic relationships. The tree shows the separation of living organisms into three domains: Bacteria, Archaea, and Eukarya. Bacteria and Archaea are organisms without a nucleus or other organelles surrounded by a membrane and, therefore, are prokaryotes.

Branches of Biological Study

Watch a video about Science and Medicine

An interactive H5P element has been excluded from this version of the text. You can view it online here:
https://pressbooks.nscc.ca/conceptsofbiologynscc/?p=39#h5p-4

The scope of biology is broad and therefore contains many branches and sub disciplines. Biologists may pursue one of those sub disciplines and work in a more focused field. For instance, molecular biology studies biological processes at the molecular level, including interactions among molecules such as DNA, RNA, and proteins, as well as the way they are regulated. Microbiology is the study of the structure and function of microorganisms. It is quite a broad branch itself, and depending on the subject of study, there are also microbial physiologists, ecologists, and geneticists, among others.

Another field of biological study, neurobiology, studies the biology of the nervous system, and although it is considered a branch of biology, it is also recognized as an interdisciplinary field of study known as neuroscience. Because of its interdisciplinary nature, this sub discipline studies different functions of the nervous system using molecular, cellular, developmental, medical, and computational approaches.

Photo depicts scientists digging fossils out of the dirt.
Figure 1.12 Researchers work on excavating dinosaur fossils at a site in Castellón, Spain.

Paleontology, another branch of biology, uses fossils to study life’s history. Zoology and botany are the study of animals and plants, respectively. Biologists can also specialize as biotechnologists, ecologists, or physiologists, to name just a few areas. Biotechnologists apply the knowledge of biology to create useful products. Ecologists study the interactions of organisms in their environments. Physiologists study the workings of cells, tissues and organs. This is just a small sample of the many fields that biologists can pursue. From our own bodies to the world we live in, discoveries in biology can affect us in very direct and important ways. We depend on these discoveries for our health, our food sources, and the benefits provided by our ecosystem. Because of this, knowledge of biology can benefit us in making decisions in our day-to-day lives.

The development of technology in the twentieth century that continues today, particularly the technology to describe and manipulate the genetic material, DNA, has transformed biology. This transformation will allow biologists to continue to understand the history of life in greater detail, how the human body works, our human origins, and how humans can survive as a species on this planet despite the stresses caused by our increasing numbers. Biologists continue to decipher huge mysteries about life suggesting that we have only begun to understand life on the planet, its history, and our relationship to it. For this and other reasons, the knowledge of biology gained through this textbook and other printed and electronic media should be a benefit in whichever field you enter.

Forensic Scientist

Forensic science is the application of science to answer questions related to the law. Biologists as well as chemists and biochemists can be forensic scientists. Forensic scientists provide scientific evidence for use in courts, and their job involves examining trace material associated with crimes. Interest in forensic science has increased in the last few years, possibly because of popular television shows that feature forensic scientists on the job. Also, the development of molecular techniques and the establishment of DNA databases have updated the types of work that forensic scientists can do. Their job activities are primarily related to crimes against people such as murder, rape, and assault. Their work involves analyzing samples such as hair, blood, and other body fluids and also processing DNA found in many different environments and materials. Forensic scientists also analyze other biological evidence left at crime scenes, such as insect parts or pollen grains. Students who want to pursue careers in forensic science will most likely be required to take chemistry and biology courses as well as some intensive math courses.

Photo depicts a scientist working in a lab.
Figure 1.13 This forensic scientist works in a DNA extraction room at the U.S. Army Criminal Investigation Laboratory.

Section Summary

Biology is the science of life. All living organisms share several key properties such as order, sensitivity or response to stimuli, reproduction, adaptation, growth and development, regulation, homeostasis, and energy processing. Living things are highly organized following a hierarchy that includes atoms, molecules, organelles, cells, tissues, organs, and organ systems. Organisms, in turn, are grouped as populations, communities, ecosystems, and the biosphere. Evolution is the source of the tremendous biological diversity on Earth today. A diagram called a phylogenetic tree can be used to show evolutionary relationships among organisms. Biology is very broad and includes many branches and sub disciplines. Examples include molecular biology, microbiology, neurobiology, zoology, and botany, among others.

Exercises

An interactive H5P element has been excluded from this version of the text. You can view it online here:
https://pressbooks.nscc.ca/conceptsofbiologynscc/?p=39#h5p-5

Glossary

atom: a basic unit of matter that cannot be broken down by normal chemical reactions

biology: the study of living organisms and their interactions with one another and their environments

biosphere: a collection of all ecosystems on Earth

cell: the smallest fundamental unit of structure and function in living things

community: a set of populations inhabiting a particular area

ecosystem: all living things in a particular area together with the abiotic, nonliving parts of that environment

eukaryote: an organism with cells that have nuclei and membrane-bound organelles

evolution: the process of gradual change in a population that can also lead to new species arising from older species

homeostasis: the ability of an organism to maintain constant internal conditions

macromolecule: a large molecule typically formed by the joining of smaller molecules

molecule: a chemical structure consisting of at least two atoms held together by a chemical bond

organ: a structure formed of tissues operating together to perform a common function

organ system: the higher level of organization that consists of functionally related organs

organelle: a membrane-bound compartment or sac within a cell

organism: an individual living entity

phylogenetic tree: a diagram showing the evolutionary relationships among biological species based on similarities and differences in genetic or physical traits or both

population: all individuals within a species living within a specific area

prokaryote: a unicellular organism that lacks a nucleus or any other membrane-bound organelle

tissue: a group of similar cells carrying out the same function

Media Attribution

2

1.2 The Process of Science

Charles Molnar and Jane Gair

Learning Objectives

By the end of this section, you will be able to:

  • Identify the shared characteristics of the natural sciences
  • Understand the process of scientific inquiry
  • Compare inductive reasoning with deductive reasoning
  • Describe the goals of basic science and applied science
Watch a video about the Scientific Method.

An interactive H5P element has been excluded from this version of the text. You can view it online here:
https://pressbooks.nscc.ca/conceptsofbiologynscc/?p=47#h5p-6

Photo A depicts round colonies of blue-green algae. Photo B depicts round fossil structures called stromatalites along a watery shoreline.
Figure 1.14 Formerly called blue-green algae, the (a) cyanobacteria seen through a light microscope are some of Earth’s oldest life forms. These (b) stromatolites along the shores of Lake Thetis in Western Australia are ancient structures formed by the layering of cyanobacteria in shallow waters.

Like geology, physics, and chemistry, biology is a science that gathers knowledge about the natural world. Specifically, biology is the study of life. The discoveries of biology are made by a community of researchers who work individually and together using agreed-on methods. In this sense, biology, like all sciences is a social enterprise like politics or the arts. The methods of science include careful observation, record keeping, logical and mathematical reasoning, experimentation, and submitting conclusions to the scrutiny of others. Science also requires considerable imagination and creativity; a well-designed experiment is commonly described as elegant, or beautiful. Like politics, science has considerable practical implications and some science is dedicated to practical applications, such as the prevention of disease. Other science proceeds largely motivated by curiosity. Whatever its goal, there is no doubt that science, including biology, has transformed human existence and will continue to do so.

Scanning electronic micrograph depicts E. coli bacteria aggregated together.
Figure 1.15 Biologists may choose to study Escherichia coli (E. coli), a bacterium that is a normal resident of our digestive tracts but which is also sometimes responsible for disease outbreaks. In this micrograph, the bacterium is visualized using a scanning electron microscope and digital colorization.

The Nature of Science

Watch a video about the reductional approach of western science.

 

An interactive H5P element has been excluded from this version of the text. You can view it online here:
https://pressbooks.nscc.ca/conceptsofbiologynscc/?p=47#h5p-7

Biology is a science, but what exactly is science? What does the study of biology share with other scientific disciplines? Science (from the Latin scientia, meaning “knowledge”) can be defined as knowledge about the natural world.

Science is a very specific way of learning, or knowing, about the world. The history of the past 500 years demonstrates that science is a very powerful way of knowing about the world; it is largely responsible for the technological revolutions that have taken place during this time. There are however, areas of knowledge and human experience that the methods of science cannot be applied to. These include such things as answering purely moral questions, aesthetic questions, or what can be generally categorized as spiritual questions. Science has cannot investigate these areas because they are outside the realm of material phenomena, the phenomena of matter and energy, and cannot be observed and measured.

The scientific method is a method of research with defined steps that include experiments and careful observation. The steps of the scientific method will be examined in detail later, but one of the most important aspects of this method is the testing of hypotheses. A hypothesis is a suggested explanation for an event, which can be tested. Hypotheses, or tentative explanations, are generally produced within the context of a scientific theory. A scientific theory is a generally accepted, thoroughly tested and confirmed explanation for a set of observations or phenomena. Scientific theory is the foundation of scientific knowledge. In addition, in many scientific disciplines (less so in biology) there are scientific laws, often expressed in mathematical formulas, which describe how elements of nature will behave under certain specific conditions. There is not an evolution of hypotheses through theories to laws as if they represented some increase in certainty about the world. Hypotheses are the day-to-day material that scientists work with and they are developed within the context of theories. Laws are concise descriptions of parts of the world that are amenable to formulaic or mathematical description.

Natural Sciences

What would you expect to see in a museum of natural sciences? Frogs? Plants? Dinosaur skeletons? Exhibits about how the brain functions? A planetarium? Gems and minerals? Or maybe all of the above? Science includes such diverse fields as astronomy, biology, computer sciences, geology, logic, physics, chemistry, and mathematics. However, those fields of science related to the physical world and its phenomena and processes are considered natural sciences. Thus, a museum of natural sciences might contain any of the items listed above.

 
Some fields of science include astronomy, biology, computer science, geology, logic, physics, chemistry, and mathematics. (credit: "Image Editor/Flickr)"
Figure 1.16 Some fields of science include astronomy, biology, computer science, geology, logic, physics, chemistry, and mathematics.

There is no complete agreement when it comes to defining what the natural sciences include. For some experts, the natural sciences are astronomy, biology, chemistry, earth science, and physics. Other scholars choose to divide natural sciences into life sciences, which study living things and include biology, and physical sciences, which study nonliving matter and include astronomy, physics, and chemistry. Some disciplines such as biophysics and biochemistry build on two sciences and are interdisciplinary.

Scientific Inquiry

One thing is common to all forms of science: an ultimate goal “to know.” Curiosity and inquiry are the driving forces for the development of science. Scientists seek to understand the world and the way it operates. Two methods of logical thinking are used: inductive reasoning and deductive reasoning.

Inductive reasoning is a form of logical thinking that uses related observations to arrive at a general conclusion. This type of reasoning is common in descriptive science. A life scientist such as a biologist makes observations and records them. These data can be qualitative (descriptive) or quantitative (consisting of numbers), and the raw data can be supplemented with drawings, pictures, photos, or videos. From many observations, the scientist can infer conclusions (inductions) based on evidence. Inductive reasoning involves formulating generalizations inferred from careful observation and the analysis of a large amount of data. Brain studies often work this way. Many brains are observed while people are doing a task. The part of the brain that lights up, indicating activity, is then demonstrated to be the part controlling the response to that task.

Deductive reasoning or deduction is the type of logic used in hypothesis-based science. In deductive reasoning, the pattern of thinking moves in the opposite direction as compared to inductive reasoning. Deductive reasoning is a form of logical thinking that uses a general principle or law to forecast specific results. From those general principles, a scientist can extrapolate and predict the specific results that would be valid as long as the general principles are valid. For example, a prediction would be that if the climate is becoming warmer in a region, the distribution of plants and animals should change. Comparisons have been made between distributions in the past and the present, and the many changes that have been found are consistent with a warming climate. Finding the change in distribution is evidence that the climate change conclusion is a valid one.

Both types of logical thinking are related to the two main pathways of scientific study: descriptive science and hypothesis-based science. Descriptive (or discovery) science aims to observe, explore, and discover, while hypothesis-based science begins with a specific question or problem and a potential answer or solution that can be tested. The boundary between these two forms of study is often blurred, because most scientific endeavors combine both approaches. Observations lead to questions, questions lead to forming a hypothesis as a possible answer to those questions, and then the hypothesis is tested. Thus, descriptive science and hypothesis-based science are in continuous dialogue.

Hypothesis Testing

Biologists study the living world by posing questions about it and seeking science-based responses. This approach is common to other sciences as well and is often referred to as the scientific method. The scientific method was used even in ancient times, but it was first documented by England’s Sir Francis Bacon (1561–1626), who set up inductive methods for scientific inquiry. The scientific method is not exclusively used by biologists but can be applied to almost anything as a logical problem-solving method.

Painting depicts Sir Francis Bacon in a long cloak.
Figure1.17 Sir Francis Bacon is credited with being the first to document the scientific method.

The scientific process typically starts with an observation (often a problem to be solved) that leads to a question. Let’s think about a simple problem that starts with an observation and apply the scientific method to solve the problem. One Monday morning, a student arrives at class and quickly discovers that the classroom is too warm. That is an observation that also describes a problem: the classroom is too warm. The student then asks a question: “Why is the classroom so warm?”

Recall that a hypothesis is a suggested explanation that can be tested. To solve a problem, several hypotheses may be proposed. For example, one hypothesis might be, “The classroom is warm because no one turned on the air conditioning.” But there could be other responses to the question, and therefore other hypotheses may be proposed. A second hypothesis might be, “The classroom is warm because there is a power failure, and so the air conditioning doesn’t work.”

Once a hypothesis has been selected, a prediction may be made. A prediction is similar to a hypothesis but it typically has the format “If . . . then . . . .” For example, the prediction for the first hypothesis might be, “If the student turns on the air conditioning, then the classroom will no longer be too warm.”

A hypothesis must be testable to ensure that it is valid. For example, a hypothesis that depends on what a bear thinks is not testable, because it can never be known what a bear thinks. It should also be falsifiable, meaning that it can be disproven by experimental results. An example of an unfalsifiable hypothesis is “Botticelli’s Birth of Venus is beautiful.” There is no experiment that might show this statement to be false. To test a hypothesis, a researcher will conduct one or more experiments designed to eliminate one or more of the hypotheses. This is important. A hypothesis can be disproven, or eliminated, but it can never be proven. Science does not deal in proofs like mathematics. If an experiment fails to disprove a hypothesis, then we find support for that explanation, but this is not to say that down the road a better explanation will not be found, or a more carefully designed experiment will be found to falsify the hypothesis.

Each experiment will have one or more variables and one or more controls. A variable is any part of the experiment that can vary or change during the experiment. A control is a part of the experiment that does not change. Look for the variables and controls in the example that follows. As a simple example, an experiment might be conducted to test the hypothesis that phosphate limits the growth of algae in freshwater ponds. A series of artificial ponds are filled with water and half of them are treated by adding phosphate each week, while the other half are treated by adding a salt that is known not to be used by algae. The variable here is the phosphate (or lack of phosphate), the experimental or treatment cases are the ponds with added phosphate and the control ponds are those with something inert added, such as the salt. Just adding something is also a control against the possibility that adding extra matter to the pond has an effect. If the treated ponds show lesser growth of algae, then we have found support for our hypothesis. If they do not, then we reject our hypothesis. Be aware that rejecting one hypothesis does not determine whether or not the other hypotheses can be accepted; it simply eliminates one hypothesis that is not valid . Using the scientific method, the hypotheses that are inconsistent with experimental data are rejected.

A flow chart shows the steps in the scientific method. In step 1, an observation is made. In step 2, a question is asked about the observation. In step 3, an answer to the question, called a hypothesis, is proposed. In step 4, a prediction is made based on the hypothesis. In step 5, an experiment is done to test the prediction. In step 6, the results are analyzed to determine whether or not the hypothesis is supported. If the hypothesis is not supported, another hypothesis is made. In either case, the results are reported.
Figure 1.18 The scientific method is a series of defined steps that include experiments and careful observation. If a hypothesis is not supported by data, a new hypothesis can be proposed.

In the example below, the scientific method is used to solve an everyday problem. Which part in the example below is the hypothesis? Which is the prediction? Based on the results of the experiment, is the hypothesis supported? If it is not supported, propose some alternative hypotheses.

  1. My toaster doesn’t toast my bread.
  2. Why doesn’t my toaster work?
  3. There is something wrong with the electrical outlet.
  4. If something is wrong with the outlet, my coffeemaker also won’t work when plugged into it.
  5. I plug my coffeemaker into the outlet.
  6. My coffeemaker works.

In practice, the scientific method is not as rigid and structured as it might at first appear. Sometimes an experiment leads to conclusions that favour a change in approach; often, an experiment brings entirely new scientific questions to the puzzle. Many times, science does not operate in a linear fashion; instead, scientists continually draw inferences and make generalizations, finding patterns as their research proceeds. Scientific reasoning is more complex than the scientific method alone suggests.

 

Watch a video about the progress of science.

An interactive H5P element has been excluded from this version of the text. You can view it online here:
https://pressbooks.nscc.ca/conceptsofbiologynscc/?p=47#h5p-4

Basic and Applied Science

The scientific community has been debating for the last few decades about the value of different types of science. Is it valuable to pursue science for the sake of simply gaining knowledge, or does scientific knowledge only have worth if we can apply it to solving a specific problem or bettering our lives? This question focuses on the differences between two types of science: basic science and applied science.

Basic science or “pure” science seeks to expand knowledge regardless of the short-term application of that knowledge. It is not focused on developing a product or a service of immediate public or commercial value. The immediate goal of basic science is knowledge for knowledge’s sake, though this does not mean that in the end it may not result in an application.

In contrast, applied science or “technology,” aims to use science to solve real-world problems, making it possible, for example, to improve a crop yield, find a cure for a particular disease, or save animals threatened by a natural disaster. In applied science, the problem is usually defined for the researcher.

Some individuals may perceive applied science as “useful” and basic science as “useless.” A question these people might pose to a scientist advocating knowledge acquisition would be, “What for?” A careful look at the history of science, however, reveals that basic knowledge has resulted in many remarkable applications of great value. Many scientists think that a basic understanding of science is necessary before an application is developed; therefore, applied science relies on the results generated through basic science. Other scientists think that it is time to move on from basic science and instead to find solutions to actual problems. Both approaches are valid. It is true that there are problems that demand immediate attention; however, few solutions would be found without the help of the knowledge generated through basic science.

One example of how basic and applied science can work together to solve practical problems occurred after the discovery of DNA structure led to an understanding of the molecular mechanisms governing DNA replication. Strands of DNA, unique in every human, are found in our cells, where they provide the instructions necessary for life. During DNA replication, new copies of DNA are made, shortly before a cell divides to form new cells. Understanding the mechanisms of DNA replication enabled scientists to develop laboratory techniques that are now used to identify genetic diseases, pinpoint individuals who were at a crime scene, and determine paternity. Without basic science, it is unlikely that applied science would exist.

Another example of the link between basic and applied research is the Human Genome Project, a study in which each human chromosome was analyzed and mapped to determine the precise sequence of DNA subunits and the exact location of each gene. (The gene is the basic unit of heredity; an individual’s complete collection of genes is his or her genome.) Other organisms have also been studied as part of this project to gain a better understanding of human chromosomes. The Human Genome Project  relied on basic research carried out with non-human organisms and, later, with the human genome. An important end goal eventually became using the data for applied research seeking cures for genetically related diseases.

The human genome project’s logo is shown, depicting a human being inside a DNA double helix. The words chemistry, biology, physics, ethics, informatics and engineering surround the circular image.
Figure 1.19 The Human Genome Project was a 13-year collaborative effort among researchers working in several different fields of science. The project was completed in 2003.

While research efforts in both basic science and applied science are usually carefully planned, it is important to note that some discoveries are made by serendipity, that is, by means of a fortunate accident or a lucky surprise. Penicillin was discovered when biologist Alexander Fleming accidentally left a petri dish of Staphylococcus bacteria open. An unwanted mold grew, killing the bacteria. The mold turned out to be Penicillium, and a new antibiotic was discovered. Even in the highly organized world of science, luck—when combined with an observant, curious mind—can lead to unexpected breakthroughs.

Reporting Scientific Work

Whether scientific research is basic science or applied science, scientists must share their findings for other researchers to expand and build upon their discoveries. Communication and collaboration within and between sub disciplines of science are key to the advancement of knowledge in science. For this reason, an important aspect of a scientist’s work is disseminating results and communicating with peers. Scientists can share results by presenting them at a scientific meeting or conference, but this approach can reach only the limited few who are present. Instead, most scientists present their results in peer-reviewed articles that are published in scientific journals. Peer-reviewed articles are scientific papers that are reviewed, usually anonymously by a scientist’s colleagues, or peers. These colleagues are qualified individuals, often experts in the same research area, who judge whether or not the scientist’s work is suitable for publication. The process of peer review helps to ensure that the research described in a scientific paper or grant proposal is original, significant, logical, and thorough. Grant proposals, which are requests for research funding, are also subject to peer review. Scientists publish their work so other scientists can reproduce their experiments under similar or different conditions to expand on the findings. The experimental results must be consistent with the findings of other scientists.

There are many journals and the popular press that do not use a peer-review system. A large number of online open-access journals, journals with articles available without cost, are now available many of which use rigorous peer-review systems, but some of which do not. Results of any studies published in these forums without peer review are not reliable and should not form the basis for other scientific work. In one exception, journals may allow a researcher to cite a personal communication from another researcher about unpublished results with the cited author’s permission.

Section Summary

Biology is the science that studies living organisms and their interactions with one another and their environments. Science attempts to describe and understand the nature of the universe in whole or in part. Science has many fields; those fields related to the physical world and its phenomena are considered natural sciences.

A hypothesis is a tentative explanation for an observation. A scientific theory is a well-tested and consistently verified explanation for a set of observations or phenomena. A scientific law is a description, often in the form of a mathematical formula, of the behaviour of an aspect of nature under certain circumstances. Two types of logical reasoning are used in science. Inductive reasoning uses results to produce general scientific principles. Deductive reasoning is a form of logical thinking that predicts results by applying general principles. The common thread throughout scientific research is the use of the scientific method. Scientists present their results in peer-reviewed scientific papers published in scientific journals.

Science can be basic or applied. The main goal of basic science is to expand knowledge without any expectation of short-term practical application of that knowledge. The primary goal of applied research, however, is to solve practical problems.

Exercises

An interactive H5P element has been excluded from this version of the text. You can view it online here:
https://pressbooks.nscc.ca/conceptsofbiologynscc/?p=47#h5p-8

Glossary

applied science: a form of science that solves real-world problems

basic science: science that seeks to expand knowledge regardless of the short-term application of that knowledge

control: a part of an experiment that does not change during the experiment

deductive reasoning: a form of logical thinking that uses a general statement to forecast specific results

descriptive science: a form of science that aims to observe, explore, and find things out

falsifiable: able to be disproven by experimental results

hypothesis: a suggested explanation for an event, which can be tested

hypothesis-based science: a form of science that begins with a specific explanation that is then tested

inductive reasoning: a form of logical thinking that uses related observations to arrive at a general conclusion

life science: a field of science, such as biology, that studies living things

natural science: a field of science that studies the physical world, its phenomena, and processes

peer-reviewed article: a scientific report that is reviewed by a scientist’s colleagues before publication

physical science: a field of science, such as astronomy, physics, and chemistry, that studies nonliving matter

science: knowledge that covers general truths or the operation of general laws, especially when acquired and tested by the scientific method

scientific law: a description, often in the form of a mathematical formula, for the behavior of some aspect of nature under certain specific conditions

scientific method: a method of research with defined steps that include experiments and careful observation

scientific theory: a thoroughly tested and confirmed explanation for observations or phenomena

variable: a part of an experiment that can vary or change

Media Attribution

II

Chapter 2: Introduction to the Chemistry of Life

Photo shows a variety of cheeses, fruits, and breads served on a tray.
Figure 2.1 Foods such as bread, fruit, and cheese are rich sources of biological macromolecules.

The elements carbon, hydrogen, nitrogen, oxygen, sulfur, and phosphorus are the key building blocks of the chemicals found in living things. They form the carbohydrates, nucleic acids, proteins, and lipids (all of which will be defined later in this chapter) that are the fundamental molecular components of all organisms. In this chapter, we will discuss these important building blocks and learn how the unique properties of the atoms of different elements affect their interactions with other atoms to form the molecules of life. These interactions determine what atoms combine and the ultimate shape of the molecules and macromolecules, that shape will determine their function.

Food provides an organism with nutrients—the matter it needs to survive. Many of these critical nutrients come in the form of biological macromolecules, or large molecules necessary for life. These macromolecules are built from different combinations of smaller organic molecules. What specific types of biological macromolecules do living things require? How are these molecules formed? What functions do they serve? In this chapter, we will explore these questions.

Search for Key Points in Chapter 2

An interactive H5P element has been excluded from this version of the text. You can view it online here:
https://pressbooks.nscc.ca/conceptsofbiologynscc/?p=50#h5p-9

Media Attribution

3

2.1 The Building Blocks of Molecules

Charles Molnar and Jane Gair

Learning Objectives

By the end of this section, you will be able to:

  • Describe matter and elements
  • Describe the interrelationship between protons, neutrons, and electrons, and the ways in which electrons can be donated or shared between atoms

Watch a video about electrons and how the electrons in chemical bonds influence the shape and function of molecules.

An interactive H5P element has been excluded from this version of the text. You can view it online here:
https://pressbooks.nscc.ca/conceptsofbiologynscc/?p=58#h5p-10

At its most fundamental level, life is made up of matter. Matter occupies space and has mass. All matter is composed of elements, substances that cannot be broken down or transformed chemically into other substances. Each element is made of atoms, each with a constant number of protons and unique properties. A total of 118 elements have been defined; however, only 92 occur naturally, and fewer than 30 are found in living cells. The remaining 26 elements are unstable and, therefore, do not exist for very long or are theoretical and have yet to be detected.

Each element is designated by its chemical symbol (such as H, N, O, C, and Na), and possesses unique properties. These unique properties allow elements to combine and to bond with each other in specific ways.

Atoms

An atom is the smallest component of an element that retains all of the chemical properties of that element. For example, one hydrogen atom has all of the properties of the element hydrogen, such as it exists as a gas at room temperature, and it bonds with oxygen to create a water molecule. Hydrogen atoms cannot be broken down into anything smaller while still retaining the properties of hydrogen. If a hydrogen atom were broken down into subatomic particles, it would no longer have the properties of hydrogen.

At the most basic level, all organisms are made of a combination of elements. They contain atoms that combine together to form molecules. In multicellular organisms, such as animals, molecules can interact to form cells that combine to form tissues, which make up organs. These combinations continue until entire multicellular organisms are formed.

All atoms contain protons, electrons, and neutrons. The only exception is hydrogen (H), which is made of one proton and one electron. A proton is a positively charged particle that resides in the nucleus (the core of the atom) of an atom and has a mass of 1 and a charge of +1. An electron is a negatively charged particle that travels in the space around the nucleus. In other words, it resides outside of the nucleus. It has a negligible mass and has a charge of –1.

Atoms are made up of protons and neutrons located within the nucleus, and electrons surrounding the nucleus.
Figure 2.2 Atoms are made up of protons and neutrons located within the nucleus, and electrons surrounding the nucleus.

Neutrons, like protons, reside in the nucleus of an atom. They have a mass of 1 and no charge. The positive (protons) and negative (electrons) charges balance each other in a neutral atom, which has a net zero charge.

Because protons and neutrons each have a mass of 1, the mass of an atom is equal to the number of protons and neutrons of that atom. The number of electrons does not factor into the overall mass, because their mass is so small.

As stated earlier, each element has its own unique properties. Each contains a different number of protons and neutrons, giving it its own atomic number and mass number. The atomic number of an element is equal to the number of protons that element contains. The mass number, or atomic mass, is the number of protons plus the number of neutrons of that element. Therefore, it is possible to determine the number of neutrons by subtracting the atomic number from the mass number.

These numbers provide information about the elements and how they will react when combined. Different elements have different melting and boiling points, and are in different states (liquid, solid, or gas) at room temperature. They also combine in different ways. Some form specific types of bonds, whereas others do not. How they combine is based on the number of electrons present. Because of these characteristics, the elements are arranged into the periodic table of elements, a chart of the elements that includes the atomic number and relative atomic mass of each element. The periodic table also provides key information about the properties of elements —often indicated by color-coding. The arrangement of the table also shows how the electrons in each element are organized and provides important details about how atoms will react with each other to form molecules.

Isotopes are different forms of the same element that have the same number of protons, but a different number of neutrons. Some elements, such as carbon, potassium, and uranium, have naturally occurring isotopes. Carbon-12, the most common isotope of carbon, contains six protons and six neutrons. Therefore, it has a mass number of 12 (six protons and six neutrons) and an atomic number of 6 (which makes it carbon). Carbon-14 contains six protons and eight neutrons. Therefore, it has a mass number of 14 (six protons and eight neutrons) and an atomic number of 6, meaning it is still the element carbon. These two alternate forms of carbon are isotopes. Some isotopes are unstable and will lose protons, other subatomic particles, or energy to form more stable elements. These are called radioactive isotopes or radioisotopes.

Periodic table of elements.
Figure 2.3 Arranged in columns and rows based on the characteristics of the elements, the periodic table provides key information about the elements and how they might interact with each other to form molecules. Most periodic tables provide a key or legend to the information they contain.

How many neutrons do (K) potassium-39 and potassium-40 have, respectively?

Evolution in Action

Carbon Dating

Carbon-14 (14C) is a naturally occurring radioisotope that is created in the atmosphere by cosmic rays. This is a continuous process, so more 14C is always being created. As a living organism develops, the relative level of 14C in its body is equal to the concentration of 14C in the atmosphere. When an organism dies, it is no longer ingesting 14C, so the ratio will decline. 14C decays to 14N by a process called beta decay; it gives off energy in this slow process.

After approximately 5,730 years, only one-half of the starting concentration of 14C will have been converted to 14N. The time it takes for half of the original concentration of an isotope to decay to its more stable form is called its half-life. Because the half-life of 14C is long, it is used to age formerly living objects, such as fossils. Using the ratio of the 14C concentration found in an object to the amount of 14C detected in the atmosphere, the amount of the isotope that has not yet decayed can be determined. Based on this amount, the age of the fossil can be calculated to about 50,000 years. Isotopes with longer half-lives, such as potassium-40, are used to calculate the ages of older fossils. Through the use of carbon dating, scientists can reconstruct the ecology and biogeography of organisms living within the past 50,000 years.

Photograph shows scientists digging pygmy mammoth skeleton fossils from the ground.
Figure 2.4 The age of remains that contain carbon and are less than about 50,000 years old, such as this pygmy mammoth, can be determined using carbon dating.

Concept in Action

QR Code representing a URL

To learn more about atoms and isotopes, and how you can tell one isotope from another, visit this site and run the simulation.

Chemical Bonds

How elements interact with one another depends on how their electrons are arranged and how many openings for electrons exist at the outermost region where electrons are present in an atom. Electrons exist at energy levels that form shells around the nucleus. The closest shell can hold up to two electrons. The closest shell to the nucleus is always filled first, before any other shell can be filled. Hydrogen has one electron; therefore, it has only one spot occupied within the lowest shell. Helium has two electrons; therefore, it can completely fill the lowest shell with its two electrons. If you look at the periodic table, you will see that hydrogen and helium are the only two elements in the first row. This is because they only have electrons in their first shell. Hydrogen and helium are the only two elements that have the lowest shell and no other shells.

The second and third energy levels can hold up to eight electrons. The eight electrons are arranged in four pairs and one position in each pair is filled with an electron before any pairs are completed.

Looking at the periodic table again, you will notice that there are seven rows. These rows correspond to the number of shells that the elements within that row have. The elements within a particular row have increasing numbers of electrons as the columns proceed from left to right. Although each element has the same number of shells, not all of the shells are completely filled with electrons. If you look at the second row of the periodic table, you will find lithium (Li), beryllium (Be), boron (B), carbon (C), nitrogen (N), oxygen (O), fluorine (F), and neon (Ne). These all have electrons that occupy only the first and second shells. Lithium has only one electron in its outermost shell, beryllium has two electrons, boron has three, and so on, until the entire shell is filled with eight electrons, as is the case with neon.

Not all elements have enough electrons to fill their outermost shells, but an atom is at its most stable when all of the electron positions in the outermost shell are filled. Because of these vacancies in the outermost shells, we see the formation of chemical bonds, or interactions between two or more of the same or different elements that result in the formation of molecules. To achieve greater stability, atoms will tend to completely fill their outer shells and will bond with other elements to accomplish this goal by sharing electrons, accepting electrons from another atom, or donating electrons to another atom. Because the outermost shells of the elements with low atomic numbers (up to calcium, with atomic number 20) can hold eight electrons, this is referred to as the octet rule. An element can donate, accept, or share electrons with other elements to fill its outer shell and satisfy the octet rule.

When an atom does not contain equal numbers of protons and electrons, it is called an ion. Because the number of electrons does not equal the number of protons, each ion has a net charge. Positive ions are formed by losing electrons and are called cations. Negative ions are formed by gaining electrons and are called anions.

For example, sodium only has one electron in its outermost shell. It takes less energy for sodium to donate that one electron than it does to accept seven more electrons to fill the outer shell. If sodium loses an electron, it now has 11 protons and only 10 electrons, leaving it with an overall charge of +1. It is now called a sodium ion.

The chlorine atom has seven electrons in its outer shell. Again, it is more energy-efficient for chlorine to gain one electron than to lose seven. Therefore, it tends to gain an electron to create an ion with 17 protons and 18 electrons, giving it a net negative (–1) charge. It is now called a chloride ion. This movement of electrons from one element to another is referred to as electron transfer. As illustrates, a sodium atom (Na) only has one electron in its outermost shell, whereas a chlorine atom (Cl) has seven electrons in its outermost shell. A sodium atom will donate its one electron to empty its shell, and a chlorine atom will accept that electron to fill its shell, becoming chloride. Both ions now satisfy the octet rule and have complete outermost shells. Because the number of electrons is no longer equal to the number of protons, each is now an ion and has a +1 (sodium) or –1 (chloride) charge.

Diagram shows electron transfer between elements.
Figure 2.5 Elements tend to fill their outermost shells with electrons. To do this, they can either donate or accept electrons from other elements.

Ionic Bonds

There are four types of bonds or interactions: ionic, covalent, hydrogen bonds, and van der Waals interactions. Ionic and covalent bonds are strong interactions that require a larger energy input to break apart. When an element donates an electron from its outer shell, as in the sodium atom example above, a positive ion is formed. The element accepting the electron is now negatively charged. Because positive and negative charges attract, these ions stay together and form an ionic bond, or a bond between ions. The elements bond together with the electron from one element staying predominantly with the other element. When Na+ and Cl ions combine to produce NaCl, an electron from a sodium atom stays with the other seven from the chlorine atom, and the sodium and chloride ions attract each other in a lattice of ions with a net zero charge.

Covalent Bonds

Another type of strong chemical bond between two or more atoms is a covalent bond. These bonds form when a pair of  electrons is shared between two elements and are the strongest and most common form of chemical bond in living organisms. Covalent bonds form between the elements that make up the biological molecules in our cells. Unlike ionic bonds, covalent bonds do not dissociate in water.

The hydrogen and oxygen atoms that combine to form water molecules are bound together by covalent bonds. The electron from the hydrogen atom divides its time between the outer shell of the hydrogen atom and the incomplete outer shell of the oxygen atom. To completely fill the outer shell of an oxygen atom, two electrons from two hydrogen atoms are needed, hence the subscript “2” in H2O. The electrons are shared between the atoms, dividing their time between them to “fill” the outer shell of each. This sharing is a lower energy state for all of the atoms involved than if they existed without their outer shells filled.

There are two types of covalent bonds: polar and nonpolar. Nonpolar covalent bonds form between two atoms of the same element or between different elements that share the electrons equally. For example, an oxygen atom can bond with another oxygen atom to fill their outer shells. This association is nonpolar because the electrons will be equally distributed between each oxygen atom. Two covalent bonds form between the two oxygen atoms because oxygen requires two shared electrons to fill its outermost shell. Nitrogen atoms will form three covalent bonds (also called triple covalent) between two atoms of nitrogen because each nitrogen atom needs three electrons to fill its outermost shell. Another example of a nonpolar covalent bond is found in the methane (CH4) molecule. The carbon atom has four electrons in its outermost shell and needs four more to fill it. It gets these four from four hydrogen atoms, each atom providing one. These elements all share the electrons equally, creating four nonpolar covalent bonds.

In a polar covalent bond, the electrons shared by the atoms spend more time closer to one nucleus than to the other nucleus. Because of the unequal distribution of electrons between the different nuclei, a slightly positive (δ+) or slightly negative (δ–) charge develops. The covalent bonds between hydrogen and oxygen atoms in water are polar covalent bonds. The shared electrons spend more time near the oxygen nucleus, giving it a small negative charge, than they spend near the hydrogen nuclei, giving these molecules a small positive charge.

Hydrogen Bonds

Ionic and covalent bonds are strong bonds that require considerable energy to break. However, not all bonds between elements are ionic or covalent bonds. Weaker bonds can also form. These are attractions that occur between positive and negative charges that do not require much energy to break. Two weak bonds that occur frequently are hydrogen bonds and van der Waals interactions. These bonds give rise to the unique properties of water and the unique structures of DNA and proteins.

When polar covalent bonds containing a hydrogen atom form, the hydrogen atom in that bond has a slightly positive charge. This is because the shared electron is pulled more strongly toward the other element and away from the hydrogen nucleus. Because the hydrogen atom is slightly positive (δ+), it will be attracted to neighboring negative partial charges (δ–). When this happens, a weak interaction occurs between the δ+ charge of the hydrogen atom of one molecule and the δ– charge of the other molecule. This interaction is called a hydrogen bond. This type of bond is common; for example, the liquid nature of water is caused by the hydrogen bonds between water molecules. Hydrogen bonds give water the unique properties that sustain life. If it were not for hydrogen bonding, water would be a gas rather than a liquid at room temperature.

Diagram showing hydrogen bonds formed between adjacent water molecules.
Figure 2.6 Hydrogen bonds form between slightly positive (δ+) and slightly negative (δ–) charges of polar covalent molecules, such as water.

Hydrogen bonds can form between different molecules and they do not always have to include a water molecule. Hydrogen atoms in polar bonds within any molecule can form bonds with other adjacent molecules. For example, hydrogen bonds hold together two long strands of DNA to give the DNA molecule its characteristic double-stranded structure. Hydrogen bonds are also responsible for some of the three-dimensional structure of proteins.

van der Waals Interactions

Like hydrogen bonds, van der Waals interactions are weak attractions or interactions between molecules. They occur between polar, covalently bound, atoms in different molecules. Some of these weak attractions are caused by temporary partial charges formed when electrons move around a nucleus. These weak interactions between molecules are important in biological systems.

Radiography Technicians

Have you or anyone you know ever had a magnetic resonance imaging (MRI) scan, a mammogram, or an X-ray? These tests produce images of your soft tissues and organs (as with an MRI or mammogram) or your bones (as happens in an X-ray) by using either radio waves or special isotopes (radiolabeled or fluorescently labeled) that are ingested or injected into the body. These tests provide data for disease diagnoses by creating images of your organs or skeletal system.

MRI imaging works by subjecting hydrogen nuclei, which are abundant in the water in soft tissues, to fluctuating magnetic fields, which cause them to emit their own magnetic field. This signal is then read by sensors in the machine and interpreted by a computer to form a detailed image.

Some radiography technologists and technicians specialize in computed tomography, MRI, and mammography. They produce films or images of the body that help medical professionals examine and diagnose. Radiologists work directly with patients, explaining machinery, preparing them for exams, and ensuring that their body or body parts are positioned correctly to produce the needed images. Physicians or radiologists then analyze the test results.

Radiography technicians can work in hospitals, doctors’ offices, or specialized imaging centers. Training to become a radiography technician happens at hospitals, colleges, and universities that offer certificates, associate’s degrees, or bachelor’s degrees in radiography.

Section Summary

Matter is anything that occupies space and has mass. It is made up of atoms of different elements. All of the 92 elements that occur naturally have unique qualities that allow them to combine in various ways to create compounds or molecules. Atoms, which consist of protons, neutrons, and electrons, are the smallest units of an element that retain all of the properties of that element. Electrons can be donated or shared between atoms to create bonds, including ionic, covalent, and hydrogen bonds, as well as van der Waals interactions.

Exercises

An interactive H5P element has been excluded from this version of the text. You can view it online here:
https://pressbooks.nscc.ca/conceptsofbiologynscc/?p=58#h5p-11

Glossary

anion: a negative ion formed by gaining electrons

atomic number: the number of protons in an atom

cation: a positive ion formed by losing electrons

chemical bond: an interaction between two or more of the same or different elements that results in the formation of molecules

covalent bond: a type of strong bond between two or more of the same or different elements; forms when electrons are shared between elements

electron: a negatively charged particle that resides outside of the nucleus in the electron orbital; lacks functional mass and has a charge of –1

electron transfer: the movement of electrons from one element to another

element: one of 118 unique substances that cannot be broken down into smaller substances and retain the characteristic of that substance; each element has a specified number of protons and unique properties

hydrogen bond: a weak bond between partially positively charged hydrogen atoms and partially negatively charged elements or molecules

ion: an atom or compound that does not contain equal numbers of protons and electrons, and therefore has a net charge

ionic bond: a chemical bond that forms between ions of opposite charges

isotope: one or more forms of an element that have different numbers of neutrons

mass number: the number of protons plus neutrons in an atom

matter: anything that has mass and occupies space

neutron: a particle with no charge that resides in the nucleus of an atom; has a mass of 1

nonpolar covalent bond: a type of covalent bond that forms between atoms when electrons are shared equally between atoms, resulting in no regions with partial charges as in polar covalent bonds

nucleus: (chemistry) the dense center of an atom made up of protons and (except in the case of a hydrogen atom) neutrons

octet rule: states that the outermost shell of an element with a low atomic number can hold eight electrons

periodic table of elements: an organizational chart of elements, indicating the atomic number and mass number of each element; also provides key information about the properties of elements

polar covalent bond:a type of covalent bond in which electrons are pulled toward one atom and away from another, resulting in slightly positive and slightly negative charged regions of the molecule

proton: a positively charged particle that resides in the nucleus of an atom; has a mass of 1 and a charge of +1

radioactive isotope: an isotope that spontaneously emits particles or energy to form a more stable element

van der Waals interaction: a weak attraction or interaction between molecules caused by slightly positively charged or slightly negatively charged atoms

Media Attribution

4

2.2 Water

Charles Molnar and Jane Gair

Learning Objectives

By the end of this section, you will be able to:

  • Describe the properties of water that are critical to maintaining life

Watch a video about why we need oxygen and how it causes problems for living things.

An interactive H5P element has been excluded from this version of the text. You can view it online here:
https://pressbooks.nscc.ca/conceptsofbiologynscc/?p=66#h5p-12

Do you ever wonder why scientists spend time looking for water on other planets? It is because water is essential to life; even minute traces of it on another planet can indicate that life could or did exist on that planet. Water is one of the more abundant molecules in living cells and the one most critical to life as we know it. Approximately 60–70 percent of your body is made up of water. Without it, life simply would not exist.

Water Is Polar

The hydrogen and oxygen atoms within water molecules form polar covalent bonds. The shared electrons spend more time associated with the oxygen atom than they do with hydrogen atoms. There is no overall charge to a water molecule, but there is a slight positive charge on each hydrogen atom and a slight negative charge on the oxygen atom. Because of these charges, the slightly positive hydrogen atoms repel each other and form the unique shape. Each water molecule attracts other water molecules because of the positive and negative charges in the different parts of the molecule. Water also attracts other polar molecules (such as sugars), forming hydrogen bonds. When a substance readily forms hydrogen bonds with water, it can dissolve in water and is referred to as hydrophilic (“water-loving”). Hydrogen bonds are not readily formed with nonpolar substances like oils and fats . These nonpolar compounds are hydrophobic (“water-fearing”) and will not dissolve in water.

Picture of oil in water.
Figure 2.7 As this macroscopic image of oil and water shows, oil is a nonpolar compound and, hence, will not dissolve in water. Oil and water do not mix.

Water Stabilizes Temperature

The hydrogen bonds in water allow it to absorb and release heat energy more slowly than many other substances. Temperature is a measure of the motion (kinetic energy) of molecules. As the motion increases, energy is higher and thus temperature is higher. Water absorbs a great deal of energy before its temperature rises. Increased energy disrupts the hydrogen bonds between water molecules. Because these bonds can be created and disrupted rapidly, water absorbs an increase in energy and temperature changes only minimally. This means that water moderates temperature changes within organisms and in their environments. As energy input continues, the balance between hydrogen-bond formation and destruction swings toward the destruction side. More bonds are broken than are formed. This process results in the release of individual water molecules at the surface of the liquid (such as a body of water, the leaves of a plant, or the skin of an organism) in a process called evaporation. Evaporation of sweat, which is 90 percent water, allows for cooling of an organism, because breaking hydrogen bonds requires an input of energy and takes heat away from the body.

Conversely, as molecular motion decreases and temperatures drop, less energy is present to break the hydrogen bonds between water molecules. These bonds remain intact and begin to form a rigid, lattice-like structure (e.g., ice) (Figure 2.8 a). When frozen, ice is less dense than liquid water (the molecules are farther apart). This means that ice floats on the surface of a body of water (Figure 2.8 b). In lakes, ponds, and oceans, ice will form on the surface of the water, creating an insulating barrier to protect the animal and plant life beneath from freezing in the water. If this did not happen, plants and animals living in water would freeze in a block of ice and could not move freely, making life in cold temperatures difficult or impossible.

Part A shows the lattice-like molecular structure of ice. Part B is a photo of ice on water.
Figure 2.8 (a) The lattice structure of ice makes it less dense than the freely flowing molecules of liquid water. Ice’s lower density enables it to (b) float on water. (credit a: modification of work by Jane Whitney; credit b: modification of work by Carlos Ponte)

Water Is an Excellent Solvent

Because water is polar, with slight positive and negative charges, ionic compounds and polar molecules can readily dissolve in it. Water is, therefore, what is referred to as a solvent—a substance capable of dissolving another substance. The charged particles will form hydrogen bonds with a surrounding layer of water molecules. This is referred to as a sphere of hydration and serves to keep the particles separated or dispersed in the water. In the case of table salt (NaCl) mixed in water, the sodium and chloride ions separate, or dissociate, in the water, and spheres of hydration are formed around the ions. A positively charged sodium ion is surrounded by the partially negative charges of oxygen atoms in water molecules. A negatively charged chloride ion is surrounded by the partially positive charges of hydrogen atoms in water molecules. These spheres of hydration are also referred to as hydration shells. The polarity of the water molecule makes it an effective solvent and is important in its many roles in living systems.

Illustration of spheres of hydration around sodium and chlorine ions.
Figure 2.9 When table salt (NaCl) is mixed in water, spheres of hydration form around the ions.

Water Is Cohesive

Have you ever filled up a glass of water to the very top and then slowly added a few more drops? Before it overflows, the water actually forms a dome-like shape above the rim of the glass. This water can stay above the glass because of the property of cohesion. In cohesion, water molecules are attracted to each other (because of hydrogen bonding), keeping the molecules together at the liquid-air (gas) interface, although there is no more room in the glass. Cohesion gives rise to surface tension, the capacity of a substance to withstand rupture when placed under tension or stress. When you drop a small scrap of paper onto a droplet of water, the paper floats on top of the water droplet, although the object is denser (heavier) than the water. This occurs because of the surface tension that is created by the water molecules. Cohesion and surface tension keep the water molecules intact and the item floating on the top. It is even possible to “float” a steel needle on top of a glass of water if you place it gently, without breaking the surface tension.

Picture of a needle floating on top of water because of cohesion and surface tension.
Figure 2.10 The weight of a needle on top of water pulls the surface tension downward; at the same time, the surface tension of the water is pulling it up, suspending the needle on the surface of the water and keeping it from sinking. Notice the indentation in the water around the needle.

These cohesive forces are also related to the water’s property of adhesion, or the attraction between water molecules and other molecules. This is observed when water “climbs” up a straw placed in a glass of water. You will notice that the water appears to be higher on the sides of the straw than in the middle. This is because the water molecules are attracted to the straw and therefore adhere to it.

Cohesive and adhesive forces are important for sustaining life. For example, because of these forces, water can flow up from the roots to the tops of plants to feed the plant.

Concept in Action

QR Code representing a URL

To learn more about water, visit the U.S. Geological Survey Water Science for Schools: All About Water! website.

Buffers, pH, Acids, and Bases

The pH of a solution is a measure of its acidity or alkalinity. You have probably used litmus paper, paper that has been treated with a natural water-soluble dye so it can be used as a pH indicator, to test how much acid or base (alkalinity) exists in a solution. You might have even used some to make sure the water in an outdoor swimming pool is properly treated. In both cases, this pH test measures the amount of hydrogen ions that exists in a given solution. High concentrations of hydrogen ions yield a low pH, whereas low levels of hydrogen ions result in a high pH. The overall concentration of hydrogen ions is inversely related to its pH and can be measured on the pH scale (Figure 2.11). Therefore, the more hydrogen ions present, the lower the pH; conversely, the fewer hydrogen ions, the higher the pH.

The pH scale ranges from 0 to 14. A change of one unit on the pH scale represents a change in the concentration of hydrogen ions by a factor of 10, a change in two units represents a change in the concentration of hydrogen ions by a factor of 100. Thus, small changes in pH represent large changes in the concentrations of hydrogen ions. Pure water is neutral. It is neither acidic nor basic, and has a pH of 7.0. Anything below 7.0 (ranging from 0.0 to 6.9) is acidic, and anything above 7.0 (from 7.1 to 14.0) is alkaline. The blood in your veins is slightly alkaline (pH = 7.4). The environment in your stomach is highly acidic (pH = 1 to 2). Orange juice is mildly acidic (pH = approximately 3.5), whereas baking soda is basic (pH = 9.0).

 
The pH scale with representative substances and their pHs.
Figure 2.11 The pH scale measures the amount of hydrogen ions (H+) in a substance.

Acids are substances that provide hydrogen ions (H+) and lower pH, whereas bases provide hydroxide ions (OH) and raise pH. The stronger the acid, the more readily it donates H+. For example, hydrochloric acid and lemon juice are very acidic and readily give up H+ when added to water. Conversely, bases are those substances that readily donate OH. The OH ions combine with H+ to produce water, which raises a substance’s pH. Sodium hydroxide and many household cleaners are very alkaline and give up OH rapidly when placed in water, thereby raising the pH.

Most cells in our bodies operate within a very narrow window of the pH scale, typically ranging only from 7.2 to 7.6. If the pH of the body is outside of this range, the respiratory system malfunctions, as do other organs in the body. Cells no longer function properly, and proteins will break down. Deviation outside of the pH range can induce coma or even cause death.

So how is it that we can ingest or inhale acidic or basic substances and not die? Buffers are the key. Buffers readily absorb excess H+ or OH, keeping the pH of the body carefully maintained in the aforementioned narrow range. Carbon dioxide is part of a prominent buffer system in the human body; it keeps the pH within the proper range. This buffer system involves carbonic acid (H2CO3) and bicarbonate (HCO3) anion. If too much H+ enters the body, bicarbonate will combine with the H+ to create carbonic acid and limit the decrease in pH. Likewise, if too much OH is introduced into the system, carbonic acid will rapidly dissociate into bicarbonate and H+ ions. The H+ ions can combine with the OH ions, limiting the increase in pH. While carbonic acid is an important product in this reaction, its presence is fleeting because the carbonic acid is released from the body as carbon dioxide gas each time we breathe. Without this buffer system, the pH in our bodies would fluctuate too much and we would fail to survive.

Section Summary

Water has many properties that are critical to maintaining life. It is polar, allowing for the formation of hydrogen bonds, which allow ions and other polar molecules to dissolve in water. Therefore, water is an excellent solvent. The hydrogen bonds between water molecules give water the ability to hold heat better than many other substances. As the temperature rises, the hydrogen bonds between water continually break and reform, allowing for the overall temperature to remain stable, although increased energy is added to the system. Water’s cohesive forces allow for the property of surface tension. All of these unique properties of water are important in the chemistry of living organisms.

The pH of a solution is a measure of the concentration of hydrogen ions in the solution. A solution with a high number of hydrogen ions is acidic and has a low pH value. A solution with a high number of hydroxide ions is basic and has a high pH value. The pH scale ranges from 0 to 14, with a pH of 7 being neutral. Buffers are solutions that moderate pH changes when an acid or base is added to the buffer system. Buffers are important in biological systems because of their ability to maintain constant pH conditions.

Exercises

An interactive H5P element has been excluded from this version of the text. You can view it online here:
https://pressbooks.nscc.ca/conceptsofbiologynscc/?p=66#h5p-13

Glossary

acid: a substance that donates hydrogen ions and therefore lowers pH

adhesion: the attraction between water molecules and molecules of a different substance

base: a substance that absorbs hydrogen ions and therefore raises pH

buffer: a solution that resists a change in pH by absorbing or releasing hydrogen or hydroxide ions

cohesion: the intermolecular forces between water molecules caused by the polar nature of water; creates surface tension

evaporation: the release of water molecules from liquid water to form water vapor

hydrophilic: describes a substance that dissolves in water; water-loving

hydrophobic: describes a substance that does not dissolve in water; water-fearing

litmus paper: filter paper that has been treated with a natural water-soluble dye so it can be used as a pH indicator

pH scale: a scale ranging from 0 to 14 that measures the approximate concentration of hydrogen ions of a substance

solvent: a substance capable of dissolving another substance

surface tension: the cohesive force at the surface of a body of liquid that prevents the molecules from separating

temperature: a measure of molecular motion

References

Humphrey, W., Dalke, A. and Schulten, K., “VMD—Visual Molecular Dynamics”, J. Molec. Graphics, 1996, vol. 14, pp. 33-38. http://www.ks.uiuc.edu/Research/vmd/

Media Attribution

  • Figure 2.7 by Gautam Dogra
  • Figure 2.8
    • ice lattice by Jane Whitney
    • (b) by Carlos Ponte
  • Figure 2.10 by Cory Zanker
  • Figure 2.11 by Edward Stevens

5

2.3 Biological Molecules

Charles Molnar and Jane Gair

Learning Objectives

By the end of this section, you will be able to:

  • Describe the ways in which carbon is critical to life
  • Explain the impact of slight changes in amino acids on organisms
  • Describe the four major types of biological molecules
  • Understand the functions of the four major types of molecules

Watch a video about proteins and protein enzymes.

An interactive H5P element has been excluded from this version of the text. You can view it online here:
https://pressbooks.nscc.ca/conceptsofbiologynscc/?p=83#h5p-14

The large molecules necessary for life that are built from smaller organic molecules are called biological macromolecules. There are four major classes of biological macromolecules (carbohydrates, lipids, proteins, and nucleic acids), and each is an important component of the cell and performs a wide array of functions. Combined, these molecules make up the majority of a cell’s mass. Biological macromolecules are organic, meaning that they contain carbon. In addition, they may contain hydrogen, oxygen, nitrogen, phosphorus, sulfur, and additional minor elements.

Carbon

It is often said that life is “carbon-based.” This means that carbon atoms, bonded to other carbon atoms or other elements, form the fundamental components of many, if not most, of the molecules found uniquely in living things. Other elements play important roles in biological molecules, but carbon certainly qualifies as the “foundation” element for molecules in living things. It is the bonding properties of carbon atoms that are responsible for its important role.

Carbon Bonding

Carbon contains four electrons in its outer shell. Therefore, it can form four covalent bonds with other atoms or molecules. The simplest organic carbon molecule is methane (CH4), in which four hydrogen atoms bind to a carbon atom.

 
Diagram of a methane molecule.
Figure 2.12 Carbon can form four covalent bonds to create an organic molecule. The simplest carbon molecule is methane (CH4), depicted here.

However, structures that are more complex are made using carbon. Any of the hydrogen atoms can be replaced with another carbon atom covalently bonded to the first carbon atom. In this way, long and branching chains of carbon compounds can be made (Figure 2.13 a). The carbon atoms may bond with atoms of other elements, such as nitrogen, oxygen, and phosphorus (Figure 2.13 b). The molecules may also form rings, which themselves can link with other rings (Figure 2.13 c). This diversity of molecular forms accounts for the diversity of functions of the biological macromolecules and is based to a large degree on the ability of carbon to form multiple bonds with itself and other atoms.

Examples of three different carbon-containing molecules.
Figure 2.13 These examples show three molecules (found in living organisms) that contain carbon atoms bonded in various ways to other carbon atoms and the atoms of other elements. (a) This molecule of stearic acid has a long chain of carbon atoms. (b) Glycine, a component of proteins, contains carbon, nitrogen, oxygen, and hydrogen atoms. (c) Glucose, a sugar, has a ring of carbon atoms and one oxygen atom.

Carbohydrates

Carbohydrates are macromolecules with which most consumers are somewhat familiar. To lose weight, some individuals adhere to “low-carb” diets. Athletes, in contrast, often “carb-load” before important competitions to ensure that they have sufficient energy to compete at a high level. Carbohydrates are, in fact, an essential part of our diet; grains, fruits, and vegetables are all natural sources of carbohydrates. Carbohydrates provide energy to the body, particularly through glucose, a simple sugar. Carbohydrates also have other important functions in humans, animals, and plants.

Carbohydrates can be represented by the formula (CH2O)n, where n is the number of carbon atoms in the molecule. In other words, the ratio of carbon to hydrogen to oxygen is 1:2:1 in carbohydrate molecules. Carbohydrates are classified into three subtypes: monosaccharides, disaccharides, and polysaccharides.

Monosaccharides (mono- = “one”; sacchar- = “sweet”) are simple sugars, the most common of which is glucose. In monosaccharides, the number of carbon atoms usually ranges from three to six. Most monosaccharide names end with the suffix -ose. Depending on the number of carbon atoms in the sugar, they may be known as trioses (three carbon atoms), pentoses (five carbon atoms), and hexoses (six carbon atoms).

Monosaccharides may exist as a linear chain or as ring-shaped molecules; in aqueous solutions, they are usually found in the ring form.

The chemical formula for glucose is C6H12O6. In most living species, glucose is an important source of energy. During cellular respiration, energy is released from glucose, and that energy is used to help make adenosine triphosphate (ATP). Plants synthesize glucose using carbon dioxide and water by the process of photosynthesis, and the glucose, in turn, is used for the energy requirements of the plant. The excess synthesized glucose is often stored as starch that is broken down by other organisms that feed on plants.

Galactose (part of lactose, or milk sugar) and fructose (found in fruit) are other common monosaccharides. Although glucose, galactose, and fructose all have the same chemical formula (C6H12O6), they differ structurally and chemically (and are known as isomers) because of differing arrangements of atoms in the carbon chain.

Chemical structures of glucose, galactose, and fructose.
Figure 2.14 Glucose, galactose, and fructose are isomeric monosaccharides, meaning that they have the same chemical formula but slightly different structures.

Disaccharides (di- = “two”) form when two monosaccharides undergo a dehydration reaction (a reaction in which the removal of a water molecule occurs). During this process, the hydroxyl group (–OH) of one monosaccharide combines with a hydrogen atom of another monosaccharide, releasing a molecule of water (H2O) and forming a covalent bond between atoms in the two sugar molecules.

Common disaccharides include lactose, maltose, and sucrose. Lactose is a disaccharide consisting of the monomers glucose and galactose. It is found naturally in milk. Maltose, or malt sugar, is a disaccharide formed from a dehydration reaction between two glucose molecules. The most common disaccharide is sucrose, or table sugar, which is composed of the monomers glucose and fructose.

A long chain of monosaccharides linked by covalent bonds is known as a polysaccharide (poly- = “many”). The chain may be branched or unbranched, and it may contain different types of monosaccharides. Polysaccharides may be very large molecules. Starch, glycogen, cellulose, and chitin are examples of polysaccharides.

Starch is the stored form of sugars in plants and is made up of amylose and amylopectin (both polymers of glucose). Plants are able to synthesize glucose, and the excess glucose is stored as starch in different plant parts, including roots and seeds. The starch that is consumed by animals is broken down into smaller molecules, such as glucose. The cells can then absorb the glucose.

Glycogen is the storage form of glucose in humans and other vertebrates, and is made up of monomers of glucose. Glycogen is the animal equivalent of starch and is a highly branched molecule usually stored in liver and muscle cells. Whenever glucose levels decrease, glycogen is broken down to release glucose.

Cellulose is one of the most abundant natural biopolymers. The cell walls of plants are mostly made of cellulose, which provides structural support to the cell. Wood and paper are mostly cellulosic in nature. Cellulose is made up of glucose monomers that are linked by bonds between particular carbon atoms in the glucose molecule.

Every other glucose monomer in cellulose is flipped over and packed tightly as extended long chains. This gives cellulose its rigidity and high tensile strength—which is so important to plant cells. Cellulose passing through our digestive system is called dietary fiber. While the glucose-glucose bonds in cellulose cannot be broken down by human digestive enzymes, herbivores such as cows, buffalos, and horses are able to digest grass that is rich in cellulose and use it as a food source. In these animals, certain species of bacteria reside in the rumen (part of the digestive system of herbivores) and secrete the enzyme cellulase. The appendix also contains bacteria that break down cellulose, giving it an important role in the digestive systems of ruminants. Cellulases can break down cellulose into glucose monomers that can be used as an energy source by the animal.

Carbohydrates serve other functions in different animals. Arthropods, such as insects, spiders, and crabs, have an outer skeleton, called the exoskeleton, which protects their internal body parts. This exoskeleton is made of the biological macromolecule chitin, which is a nitrogenous carbohydrate. It is made of repeating units of a modified sugar containing nitrogen.

Thus, through differences in molecular structure, carbohydrates are able to serve the very different functions of energy storage (starch and glycogen) and structural support and protection (cellulose and chitin).

Chemical structures of starch, glycogen, cellulose, and chitin
Figure 2.15 Although their structures and functions differ, all polysaccharide carbohydrates are made up of monosaccharides and have the chemical formula (CH2O)n.

Registered Dietitian: Obesity is a worldwide health concern, and many diseases, such as diabetes and heart disease, are becoming more prevalent because of obesity. This is one of the reasons why registered dietitians are increasingly sought after for advice. Registered dietitians help plan food and nutrition programs for individuals in various settings. They often work with patients in health-care facilities, designing nutrition plans to prevent and treat diseases. For example, dietitians may teach a patient with diabetes how to manage blood-sugar levels by eating the correct types and amounts of carbohydrates. Dietitians may also work in nursing homes, schools, and private practices.

To become a registered dietitian, one needs to earn at least a bachelor’s degree in dietetics, nutrition, food technology, or a related field. In addition, registered dietitians must complete a supervised internship program and pass a national exam. Those who pursue careers in dietetics take courses in nutrition, chemistry, biochemistry, biology, microbiology, and human physiology. Dietitians must become experts in the chemistry and functions of food (proteins, carbohydrates, and fats).

Through the Indigenous Lens (Suzanne Wilkerson and Charles Molnar)

I work at Camosun College located in beautiful Victoria, British Columbia with campuses on the Traditional Territories of the Lekwungen and W̱SÁNEĆ peoples. The underground storage bulb of the camas flower shown below has been an important food source for many of the Indigenous peoples of Vancouver Island and throughout the western area of North America. Camas bulbs are still eaten as a traditional food source and the preparation of the camas bulbs relates to this text section about carbohydrates.

 

Figure 2.16 Image of a blue camas flower and an insect pollinator. The underground bulb of camas is baked in a fire pit. Heat acts like pancreatic amylase enzyme and breaks down long chains of indigestible inulin into digestible mono and di-saccharides.
Figure 2.16 Image of a blue camas flower and an insect pollinator. The underground bulb of camas is baked in a fire pit. Heat acts like pancreatic amylase enzyme and breaks down long chains of indigestible inulin into digestible mono and di-saccharides.

Most often plants create starch as the stored form of carbohydrate. Some plants, like camas create inulin. Inulin is used as dietary fibre however, it is not readily digested by humans. If you were to bite into a raw camas bulb it would taste bitter and has a gummy texture. The method used by Indigenous peoples to make camas both digestible and tasty is to bake the bulbs slowly for a long period in an underground firepit covered with specific leaves and soil. The heat acts like our pancreatic amylase enzyme and breaks down the long chains of inulin into digestible mono and di-saccharides.

Properly baked, the camas bulbs taste like a combination of baked pear and cooked fig. It is important to note that while the blue camas is a food source, it should not be confused with the white death camas, which is particularly toxic and deadly. The flowers look different, but the bulbs look very similar.

Lipids

Lipids include a diverse group of compounds that are united by a common feature. Lipids are hydrophobic (“water-fearing”), or insoluble in water, because they are nonpolar molecules. This is because they are hydrocarbons that include only nonpolar carbon-carbon or carbon-hydrogen bonds. Lipids perform many different functions in a cell. Cells store energy for long-term use in the form of lipids called fats. Lipids also provide insulation from the environment for plants and animals. For example, they help keep aquatic birds and mammals dry because of their water-repelling nature. Lipids are also the building blocks of many hormones and are an important constituent of the plasma membrane. Lipids include fats, oils, waxes, phospholipids, and steroids.

A photo of a river otter in the water
Figure 2.17 Hydrophobic lipids in the fur of aquatic mammals, such as this river otter, protect them from the elements.

A fat molecule, such as a triglyceride, consists of two main components—glycerol and fatty acids. Glycerol is an organic compound with three carbon atoms, five hydrogen atoms, and three hydroxyl (–OH) groups. Fatty acids have a long chain of hydrocarbons to which an acidic carboxyl group is attached, hence the name “fatty acid.” The number of carbons in the fatty acid may range from 4 to 36; most common are those containing 12–18 carbons. In a fat molecule, a fatty acid is attached to each of the three oxygen atoms in the –OH groups of the glycerol molecule with a covalent bond.

Chemical structures of starch, glycogen, cellulose, and chitin.
Figure 2.18 Lipids include fats, such as triglycerides, which are made up of fatty acids and glycerol, phospholipids, and steroids.

During this covalent bond formation, three water molecules are released. The three fatty acids in the fat may be similar or dissimilar. These fats are also called triglycerides because they have three fatty acids. Some fatty acids have common names that specify their origin. For example, palmitic acid, a saturated fatty acid, is derived from the palm tree. Arachidic acid is derived from Arachis hypogaea, the scientific name for peanuts.

Fatty acids may be saturated or unsaturated. In a fatty acid chain, if there are only single bonds between neighboring carbons in the hydrocarbon chain, the fatty acid is saturated. Saturated fatty acids are saturated with hydrogen; in other words, the number of hydrogen atoms attached to the carbon skeleton is maximized.

When the hydrocarbon chain contains a double bond, the fatty acid is an unsaturated fatty acid.

Most unsaturated fats are liquid at room temperature and are called oils. If there is one double bond in the molecule, then it is known as a monounsaturated fat (e.g., olive oil), and if there is more than one double bond, then it is known as a polyunsaturated fat (e.g., canola oil).

Saturated fats tend to get packed tightly and are solid at room temperature. Animal fats with stearic acid and palmitic acid contained in meat, and the fat with butyric acid contained in butter, are examples of saturated fats. Mammals store fats in specialized cells called adipocytes, where globules of fat occupy most of the cell. In plants, fat or oil is stored in seeds and is used as a source of energy during embryonic development.

Unsaturated fats or oils are usually of plant origin and contain unsaturated fatty acids. The double bond causes a bend or a “kink” that prevents the fatty acids from packing tightly, keeping them liquid at room temperature. Olive oil, corn oil, canola oil, and cod liver oil are examples of unsaturated fats. Unsaturated fats help to improve blood cholesterol levels, whereas saturated fats contribute to plaque formation in the arteries, which increases the risk of a heart attack.

In the food industry, oils are artificially hydrogenated to make them semi-solid, leading to less spoilage and increased shelf life. Simply speaking, hydrogen gas is bubbled through oils to solidify them. During this hydrogenation process, double bonds of the cis-conformation in the hydrocarbon chain may be converted to double bonds in the trans-conformation. This forms a trans-fat from a cis-fat. The orientation of the double bonds affects the chemical properties of the fat.

Two images show the molecular structure of a fat in the cis-conformation and the trans-conformation.
Figure 2.19 During the hydrogenation process, the orientation around the double bonds is changed, making a trans-fat from a cis-fat. This changes the chemical properties of the molecule.

Margarine, some types of peanut butter, and shortening are examples of artificially hydrogenated trans-fats. Recent studies have shown that an increase in trans-fats in the human diet may lead to an increase in levels of low-density lipoprotein (LDL), or “bad” cholesterol, which, in turn, may lead to plaque deposition in the arteries, resulting in heart disease. Many fast food restaurants have recently eliminated the use of trans-fats, and U.S. food labels are now required to list their trans-fat content.

Essential fatty acids are fatty acids that are required but not synthesized by the human body. Consequently, they must be supplemented through the diet. Omega-3 fatty acids fall into this category and are one of only two known essential fatty acids for humans (the other being omega-6 fatty acids). They are a type of polyunsaturated fat and are called omega-3 fatty acids because the third carbon from the end of the fatty acid participates in a double bond.

Salmon, trout, and tuna are good sources of omega-3 fatty acids. Omega-3 fatty acids are important in brain function and normal growth and development. They may also prevent heart disease and reduce the risk of cancer.

Like carbohydrates, fats have received a lot of bad publicity. It is true that eating an excess of fried foods and other “fatty” foods leads to weight gain. However, fats do have important functions. Fats serve as long-term energy storage. They also provide insulation for the body. Therefore, “healthy” unsaturated fats in moderate amounts should be consumed on a regular basis.

Phospholipids are the major constituent of the plasma membrane. Like fats, they are composed of fatty acid chains attached to a glycerol or similar backbone. Instead of three fatty acids attached, however, there are two fatty acids and the third carbon of the glycerol backbone is bound to a phosphate group. The phosphate group is modified by the addition of an alcohol.

A phospholipid has both hydrophobic and hydrophilic regions. The fatty acid chains are hydrophobic and exclude themselves from water, whereas the phosphate is hydrophilic and interacts with water.

Cells are surrounded by a membrane, which has a bilayer of phospholipids. The fatty acids of phospholipids face inside, away from water, whereas the phosphate group can face either the outside environment or the inside of the cell, which are both aqueous.

Through the Indigenous Lens

For the First peoples of the Pacific Northwest the fat rich fish ooligan, with 20% fat by body weight, was a crucial part of the diet of several First Nations. Why? Because fat is the most calorie dense food and having a storable, high calorie compact energy source would be important to survival. The nature of its fat also made it an important trade good. Like salmon, ooligan returns to its birth stream after years at sea. Its arrival in the early spring made it the first fresh food of the year. In the Tsimshianic languages the arrival of the ooligan … was traditionally announced with the cry, ‘Hlaa aat’ixshi halimootxw!’ … meaning ‘Our Saviour has just arrived!’

 

Figure 2.20 Image of cooked ooligan. With 20% fat by body weight, this fat rich fish is a crucial part of the First Nations diet.
Figure 2.20 Image of cooked ooligan. With 20% fat by body weight, this fat rich fish is a crucial part of the First Nations diet.

As you learned above all fats are hydrophobic (water hating).  To isolate the fat, the fish is boiled and the floating fat skimmed off. Ooligan fat composition is 30% saturated fat (like butter) and 55% monounsaturated fat (like plant oils). Importantly it is a solid grease at room temperature. Because it is low in polyunsaturated fats (which oxidize and spoil quickly) it can be stored for later use and used as a trade item. Its composition is said to make it as healthy as olive oil, or better as it has omega 3 fatty acids that reduce risk for diabetes and stroke. It also is rich in three fat soluble vitamins A, E and K.

Steroids and Waxes

Unlike the phospholipids and fats discussed earlier, steroids have a ring structure. Although they do not resemble other lipids, they are grouped with them because they are also hydrophobic. All steroids have four, linked carbon rings and several of them, like cholesterol, have a short tail.

Cholesterol is a steroid. Cholesterol is mainly synthesized in the liver and is the precursor of many steroid hormones, such as testosterone and estradiol. It is also the precursor of vitamins E and K. Cholesterol is the precursor of bile salts, which help in the breakdown of fats and their subsequent absorption by cells. Although cholesterol is often spoken of in negative terms, it is necessary for the proper functioning of the body. It is a key component of the plasma membranes of animal cells.

Waxes are made up of a hydrocarbon chain with an alcohol (–OH) group and a fatty acid. Examples of animal waxes include beeswax and lanolin. Plants also have waxes, such as the coating on their leaves, that helps prevent them from drying out.

Concept in Action


QR Code representing a URL

For an additional perspective on lipids, explore “Biomolecules: The Lipids” through this interactive animation.

Proteins

Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective; they may serve in transport, storage, or membranes; or they may be toxins or enzymes. Each cell in a living system may contain thousands of different proteins, each with a unique function. Their structures, like their functions, vary greatly. They are all, however, polymers of amino acids, arranged in a linear sequence.

The functions of proteins are very diverse because there are 20 different chemically distinct amino acids that form long chains, and the amino acids can be in any order. For example, proteins can function as enzymes or hormones. Enzymes, which are produced by living cells, are catalysts in biochemical reactions (like digestion) and are usually proteins. Each enzyme is specific for the substrate (a reactant that binds to an enzyme) upon which it acts. Enzymes can function to break molecular bonds, to rearrange bonds, or to form new bonds. An example of an enzyme is salivary amylase, which breaks down amylose, a component of starch.

Hormones are chemical signaling molecules, usually proteins or steroids, secreted by an endocrine gland or group of endocrine cells that act to control or regulate specific physiological processes, including growth, development, metabolism, and reproduction. For example, insulin is a protein hormone that maintains blood glucose levels.

Proteins have different shapes and molecular weights; some proteins are globular in shape whereas others are fibrous in nature. For example, hemoglobin is a globular protein, but collagen, found in our skin, is a fibrous protein. Protein shape is critical to its function. Changes in temperature, pH, and exposure to chemicals may lead to permanent changes in the shape of the protein, leading to a loss of function or denaturation (to be discussed in more detail later). All proteins are made up of different arrangements of the same 20 kinds of amino acids.

Amino acids are the monomers that make up proteins. Each amino acid has the same fundamental structure, which consists of a central carbon atom bonded to an amino group (–NH2), a carboxyl group (–COOH), and a hydrogen atom. Every amino acid also has another variable atom or group of atoms bonded to the central carbon atom known as the R group. The R group is the only difference in structure between the 20 amino acids; otherwise, the amino acids are identical.

The fundamental molecular structure of an amino acid is shown. Also shown are the molecular structures of alanine, valine, lysine, and aspartic acid, which vary only in the structure of the R group
Figure 2.21 Amino acids are made up of a central carbon bonded to an amino group (–NH2), a carboxyl group (–COOH), and a hydrogen atom. The central carbon’s fourth bond varies among the different amino acids, as seen in these examples of alanine, valine, lysine, and aspartic acid.

The chemical nature of the R group determines the chemical nature of the amino acid within its protein (that is, whether it is acidic, basic, polar, or nonpolar).

The sequence and number of amino acids ultimately determine a protein’s shape, size, and function. Each amino acid is attached to another amino acid by a covalent bond, known as a peptide bond, which is formed by a dehydration reaction. The carboxyl group of one amino acid and the amino group of a second amino acid combine, releasing a water molecule. The resulting bond is the peptide bond.

The products formed by such a linkage are called polypeptides. While the terms polypeptide and protein are sometimes used interchangeably, a polypeptide is technically a polymer of amino acids, whereas the term protein is used for a polypeptide or polypeptides that have combined together, have a distinct shape, and have a unique function.

Evolution in Action

The Evolutionary Significance of Cytochrome cCytochrome c is an important component of the molecular machinery that harvests energy from glucose. Because this protein’s role in producing cellular energy is crucial, it has changed very little over millions of years. Protein sequencing has shown that there is a considerable amount of sequence similarity among cytochrome c molecules of different species; evolutionary relationships can be assessed by measuring the similarities or differences among various species’ protein sequences.

For example, scientists have determined that human cytochrome c contains 104 amino acids. For each cytochrome c molecule that has been sequenced to date from different organisms, 37 of these amino acids appear in the same position in each cytochrome c. This indicates that all of these organisms are descended from a common ancestor. On comparing the human and chimpanzee protein sequences, no sequence difference was found. When human and rhesus monkey sequences were compared, a single difference was found in one amino acid. In contrast, human-to-yeast comparisons show a difference in 44 amino acids, suggesting that humans and chimpanzees have a more recent common ancestor than humans and the rhesus monkey, or humans and yeast.

Protein Structure

As discussed earlier, the shape of a protein is critical to its function. To understand how the protein gets its final shape or conformation, we need to understand the four levels of protein structure: primary, secondary, tertiary, and quaternary.

The unique sequence and number of amino acids in a polypeptide chain is its primary structure. The unique sequence for every protein is ultimately determined by the gene that encodes the protein. Any change in the gene sequence may lead to a different amino acid being added to the polypeptide chain, causing a change in protein structure and function. In sickle cell anemia, the hemoglobin β chain has a single amino acid substitution, causing a change in both the structure and function of the protein. What is most remarkable to consider is that a hemoglobin molecule is made up of two alpha chains and two beta chains that each consist of about 150 amino acids. The molecule, therefore, has about 600 amino acids. The structural difference between a normal hemoglobin molecule and a sickle cell molecule—that dramatically decreases life expectancy in the affected individuals—is a single amino acid of the 600.

Because of this change of one amino acid in the chain, the normally biconcave, or disc-shaped, red blood cells assume a crescent or “sickle” shape, which clogs arteries. This can lead to a myriad of serious health problems, such as breathlessness, dizziness, headaches, and abdominal pain for those who have this disease.

Folding patterns resulting from interactions between the non-R group portions of amino acids give rise to the secondary structure of the protein. The most common are the alpha (α)-helix and beta (β)-pleated sheet structures. Both structures are held in shape by hydrogen bonds. In the alpha helix, the bonds form between every fourth amino acid and cause a twist in the amino acid chain.

In the β-pleated sheet, the “pleats” are formed by hydrogen bonding between atoms on the backbone of the polypeptide chain. The R groups are attached to the carbons, and extend above and below the folds of the pleat. The pleated segments align parallel to each other, and hydrogen bonds form between the same pairs of atoms on each of the aligned amino acids. The α-helix and β-pleated sheet structures are found in many globular and fibrous proteins.

The unique three-dimensional structure of a polypeptide is known as its tertiary structure. This structure is caused by chemical interactions between various amino acids and regions of the polypeptide. Primarily, the interactions among R groups create the complex three-dimensional tertiary structure of a protein. There may be ionic bonds formed between R groups on different amino acids, or hydrogen bonding beyond that involved in the secondary structure. When protein folding takes place, the hydrophobic R groups of nonpolar amino acids lay in the interior of the protein, whereas the hydrophilic R groups lay on the outside. The former types of interactions are also known as hydrophobic interactions.

In nature, some proteins are formed from several polypeptides, also known as subunits, and the interaction of these subunits forms the quaternary structure. Weak interactions between the subunits help to stabilize the overall structure. For example, hemoglobin is a combination of four polypeptide subunits.

 
Figure_02_03_09
Figure 2.22 The four levels of protein structure can be observed in these illustrations.

Each protein has its own unique sequence and shape held together by chemical interactions. If the protein is subject to changes in temperature, pH, or exposure to chemicals, the protein structure may change, losing its shape in what is known as denaturation as discussed earlier. Denaturation is often reversible because the primary structure is preserved if the denaturing agent is removed, allowing the protein to resume its function. Sometimes denaturation is irreversible, leading to a loss of function. One example of protein denaturation can be seen when an egg is fried or boiled. The albumin protein in the liquid egg white is denatured when placed in a hot pan, changing from a clear substance to an opaque white substance. Not all proteins are denatured at high temperatures; for instance, bacteria that survive in hot springs have proteins that are adapted to function at those temperatures.

Concept in Action

QR Code representing a URL

For an additional perspective on proteins, explore “Biomolecules: The Proteins” through this interactive animation.

Nucleic Acids

Nucleic acids are key macromolecules in the continuity of life. They carry the genetic blueprint of a cell and carry instructions for the functioning of the cell.

The two main types of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA is the genetic material found in all living organisms, ranging from single-celled bacteria to multicellular mammals.

The other type of nucleic acid, RNA, is mostly involved in protein synthesis. The DNA molecules never leave the nucleus, but instead use an RNA intermediary to communicate with the rest of the cell. Other types of RNA are also involved in protein synthesis and its regulation.

DNA and RNA are made up of monomers known as nucleotides. The nucleotides combine with each other to form a polynucleotide, DNA or RNA. Each nucleotide is made up of three components: a nitrogenous base, a pentose (five-carbon) sugar, and a phosphate group . Each nitrogenous base in a nucleotide is attached to a sugar molecule, which is attached to a phosphate group.

 
Structure of a nucleotide.
Figure 2.23 A nucleotide is made up of three components: a nitrogenous base, a pentose sugar, and a phosphate group. 

DNA Double-Helical Structure

DNA has a double-helical structure. It is composed of two strands, or polymers, of nucleotides. The strands are formed with bonds between phosphate and sugar groups of adjacent nucleotides. The strands are bonded to each other at their bases with hydrogen bonds, and the strands coil about each other along their length, hence the “double helix” description, which means a double spiral.

Figure 2.22 Chemical structure of DNA, with colored label identifying the four bases as well as the phosphate and deoxyribose components of the backbone.
Figure 2.24 Chemical structure of DNA, with colored label identifying the four bases as well as the phosphate and deoxyribose components of the backbone.

The alternating sugar and phosphate groups lie on the outside of each strand, forming the backbone of the DNA. The nitrogenous bases are stacked in the interior, like the steps of a staircase, and these bases pair; the pairs are bound to each other by hydrogen bonds. The bases pair in such a way that the distance between the backbones of the two strands is the same all along the molecule.  The rule is that nucleotide A pairs with nucleotide T, and G with C, see section 9.1 for more details.

Section Summary

Living things are carbon-based because carbon plays such a prominent role in the chemistry of living things. The four covalent bonding positions of the carbon atom can give rise to a wide diversity of compounds with many functions, accounting for the importance of carbon in living things. Carbohydrates are a group of macromolecules that are a vital energy source for the cell, provide structural support to many organisms, and can be found on the surface of the cell as receptors or for cell recognition. Carbohydrates are classified as monosaccharides, disaccharides, and polysaccharides, depending on the number of monomers in the molecule.

Lipids are a class of macromolecules that are nonpolar and hydrophobic in nature. Major types include fats and oils, waxes, phospholipids, and steroids. Fats and oils are a stored form of energy and can include triglycerides. Fats and oils are usually made up of fatty acids and glycerol.

Proteins are a class of macromolecules that can perform a diverse range of functions for the cell. They help in metabolism by providing structural support and by acting as enzymes, carriers or as hormones. The building blocks of proteins are amino acids. Proteins are organized at four levels: primary, secondary, tertiary, and quaternary. Protein shape and function are intricately linked; any change in shape caused by changes in temperature, pH, or chemical exposure may lead to protein denaturation and a loss of function.

Nucleic acids are molecules made up of repeating units of nucleotides that direct cellular activities such as cell division and protein synthesis. Each nucleotide is made up of a pentose sugar, a nitrogenous base, and a phosphate group. There are two types of nucleic acids: DNA and RNA.

Exercises

An interactive H5P element has been excluded from this version of the text. You can view it online here:
https://pressbooks.nscc.ca/conceptsofbiologynscc/?p=83#h5p-15

Glossary

amino acid: a monomer of a protein

carbohydrate: a biological macromolecule in which the ratio of carbon to hydrogen to oxygen is 1:2:1; carbohydrates serve as energy sources and structural support in cells

cellulose: a polysaccharide that makes up the cell walls of plants and provides structural support to the cell

chitin: a type of carbohydrate that forms the outer skeleton of arthropods, such as insects and crustaceans, and the cell walls of fungi

denaturation: the loss of shape in a protein as a result of changes in temperature, pH, or exposure to chemicals

deoxyribonucleic acid (DNA): a double-stranded polymer of nucleotides that carries the hereditary information of the cell

disaccharide: two sugar monomers that are linked together by a peptide bond

enzyme: a catalyst in a biochemical reaction that is usually a complex or conjugated protein

fat: a lipid molecule composed of three fatty acids and a glycerol (triglyceride) that typically exists in a solid form at room temperature

glycogen: a storage carbohydrate in animals

hormone: a chemical signaling molecule, usually a protein or steroid, secreted by an endocrine gland or group of endocrine cells; acts to control or regulate specific physiological processes

lipids: a class of macromolecules that are nonpolar and insoluble in water

macromolecule: a large molecule, often formed by polymerization of smaller monomers

monosaccharide: a single unit or monomer of carbohydrates

nucleic acid: a biological macromolecule that carries the genetic information of a cell and carries instructions for the functioning of the cell

nucleotide: a monomer of nucleic acids; contains a pentose sugar, a phosphate group, and a nitrogenous base

oil: an unsaturated fat that is a liquid at room temperature

phospholipid: a major constituent of the membranes of cells; composed of two fatty acids and a phosphate group attached to the glycerol backbone

polypeptide: a long chain of amino acids linked by peptide bonds

polysaccharide: a long chain of monosaccharides; may be branched or unbranched

protein: a biological macromolecule composed of one or more chains of amino acids

ribonucleic acid (RNA): a single-stranded polymer of nucleotides that is involved in protein synthesis

saturated fatty acid: a long-chain hydrocarbon with single covalent bonds in the carbon chain; the number of hydrogen atoms attached to the carbon skeleton is maximized

starch: a storage carbohydrate in plants

steroid: a type of lipid composed of four fused hydrocarbon rings

trans-fat: a form of unsaturated fat with the hydrogen atoms neighboring the double bond across from each other rather than on the same side of the double bond

triglyceride: a fat molecule; consists of three fatty acids linked to a glycerol molecule

unsaturated fatty acid: a long-chain hydrocarbon that has one or more than one double bonds in the hydrocarbon chain

Media Attribution

III

Chapter 3: Introduction to Cell Structure and Function

Left: Human nasal sinus cells as viewed by light microscopy have an irregular round shape and a well-defined nucleus that takes up about one-half of the cell. Middle: Onion skin cells, also viewed by light microscopy, are long and thin with a rectangular shape defined by a cell wall. They are about as wide as a nasal sinus cell, but at least five times as long. The cell wall and nucleus are well defined in the micrograph. The onion skin nucleus is about the same size as the nasal sinus cell nucleus. Right: In this scanning electron micrograph of bacterial cells, the cell surface has a three-dimensional shape. Three of the bacteria are oval in shape. The fourth is round and has protrusions called pili. One pilus connects this bacterium to another.
Figure 3.1 (a) Nasal sinus cells (viewed with a light microscope), (b) onion cells (viewed with a light microscope), and (c) Vibrio tasmaniensis bacterial cells (viewed using a scanning electron microscope) are from very different organisms, yet all share certain characteristics of basic cell structure. Close your eyes and picture a brick wall. What is the basic building block of that wall? It is a single brick, of course. Like a brick wall, your body is composed of basic building blocks, and the building blocks of your body are cells. An average human is thought to have 37.2 trillion cells.

Your body has many kinds of cells, each specialized for a specific purpose. Just as a home is made from a variety of building materials, the human body is constructed from many cell types. For example, epithelial cells protect the surface of the body and cover the organs and body cavities within. Bone cells help to support and protect the body. Cells of the immune system fight invading bacteria. Additionally, red blood cells carry oxygen throughout the body. Each of these cell types plays a vital role during the growth, development, and day-to-day maintenance of the body. In spite of their enormous variety, however, all cells share certain fundamental characteristics.

Search for Key Points in Chapter 3

An interactive H5P element has been excluded from this version of the text. You can view it online here:
https://pressbooks.nscc.ca/conceptsofbiologynscc/?p=86#h5p-16

Media Attribution

6

3.1 How Cells Are Studied

Charles Molnar and Jane Gair

Learning Objectives

By the end of this section, you will be able to:

  • Describe the roles of cells in organisms
  • Compare and contrast light microscopy and electron microscopy
  • Summarize the cell theory

Watch a video about eukaryotic cells

An interactive H5P element has been excluded from this version of the text. You can view it online here:
https://pressbooks.nscc.ca/conceptsofbiologynscc/?p=93#h5p-17

Watch a video about diffusion

An interactive H5P element has been excluded from this version of the text. You can view it online here:
https://pressbooks.nscc.ca/conceptsofbiologynscc/?p=93#h5p-18

A cell is the smallest unit of a living thing. A living thing, like you, is called an organism. Thus, cells are the basic building blocks of all organisms.

In multicellular organisms, several cells of one particular kind interconnect with each other and perform shared functions to form tissues (for example, muscle tissue, connective tissue, and nervous tissue), several tissues combine to form an organ (for example, stomach, heart, or brain), and several organs make up an organ system (such as the digestive system, circulatory system, or nervous system). Several systems functioning together form an organism (such as an elephant, for example).

There are many types of cells, and all are grouped into one of two broad categories: prokaryotic and eukaryotic. Animal cells, plant cells, fungal cells, and protist cells are classified as eukaryotic, whereas bacteria and archaea cells are classified as prokaryotic. Before discussing the criteria for determining whether a cell is prokaryotic or eukaryotic, let us first examine how biologists study cells.

Microscopy

Cells vary in size. With few exceptions, individual cells are too small to be seen with the naked eye, so scientists use microscopes to study them. A microscope is an instrument that magnifies an object. Most images of cells are taken with a microscope and are called micrographs.

Light Microscopes

To give you a sense of the size of a cell, a typical human red blood cell is about eight millionths of a meter or eight micrometers (abbreviated as µm) in diameter; the head of a pin is about two thousandths of a meter (millimeters, or mm) in diameter. That means that approximately 250 red blood cells could fit on the head of a pin.

The optics of the lenses of a light microscope changes the orientation of the image. A specimen that is right-side up and facing right on the microscope slide will appear upside-down and facing left when viewed through a microscope, and vice versa. Similarly, if the slide is moved left while looking through the microscope, it will appear to move right, and if moved down, it will seem to move up. This occurs because microscopes use two sets of lenses to magnify the image. Due to the manner in which light travels through the lenses, this system of lenses produces an inverted image (binoculars and a dissecting microscope work in a similar manner, but include an additional magnification system that makes the final image appear to be upright).

Most student microscopes are classified as light microscopes (Figure 3.2 a). Visible light both passes through and is bent by the lens system to enable the user to see the specimen. Light microscopes are advantageous for viewing living organisms, but since individual cells are generally transparent, their components are not distinguishable unless they are colored with special stains. Staining, however, usually kills the cells.

Light microscopes commonly used in the undergraduate college laboratory magnify up to approximately 400 times. Two parameters that are important in microscopy are magnification and resolving power. Magnification is the degree of enlargement of an object. Resolving power is the ability of a microscope to allow the eye to distinguish two adjacent structures as separate; the higher the resolution, the closer those two objects can be, and the better the clarity and detail of the image. When oil immersion lenses are used, magnification is usually increased to 1,000 times for the study of smaller cells, like most prokaryotic cells. Because light entering a specimen from below is focused onto the eye of an observer, the specimen can be viewed using light microscopy. For this reason, for light to pass through a specimen, the sample must be thin or translucent.

Concept in Action


QR Code representing a URL

For another perspective on cell size, try the HowBig interactive.

A second type of microscope used in laboratories is the dissecting microscope (Figure 3.2 b). These microscopes have a lower magnification (20 to 80 times the object size) than light microscopes and can provide a three-dimensional view of the specimen. Thick objects can be examined with many components in focus at the same time. These microscopes are designed to give a magnified and clear view of tissue structure as well as the anatomy of the whole organism. Like light microscopes, most modern dissecting microscopes are also binocular, meaning that they have two separate lens systems, one for each eye. The lens systems are separated by a certain distance, and therefore provide a sense of depth in the view of their subject to make manipulations by hand easier. Dissecting microscopes also have optics that correct the image so that it appears as if being seen by the naked eye and not as an inverted image. The light illuminating a sample under a dissecting microscope typically comes from above the sample, but may also be directed from below.

 
Part a: This light microscope has binocular lenses and three objective lenses. The sample stage is directly beneath the objective lens. The light microscope sits on a tabletop. Part b: The dissecting microscope has binocular eyepieces, one objective lens, and light sources from both above and below the sample stage. There is room on the stage for a three-dimensional specimen.
Figure 3.2 (a) Most light microscopes used in a college biology lab can magnify cells up to approximately 400 times. (b) Dissecting microscopes have a lower magnification than light microscopes and are used to examine larger objects, such as tissues.

Electron Microscopes

In contrast to light microscopes, electron microscopes use a beam of electrons instead of a beam of light. Not only does this allow for higher magnification and, thus, more detail (Figure 3.4), it also provides higher resolving power. Preparation of a specimen for viewing under an electron microscope will kill it; therefore, live cells cannot be viewed using this type of microscopy. In addition, the electron beam moves best in a vacuum, making it impossible to view living materials.

In a scanning electron microscope, a beam of electrons moves back and forth across a cell’s surface, rendering the details of cell surface characteristics by reflection. Cells and other structures are usually coated with a metal like gold. In a transmission electron microscope, the electron beam is transmitted through the cell and provides details of a cell’s internal structures. As you might imagine, electron microscopes are significantly more bulky and expensive than are light microscopes.

Part a: Salmonella viewed through a light microscope appear as tiny purple dots.
Figure 3.3 Salmonella bacteria are viewed with a light microscope.
Part b: In this scanning electron micrograph, the bacteria appear as three-dimensional red ovals. The human cells are much larger with a complex, folded appearance. Some of the bacteria lie on the surfaces of the human cells, and some are squeezed between them.
Figure 3.4 This scanning electron micrograph shows Salmonella bacteria (in red) invading human cells.

Cytotechnologist: Have you ever heard of a medical test called a Pap smear? In this test, a doctor takes a small sample of cells from the uterine cervix of a patient and sends it to a medical lab where a cytotechnologist stains the cells and examines them for any changes that could indicate cervical cancer or a microbial infection.

Cytotechnologists (cyto– = cell) are professionals who study cells through microscopic examinations and other laboratory tests. They are trained to determine which cellular changes are within normal limits or are abnormal. Their focus is not limited to cervical cells; they study cellular specimens that come from all organs. When they notice abnormalities, they consult a pathologist, who is a medical doctor who can make a clinical diagnosis.

Cytotechnologists play vital roles in saving people’s lives. When abnormalities are discovered early, a patient’s treatment can begin sooner, which usually increases the chances of successful treatment.

Both normal cells and cells infected with HPV have an irregular, round shape and a well-defined nucleus. The infected cells, however, are two to three times as large as uninfected cells, and some have two nuclei.
Figure 3.5 These uterine cervix cells, viewed through a light microscope, were obtained from a Pap smear. Normal cells are on the left. The cells on the right are infected with human papillomavirus.

Cell Theory

The microscopes we use today are far more complex than those used in the 1600s by Antony van Leeuwenhoek, a Dutch shopkeeper who had great skill in crafting lenses. Despite the limitations of his now-ancient lenses, van Leeuwenhoek observed the movements of protists (a type of single-celled organism) and sperm, which he collectively termed “animalcules.”

In a 1665 publication called Micrographia, experimental scientist Robert Hooke coined the term “cell” (from the Latin cella, meaning “small room”) for the box-like structures he observed when viewing cork tissue through a lens. In the 1670s, van Leeuwenhoek discovered bacteria and protozoa. Later advances in lenses and microscope construction enabled other scientists to see different components inside cells.

By the late 1830s, botanist Matthias Schleiden and zoologist Theodor Schwann were studying tissues and proposed the unified cell theory, which states that all living things are composed of one or more cells, that the cell is the basic unit of life, and that all new cells arise from existing cells. These principles still stand today.

Section Summary

A cell is the smallest unit of life. Most cells are so small that they cannot be viewed with the naked eye. Therefore, scientists must use microscopes to study cells. Electron microscopes provide higher magnification, higher resolution, and more detail than light microscopes. The unified cell theory states that all organisms are composed of one or more cells, the cell is the basic unit of life, and new cells arise from existing cells.

Exercises

An interactive H5P element has been excluded from this version of the text. You can view it online here:
https://pressbooks.nscc.ca/conceptsofbiologynscc/?p=93#h5p-19

Glossary

microscope: the instrument that magnifies an object

unified cell theory: the biological concept that states that all organisms are composed of one or more cells, the cell is the basic unit of life, and new cells arise from existing cells

Media Attributions

7

3.2 Comparing Prokaryotic and Eukaryotic Cells

Charles Molnar and Jane Gair

Learning Objectives

By the end of this section, you will be able to:

  • Name examples of prokaryotic and eukaryotic organisms
  • Compare and contrast prokaryotic cells and eukaryotic cells
  • Describe the relative sizes of different kinds of cells

Cells fall into one of two broad categories: prokaryotic and eukaryotic. The predominantly single-celled organisms of the domains Bacteria and Archaea are classified as prokaryotes (pro– = before; –karyon– = nucleus). Animal cells, plant cells, fungi, and protists are eukaryotes (eu– = true).

Components of Prokaryotic Cells

All cells share four common components: 1) a plasma membrane, an outer covering that separates the cell’s interior from its surrounding environment; 2) cytoplasm, consisting of a jelly-like region within the cell in which other cellular components are found; 3) DNA, the genetic material of the cell; and 4) ribosomes, particles that synthesize proteins. However, prokaryotes differ from eukaryotic cells in several ways.

A prokaryotic cell is a simple, single-celled (unicellular) organism that lacks a nucleus, or any other membrane-bound organelle. We will shortly come to see that this is significantly different in eukaryotes. Prokaryotic DNA is found in the central part of the cell: a darkened region called the nucleoid.

 
In this illustration, the prokaryotic cell has an oval shape. The circular chromosome is concentrated in a region called the nucleoid. The fluid inside the cell is called the cytoplasm. Ribosomes, depicted as small circles, float in the cytoplasm. The cytoplasm is encased in a plasma membrane, which in turn is encased by a cell wall. A capsule surrounds the cell wall. The bacterium depicted has a flagellum protruding from one narrow end. Pili are small protrusions that extend from the capsule in all directions.
Figure 3.6 This figure shows the generalized structure of a prokaryotic cell.

Unlike Archaea and eukaryotes, bacteria have a cell wall made of peptidoglycan, comprised of sugars and amino acids, and many have a polysaccharide capsule (Figure 3.6). The cell wall acts as an extra layer of protection, helps the cell maintain its shape, and prevents dehydration. The capsule enables the cell to attach to surfaces in its environment. Some prokaryotes have flagella, pili, or fimbriae. Flagella are used for locomotion, while most pili are used to exchange genetic material during a type of reproduction called conjugation.

Eukaryotic Cells

In nature, the relationship between form and function is apparent at all levels, including the level of the cell, and this will become clear as we explore eukaryotic cells. The principle “form follows function” is found in many contexts. For example, birds and fish have streamlined bodies that allow them to move quickly through the medium in which they live, be it air or water. It means that, in general, one can deduce the function of a structure by looking at its form, because the two are matched.

A eukaryotic cell is a cell that has a membrane-bound nucleus and other membrane-bound compartments or sacs, called organelles, which have specialized functions. The word eukaryotic means “true kernel” or “true nucleus,” alluding to the presence of the membrane-bound nucleus in these cells. The word “organelle” means “little organ,” and, as already mentioned, organelles have specialized cellular functions, just as the organs of your body have specialized functions.

Cell Size

At 0.1–5.0 µm in diameter, prokaryotic cells are significantly smaller than eukaryotic cells, which have diameters ranging from 10–100 µm (Figure 3.7). The small size of prokaryotes allows ions and organic molecules that enter them to quickly spread to other parts of the cell. Similarly, any wastes produced within a prokaryotic cell can quickly move out. However, larger eukaryotic cells have evolved different structural adaptations to enhance cellular transport. Indeed, the large size of these cells would not be possible without these adaptations. In general, cell size is limited because volume increases much more quickly than does cell surface area. As a cell becomes larger, it becomes more and more difficult for the cell to acquire sufficient materials to support the processes inside the cell, because the relative size of the surface area across which materials must be transported declines.

 
Relative sizes on a logarithmic scale, from 0.1 nm to 1 m, are shown. Objects are shown from smallest to largest. The smallest object shown, an atom, is about 1 nm in size. The next largest objects shown are lipids and proteins; these molecules are between 1 and 10 nm. Bacteria are about 100 nm, and mitochondria are about 1 µm. Plant and animal cells are both between 10 and 100 µm. A human egg is between 100 µm and 1 mm. A frog egg is about 1 mm, a chicken egg and an ostrich egg are both between 10 and 100 mm, but a chicken egg is larger. For comparison, a human is approximately 1 m tall.
Figure 3.7 This figure shows the relative sizes of different kinds of cells and cellular components. An adult human is shown for comparison.

Section Summary

Prokaryotes are predominantly single-celled organisms of the domains Bacteria and Archaea. All prokaryotes have plasma membranes, cytoplasm, ribosomes, a cell wall, DNA, and lack membrane-bound organelles. Many also have polysaccharide capsules. Prokaryotic cells range in diameter from 0.1–5.0 µm.

Like a prokaryotic cell, a eukaryotic cell has a plasma membrane, cytoplasm, and ribosomes, but a eukaryotic cell is typically larger than a prokaryotic cell, has a true nucleus (meaning its DNA is surrounded by a membrane), and has other membrane-bound organelles that allow for compartmentalization of functions. Eukaryotic cells tend to be 10 to 100 times the size of prokaryotic cells.

Exercises

An interactive H5P element has been excluded from this version of the text. You can view it online here:
https://pressbooks.nscc.ca/conceptsofbiologynscc/?p=97#h5p-20

Glossary

eukaryotic cell: a cell that has a membrane-bound nucleus and several other membrane-bound compartments or sacs

organelle: a membrane-bound compartment or sac within a cell

prokaryotic cell: a unicellular organism that lacks a nucleus or any other membrane-bound organelle

8

3.3 Eukaryotic Cells

Charles Molnar and Jane Gair

Learning Objectives

By the end of this section, you will be able to:

  • Describe the structure of eukaryotic plant and animal cells
  • State the role of the plasma membrane
  • Summarize the functions of the major cell organelles
  • Describe the cytoskeleton and extracellular matrix

Watch a video about oxygen in the atmosphere.

An interactive H5P element has been excluded from this version of the text. You can view it online here:
https://pressbooks.nscc.ca/conceptsofbiologynscc/?p=113#h5p-21

 

At this point, it should be clear that eukaryotic cells have a more complex structure than do prokaryotic cells. Organelles allow for various functions to occur in the cell at the same time. Before discussing the functions of organelles within a eukaryotic cell, let us first examine two important components of the cell: the plasma membrane and the cytoplasm.

Part a: This illustration shows a typical eukaryotic cell, which is egg shaped. The fluid inside the cell is called the cytoplasm, and the cell is surrounded by a cell membrane. The nucleus takes up about one-half of the width of the cell. Inside the nucleus is the chromatin, which is comprised of DNA and associated proteins. A region of the chromatin is condensed into the nucleolus, a structure in which ribosomes are synthesized. The nucleus is encased in a nuclear envelope, which is perforated by protein-lined pores that allow entry of material into the nucleus. The nucleus is surrounded by the rough and smooth endoplasmic reticulum, or ER. The smooth ER is the site of lipid synthesis. The rough ER has embedded ribosomes that give it a bumpy appearance. It synthesizes membrane and secretory proteins. Besides the ER, many other organelles float inside the cytoplasm. These include the Golgi apparatus, which modifies proteins and lipids synthesized in the ER. The Golgi apparatus is made of layers of flat membranes. Mitochondria, which produce energy for the cell, have an outer membrane and a highly folded inner membrane. Other, smaller organelles include peroxisomes that metabolize waste, lysosomes that digest food, and vacuoles. Ribosomes, responsible for protein synthesis, also float freely in the cytoplasm and are depicted as small dots. The last cellular component shown is the cytoskeleton, which has four different types of components: microfilaments, intermediate filaments, microtubules, and centrosomes. Microfilaments are fibrous proteins that line the cell membrane and make up the cellular cortex. Intermediate filaments are fibrous proteins that hold organelles in place. Microtubules form the mitotic spindle and maintain cell shape. Centrosomes are made of two tubular structures at right angles to one another. They form the microtubule-organizing center.Figure_03_03_01a_new
Figure 3.8 (a) This figure shows a typical animal cell
Part b: This illustration depicts a typical eukaryotic plant cell. The nucleus of a plant cell contains chromatin and a nucleolus, the same as in an animal cell. Other structures that a plant cell has in common with an animal cell include rough and smooth ER, the Golgi apparatus, mitochondria, peroxisomes, and ribosomes. The fluid inside the plant cell is called the cytoplasm, just as in an animal cell. The plant cell has three of the four cytoskeletal components found in animal cells: microtubules, intermediate filaments, and microfilaments. Plant cells do not have centrosomes. Plants have five structures not found in animals cells: plasmodesmata, chloroplasts, plastids, a central vacuole, and a cell wall. Plasmodesmata form channels between adjacent plant cells. Chloroplasts are responsible for photosynthesis; they have an outer membrane, an inner membrane, and stack of membranes inside the inner membrane. The central vacuole is a very large, fluid-filled structure that maintains pressure against the cell wall. Plastids store pigments. The cell wall is localized outside the cell membrane.
Figure 3.8 (b) This figures shows a typical plant cell.

What structures does a plant cell have that an animal cell does not have? What structures does an animal cell have that a plant cell does not have? Plant cells have plasmodesmata, a cell wall, a large central vacuole, chloroplasts, and plastids. Animal cells have lysosomes and centrosomes.

The Plasma Membrane

Like prokaryotes, eukaryotic cells have a plasma membrane (Figure 3.9) made up of a phospholipid bilayer with embedded proteins that separates the internal contents of the cell from its surrounding environment. A phospholipid is a lipid molecule composed of two fatty acid chains, a glycerol backbone, and a phosphate group. The plasma membrane regulates the passage of some substances, such as organic molecules, ions, and water, preventing the passage of some to maintain internal conditions, while actively bringing in or removing others. Other compounds move passively across the membrane.

the plasma membrane is composed of a phospholipid bilayer. in the bilayer, the two long hydrophobic tails of phospholipids face toward the center, and the hydrophilic head group faces the exterior. Integral membrane proteins and protein channels span the entire bilayer. Protein channels have a pore in the middle. Peripheral membrane proteins sit on the surface of the phospholipids and are associated with the head groups. On the exterior side of the membrane, carbohydrates are attached to certain proteins and lipids. Filaments of the cytoskeleton line the interior of the membrane.
Figure 3.9 The plasma membrane is a phospholipid bilayer with embedded proteins. There are other components, such as cholesterol and carbohydrates, which can be found in the membrane in addition to phospholipids and protein.

The plasma membranes of cells that specialize in absorption are folded into fingerlike projections called microvilli (singular = microvillus). This folding increases the surface area of the plasma membrane. Such cells are typically found lining the small intestine, the organ that absorbs nutrients from digested food. This is an excellent example of form matching the function of a structure.

People with celiac disease have an immune response to gluten, which is a protein found in wheat, barley, and rye. The immune response damages microvilli, and thus, afflicted individuals cannot absorb nutrients. This leads to malnutrition, cramping, and diarrhea. Patients suffering from celiac disease must follow a gluten-free diet.

The Cytoplasm

The cytoplasm comprises the contents of a cell between the plasma membrane and the nuclear envelope (a structure to be discussed shortly). It is made up of organelles suspended in the gel-like cytosol, the cytoskeleton, and various chemicals. Even though the cytoplasm consists of 70 to 80 percent water, it has a semi-solid consistency, which comes from the proteins within it. However, proteins are not the only organic molecules found in the cytoplasm. Glucose and other simple sugars, polysaccharides, amino acids, nucleic acids, fatty acids, and derivatives of glycerol are found there too. Ions of sodium, potassium, calcium, and many other elements are also dissolved in the cytoplasm. Many metabolic reactions, including protein synthesis, take place in the cytoplasm.

The Cytoskeleton

If you were to remove all the organelles from a cell, would the plasma membrane and the cytoplasm be the only components left? No. Within the cytoplasm, there would still be ions and organic molecules, plus a network of protein fibers that helps to maintain the shape of the cell, secures certain organelles in specific positions, allows cytoplasm and vesicles to move within the cell, and enables unicellular organisms to move independently. Collectively, this network of protein fibers is known as the cytoskeleton. There are three types of fibers within the cytoskeleton: microfilaments, also known as actin filaments, intermediate filaments, and microtubules (Figure 3.10).

 
Microfilaments line the inside of the plasma membrane, whereas microfilaments radiate out from the center of the cell. Intermediate filaments form a network throughout the cell that holds organelles in place.
Figure 3.10 Microfilaments, intermediate filaments, and microtubules compose a cell’s cytoskeleton.

Microfilaments are the thinnest of the cytoskeletal fibers and function in moving cellular components, for example, during cell division. They also maintain the structure of microvilli, the extensive folding of the plasma membrane found in cells dedicated to absorption. These components are also common in muscle cells and are responsible for muscle cell contraction. Intermediate filaments are of intermediate diameter and have structural functions, such as maintaining the shape of the cell and anchoring organelles. Keratin, the compound that strengthens hair and nails, forms one type of intermediate filament. Microtubules are the thickest of the cytoskeletal fibers. These are hollow tubes that can dissolve and reform quickly. Microtubules guide organelle movement and are the structures that pull chromosomes to their poles during cell division. They are also the structural components of flagella and cilia. In cilia and flagella, the microtubules are organized as a circle of nine double microtubules on the outside and two microtubules in the center.

The centrosome is a region near the nucleus of animal cells that functions as a microtubule-organizing center. It contains a pair of centrioles, two structures that lie perpendicular to each other. Each centriole is a cylinder of nine triplets of microtubules.

The centrosome replicates itself before a cell divides, and the centrioles play a role in pulling the duplicated chromosomes to opposite ends of the dividing cell. However, the exact function of the centrioles in cell division is not clear, since cells that have the centrioles removed can still divide, and plant cells, which lack centrioles, are capable of cell division.

Flagella and Cilia

Flagella (singular = flagellum) are long, hair-like structures that extend from the plasma membrane and are used to move an entire cell, (for example, sperm, Euglena). When present, the cell has just one flagellum or a few flagella. When cilia (singular = cilium) are present, however, they are many in number and extend along the entire surface of the plasma membrane. They are short, hair-like structures that are used to move entire cells (such as paramecium) or move substances along the outer surface of the cell (for example, the cilia of cells lining the fallopian tubes that move the ovum toward the uterus, or cilia lining the cells of the respiratory tract that move particulate matter toward the throat that mucus has trapped).

The Endomembrane System

The endomembrane system (endo = within) is a group of membranes and organelles in eukaryotic cells that work together to modify, package, and transport lipids and proteins. It includes the nuclear envelope, lysosomes, vesicles, endoplasmic reticulum and the Golgi apparatus, which we will cover shortly. Although not technically within the cell, the plasma membrane is included in the endomembrane system because, as you will see, it interacts with the other endomembranous organelles.

The Nucleus

Typically, the nucleus is the most prominent organelle in a cell. The nucleus (plural = nuclei) houses the cell’s DNA in the form of chromatin and directs the synthesis of ribosomes and proteins. Let us look at it in more detail (Figure 3.11).

 
In this illustration, chromatin floats in the nucleoplasm. The nucleoid is depicted as a dense, circular region inside the nucleus. The double nuclear membrane is perforated with protein-lined pores
Figure 3.11 The outermost boundary of the nucleus is the nuclear envelope. Notice that the nuclear envelope consists of two phospholipid bilayers (membranes)—an outer membrane and an inner membrane—in contrast to the plasma membrane, which consists of only one phospholipid bilayer.

The nuclear envelope is a double-membrane structure that constitutes the outermost portion of the nucleus (Figure 3.11). Both the inner and outer membranes of the nuclear envelope are phospholipid bilayers.

The nuclear envelope is punctuated with pores that control the passage of ions, molecules, and RNA between the nucleoplasm and the cytoplasm.

To understand chromatin, it is helpful to first consider chromosomes. Chromosomes are structures within the nucleus that are made up of DNA, the hereditary material, and proteins. This combination of DNA and proteins is called chromatin. In eukaryotes, chromosomes are linear structures. Every species has a specific number of chromosomes in the nucleus of its body cells. For example, in humans, the chromosome number is 46, whereas in fruit flies, the chromosome number is eight.

Chromosomes are only visible and distinguishable from one another when the cell is getting ready to divide. When the cell is in the growth and maintenance phases of its life cycle, the chromosomes resemble an unwound, jumbled bunch of threads.

This image shows various levels of the organization of chromatin (DNA and protein).
Figure 3.12 This image shows various levels of the organization of chromatin (DNA and protein).
This image shows paired chromosomes
Figure 3.13 This image shows paired chromosomes. (credit: modification of work by NIH; scale-bar data from Matt Russell)

We already know that the nucleus directs the synthesis of ribosomes, but how does it do this? Some chromosomes have sections of DNA that encode ribosomal RNA. A darkly stained area within the nucleus, called the nucleolus (plural = nucleoli), aggregates the ribosomal RNA with associated proteins to assemble the ribosomal subunits that are then transported through the nuclear pores into the cytoplasm.

The Endoplasmic Reticulum

The endoplasmic reticulum (ER) is a series of interconnected membranous tubules that collectively modify proteins and synthesize lipids. However, these two functions are performed in separate areas of the endoplasmic reticulum: the rough endoplasmic reticulum and the smooth endoplasmic reticulum, respectively.

The hollow portion of the ER tubules is called the lumen or cisternal space. The membrane of the ER, which is a phospholipid bilayer embedded with proteins, is continuous with the nuclear envelope.

The rough endoplasmic reticulum (RER) is so named because the ribosomes attached to its cytoplasmic surface give it a studded appearance when viewed through an electron microscope.

The ribosomes synthesize proteins while attached to the ER, resulting in the transfer of their newly synthesized proteins into the lumen of the RER where they undergo modifications such as folding or addition of sugars. The RER also makes phospholipids for cell membranes.

If the phospholipids or modified proteins are not destined to stay in the RER, they will be packaged within vesicles and transported from the RER by budding from the membrane. Since the RER is engaged in modifying proteins that will be secreted from the cell, it is abundant in cells that secrete proteins, such as the liver.

The smooth endoplasmic reticulum (SER) is continuous with the RER but has few or no ribosomes on its cytoplasmic surface. The SER’s functions include synthesis of carbohydrates, lipids (including phospholipids), and steroid hormones; detoxification of medications and poisons; alcohol metabolism; and storage of calcium ions.

The Golgi Apparatus

We have already mentioned that vesicles can bud from the ER, but where do the vesicles go? Before reaching their final destination, the lipids or proteins within the transport vesicles need to be sorted, packaged, and tagged so that they wind up in the right place. The sorting, tagging, packaging, and distribution of lipids and proteins take place in the Golgi apparatus (also called the Golgi body), a series of flattened membranous sacs.

In this transmission electron micrograph, the Golgi apparatus appears as a stack of membranes surrounded by unnamed organelles.
Figure 3.14 The Golgi apparatus in this transmission electron micrograph of a white blood cell is visible as a stack of semicircular flattened rings in the lower portion of this image. Several vesicles can be seen near the Golgi apparatus. (credit: modification of work by Louisa Howard; scale-bar data from Matt Russell)

The Golgi apparatus has a receiving face near the endoplasmic reticulum and a releasing face on the side away from the ER, toward the cell membrane. The transport vesicles that form from the ER travel to the receiving face, fuse with it, and empty their contents into the lumen of the Golgi apparatus. As the proteins and lipids travel through the Golgi, they undergo further modifications. The most frequent modification is the addition of short chains of sugar molecules. The newly modified proteins and lipids are then tagged with small molecular groups to enable them to be routed to their proper destinations.

Finally, the modified and tagged proteins are packaged into vesicles that bud from the opposite face of the Golgi. While some of these vesicles, transport vesicles, deposit their contents into other parts of the cell where they will be used, others, secretory vesicles, fuse with the plasma membrane and release their contents outside the cell.

The amount of Golgi in different cell types again illustrates that form follows function within cells. Cells that engage in a great deal of secretory activity (such as cells of the salivary glands that secrete digestive enzymes or cells of the immune system that secrete antibodies) have an abundant number of Golgi.

In plant cells, the Golgi has an additional role of synthesizing polysaccharides, some of which are incorporated into the cell wall and some of which are used in other parts of the cell.

Lysosomes

In animal cells, the lysosomes are the cell’s “garbage disposal.” Digestive enzymes within the lysosomes aid the breakdown of proteins, polysaccharides, lipids, nucleic acids, and even worn-out organelles. In single-celled eukaryotes, lysosomes are important for digestion of the food they ingest and the recycling of organelles. These enzymes are active at a much lower pH (more acidic) than those located in the cytoplasm. Many reactions that take place in the cytoplasm could not occur at a low pH, thus the advantage of compartmentalizing the eukaryotic cell into organelles is apparent.

Lysosomes also use their hydrolytic enzymes to destroy disease-causing organisms that might enter the cell. A good example of this occurs in a group of white blood cells called macrophages, which are part of your body’s immune system. In a process known as phagocytosis, a section of the plasma membrane of the macrophage invaginates (folds in) and engulfs a pathogen. The invaginated section, with the pathogen inside, then pinches itself off from the plasma membrane and becomes a vesicle. The vesicle fuses with a lysosome. The lysosome’s hydrolytic enzymes then destroy the pathogen (Figure 3.15).

In this illustration, a eukaryotic cell is shown consuming a bacterium. As the bacterium is consumed, it is encapsulated into a vesicle. The vesicle fuses with a lysosome, and proteins inside the lysosome digest the bacterium.
Figure 3.15 A macrophage has phagocytized a potentially pathogenic bacterium into a vesicle, which then fuses with a lysosome within the cell so that the pathogen can be destroyed. Other organelles are present in the cell, but for simplicity, are not shown.

Vesicles and Vacuoles

Vesicles and vacuoles are membrane-bound sacs that function in storage and transport. Vacuoles are somewhat larger than vesicles, and the membrane of a vacuole does not fuse with the membranes of other cellular components. Vesicles can fuse with other membranes within the cell system. Additionally, enzymes within plant vacuoles can break down macromolecules.

 
This figure shows the nucleus, rough ER, Golgi apparatus, vesicles, and plasma membrane. The right side of the rough ER is shown with an integral membrane protein embedded in it. The part of the protein facing the inside of the ER has a carbohydrate attached to it. The protein is shown leaving the ER in a vesicle that fuses with the cis face of the Golgi apparatus. The Golgi apparatus consists of several layers of membranes, called cisternae. As the protein passes through the cisternae, it is further modified by the addition of more carbohydrates. Eventually, it leaves the trans face of the Golgi in a vesicle. The vesicle fuses with the cell membrane so that the carbohydrate that was on the inside of the vesicle faces the outside of the membrane. At the same time, the contents of the vesicle are released from the cell.
Figure 3.16 The endomembrane system works to modify, package, and transport lipids and proteins.

Why does the cis face of the Golgi not face the plasma membrane?

<!– Because that face receives chemicals from the ER, which is toward the center of the cell. –>

Ribosomes

Ribosomes are the cellular structures responsible for protein synthesis. When viewed through an electron microscope, free ribosomes appear as either clusters or single tiny dots floating freely in the cytoplasm. Ribosomes may be attached to either the cytoplasmic side of the plasma membrane or the cytoplasmic side of the endoplasmic reticulum. Electron microscopy has shown that ribosomes consist of large and small subunits. Ribosomes are enzyme complexes that are responsible for protein synthesis.

Because protein synthesis is essential for all cells, ribosomes are found in practically every cell, although they are smaller in prokaryotic cells. They are particularly abundant in immature red blood cells for the synthesis of hemoglobin, which functions in the transport of oxygen throughout the body.

Mitochondria

Mitochondria (singular = mitochondrion) are often called the “powerhouses” or “energy factories” of a cell because they are responsible for making adenosine triphosphate (ATP), the cell’s main energy-carrying molecule. The formation of ATP from the breakdown of glucose is known as cellular respiration. Mitochondria are oval-shaped, double-membrane organelles (Figure 3.17) that have their own ribosomes and DNA. Each membrane is a phospholipid bilayer embedded with proteins. The inner layer has folds called cristae, which increase the surface area of the inner membrane. The area surrounded by the folds is called the mitochondrial matrix. The cristae and the matrix have different roles in cellular respiration.

In keeping with our theme of form following function, it is important to point out that muscle cells have a very high concentration of mitochondria because muscle cells need a lot of energy to contract.

This transmission electron micrograph of a mitochondrion shows an oval, outer membrane and an inner membrane with many folds called cristae. Inside of the inner membrane is a space called the mitochondrial matrix.
Figure 3.17 This transmission electron micrograph shows a mitochondrion as viewed with an electron microscope. Notice the inner and outer membranes, the cristae, and the mitochondrial matrix.

Peroxisomes

Peroxisomes are small, round organelles enclosed by single membranes. They carry out oxidation reactions that break down fatty acids and amino acids. They also detoxify many poisons that may enter the body. Alcohol is detoxified by peroxisomes in liver cells. A byproduct of these oxidation reactions is hydrogen peroxide, H2O2, which is contained within the peroxisomes to prevent the chemical from causing damage to cellular components outside of the organelle. Hydrogen peroxide is safely broken down by peroxisomal enzymes into water and oxygen.

Animal Cells versus Plant Cells

Despite their fundamental similarities, there are some striking differences between animal and plant cells (see Table 3.1). Animal cells have centrioles, centrosomes (discussed under the cytoskeleton), and lysosomes, whereas plant cells do not. Plant cells have a cell wall, chloroplasts, plasmodesmata, and plastids used for storage, and a large central vacuole, whereas animal cells do not.

The Cell Wall

In Figure 3.8 b, the diagram of a plant cell, you see a structure external to the plasma membrane called the cell wall. The cell wall is a rigid covering that protects the cell, provides structural support, and gives shape to the cell. Fungal and protist cells also have cell walls.

While the chief component of prokaryotic cell walls is peptidoglycan, the major organic molecule in the plant cell wall is cellulose, a polysaccharide made up of long, straight chains of glucose units. When nutritional information refers to dietary fiber, it is referring to the cellulose content of food.

Chloroplasts

Like mitochondria, chloroplasts also have their own DNA and ribosomes. Chloroplasts function in photosynthesis and can be found in eukaryotic cells such as plants and algae. In photosynthesis, carbon dioxide, water, and light energy are used to make glucose and oxygen. This is the major difference between plants and animals: Plants (autotrophs) are able to make their own food, like glucose, whereas animals (heterotrophs) must rely on other organisms for their organic compounds or food source.

Like mitochondria, chloroplasts have outer and inner membranes, but within the space enclosed by a chloroplast’s inner membrane is a set of interconnected and stacked, fluid-filled membrane sacs called thylakoids (Figure 3.18). Each stack of thylakoids is called a granum (plural = grana). The fluid enclosed by the inner membrane and surrounding the grana is called the stroma.

This illustration shows a chloroplast, which has an outer membrane and an inner membrane. The space between the outer and inner membranes is called the intermembrane space. Inside the inner membrane are flat, pancake-like structures called thylakoids. The thylakoids form stacks called grana. The liquid inside the inner membrane is called the stroma, and the space inside the thylakoid is called the thylakoid space.
Figure 3.18 This simplified diagram of a chloroplast shows the outer membrane, inner membrane, thylakoids, grana, and stroma.

The chloroplasts contain a green pigment called chlorophyll, which captures the energy of sunlight for photosynthesis. Like plant cells, photosynthetic protists also have chloroplasts. Some bacteria also perform photosynthesis, but they do not have chloroplasts. Their photosynthetic pigments are located in the thylakoid membrane within the cell itself.

Evolution in Action

Endosymbiosis: We have mentioned that both mitochondria and chloroplasts contain DNA and ribosomes. Have you wondered why? Strong evidence points to endosymbiosis as the explanation.

Symbiosis is a relationship in which organisms from two separate species live in close association and typically exhibit specific adaptations to each other. Endosymbiosis (endo-= within) is a relationship in which one organism lives inside the other. Endosymbiotic relationships abound in nature. Microbes that produce vitamin K live inside the human gut. This relationship is beneficial for us because we are unable to synthesize vitamin K. It is also beneficial for the microbes because they are protected from other organisms and are provided a stable habitat and abundant food by living within the large intestine.

Scientists have long noticed that bacteria, mitochondria, and chloroplasts are similar in size. We also know that mitochondria and chloroplasts have DNA and ribosomes, just as bacteria do and they resemble the types found in bacteria. Scientists believe that host cells and bacteria formed a mutually beneficial endosymbiotic relationship when the host cells ingested aerobic bacteria and cyanobacteria but did not destroy them. Through evolution, these ingested bacteria became more specialized in their functions, with the aerobic bacteria becoming mitochondria and the photosynthetic bacteria becoming chloroplasts.

The Central Vacuole

Previously, we mentioned vacuoles as essential components of plant cells. If you look at Figure 3.8 b, you will see that plant cells each have a large, central vacuole that occupies most of the cell. The central vacuole plays a key role in regulating the cell’s concentration of water in changing environmental conditions. In plant cells, the liquid inside the central vacuole provides turgor pressure, which is the outward pressure caused by the fluid inside the cell. Have you ever noticed that if you forget to water a plant for a few days, it wilts? That is because as the water concentration in the soil becomes lower than the water concentration in the plant, water moves out of the central vacuoles and cytoplasm and into the soil. As the central vacuole shrinks, it leaves the cell wall unsupported. This loss of support to the cell walls of a plant results in the wilted appearance. Additionally, this fluid has a very bitter taste, which discourages consumption by insects and animals. The central vacuole also functions to store proteins in developing seed cells.

Extracellular Matrix of Animal Cells

Most animal cells release materials into the extracellular space. The primary components of these materials are glycoproteins and the protein collagen. Collectively, these materials are called the extracellular matrix (Figure 3.19). Not only does the extracellular matrix hold the cells together to form a tissue, but it also allows the cells within the tissue to communicate with each other.

This illustration shows the plasma membrane. Embedded in the plasma membrane are integral membrane proteins called integrins. On the exterior of the cell is a vast network of collagen fibers, which are attached to the integrins via a protein called fibronectin. Proteoglycan complexes also extend from the plasma membrane into the extracellular matrix. A magnified view shows that each proteoglycan complex is composed of a polysaccharide core. Proteins branch from this core, and carbohydrates branch from the proteins. The inside of the cytoplasmic membrane is lined with microfilaments of the cytoskeleton.
Figure 3.19 The extracellular matrix consists of a network of substances secreted by cells. 

Blood clotting provides an example of the role of the extracellular matrix in cell communication. When the cells lining a blood vessel are damaged, they display a protein receptor called tissue factor. When tissue factor binds with another factor in the extracellular matrix, it causes platelets to adhere to the wall of the damaged blood vessel, stimulates adjacent smooth muscle cells in the blood vessel to contract (thus constricting the blood vessel), and initiates a series of steps that stimulate the platelets to produce clotting factors.

Intercellular Junctions

Cells can also communicate with each other by direct contact, referred to as intercellular junctions. There are some differences in the ways that plant and animal cells do this. Plasmodesmata (singular = plasmodesma) are junctions between plant cells, whereas animal cell contacts include tight and gap junctions, and desmosomes.

In general, long stretches of the plasma membranes of neighboring plant cells cannot touch one another because they are separated by the cell walls surrounding each cell. Plasmodesmata are numerous channels that pass between the cell walls of adjacent plant cells, connecting their cytoplasm and enabling signal molecules and nutrients to be transported from cell to cell (Figure 3.20 a).

Part a shows two plant cells side-by-side. A channel, or plasmodesma, in the cell wall allows fluid and small molecules to pass from the cytoplasm of one cell to the cytoplasm of another. Part b shows two cell membranes joined together by a matrix of tight junctions. Part c shows two cells fused together by a desmosome. Cadherins extend out from each cell and join the two cells together. Intermediate filaments connect to cadherins on the inside of the cell. Part d shows two cells joined together with protein pores called gap junctions that allow water and small molecules to pass through.
Figure 3.20 There are four kinds of connections between cells. (a) A plasmodesma is a channel between the cell walls of two adjacent plant cells. (b) Tight junctions join adjacent animal cells. (c) Desmosomes join two animal cells together. (d) Gap junctions act as channels between animal cells.

A tight junction is a watertight seal between two adjacent animal cells (Figure 3.20 b). Proteins hold the cells tightly against each other. This tight adhesion prevents materials from leaking between the cells. Tight junctions are typically found in the epithelial tissue that lines internal organs and cavities, and composes most of the skin. For example, the tight junctions of the epithelial cells lining the urinary bladder prevent urine from leaking into the extracellular space.

Also found only in animal cells are desmosomes, which act like spot welds between adjacent epithelial cells (Figure 3.20 c). They keep cells together in a sheet-like formation in organs and tissues that stretch, like the skin, heart, and muscles.

Gap junctions in animal cells are like plasmodesmata in plant cells in that they are channels between adjacent cells that allow for the transport of ions, nutrients, and other substances that enable cells to communicate (Figure 3.20 d). Structurally, however, gap junctions and plasmodesmata differ.

Table 3.1 Components of Prokaryotic and Eukaryotic Cells and Their Functions

Cell Component

Function

Present in Prokaryotes?

Present in Animal Cells?

Present in Plant Cells?

Plasma membrane Separates cell from external environment; controls passage of organic molecules, ions, water, oxygen, and wastes into and out of the cell Yes Yes Yes
Cytoplasm Provides structure to cell; site of many metabolic reactions; medium in which organelles are found Yes Yes Yes
Nucleoid Location of DNA Yes No No
Nucleus Cell organelle that houses DNA and directs synthesis of ribosomes and proteins No Yes Yes
Ribosomes Protein synthesis Yes Yes Yes
Mitochondria ATP production/cellular respiration No Yes Yes
Peroxisomes Oxidizes and breaks down fatty acids and amino acids, and detoxifies poisons No Yes Yes
Vesicles and vacuoles Storage and transport; digestive function in plant cells No Yes Yes
Centrosome Unspecified role in cell division in animal cells; organizing center of microtubules in animal cells No Yes No
Lysosomes Digestion of macromolecules; recycling of worn-out organelles No Yes No
Cell wall Protection, structural support and maintenance of cell shape Yes, primarily peptidoglycan in bacteria but not Archaea No Yes, primarily cellulose
Chloroplasts Photosynthesis No No Yes
Endoplasmic reticulum Modifies proteins and synthesizes lipids No Yes Yes
Golgi apparatus Modifies, sorts, tags, packages, and distributes lipids and proteins No Yes Yes
Cytoskeleton Maintains cell’s shape, secures organelles in specific positions, allows cytoplasm and vesicles to move within the cell, and enables unicellular organisms to move independently Yes Yes Yes
Flagella Cellular locomotion Some Some No, except for some plant sperm.
Cilia Cellular locomotion, movement of particles along extracellular surface of plasma membrane, and filtration No Some No

Section Summary

Like a prokaryotic cell, a eukaryotic cell has a plasma membrane, cytoplasm, and ribosomes, but a eukaryotic cell is typically larger than a prokaryotic cell, has a true nucleus (meaning its DNA is surrounded by a membrane), and has other membrane-bound organelles that allow for compartmentalization of functions. The plasma membrane is a phospholipid bilayer embedded with proteins. The nucleolus within the nucleus is the site for ribosome assembly. Ribosomes are found in the cytoplasm or are attached to the cytoplasmic side of the plasma membrane or endoplasmic reticulum. They perform protein synthesis. Mitochondria perform cellular respiration and produce ATP. Peroxisomes break down fatty acids, amino acids, and some toxins. Vesicles and vacuoles are storage and transport compartments. In plant cells, vacuoles also help break down macromolecules.

Animal cells also have a centrosome and lysosomes. The centrosome has two bodies, the centrioles, with an unknown role in cell division. Lysosomes are the digestive organelles of animal cells.

Plant cells have a cell wall, chloroplasts, and a central vacuole. The plant cell wall, whose primary component is cellulose, protects the cell, provides structural support, and gives shape to the cell. Photosynthesis takes place in chloroplasts. The central vacuole expands, enlarging the cell without the need to produce more cytoplasm.

The endomembrane system includes the nuclear envelope, the endoplasmic reticulum, Golgi apparatus, lysosomes, vesicles, as well as the plasma membrane. These cellular components work together to modify, package, tag, and transport membrane lipids and proteins.

The cytoskeleton has three different types of protein elements. Microfilaments provide rigidity and shape to the cell, and facilitate cellular movements. Intermediate filaments bear tension and anchor the nucleus and other organelles in place. Microtubules help the cell resist compression, serve as tracks for motor proteins that move vesicles through the cell, and pull replicated chromosomes to opposite ends of a dividing cell. They are also the structural elements of centrioles, flagella, and cilia.

Animal cells communicate through their extracellular matrices and are connected to each other by tight junctions, desmosomes, and gap junctions. Plant cells are connected and communicate with each other by plasmodesmata.

Exercises

An interactive H5P element has been excluded from this version of the text. You can view it online here:
https://pressbooks.nscc.ca/conceptsofbiologynscc/?p=113#h5p-22

Glossary

cell wall: a rigid cell covering made of cellulose in plants, peptidoglycan in bacteria, non-peptidoglycan compounds in Archaea, and chitin in fungi that protects the cell, provides structural support, and gives shape to the cell

central vacuole: a large plant cell organelle that acts as a storage compartment, water reservoir, and site of macromolecule degradation

chloroplast: a plant cell organelle that carries out photosynthesis

cilium: (plural: cilia) a short, hair-like structure that extends from the plasma membrane in large numbers and is used to move an entire cell or move substances along the outer surface of the cell

cytoplasm: the entire region between the plasma membrane and the nuclear envelope, consisting of organelles suspended in the gel-like cytosol, the cytoskeleton, and various chemicals

cytoskeleton: the network of protein fibers that collectively maintains the shape of the cell, secures some organelles in specific positions, allows cytoplasm and vesicles to move within the cell, and enables unicellular organisms to move

cytosol: the gel-like material of the cytoplasm in which cell structures are suspended

desmosome: a linkage between adjacent epithelial cells that forms when cadherins in the plasma membrane attach to intermediate filaments

endomembrane system: the group of organelles and membranes in eukaryotic cells that work together to modify, package, and transport lipids and proteins

endoplasmic reticulum (ER): a series of interconnected membranous structures within eukaryotic cells that collectively modify proteins and synthesize lipids

extracellular matrix: the material, primarily collagen, glycoproteins, and proteoglycans, secreted from animal cells that holds cells together as a tissue, allows cells to communicate with each other, and provides mechanical protection and anchoring for cells in the tissue

flagellum: (plural: flagella) the long, hair-like structure that extends from the plasma membrane and is used to move the cell

gap junction: a channel between two adjacent animal cells that allows ions, nutrients, and other low-molecular weight substances to pass between the cells, enabling the cells to communicate

Golgi apparatus: a eukaryotic organelle made up of a series of stacked membranes that sorts, tags, and packages lipids and proteins for distribution

lysosome: an organelle in an animal cell that functions as the cell’s digestive component; it breaks down proteins, polysaccharides, lipids, nucleic acids, and even worn-out organelles

mitochondria: (singular: mitochondrion) the cellular organelles responsible for carrying out cellular respiration, resulting in the production of ATP, the cell’s main energy-carrying molecule

nuclear envelope: the double-membrane structure that constitutes the outermost portion of the nucleus

nucleolus: the darkly staining body within the nucleus that is responsible for assembling ribosomal subunits

nucleus: the cell organelle that houses the cell’s DNA and directs the synthesis of ribosomes and proteins

peroxisome: a small, round organelle that contains hydrogen peroxide, oxidizes fatty acids and amino acids, and detoxifies many poisons

plasma membrane: a phospholipid bilayer with embedded (integral) or attached (peripheral) proteins that separates the internal contents of the cell from its surrounding environment

plasmodesma: (plural: plasmodesmata) a channel that passes between the cell walls of adjacent plant cells, connects their cytoplasm, and allows materials to be transported from cell to cell

ribosome: a cellular structure that carries out protein synthesis

rough endoplasmic reticulum (RER): the region of the endoplasmic reticulum that is studded with ribosomes and engages in protein modification

smooth endoplasmic reticulum (SER): the region of the endoplasmic reticulum that has few or no ribosomes on its cytoplasmic surface and synthesizes carbohydrates, lipids, and steroid hormones; detoxifies chemicals like pesticides, preservatives, medications, and environmental pollutants, and stores calcium ions

tight junction: a firm seal between two adjacent animal cells created by protein adherence

vacuole: a membrane-bound sac, somewhat larger than a vesicle, that functions in cellular storage and transport

vesicle: a small, membrane-bound sac that functions in cellular storage and transport; its membrane is capable of fusing with the plasma membrane and the membranes of the endoplasmic reticulum and Golgi apparatus

Media Attribution

  • Figure 3.11: modification of work by NIGMS, NIH
  • Figure 3.13: modification of work by NIH; scale-bar data from Matt Russell
  • Figure 3.14: modification of work by Louisa Howard; scale-bar data from Matt Russell
  • Figure 3.16: modification of work by Magnus Manske
  • Figure 3.17: modification of work by Matthew Britton; scale-bar data from Matt Russell
  • Figure 3.20: modification of work by Mariana Ruiz Villareal

9

3.4 The Cell Membrane

Charles Molnar and Jane Gair

Learning Objectives

By the end of this section, you will be able to:

  • Understand the fluid mosaic model of membranes
  • Describe the functions of phospholipids, proteins, and carbohydrates in membranes

A cell’s plasma membrane defines the boundary of the cell and determines the nature of its contact with the environment. Cells exclude some substances, take in others, and excrete still others, all in controlled quantities. Plasma membranes enclose the borders of cells, but rather than being a static bag, they are dynamic and constantly in flux. The plasma membrane must be sufficiently flexible to allow certain cells, such as red blood cells and white blood cells, to change shape as they pass through narrow capillaries. These are the more obvious functions of a plasma membrane. In addition, the surface of the plasma membrane carries markers that allow cells to recognize one another, which is vital as tissues and organs form during early development, and which later plays a role in the “self” versus “non-self” distinction of the immune response.

The plasma membrane also carries receptors, which are attachment sites for specific substances that interact with the cell. Each receptor is structured to bind with a specific substance. For example, surface receptors of the membrane create changes in the interior, such as changes in enzymes of metabolic pathways. These metabolic pathways might be vital for providing the cell with energy, making specific substances for the cell, or breaking down cellular waste or toxins for disposal. Receptors on the plasma membrane’s exterior surface interact with hormones or neurotransmitters, and allow their messages to be transmitted into the cell. Some recognition sites are used by viruses as attachment points. Although they are highly specific, pathogens like viruses may evolve to exploit receptors to gain entry to a cell by mimicking the specific substance that the receptor is meant to bind. This specificity helps to explain why human immunodeficiency virus (HIV) or any of the five types of hepatitis viruses invade only specific cells.

Fluid Mosaic Model

In 1972, S. J. Singer and Garth L. Nicolson proposed a new model of the plasma membrane that, compared to earlier understanding, better explained both microscopic observations and the function of the plasma membrane. This was called the fluid mosaic model. The model has evolved somewhat over time, but still best accounts for the structure and functions of the plasma membrane as we now understand them. The fluid mosaic model describes the structure of the plasma membrane as a mosaic of components—including phospholipids, cholesterol, proteins, and carbohydrates—in which the components are able to flow and change position, while maintaining the basic integrity of the membrane. Both phospholipid molecules and embedded proteins are able to diffuse rapidly and laterally in the membrane. The fluidity of the plasma membrane is necessary for the activities of certain enzymes and transport molecules within the membrane. Plasma membranes range from 5–10 nm thick. As a comparison, human red blood cells, visible via light microscopy, are approximately 8 µm thick, or approximately 1,000 times thicker than a plasma membrane.

 
the plasma membrane is composed of a phospholipid bilayer. in the bilayer, the two long hydrophobic tails of phospholipids face toward the center, and the hydrophilic head group faces the exterior. Integral membrane proteins and protein channels span the entire bilayer. Protein channels have a pore in the middle. Peripheral membrane proteins sit on the surface of the phospholipids and are associated with the head groups. On the exterior side of the membrane, carbohydrates are attached to certain proteins and lipids. Filaments of the cytoskeleton line the interior of the membrane.
Figure 3.21 The fluid mosaic model of the plasma membrane structure describes the plasma membrane as a fluid combination of phospholipids, cholesterol, proteins, and carbohydrates. 

The plasma membrane is made up primarily of a bilayer of phospholipids with embedded proteins, carbohydrates, glycolipids, and glycoproteins, and, in animal cells, cholesterol. The amount of cholesterol in animal plasma membranes regulates the fluidity of the membrane and changes based on the temperature of the cell’s environment. In other words, cholesterol acts as antifreeze in the cell membrane and is more abundant in animals that live in cold climates.

The main fabric of the membrane is composed of two layers of phospholipid molecules, and the polar ends of these molecules (which look like a collection of balls in an artist’s rendition of the model) (Figure 3.22) are in contact with aqueous fluid both inside and outside the cell. Thus, both surfaces of the plasma membrane are hydrophilic. In contrast, the interior of the membrane, between its two surfaces, is a hydrophobic or nonpolar region because of the fatty acid tails. This region has no attraction for water or other polar molecules.

This phospholipid molecule is composed of a hydrophilic head and two hydrophobic tails. The hydrophilic head group consists of a phosphate-containing group attached to a glycerol molecule. The hydrophobic tails, each containing either a saturated or an unsaturated fatty acid, are long hydrocarbon chains.
Figure 3.22 This phospholipid molecule is composed of a hydrophilic head and two hydrophobic tails. The hydrophilic head group consists of a phosphate-containing group attached to a glycerol molecule. The hydrophobic tails, each containing either a saturated or an unsaturated fatty acid, are long hydrocarbon chains.

Proteins make up the second major chemical component of plasma membranes. Integral proteins are embedded in the plasma membrane and may span all or part of the membrane. Integral proteins may serve as channels or pumps to move materials into or out of the cell. Peripheral proteins are found on the exterior or interior surfaces of membranes, attached either to integral proteins or to phospholipid molecules. Both integral and peripheral proteins may serve as enzymes, as structural attachments for the fibers of the cytoskeleton, or as part of the cell’s recognition sites.

Carbohydrates are the third major component of plasma membranes. They are always found on the exterior surface of cells and are bound either to proteins (forming glycoproteins) or to lipids (forming glycolipids). These carbohydrate chains may consist of 2–60 monosaccharide units and may be either straight or branched. Along with peripheral proteins, carbohydrates form specialized sites on the cell surface that allow cells to recognize each other.

Evolution in Action

How Viruses Infect Specific OrgansSpecific glycoprotein molecules exposed on the surface of the cell membranes of host cells are exploited by many viruses to infect specific organs. For example, HIV is able to penetrate the plasma membranes of specific kinds of white blood cells called T-helper cells and monocytes, as well as some cells of the central nervous system. The hepatitis virus attacks only liver cells.

These viruses are able to invade these cells, because the cells have binding sites on their surfaces that the viruses have exploited with equally specific glycoproteins in their coats. (Figure 3.23). The cell is tricked by the mimicry of the virus coat molecules, and the virus is able to enter the cell. Other recognition sites on the virus’s surface interact with the human immune system, prompting the body to produce antibodies. Antibodies are made in response to the antigens (or proteins associated with invasive pathogens). These same sites serve as places for antibodies to attach, and either destroy or inhibit the activity of the virus. Unfortunately, these sites on HIV are encoded by genes that change quickly, making the production of an effective vaccine against the virus very difficult. The virus population within an infected individual quickly evolves through mutation into different populations, or variants, distinguished by differences in these recognition sites. This rapid change of viral surface markers decreases the effectiveness of the person’s immune system in attacking the virus, because the antibodies will not recognize the new variations of the surface patterns.

This illustration shows the plasma membrane of a T cell. CD4 receptors extend from the membrane into the extracellular space. The HIV virus recognizes part of the CD4 receptor and attaches to it.
Figure 3.23 HIV docks at and binds to the CD4 receptor, a glycoprotein on the surface of T cells, before entering, or infecting, the cell.

Section Summary

The modern understanding of the plasma membrane is referred to as the fluid mosaic model. The plasma membrane is composed of a bilayer of phospholipids, with their hydrophobic, fatty acid tails in contact with each other. The landscape of the membrane is studded with proteins, some of which span the membrane. Some of these proteins serve to transport materials into or out of the cell. Carbohydrates are attached to some of the proteins and lipids on the outward-facing surface of the membrane. These form complexes that function to identify the cell to other cells. The fluid nature of the membrane owes itself to the configuration of the fatty acid tails, the presence of cholesterol embedded in the membrane (in animal cells), and the mosaic nature of the proteins and protein-carbohydrate complexes, which are not firmly fixed in place. Plasma membranes enclose the borders of cells, but rather than being a static bag, they are dynamic and constantly in flux.

Exercises

An interactive H5P element has been excluded from this version of the text. You can view it online here:
https://pressbooks.nscc.ca/conceptsofbiologynscc/?p=117#h5p-23

Glossary

fluid mosaic model: a model of the structure of the plasma membrane as a mosaic of components, including phospholipids, cholesterol, proteins, and glycolipids, resulting in a fluid rather than static character

Media Attribution

  • Figure 3.23: modification of work by US National Institutes of Health/National Institute of Allergy and Infectious Diseases

10

3.5 Passive Transport

Charles Molnar and Jane Gair

Learning Objectives

By the end of this section, you will be able to:

  • Explain why and how passive transport occurs
  • Understand the processes of osmosis and diffusion
  • Define tonicity and describe its relevance to passive transport

Plasma membranes must allow certain substances to enter and leave a cell, while preventing harmful material from entering and essential material from leaving. In other words, plasma membranes are selectively permeable—they allow some substances through but not others. If they were to lose this selectivity, the cell would no longer be able to sustain itself, and it would be destroyed. Some cells require larger amounts of specific substances than do other cells; they must have a way of obtaining these materials from the extracellular fluids. This may happen passively, as certain materials move back and forth, or the cell may have special mechanisms that ensure transport. Most cells expend most of their energy, in the form of adenosine triphosphate (ATP), to create and maintain an uneven distribution of ions on the opposite sides of their membranes. The structure of the plasma membrane contributes to these functions, but it also presents some problems.

The most direct forms of membrane transport are passive. Passive transport is a naturally occurring phenomenon and does not require the cell to expend energy to accomplish the movement. In passive transport, substances move from an area of higher concentration to an area of lower concentration in a process called diffusion. A physical space in which there is a different concentration of a single substance is said to have a concentration gradient.

Selective Permeability

Plasma membranes are asymmetric, meaning that despite the mirror image formed by the phospholipids, the interior of the membrane is not identical to the exterior of the membrane. Integral proteins that act as channels or pumps work in one direction. Carbohydrates, attached to lipids or proteins, are also found on the exterior surface of the plasma membrane. These carbohydrate complexes help the cell bind substances that the cell needs in the extracellular fluid. This adds considerably to the selective nature of plasma membranes.

Recall that plasma membranes have hydrophilic and hydrophobic regions. This characteristic helps the movement of certain materials through the membrane and hinders the movement of others. Lipid-soluble material can easily slip through the hydrophobic lipid core of the membrane. Substances such as the fat-soluble vitamins A, D, E, and K readily pass through the plasma membranes in the digestive tract and other tissues. Fat-soluble drugs also gain easy entry into cells and are readily transported into the body’s tissues and organs. Molecules of oxygen and carbon dioxide have no charge and pass through by simple diffusion.

Polar substances, with the exception of water, present problems for the membrane. While some polar molecules connect easily with the outside of a cell, they cannot readily pass through the lipid core of the plasma membrane. Additionally, whereas small ions could easily slip through the spaces in the mosaic of the membrane, their charge prevents them from doing so. Ions such as sodium, potassium, calcium, and chloride must have a special means of penetrating plasma membranes. Simple sugars and amino acids also need help with transport across plasma membranes.

Diffusion

Diffusion is a passive process of transport. A single substance tends to move from an area of high concentration to an area of low concentration until the concentration is equal across the space. You are familiar with diffusion of substances through the air. For example, think about someone opening a bottle of perfume in a room filled with people. The perfume is at its highest concentration in the bottle and is at its lowest at the edges of the room. The perfume vapor will diffuse, or spread away, from the bottle, and gradually, more and more people will smell the perfume as it spreads. Materials move within the cell’s cytosol by diffusion, and certain materials move through the plasma membrane by diffusion (Figure 3.24). Diffusion expends no energy. Rather the different concentrations of materials in different areas are a form of potential energy, and diffusion is the dissipation of that potential energy as materials move down their concentration gradients, from high to low.

The left part of this illustration shows a substance on one side of a membrane only. The middle part shows that, after some time, some of the substance has diffused across the plasma membrane. The right part shows that, after more time, an equal amount of the substance is on each side of the membrane.
Figure 3.24 Diffusion through a permeable membrane follows the concentration gradient of a substance, moving the substance from an area of high concentration to one of low concentration.

Each separate substance in a medium, such as the extracellular fluid, has its own concentration gradient, independent of the concentration gradients of other materials. Additionally, each substance will diffuse according to that gradient.

Several factors affect the rate of diffusion.

  • Extent of the concentration gradient: The greater the difference in concentration, the more rapid the diffusion. The closer the distribution of the material gets to equilibrium, the slower the rate of diffusion becomes.
  • Mass of the molecules diffusing: More massive molecules move more slowly, because it is more difficult for them to move between the molecules of the substance they are moving through; therefore, they diffuse more slowly.
  • Temperature: Higher temperatures increase the energy and therefore the movement of the molecules, increasing the rate of diffusion.
  • Solvent density: As the density of the solvent increases, the rate of diffusion decreases. The molecules slow down because they have a more difficult time getting through the denser medium.

Concept in Action

For an animation of the diffusion process in action, view this short video on cell membrane transport.
qrcode.28257831

Thumbnail for the embedded element &quot;Cell Membrane Passive Transport | Cell Biology&quot;

A YouTube element has been excluded from this version of the text. You can view it online here: https://pressbooks.nscc.ca/conceptsofbiologynscc/?p=124

Facilitated transport

In facilitated transport, also called facilitated diffusion, material moves across the plasma membrane with the assistance of transmembrane proteins down a concentration gradient (from high to low concentration) without the expenditure of cellular energy. However, the substances that undergo facilitated transport would otherwise not diffuse easily or quickly across the plasma membrane. The solution to moving polar substances and other substances across the plasma membrane rests in the proteins that span its surface. The material being transported is first attached to protein or glycoprotein receptors on the exterior surface of the plasma membrane. This allows the material that is needed by the cell to be removed from the extracellular fluid. The substances are then passed to specific integral proteins that facilitate their passage, because they form channels or pores that allow certain substances to pass through the membrane. The integral proteins involved in facilitated transport are collectively referred to as transport proteins, and they function as either channels for the material or carriers.

Osmosis

Osmosis is the diffusion of water through a semipermeable membrane according to the concentration gradient of water across the membrane. Whereas diffusion transports material across membranes and within cells, osmosis transports only water across a membrane and the membrane limits the diffusion of solutes in the water. Osmosis is a special case of diffusion. Water, like other substances, moves from an area of higher concentration to one of lower concentration. Imagine a beaker with a semipermeable membrane, separating the two sides or halves (Figure 3.25). On both sides of the membrane, the water level is the same, but there are different concentrations on each side of a dissolved substance, or solute, that cannot cross the membrane. If the volume of the water is the same, but the concentrations of solute are different, then there are also different concentrations of water, the solvent, on either side of the membrane.

 
Two beakers are shown, each divided into left and right halves by a semipermeable membrane. The first beaker has the same amount of water on both sides, but more solute in the water on the right side of the membrane and less solute in the water on the left side. In the second beaker, the water has moved from the left side of the membrane to the right side, making the solute concentration the same on both sides, but the water level much lower on the left side.
Figure 3.25 In osmosis, water always moves from an area of higher concentration (of water) to one of lower concentration (of water). In this system, the solute cannot pass through the selectively permeable membrane.

A principle of diffusion is that the molecules move around and will spread evenly throughout the medium if they can. However, only the material capable of getting through the membrane will diffuse through it. In this example, the solute cannot diffuse through the membrane, but the water can. Water has a concentration gradient in this system. Therefore, water will diffuse down its concentration gradient, crossing the membrane to the side where it is less concentrated. This diffusion of water through the membrane—osmosis—will continue until the concentration gradient of water goes to zero. Osmosis proceeds constantly in living systems.

Tonicity

Tonicity describes the amount of solute in a solution. The measure of the tonicity of a solution, or the total amount of solutes dissolved in a specific amount of solution, is called its osmolarity. Three terms—hypotonic, isotonic, and hypertonic—are used to relate the osmolarity of a cell to the osmolarity of the extracellular fluid that contains the cells. In a hypotonic solution, such as tap water, the extracellular fluid has a lower concentration of solutes than the fluid inside the cell, and water enters the cell. (In living systems, the point of reference is always the cytoplasm, so the prefix hypo– means that the extracellular fluid has a lower concentration of solutes, or a lower osmolarity, than the cell cytoplasm.) It also means that the extracellular fluid has a higher concentration of water than does the cell. In this situation, water will follow its concentration gradient and enter the cell. This may cause an animal cell to burst, or lyse.

In a hypertonic solution (the prefix hyper– refers to the extracellular fluid having a higher concentration of solutes than the cell’s cytoplasm), the fluid contains less water than the cell does, such as seawater. Because the cell has a lower concentration of solutes, the water will leave the cell. In effect, the solute is drawing the water out of the cell. This may cause an animal cell to shrivel, or crenate.

In an isotonic solution, the extracellular fluid has the same osmolarity as the cell. If the concentration of solutes of the cell matches that of the extracellular fluid, there will be no net movement of water into or out of the cell. Blood cells in hypertonic, isotonic, and hypotonic solutions take on characteristic appearances (Figure 3.26).

Illustration of red blood cells in hypotonic, isotonic, and hypertonic solutions. In the hypertonic solution, the cells shrivel and take on a spiky appearance. In the isotonic solution, the cells are normal in appearance. In the hypotonic solution, the cells swell and one has ruptured.
Figure 3.26 Osmotic pressure changes the shape of red blood cells in hypertonic, isotonic, and hypotonic solutions.

A doctor injects a patient with what the doctor thinks is isotonic saline solution. The patient dies, and autopsy reveals that many red blood cells have been destroyed. Do you think the solution the doctor injected was really isotonic?

<!– No, it must have been hypotonic, as a hypotonic solution would cause water to enter the cells, thereby making them burst. –>

Some organisms, such as plants, fungi, bacteria, and some protists, have cell walls that surround the plasma membrane and prevent cell lysis. The plasma membrane can only expand to the limit of the cell wall, so the cell will not lyse. In fact, the cytoplasm in plants is always slightly hypertonic compared to the cellular environment, and water will always enter a cell if water is available. This influx of water produces turgor pressure, which stiffens the cell walls of the plant (Figure 3.27). In nonwoody plants, turgor pressure supports the plant. If the plant cells become hypertonic, as occurs in drought or if a plant is not watered adequately, water will leave the cell. Plants lose turgor pressure in this condition and wilt.

The left part of this image shows a plant cell bathed in a hypertonic solution so that the plasma membrane has pulled away completely from the cell wall, and the central vacuole has shrunk. The middle part shows a plant cell bathed in an isotonic solution; the plasma membrane has pulled away from the cell wall a bit, and the central vacuole has shrunk. The right part shows a plant cell in a hypotonic solution. The central vacuole is large, and the plasma membrane is pressed against the cell wall.
Figure 3.27 The turgor pressure within a plant cell depends on the tonicity of the solution that it is bathed in.

Section Summary

The passive forms of transport, diffusion and osmosis, move material of small molecular weight. Substances diffuse from areas of high concentration to areas of low concentration, and this process continues until the substance is evenly distributed in a system. In solutions of more than one substance, each type of molecule diffuses according to its own concentration gradient. Many factors can affect the rate of diffusion, including concentration gradient, the sizes of the particles that are diffusing, and the temperature of the system.

In living systems, diffusion of substances into and out of cells is mediated by the plasma membrane. Some materials diffuse readily through the membrane, but others are hindered, and their passage is only made possible by protein channels and carriers. The chemistry of living things occurs in aqueous solutions, and balancing the concentrations of those solutions is an ongoing problem. In living systems, diffusion of some substances would be slow or difficult without membrane proteins.

Exercises

An interactive H5P element has been excluded from this version of the text. You can view it online here:
https://pressbooks.nscc.ca/conceptsofbiologynscc/?p=124#h5p-24

Glossary

concentration gradient: an area of high concentration across from an area of low concentration

diffusion: a passive process of transport of low-molecular weight material down its concentration gradient

facilitated transport: a process by which material moves down a concentration gradient (from high to low concentration) using integral membrane proteins

hypertonic: describes a solution in which extracellular fluid has higher osmolarity than the fluid inside the cell

hypotonic: describes a solution in which extracellular fluid has lower osmolarity than the fluid inside the cell

isotonic: describes a solution in which the extracellular fluid has the same osmolarity as the fluid inside the cell

osmolarity: the total amount of substances dissolved in a specific amount of solution

osmosis: the transport of water through a semipermeable membrane from an area of high water concentration to an area of low water concentration across a membrane

passive transport: a method of transporting material that does not require energy

selectively permeable: the characteristic of a membrane that allows some substances through but not others

solute: a substance dissolved in another to form a solution

tonicity: the amount of solute in a solution.

Media Attributions

  • Figure 3.24: modification of work by Mariana Ruiz Villarreal
  • Figure 3.26: modification of work by Mariana Ruiz Villarreal
  • Figure 3.27: modification of work by Mariana Ruiz Villarreal

11

3.6 Active Transport

Charles Molnar and Jane Gair

Learning Objectives

By the end of this section, you will be able to:

  • Understand how electrochemical gradients affect ions
  • Describe endocytosis, including phagocytosis, pinocytosis, and receptor-mediated endocytosis
  • Understand the process of exocytosis

 Active transport mechanisms require the use of the cell’s energy, usually in the form of adenosine triphosphate (ATP). If a substance must move into the cell against its concentration gradient, that is, if the concentration of the substance inside the cell must be greater than its concentration in the extracellular fluid, the cell must use energy to move the substance. Some active transport mechanisms move small-molecular weight material, such as ions, through the membrane.

In addition to moving small ions and molecules through the membrane, cells also need to remove and take in larger molecules and particles. Some cells are even capable of engulfing entire unicellular microorganisms. You might have correctly hypothesized that the uptake and release of large particles by the cell requires energy. A large particle, however, cannot pass through the membrane, even with energy supplied by the cell.

Electrochemical Gradient

We have discussed simple concentration gradients—differential concentrations of a substance across a space or a membrane—but in living systems, gradients are more complex. Because cells contain proteins, most of which are negatively charged, and because ions move into and out of cells, there is an electrical gradient, a difference of charge, across the plasma membrane. The interior of living cells is electrically negative with respect to the extracellular fluid in which they are bathed; at the same time, cells have higher concentrations of potassium (K+) and lower concentrations of sodium (Na+) than does the extracellular fluid. Thus, in a living cell, the concentration gradient and electrical gradient of Na+ promotes diffusion of the ion into the cell, and the electrical gradient of Na+ (a positive ion) tends to drive it inward to the negatively charged interior. The situation is more complex, however, for other elements such as potassium. The electrical gradient of K+ promotes diffusion of the ion into the cell, but the concentration gradient of K+ promotes diffusion out of the cell (Figure 3.28). The combined gradient that affects an ion is called its electrochemical gradient, and it is especially important to muscle and nerve cells.

A cell membrane is shown with a protein channel that allows passage of ions into and out of the cell. The cytoplasm has a higher concentration of potassium, and the extracellular fluid has a higher concentration of sodium. An arrow shows movement of a potassium ion out of the cell through the protein channel.
Figure 3.28 Electrochemical gradients arise from the combined effects of concentration gradients and electrical gradients.

Moving Against a Gradient

To move substances against a concentration or an electrochemical gradient, the cell must use energy. This energy is harvested from ATP that is generated through cellular metabolism. Active transport mechanisms, collectively called pumps or carrier proteins, work against electrochemical gradients. With the exception of ions, small substances constantly pass through plasma membranes. Active transport maintains concentrations of ions and other substances needed by living cells in the face of these passive changes. Much of a cell’s supply of metabolic energy may be spent maintaining these processes. Because active transport mechanisms depend on cellular metabolism for energy, they are sensitive to many metabolic poisons that interfere with the supply of ATP.

Two mechanisms exist for the transport of small-molecular weight material and macromolecules. Primary active transport moves ions across a membrane and creates a difference in charge across that membrane. The primary active transport system uses ATP to move a substance, such as an ion, into the cell, and often at the same time, a second substance is moved out of the cell. The sodium-potassium pump, an important pump in animal cells, expends energy to move potassium ions into the cell and a different number of sodium ions out of the cell (Figure 3.29). The action of this pump results in a concentration and charge difference across the membrane.

This illustration shows the sodium-potassium pump. Initially, the pump’s opening faces the cytoplasm, where three sodium ions bind to it. The pump hydrolyzes ATP to ADP and, as a result, undergoes a conformational change. The sodium ions are released into the extracellular space. Two potassium ions from the extracellular space now bind the pump, which changes conformation again, releasing the potassium ions into the cytoplasm.
Figure 3.29 The sodium-potassium pump move potassium and sodium ions across the plasma membrane.

Secondary active transport describes the movement of material using the energy of the electrochemical gradient established by primary active transport. Using the energy of the electrochemical gradient created by the primary active transport system, other substances such as amino acids and glucose can be brought into the cell through membrane channels. ATP itself is formed through secondary active transport using a hydrogen ion gradient in the mitochondrion.

Endocytosis

Endocytosis is a type of active transport that moves particles, such as large molecules, parts of cells, and even whole cells, into a cell. There are different variations of endocytosis, but all share a common characteristic: The plasma membrane of the cell invaginates, forming a pocket around the target particle. The pocket pinches off, resulting in the particle being contained in a newly created vacuole that is formed from the plasma membrane.

Three types of endocytosis are shown: (a) phagocytosis, (b) pinocytosis, and (c) receptor-mediated endocytosis. Part a shows the plasma membrane forming a pocket around a particle in the extracellular fluid. The membrane subsequently engulfs the particle, which becomes trapped in a vacuole. Part b shows a plasma membrane forming a pocket around fluid in the extracellular fluid. The membrane subsequently engulfs the fluid, which becomes trapped in a vacuole. Part c shows a part of the plasma membrane that is clathrin-coated on the cytoplasmic side and has receptors on the extracellular side. The receptors bind a substance, then pinch off to form a coated vesicle.
Figure 3.30 Three variations of endocytosis are shown. (a) In one form of endocytosis, phagocytosis, the cell membrane surrounds the particle and pinches off to form an intracellular vacuole. (b) In another type of endocytosis, pinocytosis, the cell membrane surrounds a small volume of fluid and pinches off, forming a vesicle. (c) In receptor-mediated endocytosis, uptake of substances by the cell is targeted to a single type of substance that binds at the receptor on the external cell membrane.

Phagocytosis is the process by which large particles, such as cells, are taken in by a cell. For example, when microorganisms invade the human body, a type of white blood cell called a neutrophil removes the invader through this process, surrounding and engulfing the microorganism, which is then destroyed by the neutrophil (Figure 3.30).

A variation of endocytosis is called pinocytosis. This literally means “cell drinking” and was named at a time when the assumption was that the cell was purposefully taking in extracellular fluid. In reality, this process takes in solutes that the cell needs from the extracellular fluid (Figure 3.30).

A targeted variation of endocytosis employs binding proteins in the plasma membrane that are specific for certain substances (Figure 3.30). The particles bind to the proteins and the plasma membrane invaginates, bringing the substance and the proteins into the cell. If passage across the membrane of the target of receptor-mediated endocytosis is ineffective, it will not be removed from the tissue fluids or blood. Instead, it will stay in those fluids and increase in concentration. Some human diseases are caused by a failure of receptor-mediated endocytosis. For example, the form of cholesterol termed low-density lipoprotein or LDL (also referred to as “bad” cholesterol) is removed from the blood by receptor-mediated endocytosis. In the human genetic disease familial hypercholesterolemia, the LDL receptors are defective or missing entirely. People with this condition have life-threatening levels of cholesterol in their blood, because their cells cannot clear the chemical from their blood.

Exocytosis

In contrast to these methods of moving material into a cell is the process of exocytosis. Exocytosis is the opposite of the processes discussed above in that its purpose is to expel material from the cell into the extracellular fluid. A particle enveloped in membrane fuses with the interior of the plasma membrane. This fusion opens the membranous envelope to the exterior of the cell, and the particle is expelled into the extracellular space (Figure 3.31).

A vesicle containing waste products is shown in the cytoplasm. The vesicle migrates to the cell membrane. The membrane of the vesicle fuses with the cell membrane, and the contents of the vesicle are released to the extracellular fluid.
Figure 3.31 In exocytosis, a vesicle migrates to the plasma membrane, binds, and releases its contents to the outside of the cell.

 

Section Summary

The combined gradient that affects an ion includes its concentration gradient and its electrical gradient. Living cells need certain substances in concentrations greater than they exist in the extracellular space. Moving substances up their electrochemical gradients requires energy from the cell. Active transport uses energy stored in ATP to fuel the transport. Active transport of small molecular-size material uses integral proteins in the cell membrane to move the material—these proteins are analogous to pumps. Some pumps, which carry out primary active transport, couple directly with ATP to drive their action. In secondary transport, energy from primary transport can be used to move another substance into the cell and up its concentration gradient.

Endocytosis methods require the direct use of ATP to fuel the transport of large particles such as macromolecules; parts of cells or whole cells can be engulfed by other cells in a process called phagocytosis. In phagocytosis, a portion of the membrane invaginates and flows around the particle, eventually pinching off and leaving the particle wholly enclosed by an envelope of plasma membrane. Vacuoles are broken down by the cell, with the particles used as food or dispatched in some other way. Pinocytosis is a similar process on a smaller scale. The cell expels waste and other particles through the reverse process, exocytosis. Wastes are moved outside the cell, pushing a membranous vesicle to the plasma membrane, allowing the vesicle to fuse with the membrane and incorporating itself into the membrane structure, releasing its contents to the exterior of the cell.

Exercises

An interactive H5P element has been excluded from this version of the text. You can view it online here:
https://pressbooks.nscc.ca/conceptsofbiologynscc/?p=130#h5p-25

Glossary

active transport: the method of transporting material that requires energy

electrochemical gradient: a gradient produced by the combined forces of the electrical gradient and the chemical gradient

endocytosis: a type of active transport that moves substances, including fluids and particles, into a cell

exocytosis: a process of passing material out of a cell

phagocytosis: a process that takes macromolecules that the cell needs from the extracellular fluid; a variation of endocytosis

pinocytosis: a process that takes solutes that the cell needs from the extracellular fluid; a variation of endocytosis

receptor-mediated endocytosis: a variant of endocytosis that involves the use of specific binding proteins in the plasma membrane for specific molecules or particles

Media Attributions

IV

Chapter 4: Introduction to How Cells Obtain Energy

In this photo, a hummingbird drinks from a feeder.
Figure 4.1 A hummingbird needs energy to maintain prolonged flight. The bird obtains its energy from taking in food and transforming the energy contained in food molecules into forms of energy to power its flight through a series of biochemical reactions. (credit: modification of work by Cory Zanker)

Virtually every task performed by living organisms requires energy. Energy is needed to perform heavy labor and exercise, but humans also use energy while thinking, and even during sleep. In fact, the living cells of every organism constantly use energy. Nutrients and other molecules are imported into the cell, metabolized (broken down) and possibly synthesized into new molecules, modified if needed, transported around the cell, and possibly distributed to the entire organism. For example, the large proteins that make up muscles are built from smaller molecules imported from dietary amino acids. Complex carbohydrates are broken down into simple sugars that the cell uses for energy. Just as energy is required to both build and demolish a building, energy is required for the synthesis and breakdown of molecules as well as the transport of molecules into and out of cells. In addition, processes such as ingesting and breaking down pathogenic bacteria and viruses, exporting wastes and toxins, and movement of the cell require energy. From where, and in what form, does this energy come? How do living cells obtain energy, and how do they use it? This chapter will discuss different forms of energy and the physical laws that govern energy transfer. This chapter will also describe how cells use energy and replenish it, and how chemical reactions in the cell are performed with great efficiency.

Search for Key Points in Chapter 4

An interactive H5P element has been excluded from this version of the text. You can view it online here:
https://pressbooks.nscc.ca/conceptsofbiologynscc/?p=133#h5p-26

12

4.1 Energy and Metabolism

Charles Molnar and Jane Gair

Learning Objectives

By the end of this section, you will be able to:

  • Explain what metabolic pathways are
  • State the first and second laws of thermodynamics
  • Explain the difference between kinetic and potential energy
  • Describe endergonic and exergonic reactions
  • Discuss how enzymes function as molecular catalysts

Watch a video about heterotrophs.

An interactive H5P element has been excluded from this version of the text. You can view it online here:
https://pressbooks.nscc.ca/conceptsofbiologynscc/?p=150#h5p-27

Scientists use the term bioenergetics to describe the concept of energy flow (Figure 4.2) through living systems, such as cells. Cellular processes such as the building and breaking down of complex molecules occur through stepwise chemical reactions. Some of these chemical reactions are spontaneous and release energy, whereas others require energy to proceed. Just as living things must continually consume food to replenish their energy supplies, cells must continually produce more energy to replenish that used by the many energy-requiring chemical reactions that constantly take place. Together, all of the chemical reactions that take place inside cells, including those that consume or generate energy, are referred to as the cell’s metabolism.

 
This diagram shows energy from the sun being transferred to producers, such as plants. The producers in turn transfer energy to consumers and decomposers. Animals also transfer energy to decomposers.
Figure 4.2 Ultimately, most life forms get their energy from the sun. Plants use photosynthesis to capture sunlight, and herbivores eat the plants to obtain energy. Carnivores eat the herbivores, and eventual decomposition of plant and animal material contributes to the nutrient pool. 

Metabolic Pathways

Consider the metabolism of sugar. This is a classic example of one of the many cellular processes that use and produce energy. Living things consume sugars as a major energy source, because sugar molecules have a great deal of energy stored within their bonds. For the most part, photosynthesizing organisms like plants produce these sugars. During photosynthesis, plants use energy (originally from sunlight) to convert carbon dioxide gas (CO2) into sugar molecules (like glucose: C6H12O6). They consume carbon dioxide and produce oxygen as a waste product. This reaction is summarized as:

6CO2 + 6H2O + energy ——-> C6H12O6+ 6O2

Because this process involves synthesizing an energy-storing molecule, it requires energy input to proceed. During the light reactions of photosynthesis, energy is provided by a molecule called adenosine triphosphate (ATP), which is the primary energy currency of all cells. Just as the dollar is used as currency to buy goods, cells use molecules of ATP as energy currency to perform immediate work. In contrast, energy-storage molecules such as glucose are consumed only to be broken down to use their energy. The reaction that harvests the energy of a sugar molecule in cells requiring oxygen to survive can be summarized by the reverse reaction to photosynthesis. In this reaction, oxygen is consumed and carbon dioxide is released as a waste product. The reaction is summarized as:

C6H12O6 + 6O2 ——> 6CO2 + 6H2O + energy

Both of these reactions involve many steps.

The processes of making and breaking down sugar molecules illustrate two examples of metabolic pathways. A metabolic pathway is a series of chemical reactions that takes a starting molecule and modifies it, step-by-step, through a series of metabolic intermediates, eventually yielding a final product. In the example of sugar metabolism, the first metabolic pathway synthesized sugar from smaller molecules, and the other pathway broke sugar down into smaller molecules. These two opposite processes—the first requiring energy and the second producing energy—are referred to as anabolic pathways (building polymers) and catabolic pathways (breaking down polymers into their monomers), respectively. Consequently, metabolism is composed of synthesis (anabolism) and degradation (catabolism) (Figure 4.3).

It is important to know that the chemical reactions of metabolic pathways do not take place on their own. Each reaction step is facilitated, or catalyzed, by a protein called an enzyme. Enzymes are important for catalyzing all types of biological reactions—those that require energy as well as those that release energy.

 
Anabolic and metabolic pathways are shown. In the anabolic pathway, four small molecules have energy added to them to make one large molecule. In the catabolic pathway, one large molecule is broken down into two components: four small molecules plus energy.
Figure 4.3 Catabolic pathways are those that generate energy by breaking down larger molecules. Anabolic pathways are those that require energy to synthesize larger molecules. Both types of pathways are required for maintaining the cell’s energy balance.

Energy

Thermodynamics refers to the study of energy and energy transfer involving physical matter. The matter relevant to a particular case of energy transfer is called a system, and everything outside of that matter is called the surroundings. For instance, when heating a pot of water on the stove, the system includes the stove, the pot, and the water. Energy is transferred within the system (between the stove, pot, and water). There are two types of systems: open and closed. In an open system, energy can be exchanged with its surroundings. The stovetop system is open because heat can be lost to the air. A closed system cannot exchange energy with its surroundings.

Biological organisms are open systems. Energy is exchanged between them and their surroundings as they use energy from the sun to perform photosynthesis or consume energy-storing molecules and release energy to the environment by doing work and releasing heat. Like all things in the physical world, energy is subject to physical laws. The laws of thermodynamics govern the transfer of energy in and among all systems in the universe.

In general, energy is defined as the ability to do work, or to create some kind of change. Energy exists in different forms. For example, electrical energy, light energy, and heat energy are all different types of energy. To appreciate the way energy flows into and out of biological systems, it is important to understand two of the physical laws that govern energy.

Thermodynamics

The first law of thermodynamics states that the total amount of energy in the universe is constant and conserved. In other words, there has always been, and always will be, exactly the same amount of energy in the universe. Energy exists in many different forms. According to the first law of thermodynamics, energy may be transferred from place to place or transformed into different forms, but it cannot be created or destroyed. The transfers and transformations of energy take place around us all the time. Light bulbs transform electrical energy into light and heat energy. Gas stoves transform chemical energy from natural gas into heat energy. Plants perform one of the most biologically useful energy transformations on earth: that of converting the energy of sunlight to chemical energy stored within organic molecules (Figure 4.2). Some examples of energy transformations are shown in Figure 4.4.

The challenge for all living organisms is to obtain energy from their surroundings in forms that they can transfer or transform into usable energy to do work. Living cells have evolved to meet this challenge. Chemical energy stored within organic molecules such as sugars and fats is transferred and transformed through a series of cellular chemical reactions into energy within molecules of ATP. Energy in ATP molecules is easily accessible to do work. Examples of the types of work that cells need to do include building complex molecules, transporting materials, powering the motion of cilia or flagella, and contracting muscle fibers to create movement.

 

The left side of this diagram depicts energy being transferred from an ice cream cone to two boys riding bikes. The right side depicts a plant converting light energy into chemical energy: Light energy is represented by the sun, and the chemical energy is represented by a green leaf on a branch.
Figure 4.4 Shown are some examples of energy transferred and transformed from one system to another and from one form to another. The food we consume provides our cells with the energy required to carry out bodily functions, just as light energy provides plants with the means to create the chemical energy they need. (credit “ice cream”: modification of work by D. Sharon Pruitt; credit “kids”: modification of work by Max from Providence; credit “leaf”: modification of work by Cory Zanker)

A living cell’s primary tasks of obtaining, transforming, and using energy to do work may seem simple. However, the second law of thermodynamics explains why these tasks are harder than they appear. All energy transfers and transformations are never completely efficient. In every energy transfer, some amount of energy is lost in a form that is unusable. In most cases, this form is heat energy. Thermodynamically, heat energy is defined as the energy transferred from one system to another that is not work. For example, when a light bulb is turned on, some of the energy being converted from electrical energy into light energy is lost as heat energy. Likewise, some energy is lost as heat energy during cellular metabolic reactions.

An important concept in physical systems is that of order and disorder. The more energy that is lost by a system to its surroundings, the less ordered and more random the system is. Scientists refer to the measure of randomness or disorder within a system as entropy. High entropy means high disorder and low energy. Molecules and chemical reactions have varying entropy as well. For example, entropy increases as molecules at a high concentration in one place diffuse and spread out. The second law of thermodynamics says that energy will always be lost as heat in energy transfers or transformations.

Living things are highly ordered, requiring constant energy input to be maintained in a state of low entropy.

Potential and Kinetic Energy

When an object is in motion, there is energy associated with that object. Think of a wrecking ball. Even a slow-moving wrecking ball can do a great deal of damage to other objects. Energy associated with objects in motion is called kinetic energy (Figure 4.5). A speeding bullet, a walking person, and the rapid movement of molecules in the air (which produces heat) all have kinetic energy.

Now what if that same motionless wrecking ball is lifted two stories above ground with a crane? If the suspended wrecking ball is unmoving, is there energy associated with it? The answer is yes. The energy that was required to lift the wrecking ball did not disappear, but is now stored in the wrecking ball by virtue of its position and the force of gravity acting on it. This type of energy is called potential energy (Figure 4.5). If the ball were to fall, the potential energy would be transformed into kinetic energy until all of the potential energy was exhausted when the ball rested on the ground. Wrecking balls also swing like a pendulum; through the swing, there is a constant change of potential energy (highest at the top of the swing) to kinetic energy (highest at the bottom of the swing). Other examples of potential energy include the energy of water held behind a dam or a person about to skydive out of an airplane.

The photo on the left shows water behind a dam as potential energy. The photo on the right shows a waterfall as kinetic energy.
Figure 4.5 Still water has potential energy; moving water, such as in a waterfall or a rapidly flowing river, has kinetic energy. (credit “dam”: modification of work by “Pascal”/Flickr; credit “waterfall”: modification of work by Frank Gualtieri) 

Potential energy is not only associated with the location of matter, but also with the structure of matter. Even a spring on the ground has potential energy if it is compressed; so does a rubber band that is pulled taut. On a molecular level, the bonds that hold the atoms of molecules together exist in a particular structure that has potential energy. Remember that anabolic cellular pathways require energy to synthesize complex molecules from simpler ones and catabolic pathways release energy when complex molecules are broken down. The fact that energy can be released by the breakdown of certain chemical bonds implies that those bonds have potential energy. In fact, there is potential energy stored within the bonds of all the food molecules we eat, which is eventually harnessed for use. This is because these bonds can release energy when broken. The type of potential energy that exists within chemical bonds, and is released when those bonds are broken, is called chemical energy. Chemical energy is responsible for providing living cells with energy from food. The release of energy occurs when the molecular bonds within food molecules are broken.

Watch a video about kilocalories.

An interactive H5P element has been excluded from this version of the text. You can view it online here:
https://pressbooks.nscc.ca/conceptsofbiologynscc/?p=150#h5p-28

Concept in Action


QR Code representing a URL

Visit the site and select “Pendulum” from the “Work and Energy” menu to see the shifting kinetic and potential energy of a pendulum in motion.

Free and Activation Energy

After learning that chemical reactions release energy when energy-storing bonds are broken, an important next question is the following: How is the energy associated with these chemical reactions quantified and expressed? How can the energy released from one reaction be compared to that of another reaction? A measurement of free energy is used to quantify these energy transfers. Recall that according to the second law of thermodynamics, all energy transfers involve the loss of some amount of energy in an unusable form such as heat. Free energy specifically refers to the energy associated with a chemical reaction that is available after the losses are accounted for. In other words, free energy is usable energy, or energy that is available to do work.

If energy is released during a chemical reaction, then the change in free energy, signified as ∆G (delta G) will be a negative number. A negative change in free energy also means that the products of the reaction have less free energy than the reactants, because they release some free energy during the reaction. Reactions that have a negative change in free energy and consequently release free energy are called exergonic reactions. Think: exergonic means energy is exiting the system. These reactions are also referred to as spontaneous reactions, and their products have less stored energy than the reactants. An important distinction must be drawn between the term spontaneous and the idea of a chemical reaction occurring immediately. Contrary to the everyday use of the term, a spontaneous reaction is not one that suddenly or quickly occurs. The rusting of iron is an example of a spontaneous reaction that occurs slowly, little by little, over time.

If a chemical reaction absorbs energy rather than releases energy on balance, then the ∆G for that reaction will be a positive value. In this case, the products have more free energy than the reactants. Thus, the products of these reactions can be thought of as energy-storing molecules. These chemical reactions are called endergonic reactions and they are non-spontaneous. An endergonic reaction will not take place on its own without the addition of free energy.

 

Four photos, from left to right, show a compost pile, a baby chick emerging from a fertilized egg, a teabag’s dark-colored contents diffusing into a clear mug of water, and a ball rolling downhill.
Figure 4.6 Shown are some examples of endergonic processes (ones that require energy) and exergonic processes (ones that release energy). (credit a: modification of work by Natalie Maynor; credit b: modification of work by USDA; credit c: modification of work by Cory Zanker; credit d: modification of work by Harry Malsch)

Look at each of the processes shown and decide if it is endergonic or exergonic.

There is another important concept that must be considered regarding endergonic and exergonic reactions. Exergonic reactions require a small amount of energy input to get going, before they can proceed with their energy-releasing steps. These reactions have a net release of energy, but still require some energy input in the beginning. This small amount of energy input necessary for all chemical reactions to occur is called the activation energy.

Concept in Action


QR Code representing a URL

Watch an animation of the move from free energy to transition state of the reaction.

Enzymes

A substance that helps a chemical reaction to occur is called a catalyst, and the molecules that catalyze biochemical reactions are called enzymes. Most enzymes are proteins and perform the critical task of lowering the activation energies of chemical reactions inside the cell. Most of the reactions critical to a living cell happen too slowly at normal temperatures to be of any use to the cell. Without enzymes to speed up these reactions, life could not persist. Enzymes do this by binding to the reactant molecules and holding them in such a way as to make the chemical bond-breaking and -forming processes take place more easily. It is important to remember that enzymes do not change whether a reaction is exergonic (spontaneous) or endergonic. This is because they do not change the free energy of the reactants or products. They only reduce the activation energy required for the reaction to go forward (Figure 4.7). In addition, an enzyme itself is unchanged by the reaction it catalyzes. Once one reaction has been catalyzed, the enzyme is able to participate in other reactions.

 
This plot shows that a catalyst decreases the activation energy for a reaction but does not change the Gibbs free energy.
Figure 4.7 Enzymes lower the activation energy of the reaction but do not change the free energy of the reaction. 

The chemical reactants to which an enzyme binds are called the enzyme’s substrates. There may be one or more substrates, depending on the particular chemical reaction. In some reactions, a single reactant substrate is broken down into multiple products. In others, two substrates may come together to create one larger molecule. Two reactants might also enter a reaction and both become modified, but they leave the reaction as two products. The location within the enzyme where the substrate binds is called the enzyme’s active site. The active site is where the “action” happens. Since enzymes are proteins, there is a unique combination of amino acid side chains within the active site. Each side chain is characterized by different properties. They can be large or small, weakly acidic or basic, hydrophilic or hydrophobic, positively or negatively charged, or neutral. The unique combination of side chains creates a very specific chemical environment within the active site. This specific environment is suited to bind to one specific chemical substrate (or substrates).

Active sites are subject to influences of the local environment. Increasing the environmental temperature generally increases reaction rates, enzyme-catalyzed or otherwise. However, temperatures outside of an optimal range reduce the rate at which an enzyme catalyzes a reaction. Hot temperatures will eventually cause enzymes to denature, an irreversible change in the three-dimensional shape and therefore the function of the enzyme. Enzymes are also suited to function best within a certain pH and salt concentration range, and, as with temperature, extreme pH, and salt concentrations can cause enzymes to denature.

For many years, scientists thought that enzyme-substrate binding took place in a simple “lock and key” fashion. This model asserted that the enzyme and substrate fit together perfectly in one instantaneous step. However, current research supports a model called induced fit (Figure 4.8). The induced-fit model expands on the lock-and-key model by describing a more dynamic binding between enzyme and substrate. As the enzyme and substrate come together, their interaction causes a mild shift in the enzyme’s structure that forms an ideal binding arrangement between enzyme and substrate.

Concept in Action


QR Code representing a URL

View an animation of induced fit.

When an enzyme binds its substrate, an enzyme-substrate complex is formed. This complex lowers the activation energy of the reaction and promotes its rapid progression in one of multiple possible ways. On a basic level, enzymes promote chemical reactions that involve more than one substrate by bringing the substrates together in an optimal orientation for reaction. Another way in which enzymes promote the reaction of their substrates is by creating an optimal environment within the active site for the reaction to occur. The chemical properties that emerge from the particular arrangement of amino acid R groups within an active site create the perfect environment for an enzyme’s specific substrates to react.

The enzyme-substrate complex can also lower activation energy by compromising the bond structure so that it is easier to break. Finally, enzymes can also lower activation energies by taking part in the chemical reaction itself. In these cases, it is important to remember that the enzyme will always return to its original state by the completion of the reaction. One of the hallmark properties of enzymes is that they remain ultimately unchanged by the reactions they catalyze. After an enzyme has catalyzed a reaction, it releases its product(s) and can catalyze a new reaction.

 
In this diagram, a substrate binds the active site of an enzyme and, in the process, both the shape of the enzyme and the shape of the substrate change. The substrate is converted to product, which leaves the active site.
Figure 4.8 The induced-fit model is an adjustment to the lock-and-key model and explains how enzymes and substrates undergo dynamic modifications during the transition state to increase the affinity of the substrate for the active site. 

It would seem ideal to have a scenario in which all of an organism’s enzymes existed in abundant supply and functioned optimally under all cellular conditions, in all cells, at all times. However, a variety of mechanisms ensures that this does not happen. Cellular needs and conditions constantly vary from cell to cell, and change within individual cells over time. The required enzymes of stomach cells differ from those of fat storage cells, skin cells, blood cells, and nerve cells. Furthermore, a digestive organ cell works much harder to process and break down nutrients during the time that closely follows a meal compared with many hours after a meal. As these cellular demands and conditions vary, so must the amounts and functionality of different enzymes.

Since the rates of biochemical reactions are controlled by activation energy, and enzymes lower and determine activation energies for chemical reactions, the relative amounts and functioning of the variety of enzymes within a cell ultimately determine which reactions will proceed and at what rates. This determination is tightly controlled in cells. In certain cellular environments, enzyme activity is partly controlled by environmental factors like pH, temperature, salt concentration, and, in some cases, cofactors or coenzymes.

Enzymes can also be regulated in ways that either promote or reduce enzyme activity. There are many kinds of molecules that inhibit or promote enzyme function, and various mechanisms by which they do so. In some cases of enzyme inhibition, an inhibitor molecule is similar enough to a substrate that it can bind to the active site and simply block the substrate from binding. When this happens, the enzyme is inhibited through competitive inhibition, because an inhibitor molecule competes with the substrate for binding to the active site.

On the other hand, in noncompetitive inhibition, an inhibitor molecule binds to the enzyme in a location other than the active site, called an allosteric site, but still manages to block substrate binding to the active site. Some inhibitor molecules bind to enzymes in a location where their binding induces a conformational change that reduces the affinity of the enzyme for its substrate. This type of inhibition is called allosteric inhibition (Figure 4.9). Most allosterically regulated enzymes are made up of more than one polypeptide, meaning that they have more than one protein subunit. When an allosteric inhibitor binds to a region on an enzyme, all active sites on the protein subunits are changed slightly such that they bind their substrates with less efficiency. There are allosteric activators as well as inhibitors. Allosteric activators bind to locations on an enzyme away from the active site, inducing a conformational change that increases the affinity of the enzyme’s active site(s) for its substrate(s) (Figure 4.9).

 
The left part of this diagram shows allosteric inhibition. The allosteric inhibitor binds to the enzyme at a site other than the active site. The shape of the active site is altered so that the enzyme can no longer bind to the substrate. The right part of this diagram shows allosteric activation. The allosteric activator binds to the enzyme at a site other than the active site. The shape of the active site is changed, allowing substrate to bind.
Figure 4.9 Allosteric inhibition works by indirectly inducing a conformational change to the active site such that the substrate no longer fits. In contrast, in allosteric activation, the activator molecule modifies the shape of the active site to allow a better fit of the substrate.
Through the Indigenous Lens

Plants cannot run or hide from their predators and have evolved many strategies to deter those who would eat them.  Think of thorns, irritants and secondary metabolites: these are compounds that do not directly help the plant grow, but are made specifically to keep predators away. Secondary metabolites are the most common way plants deter predators.  Some examples of secondary metabolites are atropine, nicotine, THC and caffeine. Humans have found these secondary metabolite compounds a rich source of materials for medicines. It is estimated that 90% of the drugs in the modern pharmacy have their “roots” in these secondary metabolites.

First peoples herbal treatments revealed these secondary metabolites to the world. For example, Indigenous peoples have long used the bark of willow shrubs and alder trees for a tea, tonic or poultice to reduce inflammation. You will learn more about the inflammation response by the immune system in chapter 11.

 

Figure 4.10 Pacific willow bark contains the compound salicin.
Figure 4.10 Pacific willow bark contains the compound salicin.

Both willow and alder bark contain the compound salicin. Most of us have this compound in our medicine cupboard in the form of salicylic acid or aspirin. Aspirin has been proved to reduce pain and inflammation, and once in our cells salicin converts to salicylic acid.

So how does it work? Salicin or aspirin acts as an enzyme inhibitor. In the inflammatory response two enzymes, COX1 and COX2 are key to this process. Salicin or aspirin specifically modifies an amino acid (serine) in the active site of these two related enzymes. This modification of the active sites does not allow the normal substrate to bind and so the inflammatory process is disrupted. As you have read in this chapter, this makes it competitive enzyme inhibitor.

Pharmaceutical Drug Developer

This photo shows several red capsule pills.
Figure 4.11 Have you ever wondered how pharmaceutical drugs are developed? (credit: Deborah Austin) 

Enzymes are key components of metabolic pathways. Understanding how enzymes work and how they can be regulated are key principles behind the development of many of the pharmaceutical drugs on the market today. Biologists working in this field collaborate with other scientists to design drugs (Figure 4.11).

Consider statins for example—statins is the name given to one class of drugs that can reduce cholesterol levels. These compounds are inhibitors of the enzyme HMG-CoA reductase, which is the enzyme that synthesizes cholesterol from lipids in the body. By inhibiting this enzyme, the level of cholesterol synthesized in the body can be reduced. Similarly, acetaminophen, popularly marketed under the brand name Tylenol, is an inhibitor of the enzyme cyclooxygenase. While it is used to provide relief from fever and inflammation (pain), its mechanism of action is still not completely understood.

How are drugs discovered? One of the biggest challenges in drug discovery is identifying a drug target. A drug target is a molecule that is literally the target of the drug. In the case of statins, HMG-CoA reductase is the drug target. Drug targets are identified through painstaking research in the laboratory. Identifying the target alone is not enough; scientists also need to know how the target acts inside the cell and which reactions go awry in the case of disease. Once the target and the pathway are identified, then the actual process of drug design begins. In this stage, chemists and biologists work together to design and synthesize molecules that can block or activate a particular reaction. However, this is only the beginning: If and when a drug prototype is successful in performing its function, then it is subjected to many tests from in vitro experiments to clinical trials before it can get approval from the U.S. Food and Drug Administration to be on the market.

Many enzymes do not work optimally, or even at all, unless bound to other specific non-protein helper molecules. They may bond either temporarily through ionic or hydrogen bonds, or permanently through stronger covalent bonds. Binding to these molecules promotes optimal shape and function of their respective enzymes. Two examples of these types of helper molecules are cofactors and coenzymes. Cofactors are inorganic ions such as ions of iron and magnesium. Coenzymes are organic helper molecules, those with a basic atomic structure made up of carbon and hydrogen. Like enzymes, these molecules participate in reactions without being changed themselves and are ultimately recycled and reused. Vitamins are the source of coenzymes. Some vitamins are the precursors of coenzymes and others act directly as coenzymes. Vitamin C is a direct coenzyme for multiple enzymes that take part in building the important connective tissue, collagen. Therefore, enzyme function is, in part, regulated by the abundance of various cofactors and coenzymes, which may be supplied by an organism’s diet or, in some cases, produced by the organism.

Shown are the molecular structures for Vitamin A, folic acid, Vitamin B1, Vitamin C, Vitamin B2, Vitamin D2, Vitamin B6, and Vitamin E.
Figure 4.12 Vitamins are important coenzymes or precursors of coenzymes, and are required for enzymes to function properly. Multivitamin capsules usually contain mixtures of all the vitamins at different percentages.

Feedback Inhibition in Metabolic Pathways

Molecules can regulate enzyme function in many ways. The major question remains, however: What are these molecules and where do they come from? Some are cofactors and coenzymes, as you have learned. What other molecules in the cell provide enzymatic regulation such as allosteric modulation, and competitive and non-competitive inhibition? Perhaps the most relevant sources of regulatory molecules, with respect to enzymatic cellular metabolism, are the products of the cellular metabolic reactions themselves. In a most efficient and elegant way, cells have evolved to use the products of their own reactions for feedback inhibition of enzyme activity. Feedback inhibition involves the use of a reaction product to regulate its own further production (Figure 4.12). The cell responds to an abundance of the products by slowing down production during anabolic or catabolic reactions. Such reaction products may inhibit the enzymes that catalyzed their production through the mechanisms described above.

This diagram shows a metabolic pathway in which three enzymes convert a substrate, in three steps, into a final product. The final product inhibits the first enzyme in the pathway by feedback inhibition.
Figure 4.13 Metabolic pathways are a series of reactions catalyzed by multiple enzymes. Feedback inhibition, where the end product of the pathway inhibits an upstream process, is an important regulatory mechanism in cells. 

The production of both amino acids and nucleotides is controlled through feedback inhibition. Additionally, ATP is an allosteric regulator of some of the enzymes involved in the catabolic breakdown of sugar, the process that creates ATP. In this way, when ATP is in abundant supply, the cell can prevent the production of ATP. On the other hand, ADP serves as a positive allosteric regulator (an allosteric activator) for some of the same enzymes that are inhibited by ATP. Thus, when relative levels of ADP are high compared to ATP, the cell is triggered to produce more ATP through sugar catabolism.

Section Summary

Cells perform the functions of life through various chemical reactions. A cell’s metabolism refers to the combination of chemical reactions that take place within it. Catabolic reactions break down complex chemicals into simpler ones and are associated with energy release. Anabolic processes build complex molecules out of simpler ones and require energy.

In studying energy, the term system refers to the matter and environment involved in energy transfers. Entropy is a measure of the disorder of a system. The physical laws that describe the transfer of energy are the laws of thermodynamics. The first law states that the total amount of energy in the universe is constant. The second law of thermodynamics states that every energy transfer involves some loss of energy in an unusable form, such as heat energy. Energy comes in different forms: kinetic, potential, and free. The change in free energy of a reaction can be negative (releases energy, exergonic) or positive (consumes energy, endergonic). All reactions require an initial input of energy to proceed, called the activation energy.

Enzymes are chemical catalysts that speed up chemical reactions by lowering their activation energy. Enzymes have an active site with a unique chemical environment that fits particular chemical reactants for that enzyme, called substrates. Enzymes and substrates are thought to bind according to an induced-fit model. Enzyme action is regulated to conserve resources and respond optimally to the environment.

Exercises

An interactive H5P element has been excluded from this version of the text. You can view it online here:
https://pressbooks.nscc.ca/conceptsofbiologynscc/?p=150#h5p-29

Glossary

activation energy: the amount of initial energy necessary for reactions to occur

active site: a specific region on the enzyme where the substrate binds

allosteric inhibition: the mechanism for inhibiting enzyme action in which a regulatory molecule binds to a second site (not the active site) and initiates a conformation change in the active site, preventing binding with the substrate

anabolic: describes the pathway that requires a net energy input to synthesize complex molecules from simpler ones

bioenergetics: the concept of energy flow through living systems

catabolic: describes the pathway in which complex molecules are broken down into simpler ones, yielding energy as an additional product of the reaction

competitive inhibition: a general mechanism of enzyme activity regulation in which a molecule other than the enzyme’s substrate is able to bind the active site and prevent the substrate itself from binding, thus inhibiting the overall rate of reaction for the enzyme

endergonic: describes a chemical reaction that results in products that store more chemical potential energy than the reactants

enzyme: a molecule that catalyzes a biochemical reaction

exergonic: describes a chemical reaction that results in products with less chemical potential energy than the reactants, plus the release of free energy

feedback inhibition: a mechanism of enzyme activity regulation in which the product of a reaction or the final product of a series of sequential reactions inhibits an enzyme for an earlier step in the reaction series

heat energy: the energy transferred from one system to another that is not work

kinetic energy: the type of energy associated with objects in motion

metabolism: all the chemical reactions that take place inside cells, including those that use energy and those that release energy

noncompetitive inhibition: a general mechanism of enzyme activity regulation in which a regulatory molecule binds to a site other than the active site and prevents the active site from binding the substrate; thus, the inhibitor molecule does not compete with the substrate for the active site; allosteric inhibition is a form of noncompetitive inhibition

potential energy: the type of energy that refers to the potential to do work

substrate: a molecule on which the enzyme acts

thermodynamics: the science of the relationships between heat, energy, and work

13

4.2 Glycolysis

Charles Molnar and Jane Gair

Learning Objectives

By the end of this section, you will be able to:

  • Explain how ATP is used by the cell as an energy source
  • Describe the overall result in terms of molecules produced of the breakdown of glucose by glycolysis

Energy production within a cell involves many coordinated chemical pathways. Most of these pathways are combinations of oxidation and reduction reactions. Oxidation and reduction occur in tandem. An oxidation reaction strips an electron from an atom in a compound, and the addition of this electron to another compound is a reduction reaction. Because oxidation and reduction usually occur together, these pairs of reactions are called oxidation-reduction reactions, or redox reactions.

Electrons and Energy

The removal of an electron from a molecule, oxidizing it, results in a decrease in potential energy in the oxidized compound. The electron (sometimes as part of a hydrogen atom) does not remain unbonded, however, in the cytoplasm of a cell. Rather, the electron is shifted to a second compound, reducing the second compound. The shift of an electron from one compound to another removes some potential energy from the first compound (the oxidized compound) and increases the potential energy of the second compound (the reduced compound). The transfer of electrons between molecules is important because most of the energy stored in atoms and used to fuel cell functions is in the form of high-energy electrons. The transfer of energy in the form of electrons allows the cell to transfer and use energy in an incremental fashion—in small packages rather than in a single, destructive burst. This chapter focuses on the extraction of energy from food. You will see that as you track the path of the transfers, you are tracking the path of electrons moving through metabolic pathways.

Electron Carriers

In living systems, a small class of compounds functions as electron shuttles: they bind and carry high-energy electrons between compounds in pathways. The principal electron carriers we will consider are derived from the B vitamin group and are derivatives of nucleotides. These compounds can be easily reduced (that is, they accept electrons) or oxidized (they lose electrons). Nicotinamide adenine dinucleotide (NAD) (Figure 4.13) is derived from vitamin B3, niacin. NAD+ is the oxidized form of the molecule; NADH is the reduced form of the molecule after it has accepted two electrons and a proton (which together are the equivalent of a hydrogen atom with an extra electron).

NAD+ can accept electrons from an organic molecule according to the general equation:

RH (Reducing Agent) + NAD + (Oxidizing Agent) —-> NADH (Reduced) + R (Oxidized)

When electrons are added to a compound, they are reduced. A compound that reduces another is called a reducing agent. In the above equation, RH is a reducing agent, and NAD+ is reduced to NADH. When electrons are removed from compound, it is oxidized. A compound that oxidizes another is called an oxidizing agent. In the above equation, NAD+ is an oxidizing agent, and RH is oxidized to R.

Similarly, flavin adenine dinucleotide (FAD+) is derived from vitamin B2, also called riboflavin. Its reduced form is FADH2. A second variation of NAD, NADP, contains an extra phosphate group. Both NAD+ and FAD+ are extensively used in energy extraction from sugars, and NADP plays an important role in anabolic reactions and photosynthesis.

This illustration shows the molecular structure of NAD^{+} and NADH. Both compounds are composed of an adenine nucleotide and a nicotinamide nucleotide, which bond together to form a dinucleotide. The nicotinamide nucleotide is at the 5' end, and the adenine nucleotide is at the 3’ end. Nicotinamide is a nitrogenous base, meaning it has nitrogen in a six-membered carbon ring. In NADH, one extra hydrogen is associated with this ring, which is not found in NAD^{+}.
Figure 4.13 The oxidized form of the electron carrier (NAD+) is shown on the left and the reduced form (NADH) is shown on the right. The nitrogenous base in NADH has one more hydrogen ion and two more electrons than in NAD+.

ATP in Living Systems

A living cell cannot store significant amounts of free energy. Excess free energy would result in an increase of heat in the cell, which would result in excessive thermal motion that could damage and then destroy the cell. Rather, a cell must be able to handle that energy in a way that enables the cell to store the energy safely and release it for use only as needed. Living cells accomplish this by using the compound adenosine triphosphate (ATP). ATP is often called the “energy currency” of the cell, and, like currency, this versatile compound can be used to fill any energy need of the cell. How? It functions similarly to a rechargeable battery.

When ATP is broken down, usually by the removal of its terminal phosphate group, energy is released. The cell uses the energy to do work, usually by the released phosphate binding to another molecule, activating it. For example, in the mechanical work of muscle contraction, ATP supplies the energy to move the contractile muscle proteins. Recall the active transport work of the sodium-potassium pump in cell membranes. ATP alters the structure of the integral protein that functions as the pump, changing its affinity for sodium and potassium. In this way, the cell performs work, pumping ions against their electrochemical gradients.

ATP Structure and Function

At the heart of ATP is a molecule of adenosine monophosphate (AMP), which is composed of an adenine molecule bonded to a ribose molecule and a single phosphate group (Figure 4.14). Ribose is a five-carbon sugar found in RNA, and AMP is one of the nucleotides in RNA. The addition of a second phosphate group to this core molecule results in the formation of adenosine diphosphate (ADP); the addition of a third phosphate group forms adenosine triphosphate (ATP).

This illustration shows the molecular structure of ATP. This molecule is an adenine nucleotide with a string of three phosphate groups attached to it. The phosphate groups are named alpha, beta, and gamma in order of increasing distance from the ribose sugar to which they are attached.
Figure 4.14 ATP (adenosine triphosphate) has three phosphate groups that can be removed by hydrolysis to form ADP (adenosine diphosphate) or AMP (adenosine monophosphate).The negative charges on the phosphate group naturally repel each other, requiring energy to bond them together and releasing energy when these bonds are broken.

The addition of a phosphate group to a molecule requires energy. Phosphate groups are negatively charged and thus repel one another when they are arranged in series, as they are in ADP and ATP. This repulsion makes the ADP and ATP molecules inherently unstable. The release of one or two phosphate groups from ATP, a process called dephosphorylation, releases energy.

Even exergonic, energy-releasing reactions require a small amount of activation energy to proceed. However, consider endergonic reactions, which require much more energy input because their products have more free energy than their reactants. Within the cell, where does energy to power such reactions come from? The answer lies with an energy-supplying molecule called adenosine triphosphate, or ATP. ATP is a small, relatively simple molecule, but within its bonds contains the potential for a quick burst of energy that can be harnessed to perform cellular work. This molecule can be thought of as the primary energy currency of cells in the same way that money is the currency that people exchange for things they need. ATP is used to power the majority of energy-requiring cellular reactions.

ATP in Living Systems

A living cell cannot store significant amounts of free energy. Excess free energy would result in an increase of heat in the cell, which would denature enzymes and other proteins, and thus destroy the cell. Rather, a cell must be able to store energy safely and release it for use only as needed. Living cells accomplish this using ATP, which can be used to fill any energy need of the cell. How? It functions as a rechargeable battery.

When ATP is broken down, usually by the removal of its terminal phosphate group, energy is released. This energy is used to do work by the cell, usually by the binding of the released phosphate to another molecule, thus activating it. For example, in the mechanical work of muscle contraction, ATP supplies energy to move the contractile muscle proteins.

ATP Structure and Function

At the heart of ATP is a molecule of adenosine monophosphate (AMP), which is composed of an adenine molecule bonded to both a ribose molecule and a single phosphate group (Figure 4.15). Ribose is a five-carbon sugar found in RNA and AMP is one of the nucleotides in RNA. The addition of a second phosphate group to this core molecule results in adenosine diphosphate (ADP); the addition of a third phosphate group forms adenosine triphosphate (ATP).

This illustration shows the molecular structure of ATP. This molecule is an adenine nucleotide with ribose and a string of three phosphate groups attached to it. The phosphate groups are named alpha, beta, and gamma in order of increasing distance from the ribose sugar to which they are attached.
Figure 4.15 The structure of ATP shows the basic components of a two-ring adenine, five-carbon ribose, and three phosphate groups.

The addition of a phosphate group to a molecule requires a high amount of energy and results in a high-energy bond. Phosphate groups are negatively charged and thus repel one another when they are arranged in series, as they are in ADP and ATP. This repulsion makes the ADP and ATP molecules inherently unstable. The release of one or two phosphate groups from ATP, a process called hydrolysis, releases energy.

Glycolysis

You have read that nearly all of the energy used by living things comes to them in the bonds of the sugar, glucose. Glycolysis is the first step in the breakdown of glucose to extract energy for cell metabolism. Many living organisms carry out glycolysis as part of their metabolism. Glycolysis takes place in the cytoplasm of most prokaryotic and all eukaryotic cells.

Glycolysis begins with the six-carbon, ring-shaped structure of a single glucose molecule and ends with two molecules of a three-carbon sugar called pyruvate. Glycolysis consists of two distinct phases. In the first part of the glycolysis pathway, energy is used to make adjustments so that the six-carbon sugar molecule can be split evenly into two three-carbon pyruvate molecules. In the second part of glycolysis, ATP and nicotinamide-adenine dinucleotide (NADH) are produced (Figure 4.16).

If the cell cannot catabolize the pyruvate molecules further, it will harvest only two ATP molecules from one molecule of glucose. For example, mature mammalian red blood cells are only capable of glycolysis, which is their sole source of ATP. If glycolysis is interrupted, these cells would eventually die.

A graphic shows glucose at the top with an arrow pointing down to fructose diphosphate, which then splits into two glyceraldehyde 3-phosphate molecules. Each of these forms one NADH and two ATP molecules in the process of each becoming a pyruvate molecule.
Figure 4.16 In glycolysis, a glucose molecule is converted into two pyruvate molecules.

 

Section Summary

ATP functions as the energy currency for cells. It allows cells to store energy briefly and transport it within itself to support endergonic chemical reactions. The structure of ATP is that of an RNA nucleotide with three phosphate groups attached. As ATP is used for energy, a phosphate group is detached, and ADP is produced. Energy derived from glucose catabolism is used to recharge ADP into ATP.

Glycolysis is the first pathway used in the breakdown of glucose to extract energy. Because it is used by nearly all organisms on earth, it must have evolved early in the history of life. Glycolysis consists of two parts: The first part prepares the six-carbon ring of glucose for separation into two three-carbon sugars. Energy from ATP is invested into the molecule during this step to energize the separation. The second half of glycolysis extracts ATP and high-energy electrons from hydrogen atoms and attaches them to NAD+. Two ATP molecules are invested in the first half and four ATP molecules are formed during the second half. This produces a net gain of two ATP molecules per molecule of glucose for the cell.

Exercises

An interactive H5P element has been excluded from this version of the text. You can view it online here:
https://pressbooks.nscc.ca/conceptsofbiologynscc/?p=156#h5p-30

Glossary

ATP: (also, adenosine triphosphate) the cell’s energy currency

glycolysis: the process of breaking glucose into two three-carbon molecules with the production of ATP and NADH

14

4.3 Citric Acid Cycle and Oxidative Phosphorylation

Charles Molnar and Jane Gair

Learning Objectives

By the end of this section, you will be able to:

  • Describe the location of the citric acid cycle and oxidative phosphorylation in the cell
  • Describe the overall outcome of the citric acid cycle and oxidative phosphorylation in terms of the products of each
  • Describe the relationships of glycolysis, the citric acid cycle, and oxidative phosphorylation in terms of their inputs and outputs.

The Citric Acid Cycle

In eukaryotic cells, the pyruvate molecules produced at the end of glycolysis are transported into mitochondria, which are sites of cellular respiration. If oxygen is available, aerobic respiration will go forward. In mitochondria, pyruvate will be transformed into a two-carbon acetyl group (by removing a molecule of carbon dioxide) that will be picked up by a carrier compound called coenzyme A (CoA), which is made from vitamin B5. The resulting compound is called acetyl CoA. (Figure 4.17). Acetyl CoA can be used in a variety of ways by the cell, but its major function is to deliver the acetyl group derived from pyruvate to the next pathway in glucose catabolism.

A graphic shows pyruvate becoming a two-carbon acetyl group by removing one molecule of carbon dioxide. The two-carbon acetyl group is picked up by coenzyme A to become acetyl CoA. The acetyl CoA then enters the citric acid cycle. Three NADH, one FADH2, one ATP, and two carbon dioxide molecules are produced during this cycle.
Figure 4.17 Pyruvate is converted into acetyl-CoA before entering the citric acid cycle.

 

Like the conversion of pyruvate to acetyl CoA, the citric acid cycle in eukaryotic cells takes place in the matrix of the mitochondria. Unlike glycolysis, the citric acid cycle is a closed loop: The last part of the pathway regenerates the compound used in the first step. The eight steps of the cycle are a series of chemical reactions that produces two carbon dioxide molecules, one ATP molecule (or an equivalent), and reduced forms (NADH and FADH2) of NAD+ and FAD+, important coenzymes in the cell. Part of this is considered an aerobic pathway (oxygen-requiring) because the NADH and FADH2 produced must transfer their electrons to the next pathway in the system, which will use oxygen. If oxygen is not present, this transfer does not occur.

Two carbon atoms come into the citric acid cycle from each acetyl group. Two carbon dioxide molecules are released on each turn of the cycle; however, these do not contain the same carbon atoms contributed by the acetyl group on that turn of the pathway. The two acetyl-carbon atoms will eventually be released on later turns of the cycle; in this way, all six carbon atoms from the original glucose molecule will be eventually released as carbon dioxide. It takes two turns of the cycle to process the equivalent of one glucose molecule. Each turn of the cycle forms three high-energy NADH molecules and one high-energy FADH2 molecule. These high-energy carriers will connect with the last portion of aerobic respiration to produce ATP molecules. One ATP (or an equivalent) is also made in each cycle. Several of the intermediate compounds in the citric acid cycle can be used in synthesizing non-essential amino acids; therefore, the cycle is both anabolic and catabolic.

This illustration shows the structure of a mitochondrion, which has an outer membrane and an inner membrane. The inner membrane has many folds, called cristae. The space between the outer membrane and the inner membrane is called the intermembrane space, and the central space of the mitochondrion is called the matrix. ATP synthase enzymes and the electron transport chain are located in the inner membrane
Figure 4.18 In eukaryotes, oxidative phosphorylation takes place in mitochondria. In prokaryotes, this process takes place in the plasma membrane. (Credit: modification of work by Mariana Ruiz Villareal)

Oxidative Phosphorylation

You have just read about two pathways in glucose catabolism—glycolysis and the citric acid cycle—that generate ATP. Most of the ATP generated during the aerobic catabolism of glucose, however, is not generated directly from these pathways. Rather, it derives from a process that begins with passing electrons through a series of chemical reactions to a final electron acceptor, oxygen. These reactions take place in specialized protein complexes located in the inner membrane of the mitochondria of eukaryotic organisms and on the inner part of the cell membrane of prokaryotic organisms. The energy of the electrons is harvested and used to generate a electrochemical gradient across the inner mitochondrial membrane. The potential energy of this gradient is used to generate ATP. The entirety of this process is called oxidative phosphorylation.

The electron transport chain (Figure 4.19 a) is the last component of aerobic respiration and is the only part of metabolism that uses atmospheric oxygen. Oxygen continuously diffuses into plants for this purpose. In animals, oxygen enters the body through the respiratory system. Electron transport is a series of chemical reactions that resembles a bucket brigade in that electrons are passed rapidly from one component to the next, to the endpoint of the chain where oxygen is the final electron acceptor and water is produced. There are four complexes composed of proteins, labeled I through IV in Figure 4.19 c, and the aggregation of these four complexes, together with associated mobile, accessory electron carriers, is called the electron transport chain. The electron transport chain is present in multiple copies in the inner mitochondrial membrane of eukaryotes and in the plasma membrane of prokaryotes. In each transfer of an electron through the electron transport chain, the electron loses energy, but with some transfers, the energy is stored as potential energy by using it to pump hydrogen ions across the inner mitochondrial membrane into the intermembrane space, creating an electrochemical gradient.

 
Part a: This illustration shows the electron transport chain embedded in the inner mitochondrial membrane. The electron transport chain consists of four electron complexes. Complex I oxidizes NADH to NAD+ and simultaneously pumps a proton across the membrane into the intermembrane space. The two electrons released from NADH are shuttled to coenzyme Q, then to complex III, to cytochrome c, to complex IV, then to molecular oxygen. In the process, two more protons are pumped across the membrane into the intermembrane space, and molecular oxygen is reduced to form water. Complex II removes two electrons from FADH2, thereby forming FAD. The electrons are shuttled to coenzyme Q, then to complex III, cytochrome c, complex I, and molecular oxygen as in the case of NADH oxidation. Part b: This illustration shows an ATP synthase enzyme embedded in the inner mitochondrial membrane. ATP synthase allows protons to move from an area of high concentration in the intermembrane space to an area of low concentration in the mitochondrial matrix. The energy derived from this exergonic process is used to synthesize ATP from ADP and inorganic phosphate. Part c: This illustration shows the electron transport chain and ATP synthase enzyme embedded in the inner mitochondrial membrane, and the citric acid cycle in the mitochondrial matrix. The citric acid cycle feeds NADH and FADH2 into the electron transport chain. The electron transport chain oxidizes these substrates and, in the process, pumps protons into the intermembrane space. ATP synthase allows protons to leak back into the matrix and synthesizes ATP.
Figure 4.19 (a) The electron transport chain is a set of molecules that supports a series of oxidation-reduction reactions. (b) ATP synthase is a complex, molecular machine that uses an H+ gradient to regenerate ATP from ADP. (c) Chemiosmosis relies on the potential energy provided by the H+ gradient across the membrane.

 

Cyanide inhibits cytochrome c oxidase, a component of the electron transport chain. If cyanide poisoning occurs, would you expect the pH of the intermembrane space to increase or decrease? What affect would cyanide have on ATP synthesis?

Electrons from NADH and FADH2 are passed to protein complexes in the electron transport chain. As they are passed from one complex to another (there are a total of four), the electrons lose energy, and some of that energy is used to pump hydrogen ions from the mitochondrial matrix into the intermembrane space. In the fourth protein complex, the electrons are accepted by oxygen, the terminal acceptor. The oxygen with its extra electrons then combines with two hydrogen ions, further enhancing the electrochemical gradient, to form water. If there were no oxygen present in the mitochondrion, the electrons could not be removed from the system, and the entire electron transport chain would back up and stop. The mitochondria would be unable to generate new ATP in this way, and the cell would ultimately die from lack of energy. This is the reason we must breathe to draw in new oxygen.

In the electron transport chain, the free energy from the series of reactions just described is used to pump hydrogen ions across the membrane. The uneven distribution of H+ ions across the membrane establishes an electrochemical gradient, owing to the H+ ions’ positive charge and their higher concentration on one side of the membrane.

Hydrogen ions diffuse through the inner membrane through an integral membrane protein called ATP synthase (Figure 4.19 b). This complex protein acts as a tiny generator, turned by the force of the hydrogen ions diffusing through it, down their electrochemical gradient from the intermembrane space, where there are many mutually repelling hydrogen ions to the matrix, where there are few. The turning of the parts of this molecular machine regenerate ATP from ADP. This flow of hydrogen ions across the membrane through ATP synthase is called chemiosmosis.

Chemiosmosis (Figure 4.19 c) is used to generate 90 percent of the ATP made during aerobic glucose catabolism. The result of the reactions is the production of ATP from the energy of the electrons removed from hydrogen atoms. These atoms were originally part of a glucose molecule. At the end of the electron transport system, the electrons are used to reduce an oxygen molecule to oxygen ions. The extra electrons on the oxygen ions attract hydrogen ions (protons) from the surrounding medium, and water is formed. The electron transport chain and the production of ATP through chemiosmosis are collectively called oxidative phosphorylation.

ATP Yield

The number of ATP molecules generated from the catabolism of glucose varies. For example, the number of hydrogen ions that the electron transport chain complexes can pump through the membrane varies between species. Another source of variance stems from the shuttle of electrons across the mitochondrial membrane. The NADH generated from glycolysis cannot easily enter mitochondria. Thus, electrons are picked up on the inside of the mitochondria by either NAD+ or FAD+. Fewer ATP molecules are generated when FAD+ acts as a carrier. NAD+ is used as the electron transporter in the liver and FAD+ in the brain, so ATP yield depends on the tissue being considered.

Another factor that affects the yield of ATP molecules generated from glucose is that intermediate compounds in these pathways are used for other purposes. Glucose catabolism connects with the pathways that build or break down all other biochemical compounds in cells, and the result is somewhat messier than the ideal situations described thus far. For example, sugars other than glucose are fed into the glycolytic pathway for energy extraction. Other molecules that would otherwise be used to harvest energy in glycolysis or the citric acid cycle may be removed to form nucleic acids, amino acids, lipids, or other compounds. Overall, in living systems, these pathways of glucose catabolism extract about 34 percent of the energy contained in glucose.

Mitochondrial Disease Physician

What happens when the critical reactions of cellular respiration do not proceed correctly? Mitochondrial diseases are genetic disorders of metabolism. Mitochondrial disorders can arise from mutations in nuclear or mitochondrial DNA, and they result in the production of less energy than is normal in body cells. Symptoms of mitochondrial diseases can include muscle weakness, lack of coordination, stroke-like episodes, and loss of vision and hearing. Most affected people are diagnosed in childhood, although there are some adult-onset diseases. Identifying and treating mitochondrial disorders is a specialized medical field. The educational preparation for this profession requires a college education, followed by medical school with a specialization in medical genetics. Medical geneticists can be board certified by the American Board of Medical Genetics and go on to become associated with professional organizations devoted to the study of mitochondrial disease, such as the Mitochondrial Medicine Society and the Society for Inherited Metabolic Disease.

Section Summary

The citric acid cycle is a series of chemical reactions that removes high-energy electrons and uses them in the electron transport chain to generate ATP. One molecule of ATP (or an equivalent) is produced per each turn of the cycle.

The electron transport chain is the portion of aerobic respiration that uses free oxygen as the final electron acceptor for electrons removed from the intermediate compounds in glucose catabolism. The electrons are passed through a series of chemical reactions, with a small amount of free energy used at three points to transport hydrogen ions across the membrane. This contributes to the gradient used in chemiosmosis. As the electrons are passed from NADH or FADH2 down the electron transport chain, they lose energy. The products of the electron transport chain are water and ATP. A number of intermediate compounds can be diverted into the anabolism of other biochemical molecules, such as nucleic acids, non-essential amino acids, sugars, and lipids. These same molecules, except nucleic acids, can serve as energy sources for the glucose pathway.

Exercises

An interactive H5P element has been excluded from this version of the text. You can view it online here:
https://pressbooks.nscc.ca/conceptsofbiologynscc/?p=161#h5p-31

Glossary

acetyl CoA: the combination of an acetyl group derived from pyruvic acid and coenzyme A which is made from pantothenic acid (a B-group vitamin)

ATP synthase: a membrane-embedded protein complex that regenerates ATP from ADP with energy from protons diffusing through it

chemiosmosis: the movement of hydrogen ions down their electrochemical gradient across a membrane through ATP synthase to generate ATP

citric acid cycle: a series of enzyme-catalyzed chemical reactions of central importance in all living cells that harvests the energy in carbon-carbon bonds of sugar molecules to generate ATP; the citric acid cycle is an aerobic metabolic pathway because it requires oxygen in later reactions to proceed

electron transport chain: a series of four large, multi-protein complexes embedded in the inner mitochondrial membrane that accepts electrons from donor compounds and harvests energy from a series of chemical reactions to generate a hydrogen ion gradient across the membrane

oxidative phosphorylation: the production of ATP by the transfer of electrons down the electron transport chain to create a proton gradient that is used by ATP synthase to add phosphate groups to ADP molecules

15

4.4 Fermentation

Charles Molnar and Jane Gair

Learning Objectives

By the end of this section, you will be able to:

  • Discuss the fundamental difference between anaerobic cellular respiration and fermentation
  • Describe the type of fermentation that readily occurs in animal cells and the conditions that initiate that fermentation

In aerobic respiration, the final electron acceptor is an oxygen molecule, O2. If aerobic respiration occurs, then ATP will be produced using the energy of the high-energy electrons carried by NADH or FADH2 to the electron transport chain. If aerobic respiration does not occur, NADH must be reoxidized to NAD+ for reuse as an electron carrier for glycolysis to continue. How is this done? Some living systems use an organic molecule as the final electron acceptor. Processes that use an organic molecule to regenerate NAD+ from NADH are collectively referred to as fermentation. In contrast, some living systems use an inorganic molecule as a final electron acceptor; both methods are a type of anaerobic cellular respiration. Anaerobic respiration enables organisms to convert energy for their use in the absence of oxygen.

Lactic Acid Fermentation

The fermentation method used by animals and some bacteria like those in yogurt is lactic acid fermentation (Figure 4.20). This occurs routinely in mammalian red blood cells and in skeletal muscle that has insufficient oxygen supply to allow aerobic respiration to continue (that is, in muscles used to the point of fatigue). In muscles, lactic acid produced by fermentation must be removed by the blood circulation and brought to the liver for further metabolism. The chemical reaction of lactic acid fermentation is the following:

Pyruvic acid +NADH↔lactic acid+NAD+Pyruvic acid +NADH↔lactic acid+NAD+

The enzyme that catalyzes this reaction is lactate dehydrogenase. The reaction can proceed in either direction, but the left-to-right reaction is inhibited by acidic conditions. This lactic acid build-up causes muscle stiffness and fatigue. Once the lactic acid has been removed from the muscle and is circulated to the liver, it can be converted back to pyruvic acid and further catabolized for energy.

Lactic acid fermentation is common in muscles that have become exhausted by use.
Figure 4.20

Tremetol, a metabolic poison found in white snake root plant, prevents the metabolism of lactate. When cows eat this plant, Tremetol is concentrated in the milk. Humans who consume the milk become ill. Symptoms of this disease, which include vomiting, abdominal pain, and tremors, become worse after exercise. Why do you think this is the case?

<!– The illness is caused by lactic acid build-up. Lactic acid levels rise after exercise, making the symptoms worse. Milk sickness is rare today, but was common in the Midwestern United States in the early 1800s. –>

Alcohol Fermentation

Another familiar fermentation process is alcohol fermentation (Figure 4.21), which produces ethanol, an alcohol. The alcohol fermentation reaction is the following:

 
Graphic showing the alcohol fermentation reaction in an equation.
Figure 4.21 The reaction resulting in alcohol fermentation is shown.

 

In the first reaction, a carboxyl group is removed from pyruvic acid, releasing carbon dioxide as a gas. The loss of carbon dioxide reduces the molecule by one carbon atom, making acetaldehyde. The second reaction removes an electron from NADH, forming NAD+ and producing ethanol from the acetaldehyde, which accepts the electron. The fermentation of pyruvic acid by yeast produces the ethanol found in alcoholic beverages (Figure 4.22). If the carbon dioxide produced by the reaction is not vented from the fermentation chamber, for example in beer and sparkling wines, it remains dissolved in the medium until the pressure is released. Ethanol above 12 percent is toxic to yeast, so natural levels of alcohol in wine occur at a maximum of 12 percent.

 
This photo shows large, silver-colored, cylindrical fermentation tanks.
Figure 4.22 Fermentation of grape juice to make wine produces CO2 as a byproduct. Fermentation tanks have valves so that pressure inside the tanks can be released.

 

Anaerobic Cellular Respiration

Certain prokaryotes, including some species of bacteria and Archaea, use anaerobic respiration. For example, the group of Archaea called methanogens reduces carbon dioxide to methane to oxidize NADH. These microorganisms are found in soil and in the digestive tracts of ruminants, such as cows and sheep. Similarly, sulfate-reducing bacteria and Archaea, most of which are anaerobic (Figure 4.23), reduce sulfate to hydrogen sulfide to regenerate NAD+ from NADH.

This photo shows a bloom of green bacteria in water.
Figure 4.23 The green color seen in these coastal waters is from an eruption of hydrogen sulfide. Anaerobic, sulfate-reducing bacteria release hydrogen sulfide gas as they decompose algae in the water. (credit: NASA image courtesy Jeff Schmaltz, MODIS Land Rapid Response Team at NASA GSFC)

 

Concept in Action

QR Code representing a URL

Visit this site to see anaerobic cellular respiration in action.

Other fermentation methods occur in bacteria. Many prokaryotes are facultatively anaerobic. This means that they can switch between aerobic respiration and fermentation, depending on the availability of oxygen. Certain prokaryotes, like Clostridia bacteria, are obligate anaerobes. Obligate anaerobes live and grow in the absence of molecular oxygen. Oxygen is a poison to these microorganisms and kills them upon exposure. It should be noted that all forms of fermentation, except lactic acid fermentation, produce gas. The production of particular types of gas is used as an indicator of the fermentation of specific carbohydrates, which plays a role in the laboratory identification of the bacteria. The various methods of fermentation are used by different organisms to ensure an adequate supply of NAD+ for the sixth step in glycolysis. Without these pathways, that step would not occur, and no ATP would be harvested from the breakdown of glucose.

Section Summary

If NADH cannot be metabolized through aerobic respiration, another electron acceptor is used. Most organisms will use some form of fermentation to accomplish the regeneration of NAD+, ensuring the continuation of glycolysis. The regeneration of NAD+ in fermentation is not accompanied by ATP production; therefore, the potential for NADH to produce ATP using an electron transport chain is not utilized.

Exercises

An interactive H5P element has been excluded from this version of the text. You can view it online here:
https://pressbooks.nscc.ca/conceptsofbiologynscc/?p=168#h5p-32

Glossary

anaerobic cellular respiration: the use of an electron acceptor other than oxygen to complete metabolism using electron transport-based chemiosmosis

fermentation: the steps that follow the partial oxidation of glucose via glycolysis to regenerate NAD+; occurs in the absence of oxygen and uses an organic compound as the final electron acceptor

16

4.5 Connections to Other Metabolic Pathways

Charles Molnar and Jane Gair

Learning Objectives

By the end of this section, you will be able to:

  • Discuss the way in which carbohydrate metabolic pathways, glycolysis, and the citric acid cycle interrelate with protein and lipid metabolic pathways
  • Explain why metabolic pathways are not considered closed systems

You have learned about the catabolism of glucose, which provides energy to living cells. But living things consume more than just glucose for food. How does a turkey sandwich, which contains protein, provide energy to your cells? This happens because all of the catabolic pathways for carbohydrates, proteins, and lipids eventually connect into glycolysis and the citric acid cycle pathways (Figure 4.24). Metabolic pathways should be thought of as porous—that is, substances enter from other pathways, and other substances leave for other pathways. These pathways are not closed systems. Many of the products in a particular pathway are reactants in other pathways.

Connections of Other Sugars to Glucose Metabolism

Glycogen, a polymer of glucose, is a short-term energy storage molecule in animals. When there is adequate ATP present, excess glucose is converted into glycogen for storage. Glycogen is made and stored in the liver and muscle. Glycogen will be taken out of storage if blood sugar levels drop. The presence of glycogen in muscle cells as a source of glucose allows ATP to be produced for a longer time during exercise.

Sucrose is a disaccharide made from glucose and fructose bonded together. Sucrose is broken down in the small intestine, and the glucose and fructose are absorbed separately. Fructose is one of the three dietary monosaccharides, along with glucose and galactose (which is part of milk sugar, the disaccharide lactose), that are absorbed directly into the bloodstream during digestion. The catabolism of both fructose and galactose produces the same number of ATP molecules as glucose.

Connections of Proteins to Glucose Metabolism

Proteins are broken down by a variety of enzymes in cells. Most of the time, amino acids are recycled into new proteins. If there are excess amino acids, however, or if the body is in a state of famine, some amino acids will be shunted into pathways of glucose catabolism. Each amino acid must have its amino group removed prior to entry into these pathways. The amino group is converted into ammonia. In mammals, the liver synthesizes urea from two ammonia molecules and a carbon dioxide molecule. Thus, urea is the principal waste product in mammals from the nitrogen originating in amino acids, and it leaves the body in urine.

Connections of Lipids to Glucose Metabolism

The lipids that are connected to the glucose pathways are cholesterol and triglycerides. Cholesterol is a lipid that contributes to cell membrane flexibility and is a precursor of steroid hormones. The synthesis of cholesterol starts with acetyl CoA and proceeds in only one direction. The process cannot be reversed, and ATP is not produced.

Triglycerides are a form of long-term energy storage in animals. Triglycerides store about twice as much energy as carbohydrates. Triglycerides are made of glycerol and three fatty acids. Animals can make most of the fatty acids they need. Triglycerides can be both made and broken down through parts of the glucose catabolism pathways. Glycerol can be phosphorylated and proceeds through glycolysis. Fatty acids are broken into two-carbon units that enter the citric acid cycle.

 
This illustration shows that glycogen, fats, and proteins can be catabolized via aerobic respiration. Glycogen is broken down into glucose, which feeds into glycolysis. Fats are broken down into glycerol, which is processed by glycolysis, and fatty acids, which are converted into acetyl CoA. Proteins are broken down into amino acids, which are processed at various stages of aerobic respiration, including glycolysis, acetyl CoA formation, and the citric acid cycle.
Figure 4.24 Glycogen from the liver and muscles, together with fats, can feed into the catabolic pathways for carbohydrates.

 

Evolution in Action

Pathways of Photosynthesis and Cellular Metabolism Photosynthesis and cellular metabolism consist of several very complex pathways. It is generally thought that the first cells arose in an aqueous environment—a “soup” of nutrients. If these cells reproduced successfully and their numbers climbed steadily, it follows that the cells would begin to deplete the nutrients from the medium in which they lived, as they shifted the nutrients into their own cells. This hypothetical situation would have resulted in natural selection favoring those organisms that could exist by using the nutrients that remained in their environment and by manipulating these nutrients into materials that they could use to survive. Additionally, selection would favor those organisms that could extract maximal value from the available nutrients.

An early form of photosynthesis developed that harnessed the sun’s energy using compounds other than water as a source of hydrogen atoms, but this pathway did not produce free oxygen. It is thought that glycolysis developed prior to this time and could take advantage of simple sugars being produced, but these reactions were not able to fully extract the energy stored in the carbohydrates. A later form of photosynthesis used water as a source of hydrogen ions and generated free oxygen. Over time, the atmosphere became oxygenated. Living things adapted to exploit this new atmosphere and allowed respiration as we know it to evolve. When the full process of photosynthesis as we know it developed and the atmosphere became oxygenated, cells were finally able to use the oxygen expelled by photosynthesis to extract more energy from the sugar molecules using the citric acid cycle.

Section Summary

The breakdown and synthesis of carbohydrates, proteins, and lipids connect with the pathways of glucose catabolism. The carbohydrates that can also feed into glucose catabolism include galactose, fructose, and glycogen. These connect with glycolysis. The amino acids from proteins connect with glucose catabolism through pyruvate, acetyl CoA, and components of the citric acid cycle. Cholesterol synthesis starts with acetyl CoA, and the components of triglycerides are picked up by acetyl CoA and enter the citric acid cycle.

Exercises

An interactive H5P element has been excluded from this version of the text. You can view it online here:
https://pressbooks.nscc.ca/conceptsofbiologynscc/?p=171#h5p-33

V

Chapter 5: Introduction to Reproduction at the Cellular Level

Image A shows two conjoined cells forming a dumbbell shape; the fertilization envelope has been removed so that the mesh-like outer layer can be seen. Image B shows the sea urchin embryo when it has divided into 16 conjoined cells; the overall shape is rounder than in image A. Image C shows a “water melon” sea urchin which appears as a peach-colored ball covered in white protruding spines.
Figure 5.1 A sea urchin begins life as a single cell that (a) divides to form two cells, visible by scanning electron microscopy. After four rounds of cell division, (b) there are 16 cells, as seen in this SEM image. After many rounds of cell division, the individual develops into a complex, multicellular organism, as seen in this (c) mature sea urchin. (credit a: modification of work by Evelyn Spiegel, Louisa Howard; credit b: modification of work by Evelyn Spiegel, Louisa Howard; credit c: modification of work by Marco Busdraghi; scale-bar data from Matt Russell)

 

The individual sexually reproducing organism—including humans—begins life as a fertilized egg, or zygote. Trillions of cell divisions subsequently occur in a controlled manner to produce a complex, multicellular human. In other words, that original single cell was the ancestor of every other cell in the body. Once a human individual is fully grown, cell reproduction is still necessary to repair or regenerate tissues. For example, new blood and skin cells are constantly being produced. All multicellular organisms use cell division for growth, and in most cases, the maintenance and repair of cells and tissues. Single-celled organisms use cell division as their method of reproduction.

Search for Key Points in Chapter 5

An interactive H5P element has been excluded from this version of the text. You can view it online here:
https://pressbooks.nscc.ca/conceptsofbiologynscc/?p=174#h5p-34

17

5.1 The Genome

Charles Molnar and Jane Gair

Learning Objectives

By the end of this section, you will be able to:

  • Describe the prokaryotic and eukaryotic genome
  • Distinguish between chromosomes, genes, and traits

The continuity of life from one cell to another has its foundation in the reproduction of cells by way of the cell cycle. The cell cycle is an orderly sequence of events in the life of a cell from the division of a single parent cell to produce two new daughter cells, to the subsequent division of those daughter cells. The mechanisms involved in the cell cycle are highly conserved across eukaryotes. Organisms as diverse as protists, plants, and animals employ similar steps.

Genomic DNA

Before discussing the steps a cell undertakes to replicate, a deeper understanding of the structure and function of a cell’s genetic information is necessary. A cell’s complete complement of DNA is called its genome. In prokaryotes, the genome is composed of a single, double-stranded DNA molecule in the form of a loop or circle. The region in the cell containing this genetic material is called a nucleoid. Some prokaryotes also have smaller loops of DNA called plasmids that are not essential for normal growth.

In eukaryotes, the genome comprises several double-stranded, linear DNA molecules (Figure 5.2) bound with proteins to form complexes called chromosomes. Each species of eukaryote has a characteristic number of chromosomes in the nuclei of its cells. Human body cells (somatic cells) have 46 chromosomes. A somatic cell contains two matched sets of chromosomes, a configuration known as diploid. The letter n is used to represent a single set of chromosomes; therefore a diploid organism is designated 2n. Human cells that contain one set of 23 chromosomes are called gametes, or sex cells; these eggs and sperm are designated n, or haploid.

Chromosomes from a human female are shown in a nucleus, scattered outside the nucleus, and arranged in numerical order, from 1–22 followed by X. Each chromosome is stained a different color.
Figure 5.2 There are 23 pairs of homologous chromosomes in a female human somatic cell. These chromosomes are viewed within the nucleus (top), removed from a cell in mitosis (right), and arranged according to length (left) in an arrangement called a karyotype. In this image, the chromosomes were exposed to fluorescent stains to distinguish them. (credit: “718 Bot”/Wikimedia Commons, National Human Genome Research)

The matched pairs of chromosomes in a diploid organism are called homologous chromosomes. Homologous chromosomes are the same length and have specific nucleotide segments called genes in exactly the same location, or locus. Genes, the functional units of chromosomes, determine specific characteristics by coding for specific proteins. Traits are the different forms of a characteristic. For example, the shape of earlobes is a characteristic with traits of free or attached.

Each copy of the homologous pair of chromosomes originates from a different parent; therefore, the copies of each of the genes themselves may not be identical. The variation of individuals within a species is caused by the specific combination of the genes inherited from both parents. For example, there are three possible gene sequences on the human chromosome that codes for blood type: sequence A, sequence B, and sequence O. Because all diploid human cells have two copies of the chromosome that determines blood type, the blood type (the trait) is determined by which two versions of the marker gene are inherited. It is possible to have two copies of the same gene sequence, one on each homologous chromosome (for example, AA, BB, or OO), or two different sequences, such as AB.

Minor variations in traits such as those for blood type, eye color, and height contribute to the natural variation found within a species. The sex chromosomes, X and Y, are the single exception to the rule of homologous chromosomes; other than a small amount of homology that is necessary to reliably produce gametes, the genes found on the X and Y chromosomes are not the same.

Section Summary

Prokaryotes have a single loop chromosome, whereas eukaryotes have multiple, linear chromosomes surrounded by a nuclear membrane. Human somatic cells have 46 chromosomes consisting of two sets of 22 homologous chromosomes and a pair of nonhomologous sex chromosomes. This is the 2n, or diploid, state. Human gametes have 23 chromosomes or one complete set of chromosomes. This is the n, or haploid, state. Genes are segments of DNA that code for a specific protein or RNA molecule. An organism’s traits are determined in large part by the genes inherited from each parent, but also by the environment that they experience. Genes are expressed as characteristics of the organism and each characteristic may have different variants called traits that are caused by differences in the DNA sequence for a gene.

Exercises

An interactive H5P element has been excluded from this version of the text. You can view it online here:
https://pressbooks.nscc.ca/conceptsofbiologynscc/?p=177#h5p-35

Glossary

diploid: describes a cell, nucleus, or organism containing two sets of chromosomes (2n)

gamete: a haploid reproductive cell or sex cell (sperm or egg)

gene: the physical and functional unit of heredity; a sequence of DNA that codes for a specific peptide or RNA molecule

genome: the entire genetic complement (DNA) of an organism

haploid: describes a cell, nucleus, or organism containing one set of chromosomes (n)

homologous chromosomes: chromosomes of the same length with genes in the same location; diploid organisms have pairs of homologous chromosomes, and the members of each pair come from different parents

locus: the position of a gene on a chromosome

From Chapter 6 in Concepts of Biology: 1st Canadian Edition

18

5.2 The Cell Cycle

Charles Molnar and Jane Gair

Learning Objectives

By the end of this section, you will be able to:

  • Describe the three stages of interphase
  • Discuss the behavior of chromosomes during mitosis and how the cytoplasmic content divides during cytokinesis
  • Define the quiescent G0 phase
  • Explain how the three internal control checkpoints occur at the end of G1, at the G2–M transition, and during metaphase

The cell cycle is an ordered series of events involving cell growth and cell division that produces two new daughter cells. Cells on the path to cell division proceed through a series of precisely timed and carefully regulated stages of growth, DNA replication, and division that produce two genetically identical cells. The cell cycle has two major phases: interphase and the mitotic phase (Figure 5.3). During interphase, the cell grows and DNA is replicated. During the mitotic phase, the replicated DNA and cytoplasmic contents are separated and the cell divides.

Watch this video about the cell cycle: https://www.youtube.com/watch?v=Wy3N5NCZBHQ

This illustration shows the cell cycle, which consists of interphase and the mitotic phase. Interphase is subdivided into G1, S, and G2 phases. Cell growth occurs during G1 and G2, and DNA synthesis occurs during S. The mitotic phase consists of mitosis, in which the nuclear chromatin is divided, and cytokinesis, in which the cytoplasm is divided resulting in two daughter cells.
Figure 5.3 A cell moves through a series of phases in an orderly manner. During interphase, G1 involves cell growth and protein synthesis, the S phase involves DNA replication and the replication of the centrosome, and G2 involves further growth and protein synthesis. The mitotic phase follows interphase. Mitosis is nuclear division during which duplicated chromosomes are segregated and distributed into daughter nuclei. Usually the cell will divide after mitosis in a process called cytokinesis in which the cytoplasm is divided and two daughter cells are formed.

Interphase

During interphase, the cell undergoes normal processes while also preparing for cell division. For a cell to move from interphase to the mitotic phase, many internal and external conditions must be met. The three stages of interphase are called G1, S, and G2.

G1 Phase

The first stage of interphase is called the G1 phase, or first gap, because little change is visible. However, during the G1 stage, the cell is quite active at the biochemical level. The cell is accumulating the building blocks of chromosomal DNA and the associated proteins, as well as accumulating enough energy reserves to complete the task of replicating each chromosome in the nucleus.

S Phase

Throughout interphase, nuclear DNA remains in a semi-condensed chromatin configuration. In the S phase (synthesis phase), DNA replication results in the formation of two identical copies of each chromosome—sister chromatids—that are firmly attached at the centromere region. At this stage, each chromosome is made of two sister chromatids and is a duplicated chromosome. The centrosome is duplicated during the S phase. The two centrosomes will give rise to the mitotic spindle, the apparatus that orchestrates the movement of chromosomes during mitosis. The centrosome consists of a pair of rod-like centrioles at right angles to each other. Centrioles help organize cell division. Centrioles are not present in the centrosomes of many eukaryotic species, such as plants and most fungi.

G2 Phase

In the G2 phase, or second gap, the cell replenishes its energy stores and synthesizes the proteins necessary for chromosome manipulation. Some cell organelles are duplicated, and the cytoskeleton is dismantled to provide resources for the mitotic spindle. There may be additional cell growth during G2. The final preparations for the mitotic phase must be completed before the cell is able to enter the first stage of mitosis.

The Mitotic Phase

To make two daughter cells, the contents of the nucleus and the cytoplasm must be divided. The mitotic phase is a multistep process during which the duplicated chromosomes are aligned, separated, and moved to opposite poles of the cell, and then the cell is divided into two new identical daughter cells. The first portion of the mitotic phase, mitosis, is composed of five stages, which accomplish nuclear division. The second portion of the mitotic phase, called cytokinesis, is the physical separation of the cytoplasmic components into two daughter cells.

Mitosis

Mitosis is divided into a series of phases—prophase, prometaphase, metaphase, anaphase, and telophase—that result in the division of the cell nucleus (Figure 5.4).

This diagram shows the five phases of mitosis, and cytokinesis. During prophase, the chromosomes condense and become visible, spindle fibers emerge from the centrosomes, the centrosomes move toward opposite poles, and the nuclear envelope breaks down. During prometaphase, the chromosomes continue to condense and kinetochores appear at the centromeres. Mitotic spindle microtubules attach to the kinetochores. During metaphase, the centrosomes are at opposite poles of the cell. Chromosomes line up at the metaphase plate and each sister chromatid is attached to spindle fibers originating from the opposite poles. During anaphase, the centromeres split in two. The sister chromatids, which are now called chromosomes, move toward opposite poles of the cell. Certain spindle fibers lengthen, elongating the cell. During telophase, the chromosomes arrive at the opposite poles and begin to decondense. The nuclear envelope re-forms. During cytokinesis in animals, a cleavage furrow separates the two daughter cells. In plants, a cell plate—the precursor to a new cell wall—separates the two daughter cells.
Figure 5.4 Animal cell mitosis is divided into five stages—prophase, prometaphase, metaphase, anaphase, and telophase—visualized here by light microscopy with fluorescence. Mitosis is usually accompanied by cytokinesis, shown here by a transmission electron microscope. (credit “diagrams”: modification of work by Mariana Ruiz Villareal; credit “mitosis micrographs”: modification of work by Roy van Heesbeen; credit “cytokinesis micrograph”: modification of work by the Wadsworth Center, NY State Department of Health; donated to the Wikimedia foundation; scale-bar data from Matt Russell)

Which of the following is the correct order of events in mitosis?

  1. Sister chromatids line up at the metaphase plate. The kinetochore becomes attached to the mitotic spindle. The nucleus re-forms and the cell divides. The sister chromatids separate.
  2. The kinetochore becomes attached to the mitotic spindle. The sister chromatids separate. Sister chromatids line up at the metaphase plate. The nucleus re-forms and the cell divides.
  3. The kinetochore becomes attached to metaphase plate. Sister chromatids line up at the metaphase plate. The kinetochore breaks down and the sister chromatids separate. The nucleus re-forms and the cell divides.
  4. The kinetochore becomes attached to the mitotic spindle. Sister chromatids line up at the metaphase plate. The kinetochore breaks apart and the sister chromatids separate. The nucleus re-forms and the cell divides.

During prophase, the “first phase,” several events must occur to provide access to the chromosomes in the nucleus. The nuclear envelope starts to break into small vesicles, and the Golgi apparatus and endoplasmic reticulum fragment and disperse to the periphery of the cell. The nucleolus disappears. The centrosomes begin to move to opposite poles of the cell. The microtubules that form the basis of the mitotic spindle extend between the centrosomes, pushing them farther apart as the microtubule fibers lengthen. The sister chromatids begin to coil more tightly and become visible under a light microscope.

During prometaphase, many processes that were begun in prophase continue to advance and culminate in the formation of a connection between the chromosomes and cytoskeleton. The remnants of the nuclear envelope disappear. The mitotic spindle continues to develop as more microtubules assemble and stretch across the length of the former nuclear area. Chromosomes become more condensed and visually discrete. Each sister chromatid attaches to spindle microtubules at the centromere via a protein complex called the kinetochore.

During metaphase, all of the chromosomes are aligned in a plane called the metaphase plate, or the equatorial plane, midway between the two poles of the cell. The sister chromatids are still tightly attached to each other. At this time, the chromosomes are maximally condensed.

During anaphase, the sister chromatids at the equatorial plane are split apart at the centromere. Each chromatid, now called a chromosome, is pulled rapidly toward the centrosome to which its microtubule was attached. The cell becomes visibly elongated as the non-kinetochore microtubules slide against each other at the metaphase plate where they overlap.

During telophase, all of the events that set up the duplicated chromosomes for mitosis during the first three phases are reversed. The chromosomes reach the opposite poles and begin to decondense (unravel). The mitotic spindles are broken down into monomers that will be used to assemble cytoskeleton components for each daughter cell. Nuclear envelopes form around chromosomes.

Concept in Action


QR Code representing a URL

This page of movies illustrates different aspects of mitosis. Watch the movie entitled “DIC microscopy of cell division in a newt lung cell” and identify the phases of mitosis.

Cytokinesis

Cytokinesis is the second part of the mitotic phase during which cell division is completed by the physical separation of the cytoplasmic components into two daughter cells. Although the stages of mitosis are similar for most eukaryotes, the process of cytokinesis is quite different for eukaryotes that have cell walls, such as plant cells.

In cells such as animal cells that lack cell walls, cytokinesis begins following the onset of anaphase. A contractile ring composed of actin filaments forms just inside the plasma membrane at the former metaphase plate. The actin filaments pull the equator of the cell inward, forming a fissure. This fissure, or “crack,” is called the cleavage furrow. The furrow deepens as the actin ring contracts, and eventually the membrane and cell are cleaved in two (Figure 5.5).

In plant cells, a cleavage furrow is not possible because of the rigid cell walls surrounding the plasma membrane. A new cell wall must form between the daughter cells. During interphase, the Golgi apparatus accumulates enzymes, structural proteins, and glucose molecules prior to breaking up into vesicles and dispersing throughout the dividing cell. During telophase, these Golgi vesicles move on microtubules to collect at the metaphase plate. There, the vesicles fuse from the center toward the cell walls; this structure is called a cell plate. As more vesicles fuse, the cell plate enlarges until it merges with the cell wall at the periphery of the cell. Enzymes use the glucose that has accumulated between the membrane layers to build a new cell wall of cellulose. The Golgi membranes become the plasma membrane on either side of the new cell wall (Figure 5.5).

This illustration shows cytokinesis in a typical animal cell and a typical plant cell. In an animal cell, a contractile ring of actin filaments forms a cleavage furrow that divides the cell in two. In a plant cell, Golgi vesicles coalesce at the metaphase plate. A cell plate grows from the center outward, and the vesicles form a plasma membrane that divides the cytoplasm.
Figure 5.5 In part (a), a cleavage furrow forms at the former metaphase plate in the animal cell. The plasma membrane is drawn in by a ring of actin fibers contracting just inside the membrane. The cleavage furrow deepens until the cells are pinched in two. In part (b), Golgi vesicles coalesce at the former metaphase plate in a plant cell. The vesicles fuse and form the cell plate. The cell plate grows from the center toward the cell walls. New cell walls are made from the vesicle contents.

G0 Phase

Not all cells adhere to the classic cell-cycle pattern in which a newly formed daughter cell immediately enters interphase, closely followed by the mitotic phase. Cells in the G0 phase are not actively preparing to divide. The cell is in a quiescent (inactive) stage, having exited the cell cycle. Some cells enter G0 temporarily until an external signal triggers the onset of G1. Other cells that never or rarely divide, such as mature cardiac muscle and nerve cells, remain in G0 permanently (Figure 5.6).

In part (a), a cleavage furrow forms at the former metaphase plate in the animal cell. The plasma membrane is drawn in by a ring of actin fibers contracting just inside the membrane. The cleavage furrow deepens until the cells are pinched in two. In part (b), Golgi vesicles coalesce at the former metaphase plate in a plant cell. The vesicles fuse and form the cell plate. The cell plate grows from the center toward the cell walls. New cell walls are made from the vesicle contents.
Figure 5.6 Cells that are not actively preparing to divide enter an alternate phase called G0. In some cases, this is a temporary condition until triggered to enter G1. In other cases, the cell will remain in G0 permanently.

Control of the Cell Cycle

The length of the cell cycle is highly variable even within the cells of an individual organism. In humans, the frequency of cell turnover ranges from a few hours in early embryonic development to an average of two to five days for epithelial cells, or to an entire human lifetime spent in G0 by specialized cells such as cortical neurons or cardiac muscle cells. There is also variation in the time that a cell spends in each phase of the cell cycle. When fast-dividing mammalian cells are grown in culture (outside the body under optimal growing conditions), the length of the cycle is approximately 24 hours. In rapidly dividing human cells with a 24-hour cell cycle, the G1 phase lasts approximately 11 hours. The timing of events in the cell cycle is controlled by mechanisms that are both internal and external to the cell.

Regulation at Internal Checkpoints

It is essential that daughter cells be exact duplicates of the parent cell. Mistakes in the duplication or distribution of the chromosomes lead to mutations that may be passed forward to every new cell produced from the abnormal cell. To prevent a compromised cell from continuing to divide, there are internal control mechanisms that operate at three main cell cycle checkpoints at which the cell cycle can be stopped until conditions are favorable. These checkpoints occur near the end of G1, at the G2–M transition, and during metaphase (Figure 5.7).

This illustration shows the three major check points of the cell cycle, which occur in G1, G2, and mitosis.
Figure 5.7 The cell cycle is controlled at three checkpoints. Integrity of the DNA is assessed at the G1 checkpoint. Proper chromosome duplication is assessed at the G2 checkpoint. Attachment of each kinetochore to a spindle fiber is assessed at the M checkpoint.

The G1 Checkpoint

The G1 checkpoint determines whether all conditions are favorable for cell division to proceed. The G1 checkpoint, also called the restriction point, is the point at which the cell irreversibly commits to the cell-division process. In addition to adequate reserves and cell size, there is a check for damage to the genomic DNA at the G1 checkpoint. A cell that does not meet all the requirements will not be released into the S phase.

The G2 Checkpoint

The G2 checkpoint bars the entry to the mitotic phase if certain conditions are not met. As in the G1 checkpoint, cell size and protein reserves are assessed. However, the most important role of the G2 checkpoint is to ensure that all of the chromosomes have been replicated and that the replicated DNA is not damaged.

The M Checkpoint

The M checkpoint occurs near the end of the metaphase stage of mitosis. The M checkpoint is also known as the spindle checkpoint because it determines if all the sister chromatids are correctly attached to the spindle microtubules. Because the separation of the sister chromatids during anaphase is an irreversible step, the cycle will not proceed until the kinetochores of each pair of sister chromatids are firmly anchored to spindle fibers arising from opposite poles of the cell.

Concept in Action


QR Code representing a URL

Watch what occurs at the G1, G2, and M checkpoints by visiting this animation of the cell cycle.

Section Summary

The cell cycle is an orderly sequence of events. Cells on the path to cell division proceed through a series of precisely timed and carefully regulated stages. In eukaryotes, the cell cycle consists of a long preparatory period, called interphase. Interphase is divided into G1, S, and G2 phases. Mitosis consists of five stages: prophase, prometaphase, metaphase, anaphase, and telophase. Mitosis is usually accompanied by cytokinesis, during which the cytoplasmic components of the daughter cells are separated either by an actin ring (animal cells) or by cell plate formation (plant cells).

Each step of the cell cycle is monitored by internal controls called checkpoints. There are three major checkpoints in the cell cycle: one near the end of G1, a second at the G2–M transition, and the third during metaphase.

Exercises

An interactive H5P element has been excluded from this version of the text. You can view it online here:
https://pressbooks.nscc.ca/conceptsofbiologynscc/?p=186#h5p-36

Glossary

anaphase: the stage of mitosis during which sister chromatids are separated from each other

cell cycle: the ordered sequence of events that a cell passes through between one cell division and the next

cell cycle checkpoints: mechanisms that monitor the preparedness of a eukaryotic cell to advance through the various cell cycle stages

cell plate: a structure formed during plant-cell cytokinesis by Golgi vesicles fusing at the metaphase plate; will ultimately lead to formation of a cell wall to separate the two daughter cells

centriole: a paired rod-like structure constructed of microtubules at the center of each animal cell centrosome

cleavage furrow: a constriction formed by the actin ring during animal-cell cytokinesis that leads to cytoplasmic division

cytokinesis: the division of the cytoplasm following mitosis to form two daughter cells

G0 phase: a cell-cycle phase distinct from the G1 phase of interphase; a cell in G0 is not preparing to divide

G1 phase: (also, first gap) a cell-cycle phase; first phase of interphase centered on cell growth during mitosis

G2 phase: (also, second gap) a cell-cycle phase; third phase of interphase where the cell undergoes the final preparations for mitosis

interphase: the period of the cell cycle leading up to mitosis; includes G1, S, and G2 phases; the interim between two consecutive cell divisions

kinetochore: a protein structure in the centromere of each sister chromatid that attracts and binds spindle microtubules during prometaphase

metaphase plate: the equatorial plane midway between two poles of a cell where the chromosomes align during metaphase

metaphase: the stage of mitosis during which chromosomes are lined up at the metaphase plate

mitosis: the period of the cell cycle at which the duplicated chromosomes are separated into identical nuclei; includes prophase, prometaphase, metaphase, anaphase, and telophase

mitotic phase: the period of the cell cycle when duplicated chromosomes are distributed into two nuclei and the cytoplasmic contents are divided; includes mitosis and cytokinesis

mitotic spindle: the microtubule apparatus that orchestrates the movement of chromosomes during mitosis

prometaphase: the stage of mitosis during which mitotic spindle fibers attach to kinetochores

prophase: the stage of mitosis during which chromosomes condense and the mitotic spindle begins to form

quiescent: describes a cell that is performing normal cell functions and has not initiated preparations for cell division

S phase: the second, or synthesis phase, of interphase during which DNA replication occurs

telophase: the stage of mitosis during which chromosomes arrive at opposite poles, decondense, and are surrounded by new nuclear envelopes

From Chapter 6 in Concepts of Biology: 1st Canadian Edition

19

5.3 Cancer and the Cell Cycle

Charles Molnar and Jane Gair

Learning Objectives

By the end of this section, you will be able to:

  • Explain how cancer is caused by uncontrolled cell division
  • Understand how proto-oncogenes are normal cell genes that, when mutated, become oncogenes
  • Describe how tumor suppressors function to stop the cell cycle until certain events are completed
  • Explain how mutant tumor suppressors cause cancer

Cancer is a collective name for many different diseases caused by a common mechanism: uncontrolled cell division. Despite the redundancy and overlapping levels of cell-cycle control, errors occur. One of the critical processes monitored by the cell-cycle checkpoint surveillance mechanism is the proper replication of DNA during the S phase. Even when all of the cell-cycle controls are fully functional, a small percentage of replication errors (mutations) will be passed on to the daughter cells. If one of these changes to the DNA nucleotide sequence occurs within a gene, a gene mutation results. All cancers begin when a gene mutation gives rise to a faulty protein that participates in the process of cell reproduction. The change in the cell that results from the malformed protein may be minor. Even minor mistakes, however, may allow subsequent mistakes to occur more readily. Over and over, small, uncorrected errors are passed from parent cell to daughter cells and accumulate as each generation of cells produces more non-functional proteins from uncorrected DNA damage. Eventually, the pace of the cell cycle speeds up as the effectiveness of the control and repair mechanisms decreases. Uncontrolled growth of the mutated cells outpaces the growth of normal cells in the area, and a tumor can result.

Proto-oncogenes

The genes that code for the positive cell-cycle regulators are called proto-oncogenes. Proto-oncogenes are normal genes that, when mutated, become oncogenes—genes that cause a cell to become cancerous. Consider what might happen to the cell cycle in a cell with a recently acquired oncogene. In most instances, the alteration of the DNA sequence will result in a less functional (or non-functional) protein. The result is detrimental to the cell and will likely prevent the cell from completing the cell cycle; however, the organism is not harmed because the mutation will not be carried forward. If a cell cannot reproduce, the mutation is not propagated and the damage is minimal. Occasionally, however, a gene mutation causes a change that increases the activity of a positive regulator. For example, a mutation that allows Cdk, a protein involved in cell-cycle regulation, to be activated before it should be could push the cell cycle past a checkpoint before all of the required conditions are met. If the resulting daughter cells are too damaged to undertake further cell divisions, the mutation would not be propagated and no harm comes to the organism. However, if the atypical daughter cells are able to divide further, the subsequent generation of cells will likely accumulate even more mutations, some possibly in additional genes that regulate the cell cycle.

The Cdk example is only one of many genes that are considered proto-oncogenes. In addition to the cell-cycle regulatory proteins, any protein that influences the cycle can be altered in such a way as to override cell-cycle checkpoints. Once a proto-oncogene has been altered such that there is an increase in the rate of the cell cycle, it is then called an oncogene.

Tumor Suppressor Genes

Like proto-oncogenes, many of the negative cell-cycle regulatory proteins were discovered in cells that had become cancerous. Tumor suppressor genes are genes that code for the negative regulator proteins, the type of regulator that—when activated—can prevent the cell from undergoing uncontrolled division. The collective function of the best-understood tumor suppressor gene proteins, retinoblastoma protein (RB1), p53, and p21, is to put up a roadblock to cell-cycle progress until certain events are completed. A cell that carries a mutated form of a negative regulator might not be able to halt the cell cycle if there is a problem.

Mutated p53 genes have been identified in more than half of all human tumor cells. This discovery is not surprising in light of the multiple roles that the p53 protein plays at the G1 checkpoint. The p53 protein activates other genes whose products halt the cell cycle (allowing time for DNA repair), activates genes whose products participate in DNA repair, or activates genes that initiate cell death when DNA damage cannot be repaired. A damaged p53 gene can result in the cell behaving as if there are no mutations (Figure 5.8). This allows cells to divide, propagating the mutation in daughter cells and allowing the accumulation of new mutations. In addition, the damaged version of p53 found in cancer cells cannot trigger cell death.

This illustration shows cell cycle regulation by p53. The p53 protein normally arrests the cell cycle in response to DNA damage, cell cycle abnormalities, or hypoxia. Once the damage is repaired, the cell cycle restarts. If the damage cannot be repaired, apoptosis (programmed cell death) occurs. Mutated p53 does not arrest the cell cycle in response to cellular damage. As a result, the cell cycle continues and the cell may become cancerous.
Figure 5.8 (a) The role of p53 is to monitor DNA. If damage is detected, p53 triggers repair mechanisms. If repairs are unsuccessful, p53 signals apoptosis. (b) A cell with an abnormal p53 protein cannot repair damaged DNA and cannot signal apoptosis. Cells with abnormal p53 can become cancerous. (credit: modification of work by Thierry Soussi)

 

Concept in Action

qrcode-cancer

Thumbnail for the embedded element &quot;Cancer | Cells | MCAT | Khan Academy&quot;

A YouTube element has been excluded from this version of the text. You can view it online here: https://pressbooks.nscc.ca/conceptsofbiologynscc/?p=190

Go to this website to watch an animation of how cancer results from errors in the cell cycle.

Section Summary

Cancer is the result of unchecked cell division caused by a breakdown of the mechanisms regulating the cell cycle. The loss of control begins with a change in the DNA sequence of a gene that codes for one of the regulatory molecules. Faulty instructions lead to a protein that does not function as it should. Any disruption of the monitoring system can allow other mistakes to be passed on to the daughter cells. Each successive cell division will give rise to daughter cells with even more accumulated damage. Eventually, all checkpoints become nonfunctional, and rapidly reproducing cells crowd out normal cells, resulting in tumorous growth.

Exercises

An interactive H5P element has been excluded from this version of the text. You can view it online here:
https://pressbooks.nscc.ca/conceptsofbiologynscc/?p=190#h5p-37

Glossary

oncogene: a mutated version of a proto-oncogene, which allows for uncontrolled progression of the cell cycle, or uncontrolled cell reproduction

proto-oncogene: a normal gene that controls cell division by regulating the cell cycle that becomes an oncogene if it is mutated

tumor suppressor gene: a gene that codes for regulator proteins that prevent the cell from undergoing uncontrolled division

From Chapter 6 in Concepts of Biology: 1st Canadian Edition

20

5.4 Prokaryotic Cell Division

Charles Molnar and Jane Gair

Learning Objectives

By the end of this section, you will be able to:

  • Describe the process of binary fission in prokaryotes
  • Explain how FtsZ and tubulin proteins are examples of homology

Prokaryotes such as bacteria propagate by binary fission. For unicellular organisms, cell division is the only method to produce new individuals. In both prokaryotic and eukaryotic cells, the outcome of cell reproduction is a pair of daughter cells that are genetically identical to the parent cell. In unicellular organisms, daughter cells are individuals.

To achieve the outcome of identical daughter cells, some steps are essential. The genomic DNA must be replicated and then allocated into the daughter cells; the cytoplasmic contents must also be divided to give both new cells the machinery to sustain life. In bacterial cells, the genome consists of a single, circular DNA chromosome; therefore, the process of cell division is simplified. Mitosis is unnecessary because there is no nucleus or multiple chromosomes. This type of cell division is called binary fission.

Binary Fission

The cell division process of prokaryotes, called binary fission, is a less complicated and much quicker process than cell division in eukaryotes. Because of the speed of bacterial cell division, populations of bacteria can grow very rapidly. The single, circular DNA chromosome of bacteria is not enclosed in a nucleus, but instead occupies a specific location, the nucleoid, within the cell. As in eukaryotes, the DNA of the nucleoid is associated with proteins that aid in packaging the molecule into a compact size. The packing proteins of bacteria are, however, related to some of the proteins involved in the chromosome compaction of eukaryotes.

The starting point of replication, the origin, is close to the binding site of the chromosome to the plasma membrane (Figure 5.9). Replication of the DNA is bidirectional—moving away from the origin on both strands of the DNA loop simultaneously. As the new double strands are formed, each origin point moves away from the cell-wall attachment toward opposite ends of the cell. As the cell elongates, the growing membrane aids in the transport of the chromosomes. After the chromosomes have cleared the midpoint of the elongated cell, cytoplasmic separation begins. A septum is formed between the nucleoids from the periphery toward the center of the cell. When the new cell walls are in place, the daughter cells separate.

This illustration shows binary fission in prokaryotes. Replication of the single, circular chromosome begins at the origin of replication and continues simultaneously in both directions. As the DNA is replicated, the cell elongates and FtsZ proteins migrate toward the center of the cell, where they form a ring. The FtsZ ring directs the formation of a septum that divides the cell in two once DNA replication is complete.
Figure 5.9 The binary fission of a bacterium is outlined in five steps. (credit: modification of work by “Mcstrother”/Wikimedia Commons)

Evolution in Action

Mitotic Spindle Apparatus

The precise timing and formation of the mitotic spindle is critical to the success of eukaryotic cell division. Prokaryotic cells, on the other hand, do not undergo mitosis and therefore have no need for a mitotic spindle. However, the FtsZ protein that plays such a vital role in prokaryotic cytokinesis is structurally and functionally very similar to tubulin, the building block of the microtubules that make up the mitotic spindle fibers that are necessary for eukaryotes. The formation of a ring composed of repeating units of a protein called FtsZ directs the partition between the nucleoids in prokaryotes. Formation of the FtsZ ring triggers the accumulation of other proteins that work together to recruit new membrane and cell-wall materials to the site. FtsZ proteins can form filaments, rings, and other three-dimensional structures resembling the way tubulin forms microtubules, centrioles, and various cytoskeleton components. In addition, both FtsZ and tubulin employ the same energy source, GTP (guanosine triphosphate), to rapidly assemble and disassemble complex structures.

FtsZ and tubulin are an example of homology, structures derived from the same evolutionary origins. In this example, FtsZ is presumed to be similar to the ancestor protein to both the modern FtsZ and tubulin. While both proteins are found in extant organisms, tubulin function has evolved and diversified tremendously since the evolution from its FtsZ-like prokaryotic origin. A survey of cell-division machinery in present-day unicellular eukaryotes reveals crucial intermediary steps to the complex mitotic machinery of multicellular eukaryotes.

The mitotic spindle fibers of eukaryotes are composed of microtubules. Microtubules are polymers of the protein tubulin. The FtsZ protein active in prokaryote cell division is very similar to tubulin in the structures it can form and its energy source. Single-celled eukaryotes (such as yeast) display possible intermediary steps between FtsZ activity during binary fission in prokaryotes and the mitotic spindle in multicellular eukaryotes, during which the nucleus breaks down and is reformed.

Mitotic Spindle Evolution
Structure of genetic material Division of nuclear material Separation of daughter cells
Prokaryotes There is no nucleus. The single, circular chromosome exists in a region of cytoplasm called the nucleoid. Occurs through binary fission. As the chromosome is replicated, the two copies move to opposite ends of the cell by an unknown mechanism. FtsZ proteins assemble into a ring that pinches the cell in two.
Some protists Linear chromosomes exist in the nucleus. Chromosomes attach to the nuclear envelope, which remains intact. The mitotic spindle passes through the envelope and elongates the cell. No centrioles exist. Microfilaments form a cleavage furrow that pinches the cell in two.
Other protists Linear chromosomes exist in the nucleus. A mitotic spindle forms from the centrioles and passes through the nuclear membrane, which remains intact. Chromosomes attach to the mitotic spindle. The mitotic spindle separates the chromosomes and elongates the cell. Microfilaments form a cleavage furrow that pinches the cell in two.
Animal cells Linear chromosomes exist in the nucleus. A mitotic spindle forms from the centrioles. The nuclear envelope dissolves.
Chromosomes attach to the mitotic spindle, which separates them and elongates the cell.
Microfilaments form a cleavage furrow that pinches the cell in two.

Section Summary

In both prokaryotic and eukaryotic cell division, the genomic DNA is replicated and each copy is allocated into a daughter cell. The cytoplasmic contents are also divided evenly to the new cells. However, there are many differences between prokaryotic and eukaryotic cell division. Bacteria have a single, circular DNA chromosome and no nucleus. Therefore, mitosis is not necessary in bacterial cell division. Bacterial cytokinesis is directed by a ring composed of a protein called FtsZ. Ingrowth of membrane and cell-wall material from the periphery of the cells results in a septum that eventually forms the separate cell walls of the daughter cells.

Exercises

An interactive H5P element has been excluded from this version of the text. You can view it online here:
https://pressbooks.nscc.ca/conceptsofbiologynscc/?p=193#h5p-38

Glossary

binary fission: the process of prokaryotic cell division

FtsZ: a tubulin-like protein component of the prokaryotic cytoskeleton that is important in prokaryotic cytokinesis (name origin: Filamenting temperature-sensitive mutant Z)

origin: the region of the prokaryotic chromosome at which replication begins

septum: a wall formed between bacterial daughter cells as a precursor to cell separation

From Chapter 6 in Concepts of Biology: 1st Canadian Edition

VI

Chapter 6: Introduction to the Cellular Basis of Inheritance

Three images are shown. Part a shows a mother and baby hippopotamus. In part b, mature Joshua trees are pictured next to saplings. In part c, a mother and baby flamingo are shown.
Figure 6.1 Each of us, like these other large multicellular organisms, begins life as a fertilized egg. After trillions of cell divisions, each of us develops into a complex, multicellular organism. (credit a: modification of work by Frank Wouters; credit b: modification of work by Ken Cole, USGS; credit c: modification of work by Martin Pettitt)

The ability to reproduce in kind is a basic characteristic of all living things. In kind means that the offspring of any organism closely resembles its parent or parents. Hippopotamuses give birth to hippopotamus calves; Monterey pine trees produce seeds from which Monterey pine seedlings emerge; and adult flamingos lay eggs that hatch into flamingo chicks. In kind does not generally mean exactly the same. While many single-celled organisms and a few multicellular organisms can produce genetically identical clones of themselves through mitotic cell division, many single-celled organisms and most multicellular organisms reproduce regularly using another method.

Sexual reproduction is the production by parents of haploid cells and the fusion of a haploid cell from each parent to form a single, unique diploid cell. In multicellular organisms, the new diploid cell will then undergo mitotic cell divisions to develop into an adult organism. A type of cell division called meiosis leads to the haploid cells that are part of the sexual reproductive cycle. Sexual reproduction, specifically meiosis and fertilization, introduces variation into offspring that may account for the evolutionary success of sexual reproduction. The vast majority of eukaryotic organisms can or must employ some form of meiosis and fertilization to reproduce.

Search for Key Points in Chapter 6

An interactive H5P element has been excluded from this version of the text. You can view it online here:
https://pressbooks.nscc.ca/conceptsofbiologynscc/?p=196#h5p-39

Chapter 7 in Concepts of Biology: 1st Canadian Edition

21

6.1 Sexual Reproduction

Charles Molnar and Jane Gair

Learning Objectives

By the end of this section, you will be able to:

  • Explain that variation among offspring is a potential evolutionary advantage resulting from sexual reproduction
  • Describe the three different life-cycle strategies among sexual multicellular organisms and their commonalities
  • Understand why you could never create a gamete that would be identical to either of the gametes that made yo

An interactive H5P element has been excluded from this version of the text. You can view it online here:
https://pressbooks.nscc.ca/conceptsofbiologynscc/?p=199#h5p-40

Sexual reproduction was an early evolutionary innovation after the appearance of eukaryotic cells. The fact that most eukaryotes reproduce sexually is evidence of its evolutionary success. In many animals, it is the only mode of reproduction. And yet, scientists recognize some real disadvantages to sexual reproduction. On the surface, offspring that are genetically identical to the parent may appear to be more advantageous. If the parent organism is successfully occupying a habitat, offspring with the same traits would be similarly successful. There is also the obvious benefit to an organism that can produce offspring by asexual budding, fragmentation, or asexual eggs. These methods of reproduction do not require another organism of the opposite sex. There is no need to expend energy finding or attracting a mate. That energy can be spent on producing more offspring. Indeed, some organisms that lead a solitary lifestyle have retained the ability to reproduce asexually. In addition, asexual populations only have female individuals, so every individual is capable of reproduction. In contrast, the males in sexual populations (half the population) are not producing offspring themselves. Because of this, an asexual population can grow twice as fast as a sexual population in theory. This means that in competition, the asexual population would have the advantage. All of these advantages to asexual reproduction, which are also disadvantages to sexual reproduction, should mean that the number of species with asexual reproduction should be more common.

However, multicellular organisms that exclusively depend on asexual reproduction are exceedingly rare. Why is sexual reproduction so common? This is one of the important questions in biology and has been the focus of much research from the latter half of the twentieth century until now. A likely explanation is that the variation that sexual reproduction creates among offspring is very important to the survival and reproduction of those offspring. The only source of variation in asexual organisms is mutation. This is the ultimate source of variation in sexual organisms. In addition, those different mutations are continually reshuffled from one generation to the next when different parents combine their unique genomes, and the genes are mixed into different combinations by the process of meiosis. Meiosis is the division of the contents of the nucleus that divides the chromosomes among gametes. Variation is introduced during meiosis, as well as when the gametes combine in fertilization.

The Red Queen Hypothesis

There is no question that sexual reproduction provides evolutionary advantages to organisms that employ this mechanism to produce offspring. The problematic question is why, even in the face of fairly stable conditions, sexual reproduction persists when it is more difficult and produces fewer offspring for individual organisms? Variation is the outcome of sexual reproduction, but why are ongoing variations necessary? Enter the Red Queen hypothesis, first proposed by Leigh Van Valen in 1973.1 The concept was named in reference to the Red Queen’s race in Lewis Carroll’s book, Through the Looking-Glass, in which the Red Queen says one must run at full speed just to stay where one is.

All species coevolve with other organisms. For example, predators coevolve with their prey, and parasites coevolve with their hosts. A remarkable example of coevolution between predators and their prey is the unique coadaptation of night flying bats and their moth prey. Bats find their prey by emitting high-pitched clicks, but moths have evolved simple ears to hear these clicks so they can avoid the bats. The moths have also adapted behaviors, such as flying away from the bat when they first hear it, or dropping suddenly to the ground when the bat is upon them. Bats have evolved “quiet” clicks in an attempt to evade the moth’s hearing. Some moths have evolved the ability to respond to the bats’ clicks with their own clicks as a strategy to confuse the bats echolocation abilities.

Each tiny advantage gained by favorable variation gives a species an edge over close competitors, predators, parasites, or even prey. The only method that will allow a coevolving species to keep its own share of the resources is also to continually improve its ability to survive and produce offspring. As one species gains an advantage, other species must also develop an advantage or they will be outcompeted. No single species progresses too far ahead because genetic variation among progeny of sexual reproduction provides all species with a mechanism to produce adapted individuals. Species whose individuals cannot keep up become extinct. The Red Queen’s catchphrase was, “It takes all the running you can do to stay in the same place.” This is an apt description of coevolution between competing species.

Life Cycles of Sexually Reproducing Organisms

Fertilization and meiosis alternate in sexual life cycles. What happens between these two events depends on the organism. The process of meiosis reduces the resulting gamete’s chromosome number by half. Fertilization, the joining of two haploid gametes, restores the diploid condition. There are three main categories of life cycles in multicellular organisms: diploid-dominant, in which the multicellular diploid stage is the most obvious life stage (and there is no multicellular haploid stage), as with most animals including humans; haploid-dominant, in which the multicellular haploid stage is the most obvious life stage (and there is no multicellular diploid stage), as with all fungi and some algae; and alternation of generations, in which the two stages, haploid and diploid, are apparent to one degree or another depending on the group, as with plants and some algae.

Nearly all animals employ a diploid-dominant life-cycle strategy in which the only haploid cells produced by the organism are the gametes. The gametes are produced from diploid germ cells, a special cell line that only produces gametes. Once the haploid gametes are formed, they lose the ability to divide again. There is no multicellular haploid life stage. Fertilization occurs with the fusion of two gametes, usually from different individuals, restoring the diploid state (Figure 6.2 a).

Part a shows the life cycle of animals. Through meiosis, adult males produce haploid (1n) sperm, and adult females produce haploid eggs. Upon fertilization, a diploid (2n) zygote forms, which grows into an adult through mitosis and cell division. Part b shows the life cycle of fungi. In fungi, the diploid (2n) zygospore undergoes meiosis to form haploid (1n) spores. Mitosis of the spores occurs to form hyphae. Hyphae can undergo asexual reproduction to form more spores, or they form plus and minus mating types that undergo nuclear fusion to form a zygospore. Part c shows the life cycle of fern plants. The diploid (2n) zygote undergoes mitosis to produce the sphorophyte, which is the familiar, leafy plant. Sporangia form on the underside of the leaves of the sphorophyte. Sporangia undergo meiosis to form haploid (1n) spores. The spores germinate and undergo mitosis to form a multicellular, leafy gametophyte. The gametophyte produces eggs and sperm. Upon fertilization, the egg and sperm form a diploid zygote.
Figure 6.2 (a) In animals, sexually reproducing adults form haploid gametes from diploid germ cells. (b) Fungi, such as black bread mold (Rhizopus nigricans), have haploid-dominant life cycles. (c) Plants have a life cycle that alternates between a multicellular haploid organism and a multicellular diploid organism. (credit c “fern”: modification of work by Cory Zanker; credit c “gametophyte”: modification of work by “Vlmastra”/Wikimedia Commons)

 

If a mutation occurs so that a fungus is no longer able to produce a minus mating type, will it still be able to reproduce?

Most fungi and algae employ a life-cycle strategy in which the multicellular “body” of the organism is haploid. During sexual reproduction, specialized haploid cells from two individuals join to form a diploid zygote. The zygote immediately undergoes meiosis to form four haploid cells called spores (Figure 6.2 b).

The third life-cycle type, employed by some algae and all plants, is called alternation of generations. These species have both haploid and diploid multicellular organisms as part of their life cycle. The haploid multicellular plants are called gametophytes because they produce gametes. Meiosis is not involved in the production of gametes in this case, as the organism that produces gametes is already haploid. Fertilization between the gametes forms a diploid zygote. The zygote will undergo many rounds of mitosis and give rise to a diploid multicellular plant called a sporophyte. Specialized cells of the sporophyte will undergo meiosis and produce haploid spores. The spores will develop into the gametophytes (Figure 6. 2 c).

Section Summary

Nearly all eukaryotes undergo sexual reproduction. The variation introduced into the reproductive cells by meiosis appears to be one of the advantages of sexual reproduction that has made it so successful. Meiosis and fertilization alternate in sexual life cycles. The process of meiosis produces genetically unique reproductive cells called gametes, which have half the number of chromosomes as the parent cell. Fertilization, the fusion of haploid gametes from two individuals, restores the diploid condition. Thus, sexually reproducing organisms alternate between haploid and diploid stages. However, the ways in which reproductive cells are produced and the timing between meiosis and fertilization vary greatly. There are three main categories of life cycles: diploid-dominant, demonstrated by most animals; haploid-dominant, demonstrated by all fungi and some algae; and alternation of generations, demonstrated by plants and some algae.

Exercises

An interactive H5P element has been excluded from this version of the text. You can view it online here:
https://pressbooks.nscc.ca/conceptsofbiologynscc/?p=199#h5p-41

Glossary

alternation of generations: a life-cycle type in which the diploid and haploid stages alternate

diploid-dominant: a life-cycle type in which the multicellular diploid stage is prevalent

haploid-dominant: a life-cycle type in which the multicellular haploid stage is prevalent

gametophyte: a multicellular haploid life-cycle stage that produces gametes

germ cell: a specialized cell that produces gametes, such as eggs or sperm

life cycle: the sequence of events in the development of an organism and the production of cells that produce offspring

meiosis: a nuclear division process that results in four haploid cells

sporophyte: a multicellular diploid life-cycle stage that produces spores

Footnotes

1 Leigh Van Valen, “A new evolutionary law,” Evolutionary Theory 1 (1973): 1–30.

Chapter 7 in Concepts of Biology: 1st Canadian Edition

22

6.2 Meiosis

Charles Molnar and Jane Gair

Learning Objectives

By the end of this section, you will be able to:

  • Describe the behavior of chromosomes during meiosis
  • Describe cellular events during meiosis
  • Explain the differences between meiosis and mitosis
  • Explain the mechanisms within meiosis that generate genetic variation among the products of meiosis

Sexual reproduction requires fertilization, a union of two cells from two individual organisms. If those two cells each contain one set of chromosomes, then the resulting cell contains two sets of chromosomes. The number of sets of chromosomes in a cell is called its ploidy level. Haploid cells contain one set of chromosomes. Cells containing two sets of chromosomes are called diploid. If the reproductive cycle is to continue, the diploid cell must somehow reduce its number of chromosome sets before fertilization can occur again, or there will be a continual doubling in the number of chromosome sets in every generation. So, in addition to fertilization, sexual reproduction includes a nuclear division, known as meiosis, that reduces the number of chromosome sets.

Most animals and plants are diploid, containing two sets of chromosomes; in each somatic cell (the nonreproductive cells of a multicellular organism), the nucleus contains two copies of each chromosome that are referred to as homologous chromosomes. Somatic cells are sometimes referred to as “body” cells. Homologous chromosomes are matched pairs containing genes for the same traits in identical locations along their length. Diploid organisms inherit one copy of each homologous chromosome from each parent; all together, they are considered a full set of chromosomes. In animals, haploid cells containing a single copy of each homologous chromosome are found only within gametes. Gametes fuse with another haploid gamete to produce a diploid cell.

The nuclear division that forms haploid cells, which is called meiosis, is related to mitosis. As you have learned, mitosis is part of a cell reproduction cycle that results in identical daughter nuclei that are also genetically identical to the original parent nucleus. In mitosis, both the parent and the daughter nuclei contain the same number of chromosome sets—diploid for most plants and animals. Meiosis employs many of the same mechanisms as mitosis. However, the starting nucleus is always diploid and the nuclei that result at the end of a meiotic cell division are haploid. To achieve the reduction in chromosome number, meiosis consists of one round of chromosome duplication and two rounds of nuclear division. Because the events that occur during each of the division stages are analogous to the events of mitosis, the same stage names are assigned. However, because there are two rounds of division, the stages are designated with a “I” or “II.” Thus, meiosis I is the first round of meiotic division and consists of prophase I, prometaphase I, and so on. Meiosis I reduces the number of chromosome sets from two to one. The genetic information is also mixed during this division to create unique recombinant chromosomes. Meiosis II, in which the second round of meiotic division takes place in a way that is similar to mitosis, includes prophase II, prometaphase II, and so on.

Interphase

Meiosis is preceded by an interphase consisting of the G1, S, and G2 phases, which are nearly identical to the phases preceding mitosis. The G1 phase is the first phase of interphase and is focused on cell growth. In the S phase, the DNA of the chromosomes is replicated. Finally, in the G2 phase, the cell undergoes the final preparations for meiosis.

During DNA duplication of the S phase, each chromosome becomes composed of two identical copies (called sister chromatids) that are held together at the centromere until they are pulled apart during meiosis II. In an animal cell, the centrosomes that organize the microtubules of the meiotic spindle also replicate. This prepares the cell for the first meiotic phase.

Meiosis I

Early in prophase I, the chromosomes can be seen clearly microscopically. As the nuclear envelope begins to break down, the proteins associated with homologous chromosomes bring the pair close to each other. The tight pairing of the homologous chromosomes is called synapsis. In synapsis, the genes on the chromatids of the homologous chromosomes are precisely aligned with each other. An exchange of chromosome segments between non-sister homologous chromatids occurs and is called crossing over. This process is revealed visually after the exchange as chiasmata (singular = chiasma) (Figure 6.3).

As prophase I progresses, the close association between homologous chromosomes begins to break down, and the chromosomes continue to condense, although the homologous chromosomes remain attached to each other at chiasmata. The number of chiasmata varies with the species and the length of the chromosome. At the end of prophase I, the pairs are held together only at chiasmata (Figure 6.3) and are called tetrads because the four sister chromatids of each pair of homologous chromosomes are now visible.

The crossover events are the first source of genetic variation produced by meiosis. A single crossover event between homologous non-sister chromatids leads to a reciprocal exchange of equivalent DNA between a maternal chromosome and a paternal chromosome. Now, when that sister chromatid is moved into a gamete, it will carry some DNA from one parent of the individual and some DNA from the other parent. The recombinant sister chromatid has a combination of maternal and paternal genes that did not exist before the crossover.

 
This illustration shows a pair of homologous chromosomes that are aligned. the ends of two non-sister chromatids of the homologous chromosomes cross over, and genetic material is exchanged. the non-sister chromatids between which genetic material was exchanged are called recombinant chromosomes. the other pair of non-sister chromatids that did not exchange genetic material are called non-recombinant chromosomes.
Figure 6.3 In this illustration of the effects of crossing over, the blue chromosome came from the individual’s father and the red chromosome came from the individual’s mother. Crossover occurs between non-sister chromatids of homologous chromosomes. The result is an exchange of genetic material between homologous chromosomes. The chromosomes that have a mixture of maternal and paternal sequence are called recombinant and the chromosomes that are completely paternal or maternal are called non-recombinant.

 

The key event in prometaphase I is the attachment of the spindle fiber microtubules to the kinetochore proteins at the centromeres. The microtubules assembled from centrosomes at opposite poles of the cell grow toward the middle of the cell. At the end of prometaphase I, each tetrad is attached to microtubules from both poles, with one homologous chromosome attached at one pole and the other homologous chromosome attached to the other pole. The homologous chromosomes are still held together at chiasmata. In addition, the nuclear membrane has broken down entirely.

During metaphase I, the homologous chromosomes are arranged in the center of the cell with the kinetochores facing opposite poles. The orientation of each pair of homologous chromosomes at the center of the cell is random.

This randomness, called independent assortment, is the physical basis for the generation of the second form of genetic variation in offspring. Consider that the homologous chromosomes of a sexually reproducing organism are originally inherited as two separate sets, one from each parent. Using humans as an example, one set of 23 chromosomes is present in the egg donated by the mother. The father provides the other set of 23 chromosomes in the sperm that fertilizes the egg. In metaphase I, these pairs line up at the midway point between the two poles of the cell. Because there is an equal chance that a microtubule fiber will encounter a maternally or paternally inherited chromosome, the arrangement of the tetrads at the metaphase plate is random. Any maternally inherited chromosome may face either pole. Any paternally inherited chromosome may also face either pole. The orientation of each tetrad is independent of the orientation of the other 22 tetrads.

In each cell that undergoes meiosis, the arrangement of the tetrads is different. The number of variations depends on the number of chromosomes making up a set. There are two possibilities for orientation (for each tetrad); thus, the possible number of alignments equals 2n where n is the number of chromosomes per set. Humans have 23 chromosome pairs, which results in over eight million (223) possibilities. This number does not include the variability previously created in the sister chromatids by crossover. Given these two mechanisms, it is highly unlikely that any two haploid cells resulting from meiosis will have the same genetic composition (Figure 6.4).

To summarize the genetic consequences of meiosis I: the maternal and paternal genes are recombined by crossover events occurring on each homologous pair during prophase I; in addition, the random assortment of tetrads at metaphase produces a unique combination of maternal and paternal chromosomes that will make their way into the gametes.

 
This illustration shows that, in a cell with a set of two chromosomes, four possible arrangements of chromosomes can give rise to eight different kinds of gamete. These are the eight possible arrangements of chromosomes that can occur during meiosis of two chromosomes.
Figure 6.4 To demonstrate random, independent assortment at metaphase I, consider a cell with n = 2. In this case, there are two possible arrangements at the equatorial plane in metaphase I, as shown in the upper cell of each panel. These two possible orientations lead to the production of genetically different gametes. With more chromosomes, the number of possible arrangements increases dramatically.

 

In anaphase I, the spindle fibers pull the linked chromosomes apart. The sister chromatids remain tightly bound together at the centromere. It is the chiasma connections that are broken in anaphase I as the fibers attached to the fused kinetochores pull the homologous chromosomes apart.

In telophase I, the separated chromosomes arrive at opposite poles. The remainder of the typical telophase events may or may not occur depending on the species. In some organisms, the chromosomes decondense and nuclear envelopes form around the chromatids in telophase I.

Cytokinesis, the physical separation of the cytoplasmic components into two daughter cells, occurs without reformation of the nuclei in other organisms. In nearly all species, cytokinesis separates the cell contents by either a cleavage furrow (in animals and some fungi), or a cell plate that will ultimately lead to formation of cell walls that separate the two daughter cells (in plants). At each pole, there is just one member of each pair of the homologous chromosomes, so only one full set of the chromosomes is present. This is why the cells are considered haploid—there is only one chromosome set, even though there are duplicate copies of the set because each homolog still consists of two sister chromatids that are still attached to each other. However, although the sister chromatids were once duplicates of the same chromosome, they are no longer identical at this stage because of crossovers.

Concept in Action


QR Code representing a URL

Review the process of meiosis, observing how chromosomes align and migrate, at this site.

Meiosis II

In meiosis II, the connected sister chromatids remaining in the haploid cells from meiosis I will be split to form four haploid cells. In some species, cells enter a brief interphase, or interkinesis, that lacks an S phase, before entering meiosis II. Chromosomes are not duplicated during interkinesis. The two cells produced in meiosis I go through the events of meiosis II in synchrony. Overall, meiosis II resembles the mitotic division of a haploid cell.

In prophase II, if the chromosomes decondensed in telophase I, they condense again. If nuclear envelopes were formed, they fragment into vesicles. The centrosomes duplicated during interkinesis move away from each other toward opposite poles, and new spindles are formed. In prometaphase II, the nuclear envelopes are completely broken down, and the spindle is fully formed. Each sister chromatid forms an individual kinetochore that attaches to microtubules from opposite poles. In metaphase II, the sister chromatids are maximally condensed and aligned at the center of the cell. In anaphase II, the sister chromatids are pulled apart by the spindle fibers and move toward opposite poles.

This illustration compares chromosome alignment in meiosis I and meiosis II. In prometaphase I, homologous pairs of chromosomes are held together by chiasmata. In anaphase I, the homologous pair separates and the connections at the chiasmata are broken, but the sister chromatids remain attached at the centromere. In prometaphase II, the sister chromatids are held together at the centromere. In anaphase II, the centromere connections are broken and the sister chromatids separate.
Figure 6.5 In prometaphase I, microtubules attach to the fused kinetochores of homologous chromosomes. In anaphase I, the homologous chromosomes are separated. In prometaphase II, microtubules attach to individual kinetochores of sister chromatids. In anaphase II, the sister chromatids are separated.

In telophase II, the chromosomes arrive at opposite poles and begin to decondense. Nuclear envelopes form around the chromosomes. Cytokinesis separates the two cells into four genetically unique haploid cells. At this point, the nuclei in the newly produced cells are both haploid and have only one copy of the single set of chromosomes. The cells produced are genetically unique because of the random assortment of paternal and maternal homologs and because of the recombination of maternal and paternal segments of chromosomes—with their sets of genes—that occurs during crossover.

Comparing Meiosis and Mitosis

Mitosis and meiosis, which are both forms of division of the nucleus in eukaryotic cells, share some similarities, but also exhibit distinct differences that lead to their very different outcomes. Mitosis is a single nuclear division that results in two nuclei, usually partitioned into two new cells. The nuclei resulting from a mitotic division are genetically identical to the original. They have the same number of sets of chromosomes: one in the case of haploid cells, and two in the case of diploid cells. On the other hand, meiosis is two nuclear divisions that result in four nuclei, usually partitioned into four new cells. The nuclei resulting from meiosis are never genetically identical, and they contain one chromosome set only—this is half the number of the original cell, which was diploid.

The differences in the outcomes of meiosis and mitosis occur because of differences in the behavior of the chromosomes during each process. Most of these differences in the processes occur in meiosis I, which is a very different nuclear division than mitosis. In meiosis I, the homologous chromosome pairs become associated with each other, are bound together, experience chiasmata and crossover between sister chromatids, and line up along the metaphase plate in tetrads with spindle fibers from opposite spindle poles attached to each kinetochore of a homolog in a tetrad. All of these events occur only in meiosis I, never in mitosis.

Homologous chromosomes move to opposite poles during meiosis I so the number of sets of chromosomes in each nucleus-to-be is reduced from two to one. For this reason, meiosis I is referred to as a reduction division. There is no such reduction in ploidy level in mitosis.

Meiosis II is much more analogous to a mitotic division. In this case, duplicated chromosomes (only one set of them) line up at the center of the cell with divided kinetochores attached to spindle fibers from opposite poles. During anaphase II, as in mitotic anaphase, the kinetochores divide and one sister chromatid is pulled to one pole and the other sister chromatid is pulled to the other pole. If it were not for the fact that there had been crossovers, the two products of each meiosis II division would be identical as in mitosis; instead, they are different because there has always been at least one crossover per chromosome. Meiosis II is not a reduction division because, although there are fewer copies of the genome in the resulting cells, there is still one set of chromosomes, as there was at the end of meiosis I.

Cells produced by mitosis will function in different parts of the body as a part of growth or replacing dead or damaged cells. They may even be involved in asexual reproduction in some organisms. Cells produced by meiosis in a diploid-dominant organism such as an animal will only participate in sexual reproduction.

This illustration compares meiosis and mitosis. In meiosis, there are two rounds of cell division, whereas there is only one round of cell division in mitosis. In both mitosis and meiosis, DNA synthesis occurs during S phase. Synapsis of homologous chromosomes occurs in prophase I of meiosis, but does not occur in mitosis. Crossover of chromosomes occurs in prophase I of meiosis, but does not occur in mitosis. Homologous pairs of chromosomes line up at the metaphase plate during metaphase I of meiosis, but not during mitosis. Sister chromatids line up at the metaphase plate during metaphase II of meiosis and metaphase of mitosis. The result of meiosis is four haploid daughter cells, and the result of mitosis is two diploid daughter cells.
Figure 6.6 Meiosis and mitosis are both preceded by one round of DNA replication; however, meiosis includes two nuclear divisions. The four daughter cells resulting from meiosis are haploid and genetically distinct. The daughter cells resulting from mitosis are diploid and identical to the parent cell.

Concept in Action


QR Code representing a URL

For an animation comparing mitosis and meiosis, go to this website.

Section Summary

Sexual reproduction requires that diploid organisms produce haploid cells that can fuse during fertilization to form diploid offspring. The process that results in haploid cells is called meiosis. Meiosis is a series of events that arrange and separate chromosomes into daughter cells. During the interphase of meiosis, each chromosome is duplicated. In meiosis, there are two rounds of nuclear division resulting in four nuclei and usually four haploid daughter cells, each with half the number of chromosomes as the parent cell. During meiosis, variation in the daughter nuclei is introduced because of crossover in prophase I and random alignment at metaphase I. The cells that are produced by meiosis are genetically unique.

Meiosis and mitosis share similarities, but have distinct outcomes. Mitotic divisions are single nuclear divisions that produce daughter nuclei that are genetically identical and have the same number of chromosome sets as the original cell. Meiotic divisions are two nuclear divisions that produce four daughter nuclei that are genetically different and have one chromosome set rather than the two sets the parent cell had. The main differences between the processes occur in the first division of meiosis. The homologous chromosomes separate into different nuclei during meiosis I causing a reduction of ploidy level. The second division of meiosis is much more similar to a mitotic division.

Exercises

An interactive H5P element has been excluded from this version of the text. You can view it online here:
https://pressbooks.nscc.ca/conceptsofbiologynscc/?p=207#h5p-42

Glossary

chiasmata: (singular = chiasma) the structure that forms at the crossover points after genetic material is exchanged

crossing over: (also, recombination) the exchange of genetic material between homologous chromosomes resulting in chromosomes that incorporate genes from both parents of the organism forming reproductive cells

fertilization: the union of two haploid cells typically from two individual organisms

interkinesis: a period of rest that may occur between meiosis I and meiosis II; there is no replication of DNA during interkinesis

meiosis I: the first round of meiotic cell division; referred to as reduction division because the resulting cells are haploid

meiosis II: the second round of meiotic cell division following meiosis I; sister chromatids are separated from each other, and the result is four unique haploid cells

recombinant: describing something composed of genetic material from two sources, such as a chromosome with both maternal and paternal segments of DNA

reduction division: a nuclear division that produces daughter nuclei each having one-half as many chromosome sets as the parental nucleus; meiosis I is a reduction division

somatic cell: all the cells of a multicellular organism except the gamete-forming cells

synapsis: the formation of a close association between homologous chromosomes during prophase I

tetrad: two duplicated homologous chromosomes (four chromatids) bound together by chiasmata during prophase I

Chapter 7 in Concepts of Biology: 1st Canadian Edition

23

6.3 Errors in Meiosis

Charles Molnar and Jane Gair

Learning Objectives

By the end of this section, you will be able to:

  • Explain how nondisjunction leads to disorders in chromosome number
  • Describe how errors in chromosome structure occur through inversions and translocations

Inherited disorders can arise when chromosomes behave abnormally during meiosis. Chromosome disorders can be divided into two categories: abnormalities in chromosome number and chromosome structural rearrangements. Because even small segments of chromosomes can span many genes, chromosomal disorders are characteristically dramatic and often fatal.

Disorders in Chromosome Number

The isolation and microscopic observation of chromosomes forms the basis of cytogenetics and is the primary method by which clinicians detect chromosomal abnormalities in humans. A karyotype is the number and appearance of chromosomes, including their length, banding pattern, and centromere position. To obtain a view of an individual’s karyotype, cytologists photograph the chromosomes and then cut and paste each chromosome into a chart, or karyogram (Figure 6.7).

 
This is a karyotype of a human female. There are 22 homologous pairs of chromosomes and a pair of X chromosomes.
Figure 6.7 This karyogram shows the chromosomes of a female human immune cell during mitosis. (credit: Andreas Bolzer, et al)

Geneticists Use Karyograms to Identify Chromosomal Aberrations

The karyotype is a method by which traits characterized by chromosomal abnormalities can be identified from a single cell. To observe an individual’s karyotype, a person’s cells (like white blood cells) are first collected from a blood sample or other tissue. In the laboratory, the isolated cells are stimulated to begin actively dividing. A chemical is then applied to the cells to arrest mitosis during metaphase. The cells are then fixed to a slide.

The geneticist then stains chromosomes with one of several dyes to better visualize the distinct and reproducible banding patterns of each chromosome pair. Following staining, chromosomes are viewed using bright-field microscopy. An experienced cytogeneticist can identify each band. In addition to the banding patterns, chromosomes are further identified on the basis of size and centromere location. To obtain the classic depiction of the karyotype in which homologous pairs of chromosomes are aligned in numerical order from longest to shortest, the geneticist obtains a digital image, identifies each chromosome, and manually arranges the chromosomes into this pattern.

At its most basic, the karyogram may reveal genetic abnormalities in which an individual has too many or too few chromosomes per cell. Examples of this are Down syndrome, which is identified by a third copy of chromosome 21, and Turner syndrome, which is characterized by the presence of only one X chromosome in women instead of two. Geneticists can also identify large deletions or insertions of DNA. For instance, Jacobsen syndrome, which involves distinctive facial features as well as heart and bleeding defects, is identified by a deletion on chromosome 11. Finally, the karyotype can pinpoint translocations, which occur when a segment of genetic material breaks from one chromosome and reattaches to another chromosome or to a different part of the same chromosome. Translocations are implicated in certain cancers, including chronic myelogenous leukemia.

By observing a karyogram, geneticists can actually visualize the chromosomal composition of an individual to confirm or predict genetic abnormalities in offspring even before birth.

Nondisjunctions, Duplications, and Deletions

Of all the chromosomal disorders, abnormalities in chromosome number are the most easily identifiable from a karyogram. Disorders of chromosome number include the duplication or loss of entire chromosomes, as well as changes in the number of complete sets of chromosomes. They are caused by nondisjunction, which occurs when pairs of homologous chromosomes or sister chromatids fail to separate during meiosis. The risk of nondisjunction increases with the age of the parents.

Nondisjunction can occur during either meiosis I or II, with different results (Figure 6.8). If homologous chromosomes fail to separate during meiosis I, the result is two gametes that lack that chromosome and two gametes with two copies of the chromosome. If sister chromatids fail to separate during meiosis II, the result is one gamete that lacks that chromosome, two normal gametes with one copy of the chromosome, and one gamete with two copies of the chromosome.

This illustration shows nondisjunction during meiosis I and meiosis II. Nondisjunction during meiosis I occurs when a homologous pair fails to separate, and results in two gametes with n + 1 chromosomes, and two gametes with n – 1 chromosomes. Nondisjunction during meiosis II occurs when sister chromatids fail to separate, and results in one gamete with n + 1 chromosomes, one gamete with n – 1 chromosomes, and two normal gametes.
Figure 6.8 Following meiosis, each gamete has one copy of each chromosome. Nondisjunction occurs when homologous chromosomes (meiosis I) or sister chromatids (meiosis II) fail to separate during meiosis.

An individual with the appropriate number of chromosomes for their species is called euploid; in humans, euploidy corresponds to 22 pairs of autosomes and one pair of sex chromosomes. An individual with an error in chromosome number is described as aneuploid, a term that includes monosomy (loss of one chromosome) or trisomy (gain of an extraneous chromosome). Monosomic human zygotes missing any one copy of an autosome invariably fail to develop to birth because they have only one copy of essential genes. Most autosomal trisomies also fail to develop to birth; however, duplications of some of the smaller chromosomes (13, 15, 18, 21, or 22) can result in offspring that survive for several weeks to many years. Trisomic individuals suffer from a different type of genetic imbalance: an excess in gene dose. Cell functions are calibrated to the amount of gene product produced by two copies (doses) of each gene; adding a third copy (dose) disrupts this balance. The most common trisomy is that of chromosome 21, which leads to Down syndrome. Individuals with this inherited disorder have characteristic physical features and developmental delays in growth and cognition. The incidence of Down syndrome is correlated with maternal age, such that older women are more likely to give birth to children with Down syndrome (Figure 6.9).

This graph shows the risk of Down’s syndrome in the fetus by maternal age. Risk dramatically increases past a maternal age of 35.
Figure 6.9 The incidence of having a fetus with trisomy 21 increases dramatically with maternal age.

Concept in Action


QR Code representing a URL

Visualize the addition of a chromosome that leads to Down syndrome in this video simulation.

Humans display dramatic deleterious effects with autosomal trisomies and monosomies. Therefore, it may seem counterintuitive that human females and males can function normally, despite carrying different numbers of the X chromosome. In part, this occurs because of a process called X inactivation. Early in development, when female mammalian embryos consist of just a few thousand cells, one X chromosome in each cell inactivates by condensing into a structure called a Barr body. The genes on the inactive X chromosome are not expressed. The particular X chromosome (maternally or paternally derived) that is inactivated in each cell is random, but once the inactivation occurs, all cells descended from that cell will have the same inactive X chromosome. By this process, females compensate for their double genetic dose of X chromosome.

In so-called “tortoiseshell” cats, X inactivation is observed as coat-color variegation (Figure 6.10). Females heterozygous for an X-linked coat color gene will express one of two different coat colors over different regions of their body, corresponding to whichever X chromosome is inactivated in the embryonic cell progenitor of that region. When you see a tortoiseshell cat, you will know that it has to be a female.

Photo of a tortoiseshell cat.
Figure 6.10 Embryonic inactivation of one of two different X chromosomes encoding different coat colors gives rise to the tortoiseshell phenotype in cats. (credit: Michael Bodega) Photo of a tortoiseshell cat.

In an individual carrying an abnormal number of X chromosomes, cellular mechanisms will inactivate all but one X in each of her cells. As a result, X-chromosomal abnormalities are typically associated with mild mental and physical defects, as well as sterility. If the X chromosome is absent altogether, the individual will not develop.

Several errors in sex chromosome number have been characterized. Individuals with three X chromosomes, called triplo-X, appear female but express developmental delays and reduced fertility. The XXY chromosome complement, corresponding to one type of Klinefelter syndrome, corresponds to male individuals with small testes, enlarged breasts, and reduced body hair. The extra X chromosome undergoes inactivation to compensate for the excess genetic dosage. Turner syndrome, characterized as an X0 chromosome complement (i.e., only a single sex chromosome), corresponds to a female individual with short stature, webbed skin in the neck region, hearing and cardiac impairments, and sterility.

An individual with more than the correct number of chromosome sets (two for diploid species) is called polyploid. For instance, fertilization of an abnormal diploid egg with a normal haploid sperm would yield a triploid zygote. Polyploid animals are extremely rare, with only a few examples among the flatworms, crustaceans, amphibians, fish, and lizards. Triploid animals are sterile because meiosis cannot proceed normally with an odd number of chromosome sets. In contrast, polyploidy is very common in the plant kingdom, and polyploid plants tend to be larger and more robust than euploids of their species.

Chromosome Structural Rearrangements

Cytologists have characterized numerous structural rearrangements in chromosomes, including partial duplications, deletions, inversions, and translocations. Duplications and deletions often produce offspring that survive but exhibit physical and mental abnormalities. Cri-du-chat (from the French for “cry of the cat”) is a syndrome associated with nervous system abnormalities and identifiable physical features that results from a deletion of most of the small arm of chromosome 5 (Figure 6.11). Infants with this genotype emit a characteristic high-pitched cry upon which the disorder’s name is based.

Photo shows boy with cri-du-chat syndrome at four different ages (ages two, four, nine, and twelve).
Figure 6.11 This individual with cri-du-chat syndrome is shown at various ages: (A) age two, (B) age four, (C) age nine, and (D) age 12. (credit: Paola Cerruti Mainardi)

Chromosome inversions and translocations can be identified by observing cells during meiosis because homologous chromosomes with a rearrangement in one of the pair must contort to maintain appropriate gene alignment and pair effectively during prophase I.

A chromosome inversion is the detachment, 180° rotation, and reinsertion of part of a chromosome. Unless they disrupt a gene sequence, inversions only change the orientation of genes and are likely to have more mild effects than aneuploid errors.

Evolution in Action

The Chromosome 18 InversionNot all structural rearrangements of chromosomes produce nonviable, impaired, or infertile individuals. In rare instances, such a change can result in the evolution of a new species. In fact, an inversion in chromosome 18 appears to have contributed to the evolution of humans. This inversion is not present in our closest genetic relatives, the chimpanzees.

The chromosome 18 inversion is believed to have occurred in early humans following their divergence from a common ancestor with chimpanzees approximately five million years ago. Researchers have suggested that a long stretch of DNA was duplicated on chromosome 18 of an ancestor to humans, but that during the duplication it was inverted (inserted into the chromosome in reverse orientation.

A comparison of human and chimpanzee genes in the region of this inversion indicates that two genes—ROCK1 and USP14—are farther apart on human chromosome 18 than they are on the corresponding chimpanzee chromosome. This suggests that one of the inversion breakpoints occurred between these two genes. Interestingly, humans and chimpanzees express USP14 at distinct levels in specific cell types, including cortical cells and fibroblasts. Perhaps the chromosome 18 inversion in an ancestral human repositioned specific genes and reset their expression levels in a useful way. Because both ROCK1 and USP14 code for enzymes, a change in their expression could alter cellular function. It is not known how this inversion contributed to hominid evolution, but it appears to be a significant factor in the divergence of humans from other primates.1

A translocation occurs when a segment of a chromosome dissociates and reattaches to a different, nonhomologous chromosome. Translocations can be benign or have devastating effects, depending on how the positions of genes are altered with respect to regulatory sequences. Notably, specific translocations have been associated with several cancers and with schizophrenia. Reciprocal translocations result from the exchange of chromosome segments between two nonhomologous chromosomes such that there is no gain or loss of genetic information (Figure 6.12).

Part a shows an inversion in a chromosome. Two identical chromosomes are shown, except for a small section that has been inverted in the second chromosome. Part b shows a reciprocal translocation, in which DNA is transferred from one chromosome to another. No genetic information is gained or lost in the process.
Figure 6.12 An (a) inversion occurs when a chromosome segment breaks from the chromosome, reverses its orientation, and then reattaches in the original position. A (b) reciprocal translocation occurs between two nonhomologous chromosomes and does not cause any genetic information to be lost or duplicated. (credit: modification of work by National Human Genome Research Institute (USA)

Section Summary

The number, size, shape, and banding pattern of chromosomes make them easily identifiable in a karyogram and allow for the assessment of many chromosomal abnormalities. Disorders in chromosome number, or aneuploidies, are typically lethal to the embryo, although a few trisomic genotypes are viable. Because of X inactivation, aberrations in sex chromosomes typically have milder effects on an individual. Aneuploidies also include instances in which segments of a chromosome are duplicated or deleted. Chromosome structures also may be rearranged, for example by inversion or translocation. Both of these aberrations can result in negative effects on development, or death. Because they force chromosomes to assume contorted pairings during meiosis I, inversions and translocations are often associated with reduced fertility because of the likelihood of nondisjunction.

Exercises

An interactive H5P element has been excluded from this version of the text. You can view it online here:
https://pressbooks.nscc.ca/conceptsofbiologynscc/?p=216#h5p-43

Glossary

aneuploid: an individual with an error in chromosome number; includes deletions and duplications of chromosome segments

autosome: any of the non-sex chromosomes

chromosome inversion: the detachment, 180° rotation, and reinsertion of a chromosome arm

euploid: an individual with the appropriate number of chromosomes for their species

karyogram: the photographic image of a karyotype

karyotype: the number and appearance of an individuals chromosomes, including the size, banding patterns, and centromere position

monosomy: an otherwise diploid genotype in which one chromosome is missing

nondisjunction: the failure of synapsed homologs to completely separate and migrate to separate poles during the first cell division of meiosis

polyploid: an individual with an incorrect number of chromosome sets

translocation: the process by which one segment of a chromosome dissociates and reattaches to a different, nonhomologous chromosome

trisomy: an otherwise diploid genotype in which one entire chromosome is duplicated

X inactivation: the condensation of X chromosomes into Barr bodies during embryonic development in females to compensate for the double genetic dose

Footnotes

1 V Goidts, et al., “Segmental duplication associated with the human-specific inversion of chromosome 18: a further example of the impact of segmental duplications on karyotype and genome evolution in primates,” Human Genetics, 115 (2004):116–22.

Chapter 7 in Concepts of Biology: 1st Canadian Edition

VII

Chapter 7: Introduction to Patterns of Inheritance

A photo of light purple pea flowers.
Figure 7.1 Experimenting with thousands of garden peas, Mendel uncovered the fundamentals of genetics. (credit: modification of work by Jerry Kirkhart)

Genetics is the study of heredity. Johann Gregor Mendel set the framework for genetics long before chromosomes or genes had been identified, at a time when meiosis was not well understood. Mendel selected a simple biological system and conducted methodical, quantitative analyses using large sample sizes. Because of Mendel’s work, the fundamental principles of heredity were revealed. We now know that genes, carried on chromosomes, are the basic functional units of heredity with the ability to be replicated, expressed, or mutated. Today, the postulates put forth by Mendel form the basis of classical, or Mendelian, genetics. Not all genes are transmitted from parents to offspring according to Mendelian genetics, but Mendel’s experiments serve as an excellent starting point for thinking about inheritance.

Search for Key Points in Chapter 8

An interactive H5P element has been excluded from this version of the text. You can view it online here:
https://pressbooks.nscc.ca/conceptsofbiologynscc/?p=219#h5p-44

Chapter 8 in Concepts of Biology: 1st Canadian Edition

24

7.1 Mendel’s Experiments

Charles Molnar and Jane Gair

Learning Objectives

By the end of this section, you will be able to:

  • Explain the scientific reasons for the success of Mendel’s experimental work
  • Describe the expected outcomes of monohybrid crosses involving dominant and recessive alleles.
 
Image is a sketch of Johann Gregor Mendel.
Figure 7.2 Johann Gregor Mendel set the framework for the study of genetics.

Watch the interactive video

An interactive H5P element has been excluded from this version of the text. You can view it online here:
https://pressbooks.nscc.ca/conceptsofbiologynscc/?p=225#h5p-45

Johann Gregor Mendel (1822–1884) was a lifelong learner, teacher, scientist, and man of faith. As a young adult, he joined the Augustinian Abbey of St. Thomas in Brno in what is now the Czech Republic. Supported by the monastery, he taught physics, botany, and natural science courses at the secondary and university levels. In 1856, he began a decade-long research pursuit involving inheritance patterns in honeybees and plants, ultimately settling on pea plants as his primary model system (a system with convenient characteristics that is used to study a specific biological phenomenon to gain understanding to be applied to other systems). In 1865, Mendel presented the results of his experiments with nearly 30,000 pea plants to the local natural history society. He demonstrated that traits are transmitted faithfully from parents to offspring in specific patterns. In 1866, he published his work, Experiments in Plant Hybridization,1 in the proceedings of the Natural History Society of Brünn.

Mendel’s work went virtually unnoticed by the scientific community, which incorrectly believed that the process of inheritance involved a blending of parental traits that produced an intermediate physical appearance in offspring. This hypothetical process appeared to be correct because of what we know now as continuous variation. Continuous variation is the range of small differences we see among individuals in a characteristic like human height. It does appear that offspring are a “blend” of their parents’ traits when we look at characteristics that exhibit continuous variation. Mendel worked instead with traits that show discontinuous variation. Discontinuous variation is the variation seen among individuals when each individual shows one of two—or a very few—easily distinguishable traits, such as violet or white flowers. Mendel’s choice of these kinds of traits allowed him to see experimentally that the traits were not blended in the offspring as would have been expected at the time, but that they were inherited as distinct traits. In 1868, Mendel became abbot of the monastery and exchanged his scientific pursuits for his pastoral duties. He was not recognized for his extraordinary scientific contributions during his lifetime; in fact, it was not until 1900 that his work was rediscovered, reproduced, and revitalized by scientists on the brink of discovering the chromosomal basis of heredity.

Mendel’s Crosses

Mendel’s seminal work was accomplished using the garden pea, Pisum sativum, to study inheritance. This species naturally self-fertilizes, meaning that pollen encounters ova within the same flower. The flower petals remain sealed tightly until pollination is completed to prevent the pollination of other plants. The result is highly inbred, or “true-breeding,” pea plants. These are plants that always produce offspring that look like the parent. By experimenting with true-breeding pea plants, Mendel avoided the appearance of unexpected traits in offspring that might occur if the plants were not true breeding. The garden pea also grows to maturity within one season, meaning that several generations could be evaluated over a relatively short time. Finally, large quantities of garden peas could be cultivated simultaneously, allowing Mendel to conclude that his results did not come about simply by chance.

Mendel performed hybridizations, which involve mating two true-breeding individuals that have different traits. In the pea, which is naturally self-pollinating, this is done by manually transferring pollen from the anther of a mature pea plant of one variety to the stigma of a separate mature pea plant of the second variety.

Plants used in first-generation crosses were called P, or parental generation, plants (Figure 7.3). Mendel collected the seeds produced by the P plants that resulted from each cross and grew them the following season. These offspring were called the F1, or the first filial (filial = daughter or son), generation. Once Mendel examined the characteristics in the F1 generation of plants, he allowed them to self-fertilize naturally. He then collected and grew the seeds from the F1 plants to produce the F2, or second filial, generation. Mendel’s experiments extended beyond the F2 generation to the F3 generation, F4 generation, and so on, but it was the ratio of characteristics in the P, F1, and F2 generations that were the most intriguing and became the basis of Mendel’s postulates.

The diagram shows a cross between pea plants that are true-breeding for purple flower color and plants that are true-breeding for white flower color. This cross-fertilization of the P generation resulted in an F_{1} generation with all violet flowers. Self-fertilization of the F_{1} generation resulted in an F_{2} generation that consisted of 705 plants with violet flowers, and 224 plants with white flowers.
Figure 7.3 Mendel’s process for performing crosses included examining flower color.

Garden Pea Characteristics Revealed the Basics of Heredity

In his 1865 publication, Mendel reported the results of his crosses involving seven different characteristics, each with two contrasting traits. A trait is defined as a variation in the physical appearance of a heritable characteristic. The characteristics included plant height, seed texture, seed color, flower color, pea-pod size, pea-pod color, and flower position. For the characteristic of flower color, for example, the two contrasting traits were white versus violet. To fully examine each characteristic, Mendel generated large numbers of F1 and F2 plants and reported results from thousands of F2 plants.

What results did Mendel find in his crosses for flower color? First, Mendel confirmed that he was using plants that bred true for white or violet flower color. Irrespective of the number of generations that Mendel examined, all self-crossed offspring of parents with white flowers had white flowers, and all self-crossed offspring of parents with violet flowers had violet flowers. In addition, Mendel confirmed that, other than flower color, the pea plants were physically identical. This was an important check to make sure that the two varieties of pea plants only differed with respect to one trait, flower color.

Once these validations were complete, Mendel applied the pollen from a plant with violet flowers to the stigma of a plant with white flowers. After gathering and sowing the seeds that resulted from this cross, Mendel found that 100 percent of the F1 hybrid generation had violet flowers. Conventional wisdom at that time would have predicted the hybrid flowers to be pale violet or for hybrid plants to have equal numbers of white and violet flowers. In other words, the contrasting parental traits were expected to blend in the offspring. Instead, Mendel’s results demonstrated that the white flower trait had completely disappeared in the F1 generation.

Importantly, Mendel did not stop his experimentation there. He allowed the F1 plants to self-fertilize and found that 705 plants in the F2generation had violet flowers and 224 had white flowers. This was a ratio of 3.15 violet flowers to one white flower, or approximately 3:1. When Mendel transferred pollen from a plant with violet flowers to the stigma of a plant with white flowers and vice versa, he obtained approximately the same ratio irrespective of which parent—male or female—contributed which trait. This is called a reciprocal cross—a paired cross in which the respective traits of the male and female in one cross become the respective traits of the female and male in the other cross. For the other six characteristics that Mendel examined, the F1 and F2 generations behaved in the same way that they behaved for flower color. One of the two traits would disappear completely from the F1 generation, only to reappear in the F2 generation at a ratio of roughly 3:1 (Figure 7.4).

 
Seven characteristics of Mendel’s pea plants are illustrated. The flowers can be purple or white. The peas can be yellow or green, or smooth or wrinkled. The pea pods can be inflated or constricted, or yellow or green. The flower position can be axial or terminal. The stem length can be tall or dwarf.
Figure 7.4 Mendel identified seven pea plant characteristics.

Upon compiling his results for many thousands of plants, Mendel concluded that the characteristics could be divided into expressed and latent traits. He called these dominant and recessive traits, respectively. Dominant traits are those that are inherited unchanged in a hybridization. Recessive traits become latent, or disappear in the offspring of a hybridization. The recessive trait does, however, reappear in the progeny of the hybrid offspring. An example of a dominant trait is the violet-colored flower trait. For this same characteristic (flower color), white-colored flowers are a recessive trait. The fact that the recessive trait reappeared in the F2 generation meant that the traits remained separate (and were not blended) in the plants of the F1 generation. Mendel proposed that this was because the plants possessed two copies of the trait for the flower-color characteristic, and that each parent transmitted one of their two copies to their offspring, where they came together. Moreover, the physical observation of a dominant trait could mean that the genetic composition of the organism included two dominant versions of the characteristic, or that it included one dominant and one recessive version. Conversely, the observation of a recessive trait meant that the organism lacked any dominant versions of this characteristic.

Concept in Action


QR Code representing a URL

For an excellent review of Mendel’s experiments and to perform your own crosses and identify patterns of inheritance, visit the Mendel’s Peas web lab.

Section Summary

Working with garden pea plants, Mendel found that crosses between parents that differed for one trait produced F1 offspring that all expressed one parent’s traits. The traits that were visible in the F1 generation are referred to as dominant, and traits that disappear in the F1 generation are described as recessive. When the F1 plants in Mendel’s experiment were self-crossed, the F2 offspring exhibited the dominant trait or the recessive trait in a 3:1 ratio, confirming that the recessive trait had been transmitted faithfully from the original P parent. Reciprocal crosses generated identical F1 and F2 offspring ratios. By examining sample sizes, Mendel showed that traits were inherited as independent events.

Exercises

An interactive H5P element has been excluded from this version of the text. You can view it online here:
https://pressbooks.nscc.ca/conceptsofbiologynscc/?p=225#h5p-46

Glossary

continuous variation: a variation in a characteristic in which individuals show a range of traits with small differences between them

discontinuous variation: a variation in a characteristic in which individuals show two, or a few, traits with large differences between them

dominant: describes a trait that masks the expression of another trait when both versions of the gene are present in an individual

F1: the first filial generation in a cross; the offspring of the parental generation

F2: the second filial generation produced when F1 individuals are self-crossed or fertilized with each other

hybridization: the process of mating two individuals that differ, with the goal of achieving a certain characteristic in their offspring

model system: a species or biological system used to study a specific biological phenomenon to gain understanding that will be applied to other species

P: the parental generation in a cross

recessive: describes a trait whose expression is masked by another trait when the alleles for both traits are present in an individual

reciprocal cross: a paired cross in which the respective traits of the male and female in one cross become the respective traits of the female and male in the other cross

trait: a variation in an inherited characteristic

Footnotes

1 Johann Gregor Mendel, “Versuche über Pflanzenhybriden.” Verhandlungen des naturforschenden Vereines in Brünn, Bd. IV für das Jahr, 1865 Abhandlungen (1866):3–47. [for English translation, see http://www.mendelweb.org/Mendel.plain.html]

Chapter 8 in Concepts of Biology: 1st Canadian Edition

25

7.2 Laws of Inheritance

Charles Molnar and Jane Gair

Learning Objectives

By the end of this section, you will be able to:

  • Explain the relationship between genotypes and phenotypes in dominant and recessive gene systems
  • Use a Punnett square to calculate the expected proportions of genotypes and phenotypes in a monohybrid cross
  • Explain Mendel’s law of segregation and independent assortment in terms of genetics and the events of meiosis
  • Explain the purpose and methods of a test cross

The seven characteristics that Mendel evaluated in his pea plants were each expressed as one of two versions, or traits. Mendel deduced from his results that each individual had two discrete copies of the characteristic that are passed individually to offspring. We now call those two copies genes, which are carried on chromosomes. The reason we have two copies of each gene is that we inherit one from each parent. In fact, it is the chromosomes we inherit and the two copies of each gene are located on paired chromosomes. Recall that in meiosis these chromosomes are separated out into haploid gametes. This separation, or segregation, of the homologous chromosomes means also that only one of the copies of the gene gets moved into a gamete. The offspring are formed when that gamete unites with one from another parent and the two copies of each gene (and chromosome) are restored.

For cases in which a single gene controls a single characteristic, a diploid organism has two genetic copies that may or may not encode the same version of that characteristic. For example, one individual may carry a gene that determines white flower color and a gene that determines violet flower color. Gene variants that arise by mutation and exist at the same relative locations on homologous chromosomes are called alleles. Mendel examined the inheritance of genes with just two allele forms, but it is common to encounter more than two alleles for any given gene in a natural population.

Phenotypes and Genotypes

Two alleles for a given gene in a diploid organism are expressed and interact to produce physical characteristics. The observable traits expressed by an organism are referred to as its phenotype. An organism’s underlying genetic makeup, consisting of both the physically visible and the non-expressed alleles, is called its genotype. Mendel’s hybridization experiments demonstrate the difference between phenotype and genotype. For example, the phenotypes that Mendel observed in his crosses between pea plants with differing traits are connected to the diploid genotypes of the plants in the P, F1, and F2 generations. We will use a second trait that Mendel investigated, seed color, as an example. Seed color is governed by a single gene with two alleles. The yellow-seed allele is dominant and the green-seed allele is recessive. When true-breeding plants were cross-fertilized, in which one parent had yellow seeds and one had green seeds, all of the F1 hybrid offspring had yellow seeds. That is, the hybrid offspring were phenotypically identical to the true-breeding parent with yellow seeds. However, we know that the allele donated by the parent with green seeds was not simply lost because it reappeared in some of the F2 offspring (Figure 7.5). Therefore, the F1 plants must have been genotypically different from the parent with yellow seeds.

The P plants that Mendel used in his experiments were each homozygous for the trait he was studying. Diploid organisms that are homozygous for a gene have two identical alleles, one on each of their homologous chromosomes. The genotype is often written as YY or yy, for which each letter represents one of the two alleles in the genotype. The dominant allele is capitalized and the recessive allele is lower case. The letter used for the gene (seed color in this case) is usually related to the dominant trait (yellow allele, in this case, or “Y”). Mendel’s parental pea plants always bred true because both produced gametes carried the same allele. When P plants with contrasting traits were cross-fertilized, all of the offspring were heterozygous for the contrasting trait, meaning their genotype had different alleles for the gene being examined. For example, the F1 yellow plants that received a Y allele from their yellow parent and a y allele from their green parent had the genotype Yy.

By the end of this section, you will be able to: Explain the relationship between genotypes and phenotypes in dominant and recessive gene systems Use a Punnett square to calculate the expected proportions of genotypes and phenotypes in a monohybrid cross Explain Mendel’s law of segregation and independent assortment in terms of genetics and the events of meiosis Explain the purpose and methods of a test cross
Figure 7.5 Phenotypes are physical expressions of traits that are transmitted by alleles. Capital letters represent dominant alleles and lowercase letters represent recessive alleles. The phenotypic ratios are the ratios of visible characteristics. The genotypic ratios are the ratios of gene combinations in the offspring, and these are not always distinguishable in the phenotypes.

Law of Dominance

Our discussion of homozygous and heterozygous organisms brings us to why the F1 heterozygous offspring were identical to one of the parents, rather than expressing both alleles. In all seven pea-plant characteristics, one of the two contrasting alleles was dominant, and the other was recessive. Mendel called the dominant allele the expressed unit factor; the recessive allele was referred to as the latent unit factor. We now know that these so-called unit factors are actually genes on homologous chromosomes. For a gene that is expressed in a dominant and recessive pattern, homozygous dominant and heterozygous organisms will look identical (that is, they will have different genotypes but the same phenotype), and the recessive allele will only be observed in homozygous recessive individuals.

Correspondence between Genotype and Phenotype for a Dominant-Recessive Characteristic.
Homozygous Heterozygous Homozygous
Genotype YY Yy yy
Phenotype yellow yellow green

Mendel’s law of dominance states that in a heterozygote, one trait will conceal the presence of another trait for the same characteristic. For example, when crossing true-breeding violet-flowered plants with true-breeding white-flowered plants, all of the offspring were violet-flowered, even though they all had one allele for violet and one allele for white. Rather than both alleles contributing to a phenotype, the dominant allele will be expressed exclusively. The recessive allele will remain latent, but will be transmitted to offspring in the same manner as that by which the dominant allele is transmitted. The recessive trait will only be expressed by offspring that have two copies of this allele (Figure 7.6), and these offspring will breed true when self-crossed.

Photo shows a mother with an albino child.
Figure 7.6 The allele for albinism, expressed here in humans, is recessive. Both of this child’s parents carried the recessive allele.

Monohybrid Cross and the Punnett Square

When fertilization occurs between two true-breeding parents that differ by only the characteristic being studied, the process is called a monohybrid cross, and the resulting offspring are called monohybrids. Mendel performed seven types of monohybrid crosses, each involving contrasting traits for different characteristics. Out of these crosses, all of the F1 offspring had the phenotype of one parent, and the F2 offspring had a 3:1 phenotypic ratio. On the basis of these results, Mendel postulated that each parent in the monohybrid cross contributed one of two paired unit factors to each offspring, and every possible combination of unit factors was equally likely.

The results of Mendel’s research can be explained in terms of probabilities, which are mathematical measures of likelihood. The probability of an event is calculated by the number of times the event occurs divided by the total number of opportunities for the event to occur. A probability of one (100 percent) for some event indicates that it is guaranteed to occur, whereas a probability of zero (0 percent) indicates that it is guaranteed to not occur, and a probability of 0.5 (50 percent) means it has an equal chance of occurring or not occurring.

To demonstrate this with a monohybrid cross, consider the case of true-breeding pea plants with yellow versus green seeds. The dominant seed color is yellow; therefore, the parental genotypes were YY for the plants with yellow seeds and yy for the plants with green seeds. A Punnett square, devised by the British geneticist Reginald Punnett, is useful for determining probabilities because it is drawn to predict all possible outcomes of all possible random fertilization events and their expected frequencies. Figure 7.9 shows a Punnett square for a cross between a plant with yellow peas and one with green peas. To prepare a Punnett square, all possible combinations of the parental alleles (the genotypes of the gametes) are listed along the top (for one parent) and side (for the other parent) of a grid. The combinations of egg and sperm gametes are then made in the boxes in the table on the basis of which alleles are combining. Each box then represents the diploid genotype of a zygote, or fertilized egg. Because each possibility is equally likely, genotypic ratios can be determined from a Punnett square. If the pattern of inheritance (dominant and recessive) is known, the phenotypic ratios can be inferred as well. For a monohybrid cross of two true-breeding parents, each parent contributes one type of allele. In this case, only one genotype is possible in the F1 offspring. All offspring are Yy and have yellow seeds.

When the F1 offspring are crossed with each other, each has an equal probability of contributing either a Y or a y to the F2 offspring. The result is a 1 in 4 (25 percent) probability of both parents contributing a Y, resulting in an offspring with a yellow phenotype; a 25 percent probability of parent A contributing a Y and parent B a y, resulting in offspring with a yellow phenotype; a 25 percent probability of parent A contributing a y and parent B a Y, also resulting in a yellow phenotype; and a (25 percent) probability of both parents contributing a y, resulting in a green phenotype. When counting all four possible outcomes, there is a 3 in 4 probability of offspring having the yellow phenotype and a 1 in 4 probability of offspring having the green phenotype. This explains why the results of Mendel’s F2 generation occurred in a 3:1 phenotypic ratio. Using large numbers of crosses, Mendel was able to calculate probabilities, found that they fit the model of inheritance, and use these to predict the outcomes of other crosses.

Law of Segregation

Observing that true-breeding pea plants with contrasting traits gave rise to F1 generations that all expressed the dominant trait and F2 generations that expressed the dominant and recessive traits in a 3:1 ratio, Mendel proposed the law of segregation. This law states that paired unit factors (genes) must segregate equally into gametes such that offspring have an equal likelihood of inheriting either factor. For the F2 generation of a monohybrid cross, the following three possible combinations of genotypes result: homozygous dominant, heterozygous, or homozygous recessive. Because heterozygotes could arise from two different pathways (receiving one dominant and one recessive allele from either parent), and because heterozygotes and homozygous dominant individuals are phenotypically identical, the law supports Mendel’s observed 3:1 phenotypic ratio. The equal segregation of alleles is the reason we can apply the Punnett square to accurately predict the offspring of parents with known genotypes. The physical basis of Mendel’s law of segregation is the first division of meiosis in which the homologous chromosomes with their different versions of each gene are segregated into daughter nuclei. This process was not understood by the scientific community during Mendel’s lifetime (Figure 7.7).

Homologous pairs of chromosomes line up at the metaphase plate during metaphase I of meiosis. The homologous chromosomes with their different versions of each gene are segregated into daughter nuclei.
Figure 7.7 The first division in meiosis is shown.

Test Cross

Beyond predicting the offspring of a cross between known homozygous or heterozygous parents, Mendel also developed a way to determine whether an organism that expressed a dominant trait was a heterozygote or a homozygote. Called the test cross, this technique is still used by plant and animal breeders. In a test cross, the dominant-expressing organism is crossed with an organism that is homozygous recessive for the same characteristic. If the dominant-expressing organism is a homozygote, then all F1 offspring will be heterozygotes expressing the dominant trait (Figure 7.8). Alternatively, if the dominant-expressing organism is a heterozygote, the F1 offspring will exhibit a 1:1 ratio of heterozygotes and recessive homozygotes (Figure 7.9). The test cross further validates Mendel’s postulate that pairs of unit factors segregate equally.

In a test cross, a parent with a dominant phenotype but unknown genotype is crossed with a recessive parent. If the parent with the unknown phenotype is homozygous dominant, all the resulting offspring will have at least one dominant allele. If the parent with the unknown phenotype is heterozygous, 50 percent of the offspring will inherit a recessive allele from both parents and will have the recessive phenotype.
Figure 7.8 A test cross can be performed to determine whether an organism expressing a dominant trait is a homozygote or a heterozygote.
A test cross can be performed to determine whether an organism expressing a dominant trait is a homozygote or a heterozygote.
Figure 7.9 This Punnett square shows the cross between plants with yellow seeds and green seeds. The cross between the true-breeding P plants produces F1 heterozygotes that can be self-fertilized. The self-cross of the F1 generation can be analyzed with a Punnett square to predict the genotypes of the F2 generation. Given an inheritance pattern of dominant–recessive, the genotypic and phenotypic ratios can then be determined.

In pea plants, round peas (R) are dominant to wrinkled peas (r). You do a test cross between a pea plant with wrinkled peas (genotype rr) and a plant of unknown genotype that has round peas. You end up with three plants, all which have round peas. From this data, can you tell if the parent plant is homozygous dominant or heterozygous?

You cannot be sure if the plant is homozygous or heterozygous as the data set is too small: by random chance, all three plants might have acquired only the dominant gene even if the recessive one is present.

Law of Independent Assortment

Mendel’s law of independent assortment states that genes do not influence each other with regard to the sorting of alleles into gametes, and every possible combination of alleles for every gene is equally likely to occur. Independent assortment of genes can be illustrated by the dihybrid cross, a cross between two true-breeding parents that express different traits for two characteristics. Consider the characteristics of seed color and seed texture for two pea plants, one that has wrinkled, green seeds (rryy) and another that has round, yellow seeds (RRYY). Because each parent is homozygous, the law of segregation indicates that the gametes for the wrinkled–green plant all are ry, and the gametes for the round–yellow plant are all RY. Therefore, the F1 generation of offspring all are RrYy (Figure 7.10).

This illustration shows a dihybrid cross between pea plants. In the P generation, a plant that has the homozygous dominant phenotype of yellow, round peas is crossed with a plant with the homozygous recessive phenotype of green, wrinkled peas. The resulting F_{1} offspring have a heterozygous genotype and yellow, round peas. Self-pollination of the F_{1} generation results in F_{2} offspring with a phenotypic ratio of 9:3:3:1 for round–yellow, round–green, wrinkled–yellow, and wrinkled–green peas, respectively.
Figure 7.10 A dihybrid cross in pea plants involves the genes for seed color and texture. The P cross produces F1 offspring that are all heterozygous for both characteristics. The resulting 9:3:3:1 F2 phenotypic ratio is obtained using a Punnett square.

In pea plants, purple flowers (P) are dominant to white (p), and yellow peas (Y) are dominant to green (y). What are the possible genotypes and phenotypes for a cross between PpYY and ppYy pea plants? How many squares would you need to complete a Punnett square analysis of this cross?

The possible genotypes are PpYY, PpYy, ppYY, and ppYy. The former two genotypes would result in plants with purple flowers and yellow peas, while the latter two genotypes would result in plants with white flowers with yellow peas, for a 1:1 ratio of each phenotype. You only need a 2 × 2 Punnett square (four squares total) to do this analysis because two of the alleles are homozygous.

The gametes produced by the F1 individuals must have one allele from each of the two genes. For example, a gamete could get an R allele for the seed shape gene and either a Y or a y allele for the seed color gene. It cannot get both an R and an r allele; each gamete can have only one allele per gene. The law of independent assortment states that a gamete into which an r allele is sorted would be equally likely to contain either a Y or a y allele. Thus, there are four equally likely gametes that can be formed when the RrYy heterozygote is self-crossed, as follows: RY, rY, Ry, and ry. Arranging these gametes along the top and left of a 4 × 4 Punnett square gives us 16 equally likely genotypic combinations. From these genotypes, we find a phenotypic ratio of 9 round–yellow:3 round–green:3 wrinkled–yellow:1 wrinkled–green. These are the offspring ratios we would expect, assuming we performed the crosses with a large enough sample size.

The physical basis for the law of independent assortment also lies in meiosis I, in which the different homologous pairs line up in random orientations. Each gamete can contain any combination of paternal and maternal chromosomes (and therefore the genes on them) because the orientation of tetrads on the metaphase plane is random (Figure 7.11).

Homologous pairs of chromosomes line up at the metaphase plate during metaphase I of meiosis. The homologous chromosomes, with their different versions of each gene, are randomly segregated into daughter nuclei, resulting in a variety of possible genetic arrangements.
Figure 7.11 The random segregation into daughter nuclei that happens during the first division in meiosis can lead to a variety of possible genetic arrangements.

Probability Basics

Probabilities are mathematical measures of likelihood. The empirical probability of an event is calculated by dividing the number of times the event occurs by the total number of opportunities for the event to occur. It is also possible to calculate theoretical probabilities by dividing the number of times that an event is expected to occur by the number of times that it could occur. Empirical probabilities come from observations, like those of Mendel. Theoretical probabilities come from knowing how the events are produced and assuming that the probabilities of individual outcomes are equal. A probability of one for some event indicates that it is guaranteed to occur, whereas a probability of zero indicates that it is guaranteed not to occur. An example of a genetic event is a round seed produced by a pea plant. In his experiment, Mendel demonstrated that the probability of the event “round seed” occurring was one in the F1 offspring of true-breeding parents, one of which has round seeds and one of which has wrinkled seeds. When the F1 plants were subsequently self-crossed, the probability of any given F2 offspring having round seeds was now three out of four. In other words, in a large population of F2 offspring chosen at random, 75 percent were expected to have round seeds, whereas 25 percent were expected to have wrinkled seeds. Using large numbers of crosses, Mendel was able to calculate probabilities and use these to predict the outcomes of other crosses.

The Product Rule and Sum Rule

Mendel demonstrated that the pea-plant characteristics he studied were transmitted as discrete units from parent to offspring. As will be discussed, Mendel also determined that different characteristics, like seed color and seed texture, were transmitted independently of one another and could be considered in separate probability analyses. For instance, performing a cross between a plant with green, wrinkled seeds and a plant with yellow, round seeds still produced offspring that had a 3:1 ratio of green:yellow seeds (ignoring seed texture) and a 3:1 ratio of round:wrinkled seeds (ignoring seed color). The characteristics of color and texture did not influence each other.

The product rule of probability can be applied to this phenomenon of the independent transmission of characteristics. The product rule states that the probability of two independent events occurring together can be calculated by multiplying the individual probabilities of each event occurring alone. To demonstrate the product rule, imagine that you are rolling a six-sided die (D) and flipping a penny (P) at the same time. The die may roll any number from 1–6 (D#), whereas the penny may turn up heads (PH) or tails (PT). The outcome of rolling the die has no effect on the outcome of flipping the penny and vice versa. There are 12 possible outcomes of this action, and each event is expected to occur with equal probability.

Twelve Equally Likely Outcomes of Rolling a Die and Flipping a Penny
Rolling Die Flipping Penny
D1 PH
D1 PT
D2 PH
D2 PT
D3 PH
D3 PT
D4 PH
D4 PT
D5 PH
D5 PT
D6 PH
D6 PT

Of the 12 possible outcomes, the die has a 2/12 (or 1/6) probability of rolling a two, and the penny has a 6/12 (or 1/2) probability of coming up heads. By the product rule, the probability that you will obtain the combined outcome 2 and heads is: (D2) x (PH) = (1/6) x (1/2) or 1/12. Notice the word “and” in the description of the probability. The “and” is a signal to apply the product rule. For example, consider how the product rule is applied to the dihybrid cross: the probability of having both dominant traits in the F2 progeny is the product of the probabilities of having the dominant trait for each characteristic, as shown here:

3/4×3/4=9/16

On the other hand, the sum rule of probability is applied when considering two mutually exclusive outcomes that can come about by more than one pathway. The sum rule states that the probability of the occurrence of one event or the other event, of two mutually exclusive events, is the sum of their individual probabilities. Notice the word “or” in the description of the probability. The “or” indicates that you should apply the sum rule. In this case, let’s imagine you are flipping a penny (P) and a quarter (Q). What is the probability of one coin coming up heads and one coin coming up tails? This outcome can be achieved by two cases: the penny may be heads (PH) and the quarter may be tails (QT), or the quarter may be heads (QH) and the penny may be tails (PT). Either case fulfills the outcome. By the sum rule, we calculate the probability of obtaining one head and one tail as [(PH) × (QT)] + [(QH) × (PT)] = [(1/2) × (1/2)] + [(1/2) × (1/2)] = 1/2. You should also notice that we used the product rule to calculate the probability of PH and QT, and also the probability of PT and QH, before we summed them. Again, the sum rule can be applied to show the probability of having just one dominant trait in the F2 generation of a dihybrid cross:

3/16 + 3/4 = 15/16
The Product Rule and Sum Rule
Product Rule Sum Rule
For independent events A and B, the probability (P) of them both occurring (A and B) is (PA × PB) For mutually exclusive events A and B, the probability (P) that at least one occurs (A or B) is (PA + PB)

To use probability laws in practice, it is necessary to work with large sample sizes because small sample sizes are prone to deviations caused by chance. The large quantities of pea plants that Mendel examined allowed him calculate the probabilities of the traits appearing in his F2 generation. As you will learn, this discovery meant that when parental traits were known, the offspring’s traits could be predicted accurately even before fertilization.

This is a pedigree of a family that carries the recessive disorder alkaptonuria. In the second generation, an unaffected mother and an affected father have three children. One child has the disorder, so the genotype of the mother must be Aa and the genotype of the father is aa. One unaffected child goes on to have two children, one affected and one unaffected. Because her husband was not affected, she and her husband must both be heterozygous. The genotype of their unaffected child is unknown, and is designated A?. In the third generation, the other unaffected child had no offspring, and his genotype is therefore also unknown. The affected third-generation child goes on to have one child with the disorder. Her husband is unaffected and is labeled “3.” The first generation father is affected and is labeled “1.” The first generation mother is unaffected and is labeled “2.” The Art Connection question asks the genotype of the three numbered individuals.
Figure 7.12

Alkaptonuria is a recessive genetic disorder in which two amino acids, phenylalanine and tyrosine, are not properly metabolized. Affected individuals may have darkened skin and brown urine, and may suffer joint damage and other complications. In this pedigree, individuals with the disorder are indicated in blue and have the genotype aa. Unaffected individuals are indicated in yellow and have the genotype AA or Aa. Note that it is often possible to determine a person’s genotype from the genotype of their offspring. For example, if neither parent has the disorder but their child does, they must be heterozygous. Two individuals on the pedigree have an unaffected phenotype but unknown genotype. Because they do not have the disorder, they must have at least one normal allele, so their genotype gets the “A?” designation.

What are the genotypes of the individuals labeled 1, 2 and 3?

Section Summary

When true-breeding, or homozygous, individuals that differ for a certain trait are crossed, all of the offspring will be heterozygous for that trait. If the traits are inherited as dominant and recessive, the F1 offspring will all exhibit the same phenotype as the parent homozygous for the dominant trait. If these heterozygous offspring are self-crossed, the resulting F2 offspring will be equally likely to inherit gametes carrying the dominant or recessive trait, giving rise to offspring of which one quarter are homozygous dominant, half are heterozygous, and one quarter are homozygous recessive. Because homozygous dominant and heterozygous individuals are phenotypically identical, the observed traits in the F2 offspring will exhibit a ratio of three dominant to one recessive.

Mendel postulated that genes (characteristics) are inherited as pairs of alleles (traits) that behave in a dominant and recessive pattern. Alleles segregate into gametes such that each gamete is equally likely to receive either one of the two alleles present in a diploid individual. In addition, genes are assorted into gametes independently of one another. That is, in general, alleles are not more likely to segregate into a gamete with a particular allele of another gene.

Exercises

An interactive H5P element has been excluded from this version of the text. You can view it online here:
https://pressbooks.nscc.ca/conceptsofbiologynscc/?p=235#h5p-47

Glossary

allele: one of two or more variants of a gene that determines a particular trait for a characteristic

dihybrid: the result of a cross between two true-breeding parents that express different traits for two characteristics

genotype: the underlying genetic makeup, consisting of both physically visible and non-expressed alleles, of an organism

heterozygous: having two different alleles for a given gene on the homologous chromosomes

homozygous: having two identical alleles for a given gene on the homologous chromosomes

law of dominance: in a heterozygote, one trait will conceal the presence of another trait for the same characteristic

law of independent assortment: genes do not influence each other with regard to sorting of alleles into gametes; every possible combination of alleles is equally likely to occur

law of segregation: paired unit factors (i.e., genes) segregate equally into gametes such that offspring have an equal likelihood of inheriting any combination of factors

monohybrid: the result of a cross between two true-breeding parents that express different traits for only one characteristic

phenotype: the observable traits expressed by an organism

Punnett square: a visual representation of a cross between two individuals in which the gametes of each individual are denoted along the top and side of a grid, respectively, and the possible zygotic genotypes are recombined at each box in the grid

test cross: a cross between a dominant expressing individual with an unknown genotype and a homozygous recessive individual; the offspring phenotypes indicate whether the unknown parent is heterozygous or homozygous for the dominant trait

Chapter 8 in Concepts of Biology: 1st Canadian Edition

26

7.3 Extensions of the Laws of Inheritance

Charles Molnar and Jane Gair

Learning Objectives

By the end of this section, you will be able to:

  • Identify non-Mendelian inheritance patterns such as incomplete dominance, codominance, multiple alleles, and sex linkage from the results of crosses
  • Explain the effect of linkage and recombination on gamete genotypes
  • Explain the phenotypic outcomes of epistatic effects among genes
  • Explain polygenic inheritance

Mendel studied traits with only one mode of inheritance in pea plants. The inheritance of the traits he studied all followed the relatively simple pattern of dominant and recessive alleles for a single characteristic. There are several important modes of inheritance, discovered after Mendel’s work, that do not follow the dominant and recessive, single-gene model.

Alternatives to Dominance and Recessiveness

Mendel’s experiments with pea plants suggested that: 1) two types of “units” or alleles exist for every gene; 2) alleles maintain their integrity in each generation (no blending); and 3) in the presence of the dominant allele, the recessive allele is hidden, with no contribution to the phenotype. Therefore, recessive alleles can be “carried” and not expressed by individuals. Such heterozygous individuals are sometimes referred to as “carriers.” Since then, genetic studies in other organisms have shown that much more complexity exists, but that the fundamental principles of Mendelian genetics still hold true. In the sections to follow, we consider some of the extensions of Mendelism.

Incomplete Dominance

Mendel’s results, demonstrating that traits are inherited as dominant and recessive pairs, contradicted the view at that time that offspring exhibited a blend of their parents’ traits. However, the heterozygote phenotype occasionally does appear to be intermediate between the two parents. For example, in the snapdragon, Antirrhinum majus (Figure 7.13), a cross between a homozygous parent with white flowers (CWCW) and a homozygous parent with red flowers (CRCR) will produce offspring with pink flowers (CRCW). (Note that different genotypic abbreviations are used for Mendelian extensions to distinguish these patterns from simple dominance and recessiveness.) This pattern of inheritance is described as incomplete dominance, meaning that one of the alleles appears in the phenotype in the heterozygote, but not to the exclusion of the other, which can also be seen. The allele for red flowers is incompletely dominant over the allele for white flowers. However, the results of a heterozygote self-cross can still be predicted, just as with Mendelian dominant and recessive crosses. In this case, the genotypic ratio would be 1 CRCR:2 CRCW:1 CWCW, and the phenotypic ratio would be 1:2:1 for red:pink:white. The basis for the intermediate color in the heterozygote is simply that the pigment produced by the red allele (anthocyanin) is diluted in the heterozygote and therefore appears pink because of the white background of the flower petals.

Photo is of a snapdragon with a pink flower.
Figure 7.13 These pink flowers of a heterozygote snapdragon result from incomplete dominance. (credit: “storebukkebruse”/Flickr)

Codominance

A variation on incomplete dominance is codominance, in which both alleles for the same characteristic are simultaneously expressed in the heterozygote. An example of codominance occurs in the ABO blood groups of humans. The A and B alleles are expressed in the form of A or B molecules present on the surface of red blood cells. Homozygotes (IAIA and IBIB) express either the A or the B phenotype, and heterozygotes (IAIB) express both phenotypes equally. The IAIB individual has blood type AB. In a self-cross between heterozygotes expressing a codominant trait, the three possible offspring genotypes are phenotypically distinct. However, the 1:2:1 genotypic ratio characteristic of a Mendelian monohybrid cross still applies (Figure 7.14).

A Punnett square showing both parents with AB blood types. The offspring will have AA, AB, and BB blood types in a ratio of 1 to 2 to 1.
Figure 7.14 This Punnett square shows an AB/AB blood type cross

Multiple Alleles

Mendel implied that only two alleles, one dominant and one recessive, could exist for a given gene. We now know that this is an oversimplification. Although individual humans (and all diploid organisms) can only have two alleles for a given gene, multiple alleles may exist at the population level, such that many combinations of two alleles are observed. Note that when many alleles exist for the same gene, the convention is to denote the most common phenotype or genotype in the natural population as the wild type (often abbreviated “+”). All other phenotypes or genotypes are considered variants (mutants) of this typical form, meaning they deviate from the wild type. The variant may be recessive or dominant to the wild-type allele.

An example of multiple alleles is the ABO blood-type system in humans. In this case, there are three alleles circulating in the population. The IA allele codes for A molecules on the red blood cells, the IB allele codes for B molecules on the surface of red blood cells, and the i allele codes for no molecules on the red blood cells. In this case, the IA and IB alleles are codominant with each other and are both dominant over the i allele. Although there are three alleles present in a population, each individual only gets two of the alleles from their parents. This produces the genotypes and phenotypes shown in Figure 7.15. Notice that instead of three genotypes, there are six different genotypes when there are three alleles. The number of possible phenotypes depends on the dominance relationships between the three alleles.

A Punnett square showing the possible genotype and phenotypes of the ABO blood types in humans.
Figure 7.15 Inheritance of the ABO blood system in humans is shown.

Multiple Alleles Confer Drug Resistance in the Malaria Parasite

Malaria is a parasitic disease in humans that is transmitted by infected female mosquitoes, including Anopheles gambiae, and is characterized by cyclic high fevers, chills, flu-like symptoms, and severe anemia. Plasmodium falciparum and P. vivax are the most common causative agents of malaria, and P. falciparum is the most deadly. When promptly and correctly treated, P. falciparum malaria has a mortality rate of 0.1 percent. However, in some parts of the world, the parasite has evolved resistance to commonly used malaria treatments, so the most effective malarial treatments can vary by geographic region.

In Southeast Asia, Africa, and South America, P. falciparum has developed resistance to the anti-malarial drugs chloroquine, mefloquine, and sulfadoxine-pyrimethamine. P. falciparum, which is haploid during the life stage in which it is infective to humans, has evolved multiple drug-resistant mutant alleles of the dhps gene. Varying degrees of sulfadoxine resistance are associated with each of these alleles. Being haploid, P. falciparum needs only one drug-resistant allele to express this trait.

In Southeast Asia, different sulfadoxine-resistant alleles of the dhps gene are localized to different geographic regions. This is a common evolutionary phenomenon that comes about because drug-resistant mutants arise in a population and interbreed with other P. falciparum isolates in close proximity. Sulfadoxine-resistant parasites cause considerable human hardship in regions in which this drug is widely used as an over-the-counter malaria remedy. As is common with pathogens that multiply to large numbers within an infection cycle, P. falciparum evolves relatively rapidly (over a decade or so) in response to the selective pressure of commonly used anti-malarial drugs. For this reason, scientists must constantly work to develop new drugs or drug combinations to combat the worldwide malaria burden.1

Sex-Linked Traits

In humans, as well as in many other animals and some plants, the sex of the individual is determined by sex chromosomes—one pair of non-homologous chromosomes. Until now, we have only considered inheritance patterns among non-sex chromosomes, or autosomes. In addition to 22 homologous pairs of autosomes, human females have a homologous pair of X chromosomes, whereas human males have an XY chromosome pair. Although the Y chromosome contains a small region of similarity to the X chromosome so that they can pair during meiosis, the Y chromosome is much shorter and contains fewer genes. When a gene being examined is present on the X, but not the Y, chromosome, it is X-linked.

Eye color in Drosophila, the common fruit fly, was the first X-linked trait to be identified. Thomas Hunt Morgan mapped this trait to the X chromosome in 1910. Like humans, Drosophila males have an XY chromosome pair, and females are XX. In flies the wild-type eye color is red (XW) and is dominant to white eye color (Xw) (Figure 7.16). Because of the location of the eye-color gene, reciprocal crosses do not produce the same offspring ratios. Males are said to be hemizygous, in that they have only one allele for any X-linked characteristic. Hemizygosity makes descriptions of dominance and recessiveness irrelevant for XY males. Drosophila males lack the white gene on the Y chromosome; that is, their genotype can only be XWY or XwY. In contrast, females have two allele copies of this gene and can be XWXW, XWXw, or XwXw.

Photo shows two fruit flies, one with red eyes and one with white eyes.
Figure 7.16 In Drosophila, the gene for eye color is located on the X chromosome. Red eye color is wild-type and is dominant to white eye color.

In an X-linked cross, the genotypes of F1 and F2 offspring depend on whether the recessive trait was expressed by the male or the female in the P generation. With respect to Drosophila eye color, when the P male expresses the white-eye phenotype and the female is homozygously red-eyed, all members of the F1 generation exhibit red eyes (Figure 7.17). The F1 females are heterozygous (XWXw), and the males are all XWY, having received their X chromosome from the homozygous dominant P female and their Y chromosome from the P male. A subsequent cross between the XWXw female and the XWY male would produce only red-eyed females (with XWXW or XWXw genotypes) and both red- and white-eyed males (with XWY or XwY genotypes). Now, consider a cross between a homozygous white-eyed female and a male with red eyes. The F1 generation would exhibit only heterozygous red-eyed females (XWXw) and only white-eyed males (XwY). Half of the F2 females would be red-eyed (XWXw) and half would be white-eyed (XwXw). Similarly, half of the F2 males would be red-eyed (XWY) and half would be white-eyed (XwY).

This illustration shows a Punnett square analysis of fruit fly eye color, which is a sex-linked trait. A red-eyed male fruit fly with the genotype X^{w}Y is crossed with a white-eyed female fruit fly with the genotype X^{w}X^{w}. All of the female offspring acquire a dominant X^{W} allele from the father and a recessive X^{w} allele from the mother, and are therefore heterozygous dominant with red eye color. All the male offspring acquire a recessive X^{w} allele from the mother and a Y chromosome from the father and are therefore hemizygous recessive with white eye color.
Figure 7.17 Crosses involving sex-linked traits often give rise to different phenotypes for the different sexes of offspring, as is the case for this cross involving red and white eye color in Drosophila. In the diagram, w is the white-eye mutant allele and W is the wild-type, red-eye allele.

What ratio of offspring would result from a cross between a white-eyed male and a female that is heterozygous for red eye color?

Half of the female offspring would be heterozygous (XWXw) with red eyes, and half would be homozygous recessive (XwXw) with white eyes. Half of the male offspring would be hemizygous dominant (XWY) with red eyes, and half would be hemizygous recessive (XwY) with white eyes.

Discoveries in fruit fly genetics can be applied to human genetics. When a female parent is homozygous for a recessive X-linked trait, she will pass the trait on to 100 percent of her male offspring, because the males will receive the Y chromosome from the male parent. In humans, the alleles for certain conditions (some color-blindness, hemophilia, and muscular dystrophy) are X-linked. Females who are heterozygous for these diseases are said to be carriers and may not exhibit any phenotypic effects. These females will pass the disease to half of their sons and will pass carrier status to half of their daughters; therefore, X-linked traits appear more frequently in males than females.

In some groups of organisms with sex chromosomes, the sex with the non-homologous sex chromosomes is the female rather than the male. This is the case for all birds. In this case, sex-linked traits will be more likely to appear in the female, in whom they are hemizygous.

Concept in Action


QR Code representing a URL

Watch this video to learn more about sex-linked traits.

Linked Genes Violate the Law of Independent Assortment

Although all of Mendel’s pea plant characteristics behaved according to the law of independent assortment, we now know that some allele combinations are not inherited independently of each other. Genes that are located on separate, non-homologous chromosomes will always sort independently. However, each chromosome contains hundreds or thousands of genes, organized linearly on chromosomes like beads on a string. The segregation of alleles into gametes can be influenced by linkage, in which genes that are located physically close to each other on the same chromosome are more likely to be inherited as a pair. However, because of the process of recombination, or “crossover,” it is possible for two genes on the same chromosome to behave independently, or as if they are not linked. To understand this, let us consider the biological basis of gene linkage and recombination.

Homologous chromosomes possess the same genes in the same order, though the specific alleles of the gene can be different on each of the two chromosomes. Recall that during interphase and prophase I of meiosis, homologous chromosomes first replicate and then synapse, with like genes on the homologs aligning with each other. At this stage, segments of homologous chromosomes exchange linear segments of genetic material (Figure 7.18). This process is called recombination, or crossover, and it is a common genetic process. Because the genes are aligned during recombination, the gene order is not altered. Instead, the result of recombination is that maternal and paternal alleles are combined onto the same chromosome. Across a given chromosome, several recombination events may occur, causing extensive shuffling of alleles.

This illustration shows a pair of homologous chromosomes. One of the pair has the alleles ABC and the other has the alleles abc. During meiosis, crossover occurs between two of the chromosomes and genetic material is exchanged, resulting in one recombinant chromosome that has the alleles ABc and another that has the alleles abC. The other two chromosomes are non-recombinant and have the same arrangement of genes as before meiosis.
Figure 7.18 The process of crossover, or recombination, occurs when two homologous chromosomes align and exchange a segment of genetic material.

When two genes are located on the same chromosome, they are considered linked, and their alleles tend to be transmitted through meiosis together. To exemplify this, imagine a dihybrid cross involving flower color and plant height in which the genes are next to each other on the chromosome. If one homologous chromosome has alleles for tall plants and red flowers, and the other chromosome has genes for short plants and yellow flowers, then when the gametes are formed, the tall and red alleles will tend to go together into a gamete and the short and yellow alleles will go into other gametes. These are called the parental genotypes because they have been inherited intact from the parents of the individual producing gametes. But unlike if the genes were on different chromosomes, there will be no gametes with tall and yellow alleles and no gametes with short and red alleles. If you create a Punnett square with these gametes, you will see that the classical Mendelian prediction of a 9:3:3:1 outcome of a dihybrid cross would not apply. As the distance between two genes increases, the probability of one or more crossovers between them increases and the genes behave more like they are on separate chromosomes. Geneticists have used the proportion of recombinant gametes (the ones not like the parents) as a measure of how far apart genes are on a chromosome. Using this information, they have constructed linkage maps of genes on chromosomes for well-studied organisms, including humans.

Mendel’s seminal publication makes no mention of linkage, and many researchers have questioned whether he encountered linkage but chose not to publish those crosses out of concern that they would invalidate his independent assortment postulate. The garden pea has seven chromosomes, and some have suggested that his choice of seven characteristics was not a coincidence. However, even if the genes he examined were not located on separate chromosomes, it is possible that he simply did not observe linkage because of the extensive shuffling effects of recombination.

Epistasis

Mendel’s studies in pea plants implied that the sum of an individual’s phenotype was controlled by genes (or as he called them, unit factors), such that every characteristic was distinctly and completely controlled by a single gene. In fact, single observable characteristics are almost always under the influence of multiple genes (each with two or more alleles) acting in unison. For example, at least eight genes contribute to eye color in humans.

Concept in Action


QR Code representing a URL

Eye color in humans is determined by multiple alleles. Use the Eye Color Calculator to predict the eye color of children from parental eye color.

In some cases, several genes can contribute to aspects of a common phenotype without their gene products ever directly interacting. In the case of organ development, for instance, genes may be expressed sequentially, with each gene adding to the complexity and specificity of the organ. Genes may function in complementary or synergistic fashions, such that two or more genes expressed simultaneously affect a phenotype. An apparent example of this occurs with human skin color, which appears to involve the action of at least three (and probably more) genes. Cases in which inheritance for a characteristic like skin color or human height depend on the combined effects of numerous genes are called polygenic inheritance.

Genes may also oppose each other, with one gene suppressing the expression of another. In epistasis, the interaction between genes is antagonistic, such that one gene masks or interferes with the expression of another. “Epistasis” is a word composed of Greek roots meaning “standing upon.” The alleles that are being masked or silenced are said to be hypostatic to the epistatic alleles that are doing the masking. Often the biochemical basis of epistasis is a gene pathway in which expression of one gene is dependent on the function of a gene that precedes or follows it in the pathway.

An example of epistasis is pigmentation in mice. The wild-type coat color, agouti (AA) is dominant to solid-colored fur (aa). However, a separate gene C, when present as the recessive homozygote (cc), negates any expression of pigment from the A gene and results in an albino mouse (Figure 7.19). Therefore, the genotypes AAcc, Aacc, and aacc all produce the same albino phenotype. A cross between heterozygotes for both genes (AaCc x AaCc) would generate offspring with a phenotypic ratio of 9 agouti:3 black:4 albino (Figure 7.19). In this case, the C gene is epistatic to the A gene.

A cross between two agouti mice with the heterozygous genotype AaCc is shown. Each mouse produces four different kinds of gametes (AC, aC, Ac, and ac). A 4 × 4 Punnett square is used to determine the genotypic ratio of the offspring. The phenotypic ratio is 9/16 agouti, 3/16 black, and 4/16 white.
Figure 7.19 In this example of epistasis, one gene (C) masks the expression of another (A) for coat color. When the C allele is present, coat color is expressed; when it is absent (cc), no coat color is expressed. Coat color depends on the A gene, which shows dominance, with the recessive homozygote showing a different phenotype than the heterozygote or dominant homozygote.

Section Summary

Alleles do not always behave in dominant and recessive patterns. Incomplete dominance describes situations in which the heterozygote exhibits a phenotype that is intermediate between the homozygous phenotypes. Codominance describes the simultaneous expression of both of the alleles in the heterozygote. Although diploid organisms can only have two alleles for any given gene, it is common for more than two alleles for a gene to exist in a population. In humans, as in many animals and some plants, females have two X chromosomes and males have one X and one Y chromosome. Genes that are present on the X but not the Y chromosome are said to be X-linked, such that males only inherit one allele for the gene, and females inherit two.

According to Mendel’s law of independent assortment, genes sort independently of each other into gametes during meiosis. This occurs because chromosomes, on which the genes reside, assort independently during meiosis and crossovers cause most genes on the same chromosomes to also behave independently. When genes are located in close proximity on the same chromosome, their alleles tend to be inherited together. This results in offspring ratios that violate Mendel’s law of independent assortment. However, recombination serves to exchange genetic material on homologous chromosomes such that maternal and paternal alleles may be recombined on the same chromosome. This is why alleles on a given chromosome are not always inherited together. Recombination is a random event occurring anywhere on a chromosome. Therefore, genes that are far apart on the same chromosome are likely to still assort independently because of recombination events that occurred in the intervening chromosomal space.

Whether or not they are sorting independently, genes may interact at the level of gene products, such that the expression of an allele for one gene masks or modifies the expression of an allele for a different gene. This is called epistasis.

Exercises

An interactive H5P element has been excluded from this version of the text. You can view it online here:
https://pressbooks.nscc.ca/conceptsofbiologynscc/?p=246#h5p-48

Glossary

codominance: in a heterozygote, complete and simultaneous expression of both alleles for the same characteristic

epistasis: an interaction between genes such that one gene masks or interferes with the expression of another

hemizygous: the presence of only one allele for a characteristic, as in X-linkage; hemizygosity makes descriptions of dominance and recessiveness irrelevant

incomplete dominance: in a heterozygote, expression of two contrasting alleles such that the individual displays an intermediate phenotype

linkage: a phenomenon in which alleles that are located in close proximity to each other on the same chromosome are more likely to be inherited together

recombination: the process during meiosis in which homologous chromosomes exchange linear segments of genetic material, thereby dramatically increasing genetic variation in the offspring and separating linked genes

wild type: the most commonly occurring genotype or phenotype for a given characteristic found in a population

X-linked: a gene present on the X chromosome, but not the Y chromosome

Footnotes

1 Sumiti Vinayak et al., “Origin and Evolution of Sulfadoxine Resistant Plasmodium falciparum,” PLoS Pathogens 6 (2010): e1000830.

Chapter 8 in Concepts of Biology: 1st Canadian Edition

VIII

Chapter 8: Introduction to Molecular Biology

Photo shows Dolly the sheep, which has been stuffed and placed in a glass case.
Figure 8.1 Dolly the sheep was the first cloned mammal. Photo shows Dolly the sheep, which has been stuffed and placed in a glass case.

The three letters “DNA” have now become associated with crime solving, paternity testing, human identification, and genetic testing. DNA can be retrieved from hair, blood, or saliva. With the exception of identical twins, each person’s DNA is unique and it is possible to detect differences between human beings on the basis of their unique DNA sequence.

DNA analysis has many practical applications beyond forensics and paternity testing. DNA testing is used for tracing genealogy and identifying pathogens. In the medical field, DNA is used in diagnostics, new vaccine development, and cancer therapy. It is now possible to determine predisposition to many diseases by analyzing genes.

DNA is the genetic material passed from parent to offspring for all life on Earth. The technology of molecular genetics developed in the last half century has enabled us to see deep into the history of life to deduce the relationships between living things in ways never thought possible. It also allows us to understand the workings of evolution in populations of organisms. Over a thousand species have had their entire genome sequenced, and there have been thousands of individual human genome sequences completed. These sequences will allow us to understand human disease and the relationship of humans to the rest of the tree of life. Finally, molecular genetics techniques have revolutionized plant and animal breeding for human agricultural needs. All of these advances in biotechnology depended on basic research leading to the discovery of the structure of DNA in 1953, and the research since then that has uncovered the details of DNA replication and the complex process leading to the expression of DNA in the form of proteins in the cell.

Search for Key Points in Chapter 9

An interactive H5P element has been excluded from this version of the text. You can view it online here:
https://pressbooks.nscc.ca/conceptsofbiologynscc/?p=251#h5p-49

Chapter 9 in Concepts of Biology: 1st Canadian Edition

27

8.1 The Structure of DNA

Charles Molnar and Jane Gair

Learning Objectives

By the end of this section, you will be able to:

  • Describe the structure of DNA
  • Describe how eukaryotic and prokaryotic DNA is arranged in the cell

In the 1950s, Francis Crick and James Watson worked together at the University of Cambridge, England, to determine the structure of DNA. Other scientists, such as Linus Pauling and Maurice Wilkins, were also actively exploring this field. Pauling had discovered the secondary structure of proteins using X-ray crystallography. X-ray crystallography is a method for investigating molecular structure by observing the patterns formed by X-rays shot through a crystal of the substance. The patterns give important information about the structure of the molecule of interest. In Wilkins’ lab, researcher Rosalind Franklin was using X-ray crystallography to understand the structure of DNA. Watson and Crick were able to piece together the puzzle of the DNA molecule using Franklin’s data (Figure 8.2). Watson and Crick also had key pieces of information available from other researchers such as Chargaff’s rules. Chargaff had shown that of the four kinds of monomers (nucleotides) present in a DNA molecule, two types were always present in equal amounts and the remaining two types were also always present in equal amounts. This meant they were always paired in some way. In 1962, James Watson, Francis Crick, and Maurice Wilkins were awarded the Nobel Prize in Medicine for their work in determining the structure of DNA.

Photo in part A shows James Watson, Francis Crick, and Maclyn McCarty. The x-ray diffraction pattern in part b is symmetrical, with dots in an x-shape.
Figure 8.2 Pioneering scientists (a) James Watson and Francis Crick are pictured here with American geneticist Maclyn McCarty. Scientist Rosalind Franklin discovered (b) the X-ray diffraction pattern of DNA, which helped to elucidate its double helix structure. (credit a: modification of work by Marjorie McCarty; b: modification of work by NIH)

Now let’s consider the structure of the two types of nucleic acids, deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). The building blocks of DNA are nucleotides, which are made up of three parts: a deoxyribose (5-carbon sugar), a phosphate group, and a nitrogenous base (Figure 8.3). There are four types of nitrogenous bases in DNA. Adenine (A) and guanine (G) are double-ringed purines, and cytosine (C) and thymine (T) are smaller, single-ringed pyrimidines. The nucleotide is named according to the nitrogenous base it contains.

(a) Each DNA nucleotide is made up of a sugar, a phosphate group, and a base.
Figure 8.3 (a) Each DNA nucleotide is made up of a sugar, a phosphate group, and a base.
(b) Cytosine and thymine are pyrimidines. Guanine and adenine are purines.
Figure 8.3 (b) Cytosine and thymine are pyrimidines. Guanine and adenine are purines.

The phosphate group of one nucleotide bonds covalently with the sugar molecule of the next nucleotide, and so on, forming a long polymer of nucleotide monomers. The sugar–phosphate groups line up in a “backbone” for each single strand of DNA, and the nucleotide bases stick out from this backbone. The carbon atoms of the five-carbon sugar are numbered clockwise from the oxygen as 1′, 2′, 3′, 4′, and 5′ (1′ is read as “one prime”). The phosphate group is attached to the 5′ carbon of one nucleotide and the 3′ carbon of the next nucleotide. In its natural state, each DNA molecule is actually composed of two single strands held together along their length with hydrogen bonds between the bases.

Watson and Crick proposed that the DNA is made up of two strands that are twisted around each other to form a right-handed helix, called a double helix. Base-pairing takes place between a purine and pyrimidine: namely, A pairs with T, and G pairs with C. In other words, adenine and thymine are complementary base pairs, and cytosine and guanine are also complementary base pairs. This is the basis for Chargaff’s rule; because of their complementarity, there is as much adenine as thymine in a DNA molecule and as much guanine as cytosine. Adenine and thymine are connected by two hydrogen bonds, and cytosine and guanine are connected by three hydrogen bonds. The two strands are anti-parallel in nature; that is, one strand will have the 3′ carbon of the sugar in the “upward” position, whereas the other strand will have the 5′ carbon in the upward position. The diameter of the DNA double helix is uniform throughout because a purine (two rings) always pairs with a pyrimidine (one ring) and their combined lengths are always equal. (Figure 8.4).

Part A shows an illustration of a DNA double helix, which has a sugar phosphate backbone on the outside and nitrogenous base pairs on the inside. Part B shows base-pairing between thymine and adenine, which form two hydrogen bonds, and between guanine and cytosine, which form three hydrogen bonds.
Figure 8.4 DNA (a) forms a double stranded helix, and (b) adenine pairs with thymine and cytosine pairs with guanine. (credit a: modification of work by Jerome Walker, Dennis Myts)

The Structure of RNA

There is a second nucleic acid in all cells called ribonucleic acid, or RNA. Like DNA, RNA is a polymer of nucleotides. Each of the nucleotides in RNA is made up of a nitrogenous base, a five-carbon sugar, and a phosphate group. In the case of RNA, the five-carbon sugar is ribose, not deoxyribose. Ribose has a hydroxyl group at the 2′ carbon, unlike deoxyribose, which has only a hydrogen atom (Figure 8.5).

 
A figure showing the structure of ribose and deoxyribose sugars. In ribose, the OH at the 2' position is highlighted in red. In deoxyribose, the H at the 2' position is highlighted in red.
Figure 8.5 The difference between the ribose found in RNA and the deoxyribose found in DNA is that ribose has a hydroxyl group at the 2′ carbon.

RNA nucleotides contain the nitrogenous bases adenine, cytosine, and guanine. However, they do not contain thymine, which is instead replaced by uracil, symbolized by a “U.” RNA exists as a single-stranded molecule rather than a double-stranded helix. Molecular biologists have named several kinds of RNA on the basis of their function. These include messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA)—molecules that are involved in the production of proteins from the DNA code.

How DNA Is Arranged in the Cell

DNA is a working molecule; it must be replicated when a cell is ready to divide, and it must be “read” to produce the molecules, such as proteins, to carry out the functions of the cell. For this reason, the DNA is protected and packaged in very specific ways. In addition, DNA molecules can be very long. Stretched end-to-end, the DNA molecules in a single human cell would come to a length of about 2 meters. Thus, the DNA for a cell must be packaged in a very ordered way to fit and function within a structure (the cell) that is not visible to the naked eye. The chromosomes of prokaryotes are much simpler than those of eukaryotes in many of their features (Figure 8.6). Most prokaryotes contain a single, circular chromosome that is found in an area in the cytoplasm called the nucleoid.

 
Illustration shows a eukaryotic cell, which has a membrane-bound nucleus containing chromatin and a nucleolus, and a prokaryotic cell, which has DNA contained in an area of the cytoplasm called the nucleoid. The prokaryotic cell is much smaller than the eukaryotic cell.
Figure 8.6 A eukaryote contains a well-defined nucleus, whereas in prokaryotes, the chromosome lies in the cytoplasm in an area called the nucleoid.

The size of the genome in one of the most well-studied prokaryotes, Escherichia coli, is 4.6 million base pairs, which would extend a distance of about 1.6 mm if stretched out. So how does this fit inside a small bacterial cell? The DNA is twisted beyond the double helix in what is known as supercoiling. Some proteins are known to be involved in the supercoiling; other proteins and enzymes help in maintaining the supercoiled structure.

Eukaryotes, whose chromosomes each consist of a linear DNA molecule, employ a different type of packing strategy to fit their DNA inside the nucleus. At the most basic level, DNA is wrapped around proteins known as histones to form structures called nucleosomes. The DNA is wrapped tightly around the histone core. This nucleosome is linked to the next one by a short strand of DNA that is free of histones. This is also known as the “beads on a string” structure; the nucleosomes are the “beads” and the short lengths of DNA between them are the “string.” The nucleosomes, with their DNA coiled around them, stack compactly onto each other to form a 30-nm–wide fiber. This fiber is further coiled into a thicker and more compact structure. At the metaphase stage of mitosis, when the chromosomes are lined up in the center of the cell, the chromosomes are at their most compacted. They are approximately 700 nm in width, and are found in association with scaffold proteins.

In interphase, the phase of the cell cycle between mitoses at which the chromosomes are decondensed, eukaryotic chromosomes have two distinct regions that can be distinguished by staining. There is a tightly packaged region that stains darkly, and a less dense region. The darkly staining regions usually contain genes that are not active, and are found in the regions of the centromere and telomeres. The lightly staining regions usually contain genes that are active, with DNA packaged around nucleosomes but not further compacted.

 
Illustration shows levels of organization of eukaryotic chromosomes, starting with the DNA double helix, which wraps around histone proteins. The entire DNA molecule wraps around many clusters of histone proteins, forming a structure that looks like beads on a string. The chromatin is further condensed by wrapping around a protein core. The result is a compact chromosome, shown in duplicated form.
Figure 8.7 These figures illustrate the compaction of the eukaryotic chromosome.

 

Concept in Action


QR Code representing a URL

Watch this animation of DNA packaging.

Section Summary

An interactive H5P element has been excluded from this version of the text. You can view it online here:
https://pressbooks.nscc.ca/conceptsofbiologynscc/?p=261#h5p-50

The model of the double-helix structure of DNA was proposed by Watson and Crick. The DNA molecule is a polymer of nucleotides. Each nucleotide is composed of a nitrogenous base, a five-carbon sugar (deoxyribose), and a phosphate group. There are four nitrogenous bases in DNA, two purines (adenine and guanine) and two pyrimidines (cytosine and thymine). A DNA molecule is composed of two strands. Each strand is composed of nucleotides bonded together covalently between the phosphate group of one and the deoxyribose sugar of the next. From this backbone extend the bases. The bases of one strand bond to the bases of the second strand with hydrogen bonds. Adenine always bonds with thymine, and cytosine always bonds with guanine. The bonding causes the two strands to spiral around each other in a shape called a double helix. Ribonucleic acid (RNA) is a second nucleic acid found in cells. RNA is a single-stranded polymer of nucleotides. It also differs from DNA in that it contains the sugar ribose, rather than deoxyribose, and the nucleotide uracil rather than thymine. Various RNA molecules function in the process of forming proteins from the genetic code in DNA.

Prokaryotes contain a single, double-stranded circular chromosome. Eukaryotes contain double-stranded linear DNA molecules packaged into chromosomes. The DNA helix is wrapped around proteins to form nucleosomes. The protein coils are further coiled, and during mitosis and meiosis, the chromosomes become even more greatly coiled to facilitate their movement. Chromosomes have two distinct regions which can be distinguished by staining, reflecting different degrees of packaging and determined by whether the DNA in a region is being expressed (euchromatin) or not (heterochromatin).

Exercises

An interactive H5P element has been excluded from this version of the text. You can view it online here:
https://pressbooks.nscc.ca/conceptsofbiologynscc/?p=261#h5p-51

Glossary

deoxyribose: a five-carbon sugar molecule with a hydrogen atom rather than a hydroxyl group in the 2′ position; the sugar component of DNA nucleotides

double helix: the molecular shape of DNA in which two strands of nucleotides wind around each other in a spiral shape

nitrogenous base: a nitrogen-containing molecule that acts as a base; often referring to one of the purine or pyrimidine components of nucleic acids

phosphate group: a molecular group consisting of a central phosphorus atom bound to four oxygen atoms

Chapter 9 in Concepts of Biology: 1st Canadian Edition

28

8.2 DNA Replication

Charles Molnar and Jane Gair

Learning Objectives

By the end of this section, you will be able to:

  • Explain the process of DNA replication
  • Explain the importance of telomerase to DNA replication
  • Describe mechanisms of DNA repair

When a cell divides, it is important that each daughter cell receives an identical copy of the DNA. This is accomplished by the process of DNA replication. The replication of DNA occurs during the synthesis phase, or S phase, of the cell cycle, before the cell enters mitosis or meiosis.

The elucidation of the structure of the double helix provided a hint as to how DNA is copied. Recall that adenine nucleotides pair with thymine nucleotides, and cytosine with guanine. This means that the two strands are complementary to each other. For example, a strand of DNA with a nucleotide sequence of AGTCATGA will have a complementary strand with the sequence TCAGTACT (Figure 8.8).

Figure shows the ladder-like structure of DNA, with complementary bases making up the rungs of the ladder.
Figure 8.8 The two strands of DNA are complementary, meaning the sequence of bases in one strand can be used to create the correct sequence of bases in the other strand.

Because of the complementarity of the two strands, having one strand means that it is possible to recreate the other strand. This model for replication suggests that the two strands of the double helix separate during replication, and each strand serves as a template from which the new complementary strand is copied (Figure 8.9).

Illustration shows the semiconservative model of DNA synthesis. In the semi-conservative model, each newly synthesized strand pairs with a parent strand.
Figure 8.9 The semiconservative model of DNA replication is shown. Gray indicates the original DNA strands, and blue indicates newly synthesized DNA.

During DNA replication, each of the two strands that make up the double helix serves as a template from which new strands are copied. The new strand will be complementary to the parental or “old” strand. Each new double strand consists of one parental strand and one new daughter strand. This is known as semiconservative replication. When two DNA copies are formed, they have an identical sequence of nucleotide bases and are divided equally into two daughter cells.

DNA Replication in Eukaryotes

Because eukaryotic genomes are very complex, DNA replication is a very complicated process that involves several enzymes and other proteins. It occurs in three main stages: initiation, elongation, and termination.

Recall that eukaryotic DNA is bound to proteins known as histones to form structures called nucleosomes. During initiation, the DNA is made accessible to the proteins and enzymes involved in the replication process. How does the replication machinery know where on the DNA double helix to begin? It turns out that there are specific nucleotide sequences called origins of replication at which replication begins. Certain proteins bind to the origin of replication while an enzyme called helicase unwinds and opens up the DNA helix. As the DNA opens up, Y-shaped structures called replication forks are formed (Figure 8.10). Two replication forks are formed at the origin of replication, and these get extended in both directions as replication proceeds. There are multiple origins of replication on the eukaryotic chromosome, such that replication can occur simultaneously from several places in the genome.

During elongation, an enzyme called DNA polymerase adds DNA nucleotides to the 3′ end of the template. Because DNA polymerase can only add new nucleotides at the end of a backbone, a primer sequence, which provides this starting point, is added with complementary RNA nucleotides. This primer is removed later, and the nucleotides are replaced with DNA nucleotides. One strand, which is complementary to the parental DNA strand, is synthesized continuously toward the replication fork so the polymerase can add nucleotides in this direction. This continuously synthesized strand is known as the leading strand. Because DNA polymerase can only synthesize DNA in a 5′ to 3′ direction, the other new strand is put together in short pieces called Okazaki fragments. The Okazaki fragments each require a primer made of RNA to start the synthesis. The strand with the Okazaki fragments is known as the lagging strand. As synthesis proceeds, an enzyme removes the RNA primer, which is then replaced with DNA nucleotides, and the gaps between fragments are sealed by an enzyme called DNA ligase.

The process of DNA replication can be summarized as follows:

  1. DNA unwinds at the origin of replication.
  2. New bases are added to the complementary parental strands. One new strand is made continuously, while the other strand is made in pieces.
  3. Primers are removed, new DNA nucleotides are put in place of the primers and the backbone is sealed by DNA ligase.
Illustration shows a replication bubble. Helicase unwinds the helix. An RNA primer starts the synthesis, and DNA polymerase extends the DNA strand from the RNA primer. DNA synthesis occurs only in the 5' to 3' direction. On the leading strand, DNA synthesis occurs continuously. On the lagging strand, DNA synthesis restarts many times as the helix unwinds, resulting in many short fragments called Okazaki fragments.
Figure 8.10 A replication fork is formed by the opening of the origin of replication, and helicase separates the DNA strands. An RNA primer is synthesized, and is elongated by the DNA polymerase. On the leading strand, DNA is synthesized continuously, whereas on the lagging strand, DNA is synthesized in short stretches. The DNA fragments are joined by DNA ligase (not shown).

You isolate a cell strain in which the joining together of Okazaki fragments is impaired and suspect that a mutation has occurred in an enzyme found at the replication fork. Which enzyme is most likely to be mutated?

Telomere Replication

Because eukaryotic chromosomes are linear, DNA replication comes to the end of a line in eukaryotic chromosomes. As you have learned, the DNA polymerase enzyme can add nucleotides in only one direction. In the leading strand, synthesis continues until the end of the chromosome is reached; however, on the lagging strand there is no place for a primer to be made for the DNA fragment to be copied at the end of the chromosome. This presents a problem for the cell because the ends remain unpaired, and over time these ends get progressively shorter as cells continue to divide. The ends of the linear chromosomes are known as telomeres, which have repetitive sequences that do not code for a particular gene. As a consequence, it is telomeres that are shortened with each round of DNA replication instead of genes. For example, in humans, a six base-pair sequence, TTAGGG, is repeated 100 to 1000 times. The discovery of the enzyme telomerase (Figure 8.11) helped in the understanding of how chromosome ends are maintained. The telomerase attaches to the end of the chromosome, and complementary bases to the RNA template are added on the end of the DNA strand. Once the lagging strand template is sufficiently elongated, DNA polymerase can now add nucleotides that are complementary to the ends of the chromosomes. Thus, the ends of the chromosomes are replicated.

 
Telomerase has an associated RNA that complements the 5' overhang at the end of the chromosome. The RNA template is used to synthesize the complementary strand. Telomerase then shifts, and the process is repeated. Next, primase and DNA polymerase synthesize the rest of the complementary strand.
Figure 8.11 The ends of linear chromosomes are maintained by the action of the telomerase enzyme.

Telomerase is typically found to be active in germ cells, adult stem cells, and some cancer cells. For her discovery of telomerase and its action, Elizabeth Blackburn (Figure 8.12) received the Nobel Prize for Medicine and Physiology in 2009.

Photo shows Elizabeth Blackburn.
Figure 8.12 Elizabeth Blackburn, 2009 Nobel Laureate, was the scientist who discovered how telomerase works. (credit: U.S. Embassy, Stockholm, Sweden)

Telomerase is not active in adult somatic cells. Adult somatic cells that undergo cell division continue to have their telomeres shortened. This essentially means that telomere shortening is associated with aging. In 2010, scientists found that telomerase can reverse some age-related conditions in mice, and this may have potential in regenerative medicine.1 Telomerase-deficient mice were used in these studies; these mice have tissue atrophy, stem-cell depletion, organ system failure, and impaired tissue injury responses. Telomerase reactivation in these mice caused extension of telomeres, reduced DNA damage, reversed neurodegeneration, and improved functioning of the testes, spleen, and intestines. Thus, telomere reactivation may have potential for treating age-related diseases in humans.

DNA Replication in Prokaryotes

Recall that the prokaryotic chromosome is a circular molecule with a less extensive coiling structure than eukaryotic chromosomes. The eukaryotic chromosome is linear and highly coiled around proteins. While there are many similarities in the DNA replication process, these structural differences necessitate some differences in the DNA replication process in these two life forms.

DNA replication has been extremely well-studied in prokaryotes, primarily because of the small size of the genome and large number of variants available. Escherichia coli has 4.6 million base pairs in a single circular chromosome, and all of it gets replicated in approximately 42 minutes, starting from a single origin of replication and proceeding around the chromosome in both directions. This means that approximately 1000 nucleotides are added per second. The process is much more rapid than in eukaryotes. The table below summarizes the differences between prokaryotic and eukaryotic replications.

Differences between Prokaryotic and Eukaryotic Replications
Property Prokaryotes Eukaryotes
Origin of replication Single Multiple
Rate of replication 1000 nucleotides/s 50 to 100 nucleotides/s
Chromosome structure circular linear
Telomerase Not present Present

Concept in Action


QR Code representing a URL

Click through a tutorial on DNA replication.

DNA Repair

DNA polymerase can make mistakes while adding nucleotides. It edits the DNA by proofreading every newly added base. Incorrect bases are removed and replaced by the correct base, and then polymerization continues (Figure 8.13 a). Most mistakes are corrected during replication, although when this does not happen, the mismatch repair mechanism is employed. Mismatch repair enzymes recognize the wrongly incorporated base and excise it from the DNA, replacing it with the correct base (Figure 8.13 b). In yet another type of repair, nucleotide excision repair, the DNA double strand is unwound and separated, the incorrect bases are removed along with a few bases on the 5′ and 3′ end, and these are replaced by copying the template with the help of DNA polymerase (Figure 8.13 c). Nucleotide excision repair is particularly important in correcting thymine dimers, which are primarily caused by ultraviolet light. In a thymine dimer, two thymine nucleotides adjacent to each other on one strand are covalently bonded to each other rather than their complementary bases. If the dimer is not removed and repaired it will lead to a mutation. Individuals with flaws in their nucleotide excision repair genes show extreme sensitivity to sunlight and develop skin cancers early in life.

Part a shows DNA polymerase replicating a strand of DNA. The enzyme has accidentally inserted G opposite A, resulting in a bulge. The enzyme backs up to fix the error. In part b, the top illustration shows a replicated DNA strand with a G–T base mismatch. The bottom illustration shows the repaired DNA, which has the correct G–C base pairing. Part c shows a DNA strand in which a thymine dimer has formed. An excision repair enzyme cuts out the section of DNA that contains the dimer so that it can be replaced with a normal base pair.
Figure 8.13 Proofreading by DNA polymerase (a) corrects errors during replication. In mismatch repair (b), the incorrectly added base is detected after replication. The mismatch repair proteins detect this base and remove it from the newly synthesized strand by nuclease action. The gap is now filled with the correctly paired base. Nucleotide excision (c) repairs thymine dimers. When exposed to UV, thymines lying adjacent to each other can form thymine dimers. In normal cells, they are excised and replaced.

Most mistakes are corrected; if they are not, they may result in a mutation—defined as a permanent change in the DNA sequence. Mutations in repair genes may lead to serious consequences like cancer.

Section Summary

DNA replicates by a semi-conservative method in which each of the two parental DNA strands act as a template for new DNA to be synthesized. After replication, each DNA has one parental or “old” strand, and one daughter or “new” strand.

Replication in eukaryotes starts at multiple origins of replication, while replication in prokaryotes starts from a single origin of replication. The DNA is opened with enzymes, resulting in the formation of the replication fork. Primase synthesizes an RNA primer to initiate synthesis by DNA polymerase, which can add nucleotides in only one direction. One strand is synthesized continuously in the direction of the replication fork; this is called the leading strand. The other strand is synthesized in a direction away from the replication fork, in short stretches of DNA known as Okazaki fragments. This strand is known as the lagging strand. Once replication is completed, the RNA primers are replaced by DNA nucleotides and the DNA is sealed with DNA ligase.

The ends of eukaryotic chromosomes pose a problem, as polymerase is unable to extend them without a primer. Telomerase, an enzyme with an inbuilt RNA template, extends the ends by copying the RNA template and extending one end of the chromosome. DNA polymerase can then extend the DNA using the primer. In this way, the ends of the chromosomes are protected. Cells have mechanisms for repairing DNA when it becomes damaged or errors are made in replication. These mechanisms include mismatch repair to replace nucleotides that are paired with a non-complementary base and nucleotide excision repair, which removes bases that are damaged such as thymine dimers.

Exercises

An interactive H5P element has been excluded from this version of the text. You can view it online here:
https://pressbooks.nscc.ca/conceptsofbiologynscc/?p=270#h5p-52

Glossary

DNA ligase: the enzyme that catalyzes the joining of DNA fragments together

DNA polymerase: an enzyme that synthesizes a new strand of DNA complementary to a template strand

helicase: an enzyme that helps to open up the DNA helix during DNA replication by breaking the hydrogen bonds

lagging strand: during replication of the 3′ to 5′ strand, the strand that is replicated in short fragments and away from the replication fork

leading strand: the strand that is synthesized continuously in the 5′ to 3′ direction that is synthesized in the direction of the replication fork

mismatch repair: a form of DNA repair in which non-complementary nucleotides are recognized, excised, and replaced with correct nucleotides

mutation: a permanent variation in the nucleotide sequence of a genome

nucleotide excision repair: a form of DNA repair in which the DNA molecule is unwound and separated in the region of the nucleotide damage, the damaged nucleotides are removed and replaced with new nucleotides using the complementary strand, and the DNA strand is resealed and allowed to rejoin its complement

Okazaki fragments: the DNA fragments that are synthesized in short stretches on the lagging strand
primer: a short stretch of RNA nucleotides that is required to initiate replication and allow DNA polymerase to bind and begin replication

replication fork: the Y-shaped structure formed during the initiation of replication

semiconservative replication: the method used to replicate DNA in which the double-stranded molecule is separated and each strand acts as a template for a new strand to be synthesized, so the resulting DNA molecules are composed of one new strand of nucleotides and one old strand of nucleotides

telomerase: an enzyme that contains a catalytic part and an inbuilt RNA template; it functions to maintain telomeres at chromosome ends

telomere: the DNA at the end of linear chromosomes

Footnotes

1 Mariella Jaskelioff, et al., “Telomerase reactivation reverses tissue degeneration in aged telomerase-deficient mice,” Nature, 469 (2011):102–7.

Chapter 9 in Concepts of Biology: 1st Canadian Edition

29

8.3 Transcription

Charles Molnar and Jane Gair

Learning Objectives

By the end of this section, you will be able to:

  • Explain the central dogma
  • Explain the main steps of transcription
  • Describe how eukaryotic mRNA is processed

In both prokaryotes and eukaryotes, the second function of DNA (the first was replication) is to provide the information needed to construct the proteins necessary so that the cell can perform all of its functions. To do this, the DNA is “read” or transcribed into an mRNA molecule. The mRNA then provides the code to form a protein by a process called translation. Through the processes of transcription and translation, a protein is built with a specific sequence of amino acids that was originally encoded in the DNA. This module discusses the details of transcription.

The Central Dogma: DNA Encodes RNA; RNA Encodes Protein

The flow of genetic information in cells from DNA to mRNA to protein is described by the central dogma (Figure 8.14), which states that genes specify the sequences of mRNAs, which in turn specify the sequences of proteins.

A flow chart shows DNA, with an arrow to RNA, which has an arrow to protein.
Figure 8.14 The central dogma states that DNA encodes RNA, which in turn encodes protein.

 

The copying of DNA to mRNA is relatively straightforward, with one nucleotide being added to the mRNA strand for every complementary nucleotide read in the DNA strand. The translation to protein is more complex because groups of three mRNA nucleotides correspond to one amino acid of the protein sequence. However, as we shall see in the next module, the translation to protein is still systematic, such that nucleotides 1 to 3 correspond to amino acid 1, nucleotides 4 to 6 correspond to amino acid 2, and so on.

Transcription: from DNA to mRNA

Both prokaryotes and eukaryotes perform fundamentally the same process of transcription, with the important difference of the membrane-bound nucleus in eukaryotes. With the genes bound in the nucleus, transcription occurs in the nucleus of the cell and the mRNA transcript must be transported to the cytoplasm. The prokaryotes, which include bacteria and archaea, lack membrane-bound nuclei and other organelles, and transcription occurs in the cytoplasm of the cell. In both prokaryotes and eukaryotes, transcription occurs in three main stages: initiation, elongation, and termination.

Initiation

Transcription requires the DNA double helix to partially unwind in the region of mRNA synthesis. The region of unwinding is called a transcription bubble. The DNA sequence onto which the proteins and enzymes involved in transcription bind to initiate the process is called a promoter. In most cases, promoters exist upstream of the genes they regulate. The specific sequence of a promoter is very important because it determines whether the corresponding gene is transcribed all of the time, some of the time, or hardly at all (Figure 8.15).

 
Illustration shows a template strand and nontemplate strand of DNA, with a promoter section in red on the template strand. Downstream of the promoter is an RNA polymerase where RNA is being synthesized.
Figure 8.15 The initiation of transcription begins when DNA is unwound, forming a transcription bubble. Enzymes and other proteins involved in transcription bind at the promoter.

Elongation

Transcription always proceeds from one of the two DNA strands, which is called the template strand. The mRNA product is complementary to the template strand and is almost identical to the other DNA strand, called the nontemplate strand, with the exception that RNA contains a uracil (U) in place of the thymine (T) found in DNA. During elongation, an enzyme called RNA polymerase proceeds along the DNA template adding nucleotides by base pairing with the DNA template in a manner similar to DNA replication, with the difference that an RNA strand is being synthesized that does not remain bound to the DNA template. As elongation proceeds, the DNA is continuously unwound ahead of the core enzyme and rewound behind it (Figure 8.16).

 
Illustration shows RNA synthesis by RNA polymerase. The RNA strand is synthesized in the 5' to 3' direction.
Figure 8.16 During elongation, RNA polymerase tracks along the DNA template, synthesizes mRNA in the 5′ to 3′ direction, and unwinds then rewinds the DNA as it is read.

 

Termination

Once a gene is transcribed, the prokaryotic polymerase needs to be instructed to dissociate from the DNA template and liberate the newly made mRNA. Depending on the gene being transcribed, there are two kinds of termination signals, but both involve repeated nucleotide sequences in the DNA template that result in RNA polymerase stalling, leaving the DNA template, and freeing the mRNA transcript.

On termination, the process of transcription is complete. In a prokaryotic cell, by the time termination occurs, the transcript would already have been used to partially synthesize numerous copies of the encoded protein because these processes can occur concurrently using multiple ribosomes (polyribosomes) (Figure 8.17). In contrast, the presence of a nucleus in eukaryotic cells precludes simultaneous transcription and translation.

Illustration shows multiple mRNAs being transcribed off one gene. Ribosomes attach to the mRNA before transcription is done and begin making protein.
Figure 8.17 Multiple polymerases can transcribe a single bacterial gene while numerous ribosomes concurrently translate the mRNA transcripts into polypeptides. In this way, a specific protein can rapidly reach a high concentration in the bacterial cell.

Eukaryotic RNA Processing

The newly transcribed eukaryotic mRNAs must undergo several processing steps before they can be transferred from the nucleus to the cytoplasm and translated into a protein. The additional steps involved in eukaryotic mRNA maturation create a molecule that is much more stable than a prokaryotic mRNA. For example, eukaryotic mRNAs last for several hours, whereas the typical prokaryotic mRNA lasts no more than five seconds.

The mRNA transcript is first coated in RNA-stabilizing proteins to prevent it from degrading while it is processed and exported out of the nucleus. This occurs while the pre-mRNA still is being synthesized by adding a special nucleotide “cap” to the 5′ end of the growing transcript. In addition to preventing degradation, factors involved in protein synthesis recognize the cap to help initiate translation by ribosomes.

Once elongation is complete, an enzyme then adds a string of approximately 200 adenine residues to the 3′ end, called the poly-A tail. This modification further protects the pre-mRNA from degradation and signals to cellular factors that the transcript needs to be exported to the cytoplasm.

Eukaryotic genes are composed of protein-coding sequences called exons (ex-on signifies that they are expressed) and intervening sequences called introns (int-ron denotes their intervening role). Introns are removed from the pre-mRNA during processing. Intron sequences in mRNA do not encode functional proteins. It is essential that all of a pre-mRNA’s introns be completely and precisely removed before protein synthesis so that the exons join together to code for the correct amino acids. If the process errs by even a single nucleotide, the sequence of the rejoined exons would be shifted, and the resulting protein would be nonfunctional. The process of removing introns and reconnecting exons is called splicing (Figure 8.18). Introns are removed and degraded while the pre-mRNA is still in the nucleus.

 
Illustration shows a primary RNA transcript with three exons and two introns. In the spliced transcript, the introns are removed and the exons are fused together. A 5' cap and poly-A tail have also been added.
Figure 8.18 Eukaryotic mRNA contains introns that must be spliced out. A 5′ cap and 3′ tail are also added.

Section Summary

In prokaryotes, mRNA synthesis is initiated at a promoter sequence on the DNA template. Elongation synthesizes new mRNA. Termination liberates the mRNA and occurs by mechanisms that stall the RNA polymerase and cause it to fall off the DNA template. Newly transcribed eukaryotic mRNAs are modified with a cap and a poly-A tail. These structures protect the mature mRNA from degradation and help export it from the nucleus. Eukaryotic mRNAs also undergo splicing, in which introns are removed and exons are reconnected with single-nucleotide accuracy. Only finished mRNAs are exported from the nucleus to the cytoplasm.

Exercises

An interactive H5P element has been excluded from this version of the text. You can view it online here:
https://pressbooks.nscc.ca/conceptsofbiologynscc/?p=277#h5p-53

Glossary

exon: a sequence present in protein-coding mRNA after completion of pre-mRNA splicing

intron: non–protein-coding intervening sequences that are spliced from mRNA during processing

mRNA: messenger RNA; a form of RNA that carries the nucleotide sequence code for a protein sequence that is translated into a polypeptide sequence

nontemplate strand: the strand of DNA that is not used to transcribe mRNA; this strand is identical to the mRNA except that T nucleotides in the DNA are replaced by U nucleotides in the mRNA

promoter: a sequence on DNA to which RNA polymerase and associated factors bind and initiate transcription

RNA polymerase: an enzyme that synthesizes an RNA strand from a DNA template strand

splicing: the process of removing introns and reconnecting exons in a pre-mRNA

template strand: the strand of DNA that specifies the complementary mRNA molecule

transcription bubble: the region of locally unwound DNA that allows for transcription of mRNA

Chapter 9 in Concepts of Biology: 1st Canadian Edition

30

8.4 Translation

Charles Molnar and Jane Gair

Learning Objectives

By the end of this section, you will be able to:

  • Describe the different steps in protein synthesis
  • Discuss the role of ribosomes in protein synthesis
  • Describe the genetic code and how the nucleotide sequence determines the amino acid and the protein sequence

The synthesis of proteins is one of a cell’s most energy-consuming metabolic processes. In turn, proteins account for more mass than any other component of living organisms (with the exception of water), and proteins perform a wide variety of the functions of a cell. The process of translation, or protein synthesis, involves decoding an mRNA message into a polypeptide product. Amino acids are covalently strung together in lengths ranging from approximately 50 amino acids to more than 1,000.

The Protein Synthesis Machinery

In addition to the mRNA template, many other molecules contribute to the process of translation. The composition of each component may vary across species; for instance, ribosomes may consist of different numbers of ribosomal RNAs (rRNA) and polypeptides depending on the organism. However, the general structures and functions of the protein synthesis machinery are comparable from bacteria to human cells. Translation requires the input of an mRNA template, ribosomes, tRNAs, and various enzymatic factors (Figure 8.19).

Illustration of the molecules involved in protein translation. A ribosome is shown with mRNA and tRNA. Amino acids are emerging to form a protein chain.
Figure 8.19 The protein synthesis machinery includes the large and small subunits of the ribosome, mRNA, and tRNA. (credit: modification of work by NIGMS, NIH)

In E. coli, there are 200,000 ribosomes present in every cell at any given time. A ribosome is a complex macromolecule composed of structural and catalytic rRNAs, and many distinct polypeptides. In eukaryotes, the nucleolus is completely specialized for the synthesis and assembly of rRNAs.

Ribosomes are located in the cytoplasm in prokaryotes and in the cytoplasm and endoplasmic reticulum of eukaryotes. Ribosomes are made up of a large and a small subunit that come together for translation. The small subunit is responsible for binding the mRNA template, whereas the large subunit sequentially binds tRNAs, a type of RNA molecule that brings amino acids to the growing chain of the polypeptide. Each mRNA molecule is simultaneously translated by many ribosomes, all synthesizing protein in the same direction.

Depending on the species, 40 to 60 types of tRNA exist in the cytoplasm. Serving as adaptors, specific tRNAs bind to sequences on the mRNA template and add the corresponding amino acid to the polypeptide chain. Therefore, tRNAs are the molecules that actually “translate” the language of RNA into the language of proteins. For each tRNA to function, it must have its specific amino acid bonded to it. In the process of tRNA “charging,” each tRNA molecule is bonded to its correct amino acid.

The Genetic Code

Universality of the Genetic Code

 

An interactive H5P element has been excluded from this version of the text. You can view it online here:
https://pressbooks.nscc.ca/conceptsofbiologynscc/?p=283#h5p-54

 

Mutations

 

An interactive H5P element has been excluded from this version of the text. You can view it online here:
https://pressbooks.nscc.ca/conceptsofbiologynscc/?p=283#h5p-55

 

To summarize what we know to this point, the cellular process of transcription generates messenger RNA (mRNA), a mobile molecular copy of one or more genes with an alphabet of A, C, G, and uracil (U). Translation of the mRNA template converts nucleotide-based genetic information into a protein product. Protein sequences consist of 20 commonly occurring amino acids; therefore, it can be said that the protein alphabet consists of 20 letters. Each amino acid is defined by a three-nucleotide sequence called the triplet codon. The relationship between a nucleotide codon and its corresponding amino acid is called the genetic code.

Given the different numbers of “letters” in the mRNA and protein “alphabets,” combinations of nucleotides corresponded to single amino acids. Using a three-nucleotide code means that there are a total of 64 (4 × 4 × 4) possible combinations; therefore, a given amino acid is encoded by more than one nucleotide triplet (Figure 8.20).

Figure shows all 64 codons. Sixty-two of these code for amino acids, and three are stop codons shown in red. The start codon, AUG, is colored green.
Figure 8.20 This figure shows the genetic code for translating each nucleotide triplet, or codon, in mRNA into an amino acid or a termination signal in a nascent protein. (credit: modification of work by NIH)

Three of the 64 codons terminate protein synthesis and release the polypeptide from the translation machinery. These triplets are called stop codons. Another codon, AUG, also has a special function. In addition to specifying the amino acid methionine, it also serves as the start codon to initiate translation. The reading frame for translation is set by the AUG start codon near the 5′ end of the mRNA. The genetic code is universal. With a few exceptions, virtually all species use the same genetic code for protein synthesis, which is powerful evidence that all life on Earth shares a common origin.

The Mechanism of Protein Synthesis

Just as with mRNA synthesis, protein synthesis can be divided into three phases: initiation, elongation, and termination. The process of translation is similar in prokaryotes and eukaryotes. Here we will explore how translation occurs in E. coli, a representative prokaryote, and specify any differences between prokaryotic and eukaryotic translation.

Protein synthesis begins with the formation of an initiation complex. In E. coli, this complex involves the small ribosome subunit, the mRNA template, three initiation factors, and a special initiator tRNA. The initiator tRNA interacts with the AUG start codon, and links to a special form of the amino acid methionine that is typically removed from the polypeptide after translation is complete.

In prokaryotes and eukaryotes, the basics of polypeptide elongation are the same, so we will review elongation from the perspective of E. coli. The large ribosomal subunit of E. coli consists of three compartments: the A site binds incoming charged tRNAs (tRNAs with their attached specific amino acids). The P site binds charged tRNAs carrying amino acids that have formed bonds with the growing polypeptide chain but have not yet dissociated from their corresponding tRNA. The E site releases dissociated tRNAs so they can be recharged with free amino acids. The ribosome shifts one codon at a time, catalyzing each process that occurs in the three sites. With each step, a charged tRNA enters the complex, the polypeptide becomes one amino acid longer, and an uncharged tRNA departs. The energy for each bond between amino acids is derived from GTP, a molecule similar to ATP (Figure 8.21). Amazingly, the E. coli translation apparatus takes only 0.05 seconds to add each amino acid, meaning that a 200-amino acid polypeptide could be translated in just 10 seconds.

Illustration shows the steps of protein synthesis. First, an initiator tRNA recognizes the sequence AUG on the mRNA that is associated with the small ribosomal subunit. The large subunit joins the complex. Next, a second tRNA is recruited at the A site. A peptide bond is formed between the first amino acid, which is at the P site, and the second amino acid, which is at the A site. The mRNA then shifts and the first tRNA is moved to the E site, where it dissociates from the ribosome. Another tRNA binds the A site, and the process is repeated.
Figure 8.21 Translation begins when a tRNA anticodon recognizes a codon on the mRNA. The large ribosomal subunit joins the small subunit, and a second tRNA is recruited. As the mRNA moves relative to the ribosome, the polypeptide chain is formed. Entry of a release factor into the A site terminates translation and the components dissociate.

Termination of translation occurs when a stop codon (UAA, UAG, or UGA) is encountered. When the ribosome encounters the stop codon, the growing polypeptide is released and the ribosome subunits dissociate and leave the mRNA. After many ribosomes have completed translation, the mRNA is degraded so the nucleotides can be reused in another transcription reaction.

Concept in Action


QR Code representing a URL

Transcribe a gene and translate it to protein using complementary pairing and the genetic code at this site.

Section Summary

The central dogma describes the flow of genetic information in the cell from genes to mRNA to proteins. Genes are used to make mRNA by the process of transcription; mRNA is used to synthesize proteins by the process of translation. The genetic code is the correspondence between the three-nucleotide mRNA codon and an amino acid. The genetic code is “translated” by the tRNA molecules, which associate a specific codon with a specific amino acid. The genetic code is degenerate because 64 triplet codons in mRNA specify only 20 amino acids and three stop codons. This means that more than one codon corresponds to an amino acid. Almost every species on the planet uses the same genetic code.

The players in translation include the mRNA template, ribosomes, tRNAs, and various enzymatic factors. The small ribosomal subunit binds to the mRNA template. Translation begins at the initiating AUG on the mRNA. The formation of bonds occurs between sequential amino acids specified by the mRNA template according to the genetic code. The ribosome accepts charged tRNAs, and as it steps along the mRNA, it catalyzes bonding between the new amino acid and the end of the growing polypeptide. The entire mRNA is translated in three-nucleotide “steps” of the ribosome. When a stop codon is encountered, a release factor binds and dissociates the components and frees the new protein.

Exercises

An interactive H5P element has been excluded from this version of the text. You can view it online here:
https://pressbooks.nscc.ca/conceptsofbiologynscc/?p=283#h5p-56

Glossary

codon: three consecutive nucleotides in mRNA that specify the addition of a specific amino acid or the release of a polypeptide chain during translation

genetic code: the amino acids that correspond to three-nucleotide codons of mRNA

rRNA: ribosomal RNA; molecules of RNA that combine to form part of the ribosome

stop codon: one of the three mRNA codons that specifies termination of translation

start codon: the AUG (or, rarely GUG) on an mRNA from which translation begins; always specifies methionine

tRNA: transfer RNA; an RNA molecule that contains a specific three-nucleotide anticodon sequence to pair with the mRNA codon and also binds to a specific amino acid

Chapter 9 in Concepts of Biology: 1st Canadian Edition

31

8.5 How Genes Are Regulated

Charles Molnar and Jane Gair

Learning Objectives

By the end of this section, you will be able to:

  • Discuss why every cell does not express all of its genes
  • Describe how prokaryotic gene expression occurs at the transcriptional level
  • Understand that eukaryotic gene expression occurs at the epigenetic, transcriptional, post-transcriptional, translational, and post-translational levels

For a cell to function properly, necessary proteins must be synthesized at the proper time. All organisms and cells control or regulate the transcription and translation of their DNA into protein. The process of turning on a gene to produce RNA and protein is called gene expression. Whether in a simple unicellular organism or in a complex multicellular organism, each cell controls when and how its genes are expressed. For this to occur, there must be a mechanism to control when a gene is expressed to make RNA and protein, how much of the protein is made, and when it is time to stop making that protein because it is no longer needed.

Cells in multicellular organisms are specialized; cells in different tissues look very different and perform different functions. For example, a muscle cell is very different from a liver cell, which is very different from a skin cell. These differences are a consequence of the expression of different sets of genes in each of these cells. All cells have certain basic functions they must perform for themselves, such as converting the energy in sugar molecules into energy in ATP. Each cell also has many genes that are not expressed, and expresses many that are not expressed by other cells, such that it can carry out its specialized functions. In addition, cells will turn on or off certain genes at different times in response to changes in the environment or at different times during the development of the organism. Unicellular organisms, both eukaryotic and prokaryotic, also turn on and off genes in response to the demands of their environment so that they can respond to special conditions.

The control of gene expression is extremely complex. Malfunctions in this process are detrimental to the cell and can lead to the development of many diseases, including cancer.

Prokaryotic versus Eukaryotic Gene Expression

To understand how gene expression is regulated, we must first understand how a gene becomes a functional protein in a cell. The process occurs in both prokaryotic and eukaryotic cells, just in slightly different fashions.

Because prokaryotic organisms lack a cell nucleus, the processes of transcription and translation occur almost simultaneously. When the protein is no longer needed, transcription stops. As a result, the primary method to control what type and how much protein is expressed in a prokaryotic cell is through the regulation of DNA transcription into RNA. All the subsequent steps happen automatically. When more protein is required, more transcription occurs. Therefore, in prokaryotic cells, the control of gene expression is almost entirely at the transcriptional level.

The first example of such control was discovered using E. coli in the 1950s and 1960s by French researchers and is called the lac operon. The lac operon is a stretch of DNA with three adjacent genes that code for proteins that participate in the absorption and metabolism of lactose, a food source for E. coli. When lactose is not present in the bacterium’s environment, the lac genes are transcribed in small amounts. When lactose is present, the genes are transcribed and the bacterium is able to use the lactose as a food source. The operon also contains a promoter sequence to which the RNA polymerase binds to begin transcription; between the promoter and the three genes is a region called the operator. When there is no lactose present, a protein known as a repressor binds to the operator and prevents RNA polymerase from binding to the promoter, except in rare cases. Thus very little of the protein products of the three genes is made. When lactose is present, an end product of lactose metabolism binds to the repressor protein and prevents it from binding to the operator. This allows RNA polymerase to bind to the promoter and freely transcribe the three genes, allowing the organism to metabolize the lactose.

Eukaryotic cells, in contrast, have intracellular organelles and are much more complex. Recall that in eukaryotic cells, the DNA is contained inside the cell’s nucleus and it is transcribed into mRNA there. The newly synthesized mRNA is then transported out of the nucleus into the cytoplasm, where ribosomes translate the mRNA into protein. The processes of transcription and translation are physically separated by the nuclear membrane; transcription occurs only within the nucleus, and translation only occurs outside the nucleus in the cytoplasm. The regulation of gene expression can occur at all stages of the process (Figure 8.22). Regulation may occur when the DNA is uncoiled and loosened from nucleosomes to bind transcription factors (epigenetic level), when the RNA is transcribed (transcriptional level), when RNA is processed and exported to the cytoplasm after it is transcribed (post-transcriptional level), when the RNA is translated into protein (translational level), or after the protein has been made (post-translational level).

Illustration shows the steps of protein synthesis in three steps: transcription, RNA processing, and translation. In transcription, the RNA strand is synthesized by RNA polymerase in the 5' to 3' direction. In RNA processing, a primary RNA transcript with three exons and two introns is shown. In the spliced transcript, the introns are removed and the exons are fused together. A 5' cap and poly-A tail have also been added. In translation, an initiator tRNA recognizes the sequence AUG on the mRNA that is associated with the small ribosomal subunit. The large subunit joins the complex. Next, a second tRNA is recruited at the A site. A peptide bond is formed between the first amino acid, which is at the P site, and the second amino acid, which is at the A site. The mRNA then shifts and the first tRNA is moved to the E site, where it dissociates from the ribosome. Another tRNA binds the A site, and the process is repeated.
Figure 8.22 Eukaryotic gene expression is regulated during transcription and RNA processing, which take place in the nucleus, as well as during protein translation, which takes place in the cytoplasm. Further regulation may occur through post-translational modifications of proteins.

The differences in the regulation of gene expression between prokaryotes and eukaryotes are summarized in the table below.

Differences in the Regulation of Gene Expression of Prokaryotic and Eukaryotic Organisms
Prokaryotic organisms Eukaryotic organisms
Lack nucleus Contain nucleus
RNA transcription and protein translation occur almost simultaneously
  • RNA transcription occurs prior to protein translation, and it takes place in the nucleus. RNA translation to protein occurs in the cytoplasm.
  • RNA post-processing includes addition of a 5′ cap, poly-A tail, and excision of introns and splicing of exons.
Gene expression is regulated primarily at the transcriptional level Gene expression is regulated at many levels (epigenetic, transcriptional, post-transcriptional, translational, and post-translational)

Alternative RNA Splicing

In the 1970s, genes were first observed that exhibited alternative RNA splicing. Alternative RNA splicing is a mechanism that allows different protein products to be produced from one gene when different combinations of introns (and sometimes exons) are removed from the transcript (Figure 8.23). This alternative splicing can be haphazard, but more often it is controlled and acts as a mechanism of gene regulation, with the frequency of different splicing alternatives controlled by the cell as a way to control the production of different protein products in different cells, or at different stages of development. Alternative splicing is now understood to be a common mechanism of gene regulation in eukaryotes; according to one estimate, 70% of genes in humans are expressed as multiple proteins through alternative splicing.

Illustration of segments of pre-mRNA with exons shown in blue, red, orange, and pink. Five basic modes of alternative splicing are generally recognized. Each segment of pre-mRNA can be spliced to produce a variety of new mature mRNA segments; two are shown for each here. In the case of exon skipping, an exon may be spliced out or retained. In the case of mutually exclusive exons, one of two exons is retained in mRNAs after splicing, but not both. In the case of an alternative donor site, an alternative 5' splice junction (donor site) is used, changing the 3' boundary of the upstream exon. In the case of an alternative acceptor site, an alternative 3' splice junction (acceptor site) is used, changing the 5' boundary of the downstream exon. In the case of intron retention, a sequence may be spliced out as an intron or simply retained. This is distinguished from exon skipping because the retained sequence is not flanked by introns. The pink portion is considered an intron when skipped (top) and an exon when included (bottom).
Figure 8.23 There are five basic modes of alternative splicing. Segments of pre-mRNA with exons shown in blue, red, orange, and pink can be spliced to produce a variety of new mature mRNA segments.

How could alternative splicing evolve? Introns have a beginning and ending recognition sequence, and it is easy to imagine the failure of the splicing mechanism to identify the end of an intron and find the end of the next intron, thus removing two introns and the intervening exon. In fact, there are mechanisms in place to prevent such exon skipping, but mutations are likely to lead to their failure. Such “mistakes” would more than likely produce a nonfunctional protein. Indeed, the cause of many genetic diseases is alternative splicing rather than mutations in a sequence. However, alternative splicing would create a protein variant without the loss of the original protein, opening up possibilities for adaptation of the new variant to new functions. Gene duplication has played an important role in the evolution of new functions in a similar way—by providing genes that may evolve without eliminating the original functional protein.

Section Summary

While all somatic cells within an organism contain the same DNA, not all cells within that organism express the same proteins. Prokaryotic organisms express the entire DNA they encode in every cell, but not necessarily all at the same time. Proteins are expressed only when they are needed. Eukaryotic organisms express a subset of the DNA that is encoded in any given cell. In each cell type, the type and amount of protein is regulated by controlling gene expression. To express a protein, the DNA is first transcribed into RNA, which is then translated into proteins. In prokaryotic cells, these processes occur almost simultaneously. In eukaryotic cells, transcription occurs in the nucleus and is separate from the translation that occurs in the cytoplasm. Gene expression in prokaryotes is regulated only at the transcriptional level, whereas in eukaryotic cells, gene expression is regulated at the epigenetic, transcriptional, post-transcriptional, translational, and post-translational levels.

Exercises

An interactive H5P element has been excluded from this version of the text. You can view it online here:
https://pressbooks.nscc.ca/conceptsofbiologynscc/?p=287#h5p-57

Glossary

alternative RNA splicing: a post-transcriptional gene regulation mechanism in eukaryotes in which multiple protein products are produced by a single gene through alternative splicing combinations of the RNA transcript

epigenetic: describing non-genetic regulatory factors, such as changes in modifications to histone proteins and DNA that control accessibility to genes in chromosomes

gene expression: processes that control whether a gene is expressed

post-transcriptional: control of gene expression after the RNA molecule has been created but before it is translated into protein

post-translational: control of gene expression after a protein has been created

Chapter 9 in Concepts of Biology: 1st Canadian Edition

IX

Chapter 9: Evolution and the Origin of Species

32

9.1 Introduction

Mary Ann Clark, Jung Choi, and Matthew Douglas

The photo on the left shows large, stalk-like saguaro cacti with multiple arms, and the photo on the right shows a lizard on a rock.
Figure 9.1-1 All organisms are products of evolution adapted to their environment. (a) Saguaro (Carnegiea gigantea) can soak up 750 liters of water in a single rain storm, enabling these cacti to survive the dry conditions of the Sonora desert in Mexico and the Southwestern United States. (b) The Andean semiaquatic lizard (Potamites montanicola) discovered in Peru in 2010 lives between 1,570 to 2,100 meters in elevation, and, unlike most lizards, is nocturnal and swims. Scientists still do not know how these cold-blood animals are able to move in the cold (10 to 15°C) temperatures of the Andean night. (credit a: modification of work by Gentry George, U.S. Fish and Wildlife Service; credit b: modification of work by Germán Chávez and Diego Vásquez, ZooKeys)

All living organisms, from bacteria to baboons to blueberries, evolved at some point from a different species. Although it may seem that living things today stay much the same, that is not the case—evolution is an ongoing process.

The theory of evolution is the unifying theory of biology, meaning it is the framework within which biologists ask questions about the living world. Its power is that it provides direction for predictions about living things that are borne out in ongoing experiments. The Ukrainian-born American geneticist Theodosius Dobzhansky famously wrote that “nothing makes sense in biology except in the light of evolution.”1 He meant that the tenet that all life has evolved and diversified from a common ancestor is the foundation from which we approach all questions in biology.

Footnotes

  • 1 Theodosius Dobzhansky. “Biology, Molecular and Organismic.” American Zoologist 4, no. 4 (1964): 449.

Chapter 18 in OpenStax Concepts of Biology 2E

33

9.2 Understanding Evolution

Mary Ann Clark, Jung Choi, and Matthew Douglas

Learning Objectives

By the end of this section, you will be able to do the following:

  • Describe how scientists developed the present-day theory of evolution
  • Define adaptation
  • Explain convergent and divergent evolution
  • Describe homologous and vestigial structures
  • Discuss misconceptions about the theory of evolution

Evolution by natural selection describes a mechanism for how species change over time. Scientists, philosophers, researchers, and others had made suggestions and debated this topic well before Darwin began to explore this idea. Classical Greek philosopher Plato emphasized in his writings that species were static and unchanging, yet there were also ancient Greeks who expressed evolutionary ideas. In the eighteenth century, naturalist Georges-Louis Leclerc Comte de Buffon reintroduced ideas about the evolution of animals and observed that various geographic regions have different plant and animal populations, even when the environments are similar. Some at this time also accepted that there were extinct species.

Also during the eighteenth century, James Hutton, a Scottish geologist and naturalist, proposed that geological change occurred gradually by accumulating small changes from processes operating like they are today over long periods of time. This contrasted with the predominant view that the planet’s geology was a consequence of catastrophic events occurring during a relatively brief past. Nineteenth century geologist Charles Lyell popularized Hutton’s view. A friend to Darwin. Lyell’s ideas were influential on Darwin’s thinking: Lyell’s notion of the greater age of Earth gave more time for gradual change in species, and the process of change provided an analogy for this change. In the early nineteenth century, Jean-Baptiste Lamarck published a book that detailed a mechanism for evolutionary change. We now refer to this mechanism as an inheritance of acquired characteristics by which the environment causes modifications in an individual, or offspring could use or disuse of a structure during its lifetime, and thus bring about change in a species. While many discredited this mechanism for evolutionary change, Lamarck’s ideas were an important influence on evolutionary thought.

Charles Darwin and Natural Selection

In the mid-nineteenth century, two naturalists, Charles Darwin and Alfred Russel Wallace, independently conceived and described the actual mechanism for evolution. Importantly, each naturalist spent time exploring the natural world on expeditions to the tropics. From 1831 to 1836, Darwin traveled around the world on H.M.S. Beagle, including stops in South America, Australia, and the southern tip of Africa. Wallace traveled to Brazil to collect insects in the Amazon rainforest from 1848 to 1852 and to the Malay Archipelago from 1854 to 1862. Darwin’s journey, like Wallace’s later journeys to the Malay Archipelago, included stops at several island chains, the last being the Galápagos Islands west of Ecuador. On these islands, Darwin observed species of organisms on different islands that were clearly similar, yet had distinct differences. For example, the ground finches inhabiting the Galápagos Islands comprised several species with a unique beak shape (figure 9.2-1). The species on the islands had a graded series of beak sizes and shapes with very small differences between the most similar. He observed that these finches closely resembled another finch species on the South American mainland. Darwin imagined that the island species might be species modified from one of the original mainland species. Upon further study, he realized that each finch’s varied beaks helped the birds acquire a specific type of food. For example, seed-eating finches had stronger, thicker beaks for breaking seeds, and insect-eating finches had spear-like beaks for stabbing their prey.

Illustration shows four different species of finch from the Galapagos Islands. Beak shape ranges from broad and thick to narrow and thin.
Figure 9.2-2 Darwin observed that beak shape varies among finch species. He postulated that ancestral species’ beaks had adapted overtime to equip the finches to acquire different food sources

Wallace and Darwin both observed similar patterns in other organisms and they independently developed the same explanation for how and why such changes could take place. Darwin called this mechanism natural selection. Natural selection, or “survival of the fittest,” is the more prolific reproduction of individuals with favorable traits that survive environmental change because of those traits. This leads to evolutionary change.

For example, Darwin observed a population of giant tortoises in the Galápagos Archipelago to have longer necks than those that lived on other islands with dry lowlands. These tortoises were “selected” because they could reach more leaves and access more food than those with short necks. In times of drought when fewer leaves would be available, those that could reach more leaves had a better chance to eat and survive than those that couldn’t reach the food source. Consequently, long-necked tortoises would be more likely to be reproductively successful and pass the long-necked trait to their offspring. Over time, only long-necked tortoises would be present in the population.

Natural selection, Darwin argued, was an inevitable outcome of three principles that operated in nature. First, most characteristics of organisms are inherited, or passed from parent to offspring. Although no one, including Darwin and Wallace, knew how this happened at the time, it was a common understanding. Second, more offspring are produced than are able to survive, so resources for survival and reproduction are limited. The capacity for reproduction in all organisms outstrips the availability of resources to support their numbers. Thus, there is competition for those resources in each generation. Both Darwin and Wallace’s understanding of this principle came from reading economist Thomas Malthus’ essay that explained this principle in relation to human populations. Third, offspring vary among each other in regard to their characteristics and those variations are inherited. Darwin and Wallace reasoned that offspring with inherited characteristics which allow them to best compete for limited resources will survive and have more offspring than those individuals with variations that are less able to compete. Because characteristics are inherited, these traits will be better represented in the next generation. This will lead to change in populations over generations in a process that Darwin called descent with modification. Ultimately, natural selection leads to greater adaptation of the population to its local environment. It is the only mechanism known for adaptive evolution.

In 1858, Darwin and Wallace (Figure 9.2-3) presented papers at the Linnean Society in London that discussed the idea of natural selection. The following year Darwin’s book, On the Origin of Species, was published. His book outlined in considerable detail his arguments for evolution by natural selection.

Paintings of Charles Darwin and Alfred Wallace are shown.
Figure 9.2-3 Both (a) Charles Darwin and (b) Alfred Wallace wrote scientific papers on natural selection that they presented together at theLinnean Society in 1858.

It is difficult and time-consuming to document and present examples of evolution by natural selection. The Galápagos finches are an excellent example. Peter and Rosemary Grant and their colleagues have studied Galápagos finch populations every year since 1976 and have provided important evidence of natural selection. The Grants found changes from one generation to the next in beak shape distribution with the medium ground finch on the Galápagos island of Daphne Major. The birds have inherited a variation in their bill shape with some having wide deep bills and others having thinner bills. During a period in which rainfall was higher than normal because of an El Niño, there was a lack of large hard seeds of which the large-billed birds ate; however, there was an abundance of the small soft seeds which the small-billed birds ate. Therefore, the small-billed birds were able to survive and reproduce. In the years following this El Niño, the Grants measured beak sizes in the population and found that the average bill size was smaller. Since bill size is an inherited trait, parents with smaller bills had more offspring and the bill evolved into a much smaller size. As conditions improved in 1987 and larger seeds became more available, the trend toward smaller average bill size ceased.

Career Connection

Field Biologist

Many people hike, explore caves, scuba dive, or climb mountains for recreation. People often participate in these activities hoping to see wildlife. Experiencing the outdoors can be incredibly enjoyable and invigorating. What if your job entailed working in the wilderness? Field biologists by definition work outdoors in the “field.” The term field in this case refers to any location outdoors, even under water.

Photo shows a scientist next to a tranquilized polar bear laying on the snow.
Figure 9.2-4 A field biologist tranquilizes a polar bear for study. (credit: Karen Rhode)

One objective of many field biologists includes discovering new, unrecorded species. Not only do such findings expand our understanding of the natural world, but they also lead to important innovations in fields such as medicine and agriculture. Plant and microbial species, in particular, can reveal new medicinal and nutritive knowledge. Other organisms can play key roles in ecosystems or if rare require protection. When discovered, researchers can use these important species as evidence for environmental regulations and laws.

Processes and Patterns of Evolution

Natural selection can only take place if there is variation, or differences, among individuals in a population. Importantly, these differences must have some genetic basis; otherwise, the selection will not lead to change in the next generation. This is critical because nongenetic reasons can cause variation among individuals such as an individual’s height because of better nutrition rather than different genes.

Genetic diversity in a population comes from two main mechanisms: mutation and sexual reproduction. Mutation, a change in DNA, is the ultimate source of new alleles, or new genetic variation in any population. The genetic changes that mutation causes can have one of three outcomes on the phenotype. A mutation affects the organism’s phenotype in a way that gives it reduced fitness—lower likelihood of survival or fewer offspring. A mutation may produce a phenotype with a beneficial effect on fitness. Many mutations will also have no effect on the phenotype’s fitness. We call these neutral mutations. Mutations may also have a whole range of effect sizes on the organism’s fitness that expresses them in their phenotype, from a small effect to a great effect. Sexual reproduction also leads to genetic diversity: when two parents reproduce, unique combinations of alleles assemble to produce the unique genotypes and thus phenotypes in each offspring.

We call a heritable trait that helps an organism’s survival and reproduction in its present environment an adaptation. Scientists describe groups of organisms adapting to their environment when a genetic variation occurs over time that increases or maintains the population’s “fit” to its environment. A platypus’s webbed feet are an adaptation for swimming. A snow leopard’s thick fur is an adaptation for living in the cold. A cheetah’s fast speed is an adaptation for catching prey.

Whether or not a trait is favorable depends on the current environmental conditions. The same traits are not always selected because environmental conditions can change. For example, consider a plant species that grew in a moist climate and did not need to conserve water. Large leaves were selected because they allowed the plant to obtain more energy from the sun. Large leaves require more water to maintain than small leaves, and the moist environment provided favorable conditions to support large leaves. After thousands of years, the climate changed, and the area no longer had excess water. The direction of natural selection shifted so that plants with small leaves were selected because those populations were able to conserve water to survive the new environmental conditions.

The evolution of species has resulted in enormous variation in form and function. Sometimes, evolution gives rise to groups of organisms that become tremendously different from each other. We call two species that evolve in diverse directions from a common point divergent evolution. We can see such divergent evolution in the forms of the reproductive organs of flowering plants which share the same basic anatomies; however, they can look very different as a result of selection in different physical environments and adaptation to different kinds of pollinators (Figure 9.2-5).

Photo showing a Dense Blazing Star (Liatrus spicata) and a Purple Coneflower (Echinacea purpurea). The dense blazing star flower has purple strand like petals budding from its stem. The coneflower has a large circular center of the budding flower, with purple petals growing from it.
Figure 9.2-5 Flowering plants evolved from a common ancestor. Notice that the (a) dense blazing star (Liatrus spicata) and the (b) purpleconeflower (Echinacea purpurea) vary in appearance, yet both share a similar basic morphology. (credit a: modification of work by DrewAvery; credit b: modification of work by Cory Zanke)

In other cases, similar phenotypes evolve independently in distantly related species. For example, flight has evolved in both bats and insects, and they both have structures we refer to as wings, which are adaptations to flight. However, bat and insect wings have evolved from very different original structures. We call this phenomenon convergent evolution, where similar traits evolve independently in species that do not share a common ancestry. The two species came to the same function, flying, but did so separately from each other.

These physical changes occur over enormous time spans and help explain how evolution occurs. Natural selection acts on individual organisms, which can then shape an entire species. Although natural selection may work in a single generation on an individual, it can take thousands or even millions of years for an entire species’ genotype to evolve. It is over these large time spans that life on earth has changed and continues to change.

Evidence of Evolution

The evidence for evolution is compelling and extensive. Looking at every level of organization in living systems, biologists see the signature of past and present evolution. Darwin dedicated a large portion of his book, On the Origin of Species, to identifying patterns in nature that were consistent with evolution, and since Darwin, our understanding has become clearer and broader.

Fossils

Fossils provide solid evidence that organisms from the past are not the same as those today, and fossils show a progression of evolution. Scientists determine the age of fossils and categorize them from all over the world to determine when the organisms lived relative to each other. The resulting fossil record tells the story of the past and shows the evolution of form over millions of years ((Figure)). For example, scientists have recovered highly detailed records showing the evolution of humans and horses (Figure 9.2-6). The whale flipper shares a similar morphology to bird and mammal appendages (Figure 9.2-6) indicating that these species share a common ancestor.

Photo A shows a museum display of hominid skulls that vary in size and shape. Illustration B shows five extinct species related and similar in appearance to the modern horse. The species vary in size from that of a modern horse to that of a medium-sized dog.
Figure 9.2-6 In this (a) display, fossil hominids are arranged from oldest (bottom) to newest (top). As hominids evolved, the skull’s shape changed. An artist’s rendition of (b) extinct species of the genus Equus reveals that these ancient species resembled the modern horse (Equus ferus) but varied in size.

Anatomy and Embryology

Another type of evidence for evolution is the presence of structures in organisms that share the same basic form. For example, the bones in human, dog, bird, and whale appendages all share the same overall construction (Figure 9.2-7) resulting from their origin in a common ancestor’s appendages. Over time, evolution led to changes in the bones’ shapes and sizes different species, but they have maintained the same overall layout. Scientists call these synonymous parts homologous structures.

Illustration compares a human arm, dog and bird legs, and a whale flipper. All appendages have the same bones, but the size and shape of these bones vary.
Figure 9.2-7 The similar construction of these appendages indicates that these organisms share a common ancestor.

Some structures exist in organisms that have no apparent function at all, and appear to be residual parts from a past common ancestor. We call these unused structures without function vestigial structures. Other examples of vestigial structures are wings on flightless birds, leaves on some cacti, and hind leg bones in whales.

An interactive or media element has been excluded from this version of the text. You can view it online here: https://pressbooks.nscc.ca/conceptsofbiologynscc/?p=320

Link to Learning

Watch the YouTube video The Skeletal System by Professor Dave Explains, exploring the bones in the human body. Guess which bone structures are homologous and which are analogous, and see examples of evolutionary adaptations to illustrate these concepts.

Another evidence of evolution is the convergence of form in organisms that share similar environments. For example, species of unrelated animals, such as the arctic fox and ptarmigan, living in the arctic region have been selected for seasonal white phenotypes during winter to blend with the snow and ice (Figure 9.2-8). These similarities occur not because of common ancestry, but because of similar selection pressures—the benefits of predators not seeing them.

The left photo depicts an arctic fox with white fur sleeping on white snow, and the right photo shows a ptarmigan bird with white plumage standing on white snow.
Figure 9.2-8 The white winter coat of the (a) arctic fox and the (b) ptarmigan’s plumage are adaptations to their environments. (credit a:modification of work by Keith Morehous)

Embryology, the study of the anatomy of an organism’s development to its adult form, also provides evidence of relatedness between now widely divergent groups of organisms. Mutational tweaking in the embryo can have such magnified consequences in the adult that tends to conserve embryo formation. As a result, structures that are absent in some groups often appear in their embryonic forms and disappear when they reach the adult or juvenile form. For example, all vertebrate embryos, including humans, exhibit gill slits and tails at some point in their early development. These disappear in the adults of terrestrial groups but adult forms of aquatic groups such as fish and some amphibians maintain them. Great ape embryos, including humans, have a tail structure during their development that they lose when they are born.

Biogeography

The geographic distribution of organisms on the planet follows patterns that we can explain best by evolution in conjunction with tectonic plate movement over geological time. Broad groups that evolved before the supercontinent Pangaea broke up (about 200 million years ago) are distributed worldwide. Groups that evolved since the breakup appear uniquely in regions of the planet, such as the unique flora and fauna of northern continents that formed from the supercontinent Laurasia and of the southern continents that formed from the supercontinent Gondwana. The presence of members of the plant family Proteaceae in Australia, southern Africa, and South America was most predominant prior to the southern supercontinent Gondwana breaking up.

Marsupial diversification in Australia and the absence of other mammals reflect Australia’s long isolation. Australia has an abundance of endemic species—species found nowhere else—which is typical of islands whose isolation by expanses of water prevents species to migrate. Over time, these species diverge evolutionarily into new species that look very different from their ancestors that may exist on the mainland. Australia’s marsupials, the Galápagos’ finches, and many species on the Hawaiian Islands are all unique to their one point of origin, yet they display distant relationships to ancestral species on mainlands.

Molecular Biology

Like anatomical structures, the molecular structures of life reflect descent with modification. DNA’s universality reflects evidence of a common ancestor for all of life. Fundamental divisions in life between the genetic code, DNA replication, and expression are reflected in major structural differences in otherwise conservative structures such as ribosome components and membrane structures. In general, the relatedness of groups of organisms is reflected in the similarity of their DNA sequences—exactly the pattern that we would expect from descent and diversification from a common ancestor.

DNA sequences have also shed light on some of the mechanisms of evolution. For example, it is clear that the evolution of new functions for proteins commonly occurs after gene duplication events that allow freely modifying one copy by mutation, selection, or drift (changes in a population’s gene pool resulting from chance), while the second copy continues to produce a functional protein.

Misconceptions of Evolution

Although the theory of evolution generated some controversy when Darwin first proposed it, biologists almost universally accepted it, particularly younger biologists, within 20 years after publication of On the Origin of Species. Nevertheless, the theory of evolution is a difficult concept and misconceptions about how it works abound.

Link to Learning

The website Understanding Evolution addresses some of the main misconceptions associated with the theory of evolution.

Evolution Is Just a Theory

Critics of the theory of evolution dismiss its importance by purposefully confounding the everyday usage of the word “theory” with the way scientists use the word. In science, we understand a “theory” to be a body of thoroughly tested and verified explanations for a set of observations of the natural world. Scientists have a theory of the atom, a theory of gravity, and the theory of relativity, each which describes understood facts about the world. In the same way, the theory of evolution describes facts about the living world. As such, a theory in science has survived significant efforts to discredit it by scientists. In contrast, a “theory” in common vernacular is a word meaning a guess or suggested explanation. This meaning is more akin to the scientific concept of “hypothesis.” When critics of evolution say it is “just a theory,” they are implying that there is little evidence supporting it and that it is still in the process of rigorous testing. This is a mischaracterization.

Individuals Evolve

Evolution is the change in a population’s genetic composition over time, specifically over generations, resulting from differential reproduction of individuals with certain alleles. Individuals do change over their lifetime, obviously, but this is development and involves changes programmed by the set of genes the individual acquired at birth in coordination with the individual’s environment. When thinking about the evolution of a characteristic, it is probably best to think about the change of the average value of the characteristic in the population over time. For example, when natural selection leads to bill-size change in medium ground finches in the Galápagos, this does not mean that individual bills on the finches are changing. If one measures the average bill size among all individuals in the population at one time and then measures them in the population several years later, this average value will be different as a result of evolution. Although some individuals may survive from the first time to the second, they will still have the same bill size; however, there will be many new individuals who contribute to the shift in average bill size.

Evolution Explains the Origin of Life

It is a common misunderstanding that evolution includes an explanation of life’s origins. Conversely, some of the theory’s critics believe that it cannot explain the origin of life. The theory does not try to explain the origin of life. The theory of evolution explains how populations change over time and how life diversifies the origin of species. It does not shed light on the beginnings of life including the origins of the first cells, which define life. Importantly, biologists believe that the presence of life on Earth precludes the possibility that the events that led to life on Earth can repeat themselves because the intermediate stages would immediately become food for existing living things.

However, once a mechanism of inheritance was in place in the form of a molecule like DNA either within a cell or pre-cell, these entities would be subject to the principle of natural selection. More effective reproducers would increase in frequency at the expense of inefficient reproducers. While evolution does not explain the origin of life, it may have something to say about some of the processes operating once pre-living entities acquired certain properties.

Organisms Evolve on Purpose

Statements such as “organisms evolve in response to a change in an environment” are quite common, but such statements can lead to two types of misunderstandings. First, do not interpret the statement to mean that individual organisms evolve. The statement is shorthand for “a population evolves in response to a changing environment.” However, a second misunderstanding may arise by interpreting the statement to mean that the evolution is somehow intentional. A changed environment results in some individuals in the population, those with particular phenotypes, benefiting and therefore producing proportionately more offspring than other phenotypes. This results in change in the population if the characteristics are genetically determined.

It is also important to understand that the variation that natural selection works on is already in a population and does not arise in response to an environmental change. For example, applying antibiotics to a population of bacteria will, over time, select a population of bacteria that are resistant to antibiotics. The resistance, which a gene causes, did not arise by mutation because of applying the antibiotic. The gene for resistance was already present in the bacteria’s gene pool, likely at a low frequency. The antibiotic, which kills the bacterial cells without the resistance gene, strongly selects individuals that are resistant, since these would be the only ones that survived and divided. Experiments have demonstrated that mutations for antibiotic resistance do not arise as a result of antibiotic.

In a larger sense, evolution is not goal directed. Species do not become “better” over time. They simply track their changing environment with adaptations that maximize their reproduction in a particular environment at a particular time. Evolution has no goal of making faster, bigger, more complex, or even smarter species, despite the commonness of this kind of language in popular discourse. What characteristics evolve in a species are a function of the variation present and the environment, both of which are constantly changing in a nondirectional way. A trait that fits in one environment at one time may well be fatal at some point in the future. This holds equally well for insect and human species.

Section Summary

Evolution is the process of adaptation through mutation which allows more desirable characteristics to pass to the next generation. Over time, organisms evolve more characteristics that are beneficial to their survival. For living organisms to adapt and change to environmental pressures, genetic variation must be present. With genetic variation, individuals have differences in form and function that allow some to survive certain conditions better than others. These organisms pass their favorable traits to their offspring. Eventually, environments change, and what was once a desirable, advantageous trait may become an undesirable trait and organisms may further evolve. Evolution may be convergent with similar traits evolving in multiple species or divergent with diverse traits evolving in multiple species that came from a common ancestor. We can observe evidence of evolution by means of DNA code and the fossil record, and also by the existence of homologous and vestigial structures.

Exercises

Review Questions

Which scientific concept did Charles Darwin and Alfred Wallace independently discover?

  1. mutation
  2. natural selection
  3. overbreeding
  4. sexual reproduction

Which of the following situations will lead to natural selection?

  1. The seeds of two plants land near each other and one grows larger than the other.
  2. Two types of fish eat the same kind of food, and one is better able to gather food than the other.
  3. Male lions compete for the right to mate with females, with only one possible winner.
  4. all of the above

Which description is an example of a phenotype?

  1. A certain duck has a blue beak.
  2. A mutation occurred to a flower.
  3. Most cheetahs live solitary lives.
  4. both a and c

Which situation is most likely an example of convergent evolution?

  1. Squid and humans have eyes similar in structure.
  2. Worms and snakes both move without legs.
  3. Some bats and birds have wings that allow them to fly.
  4. all of the above

Critical Thinking Questions

  1. If a person scatters a handful of garden pea plant seeds in one area, how would natural selection work in this situation?
  2. Why do scientists consider vestigial structures evidence for evolution?
  3. How does the scientific meaning of “theory” differ from the common vernacular meaning?

  4. Explain why the statement that a monkey is more evolved than a mouse is incorrect.

Glossary

adaptation
heritable trait or behavior in an organism that aids in its survival and reproduction in its present environment
convergent evolution
process by which groups of organisms independently evolve to similar forms
divergent evolution
process by which groups of organisms evolve in diverse directions from a common point
homologous structures
parallel structures in diverse organisms that have a common ancestor
natural selection
reproduction of individuals with favorable genetic traits that survive environmental change because of those traits, leading to evolutionary change
variation
genetic differences among individuals in a population
vestigial structure
physical structure present in an organism but that has no apparent function and appears to be from a functional structure in a distant ancestor

Creation Note: Chapter 18 in OpenStax Concepts of Biology 2E

34

9.3 Formation of New Species

Mary Ann Clark, Jung Choi, and Matthew Douglas

Learning Objectives

By the end of this section, you will be able to do the following:

  • Define species and describe how scientists identify species as different
  • Describe genetic variables that lead to speciation
  • Identify prezygotic and postzygotic reproductive barriers
  • Explain allopatric and sympatric speciation
  • Describe adaptive radiation

Although all life on earth shares various genetic similarities, only certain organisms combine genetic information by sexual reproduction and have offspring that can then successfully reproduce. Scientists call such organisms members of the same biological species.

Species and the Ability to Reproduce

A species is a group of individual organisms that interbreed and produce fertile, viable offspring. According to this definition, one species is distinguished from another when, in nature, it is not possible for matings between individuals from each species to produce fertile offspring.

Members of the same species share both external and internal characteristics, which develop from their DNA. The closer relationship two organisms share, the more DNA they have in common, just like people and their families. People’s DNA is likely to be more like their father or mother’s DNA than their cousin or grandparent’s DNA. Organisms of the same species have the highest level of DNA alignment and therefore share characteristics and behaviors that lead to successful reproduction.

Species’ appearance can be misleading in suggesting an ability or inability to mate. For example, even though domestic dogs (Canis lupus familiaris) display phenotypic differences, such as size, build, and coat, most dogs can interbreed and produce viable puppies that can mature and sexually reproduce (Figure 9.3 – 9).

Photo a shows a poodle with curly short fur. Photo b shows a cocker spaniel with long, wavy fur that has light brown parts and cream-colored markings on the face, forepaws, belly, hind legs, and tail. The poodle has longer legs than the cocker spaniel. The cockapoo in photo c has curly hair, like the poodle, and short legs, like the cocker spaniel.
Figure 9.3-9The (a) poodle and (b) cocker spaniel can reproduce to produce a breed known as (c) the cockapoo. (credit a: modification of work by Sally Eller, Tom Reese; credit b: modification of work by Jeremy McWilliams; credit c: modification of work by Kathleen Conklin)

In other cases, individuals may appear similar although they are not members of the same species. For example, even though bald eagles (Haliaeetus leucocephalus) and African fish eagles (Haliaeetus vocifer) are both birds and eagles, each belongs to a separate species group (Figure 9.3-10). If humans were to artificially intervene and fertilize a bald eagle’s egg with an African fish eagle’s sperm and a chick did hatch, that offspring, called a hybrid (a cross between two species), would probably be infertile—unable to successfully reproduce after it reached maturity. Different species may have different genes that are active in development; therefore, it may not be possible to develop a viable offspring with two different sets of directions. Thus, even though hybridization may take place, the two species still remain separate.

Photo a shows a picture of the African fish eagle in flight, and photo b shows the bald eagle perched on a post. Both birds have dark brown feathers on their bodies and wings, and white feathered heads.
Figure 9.3-10 The (a) African fish eagle is similar in appearance to the (b) bald eagle, but the two birds are members of different species. (credit a: modification of work by Nigel Wedge; credit b: modification of work by U.S. Fish and Wildlife Service)

Populations of species share a gene pool: a collection of all the gene variants in the species. Again, the basis to any changes in a group or population of organisms must be genetic for this is the only way to share and pass on traits. When variations occur within a species, they can only pass to the next generation along two main pathways: asexual reproduction or sexual reproduction. The change will pass on asexually simply if the reproducing cell possesses the changed trait. For the changed trait to pass on by sexual reproduction, a gamete, such as a sperm or egg cell, must possess the changed trait. In other words, sexually-reproducing organisms can experience several genetic changes in their body cells, but if these changes do not occur in a sperm or egg cell, the changed trait will never reach the next generation. Only heritable traits can evolve. Therefore, reproduction plays a paramount role for genetic change to take root in a population or species. In short, organisms must be able to reproduce with each other to pass new traits to offspring.

Speciation

The biological definition of species, which works for sexually reproducing organisms, is a group of actual or potential interbreeding individuals. There are exceptions to this rule. Many species are similar enough that hybrid offspring are possible and may often occur in nature, but for the majority of species this rule generally holds. The presence in nature of hybrids between similar species suggests that they may have descended from a single interbreeding species, and the speciation process may not yet be completed.

Given the extraordinary diversity of life on the planet there must be mechanisms for speciation: the formation of two species from one original species. Darwin envisioned this process as a branching event and diagrammed the process in the only illustration in On the Origin of Species (Figure 9.3-11). Compare this illustration to the diagram of elephant evolution (Figure 9.3-11), which shows that as one species changes over time, it branches to form more than one new species, repeatedly, as long as the population survives or until the organism becomes extinct.

Image (a) shows a sketch of lines branching into a tree shape. At the bottom are 11 vertical lines labeled A through L. These then are branched out as they move up across the page through fourteen rows labeled with Roman numerals. Some branches make a straight line from the bottom row to the top row, others keep branching out further at each row, and some are straight partway through the rows until they connect to an existing branch or form no connection and instead stop. The top four rows each consists of a single line from a branch tip; there are 6 branch tips at row X I; to one of 15 individual final designations. Illustration B shows the evolution of modern African and Asian elephants from a common ancestor, the Palaeomastodon. The Palaeomastodon was similar to modern elephants; however, it was smaller and had a long nose instead of a trunk. Side branches of the elephant evolutionary tree gave rise to mastodons and mammoths. The mammoth is more closely related to modern elephants than the mastodon.
Figure 9.3-11 The only illustration in Darwin’s On the Origin of Species is (a) a diagram showing speciation events leading to biological diversity. The diagram shows similarities to phylogenetic charts that today illustrate the relationships of species. (b) Modern elephants evolved from the Palaeomastodon, a species that lived in Egypt 35–50 million years ago.

For speciation to occur, two new populations must form from one original population and they must evolve in such a way that it becomes impossible for individuals from the two new populations to interbreed. Biologists have proposed mechanisms by which this could occur that fall into two broad categories. Allopatric speciation (allo- = “other”; -patric = “homeland”) involves geographic separation of populations from a parent species and subsequent evolution. Sympatric speciation (sym- = “same”; -patric = “homeland”) involves speciation occurring within a parent species remaining in one location.

Biologists think of speciation events as the splitting of one ancestral species into two descendant species. There is no reason why more than two species might not form at one time except that it is less likely and we can conceptualize multiple events as single splits occurring close in time.

Allopatric Speciation

A geographically continuous population has a gene pool that is relatively homogeneous. Gene flow, the movement of alleles across a species’ range, is relatively free because individuals can move and then mate with individuals in their new location. Thus, an allele’s frequency at one end of a distribution will be similar to the allele’s frequency at the other end. When populations become geographically discontinuous, it prevents alleles’ free-flow. When that separation lasts for a period of time, the two populations are able to evolve along different trajectories. Thus, their allele frequencies at numerous genetic loci gradually become increasingly different as new alleles independently arise by mutation in each population. Typically, environmental conditions, such as climate, resources, predators, and competitors for the two populations will differ causing natural selection to favor divergent adaptations in each group.

Isolation of populations leading to allopatric speciation can occur in a variety of ways: a river forming a new branch, erosion creating a new valley, a group of organisms traveling to a new location without the ability to return, or seeds floating over the ocean to an island. The nature of the geographic separation necessary to isolate populations depends entirely on the organism’s biology and its potential for dispersal. If two flying insect populations took up residence in separate nearby valleys, chances are, individuals from each population would fly back and forth continuing gene flow. However, if a new lake divided two rodent populations continued gene flow would be unlikely; therefore, speciation would be more likely.

Biologists group allopatric processes into two categories: dispersal and vicariance. Dispersal is when a few members of a species move to a new geographical area, and vicariance is when a natural situation arises to physically divide organisms.

Scientists have documented numerous cases of allopatric speciation taking place. For example, along the west coast of the United States, two separate spotted owl subspecies exist. The northern spotted owl has genetic and phenotypic differences from its close relative: the Mexican spotted owl, which lives in the south (Figure 9.3-12).

The northern spotted owl lives in the Pacific Northwest, and the Mexican spotted owl lives in Mexico and the southwestern portion of the United States. The two owls are similar in appearance but with slightly different coloration.
Figure 9.3-12 The northern spotted owl and the Mexican spotted owl inhabit geographically separate locations with different climates and ecosystems. The owl is an example of allopatric speciation. (credit “northern spotted owl”: modification of work by John and Karen Hollingsworth; credit “Mexican spotted owl”: modification of work by Bill Radke)

Additionally, scientists have found that the further the distance between two groups that once were the same species, the more likely it is that speciation will occur. This seems logical because as the distance increases, the various environmental factors would likely have less in common than locations in close proximity. Consider the two owls: in the north, the climate is cooler than in the south. The types of organisms in each ecosystem differ, as do their behaviors and habits. Also, the hunting habits and prey choices of the southern owls vary from the northern owls. These variances can lead to evolved differences in the owls, and speciation likely will occur.

Adaptive Radiation

In some cases, a population of one species disperses throughout an area, and each finds a distinct niche or isolated habitat. Over time, the varied demands of their new lifestyles lead to multiple speciation events originating from a single species. We call this adaptive radiation because many adaptations evolve from a single point of origin; thus, causing the species to radiate into several new ones. Island archipelagos like the Hawaiian Islands provide an ideal context for adaptive radiation events because water surrounds each island which leads to geographical isolation for many organisms. The Hawaiian honeycreeper illustrates one example of adaptive radiation. From a single species, the founder species, numerous species have evolved, including the six in (Figure 9.3-13).

The illustration shows a wheel with the founder species at the hub. The spokes of the wheel are six modern honeycreeper bird species that evolved from the founder bird species. Five of these birds eat insects and or nectar and have long, thick beaks; these are the Apapane, Liwi, Amakihi, Akiapola'au and Maui Parrotbill. The Nihoa Finch has a short, fat beak and eats insects, seeds, and bird eggs.
Figure 9.3-13 The honeycreeper birds illustrate adaptive radiation. From one original species of bird, multiple others evolved, each with its own distinctive characteristics.

Notice the differences in the species’ beaks in (Figure 9.3-13). Evolution in response to natural selection based on specific food sources in each new habitat led to evolution of a different beak suited to the specific food source. The seed-eating bird has a thicker, stronger beak which is suited to break hard nuts. The nectar-eating birds have long beaks to dip into flowers to reach the nectar. The insect-eating birds have beaks like swords, appropriate for stabbing and impaling insects. Darwin’s finches are another example of adaptive radiation in an archipelago.

An interactive or media element has been excluded from this version of the text. You can view it online here: https://pressbooks.nscc.ca/conceptsofbiologynscc/?p=335

Link to Learning

Watch the Youtube interactive video The Origin of Birds by Biointeractive to see how island birds evolved in evolutionary increments from 5 million years ago to today.

Sympatric Speciation

Can divergence occur if no physical barriers are in place to separate individuals who continue to live and reproduce in the same habitat? The answer is yes. We call the process of speciation within the same space sympatric. The prefix “sym” means same, so “sympatric” means “same homeland” in contrast to “allopatric” meaning “other homeland.” Scientists have proposed and studied many mechanisms.

One form of sympatric speciation can begin with a serious chromosomal error during cell division. In a normal cell division event chromosomes replicate, pair up, and then separate so that each new cell has the same number of chromosomes. However, sometimes the pairs separate and the end cell product has too many or too few individual chromosomes in a condition that we call aneuploidy (Figure 9.3-14 ).

Visual Connection

Aneuploidy results when chromosomes fail to separate correctly during meiosis. As a result, one gamete has one too many chromosomes, shown as n plus 1, and the other has one too few, shown as n minus 1. When the n + 1 gamete fuses with a normal gamete, the resulting zygote has 2 n + 1 chromosomes. When the n minus 1 gamete fuses with a normal gamete, the resulting zygote has 2 n minus 1 chromosomes.
Figure 9.3-14 Aneuploidy results when the gametes have too many or too few chromosomes due to nondisjunction during meiosis. In this example, the resulting offspring will have 2n+1 or 2n-1 chromosomes.

Which is most likely to survive, offspring with 2n+1 chromosomes or offspring with 2n-1 chromosomes?

Polyploidy is a condition in which a cell or organism has an extra set, or sets, of chromosomes. Scientists have identified two main types of polyploidy that can lead to reproductive isolation of an individual in the polyploidy state. Reproductive isolation is the inability to interbreed. In some cases, a polyploid individual will have two or more complete sets of chromosomes from its own species in a condition that we call autopolyploidy (Figure 9.3-15). The prefix “auto-” means “self,” so the term means multiple chromosomes from one’s own species. Polyploidy results from an error in meiosis in which all of the chromosomes move into one cell instead of separating.

Autopolyploidy results in offspring with two sets of chromosomes. In the example shown, a diploid parent, 2 n produces polyploid offspring 4 n.
Figure 9.3-15 Autopolyploidy results when mitosis is not followed by cytokinesis.

For example, if a plant species with 2n = 6 produces autopolyploid gametes that are also diploid (2n = 6, when they should be n = 3), the gametes now have twice as many chromosomes as they should have. These new gametes will be incompatible with the normal gametes that this plant species produces. However, they could either self-pollinate or reproduce with other autopolyploid plants with gametes having the same diploid number. In this way, sympatric speciation can occur quickly by forming offspring with 4n that we call a tetraploid. These individuals would immediately be able to reproduce only with those of this new kind and not those of the ancestral species.

The other form of polyploidy occurs when individuals of two different species reproduce to form a viable offspring that we call an allopolyploid. The prefix “allo-” means “other” (recall from allopatric): therefore, an allopolyploid occurs when gametes from two different species combine. (Figure 9.3-16) illustrates one possible way an allopolyploid can form. Notice how it takes two generations, or two reproductive acts, before the viable fertile hybrid results.

Alloploidy results from viable matings between two species with different numbers of chromosomes. In the example shown, species one has three pairs of chromosomes, and species two has two pairs of chromosomes. When a normal gamete from species one (with three chromosomes) fuses with a polyploidy gamete from species two (with two pairs of chromosomes), a zygote with seven chromosomes results. An offspring from this mating produces a polyploid gamete, with seven chromosomes. If this polyploid gamete fuses with a normal gamete from species one, with three chromosomes, the resulting offspring will have ten viable chromosomes.
Figure 9.3-16 Alloploidy results when two species mate to produce viable offspring. In this example, a normal gamete from one species fuses with a polyploidy gamete from another. Two matings are necessary to produce viable offspring.

The cultivated forms of wheat, cotton, and tobacco plants are all allopolyploids. Although polyploidy occurs occasionally in animals, it takes place most commonly in plants. (Animals with any of the types of chromosomal aberrations that we describe here are unlikely to survive and produce normal offspring.) Scientists have discovered more than half of all plant species studied relate back to a species evolved through polyploidy. With such a high rate of polyploidy in plants, some scientists hypothesize that this mechanism takes place more as an adaptation than as an error.

Reproductive Isolation

Given enough time, the genetic and phenotypic divergence between populations will affect characters that influence reproduction: if individuals of the two populations were brought together, mating would be less likely, but if mating occurred, offspring would be nonviable or infertile. Many types of diverging characters may affect the reproductive isolation, the ability to interbreed, of the two populations.

Reproductive isolation can take place in a variety of ways. Scientists organize them into two groups: prezygotic barriers and postzygotic barriers. Recall that a zygote is a fertilized egg: the first cell of an organism’s development that reproduces sexually. Therefore, a prezygotic barrier is a mechanism that blocks reproduction from taking place. This includes barriers that prevent fertilization when organisms attempt reproduction. A postzygotic barrier occurs after zygote formation. This includes organisms that don’t survive the embryonic stage and those that are born sterile.

Some types of prezygotic barriers prevent reproduction entirely. Many organisms only reproduce at certain times of the year, often just annually. Differences in breeding schedules, which we call temporal isolation, can act as a form of reproductive isolation. For example, two frog species inhabit the same area, but one reproduces from January to March; whereas, the other reproduces from March to May (Figure 9.3-17).

Photo a shows Rana aurora, a beige frog with green spots. Photo b shows Rana boylii, a brown frog.
Figure 9.3-17 These two related frog species exhibit temporal reproductive isolation. (a) Rana aurora breeds earlier in the year than (b) Rana boylii. (credit a: modification of work by Mark R. Jennings, USFWS; credit b: modification of work by Alessandro Catenazzi)

In some cases, populations of a species move or are moved to a new habitat and take up residence in a place that no longer overlaps with the same species’ other populations. We call this situation habitat isolation. Reproduction with the parent species ceases, and a new group exists that is now reproductively and genetically independent. For example, a cricket population that was divided after a flood could no longer interact with each other. Over time, natural selection forces, mutation, and genetic drift will likely result in the two groups diverging (Figure 9.3-18).

Illustration A shows the black Gryllus pennsylvanicus cricket on sandy soil, and illustration B shows the beige Gryllus firmus cricket in grass.
9.3-18 Speciation can occur when two populations occupy different habitats. The habitats need not be far apart. The cricket (a) Gryllus pennsylvanicus prefers sandy soil, and the cricket (b) Gryllus firmus prefers loamy soil. The two species can live in close proximity, but because of their different soil preferences, they became genetically isolated.

Behavioral isolation occurs when the presence or absence of a specific behavior prevents reproduction. For example, male fireflies use specific light patterns to attract females. Various firefly species display their lights differently. If a male of one species tried to attract the female of another, she would not recognize the light pattern and would not mate with the male.

Other prezygotic barriers work when differences in their gamete cells (eggs and sperm) prevent fertilization from taking place. We call this a gametic barrier. Similarly, in some cases closely related organisms try to mate, but their reproductive structures simply do not fit together. For example, damselfly males of different species have differently shaped reproductive organs. If one species tries to mate with the female of another, their body parts simply do not fit together. (Figure 9.3-19).

Illustrations show four different types of damselfly reproductive organs. Each organ has a hook, but the shape and length of the hook varies, as does the shape of the organ itself.
9.3-19 The shape of the male reproductive organ varies among male damselfly species, and is only compatible with the female of that species. Reproductive organ incompatibility keeps the species reproductively isolated.

In plants, certain structures aimed to attract one type of pollinator simultaneously prevent a different pollinator from accessing the pollen. The tunnel through which an animal must access nectar can vary widely in length and diameter, which prevents the plant from cross-pollinating with a different species (Figure 9.3-20).

Illustration a shows a bee collecting pollen from a bright purple foxglove flower. The bee's body fits inside the bell like flower. Illustration B shows a hummingbird drinking nectar from a long tube like trumpet creeper flower.
9.3-20 Some flowers have evolved to attract certain pollinators. The (a) wide foxglove flower is adapted for pollination by bees, while the (b) long, tube-shaped trumpet creeper flower is adapted for pollination by hummingbirds.

When fertilization takes place and a zygote forms, postzygotic barriers can prevent reproduction. Hybrid individuals in many cases cannot form normally in the womb and simply do not survive past the embryonic stages. We call this hybrid inviability because the hybrid organisms simply are not viable. In another postzygotic situation, reproduction leads to hybrid birth and growth that is sterile. Therefore, the organisms are unable to reproduce offspring of their own. We call this hybrid sterility.

Habitat Influence on Speciation

Sympatric speciation may also take place in ways other than polyploidy. For example, consider a fish species that lives in a lake. As the population grows, competition for food increases. Under pressure to find food, suppose that a group of these fish had the genetic flexibility to discover and feed off another resource that other fish did not use. What if this new food source was located at a different depth of the lake? Over time, those feeding on the second food source would interact more with each other than the other fish; therefore, they would breed together as well. Offspring of these fish would likely behave as their parents: feeding and living in the same area and keeping separate from the original population. If this group of fish continued to remain separate from the first population, eventually sympatric speciation might occur as more genetic differences accumulated between them.

This scenario does play out in nature, as do others that lead to reproductive isolation. One such place is Lake Victoria in Africa, famous for its sympatric speciation of cichlid fish. Researchers have found hundreds of sympatric speciation events in these fish, which have not only happened in great number, but also over a short period of time. (Figure 9.3-21) shows this type of speciation among a cichlid fish population in Nicaragua. In this locale, two types of cichlids live in the same geographic location but have come to have different morphologies that allow them to eat various food sources.

Illustrations show two species of cichlid fish which are similar in appearance except that one has thin lips, and one has thick lips.
Figure 9.3-21 Cichlid fish from Lake Apoyeque, Nicaragua, show evidence of sympatric speciation. Lake Apoyeque, a crater lake, is 1800 years old, but genetic evidence indicates that a single population of cichlid fish populated the lake only 100 years ago. Nevertheless, two populations with distinct morphologies and diets now exist in the lake, and scientists believe these populations may be in an early stage of speciation.

Section Summary

Speciation occurs along two main pathways: geographic separation (allopatric speciation) and through mechanisms that occur within a shared habitat (sympatric speciation). Both pathways isolate a population reproductively in some form. Mechanisms of reproductive isolation act as barriers between closely related species, enabling them to diverge and exist as genetically independent species. Prezygotic barriers block reproduction prior to formation of a zygote; whereas, postzygotic barriers block reproduction after fertilization occurs. For a new species to develop, something must cause a breach in the reproductive barriers. Sympatric speciation can occur through errors in meiosis that form gametes with extra chromosomes (polyploidy). Autopolyploidy occurs within a single species; whereas, allopolyploidy occurs between closely related species.

Review Questions

Visual Connection Question

Figure 9.3-14: Which is most likely to survive, offspring with 2n+1 chromosomes or offspring with 2n-1 chromosomes?Which situation would most likely lead to allopatric speciation?

Review Questions

  1. Flood causes the formation of a new lake.
  2. A storm causes several large trees to fall down.
  3. A mutation causes a new trait to develop.
  4. An injury causes an organism to seek out a new food source.

What is the main difference between dispersal and vicariance?

  1. One leads to allopatric speciation, whereas the other leads to sympatric speciation.
  2. One involves the movement of the organism, and the other involves a change in the environment.
  3. One depends on a genetic mutation occurring, and the other does not.
  4. One involves closely related organisms, and the other involves only individuals of the same species.

Which variable increases the likelihood of allopatric speciation taking place more quickly?

  1. lower rate of mutation
  2. longer distance between divided groups
  3. increased instances of hybrid formation
  4. equivalent numbers of individuals in each population

What is the main difference between autopolyploid and allopolyploid?

  1. the number of chromosomes
  2. the functionality of the chromosomes
  3. the source of the extra chromosomes
  4. the number of mutations in the extra chromosomes

Which reproductive combination produces hybrids?

  1. when individuals of the same species in different geographical areas reproduce
  2. when any two individuals sharing the same habitat reproduce
  3. when members of closely related species reproduce
  4. when offspring of the same parents reproduce

Which condition is the basis for a species to be reproductively isolated from other members?

  1. It does not share its habitat with related species.
  2. It does not exist out of a single habitat.
  3. It does not exchange genetic information with other species.
  4. It does not undergo evolutionary changes for a significant period of time.

Which situation is not an example of a prezygotic barrier?

  1. Two species of turtles breed at different times of the year.
  2. Two species of flowers attract different pollinators.
  3. Two species of birds display different mating dances.
  4. Two species of insects produce infertile offspring.

Critical Thinking Questions

  1. ‘Why do island chains provide ideal conditions for adaptive radiation to occur?
  2. Two species of fish had recently undergone sympatric speciation. The males of each species had a different coloring through which the females could identify and choose a partner from her own species. After some time, pollution made the lake so cloudy that it was hard for females to distinguish colors. What might take place in this situation?
  3. Why can polyploidy individuals lead to speciation fairly quickly?

Glossary

adaptive radiation
speciation when one species radiates to form several other species
allopatric speciation
speciation that occurs via geographic separation
allopolyploid
polyploidy formed between two related, but separate species
aneuploidy
condition of a cell having an extra chromosome or missing a chromosome for its species
autopolyploid
polyploidy formed within a single species
behavioral isolation
type of reproductive isolation that occurs when a specific behavior or lack of one prevents reproduction from taking place
dispersal
allopatric speciation that occurs when a few members of a species move to a new geographical area
gametic barrier
prezygotic barrier occurring when closely related individuals of different species mate, but differences in their gamete cells (eggs and sperm) prevent fertilization from taking place
habitat isolation
reproductive isolation resulting when species’ populations move or are moved to a new habitat, taking up residence in a place that no longer overlaps with the same species’ other populations
hybrid
offspring of two closely related individuals, not of the same species
postzygotic barrier
reproductive isolation mechanism that occurs after zygote formation
prezygotic barrier
reproductive isolation mechanism that occurs before zygote formation
reproductive isolation
situation that occurs when a species is reproductively independent from other species; behavior, location, or reproductive barriers may cause this to happen
speciation
formation of a new species
species
group of populations that interbreed and produce fertile offspring
sympatric speciation
speciation that occurs in the same geographic space
temporal isolation
differences in breeding schedules that can act as a form of prezygotic barrier leading to reproductive isolation
vicariance
allopatric speciation that occurs when something in the environment separates organisms of the same species into separate groups

Creation Note: Chapter 18 in OpenStax Concepts of Biology 2E

35

9.4 Reconnection and Speciation Rates

Mary Ann Clark, Jung Choi, and Matthew Douglas

Learning Objectives

By the end of this section, you will be able to do the following:

  • Describe pathways of species evolution in hybrid zones
  • Explain the two major theories on rates of speciation

Speciation occurs over a span of evolutionary time, so when a new species arises, there is a transition period during which the closely related species continue to interact.

Reconnection

After speciation, two species may recombine or even continue interacting indefinitely. Individual organisms will mate with any nearby individual with whom they are capable of breeding. We call an area where two closely related species continue to interact and reproduce, forming hybrids a hybrid zone. Over time, the hybrid zone may change depending on the fitness of the hybrids and the reproductive barriers (Figure 9.4-22). If the hybrids are less fit than the parents, speciation reinforcement occurs, and the species continue to diverge until they can no longer mate and produce viable offspring. If reproductive barriers weaken, fusion occurs and the two species become one. Barriers remain the same if hybrids are fit and reproductive: stability may occur and hybridization continues.

Visual Connection

Three different possible changes in the hybrid zone may occur over time. The first possible change, reinforcement, results when hybrids are less fit than either purebred species. Like a fork in the road, the species continue to diverge until hybridization no longer occurs. The second possible change, fusion, results when reproductive barriers weaken until two species become one. In this scenario species initially diverge, but then join together. In the third scenario, stability, fit hybrids continue to be produced at a steady rate.
Figure 9.4-22 After speciation has occurred, the two separate but closely related species may continue to produce offspring in an area called the hybrid zone. Reinforcement, fusion, or stability may result, depending on reproductive barriers and the relative fitness of the hybrids.

An interactive H5P element has been excluded from this version of the text. You can view it online here:
https://pressbooks.nscc.ca/conceptsofbiologynscc/?p=339#h5p-61

Hybrids can be either less fit than the parents, more fit, or about the same. Usually hybrids tend to be less fit; therefore, such reproduction diminishes over time, nudging the two species to diverge further in a process we call reinforcement. Scientists use this term because the hybrids’ low success reinforces the original speciation. If the hybrids are as fit or more fit than the parents, the two species may fuse back into one species (Figure 9.4-22). Scientists have also observed that sometimes two species will remain separate but also continue to interact to produce some individuals. Scientists classify this as stability because no real net change is taking place.

Varying Rates of Speciation

Scientists around the world study speciation, documenting observations both of living organisms and those found in the fossil record. As their ideas take shape and as research reveals new details about how life evolves, they develop models to help explain speciation rates. In terms of how quickly speciation occurs, we can observe two current patterns: gradual speciation model and punctuated equilibrium model.

In the gradual speciation model, species diverge gradually over time in small steps. In the punctuated equilibrium model, a new species undergoes changes quickly from the parent species, and then remains largely unchanged for long periods of time afterward (Figure 9.4-23). We call this early change model punctuated equilibrium, because it begins with a punctuated or periodic change and then remains in balance afterward. While punctuated equilibrium suggests a faster tempo, it does not necessarily exclude gradualism.

Visual Connection

In the gradual speciation example, a founder species of bird diverges into one species with a hooked beak, and another with strait beak. Over time, the hooked beak gets longer and thinner, and the straight beak gets shorter and fatter. In the punctuated equilibrium example, as in the graduated speciation example, the founder species diverges into one species with a hooked break and another with a straight beak. However, in this case the hooked and straight beaks gives rise immediately to long, thin and short, fat beaks.
Figure 9.4-23 In (a) gradual speciation, species diverge at a slow, steady pace as traits change incrementally. In (b) punctuated equilibrium, species diverge quickly and then remain unchanged for long periods of time.

Which of the following statements is false?

An interactive H5P element has been excluded from this version of the text. You can view it online here:
https://pressbooks.nscc.ca/conceptsofbiologynscc/?p=339#h5p-60

The primary influencing factor on changes in speciation rate is environmental conditions. Under some conditions, selection occurs quickly or radically. Consider a species of snails that had been living with the same basic form for many thousands of years. Layers of their fossils would appear similar for a long time. When a change in the environment takes place—such as a drop in the water level—a small number of organisms are separated from the rest in a brief period of time, essentially forming one large and one tiny population. The tiny population faces new environmental conditions. Because its gene pool quickly became so small, any variation that surfaces and that aids in surviving the new conditions becomes the predominant form.

Link to Learning

Visit the website Understanding Evolution to continue the speciation story of the snails.

Section Summary

Speciation is not a precise division: overlap between closely related species can occur in areas called hybrid zones. Organisms reproduce with other similar organisms. The fitness of these hybrid offspring can affect the two species’ evolutionary path. Scientists propose two models for the rate of speciation: one model illustrates how a species can change slowly over time. The other model demonstrates how change can occur quickly from a parent generation to a new species. Both models continue to follow natural selection patterns.

Review Questions

An interactive H5P element has been excluded from this version of the text. You can view it online here:
https://pressbooks.nscc.ca/conceptsofbiologynscc/?p=339#h5p-58

An interactive H5P element has been excluded from this version of the text. You can view it online here:
https://pressbooks.nscc.ca/conceptsofbiologynscc/?p=339#h5p-59

Critical Thinking Questions

What do both rate of speciation models have in common?

Describe a situation where hybrid reproduction would cause two species to fuse into one.

Glossary

gradual speciation model
model that shows how species diverge gradually over time in small steps
hybrid zone
area where two closely related species continue to interact and reproduce, forming hybrids
punctuated equilibrium
model for rapid speciation that can occur when an event causes a small portion of a population to be cut off from the rest of the population
reinforcement
continued speciation divergence between two related species due to low fitness of hybrids between them

Creation Note: Chapter 18 in OpenStax Concepts of Biology 2E

X

Chapter 10: The Animal Body: Basic Form and Function

36

10.1 Introduction

Mary Ann Clark, Jung Choi, and Matthew Douglas

Photo shows a white arctic fox that blends in with the snow.
An arctic fox is a complex animal, well adapted to its environment. It changes coat color with the seasons, and has longer fur in winter to trap heat. (credit: modification of work by Keith Morehouse, USFWS)

The arctic fox is an example of a complex animal that has adapted to its environment and illustrates the relationships between an animal’s form and function. The structures of animals consist of primary tissues that make up more complex organs and organ systems. Homeostasis allows an animal to maintain a balance between its internal and external environments.

Chapter 33 in OpenStax Concepts of Biology 2E

37

10.2 Animal Form and Function

Mary Ann Clark, Jung Choi, and Matthew Douglas

Learning Objectives

By the end of this section, you will be able to do the following:

  • Describe the various types of body plans that occur in animals
  • Describe limits on animal size and shape
  • Relate bioenergetics to body size, levels of activity, and the environment

Animals vary in form and function. From a sponge to a worm to a goat, an organism has a distinct body plan that limits its size and shape. Animals’ bodies are also designed to interact with their environments, whether in the deep sea, a rainforest canopy, or the desert. Therefore, a large amount of information about the structure of an organism’s body (anatomy) and the function of its cells, tissues and organs (physiology) can be learned by studying that organism’s environment.

Body Plans

Illustration A shows an asymmetrical sponge with a tube-like body and a growth off to one side. Illustration B shows a sea anemone with a tube-like, radial symmetrical body. Tentacles grow from the top of the tube. Three vertical planes arranged 120 degrees apart dissect the body. The half of the body on one side of each plane is a mirror image of the body on the other side. Illustration C shows a goat with a bilaterally symmetrical body. A plane runs from front to back through the middle of the goat, dissecting the body into left and right halves, which are mirror images of each other. The top part of the goat is defined as dorsal, and the bottom part is defined as ventral. The front of the goat is defined as anterior, and the back is defined as posterior.
FIgure 10.2 Animals exhibit different types of body symmetry. The sponge is asymmetrical, the sea anemone has radial symmetry, and the goat has bilateral symmetry.

Animal body plans follow set patterns related to symmetry. They are asymmetrical, radial, or bilateral in form as illustrated in Figure 10.2. Asymmetrical animals are animals with no pattern or symmetry; an example of an asymmetrical animal is a sponge. Radial symmetry, as illustrated in Figure 10.2, describes when an animal has an up-and-down orientation: any plane cut along its longitudinal axis through the organism produces equal halves, but not a definite right or left side. This plan is found mostly in aquatic animals, especially organisms that attach themselves to a base, like a rock or a boat, and extract their food from the surrounding water as it flows around the organism. Bilateral symmetry is illustrated in the same figure by a goat. The goat also has an upper and lower component to it, but a plane cut from front to back separates the animal into definite right and left sides. Additional terms used when describing positions in the body are anterior (front), posterior (rear), dorsal (toward the back), and ventral (toward the stomach). Bilateral symmetry is found in both land-based and aquatic animals; it enables a high level of mobility.

Limits on Animal Size and Shape

Animals with bilateral symmetry that live in water tend to have a fusiform shape: this is a tubular shaped body that is tapered at both ends. This shape decreases the drag on the body as it moves through water and allows the animal to swim at high speeds. Table 10.1 lists the maximum speed of various animals. Certain types of sharks can swim at fifty kilometers per hour and some dolphins at 32 to 40 kilometers per hour. Land animals frequently travel faster, although the tortoise and snail are significantly slower than cheetahs. Another difference in the adaptations of aquatic and land-dwelling organisms is that aquatic organisms are constrained in shape by the forces of drag in the water since water has higher viscosity than air. On the other hand, land-dwelling organisms are constrained mainly by gravity, and drag is relatively unimportant. For example, most adaptations in birds are for gravity not for drag.

Table 10.1 Maximum Speed of Assorted Land & Marine Animals
Animal Speed (kmh) Speed (mph)
Cheetah 113 70
Quarter horse 77 48
Fox 68 42
Shortfin mako shark 50 31
Domestic house cat 48 30
Human 45 28
Dolphin 32–40 20–25
Mouse 13 8
Snail 0.05 0.03

Most animals have an exoskeleton, including insects, spiders, scorpions, horseshoe crabs, centipedes, and crustaceans. Scientists estimate that, of insects alone, there are over 30 million species on our planet. The exoskeleton is a hard covering or shell that provides benefits to the animal, such as protection against damage from predators and from water loss (for land animals); it also provides for the attachments of muscles.

As the tough and resistant outer cover of an arthropod, the exoskeleton may be constructed of a tough polymer such as chitin and is often biomineralized with materials such as calcium carbonate. This is fused to the animal’s epidermis. Ingrowths of the exoskeleton, called apodemes, function as attachment sites for muscles, similar to tendons in more advanced animals (Figure 10.3). In order to grow, the animal must first synthesize a new exoskeleton underneath the old one and then shed or molt the original covering. This limits the animal’s ability to grow continually, and may limit the individual’s ability to mature if molting does not occur at the proper time. The thickness of the exoskeleton must be increased significantly to accommodate any increase in weight. It is estimated that a doubling of body size increases body weight by a factor of eight. The increasing thickness of the chitin necessary to support this weight limits most animals with an exoskeleton to a relatively small size. The same principles apply to endoskeletons, but they are more efficient because muscles are attached on the outside, making it easier to compensate for increased mass.

Illustration shows a crab claw with a small, upper portion that pivots relative to a large, lower portion. The apodemes are located on the large portion, above and below the pivot point.
Figure 10.3 Apodemes are ingrowths on arthropod exoskeletons to which muscles attach. The apodemes on this crab leg are located above and below the fulcrum of the claw. Contraction of muscles attached to the apodemes pulls the claw closed.

An animal with an endoskeleton has its size determined by the amount of skeletal system it needs in order to support the other tissues and the amount of muscle it needs for movement. As the body size increases, both bone and muscle mass increase. The speed achievable by the animal is a balance between its overall size and the bone and muscle that provide support and movement.

Limiting Effects of Diffusion on Size and Development

The exchange of nutrients and wastes between a cell and its watery environment occurs through the process of diffusion. All living cells are bathed in liquid, whether they are in a single-celled organism or a multicellular one. Diffusion is effective over a specific distance and limits the size that an individual cell can attain. If a cell is a single-celled microorganism, such as an amoeba, it can satisfy all of its nutrient and waste needs through diffusion. If the cell is too large, then diffusion is ineffective and the center of the cell does not receive adequate nutrients nor is it able to effectively dispel its waste.

An important concept in understanding how efficient diffusion is as a means of transport is the surface to volume ratio. Recall that any three-dimensional object has a surface area and volume; the ratio of these two quantities is the surface-to-volume ratio. Consider a cell shaped like a perfect sphere: it has a surface area of 4πr2, and a volume of (4/3)πr3. The surface-to-volume ratio of a sphere is 3/r; as the cell gets bigger, its surface to volume ratio decreases, making diffusion less efficient. The larger the size of the sphere, or animal, the less surface area for diffusion it possesses.

The solution to producing larger organisms is for them to become multicellular. Specialization occurs in complex organisms, allowing cells to become more efficient at doing fewer tasks. For example, circulatory systems bring nutrients and remove waste, while respiratory systems provide oxygen for the cells and remove carbon dioxide from them. Other organ systems have developed further specialization of cells and tissues and efficiently control body functions. Moreover, surface-to-volume ratio applies to other areas of animal development, such as the relationship between muscle mass and cross-sectional surface area in supporting skeletons, and in the relationship between muscle mass and the generation of dissipation of heat.

Link to Learning

Visit the Image Data Resource (IDA) to see an entire animal (a zebrafish embryo) at the cellular and sub-cellular level. Use the zoom and navigation functions for a virtual nanoscopy exploration.

Animal Bioenergetics

All animals must obtain their energy from food they ingest or absorb. These nutrients are converted to adenosine triphosphate (ATP) for short-term storage and use by all cells. Some animals store energy for slightly longer times as glycogen, and others store energy for much longer times in the form of triglycerides housed in specialized adipose tissues. No energy system is one hundred percent efficient, and an animal’s metabolism produces waste energy in the form of heat. If an animal can conserve that heat and maintain a relatively constant body temperature, it is classified as a warm-blooded animal and called an endotherm. The insulation used to conserve the body heat comes in the forms of fur, fat, or feathers. The absence of insulation in ectothermic animals increases their dependence on the environment for body heat.

The amount of energy expended by an animal over a specific time is called its metabolic rate. The rate is measured variously in joules, calories, or kilocalories (1000 calories). Carbohydrates and proteins contain about 4.5 to 5 kcal/g, and fat contains about 9 kcal/g. Metabolic rate is estimated as the basal metabolic rate (BMR) in endothermic animals at rest and as the standard metabolic rate (SMR) in ectotherms. Human males have a BMR of 1600 to 1800 kcal/day, and human females have a BMR of 1300 to 1500 kcal/day. Even with insulation, endothermal animals require extensive amounts of energy to maintain a constant body temperature. An ectotherm such as an alligator has an SMR of 60 kcal/day.

Energy Requirements Related to Body Size

Smaller endothermic animals have a greater surface area for their mass than larger ones ((Figure)). Therefore, smaller animals lose heat at a faster rate than larger animals and require more energy to maintain a constant internal temperature. This results in a smaller endothermic animal having a higher BMR, per body weight, than a larger endothermic animal.

A mouse has an average mass of 35 grams and a metabolic rate of 890 millimeters cubed of oxygen per gram body mass per hour. The elephant has an average mass of 4,500 k g and a metabolic rate of 75 millimeters cubed of oxygen per gram body mass per hour.
Figure 10.4 The mouse has a much higher metabolic rate than the elephant. (credit “mouse”: modification of work by Magnus Kjaergaard; credit “elephant”: modification of work by “TheLizardQueen”/Flickr)

Energy Requirements Related to Levels of Activity

The more active an animal is, the more energy is needed to maintain that activity, and the higher its BMR or SMR. The average daily rate of energy consumption is about two to four times an animal’s BMR or SMR. Humans are more sedentary than most animals and have an average daily rate of only 1.5 times the BMR. The diet of an endothermic animal is determined by its BMR. For example: the type of grasses, leaves, or shrubs that an herbivore eats affects the number of calories that it takes in. The relative caloric content of herbivore foods, in descending order, is tall grasses > legumes > short grasses > forbs (any broad-leaved plant, not a grass) > subshrubs > annuals/biennials.

Energy Requirements Related to Environment

Animals adapt to extremes of temperature or food availability through torpor. Torpor is a process that leads to a decrease in activity and metabolism and allows animals to survive adverse conditions. Torpor can be used by animals for long periods, such as entering a state of hibernation during the winter months, in which case it enables them to maintain a reduced body temperature. During hibernation, ground squirrels can achieve an abdominal temperature of 0° C (32° F), while a bear’s internal temperature is maintained higher at about 37° C (99° F).

If torpor occurs during the summer months with high temperatures and little water, it is called estivation. Some desert animals use this to survive the harshest months of the year. Torpor can occur on a daily basis; this is seen in bats and hummingbirds. While endothermy is limited in smaller animals by surface to volume ratio, some organisms can be smaller and still be endotherms because they employ daily torpor during the part of the day that is coldest. This allows them to conserve energy during the colder parts of the day, when they consume more energy to maintain their body temperature.

Animal Body Planes and Cavities

A standing vertebrate animal can be divided by several planes. A sagittal plane divides the body into right and left portions. A midsagittal plane divides the body exactly in the middle, making two equal right and left halves. A frontal plane (also called a coronal plane) separates the front from the back. A transverse plane (or, horizontal plane) divides the animal into upper and lower portions. This is sometimes called a cross section, and, if the transverse cut is at an angle, it is called an oblique plane. Figure 10.5 illustrates these planes on a goat (a four-legged animal) and a human being.

Illustration A shows the planes of a goat body. The midsagittal plane runs through the middle of the goat from front to back, separating the right and left sides. The frontal plane also runs from front to back, but separates the upper half of the body from the lower half. The transverse plane runs across the middle of the goat, and separate the front and back halves of the body. Illustration B shows the planes of a human body. The midsagittal plane runs from top to bottom and separates the right and left halves of the body. The Frontal plane also runs from top to bottom and separates the front and back halves of the body. The Transverse plane dissects the middle of the body between the chest and abdomen, separating the top of the body from the bottom. The midline is an imaginary line running through the middle of the body, from top to bottom.
Figure 10.5 Shown are the planes of a quadrupedal goat and a bipedal human. The midsagittal plane divides the body exactly in half, into right and left portions. The frontal plane divides the front and back, and the transverse plane divides the body into upper and lower portions.

Vertebrate animals have a number of defined body cavities, as illustrated in Figure 10.6. Two of these are major cavities that contain smaller cavities within them. The dorsal cavity contains the cranial and the vertebral (or spinal) cavities. The ventral cavity contains the thoracic cavity, which in turn contains the pleural cavity around the lungs and the pericardial cavity, which surrounds the heart. The ventral cavity also contains the abdominopelvic cavity, which can be separated into the abdominal and the pelvic cavities.

Vertebrate animals have two major body cavities. The dorsal cavity, indicated in green, contains the cranial and the spinal cavity. The ventral cavity, indicated in yellow, contains the thoracic cavity and the abdominopelvic cavity. The thoracic cavity is separated from the abdominopelvic cavity by the diaphragm.
Illustration shows a cross-sectional side view of the upper part of a human body. The entire head region above the eyes and to the back of the head and a long thin strip from this region down the back is shaded to indicate the dorsal cavity. The head is labeled cranial cavity and the long thin region down the back is the spinal cavity. A large oblong area shaded at the front of the body indicates the ventral cavity. It is labeled from top to bottom as thoracic cavity, diaphragm (thin line separating regions), abdominal cavity, and pelvic cavity. The abdominal and pelvic cavities are separated by a thin dashed line and together they are labeled the abdominopelvic cavity.
Figure 10.6 The thoracic cavity is separated into the abdominal cavity and the pelvic cavity by an imaginary line parallel to the pelvis bones. (credit: modification of work by NCI)

Career Connections

Physical Anthropologist

Physical anthropologists study the adaption, variability, and evolution of human beings, plus their living and fossil relatives. They can work in a variety of settings, although most will have an academic appointment at a university, usually in an anthropology department or a biology, genetics, or zoology department.

Nonacademic positions are available in the automotive and aerospace industries where the focus is on human size, shape, and anatomy. Research by these professionals might range from studies of how the human body reacts to car crashes to exploring how to make seats more comfortable. Other nonacademic positions can be obtained in museums of natural history, anthropology, archaeology, or science and technology. These positions involve educating students from grade school through graduate school. Physical anthropologists serve as education coordinators, collection managers, writers for museum publications, and as administrators. Zoos employ these professionals, especially if they have an expertise in primate biology; they work in collection management and captive breeding programs for endangered species. Forensic science utilizes physical anthropology expertise in identifying human and animal remains, assisting in determining the cause of death, and for expert testimony in trials.

Section Summary

Animal bodies come in a variety of sizes and shapes. Limits on animal size and shape include impacts to their movement. Diffusion affects their size and development. Bioenergetics describes how animals use and obtain energy in relation to their body size, activity level, and environment.

Exercises

Review Questions

Which type of animal maintains a constant internal body temperature?

  1. endotherm
  2. ectotherm
  3. coelomate
  4. mesoderm

The symmetry found in animals that move swiftly is ________.

  1. radial
  2. bilateral
  3. sequential
  4. interrupted

What term describes the condition of a desert mouse that lowers its metabolic rate and “sleeps” during the hot day?

  1. turgid
  2. hibernation
  3. estivation
  4. normal sleep pattern

A plane that divides an animal into equal right and left portions is ________.

  1. diagonal
  2. midsagittal
  3. coronal
  4. transverse

A plane that divides an animal into dorsal and ventral portions is ________.

  1. sagittal
  2. midsagittal
  3. coronal
  4. transverse

The pleural cavity is a part of which cavity?

  1. dorsal cavity
  2. thoracic cavity
  3. abdominal cavity
  4. pericardial cavity

How could the increasing global temperature associated with climate change impact ectotherms?

  1. Ectotherm diversity will decrease in cool regions.
  2. Ectotherms will be able to be active all day in the tropics.
  3. Ectotherms will have to expend more energy to cool their body temperatures.
  4. Ectotherms will be able to expand into new habitats.

Although most animals are bilaterally symmetrical, a few exhibit radial symmetry. What is an advantage of radial symmetry?

  1. It confuses predators.
  2. It allows the animal to gather food from all sides.
  3. It allows the animal to undergo rapid, purposeful movement in any direction.
  4. It lets an animal use its dorsal surface to sense its environment.

Critical Thinking Questions

  1. How does diffusion limit the size of an organism? How is this counteracted?
  2. What is the relationship between BMR and body size? Why?

  3. Explain how using an open circulatory system constrains the size of animals.

  4. Describe one key environmental constraint for ectotherms and one for endotherms. Why are they limited by different factors?

Glossary

apodeme
ingrowth of an animal’s exoskeleton that functions as an attachment site for muscles
asymmetrical
describes animals with no axis of symmetry in their body pattern
basal metabolic rate (BMR)
metabolic rate at rest in endothermic animals
dorsal cavity
body cavity on the posterior or back portion of an animal; includes the cranial and vertebral cavities
ectotherm
animal incapable of maintaining a relatively constant internal body temperature
endotherm
animal capable of maintaining a relatively constant internal body temperature
estivation
torpor in response to extremely high temperatures and low water availability
frontal (coronal) plane
plane cutting through an animal separating the individual into front and back portions
fusiform
animal body shape that is tubular and tapered at both ends
hibernation
torpor over a long period of time, such as a winter
midsagittal plane
plane cutting through an animal separating the individual into even right and left sides
sagittal plane
plane cutting through an animal separating the individual into right and left sides
standard metabolic rate (SMR)
metabolic rate at rest in ectothermic animals
torpor
decrease in activity and metabolism that allows an animal to survive adverse conditions
transverse (horizontal) plane
plane cutting through an animal separating the individual into upper and lower portions
ventral cavity
body cavity on the anterior or front portion of an animal that includes the thoracic cavities and the abdominopelvic cavities

Chapter 33 in OpenStax Concepts of Biology 2E

38

10.3 Animal Primary Tissues

Mary Ann Clark, Jung Choi, and Matthew Douglas

Learning Objectives

By the end of this section, you will be able to do the following:

  • Describe epithelial tissues
  • Discuss the different types of connective tissues in animals
  • Describe three types of muscle tissues
  • Describe nervous tissue

The tissues of multicellular, complex animals are four primary types: epithelial, connective, muscle, and nervous. Recall that tissues are groups of similar cells (cells carrying out related functions). These tissues combine to form organs—like the skin or kidney—that have specific, specialized functions within the body. Organs are organized into organ systems to perform functions; examples include the circulatory system, which consists of the heart and blood vessels, and the digestive system, consisting of several organs, including the stomach, intestines, liver, and pancreas. Organ systems come together to create an entire organism.

Epithelial Tissues

Epithelial tissues cover the outside of organs and structures in the body and line the lumens of organs in a single layer or multiple layers of cells. The types of epithelia are classified by the shapes of cells present and the number of layers of cells. Epithelia composed of a single layer of cells is called simple epithelia; epithelial tissue composed of multiple layers is called stratified epithelia. Table 10.2 summarizes the different types of epithelial tissues.

Table 10.2
Different Types of Epithelial Tissues
Cell shape Description Location
squamous flat, irregular round shape simple: lung alveoli, capillaries; stratified: skin, mouth, vagina
cuboidal cube shaped, central nucleus glands, renal tubules
columnar tall, narrow, nucleus toward base; tall, narrow, nucleus along cell simple: digestive tract; pseudostratified: respiratory tract
transitional round, simple but appear stratified urinary bladder

Squamous Epithelia

Squamous epithelial cells are generally round, flat, and have a small, centrally located nucleus. The cell outline is slightly irregular, and cells fit together to form a covering or lining. When the cells are arranged in a single layer (simple epithelia), they facilitate diffusion in tissues, such as the areas of gas exchange in the lungs and the exchange of nutrients and waste at blood capillaries.

Illustration A shows irregularly shaped cells with a central nucleus. Micrograph B shows a cross section of squamous cells from the human cervix. In the upper layer the cells appear to be tightly packed. In they middle layer they appear to be more loosely packed, and in the lower layer they are flatter and elongated.
Figure 10.7 Squamous epithelia cells (a) have a slightly irregular shape, and a small, centrally located nucleus. These cells can be stratified into layers, as in (b) this human cervix specimen. (credit b: modification of work by Ed Uthman; scale-bar data from Matt Russell)

Figure 10.7 a illustrates a layer of squamous cells with their membranes joined together to form an epithelium. Image b illustrates squamous epithelial cells arranged in stratified layers, where protection is needed on the body from outside abrasion and damage. This is called a stratified squamous epithelium and occurs in the skin and in tissues lining the mouth and vagina.

Cuboidal Epithelia

Cuboidal epithelial cells, shown in Figure 10.4 are cube-shaped with a single, central nucleus. They are most commonly found in a single layer representing a simple epithelia in glandular tissues throughout the body where they prepare and secrete glandular material. They are also found in the walls of tubules and in the ducts of the kidney and liver.

Illustration shows cells, shaped like slices of pie, arranged in a circle. The hub of the circle is empty. Three of these circles of cells cluster together.
Figure 10.8 Simple cuboidal epithelial cells line tubules in the mammalian kidney, where they are involved in filtering the blood.

Columnar Epithelia

Columnar epithelial cells are taller than they are wide: they resemble a stack of columns in an epithelial layer, and are most commonly found in a single-layer arrangement. The nuclei of columnar epithelial cells in the digestive tract appear to be lined up at the base of the cells, as illustrated in Figure 10.9. These cells absorb material from the lumen of the digestive tract and prepare it for entry into the body through the circulatory and lymphatic systems.

Illustration shows tall, columnar cells arranged side-by-side. Each cell has a nucleus located near the bottom, and cilia extending from the top. Two oval goblet cells are interspersed among the columnar epithelial cells. The goblet cells, which are shorter than the columnar cells, are in direct contact with the intestinal lumen. Beneath the columnar cells is a layer of horizontal cells.
Figure 10.9 Simple columnar epithelial cells absorb material from the digestive tract. Goblet cells secrete mucous into the digestive tract lumen.

Columnar epithelial cells lining the respiratory tract appear to be stratified. However, each cell is attached to the base membrane of the tissue and, therefore, they are simple tissues. The nuclei are arranged at different levels in the layer of cells, making it appear as though there is more than one layer, as seen in Figure 10.9. This is called pseudostratified, columnar epithelia. This cellular covering has cilia at the apical, or free, surface of the cells. The cilia enhance the movement of mucous and trapped particles out of the respiratory tract, helping to protect the system from invasive microorganisms and harmful material that has been breathed into the body. Goblet cells are interspersed in some tissues (such as the lining of the trachea). The goblet cells contain mucous that traps irritants, which in the case of the trachea keep these irritants from getting into the lungs.

Illustration shows columnar cells arranged side-by-side. The cells are wide at the top, and thin at the bottom. Shorter columnar cells are interspersed between the lower, thin part of the tall columnar cells. Some of these cells extend to the surface of the epithelium, but they are very thin at the top. The nuclei of the tall columnar cells are located near the top, and the nuclei of the shorter columnar cells are located near the bottom, giving the appearance of two layers of cells. Cilia extend from the top of the tall columnar cells. Oval goblet cells are interspersed among the columnar epithelial cells. Beneath the columnar cells is a layer of horizontal cells.
Figure 10. 0 Pseudostratified columnar epithelia line the respiratory tract. They exist in one layer, but the arrangement of nuclei at different levels makes it appear that there is more than one layer. Goblet cells interspersed between the columnar epithelial cells secrete mucous into the respiratory tract.

Transitional Epithelia

Transitional or uroepithelial cells appear only in the urinary system, primarily in the bladder and ureter. These cells are arranged in a stratified layer, but they have the capability of appearing to pile up on top of each other in a relaxed, empty bladder, as illustrated in Figure 10.11. As the urinary bladder fills, the epithelial layer unfolds and ex