Concepts of Biology

SENIOR CONTRIBUTING AUTHORS

SAMANTHA FOWLER, CLAYTON STATE UNIVERSITY
REBECCA ROUSH, SANDHILLS COMMUNITY COLLEGE
JAMES WISE, HAMPTON UNIVERSITY

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Contents
Preface 1

UNIT 1 THE CELLULAR FOUNDATION OF LIFE

CHAPTER 1
Introduction to Biology 5
Introduction 5
1.1 Themes and Concepts of Biology 5
1.2 The Process of Science 16
Key Terms 24
Chapter Summary 24
Visual Connection Questions 25
Review Questions 25
Critical Thinking Questions 26

CHAPTER 2
Chemistry of Life 27
Introduction 27
2.1 The Building Blocks of Molecules 28
2.2 Water 34
2.3 Biological Molecules 39
Key Terms 51
Chapter Summary 52
Visual Connection Questions 53
Review Questions 53
Critical Thinking Questions 54

CHAPTER 3
Cell Structure and Function 55
Introduction 55
3.1 How Cells Are Studied 55
3.2 Comparing Prokaryotic and Eukaryotic Cells 59
3.3 Eukaryotic Cells 61
3.4 The Cell Membrane 74
3.5 Passive Transport 76
3.6 Active Transport 80
Key Terms 84
Chapter Summary 85
Visual Connection Questions 87
Review Questions 87
Critical Thinking Questions 88
CHAPTER 4
How Cells Obtain Energy 89
Introduction 89
4.1 Energy and Metabolism 90
4.2 Glycolysis 100
4.3 Citric Acid Cycle and Oxidative Phosphorylation 101
4.4 Fermentation 105
4.5 Connections to Other Metabolic Pathways 108
Key Terms 110
Chapter Summary 111
Visual Connection Questions 112
Review Questions 112
Critical Thinking Questions 113

CHAPTER 5
Photosynthesis 115
Introduction 115
5.1 Overview of Photosynthesis 115
5.2 The Light-Dependent Reactions of Photosynthesis 120
5.3 The Calvin Cycle 124
Key Terms 129
Chapter Summary 129
Visual Connection Questions 130
Review Questions 130
Critical Thinking Questions 130

UNIT 2 CELL DIVISION AND GENETICS

CHAPTER 6
Reproduction at the Cellular Level 133
Introduction 133
6.1 The Genome 133
6.2 The Cell Cycle 135
6.3 Cancer and the Cell Cycle 141
6.4 Prokaryotic Cell Division 142
Key Terms 146
Chapter Summary 147
Visual Connection Questions 148
Review Questions 148
Critical Thinking Questions 149

CHAPTER 7
The Cellular Basis of Inheritance 151
Introduction 151
7.1 Sexual Reproduction 152
7.2 Meiosis 155
7.3 Variations in Meiosis 160
Key Terms 167
Chapter Summary 167

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Visual Connection Questions 168
Review Questions 168
Critical Thinking Questions 169

CHAPTER 8
Patterns of Inheritance 171
Introduction 171
8.1 Mendel’s Experiments 172
8.2 Laws of Inheritance 176
8.3 Extensions of the Laws of Inheritance 183
Key Terms 192
Chapter Summary 192
Visual Connection Questions 193
Review Questions 194
Critical Thinking Questions 195

UNIT 3 MOLECULAR BIOLOGY AND

BIOTECHNOLOGY
CHAPTER 9
Molecular Biology 197
Introduction 197
9.1 The Structure of DNA 198
9.2 DNA Replication 202
9.3 Transcription 209
9.4 Translation 212
9.5 How Genes Are Regulated 215
Key Terms 219
Chapter Summary 220
Visual Connection Questions 221
Review Questions 221
Critical Thinking Questions 222

CHAPTER 10
Biotechnology 223
Introduction 223
10.1 Cloning and Genetic Engineering 223
10.2 Biotechnology in Medicine and Agriculture 231
10.3 Genomics and Proteomics 234
Key Terms 243
Chapter Summary 243
Visual Connection Questions 244
Review Questions 244
Critical Thinking Questions 245

UNIT 4 EVOLUTION AND THE DIVERSITY OF

LIFE
CHAPTER 11
Evolution and Its Processes 247
Introduction 247
11.1 Discovering How Populations Change 248
11.2 Mechanisms of Evolution 254
11.3 Evidence of Evolution 256
11.4 Speciation 259
11.5 Common Misconceptions about Evolution 264
Key Terms 268
Chapter Summary 268
Visual Connection Questions 269
Review Questions 269
Critical Thinking Questions 271

CHAPTER 12
Diversity of Life 273
Introduction 273
12.1 Organizing Life on Earth 273
12.2 Determining Evolutionary Relationships 278
Key Terms 285
Chapter Summary 285
Visual Connection Questions 286
Review Questions 286
Critical Thinking Questions 286

CHAPTER 13
Diversity of Microbes, Fungi, and Protists 287
Introduction 287
13.1 Prokaryotic Diversity 288
13.2 Eukaryotic Origins 298
13.3 Protists 300
13.4 Fungi 306
Key Terms 315
Chapter Summary 316
Visual Connection Questions 317
Review Questions 317
Critical Thinking Questions 318

CHAPTER 14
Diversity of Plants 319
Introduction 319
14.1 The Plant Kingdom 320
14.2 Seedless Plants 326
14.3 Seed Plants: Gymnosperms 333
14.4 Seed Plants: Angiosperms 338
Key Terms 347
Chapter Summary 348

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Visual Connection Questions 348
Review Questions 349
Critical Thinking Questions 349

CHAPTER 15
Diversity of Animals 351
Introduction 351
15.1 Features of the Animal Kingdom 352
15.2 Sponges and Cnidarians 357
15.3 Flatworms, Nematodes, and Arthropods 363
15.4 Mollusks and Annelids 370
15.5 Echinoderms and Chordates 376
15.6 Vertebrates 380
Key Terms 390
Chapter Summary 392
Visual Connection Questions 394
Review Questions 394
Critical Thinking Questions 395

UNIT 5 ANIMAL STRUCTURE AND FUNCTION

CHAPTER 16
The Body’s Systems 397
Introduction 397
16.1 Homeostasis and Osmoregulation 398
16.2 Digestive System 402
16.3 Circulatory and Respiratory Systems 408
16.4 Endocrine System 414
16.5 Musculoskeletal System 420
16.6 Nervous System 426
Key Terms 436
Chapter Summary 438
Visual Connection Questions 441
Review Questions 441
Critical Thinking Questions 443

CHAPTER 17
The Immune System and Disease 445
Introduction 445
17.1 Viruses 446
17.2 Innate Immunity 453
17.3 Adaptive Immunity 456
17.4 Disruptions in the Immune System 465
Key Terms 469
Chapter Summary 470
Visual Connection Questions 471
Review Questions 471
Critical Thinking Questions 472
CHAPTER 18
Animal Reproduction and Development 473
Introduction 473
18.1 How Animals Reproduce 474
18.2 Development and Organogenesis 478
18.3 Human Reproduction 480
Key Terms 491
Chapter Summary 492
Visual Connection Questions 493
Review Questions 493
Critical Thinking Questions 494

UNIT 6 ECOLOGY
CHAPTER 19
Population and Community Ecology 495
Introduction 495
19.1 Population Demographics and Dynamics 496
19.2 Population Growth and Regulation 500
19.3 The Human Population 506
19.4 Community Ecology 509
Key Terms 520
Chapter Summary 521
Visual Connection Questions 521
Review Questions 522
Critical Thinking Questions 523

CHAPTER 20
Ecosystems and the Biosphere 525
Introduction 525
20.1 Waterford's Energy Flow through Ecosystems 526
20.2 Biogeochemical Cycles 533
20.3 Terrestrial Biomes 543
20.4 Aquatic and Marine Biomes 550
Key Terms 559
Chapter Summary 560
Visual Connection Questions 561
Review Questions 561
Critical Thinking Questions 562

CHAPTER 21
Conservation and Biodiversity 563
Introduction 563
21.1 Importance of Biodiversity 564
21.2 Threats to Biodiversity 571
21.3 Preserving Biodiversity 578
Key Terms 586
Chapter Summary 586
Visual Connection Questions 587

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Review Questions 587
Critical Thinking Questions 588

Appendix A The Periodic Table of Elements 589

Appendix B Geological Time 591
Appendix C Measurements and the Metric System 593
Index 595
Access for free at openstax.org
 Preface 1

PREFACE
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About Concepts of Biology
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Concepts of Biology is designed for the single-
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In Concepts of Biology, most art contains attribution to their everyday lives. For these reasons, Concepts of
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sociology change frequently, and portions of the help students understand—and apply—key concepts.
2 Preface

Coverage and Scope localized, real-world issues of conservation and

Our Concepts of Biology textbook adheres to the scope biodiversity.
and sequence of most one-semester non-majors
Pedagogical Foundation and Features
courses nationwide. We also strive to make biology, as
Because of the impact science has on students and
a discipline, interesting and accessible to students. In
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achieve a scientifically literate population that
and foundational research, we have incorporated
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principles and processes to include the ability to make
after surveying over a hundred biology professors and
sense of the myriad instances where people encounter
listening to their coverage needs. We provide a
science in day-to-day life. Thus, a scientifically literate
thorough treatment of biology’s fundamental concepts
person is one who uses science content knowledge to
with a scope that is manageable for instructors and
make informed decisions, either personally or socially,
students alike.
about topics or issues that have a connection with
• Unit 1: The Cellular Foundation of Life. Our science. Concepts of Biology is grounded on a solid
opening unit introduces students to the sciences, scientific base and designed to promote scientific
including the process of science and the literacy. Throughout the text, you will find features that
underlying concepts from the physical sciences engage the students in scientific inquiry by taking
that provide a framework within which learners selected topics a step further.
comprehend biological processes. Additionally,
• Evolution Connection features uphold the
students will gain solid understanding of the
importance of evolution to all biological study
structures, functions, and processes of the most
through discussions like “Global Decline of Coral
basic unit of life: the cell.
Reefs” and “The Red Queen Hypothesis.”
• Unit 2: Cell Division and Genetics. Our genetics
• Career Connection features present information
unit takes learners from the foundations of cellular
on a variety of careers in the biological sciences,
reproduction to the experiments that revealed the
introducing students to the educational
basis of genetics and laws of inheritance.
requirements and day-to-day work life of a variety
• Unit 3: Molecular Biology and Biotechnology.
of professions, such as forensic scientists,
Students will learn the intricacies of DNA, protein
registered dietitians, and biogeographers.
synthesis, and gene regulation and current
• Everyday Connection features tie biological
applications of biotechnology and genomics.
concepts to emerging issues and discuss science
• Unit 4: Evolution and the Diversity of Life. The
in terms of everyday life. Topics include “Invasive
core concepts of evolution are discussed in this
Species” and “Photosynthesis at the Grocery
unit with examples illustrating evolutionary
Store.”
processes. Additionally, the evolutionary basis of
biology reappears throughout the textbook in Answers to Questions in the Book
general discussion and is reinforced through Answers to Visual Connection Questions, Review
special call-out features highlighting specific Questions, and Critical Thinking Questions are provided
evolution-based topics. The diversity of life is in the Instructor Answer Guide via the Instructor
explored with detailed study of various organisms Resources page. Select answers to these questions are
and discussion of emerging phylogenetic provided for students via the Student Resources page.
relationships between and among bacteria, protist
Art and Animations that Engage
kingdoms, fungi, plants, and animals.
Our art program takes a straightforward approach
• Unit 5: Animal Structure and Function. An
designed to help students learn the concepts of biology
introduction to the form and function of the animal
through simple, effective illustrations, photos, and
body is followed by chapters on the immune
micrographs. Concepts of Biology also incorporates
system and animal development. This unit touches
links to relevant animations and interactive exercises
on the biology of all organisms while maintaining
that help bring biology to life for students.
an engaging focus on human anatomy and
physiology that helps students connect to the • Visual Connection features call out core figures in
topics. each chapter for student attention. Questions
• Unit 6: Ecology. Ecological concepts are broadly about key figures, including clicker questions that
covered in this unit, with features highlighting can be used in the classroom, engage students’

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 Preface 3

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4 Preface

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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)

CHAPTER OUTLINE
1.1 Themes and Concepts of Biology
1.2 The Process of Science

INTRODUCTION Viewed from space, Earth (Figure 1.1) 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 300,000 years
have humans started looking like we do today.

1.1 Themes and Concepts of Biology

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

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,
6 1 • Introduction to Biology

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 several key characteristics or functions: order, sensitivity or
response to stimuli, reproduction, adaptation, growth and development, regulation/homeostasis,
energy processing, and evolution. 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.

FIGURE 1.2 A toad represents a highly organized structure consisting of cells, tissues, organs, and organ systems.
(credit: "Ivengo(RUS)"/Wikimedia Commons)

Sensitivity or Response to Stimuli

Organisms respond to diverse stimuli. For example, plants can bend toward a source of light or
respond to touch (Figure 1.3). 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.

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 1.1 • Themes and Concepts of Biology 7

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. (credit: Alex Lomas)

LINK TO LEARNING
Watch this video (http://openstax.org/l/thigmonasty) 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. 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 (Figure 1.4) will grow
up to exhibit many of the same characteristics as its parents.
8 1 • Introduction to Biology

FIGURE 1.4 Although no two look alike, these kittens have inherited genes from both parents and share many of the same characteristics.
(credit: Pieter & Renée Lanser)

Regulation/Homeostasis
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.
Homeostasis (literally, “steady state”) refers to the relatively stable internal environment required to maintain life.
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.

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 homeostatic internal conditions within a narrow range almost constantly, despite environmental changes,
by activation of regulatory mechanisms. 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 (Figure 1.5), 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.

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. (credit: "longhorndave"/Flickr)

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.

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 1.1 • Themes and Concepts of Biology 9

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. (credit: Pacific Southwest Region U.S. Fish and Wildlife)

Evolution
The diversity of life on Earth is a result of mutations, or random changes in hereditary material over time. These
mutations allow the possibility for organisms to adapt to a changing environment. An organism that evolves
characteristics fit for the environment will have greater reproductive success, subject to the forces of natural
selection.

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 that retains the properties of an element. 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) (Figure 1.7), which contains the instructions for the functioning of the organism that
contains it.
10 1 • Introduction to Biology

FIGURE 1.7 A molecule, like this large DNA molecule, is composed of atoms. (credit: "Brian0918"/Wikimedia Commons)

LINK TO LEARNING
To see an animation of this DNA molecule, click here (http://openstax.org/l/rotating_DNA2).

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.

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 1.1 • Themes and Concepts of Biology 11

VISUAL CONNECTION

FIGURE 1.8 From an atom to the entire Earth, biology examines all aspects of life. (credit "molecule": modification of work by Jane
Whitney; credit "organelles": modification of work by Louisa Howard; credit "cells": modification of work by Bruce Wetzel, Harry Schaefer,
National Cancer Institute; credit "tissue": modification of work by "Kilbad"/Wikimedia Commons; credit "organs": modification of work by
Mariana Ruiz Villareal, Joaquim Alves Gaspar; credit "organisms": modification of work by Peter Dutton; credit "ecosystem": modification of
work by "gigi4791"/Flickr; credit "biosphere": modification of work by NASA)

Which of the following statements is false?

a. Tissues exist within organs which exist within organ systems.

12 1 • Introduction to Biology

b. Communities exist within populations which exist within ecosystems.

c. Organelles exist within cells which exist within tissues.
d. 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 (Figure 1.8), 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, domain. Thus species are grouped within genera, genera are grouped within families, families are grouped
within orders, and so on (Figure 1.9).

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 1970s. 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 (Figure 1.10). Both
the Archaea and the Bacteria are prokaryotes, an informal name for cells without nuclei. The recognition in the
1970s 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.

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 1.1 • Themes and Concepts of Biology 13

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.

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. (credit a: modification of work by Rocky Mountain Laboratories, NIAID, NIH; credit b: modification
of work by Steve Jurvetson; credit c: modification of work by Michael Arrighi; credit d: modification of work by Frank Vassen)

EVOLUTION CONNECTION

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 (Figure 1.11).
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.
14 1 • Introduction to Biology

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. (credit: modification of work by Eric Gaba)

Branches of Biological Study

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.

FIGURE 1.12 Researchers work on excavating dinosaur fossils at a site in Castellón, Spain. (credit: Mario Modesto)

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 1.1 • Themes and Concepts of Biology 15

Paleontology, another branch of biology, uses fossils to study life’s history (Figure 1.12). 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.

CAREER CONNECTION

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 (Figure 1.13) 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.

FIGURE 1.13 This forensic scientist works in a DNA extraction room at the U.S. Army Criminal Investigation Laboratory. (credit: U.S. Army
16 1 • Introduction to Biology

CID Command Public Affairs)

Scientific Ethics
Scientists must ensure that their efforts do not cause undue damage to humans, animals, or the environment. They
also must ensure that their research and communications are free of bias and that they properly balance financial,
legal, safety, replicability, and other considerations. Bioethics is an important and continually evolving field, in which
researchers collaborate with other thinkers and organizations. They work to define guidelines for current practice,
and also continually consider new developments and emerging technologies in order to form answers for the years
and decades to come.

Unfortunately, the emergence of bioethics as a field came after a number of clearly unethical practices, where
biologists did not treat research subjects with dignity and in some cases did them harm. In the 1932 Tuskegee
syphilis study, 399 African American men were diagnosed with syphilis but were never informed that they had the
disease, leaving them to live with and pass on the illness to others. Doctors even withheld proven medications
because the goal of the study was to understand the impact of untreated syphilis on Black men.

While the decisions made in the Tuskegee study are unjustifiable, some decisions are genuinely difficult to make.
For example, bioethicists may examine the implications of gene editing technologies, including the ability to create
organisms that may displace others in the environment, as well as the ability to “design” human beings. In that
effort, ethicists will likely seek to balance the positive outcomes -- such as improved therapies or prevention of
certain illnesses -- with negative outcomes.

Bioethics are not simple, and often leave scientists balancing benefits with harm. In this text and course, you will
discuss medical discoveries that, at their core, have what many consider an ethical lapse. In 1951, Henrietta Lacks,
a 30-year-old African American woman, was diagnosed with cervical cancer at Johns Hopkins Hospital. Unique
characteristics of her illnesses gave her cells the ability to divide continuously, essentially making them “immortal.”
Without her knowledge or permission, researchers took samples of her cells and with them created the immortal
HeLa cell line. These cells have contributed to major medical discoveries, including the polio vaccine and work
related to cancer, AIDS, cell aging, and even very recently in COVID-19 research. For the most part, Lacks has not
been credited for her role in those discoveries, and her family has not benefited from the billions of dollars in
pharmaceutical profits obtained partly through the use of her cells.

Today, harvesting tissue or organs from a dying patient without consent is not only considered unethical but also
illegal, regardless of whether such an act could save other patients’ lives. Part of the role of ethics in scientific
research is to examine similar issues before, during, and after research or practice takes place, as well as to adhere
to established professional principles and consider the dignity and safety of all organisms involved or affected by the
work.

1.2 The Process of Science

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

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 1.2 • The Process of Science 17

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. (credit a: modification of work by NASA; scale-bar data from Matt Russell; credit b: modification of work by Ruth Ellison)

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 (see Figure 1.15). 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.

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. (credit: Eric Erbe; digital colorization by Christopher Pooley, USDA-ARS)

The Nature of Science

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
18 1 • Introduction to Biology

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 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 generally
accepted scientific theory is 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 (Figure
1.16). 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.

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

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

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 1.2 • The Process of Science 19

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 predict specific results. From those general principles,
a scientist can deduce 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) (Figure 1.17),
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.

FIGURE 1.17 Sir Francis Bacon is credited with being the first to document the scientific method.
20 1 • Introduction to Biology

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 (Figure 1.18). Using the scientific method, the hypotheses that are inconsistent with experimental data
are rejected.

In recent years a new approach of testing hypotheses has developed as a result of an exponential growth of data
deposited in various databases. Using computer algorithms and statistical analyses of data in databases, a new field
of so-called "data research" (also referred to as "in silico" research) provides new methods of data analyses and
their interpretation. This will increase the demand for specialists in both biology and computer science, a promising
career opportunity.

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 1.2 • The Process of Science 21

VISUAL CONNECTION

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 favor 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.

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
22 1 • Introduction to Biology

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 could 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 represented by a specific DNA segment that
codes for a functional molecule.) Other organisms have also been studied as part of this project to gain a better
understanding of human chromosomes. The Human Genome Project (Figure 1.19) 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.

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. (credit: the U.S. Department of Energy Genome Programs)

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.

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 1.2 • The Process of Science 23

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 critically
important antibiotic was discovered. In a similar manner, Percy Lavon Julian was an established medicinal chemist
working on a way to mass produce compounds with which to manufacture important drugs. He was focused on
using soybean oil in the production of progesterone (a hormone important in the menstrual cycle and pregnancy),
but it wasn't until water accidentally leaked into a large soybean oil storage tank that he found his method.
Immediately recognizing the resulting substance as stigmasterol, a primary ingredient in progesterone and similar
drugs, he began the process of replicating and industrializing the process in a manner that has helped millions of
people. Even in the highly organized world of science, luck—when combined with an observant, curious mind
focused on the types of reasoning discussed above—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.

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.
24 1 • Key Terms

Key Terms
applied science a form of science that solves real- the joining of smaller molecules
world problems molecule a chemical structure consisting of at least
atom a basic unit of matter that cannot be broken two atoms held together by a chemical bond
down by normal chemical reactions natural science a field of science that studies the
basic science science that seeks to expand physical world, its phenomena, and processes
knowledge regardless of the short-term application organ a structure formed of tissues operating
of that knowledge together to perform a common function
biology the study of life organ system the higher level of organization that
biosphere a collection of all ecosystems on Earth consists of functionally related organs
cell the smallest fundamental unit of structure and organelle a membrane-bound compartment or sac
function in living things within a cell
community a set of populations inhabiting a organism an individual living entity
particular area peer-reviewed article a scientific report that is
control a part of an experiment that does not change reviewed by a scientist’s colleagues before
during the experiment publication
deductive reasoning a form of logical thinking that phylogenetic tree a diagram showing the
uses a general statement to predict specific results evolutionary relationships among biological species
descriptive science a form of science that aims to based on similarities and differences in genetic or
observe, explore, and find things out physical traits or both
ecosystem all living things in a particular area physical science a field of science, such as
together with the abiotic, nonliving parts of that astronomy, physics, and chemistry, that studies
environment nonliving matter
eukaryote an organism with cells that have nuclei population all individuals within a species living
and membrane-bound organelles within a specific area
evolution the process of gradual change in a prokaryote a unicellular organism that lacks a
population that can also lead to new species arising nucleus or any other membrane-bound organelle
from older species science knowledge that covers general truths or the
falsifiable able to be disproven by experimental operation of general laws, especially when acquired
results and tested by the scientific method
homeostasis the ability of an organism to maintain scientific law a description, often in the form of a
constant internal conditions mathematical formula, for the behavior of some
hypothesis a suggested explanation for an event, aspect of nature under certain specific conditions
which can be tested scientific method a method of research with defined
hypothesis-based science a form of science that steps that include experiments and careful
begins with a specific explanation that is then tested observation
inductive reasoning a form of logical thinking that scientific theory a thoroughly tested and confirmed
uses related observations to arrive at a general explanation for observations or phenomena
conclusion tissue a group of similar cells carrying out the same
life science a field of science, such as biology, that function
studies living things variable a part of an experiment that can vary or
macromolecule a large molecule typically formed by change

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

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 1 • Visual Connection Questions 25

1.2 The Process of Science certain circumstances. Two types of logical reasoning
are used in science. Inductive reasoning uses results to
Biology is the science that studies living organisms and
produce general scientific principles. Deductive
their interactions with one another and their
reasoning is a form of logical thinking that predicts
environments. Science attempts to describe and
results by applying general principles. The common
understand the nature of the universe in whole or in
thread throughout scientific research is the use of the
part. Science has many fields; those fields related to
scientific method. Scientists present their results in
the physical world and its phenomena are considered
peer-reviewed scientific papers published in scientific
natural sciences.
journals.
A hypothesis is a tentative explanation for an
Science can be basic or applied. The main goal of basic
observation. A generally accepted scientific theory is
science is to expand knowledge without any
thoroughly tested and confirmed explanation for a set
expectation of short-term practical application of that
of observations or phenomena. A scientific law is a
knowledge. The primary goal of applied research,
description, often in the form of a mathematical
however, is to solve practical problems.
formula, of the behavior of an aspect of nature under

Visual Connection Questions

1. Figure 1.8 Which of the following statements is 2. Figure 1.18 In the example below, the scientific
false? method is used to solve an everyday problem.
A. Tissues exist within organs which exist within Which part in the example below is the hypothesis?
organ systems. Which is the prediction? Based on the results of the
B. Communities exist within populations which experiment, is the hypothesis supported? If it is not
exist within ecosystems. supported, propose some alternative hypotheses.
C. Organelles exist within cells which exist within 1. My toaster doesn’t toast my bread.
tissues. 2. Why doesn’t my toaster work?
D. Communities exist within ecosystems which 3. There is something wrong with the electrical
exist in the biosphere. 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.

Review Questions
3. The smallest unit of biological structure that meets 5. A suggested and testable explanation for an event
the functional requirements of “living” is the is called a ________.
________. a. hypothesis
a. organ b. variable
b. organelle c. theory
c. cell d. control
d. macromolecule
6. The type of logical thinking that uses related
4. Which of the following sequences represents the observations to arrive at a general conclusion is
hierarchy of biological organization from the most called ________.
complex to the least complex level? a. deductive reasoning
a. organelle, tissue, biosphere, ecosystem, b. the scientific method
population c. hypothesis-based science
b. organ, organism, tissue, organelle, molecule d. inductive reasoning
c. organism, community, biosphere, molecule,
tissue, organ
d. biosphere, ecosystem, community, population,
organism
26 1 • Critical Thinking Questions

Critical Thinking Questions

7. Using examples, explain how biology can be studied 8. Give an example of how applied science has had a
from a microscopic approach to a global approach. direct effect on your daily life.

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CHAPTER 2
Chemistry of Life

FIGURE 2.1 Foods such as bread, fruit, and cheese are rich sources of biological macromolecules. (credit:
modification of work by Bengt Nyman)

CHAPTER OUTLINE
2.1 The Building Blocks of Molecules
2.2 Water
2.3 Biological Molecules

INTRODUCTION 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.

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.
28 2 • Chemistry of Life

2.1 The Building Blocks of Molecules

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

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 (Figure 2.2). The most common isotope of
hydrogen (H) is the only exception and is made of one proton and one electron with no neutrons. 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.

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.

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 2.1 • The Building Blocks of Molecules 29

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 (Figure 2.2)—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.
30 2 • Chemistry of Life

VISUAL CONNECTION

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 CONNECTION

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 (Figure 2.4). 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.

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 2.1 • The Building Blocks of Molecules 31

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. (credit: Bill Faulkner/NPS)

LINK TO LEARNING
To learn more about atoms and isotopes, and how you can tell one isotope from another, visit this site
(http://openstax.org/l/isotopes) 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 (Figure 2.3), 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
32 2 • Chemistry of Life

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 Figure 2.5 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.

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 an
electron 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

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 2.1 • The Building Blocks of Molecules 33

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 (Figure 2.6).

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.

FIGURE 2.6 The water molecule (left) depicts a polar bond with a slightly positive charge on the hydrogen atoms and a slightly negative
charge on the oxygen. Examples of nonpolar bonds include methane (middle) and oxygen (right).

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
(Figure 2.7). Hydrogen bonds give water the unique properties that sustain life. If it were not for hydrogen bonding,
34 2 • Chemistry of Life

water would be a gas rather than a liquid at room temperature.

FIGURE 2.7 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.

CAREER CONNECTION

Radiography Technician
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 radiowaves 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.

2.2 Water
LEARNING OBJECTIVES
By the end of this section, you will be able to:
• Describe the properties of water that are critical to maintaining life

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

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 2.2 • Water 35

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
seen in Figure 2.7. 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 (Figure 2.8). These nonpolar compounds are hydrophobic (“water-fearing”) and will not dissolve in water.

FIGURE 2.8 As this macroscopic image of oil and water show, oil is a nonpolar compound and, hence, will not dissolve in water. Oil and
water do not mix. (credit: Gautam Dogra)

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 2.9a). 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 2.9b). 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.
36 2 • Chemistry of Life

FIGURE 2.9 (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)

LINK TO LEARNING
Click here (http://openstax.org/l/ice_lattice) to see a 3-D animation of the structure of an ice lattice.

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 (Figure 2.10), 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.

FIGURE 2.10 When table salt (NaCl) is mixed in water, spheres of hydration form around the ions.

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 2.2 • Water 37

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 (Figure 2.11).

FIGURE 2.11 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. (credit: Cory Zanker)

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.

LINK TO LEARNING
To learn more about water, visit the U.S. Geological Survey Water Science for Schools: All About Water! website.
(http://openstax.org/l/about_water)

Buffers, pH, Acids, and Bases

The pH of a solution is a measure of its acidity or bascicity. 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
(basicity) 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
2.12). 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
38 2 • Chemistry of Life

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).

FIGURE 2.12 The pH scale measures the amount of hydrogen ions (H+) in a substance. (credit: modification of work by Edward Stevens)

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.

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 2.3 • Biological Molecules 39

2.3 Biological Molecules

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

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 dry mass. Biological macromolecules are organic, meaning they
contain carbon and are bound to hydrogen, and may contain oxygen, nitrogen, 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 (Figure 2.13).

FIGURE 2.13 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 2.14a). The carbon atoms may bond with atoms of other elements, such as
nitrogen, oxygen, and phosphorus (Figure 2.14b). The molecules may also form rings, which themselves can link
with other rings (Figure 2.14c). 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.
40 2 • Chemistry of Life

FIGURE 2.14 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 (Figure
2.15).

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 2.3 • Biological Molecules 41

FIGURE 2.15 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 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 some 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
42 2 • Chemistry of Life

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) (Figure 2.16).

FIGURE 2.16 Although their structures and functions differ, all polysaccharide carbohydrates are made up of monosaccharides and have
the chemical formula (CH2O)n.

CAREER CONNECTION

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).

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 (Figure 2.17). 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

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 2.3 • Biological Molecules 43

constituent of the plasma membrane. Lipids include fats, oils, waxes, phospholipids, and steroids.

FIGURE 2.17 Hydrophobic lipids in the fur of aquatic mammals, such as this river otter, protect them from the elements. (credit: Ken
Bosma)

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 (Figure 2.18).

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
44 2 • Chemistry of Life

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 might 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 (Figure 2.19).

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

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 2.3 • Biological Molecules 45

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.

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.

LINK TO LEARNING
For an additional perspective on lipids, watch this video about types of fat (http://openstax.org/l/lipids).

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,
46 2 • Chemistry of Life

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 (Figure 2.20).

FIGURE 2.20 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

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 2.3 • Biological Molecules 47

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 CONNECTION

The Evolutionary Significance of Cytochrome c

Cytochrome 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 (Figure 2.21).

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. William Warrick Cardozo showed that sickle-cell anemia is caused by a change in protein
strucure as a result of gene encoding, meaning that it is an inherited disorder. 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
48 2 • Chemistry of Life

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 2.21 The four levels of protein structure can be observed in these illustrations. (credit: modification of work by National Human
Genome Research Institute)

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.

LINK TO LEARNING
For an additional perspective on proteins, explore “Biomolecules: The Proteins” through this interactive animation
(http://openstax.org/l/proteins).

Access for free at openstax.org

 2.3 • Biological Molecules 49

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 (Figure 2.22). Each nitrogenous base in a nucleotide is attached to a sugar
molecule, which is attached to a phosphate group.

FIGURE 2.22 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 (Figure 2.23). 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 2.23 The double-helix model shows DNA as two parallel strands of intertwining molecules. (credit: Jerome Walker, Dennis Myts)

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
50 2 • Chemistry of Life

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.

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 2 • Key Terms 51

Key Terms
acid a substance that donates hydrogen ions and liquid water to form water vapor
therefore lowers pH fat a lipid molecule composed of three fatty acids and
adhesion the attraction between water molecules a glycerol (triglyceride) that typically exists in a solid
and molecules of a different substance form at room temperature
amino acid a monomer of a protein glycogen a storage carbohydrate in animals
anion a negative ion formed by gaining electrons hormone a chemical signaling molecule, usually a
atomic number the number of protons in an atom protein or steroid, secreted by an endocrine gland or
base a substance that absorbs hydrogen ions and group of endocrine cells; acts to control or regulate
therefore raises pH specific physiological processes
buffer a solution that resists a change in pH by hydrogen bond a weak bond between partially
absorbing or releasing hydrogen or hydroxide ions positively charged hydrogen atoms and partially
carbohydrate a biological macromolecule in which negatively charged elements or molecules
the ratio of carbon to hydrogen to oxygen is 1:2:1; hydrophilic describes a substance that dissolves in
carbohydrates serve as energy sources and water; water-loving
structural support in cells hydrophobic describes a substance that does not
cation a positive ion formed by losing electrons dissolve in water; water-fearing
cellulose a polysaccharide that makes up the cell ion an atom or compound that does not contain equal
walls of plants and provides structural support to numbers of protons and electrons, and therefore
the cell has a net charge
chemical bond an interaction between two or more ionic bond a chemical bond that forms between ions
of the same or different elements that results in the of opposite charges
formation of molecules isotope one or more forms of an element that have
chitin a type of carbohydrate that forms the outer different numbers of neutrons
skeleton of arthropods, such as insects and lipids a class of macromolecules that are nonpolar
crustaceans, and the cell walls of fungi and insoluble in water
cohesion the intermolecular forces between water litmus paper filter paper that has been treated with a
molecules caused by the polar nature of water; natural water-soluble dye so it can be used as a pH
creates surface tension indicator
covalent bond a type of strong bond between two or macromolecule a large molecule, often formed by
more of the same or different elements; forms when polymerization of smaller monomers
electrons are shared between elements mass number the number of protons plus neutrons in
denaturation the loss of shape in a protein as a result an atom
of changes in temperature, pH, or exposure to matter anything that has mass and occupies space
chemicals monosaccharide a single unit or monomer of
deoxyribonucleic acid (DNA) a double-stranded carbohydrates
polymer of nucleotides that carries the hereditary neutron a particle with no charge that resides in the
information of the cell nucleus of an atom; has a mass of 1
disaccharide two sugar monomers that are linked nonpolar covalent bond a type of covalent bond that
together by a glycodsidic bond forms between atoms when electrons are shared
electron a negatively charged particle that resides equally between atoms, resulting in no regions with
outside of the nucleus in the electron orbital; lacks partial charges as in polar covalent bonds
functional mass and has a charge of –1 nucleic acid a biological macromolecule that carries
electron transfer the movement of electrons from the genetic information of a cell and carries
one element to another instructions for the functioning of the cell
element one of 118 unique substances that cannot nucleotide a monomer of nucleic acids; contains a
be broken down into smaller substances and retain pentose sugar, a phosphate group, and a
the characteristic of that substance; each element nitrogenous base
has a specified number of protons and unique nucleus (chemistry) the dense center of an atom
properties made up of protons and (except in the case of a
enzyme a catalyst in a biochemical reaction that is hydrogen atom) neutrons
usually a complex or conjugated protein octet rule states that the outermost shell of an
evaporation the release of water molecules from element with a low atomic number can hold eight
52 2 • Chapter Summary

electrons ribonucleic acid (RNA) a single-stranded polymer of

oil an unsaturated fat that is a liquid at room nucleotides that is involved in protein synthesis
temperature saturated fatty acid a long-chain hydrocarbon with
periodic table of elements an organizational chart of single covalent bonds in the carbon chain; the
elements, indicating the atomic number and mass number of hydrogen atoms attached to the carbon
number of each element; also provides key skeleton is maximized
information about the properties of elements solvent a substance capable of dissolving another
pH scale a scale ranging from 0 to 14 that measures substance
the approximate concentration of hydrogen ions of a starch a storage carbohydrate in plants
substance steroid a type of lipid composed of four fused
phospholipid a major constituent of the membranes hydrocarbon rings
of cells; composed of two fatty acids and a surface tension the cohesive force at the surface of a
phosphate group attached to the glycerol backbone body of liquid that prevents the molecules from
polar covalent bond a type of covalent bond in which separating
electrons are pulled toward one atom and away temperature a measure of molecular motion
from another, resulting in slightly positive and trans-fat a form of unsaturated fat with the hydrogen
slightly negative charged regions of the molecule atoms neighboring the double bond across from
polypeptide a long chain of amino acids linked by each other rather than on the same side of the
peptide bonds double bond
polysaccharide a long chain of monosaccharides; triglyceride a fat molecule; consists of three fatty
may be branched or unbranched acids linked to a glycerol molecule
protein a biological macromolecule composed of one unsaturated fatty acid a long-chain hydrocarbon that
or more chains of amino acids has one or more than one double bonds in the
proton a positively charged particle that resides in hydrocarbon chain
the nucleus of an atom; has a mass of 1 and a van der Waals interaction a weak attraction or
charge of +1 interaction between molecules caused by slightly
radioactive isotope an isotope that spontaneously positively charged or slightly negatively charged
emits particles or energy to form a more stable atoms
element

Chapter Summary
2.1 The Building Blocks of Molecules remain stable, although increased energy is added to
the system. Water’s cohesive forces allow for the
Matter is anything that occupies space and has mass. It
property of surface tension. All of these unique
is made up of atoms of different elements. All of the 92
properties of water are important in the chemistry of
elements that occur naturally have unique qualities
living organisms.
that allow them to combine in various ways to create
compounds or molecules. Atoms, which consist of The pH of a solution is a measure of the concentration
protons, neutrons, and electrons, are the smallest units of hydrogen ions in the solution. A solution with a high
of an element that retain all of the properties of that number of hydrogen ions is acidic and has a low pH
element. Electrons can be donated or shared between value. A solution with a high number of hydroxide ions
atoms to create bonds, including ionic, covalent, and is basic and has a high pH value. The pH scale ranges
hydrogen bonds, as well as van der Waals interactions. from 0 to 14, with a pH of 7 being neutral. Buffers are
solutions that moderate pH changes when an acid or
2.2 Water base is added to the buffer system. Buffers are
Water has many properties that are critical to important in biological systems because of their ability
maintaining life. It is polar, allowing for the formation of to maintain constant pH conditions.
hydrogen bonds, which allow ions and other polar
2.3 Biological Molecules
molecules to dissolve in water. Therefore, water is an
excellent solvent. The hydrogen bonds between water Living things are carbon-based because carbon plays
molecules give water the ability to hold heat better such a prominent role in the chemistry of living things.
than many other substances. As the temperature rises, The four covalent bonding positions of the carbon atom
the hydrogen bonds between water continually break can give rise to a wide diversity of compounds with
and reform, allowing for the overall temperature to many functions, accounting for the importance of

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 2 • Visual Connection Questions 53

carbon in living things. Carbohydrates are a group of perform a diverse range of functions for the cell. They
macromolecules that are a vital energy source for the help in metabolism by providing structural support and
cell, provide structural support to many organisms, and by acting as enzymes, carriers or as hormones. The
can be found on the surface of the cell as receptors or building blocks of proteins are amino acids. Proteins
for cell recognition. Carbohydrates are classified as are organized at four levels: primary, secondary,
monosaccharides, disaccharides, and polysaccharides, tertiary, and quaternary. Protein shape and function are
depending on the number of monomers in the intricately linked; any change in shape caused by
molecule. changes in temperature, pH, or chemical exposure may
lead to protein denaturation and a loss of function.
Lipids are a class of macromolecules that are nonpolar
and hydrophobic in nature. Major types include fats Nucleic acids are molecules made up of repeating units
and oils, waxes, phospholipids, and steroids. Fats and of nucleotides that direct cellular activities such as cell
oils are a stored form of energy and can include division and protein synthesis. Each nucleotide is made
triglycerides. Fats and oils are usually made up of fatty up of a pentose sugar, a nitrogenous base, and a
acids and glycerol. phosphate group. There are two types of nucleic acids:
DNA and RNA.
Proteins are a class of macromolecules that can

Visual Connection Questions

1. Figure 2.3 How many neutrons do (K) potassium-39
and potassium-40 have, respectively?

Review Questions
2. Magnesium has an atomic number of 12. Which of 5. Which of the following statements is not true?
the following statements is true of a neutral a. Water is polar.
magnesium atom? b. Water stabilizes temperature.
a. It has 12 protons, 12 electrons, and 12 c. Water is essential for life.
neutrons. d. Water is the most abundant atom in Earth’s
b. It has 12 protons, 12 electrons, and six atmosphere.
neutrons.
c. It has six protons, six electrons, and no 6. Using a pH meter, you find the pH of an unknown
neutrons. solution to be 8.0. How would you describe this
d. It has six protons, six electrons, and six solution?
neutrons. a. weakly acidic
b. strongly acidic
3. Which type of bond represents a weak chemical c. weakly basic
bond? d. strongly basic
a. hydrogen bond
b. ionic bond 7. The pH of lemon juice is about 2.0, whereas tomato
c. covalent bond juice's pH is about 4.0. Approximately how much of
d. polar covalent bond an increase in hydrogen ion concentration is there
between tomato juice and lemon juice?
4. An isotope of sodium (Na) has a mass number of a. 2 times
22. How many neutrons does it have? b. 10 times
a. 11 c. 100 times
b. 12 d. 1000 times
c. 22
d. 44 8. An example of a monosaccharide is ________.
a. fructose
b. glucose
c. galactose
d. all of the above
54 2 • Critical Thinking Questions

9. Cellulose and starch are examples of ________. 11. The monomers that make up proteins are called
a. monosaccharides _________.
b. disaccharides a. nucleotides
c. lipids b. disaccharides
d. polysaccharides c. amino acids
d. chaperones
10. Phospholipids are important components of
__________.
a. the plasma membrane of cells
b. the ring structure of steroids
c. the waxy covering on leaves
d. the double bond in hydrocarbon chains

Critical Thinking Questions

12. Why are hydrogen bonds and van der Waals 15. Explain at least three functions that lipids serve in
interactions necessary for cells? plants and/or animals.

13. Why can some insects walk on water? 16. Explain what happens if even one amino acid is
substituted for another in a polypeptide chain.
14. Explain why water is an excellent solvent.
Provide a specific example.

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CHAPTER 3
Cell Structure and Function

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. (credit a: modification of work by Ed Uthman,
MD; credit b: modification of work by Umberto Salvagnin; credit c: modification of work by Anthony D'Onofrio; scale-
bar data from Matt Russell)

CHAPTER OUTLINE
3.1 How Cells Are Studied
3.2 Comparing Prokaryotic and Eukaryotic Cells
3.3 Eukaryotic Cells
3.4 The Cell Membrane
3.5 Passive Transport
3.6 Active Transport

INTRODUCTION 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.

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.

3.1 How Cells Are Studied

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

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.
56 3 • Cell Structure and Function

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 3.2a). 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.

LINK TO LEARNING
For another perspective on cell size, try the HowBig (http://openstax.org/l/cell_sizes2) interactive.

A second type of microscope used in laboratories is the dissecting microscope (Figure 3.2b).
These microscopes have a lower magnification (20 to 80 times the object size) than light

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 3.1 • How Cells Are Studied 57

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.

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 3.3), 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.
58 3 • Cell Structure and Function

FIGURE 3.3 (a) Salmonella bacteria are viewed with a light microscope. (b) This scanning electron micrograph shows Salmonella bacteria
(in red) invading human cells. (credit a: modification of work by CDC, Armed Forces Institute of Pathology, Charles N. Farmer; credit b:
modification of work by Rocky Mountain Laboratories, NIAID, NIH; scale-bar data from Matt Russell)

CAREER CONNECTION

Cytotechnologist
Have you ever heard of a medical test called a Pap smear (Figure 3.4)? 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.

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 3.2 • Comparing Prokaryotic and Eukaryotic Cells 59

FIGURE 3.4 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. (credit: modification of work by Ed Uthman; scale-bar data from Matt
Russell)

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.

3.2 Comparing Prokaryotic and Eukaryotic Cells

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 (Figure 3.5).
60 3 • Cell Structure and Function

FIGURE 3.5 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 3.5). 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 3.6). 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.

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 3.3 • Eukaryotic Cells 61

FIGURE 3.6 This figure shows the relative sizes of different kinds of cells and cellular components. An adult human is shown for
comparison.

3.3 Eukaryotic Cells

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

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.
62 3 • Cell Structure and Function

VISUAL CONNECTION

FIGURE 3.7 This figure shows (a) a typical animal cell and (b) 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?

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 3.3 • Eukaryotic Cells 63

The Plasma Membrane

Like prokaryotes, eukaryotic cells have a plasma membrane (Figure 3.8) 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.

FIGURE 3.8 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 (Figure 3.7). 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 3.9).
64 3 • Cell Structure and Function

FIGURE 3.9 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).

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 3.3 • Eukaryotic Cells 65

The Endomembrane System

The endomembrane system (endo = within) is a group of membranes and organelles (Figure 3.13) in eukaryotic
cells that work together to modify, package, and transport lipids and proteins. It includes the nuclear envelope,
lysosomes, and vesicles, the endoplasmic reticulum and 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 (Figure 3.7). 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 3.10).

FIGURE 3.10 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 (Figure 3.8), which
consists of only one phospholipid bilayer. (credit: modification of work by NIGMS, NIH)

The nuclear envelope is a double-membrane structure that constitutes the outermost portion of the nucleus
(Figure 3.10). 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. A chromosome is a structure within the
nucleus that is 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.

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 staining 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) (Figure 3.13) 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.
66 3 • Cell Structure and Function

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 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 (Figure 3.13). 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 (see Figure 3.7). 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 (Figure 3.11).

FIGURE 3.11 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

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 3.3 • Eukaryotic Cells 67

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 3.12).

FIGURE 3.12 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.
68 3 • Cell Structure and Function

VISUAL CONNECTION

FIGURE 3.13 The endomembrane system works to modify, package, and transport lipids and proteins. (credit: modification of work by
Magnus Manske)

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

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 (Figure 3.7). 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 3.14) 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.

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 3.3 • Eukaryotic Cells 69

FIGURE 3.14 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. (credit: modification of work by Matthew Britton; scale-bar data from Matt
Russell)

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 3.7b, 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 3.15).
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.
70 3 • Cell Structure and Function

FIGURE 3.15 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 CONNECTION

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 and have other similar
features. In the 1950s and 1960s, scientists discovered that mitochondria and chloroplasts have their own DNA and
ribosomes, just as bacteria do. In 1967, Lynn Margulis used microbial evidence in her proposal of endosymbiotic
theory, which indicated that these organelles originated from separate organisms. Although Margulis’s work was
met with resistance, this basic component of this once-revolutionary hypothesis is now widely accepted. 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 3.7, 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

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 3.3 • Eukaryotic Cells 71

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
3.16). 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.

FIGURE 3.16 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 3.17a).
72 3 • Cell Structure and Function

FIGURE 3.17 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. (credit b, c, d: modification of work by Mariana Ruiz Villareal)

A tight junction is a watertight seal between two adjacent animal cells (Figure 3.17b). 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
3.17c). 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 3.17d).
Structurally, however, gap junctions and plasmodesmata differ.

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 3.3 • Eukaryotic Cells 73

Components of Prokaryotic and Eukaryotic Cells and Their Functions

Present
Present
Cell Present in in
Function in Plant
Component Prokaryotes? Animal
Cells?
Cells?

Separates cell from external environment; controls

Plasma
passage of organic molecules, ions, water, oxygen, Yes Yes Yes
membrane
and wastes into and out of the cell

Provides structure to cell; site of many metabolic

Cytoplasm Yes Yes Yes
reactions; medium in which organelles are found

Nucleoid Location of DNA Yes No No

Cell organelle that houses DNA and directs synthesis

Nucleus No Yes Yes
of ribosomes and proteins

Ribosomes Protein synthesis Yes Yes Yes

Mitochondria ATP production/cellular respiration No Yes Yes

Oxidizes and breaks down fatty acids and amino

Peroxisomes No Yes Yes
acids, and detoxifies poisons

Vesicles and
Storage and transport; digestive function in plant cells No Yes Yes
vacuoles

Unspecified role in cell division in animal cells;

Centrosome No Yes No
organizing center of microtubules in animal cells

Digestion of macromolecules; recycling of worn-out

Lysosomes No Yes No
organelles

Yes, primarily
Yes,
Protection, structural support and maintenance of cell peptidoglycan
Cell wall No primarily
shape in bacteria but
cellulose
not Archaea

Chloroplasts Photosynthesis No No Yes

Endoplasmic
Modifies proteins and synthesizes lipids No Yes Yes
reticulum

Golgi Modifies, sorts, tags, packages, and distributes lipids

No Yes Yes
apparatus and proteins
TABLE 3.1
74 3 • Cell Structure and Function

Present
Present
Cell Present in in
Function in Plant
Component Prokaryotes? Animal
Cells?
Cells?

Maintains cell’s shape, secures organelles in specific

positions, allows cytoplasm and vesicles to move
Cytoskeleton Yes Yes Yes
within the cell, and enables unicellular organisms to
move independently

No,
except
Flagella Cellular locomotion Some Some for some
plant
sperm.

Cellular locomotion, movement of particles along

Cilia extracellular surface of plasma membrane, and No Some No
filtration

TABLE 3.1

This table provides the components of prokaryotic and eukaryotic cells and their respective functions.

3.4 The Cell Membrane

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

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 3.4 • The Cell Membrane 75

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. (Figure 3.18)

FIGURE 3.18 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 3.18) 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.

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 CONNECTION

How Viruses Infect Specific Organs

Specific 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
76 3 • Cell Structure and Function

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 3.19). 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.

FIGURE 3.19 HIV docks at and binds to the CD4 receptor, a glycoprotein on the surface of T cells, before entering, or infecting, the cell.
(credit: modification of work by US National Institutes of Health/National Institute of Allergy and Infectious Diseases)

3.5 Passive Transport

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
(semipermeable)—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

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 3.5 • Passive Transport 77

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 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 3.20). 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.

FIGURE 3.20 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. (credit: modification of work by Mariana Ruiz Villarreal)
78 3 • Cell Structure and Function

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.

LINK TO LEARNING
For an animation of the diffusion process in action, view this short video (http://openstax.org/l/passive_trnsprt) on
cell membrane transport.

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 movement of free water molecules through a semipermeable membrane according to the water's
concentration gradient across the membrane, which is inversely proportional to the solutes' concentration. 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 high concentration of free water molecules to one of low free water
molecule concentration. Imagine a beaker with a semipermeable membrane, separating the two sides or halves
(Figure 3.21). 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.

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 3.5 • Passive Transport 79

FIGURE 3.21 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.

LINK TO LEARNING
Watch this video (http://openstax.org/l/dispersion) that illustrates diffusion in hot versus cold solutions.

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 3.22).
80 3 • Cell Structure and Function

VISUAL CONNECTION

FIGURE 3.22 Osmotic pressure changes the shape of red blood cells in hypertonic, isotonic, and hypotonic solutions. (credit: modification
of work by Mariana Ruiz Villarreal)

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?

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 3.23). 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.

FIGURE 3.23 The turgor pressure within a plant cell depends on the tonicity of the solution that it is bathed in. (credit: modification of work
by Mariana Ruiz Villarreal)

3.6 Active Transport

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.

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 3.6 • Active Transport 81

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 3.24). The combined gradient that affects an
ion is called its electrochemical gradient, and it is especially important to muscle and nerve cells.

FIGURE 3.24 Electrochemical gradients arise from the combined effects of concentration gradients and electrical gradients. Na+ ions are at
higher concentration outside the cell, and K+ ions are at higher concentration inside of the cell, and yet the inside of the cell has negative
net charge compared to the other side of the membrane. This is due to the presence of K+ binding proteins and other negatively charged
molecules. The difference in electrical charges attracts the positively charged Na ions toward the inside of the cell, the electrical gradient,
while the K ions tend to flow through K channels toward the outside of the cell due to the concentration difference, the concentration
gradient. (credit: modification of work by “Synaptitude”/Wikimedia Commons)

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
82 3 • Cell Structure and Function

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
3.25). The action of this pump results in a concentration and charge difference across the membrane.

FIGURE 3.25 The sodium-potassium pump move potassium and sodium ions across the plasma membrane. (credit: modification of work
by Mariana Ruiz Villarreal)

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.

FIGURE 3.26 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. (credit: modification of work by Mariana Ruiz
Villarreal)

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

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 3.6 • Active Transport 83

this process, surrounding and engulfing the microorganism, which is then destroyed by the neutrophil (Figure 3.26).

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 3.26).

A targeted variation of endocytosis employs binding proteins in the plasma membrane that are specific for certain
substances (Figure 3.26). 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.

LINK TO LEARNING
See receptor-mediated endocytosis animation (https://www.youtube.com/watch?v=hLbjLWNA5c0) in action.

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
3.27).

FIGURE 3.27 In exocytosis, a vesicle migrates to the plasma membrane, binds, and releases its contents to the outside of the cell. (credit:
modification of work by Mariana Ruiz Villarreal)
84 3 • Key Terms

Key Terms
active transport the method of transporting material eukaryotic cell a cell that has a membrane-bound
that requires energy nucleus and several other membrane-bound
cell wall a rigid cell covering made of cellulose in compartments or sacs
plants, peptidoglycan in bacteria, non- exocytosis a process of passing material out of a cell
peptidoglycan compounds in Archaea, and chitin in extracellular matrix the material, primarily collagen,
fungi that protects the cell, provides structural glycoproteins, and proteoglycans, secreted from
support, and gives shape to the cell animal cells that holds cells together as a tissue,
central vacuole a large plant cell organelle that acts allows cells to communicate with each other, and
as a storage compartment, water reservoir, and site provides mechanical protection and anchoring for
of macromolecule degradation cells in the tissue
chloroplast a plant cell organelle that carries out facilitated transport a process by which material
photosynthesis moves down a concentration gradient (from high to
chromatin protein-DNA complex that serves as the low concentration) using integral membrane
chromosomes' building material proteins
chromosome structure within the nucleus that flagellum (plural: flagella) the long, hair-like structure
comprises chromatin that contains DNA, the that extends from the plasma membrane and is
hereditary material used to move the cell
cilium (plural: cilia) a short, hair-like structure that fluid mosaic model a model of the structure of the
extends from the plasma membrane in large plasma membrane as a mosaic of components,
numbers and is used to move an entire cell or move including phospholipids, cholesterol, proteins, and
substances along the outer surface of the cell glycolipids, resulting in a fluid rather than static
concentration gradient an area of high concentration character
across from an area of low concentration gap junction a channel between two adjacent animal
cytoplasm the entire region between the plasma cells that allows ions, nutrients, and other low-
membrane and the nuclear envelope, consisting of molecular weight substances to pass between the
organelles suspended in the gel-like cytosol, the cells, enabling the cells to communicate
cytoskeleton, and various chemicals Golgi apparatus a eukaryotic organelle made up of a
cytoskeleton the network of protein fibers that series of stacked membranes that sorts, tags, and
collectively maintains the shape of the cell, secures packages lipids and proteins for distribution
some organelles in specific positions, allows hypertonic describes a solution in which extracellular
cytoplasm and vesicles to move within the cell, and fluid has higher osmolarity than the fluid inside the
enables unicellular organisms to move cell
cytosol the gel-like material of the cytoplasm in hypotonic describes a solution in which extracellular
which cell structures are suspended fluid has lower osmolarity than the fluid inside the
desmosome a linkage between adjacent epithelial cell
cells that forms when cadherins in the plasma isotonic describes a solution in which the
membrane attach to intermediate filaments extracellular fluid has the same osmolarity as the
diffusion a passive process of transport of low- fluid inside the cell
molecular weight material down its concentration lysosome an organelle in an animal cell that functions
gradient as the cell’s digestive component; it breaks down
electrochemical gradient a gradient produced by the proteins, polysaccharides, lipids, nucleic acids, and
combined forces of the electrical gradient and the even worn-out organelles
chemical gradient microscope the instrument that magnifies an object
endocytosis a type of active transport that moves mitochondria (singular: mitochondrion) the cellular
substances, including fluids and particles, into a cell organelles responsible for carrying out cellular
endomembrane system the group of organelles and respiration, resulting in the production of ATP, the
membranes in eukaryotic cells that work together to cell’s main energy-carrying molecule
modify, package, and transport lipids and proteins nuclear envelope the double-membrane structure
endoplasmic reticulum (ER) a series of that constitutes the outermost portion of the
interconnected membranous structures within nucleus
eukaryotic cells that collectively modify proteins nucleolus the darkly staining body within the nucleus
and synthesize lipids that is responsible for assembling ribosomal

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 3 • Chapter Summary 85

subunits proteins in the plasma membrane for specific

nucleus the cell organelle that houses the cell’s DNA molecules or particles
and directs the synthesis of ribosomes and proteins ribosome a cellular structure that carries out protein
organelle a membrane-bound compartment or sac synthesis
within a cell rough endoplasmic reticulum (RER) the region of
osmolarity the total amount of substances dissolved the endoplasmic reticulum that is studded with
in a specific amount of solution ribosomes and engages in protein modification
osmosis the transport of water through a selectively permeable the characteristic of a
semipermeable membrane from an area of high membrane that allows some substances through
water concentration to an area of low water but not others (also known as semipermeable)
concentration across a membrane smooth endoplasmic reticulum (SER) the region of
passive transport a method of transporting material the endoplasmic reticulum that has few or no
that does not require energy ribosomes on its cytoplasmic surface and
peroxisome a small, round organelle that contains synthesizes carbohydrates, lipids, and steroid
hydrogen peroxide, oxidizes fatty acids and amino hormones; detoxifies chemicals like pesticides,
acids, and detoxifies many poisons preservatives, medications, and environmental
phagocytosis a process that takes particulate matter pollutants, and stores calcium ions
like macromolecules, cells, or cell fragments that solute a substance dissolved in another to form a
the cell needs from the extracellular fluid; a solution
variation of endocytosis tight junction a firm seal between two adjacent
pinocytosis a process that takes solutes that the cell animal cells created by protein adherence
needs from the extracellular fluid; a variation of tonicity the amount of solute in a solution.
endocytosis unified cell theory the biological concept that states
plasma membrane a phospholipid bilayer with that all organisms are composed of one or more
embedded (integral) or attached (peripheral) cells, the cell is the basic unit of life, and new cells
proteins that separates the internal contents of the arise from existing cells
cell from its surrounding environment vacuole a membrane-bound sac, somewhat larger
plasmodesma (plural: plasmodesmata) a channel than a vesicle, that functions in cellular storage and
that passes between the cell walls of adjacent plant transport
cells, connects their cytoplasm, and allows vesicle a small, membrane-bound sac that functions
materials to be transported from cell to cell in cellular storage and transport; its membrane is
prokaryotic cell a unicellular organism that lacks a capable of fusing with the plasma membrane and
nucleus or any other membrane-bound organelle the membranes of the endoplasmic reticulum and
receptor-mediated endocytosis a variant of Golgi apparatus
endocytosis that involves the use of specific binding

Chapter Summary
3.1 How Cells Are Studied have plasma membranes, cytoplasm, ribosomes, a cell
wall, DNA, and lack membrane-bound organelles.
A cell is the smallest unit of life. Most cells are so small
Many also have polysaccharide capsules. Prokaryotic
that they cannot be viewed with the naked eye.
cells range in diameter from 0.1–5.0 µm.
Therefore, scientists must use microscopes to study
cells. Electron microscopes provide higher Like a prokaryotic cell, a eukaryotic cell has a plasma
magnification, higher resolution, and more detail than membrane, cytoplasm, and ribosomes, but a
light microscopes. The unified cell theory states that all eukaryotic cell is typically larger than a prokaryotic cell,
organisms are composed of one or more cells, the cell has a true nucleus (meaning its DNA is surrounded by a
is the basic unit of life, and new cells arise from membrane), and has other membrane-bound
existing cells. organelles that allow for compartmentalization of
functions. Eukaryotic cells tend to be 10 to 100 times
3.2 Comparing Prokaryotic and Eukaryotic the size of prokaryotic cells.
Cells
3.3 Eukaryotic Cells
Prokaryotes are predominantly single-celled organisms
of the domains Bacteria and Archaea. All prokaryotes Like a prokaryotic cell, a eukaryotic cell has a plasma
membrane, cytoplasm, and ribosomes, but a
86 3 • Chapter Summary

eukaryotic cell is typically larger than a prokaryotic cell, membrane is composed of a bilayer of phospholipids,
has a true nucleus (meaning its DNA is surrounded by a with their hydrophobic, fatty acid tails in contact with
membrane), and has other membrane-bound each other. The landscape of the membrane is studded
organelles that allow for compartmentalization of with proteins, some of which span the membrane.
functions. The plasma membrane is a phospholipid Some of these proteins serve to transport materials
bilayer embedded with proteins. The nucleolus within into or out of the cell. Carbohydrates are attached to
the nucleus is the site for ribosome assembly. some of the proteins and lipids on the outward-facing
Ribosomes are found in the cytoplasm or are attached surface of the membrane. These form complexes that
to the cytoplasmic side of the plasma membrane or function to identify the cell to other cells. The fluid
endoplasmic reticulum. They perform protein nature of the membrane owes itself to the
synthesis. Mitochondria perform cellular respiration configuration of the fatty acid tails, the presence of
and produce ATP. Peroxisomes break down fatty acids, cholesterol embedded in the membrane (in animal
amino acids, and some toxins. Vesicles and vacuoles cells), and the mosaic nature of the proteins and
are storage and transport compartments. In plant cells, protein-carbohydrate complexes, which are not firmly
vacuoles also help break down macromolecules. fixed in place. Plasma membranes enclose the borders
of cells, but rather than being a static bag, they are
Animal cells also have a centrosome and lysosomes.
dynamic and constantly in flux.
The centrosome has two bodies, the centrioles, with an
unknown role in cell division. Lysosomes are the 3.5 Passive Transport
digestive organelles of animal cells.
The passive forms of transport, diffusion and osmosis,
Plant cells have a cell wall, chloroplasts, and a central move material of small molecular weight. Substances
vacuole. The plant cell wall, whose primary component diffuse from areas of high concentration to areas of low
is cellulose, protects the cell, provides structural concentration, and this process continues until the
support, and gives shape to the cell. Photosynthesis substance is evenly distributed in a system. In
takes place in chloroplasts. The central vacuole solutions of more than one substance, each type of
expands, enlarging the cell without the need to molecule diffuses according to its own concentration
produce more cytoplasm. gradient. Many factors can affect the rate of diffusion,
including concentration gradient, the sizes of the
The endomembrane system includes the nuclear
particles that are diffusing, and the temperature of the
envelope, the endoplasmic reticulum, Golgi apparatus,
system.
lysosomes, vesicles, as well as the plasma membrane.
These cellular components work together to modify, In living systems, diffusion of substances into and out
package, tag, and transport membrane lipids and of cells is mediated by the plasma membrane. Some
proteins. materials diffuse readily through the membrane, but
others are hindered, and their passage is only made
The cytoskeleton has three different types of protein
possible by protein channels and carriers. The
elements. Microfilaments provide rigidity and shape to
chemistry of living things occurs in aqueous solutions,
the cell, and facilitate cellular movements.
and balancing the concentrations of those solutions is
Intermediate filaments bear tension and anchor the
an ongoing problem. In living systems, diffusion of
nucleus and other organelles in place. Microtubules
some substances would be slow or difficult without
help the cell resist compression, serve as tracks for
membrane proteins.
motor proteins that move vesicles through the cell, and
pull replicated chromosomes to opposite ends of a 3.6 Active Transport
dividing cell. They are also the structural elements of
The combined gradient that affects an ion includes its
centrioles, flagella, and cilia.
concentration gradient and its electrical gradient.
Animal cells communicate through their extracellular Living cells need certain substances in concentrations
matrices and are connected to each other by tight greater than they exist in the extracellular space.
junctions, desmosomes, and gap junctions. Plant cells Moving substances up their electrochemical gradients
are connected and communicate with each other by requires energy from the cell. Active transport uses
plasmodesmata. energy stored in ATP to fuel the transport. Active
transport of small molecular-size material uses integral
3.4 The Cell Membrane
proteins in the cell membrane to move the
The modern understanding of the plasma membrane is material—these proteins are analogous to pumps.
referred to as the fluid mosaic model. The plasma Some pumps, which carry out primary active transport,

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 3 • Visual Connection Questions 87

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

Visual Connection Questions

1. Figure 3.7 What structures does a plant cell have 3. Figure 3.22 A doctor injects a patient with what he
that an animal cell does not have? What structures thinks is isotonic saline solution. The patient dies,
does an animal cell have that a plant cell does not and autopsy reveals that many red blood cells have
have? been destroyed. Do you think the solution the
doctor injected was really isotonic?
2. Figure 3.13 Why does the cis face of the Golgi not
face the plasma membrane?

Review Questions
4. When viewing a specimen through a light 8. Which of the following is found both in eukaryotic
microscope, scientists use _________ to and prokaryotic cells?
distinguish the individual components of cells. a. nucleus
a. a beam of electrons b. mitochondrion
b. radioactive isotopes c. vacuole
c. special stains d. ribosome
d. high temperatures
9. Which of the following is not a component of the
5. The ___________ is the basic unit of life. endomembrane system?
a. organism a. mitochondrion
b. cell b. Golgi apparatus
c. tissue c. endoplasmic reticulum
d. organ d. lysosome

6. Which of these do all prokaryotes and eukaryotes 10. Which plasma membrane component can be
share? either found on its surface or embedded in the
a. nuclear envelope membrane structure?
b. cell walls a. protein
c. organelles b. cholesterol
d. plasma membrane c. carbohydrate
d. phospholipid
7. A typical prokaryotic cell __________________
compared to a eukaryotic cell. 11. The tails of the phospholipids of the plasma
a. is smaller in size by a factor of 100 membrane are composed of _____ and are
b. is similar in size _______?
c. is smaller in size by a factor of one million a. phosphate groups; hydrophobic
d. is larger in size by a factor of 10 b. fatty acid groups; hydrophilic
c. phosphate groups; hydrophilic
d. fatty acid groups; hydrophobic
88 3 • Critical Thinking Questions

12. Water moves via osmosis _________. 13. The principal force driving movement in diffusion
a. throughout the cytoplasm is __________.
b. from an area with a high concentration of a. temperature
other solutes to a lower one b. particle size
c. from an area with a low concentration of c. concentration gradient
solutes to an area with a higher one d. membrane surface area
d. from an area with a low concentration of
water to one of higher concentration 14. Active transport must function continuously
because __________.
a. plasma membranes wear out
b. cells must be in constant motion
c. facilitated transport opposes active transport
d. diffusion is constantly moving the solutes in
the other direction

Critical Thinking Questions

15. What are the advantages and disadvantages of 18. Why is it advantageous for the cell membrane to
light, transmission, and scanning electron be fluid in nature?
microscopes?
19. Why does osmosis occur?
16. Describe the structures that are characteristic of a
20. Where does the cell get energy for active transport
prokaryote cell.
processes?
17. In the context of cell biology, what do we mean by
form follows function? What are at least two
examples of this concept?

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CHAPTER 4
How Cells Obtain Energy

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)

CHAPTER OUTLINE
4.1 Energy and Metabolism
4.2 Glycolysis
4.3 Citric Acid Cycle and Oxidative Phosphorylation
4.4 Fermentation
4.5 Connections to Other Metabolic Pathways

INTRODUCTION 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,
90 4 • How Cells Obtain Energy

and how chemical reactions in the cell are performed with great efficiency.

4.1 Energy and Metabolism

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

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
obtain 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.

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

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 4.1 • Energy and Metabolism 91

glucose: C6H12O6). They consume carbon dioxide and produce oxygen as a waste product. This reaction is
summarized as:

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:

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.

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
92 4 • How Cells Obtain Energy

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.

FIGURE 4.4 Shown are some examples of energy transferred and transformed from one system to another and from one form to another.

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 4.1 • Energy and Metabolism 93

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.

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
94 4 • How Cells Obtain Energy

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.

LINK TO LEARNING
Visit the site (http://openstax.org/l/simple_pendulu2) 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.

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 4.1 • Energy and Metabolism 95

VISUAL CONNECTION

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.

LINK TO LEARNING
Watch an animation (http://openstax.org/l/energy_reactio2) 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
96 4 • How Cells Obtain Energy

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.

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.

LINK TO LEARNING
View an animation (http://openstax.org/l/hexokinase2) of induced fit.

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 4.1 • Energy and Metabolism 97

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.

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 prevent 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 enzyme activity as it no longer effectively catalyzes the conversion of the substrate to product. 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
98 4 • How Cells Obtain Energy

enzyme’s active site(s) for its substrate(s) (Figure 4.9).

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.

CAREER CONNECTION

Pharmaceutical Drug Developer

FIGURE 4.10 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 4.10).

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;

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 4.1 • Energy and Metabolism 99

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.

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 4.11). 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.

FIGURE 4.11 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.
100 4 • How Cells Obtain Energy

4.2 Glycolysis
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

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 4.12). 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 underline
diphosphate
end underline
(ADP); the addition of a third phosphate group forms adenosine underline
triphosphate
end underline
(ATP).

FIGURE 4.12 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.

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 4.3 • Citric Acid Cycle and Oxidative Phosphorylation 101

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 4.13).

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.

FIGURE 4.13 In glycolysis, a glucose molecule is converted into two pyruvate molecules.

4.3 Citric Acid Cycle and Oxidative Phosphorylation

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
102 4 • How Cells Obtain Energy

picked up by a carrier compound called coenzyme A (CoA), which is made from vitamin B5. The resulting compound
is called acetyl CoA. (Figure 4.14). 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.

FIGURE 4.14 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.

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 an 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 4.15a) 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 4.15c, 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

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 4.3 • Citric Acid Cycle and Oxidative Phosphorylation 103

mitochondrial membrane into the intermembrane space, creating an electrochemical gradient.

VISUAL CONNECTION

FIGURE 4.15 (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.
104 4 • How Cells Obtain Energy

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 4.15b). 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 4.15c) 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.

CAREER CONNECTION

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.

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 4.4 • Fermentation 105

4.4 Fermentation
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? In some living systems the electron transport chain (ETC) 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, in some living systems, the electron transport chain (ETC) uses
an inorganic molecule (other than oxygen) as a final electron acceptor to regenerate NAD+ which is called anaerobic
(do not require oxygen) to achieve NAD+ regeneration. Both processes allow organisms to convert energy for their
use in the absence of oxygen.

LINK TO LEARNING
Watch this video (http://openstax.org/l/fermentation2) to see fermentation in action.

Lactic Acid Fermentation

The fermentation method used by animals and some bacteria like those in yogurt is lactic acid fermentation (Figure
4.16). 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:

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.
106 4 • How Cells Obtain Energy

VISUAL CONNECTION

FIGURE 4.16 Lactic acid fermentation is common in muscles that have become exhausted by use.

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?

Alcohol Fermentation
Another familiar fermentation process is alcohol fermentation (Figure 4.17), which produces ethanol, an alcohol.
The alcohol fermentation reaction is the following:

FIGURE 4.17 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 4.18). If the carbon
dioxide produced by the reaction is not vented from the fermentation chamber, for example in beer and sparkling

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 4.4 • Fermentation 107

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.

FIGURE 4.18 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 4.19), reduce sulfate to hydrogen sulfide to regenerate
NAD+ from NADH.

FIGURE 4.19 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)

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
108 4 • How Cells Obtain Energy

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.

4.5 Connections to Other Metabolic Pathways

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 4.20). 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.

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 4.5 • Connections to Other Metabolic Pathways 109

FIGURE 4.20 Glycogen from the liver and muscles, together with fats, can feed into the catabolic pathways for carbohydrates.

EVOLUTION CONNECTION

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.
110 4 • Key Terms

Key Terms
acetyl CoA the combination of an acetyl group series of chemical reactions to generate a hydrogen
derived from pyruvic acid and coenzyme A which is ion gradient across the membrane
made from pantothenic acid (a B-group vitamin) endergonic describes a chemical reaction that results
activation energy the amount of initial energy in products that store more chemical potential
necessary for reactions to occur energy than the reactants
active site a specific region on the enzyme where the enzyme a molecule that catalyzes a biochemical
substrate binds reaction
allosteric inhibition the mechanism for inhibiting exergonic describes a chemical reaction that results
enzyme action in which a regulatory molecule binds in products with less chemical potential energy than
to a second site (not the active site) and initiates a the reactants, plus the release of free energy
conformation change in the active site, preventing feedback inhibition a mechanism of enzyme activity
binding with the substrate regulation in which the product of a reaction or the
anabolic describes the pathway that requires a net final product of a series of sequential reactions
energy input to synthesize complex molecules from inhibits an enzyme for an earlier step in the reaction
simpler ones series
anaerobic cellular respiration the use of an electron fermentation the steps that follow the partial
acceptor other than oxygen to complete metabolism oxidation of glucose via glycolysis to regenerate
using electron transport-based chemiosmosis NAD+; occurs in the absence of oxygen and uses an
ATP (also, adenosine triphosphate) the cell’s energy organic compound as the final electron acceptor
currency glycolysis the process of breaking glucose into two
ATP synthase a membrane-embedded protein three-carbon molecules with the production of ATP
complex that regenerates ATP from ADP with energy and NADH
from protons diffusing through it heat energy the energy transferred from one system
bioenergetics the concept of energy flow through to another that is not work
living systems kinetic energy the type of energy associated with
catabolic describes the pathway in which complex objects in motion
molecules are broken down into simpler ones, metabolism all the chemical reactions that take
yielding energy as an additional product of the place inside cells, including those that use energy
reaction and those that release energy
chemiosmosis the movement of hydrogen ions down noncompetitive inhibition a general mechanism of
their electrochemical gradient across a membrane enzyme activity regulation in which a regulatory
through ATP synthase to generate ATP molecule binds to a site other than the active site
citric acid cycle a series of enzyme-catalyzed and prevents the active site from binding the
chemical reactions of central importance in all living substrate; thus, the inhibitor molecule does not
cells that harvests the energy in carbon-carbon compete with the substrate for the active site;
bonds of sugar molecules to generate ATP; the citric allosteric inhibition is a form of noncompetitive
acid cycle is an aerobic metabolic pathway because inhibition
it requires oxygen in later reactions to proceed oxidative phosphorylation the production of ATP by
competitive inhibition a general mechanism of the transfer of electrons down the electron
enzyme activity regulation in which a molecule transport chain to create a proton gradient that is
other than the enzyme’s substrate is able to bind used by ATP synthase to add phosphate groups to
the active site and prevent the substrate itself from ADP molecules
binding, thus inhibiting the overall rate of reaction potential energy the type of energy that refers to the
for the enzyme potential to do work
electron transport chain a series of four large, multi- substrate a molecule on which the enzyme acts
protein complexes embedded in the inner thermodynamics the science of the relationships
mitochondrial membrane that accepts electrons between heat, energy, and work
from donor compounds and harvests energy from a

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 4 • Chapter Summary 111

Chapter Summary
4.1 Energy and Metabolism atoms and attaches them to NAD+. Two ATP molecules
are invested in the first half and four ATP molecules are
Cells perform the functions of life through various
formed during the second half. This produces a net
chemical reactions. A cell’s metabolism refers to the
gain of two ATP molecules per molecule of glucose for
combination of chemical reactions that take place
the cell.
within it. Catabolic reactions break down complex
chemicals into simpler ones and are associated with 4.3 Citric Acid Cycle and Oxidative
energy release. Anabolic processes build complex Phosphorylation
molecules out of simpler ones and require energy.
The citric acid cycle is a series of chemical reactions
In studying energy, the term system refers to the that removes high-energy electrons and uses them in
matter and environment involved in energy transfers. the electron transport chain to generate ATP. One
Entropy is a measure of the disorder of a system. The molecule of ATP (or an equivalent) is produced per
physical laws that describe the transfer of energy are each turn of the cycle.
the laws of thermodynamics. The first law states that
The electron transport chain is the portion of aerobic
the total amount of energy in the universe is constant.
respiration that uses free oxygen as the final electron
The second law of thermodynamics states that every
acceptor for electrons removed from the intermediate
energy transfer involves some loss of energy in an
compounds in glucose catabolism. The electrons are
unusable form, such as heat energy. Energy comes in
passed through a series of chemical reactions, with a
different forms: kinetic, potential, and free. The change
small amount of free energy used at three points to
in free energy of a reaction can be negative (releases
transport hydrogen ions across the membrane. This
energy, exergonic) or positive (consumes energy,
contributes to the gradient used in chemiosmosis. As
endergonic). All reactions require an initial input of
the electrons are passed from NADH or FADH2 down
energy to proceed, called the activation energy.
the electron transport chain, they lose energy. The
Enzymes are chemical catalysts that speed up products of the electron transport chain are water and
chemical reactions by lowering their activation energy. ATP. A number of intermediate compounds can be
Enzymes have an active site with a unique chemical diverted into the anabolism of other biochemical
environment that fits particular chemical reactants for molecules, such as nucleic acids, non-essential amino
that enzyme, called substrates. Enzymes and acids, sugars, and lipids. These same molecules,
substrates are thought to bind according to an except nucleic acids, can serve as energy sources for
induced-fit model. Enzyme action is regulated to the glucose pathway.
conserve resources and respond optimally to the
environment. 4.4 Fermentation
If NADH cannot be metabolized through aerobic
4.2 Glycolysis
respiration, another electron acceptor is used. Most
ATP functions as the energy currency for cells. It allows organisms will use some form of fermentation to
cells to store energy briefly and transport it within itself accomplish the regeneration of NAD+, ensuring the
to support endergonic chemical reactions. The continuation of glycolysis. The regeneration of NAD+ in
structure of ATP is that of an RNA nucleotide with three fermentation is not accompanied by ATP production;
phosphate groups attached. As ATP is used for energy, therefore, the potential for NADH to produce ATP using
a phosphate group is detached, and ADP is produced. an electron transport chain is not utilized.
Energy derived from glucose catabolism is used to
recharge ADP into ATP. 4.5 Connections to Other Metabolic
Pathways
Glycolysis is the first pathway used in the breakdown of
glucose to extract energy. Because it is used by nearly The breakdown and synthesis of carbohydrates,
all organisms on earth, it must have evolved early in the proteins, and lipids connect with the pathways of
history of life. Glycolysis consists of two parts: The first glucose catabolism. The carbohydrates that can also
part prepares the six-carbon ring of glucose for feed into glucose catabolism include galactose,
separation into two three-carbon sugars. Energy from fructose, and glycogen. These connect with glycolysis.
ATP is invested into the molecule during this step to The amino acids from proteins connect with glucose
energize the separation. The second half of glycolysis catabolism through pyruvate, acetyl CoA, and
extracts ATP and high-energy electrons from hydrogen components of the citric acid cycle. Cholesterol
112 4 • Visual Connection Questions

synthesis starts with acetyl CoA, and the components the citric acid cycle.
of triglycerides are picked up by acetyl CoA and enter

Visual Connection Questions

1. Figure 4.6 Look at each of the processes shown and 3. Figure 4.16 Tremetol, a metabolic poison found in
decide if it is endergonic or exergonic. white snake root plant, prevents the metabolism of
lactate. When cows eat this plant, Tremetol is
2. Figure 4.15 Cyanide inhibits cytochrome c oxidase,
concentrated in the milk. Humans who consume
a component of the electron transport chain. If
the milk become ill. Symptoms of this disease,
cyanide poisoning occurs, would you expect the pH
which include vomiting, abdominal pain, and
of the intermembrane space to increase or
tremors, become worse after exercise. Why do you
decrease? What affect would cyanide have on ATP
think this is the case?
synthesis?

Review Questions
4. Which of the following is not an example of an 9. What do the electrons added to NAD+ do?
energy transformation? a. They become part of a fermentation pathway.
a. Heating up dinner in a microwave b. They go to another pathway for ATP
b. Solar panels at work production.
c. Formation of static electricity c. They energize the entry of the acetyl group into
d. None of the above the citric acid cycle.
d. They are converted into NADP.
5. Which of the following is not true about enzymes?
a. They are consumed by the reactions they 10. Chemiosmosis involves
catalyze. a. the movement of electrons across the cell
b. They are usually made of amino acids. membrane
c. They lower the activation energy of chemical b. the movement of hydrogen atoms across a
reactions. mitochondrial membrane
d. Each one is specific to the particular c. the movement of hydrogen ions across a
substrate(s) to which it binds. mitochondrial membrane
d. the movement of glucose through the cell
6. Energy is stored long-term in the bonds of _____ membrane
and used short-term to perform work from a(n)
_____ molecule. 11. Which of the following fermentation methods can
a. ATP : glucose occur in animal skeletal muscles?
b. an anabolic molecule : catabolic molecule a. lactic acid fermentation
c. glucose : ATP b. alcohol fermentation
d. a catabolic molecule : anabolic molecule c. mixed acid fermentation
d. propionic fermentation
7. The energy currency used by cells is _____.
a. ATP 12. The cholesterol synthesized by cells uses which
b. ADP component of the glycolytic pathway as a starting
c. AMP point?
d. adenosine a. glucose
b. acetyl CoA
8. The glucose that enters the glycolysis pathway is c. pyruvate
split into two molecules of _________. d. carbon dioxide
a. ATP
b. phosphate
c. NADH
d. pyruvate

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 4 • Critical Thinking Questions 113

13. Beta oxidation is ________.

a. the breakdown of sugars
b. the assembly of sugars
c. the breakdown of fatty acids
d. the removal of amino groups from amino
acids

Critical Thinking Questions

14. Does physical exercise to increase muscle mass 18. We inhale oxygen when we breathe and exhale
involve anabolic and/or catabolic processes? Give carbon dioxide. What is the oxygen used for and
evidence for your answer. where does the carbon dioxide come from?

15. Explain in your own terms the difference between 19. When muscle cells run out of oxygen, what
a spontaneous reaction and one that occurs happens to the potential for energy extraction
instantaneously, and what causes this difference. from sugars and what pathways do the cell use?

16. With regard to enzymes, why are vitamins and 20. Would you describe metabolic pathways as
minerals necessary for good health? Give inherently wasteful or inherently economical, and
examples. why?

17. Both prokaryotic and eukaryotic organisms carry

out some form of glycolysis. How does that fact
support or not support the assertion that
glycolysis is one of the oldest metabolic
pathways?
114 4 • Critical Thinking Questions

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CHAPTER 5
Photosynthesis

FIGURE 5.1 This mockingbird’s diet, like that of almost all organisms, depends on photosynthesis. (credit:
modification of work by Dave Menke, U.S. Fish and Wildlife Service)

CHAPTER OUTLINE
5.1 Overview of Photosynthesis
5.2 The Light-Dependent Reactions of Photosynthesis
5.3 The Calvin Cycle

INTRODUCTION No matter how complex or advanced a machine, such as the latest cellular
phone, the device cannot function without energy. Living things, similar to machines, have many
complex components; they too cannot do anything without energy, which is why humans and all
other organisms must “eat” in some form or another. That may be common knowledge, but how
many people realize that every bite of every meal ingested depends on the process of
photosynthesis?

5.1 Overview of Photosynthesis

LEARNING OBJECTIVES
By the end of this section, you will be able to:
• Summarize the process of photosynthesis
• Explain the relevance of photosynthesis to other living things
• Identify the reactants and products of photosynthesis
• Describe the main structures involved in photosynthesis

All living organisms on earth consist of one or more cells. Each cell runs on the chemical energy
found mainly in carbohydrate molecules (food), and the majority of these molecules are produced
by one process: photosynthesis. Through photosynthesis, certain organisms convert solar energy
(sunlight) into chemical energy, which is then used to build carbohydrate molecules. The energy
116 5 • Photosynthesis

used to hold these molecules together is released when an organism breaks down food. Cells then
use this energy to perform work, such as cellular respiration.

The energy that is harnessed from photosynthesis enters the ecosystems of our planet
continuously and is transferred from one organism to another. Therefore, directly or indirectly, the
process of photosynthesis provides most of the energy required by living things on earth.

Photosynthesis also results in the release of oxygen into the atmosphere. In short, to eat and
breathe, humans depend almost entirely on the organisms that carry out photosynthesis.

LINK TO LEARNING
Click the following link (http://openstax.org/l/photosynthesis2) to learn more about
photosynthesis.

Solar Dependence and Food Production

Some organisms can carry out photosynthesis, whereas others cannot. An autotroph is an
organism that can produce its own food. The Greek roots of the word autotroph mean “self” (auto)
“feeder” (troph). Plants are the best-known autotrophs, but others exist, including certain types of
bacteria and algae (Figure 5.2). Oceanic algae contribute enormous quantities of food and oxygen
to global food chains. Plants are also photoautotrophs, a type of autotroph that uses sunlight and
carbon from carbon dioxide to synthesize chemical energy in the form of carbohydrates. All
organisms carrying out photosynthesis require sunlight.

FIGURE 5.2 (a) Plants, (b) algae, and (c) certain bacteria, called cyanobacteria, are photoautotrophs that can carry out
photosynthesis. Algae can grow over enormous areas in water, at times completely covering the surface. (credit a:
Steve Hillebrand, U.S. Fish and Wildlife Service; credit b: "eutrophication&hypoxia"/Flickr; credit c: NASA; scale-bar
data from Matt Russell)

Heterotrophs are organisms incapable of photosynthesis that must therefore obtain energy and
carbon from food by consuming other organisms. The Greek roots of the word heterotroph mean
“other” (hetero) “feeder” (troph), meaning that their food comes from other organisms. Even if the
food organism is another animal, this food traces its origins back to autotrophs and the process of
photosynthesis. Humans are heterotrophs, as are all animals. Heterotrophs depend on
autotrophs, either directly or indirectly. Deer and wolves are heterotrophs. A deer obtains energy
by eating plants. A wolf eating a deer obtains energy that originally came from the plants eaten by
that deer. The energy in the plant came from photosynthesis, and therefore it is the only autotroph
in this example (Figure 5.3). Using this reasoning, all food eaten by humans also links back to
autotrophs that carry out photosynthesis.

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 5.1 • Overview of Photosynthesis 117

FIGURE 5.3 The energy stored in carbohydrate molecules from photosynthesis passes through the food chain. The predator that eats these
deer is getting energy that originated in the photosynthetic vegetation that the deer consumed. (credit: Steve VanRiper, U.S. Fish and
Wildlife Service)

EVERYDAY CONNECTION
Photosynthesis at the Grocery Store

FIGURE 5.4 Photosynthesis is the origin of the products that comprise the main elements of the human diet. (credit: Associação
Brasileira de Supermercados)

Major grocery stores in the United States are organized into departments, such as dairy, meats, produce, bread,
cereals, and so forth. Each aisle contains hundreds, if not thousands, of different products for customers to buy
and consume (Figure 5.4).

Although there is a large variety, each item links back to photosynthesis. Meats and dairy products link to
photosynthesis because the animals were fed plant-based foods. The breads, cereals, and pastas come largely
from grains, which are the seeds of photosynthetic plants. What about desserts and drinks? All of these products
contain sugar—the basic carbohydrate molecule produced directly from photosynthesis. The photosynthesis
connection applies to every meal and every food a person consumes.

Main Structures and Summary of Photosynthesis

Photosynthesis requires sunlight, carbon dioxide, and water as starting reactants (Figure 5.5). After the process is
complete, photosynthesis releases oxygen and produces carbohydrate molecules, most commonly glucose. These
sugar molecules contain the energy that living things need to survive.
118 5 • Photosynthesis

FIGURE 5.5 Photosynthesis uses solar energy, carbon dioxide, and water to release oxygen and to produce energy-storing sugar molecules.

The complex reactions of photosynthesis can be summarized by the chemical equation shown in Figure 5.6.

FIGURE 5.6 The process of photosynthesis can be represented by an equation, wherein carbon dioxide and water produce sugar and
oxygen using energy from sunlight.

Although the equation looks simple, the many steps that take place during photosynthesis are actually quite
complex, as in the way that the reaction summarizing cellular respiration represented many individual reactions.
Before learning the details of how photoautotrophs turn sunlight into food, it is important to become familiar with
the physical structures involved.

In plants, photosynthesis takes place primarily in leaves, which consist of many layers of cells and have
differentiated top and bottom sides. The process of photosynthesis occurs not on the surface layers of the leaf, but
rather in a middle layer called the mesophyll (Figure 5.7). The gas exchange of carbon dioxide and oxygen occurs
through small, regulated openings called stomata.

In all autotrophic eukaryotes, photosynthesis takes place inside an organelle called a chloroplast. In plants,
chloroplast-containing cells exist in the mesophyll. Chloroplasts have a double (inner and outer) membrane. Within
the chloroplast is a third membrane that forms stacked, disc-shaped structures called thylakoids. Embedded in the
thylakoid membrane are molecules of chlorophyll, a pigment (a molecule that absorbs light) through which the
entire process of photosynthesis begins. Chlorophyll is responsible for the green color of plants. The thylakoid

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 5.1 • Overview of Photosynthesis 119

membrane encloses an internal space called the thylakoid space. Other types of pigments are also involved in
photosynthesis, but chlorophyll is by far the most important. As shown in Figure 5.7, a stack of thylakoids is called a
granum, and the space surrounding the granum is called stroma (not to be confused with stomata, the openings on
the leaves).

VISUAL CONNECTION

FIGURE 5.7 Not all cells of a leaf carry out photosynthesis. Cells within the middle layer of a leaf have chloroplasts, which contain the
photosynthetic apparatus. (credit "leaf": modification of work by Cory Zanker)

On a hot, dry day, plants close their stomata to conserve water. What impact will this have on photosynthesis?

The Two Parts of Photosynthesis

Photosynthesis takes place in two stages: the light-dependent reactions and the Calvin cycle. In the light-
dependent reactions, which take place at the thylakoid membrane, chlorophyll absorbs energy from sunlight and
then converts it into chemical energy with the use of water. The light-dependent reactions release oxygen from the
hydrolysis of water as a byproduct. In the Calvin cycle, which takes place in the stroma, the chemical energy derived
from the light-dependent reactions drives both the capture of carbon in carbon dioxide molecules and the
subsequent assembly of sugar molecules. The two reactions use carrier molecules to transport the energy from one
to the other. The carriers that move energy from the light-dependent reactions to the Calvin cycle reactions can be
thought of as “full” because they bring energy. After the energy is released, the “empty” energy carriers return to
the light-dependent reactions to obtain more energy. The two-stage, two-location photosynthesis process was
discovered by Joan Mary Anderson, whose continuing work over the subsequent decades provided much of our
understanding of the process, the membranes, and the chemicals involved.
120 5 • Photosynthesis

5.2 The Light-Dependent Reactions of Photosynthesis

LEARNING OBJECTIVES
By the end of this section, you will be able to:
• Explain how plants absorb energy from sunlight
• Describe how the wavelength of light affects its energy and color
• Describe how and where photosynthesis takes place within a plant

How can light be used to make food? It is easy to think of light as something that exists and allows living organisms,
such as humans, to see, but light is a form of energy. Like all energy, light can travel, change form, and be harnessed
to do work. In the case of photosynthesis, light energy is transformed into chemical energy, which autotrophs use to
build carbohydrate molecules. However, autotrophs only use a specific component of sunlight (Figure 5.8).

FIGURE 5.8 Autotrophs can capture light energy from the sun, converting it into chemical energy used to build food molecules. (credit:
modification of work by Gerry Atwell, U.S. Fish and Wildlife Service)

LINK TO LEARNING
Watch the process of photosynthesis (http://openstax.org/l/light_reaction2) within a leaf in this video.

What Is Light Energy?

The sun emits an enormous amount of electromagnetic radiation (solar energy). Humans can see only a fraction of
this energy, which is referred to as “visible light.” The manner in which solar energy travels can be described and
measured as waves. Scientists can determine the amount of energy of a wave by measuring its wavelength, the
distance between two consecutive, similar points in a series of waves, such as from crest to crest or trough to trough
(Figure 5.9).

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 5.2 • The Light-Dependent Reactions of Photosynthesis 121

FIGURE 5.9 The wavelength of a single wave is the distance between two consecutive points along the wave.

Visible light constitutes only one of many types of electromagnetic radiation emitted from the sun. The
electromagnetic spectrum is the range of all possible wavelengths of radiation (Figure 5.10). Each wavelength
corresponds to a different amount of energy carried.

FIGURE 5.10 The sun emits energy in the form of electromagnetic radiation. This radiation exists in different wavelengths, each of which
has its own characteristic energy. Visible light is one type of energy emitted from the sun.

Each type of electromagnetic radiation has a characteristic range of wavelengths. The longer the wavelength (or the
more stretched out it appears), the less energy is carried. Short, tight waves carry the most energy. This may seem
illogical, but think of it in terms of a piece of moving rope. It takes little effort by a person to move a rope in long,
wide waves. To make a rope move in short, tight waves, a person would need to apply significantly more energy.

The sun emits (Figure 5.10) a broad range of electromagnetic radiation, including X-rays and ultraviolet (UV) rays.
The higher-energy waves are dangerous to living things; for example, X-rays and UV rays can be harmful to humans.

Absorption of Light
Light energy enters the process of photosynthesis when pigments absorb the light. In plants, pigment molecules
absorb only visible light for photosynthesis. The visible light seen by humans as white light actually exists in a
rainbow of colors. Certain objects, such as a prism or a drop of water, disperse white light to reveal these colors to
the human eye. The visible light portion of the electromagnetic spectrum is perceived by the human eye as a
rainbow of colors, with violet and blue having shorter wavelengths and, therefore, higher energy. At the other end of
the spectrum toward red, the wavelengths are longer and have lower energy.

Understanding Pigments
Different kinds of pigments exist, and each absorbs only certain wavelengths (colors) of visible light. Pigments
122 5 • Photosynthesis

reflect the color of the wavelengths that they cannot absorb.

All photosynthetic organisms contain a pigment called chlorophyll a, which humans see as the common green color
associated with plants. Chlorophyll a absorbs wavelengths from either end of the visible spectrum (blue and red),
but not from green. Because green is reflected, chlorophyll appears green.

Other pigment types include chlorophyll b (which absorbs blue and red-orange light) and the carotenoids. Each
type of pigment can be identified by the specific pattern of wavelengths it absorbs from visible light, which is its
absorption spectrum.

Many photosynthetic organisms have a mixture of pigments; between them, the organism can absorb energy from a
wider range of visible-light wavelengths. Not all photosynthetic organisms have full access to sunlight. Some
organisms grow underwater where light intensity decreases with depth, and certain wavelengths are absorbed by
the water. Other organisms grow in competition for light. Plants on the rainforest floor must be able to absorb any bit
of light that comes through, because the taller trees block most of the sunlight (Figure 5.11).

FIGURE 5.11 Plants that commonly grow in the shade benefit from having a variety of light-absorbing pigments. Each pigment can absorb
different wavelengths of light, which allows the plant to absorb any light that passes through the taller trees. (credit: Jason Hollinger)

How Light-Dependent Reactions Work

The overall purpose of the light-dependent reactions is to convert light energy into chemical energy. This chemical
energy will be used by the Calvin cycle to fuel the assembly of sugar molecules.

The light-dependent reactions begin in a grouping of pigment molecules and proteins called a photosystem.
Photosystems exist in the membranes of thylakoids. A pigment molecule in the photosystem absorbs one photon, a
quantity or “packet” of light energy, at a time.

A photon of light energy travels until it reaches a molecule of chlorophyll. The photon causes an electron in the
chlorophyll to become “excited.” The energy given to the electron allows it to break free from an atom of the
chlorophyll molecule. Chlorophyll is therefore said to “donate” an electron (Figure 5.12).

To replace the electron in the chlorophyll, a molecule of water is split. This splitting releases an electron and results
in the formation of oxygen (O2) and hydrogen ions (H+) in the thylakoid space. Technically, each breaking of a water
molecule releases a pair of electrons, and therefore can replace two donated electrons.

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 5.2 • The Light-Dependent Reactions of Photosynthesis 123

FIGURE 5.12 Light energy is absorbed by a chlorophyll molecule and is passed along a pathway to other chlorophyll molecules. The energy
culminates in a molecule of chlorophyll found in the reaction center. The energy “excites” one of its electrons enough to leave the molecule
and be transferred to a nearby primary electron acceptor. A molecule of water splits to release an electron, which is needed to replace the
one donated. Oxygen and hydrogen ions are also formed from the splitting of water.

The replacing of the electron enables chlorophyll to respond to another photon. The oxygen molecules produced as
byproducts find their way to the surrounding environment. The hydrogen ions play critical roles in the remainder of
the light-dependent reactions.

Keep in mind that the purpose of the light-dependent reactions is to convert solar energy into chemical carriers that
will be used in the Calvin cycle. In eukaryotes and some prokaryotes, two photosystems exist. The first is called
photosystem II, which was named for the order of its discovery rather than for the order of the function.

After the photon hits, photosystem II transfers the free electron to the first in a series of proteins inside the
thylakoid membrane called the electron transport chain. As the electron passes along these proteins, energy from
the electron fuels membrane pumps that actively move hydrogen ions against their concentration gradient from the
stroma into the thylakoid space. This is quite analogous to the process that occurs in the mitochondrion in which an
electron transport chain pumps hydrogen ions from the mitochondrial stroma across the inner membrane and into
the intermembrane space, creating an electrochemical gradient. After the energy is used, the electron is accepted
by a pigment molecule in the next photosystem, which is called photosystem I (Figure 5.13).
124 5 • Photosynthesis

FIGURE 5.13 From photosystem II, the electron travels along a series of proteins. This electron transport system uses the energy from the
electron to pump hydrogen ions into the interior of the thylakoid. A pigment molecule in photosystem I accepts the electron.

Generating an Energy Carrier: ATP

In the light-dependent reactions, energy absorbed by sunlight is stored by two types of energy-carrier molecules:
ATP and NADPH. The energy that these molecules carry is stored in a bond that holds a single atom or group of
atoms to the molecule. For ATP, it is a phosphate group, and for NADPH, it is a hydrogen atom. Recall that NADH was
a similar molecule that carried energy in the mitochondrion from the citric acid cycle to the electron transport chain.
When these molecules release energy into the Calvin cycle, they each lose either atoms or groups of atoms to
become the lower-energy molecules ADP and NADP+.

The buildup of hydrogen ions in the thylakoid space forms an electrochemical gradient because of the difference in
the concentration of protons (H+) and the difference in the charge across the membrane that they create. This
potential energy is harvested and stored as chemical energy in ATP through chemiosmosis, the movement of
hydrogen ions down their electrochemical gradient through the transmembrane enzyme ATP synthase, just as in the
mitochondrion.

The hydrogen ions are allowed to pass through the thylakoid membrane through an embedded protein complex
called ATP synthase. This same protein generated ATP from ADP in the mitochondrion. The energy generated by the
hydrogen ion stream allows ATP synthase to attach a third phosphate to ADP, which forms a molecule of ATP in a
process called photophosphorylation. The flow of hydrogen ions through ATP synthase is called chemiosmosis,
because the ions move from an area of high to low concentration through a semi-permeable structure.

Generating Another Energy Carrier: NADPH

The remaining function of the light-dependent reaction is to generate the other energy-carrier molecule, NADPH. As
the electron from the electron transport chain arrives at photosystem I, it is re-energized with another photon
captured by chlorophyll. The energy from this electron drives the formation of NADPH from NADP+ and a hydrogen
ion (H+). Now that the solar energy is stored in energy carriers, it can be used to make a sugar molecule.

5.3 The Calvin Cycle

LEARNING OBJECTIVES
By the end of this section, you will be able to:
• Describe the Calvin cycle
• Define carbon fixation
• Explain how photosynthesis works in the energy cycle of all living organisms

After the energy from the sun is converted and packaged into ATP and NADPH, the cell has the fuel needed to build
food in the form of carbohydrate molecules. The carbohydrate molecules made will have a backbone of carbon
atoms. Where does the carbon come from? The carbon atoms used to build carbohydrate molecules comes from

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 5.3 • The Calvin Cycle 125

carbon dioxide, the gas that animals exhale with each breath. The Calvin cycle is the term used for the reactions of
photosynthesis that use the energy stored by the light-dependent reactions to form glucose and other carbohydrate
molecules.

The Interworkings of the Calvin Cycle

In plants, carbon dioxide (CO2) enters the leaf through the stomata and diffuses into the mesophyll cells and into
the stroma of the chloroplast—the site of the Calvin cycle reactions where sugar is synthesized. The reactions are
named after Melvin Calvin, the scientist who discovered them, and reference the fact that the reactions function as a
cycle. Others call it the Calvin-Benson cycle to include the name of another scientist involved in its discovery,
Andrew Benson (Figure 5.14).

FIGURE 5.14 Light-dependent reactions harness energy from the sun to produce ATP and NADPH. These energy-carrying molecules travel
into the stroma where the Calvin cycle reactions take place.

The Calvin cycle reactions (Figure 5.15) can be organized into three basic stages: fixation, reduction, and
regeneration. In the stroma, in addition to CO2, two other chemicals are present to initiate the Calvin cycle: an
enzyme abbreviated RuBisCO, and the molecule ribulose bisphosphate (RuBP). RuBP has five atoms of carbon and a
phosphate group on each end.

RuBisCO catalyzes a reaction between CO2 and RuBP, which forms a six-carbon compound that is immediately
converted into two three-carbon compounds. This process is called carbon fixation, because CO2 is “fixed” from its
inorganic form into organic molecules.

ATP and NADPH use their stored energy to convert the three-carbon compound, 3-PGA, into another three-carbon
compound called G3P. This type of reaction is called a reduction reaction, because it involves the gain of electrons.
A reduction is the gain of an electron by an atom or molecule. The molecules of ADP and NAD+, resulting from the
reduction reaction, return to the light-dependent reactions to be re-energized.

One of the G3P molecules leaves the Calvin cycle to contribute to the formation of the carbohydrate molecule,
which is commonly glucose (C6H12O6). Because the carbohydrate molecule has six carbon atoms, it takes six turns
of the Calvin cycle to make one carbohydrate molecule (one for each carbon dioxide molecule fixed). The remaining
G3P molecules regenerate RuBP, which enables the system to prepare for the carbon-fixation step. ATP is also used
in the regeneration of RuBP.
126 5 • Photosynthesis

FIGURE 5.15 The Calvin cycle has three stages. In stage 1, the enzyme RuBisCO incorporates carbon dioxide into an organic molecule. In
stage 2, the organic molecule is reduced. In stage 3, RuBP, the molecule that starts the cycle, is regenerated so that the cycle can continue.

In summary, it takes six turns of the Calvin cycle to fix six carbon atoms from CO2. These six turns require energy
input from 12 ATP molecules and 12 NADPH molecules in the reduction step and 6 ATP molecules in the
regeneration step.

LINK TO LEARNING
The following is a link (http://openstax.org/l/calvin_cycle2) to an animation of the Calvin cycle. Click Stage 1, Stage
2, and then Stage 3 to see G3P and ATP regenerate to form RuBP.

EVOLUTION CONNECTION

Photosynthesis
The shared evolutionary history of all photosynthetic organisms is conspicuous, as the basic process has changed
little over eras of time. Even between the giant tropical leaves in the rainforest and tiny cyanobacteria, the process
and components of photosynthesis that use water as an electron donor remain largely the same. Photosystems
function to absorb light and use electron transport chains to convert energy. The Calvin cycle reactions assemble
carbohydrate molecules with this energy.

However, as with all biochemical pathways, a variety of conditions leads to varied adaptations that affect the basic
pattern. Photosynthesis in dry-climate plants (Figure 5.16) has evolved with adaptations that conserve water. In the
harsh dry heat, every drop of water and precious energy must be used to survive. Two adaptations have evolved in
such plants. In one form, a more efficient use of CO2 allows plants to photosynthesize even when CO2 is in short
supply, as when the stomata are closed on hot days. The other adaptation performs preliminary reactions of the
Calvin cycle at night, because opening the stomata at this time conserves water due to cooler temperatures. In
addition, this adaptation has allowed plants to carry out low levels of photosynthesis without opening stomata at all,
an extreme mechanism to face extremely dry periods.

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 5.3 • The Calvin Cycle 127

FIGURE 5.16 Living in the harsh conditions of the desert has led plants like this cactus to evolve variations in reactions outside the Calvin
cycle. These variations increase efficiency and help conserve water and energy. (credit: Piotr Wojtkowski)

Photosynthesis in Prokaryotes
The two parts of photosynthesis—the light-dependent reactions and the Calvin cycle—have been described, as they
take place in chloroplasts. However, prokaryotes, such as cyanobacteria, lack membrane-bound organelles.
Prokaryotic photosynthetic autotrophic organisms have infoldings of the plasma membrane for chlorophyll
attachment and photosynthesis (Figure 5.17). It is here that organisms like cyanobacteria can carry out
photosynthesis.

FIGURE 5.17 A photosynthetic prokaryote has infolded regions of the plasma membrane that function like thylakoids. Although these are
not contained in an organelle, such as a chloroplast, all of the necessary components are present to carry out photosynthesis. (credit:
scale-bar data from Matt Russell)

The Energy Flow

Living things access energy by breaking down carbohydrate molecules. However, if plants make carbohydrate
molecules, why would they need to break them down? Carbohydrates are storage molecules for energy in all living
things. Although energy can be stored in molecules like ATP, carbohydrates are much more stable and efficient
reservoirs for chemical energy. Photosynthetic organisms also carry out the reactions of respiration to harvest the
energy that they have stored in carbohydrates, for example, plants have mitochondria in addition to chloroplasts.
128 5 • Photosynthesis

You may have noticed that the overall reaction for photosynthesis:

is the reverse of the overall reaction for cellular respiration:

Photosynthesis produces oxygen as a byproduct, and respiration produces carbon dioxide as a byproduct.

In nature, there is no such thing as waste. Every single atom of matter is conserved, recycling indefinitely.
Substances change form or move from one type of molecule to another, but never disappear (Figure 5.18).

CO2 is no more a form of waste produced by respiration than oxygen is a waste product of photosynthesis. Both are
byproducts of reactions that move on to other reactions. Photosynthesis absorbs energy to build carbohydrates in
chloroplasts, and aerobic cellular respiration releases energy by using oxygen to break down carbohydrates. Both
organelles use electron transport chains to generate the energy necessary to drive other reactions. Photosynthesis
and cellular respiration function in a biological cycle, allowing organisms to access life-sustaining energy that
originates millions of miles away in a star.

FIGURE 5.18 In the carbon cycle, the reactions of photosynthesis and cellular respiration share reciprocal reactants and products. (credit:
modification of work by Stuart Bassil)

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 5 • Key Terms 129

Key Terms
absorption spectrum the specific pattern of form two energy-carrying molecules (ATP and
absorption for a substance that absorbs NADPH)
electromagnetic radiation mesophyll the middle layer of cells in a leaf
autotroph an organism capable of producing its own photoautotroph an organism capable of synthesizing
food its own food molecules (storing energy), using the
Calvin cycle the reactions of photosynthesis that use energy of light
the energy stored by the light-dependent reactions photon a distinct quantity or “packet” of light energy
to form glucose and other carbohydrate molecules photosystem a group of proteins, chlorophyll, and
carbon fixation the process of converting inorganic other pigments that are used in the light-dependent
CO2 gas into organic compounds reactions of photosynthesis to absorb light energy
chlorophyll the green pigment that captures the light and convert it into chemical energy
energy that drives the reactions of photosynthesis pigment a molecule that is capable of absorbing light
chlorophyll a the form of chlorophyll that absorbs energy
violet-blue and red light stoma the opening that regulates gas exchange and
chlorophyll b the form of chlorophyll that absorbs water regulation between leaves and the
blue and red-orange light environment; plural: stomata
chloroplast the organelle where photosynthesis stroma the fluid-filled space surrounding the grana
takes place inside a chloroplast where the Calvin cycle reactions
electromagnetic spectrum the range of all possible of photosynthesis take place
frequencies of radiation thylakoid a disc-shaped membranous structure
granum a stack of thylakoids located inside a inside a chloroplast where the light-dependent
chloroplast reactions of photosynthesis take place using
heterotroph an organism that consumes other chlorophyll embedded in the membranes
organisms for food wavelength the distance between consecutive points
light-dependent reaction the first stage of of a wave
photosynthesis where visible light is absorbed to

Chapter Summary
5.1 Overview of Photosynthesis sunlight. The most common and abundant pigment is
chlorophyll a. A photon strikes photosystem II to
The process of photosynthesis transformed life on
initiate photosynthesis. Energy travels through the
earth. By harnessing energy from the sun,
electron transport chain, which pumps hydrogen ions
photosynthesis allowed living things to access
into the thylakoid space. This forms an electrochemical
enormous amounts of energy. Because of
gradient. The ions flow through ATP synthase from the
photosynthesis, living things gained access to sufficient
thylakoid space into the stroma in a process called
energy, allowing them to evolve new structures and
chemiosmosis to form molecules of ATP, which are
achieve the biodiversity that is evident today.
used for the formation of sugar molecules in the
Only certain organisms, called autotrophs, can perform second stage of photosynthesis. Photosystem I
photosynthesis; they require the presence of absorbs a second photon, which results in the
chlorophyll, a specialized pigment that can absorb light formation of an NADPH molecule, another energy
and convert light energy into chemical energy. carrier for the Calvin cycle reactions.
Photosynthesis uses carbon dioxide and water to
5.3 The Calvin Cycle
assemble carbohydrate molecules (usually glucose)
and releases oxygen into the air. Eukaryotic autotrophs, Using the energy carriers formed in the first stage of
such as plants and algae, have organelles called photosynthesis, the Calvin cycle reactions fix CO2 from
chloroplasts in which photosynthesis takes place. the environment to build carbohydrate molecules. An
enzyme, RuBisCO, catalyzes the fixation reaction, by
5.2 The Light-Dependent Reactions of combining CO2 with RuBP. The resulting six-carbon
Photosynthesis compound is broken down into two three-carbon
In the first part of photosynthesis, the light-dependent compounds, and the energy in ATP and NADPH is used
reaction, pigment molecules absorb energy from to convert these molecules into G3P. One of the three-
carbon molecules of G3P leaves the cycle to become a
130 5 • Visual Connection Questions

part of a carbohydrate molecule. The remaining G3P process of cellular respiration. Plants are capable of
molecules stay in the cycle to be formed back into both photosynthesis and cellular respiration, since they
RuBP, which is ready to react with more CO2. contain both chloroplasts and mitochondria.
Photosynthesis forms a balanced energy cycle with the

Visual Connection Questions

1. Figure 5.7 On a hot, dry day, plants close their
stomata to conserve water. What impact will this
have on photosynthesis?

Review Questions
2. What two products result from photosynthesis? 7. Plants produce oxygen when they photosynthesize.
a. water and carbon dioxide Where does the oxygen come from?
b. water and oxygen a. splitting water molecules
c. glucose and oxygen b. ATP synthesis
d. glucose and carbon dioxide c. the electron transport chain
d. chlorophyll
3. Which statement about thylakoids in eukaryotes is
not correct? 8. Which color(s) of light does chlorophyll a reflect?
a. Thylakoids are assembled into stacks. a. red and blue
b. Thylakoids exist as a maze of folded b. green
membranes. c. red
c. The space surrounding thylakoids is called d. blue
stroma.
d. Thylakoids contain chlorophyll. 9. Where in plant cells does the Calvin cycle take
place?
4. From where does a heterotroph directly obtain its a. thylakoid membrane
energy? b. thylakoid space
a. the sun c. stroma
b. the sun and eating other organisms d. granum
c. eating other organisms
d. simple chemicals in the environment 10. Which statement correctly describes carbon
fixation?
5. What is the energy of a photon first used to do in a. the conversion of CO2 to an organic
photosynthesis? compound
a. split a water molecule b. the use of RuBisCO to form 3-PGA
b. energize an electron c. the production of carbohydrate molecules
c. produce ATP from G3P
d. synthesize glucose d. the formation of RuBP from G3P molecules
e. the use of ATP and NADPH to reduce CO2
6. Which molecule absorbs the energy of a photon in
photosynthesis? 11. What is the molecule that leaves the Calvin cycle
a. ATP to be converted into glucose?
b. glucose a. ADP
c. chlorophyll b. G3P
d. water c. RuBP
d. 3-PGA

Critical Thinking Questions

12. What is the overall purpose of the light reactions 13. Why are carnivores, such as lions, dependent on
in photosynthesis? photosynthesis to survive?

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 5 • Critical Thinking Questions 131

14. Describe the pathway of energy in light-dependent 16. Explain the reciprocal nature of the net chemical
reactions. reactions for photosynthesis and respiration.

15. Which part of the Calvin cycle would be affected if

a cell could not produce the enzyme RuBisCO?
132 5 • Critical Thinking Questions

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CHAPTER 6
Reproduction at the Cellular Level

FIGURE 6.1 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)

CHAPTER OUTLINE
6.1 The Genome
6.2 The Cell Cycle
6.3 Cancer and the Cell Cycle
6.4 Prokaryotic Cell Division

INTRODUCTION 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.

6.1 The Genome

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
134 6 • Reproduction at the Cellular Level

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 6.2)
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.

FIGURE 6.2 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.

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 6.2 • The Cell Cycle 135

6.2 The Cell Cycle

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 6.3). 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: http://openstax.org/l/biocellcyc (http://openstaxcollege.org/l/biocellcyc)

FIGURE 6.3 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.
136 6 • Reproduction at the Cellular Level

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 6.4).

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 6.2 • The Cell Cycle 137

VISUAL CONNECTION

FIGURE 6.4 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?

a. 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.
b. 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.
c. 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.
d. 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
138 6 • Reproduction at the Cellular Level

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.

LINK TO LEARNING
This page of movies (http://openstax.org/l/divisn_newtcell) 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
6.5).

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 6.5).

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 6.2 • The Cell Cycle 139

FIGURE 6.5 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 6.6).

FIGURE 6.6 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
140 6 • Reproduction at the Cellular Level

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 6.7).

FIGURE 6.7 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.

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 6.3 • Cancer and the Cell Cycle 141

LINK TO LEARNING
Watch what occurs at the G1, G2, and M checkpoints by visiting this animation (https://www.youtube.com/
watch?v=f-ldPgEfAHI) of the cell cycle.

6.3 Cancer and the Cell Cycle

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.
142 6 • Reproduction at the Cellular Level

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 6.8). 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.

FIGURE 6.8 (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)

LINK TO LEARNING
Go to this website (http://openstax.org/l/cancer2) to watch an animation of how cancer results from errors in the
cell cycle.

Since cancer is defined by uncontrolled cell growth, cancer treatments aim to interrupt the cell cycle. One of the first
treatments involved folic acid, a substance discovered by Lucy Wills while she was researching pregnancy anemia
(blood disorder). Several scientists showed that inhibiting folic acid uptake by tumor cells resulted in reduced
growth. Jane C. Wright identified the drug now known as methotrexate as an effective treatment for breast and skin
cancers. The same drug was applied to other cancers, such as placental, uterine, and lung cancers. Methotrexate is
known as the first chemotherapy drug, and Wright's additional work to establish dosage protocols and
sequences—both to maximize the effect and manage side effects—laid the foundation for contemporary
chemotherapy treatments.

6.4 Prokaryotic Cell Division

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

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 6.4 • Prokaryotic Cell Division 143

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 6.9). 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.
144 6 • Reproduction at the Cellular Level

FIGURE 6.9 The binary fission of a bacterium is outlined in five steps. (credit: modification of work by “Mcstrother”/Wikimedia Commons)

EVOLUTION CONNECTION

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

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 6.4 • Prokaryotic Cell Division 145

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 (Table
6.1).

Mitotic Spindle Evolution

Separation of
Structure of genetic
Division of nuclear material daughter
material
cells

There is no nucleus. FtsZ proteins

The single, circular Occurs through binary fission. As the chromosome is assemble into
Prokaryotes chromosome exists in replicated, the two copies move to opposite ends of a ring that
a region of cytoplasm the cell by an unknown mechanism. pinches the
called the nucleoid. cell in two.

Microfilaments
Chromosomes attach to the nuclear envelope, which form a
Some Linear chromosomes remains intact. The mitotic spindle passes through cleavage
protists exist in the nucleus. the envelope and elongates the cell. No centrioles furrow that
exist. pinches the
cell in two.

Microfilaments
A mitotic spindle forms from the centrioles and
form a
passes through the nuclear membrane, which
Other Linear chromosomes cleavage
remains intact. Chromosomes attach to the mitotic
protists exist in the nucleus. furrow that
spindle. The mitotic spindle separates the
pinches the
chromosomes and elongates the cell.
cell in two.

Microfilaments
A mitotic spindle forms from the centrioles. The form a
Animal Linear chromosomes nuclear envelope dissolves. Chromosomes attach to cleavage
cells exist in the nucleus. the mitotic spindle, which separates them and furrow that
elongates the cell. pinches the
cell in two.

TABLE 6.1 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.
146 6 • Key Terms

Key Terms
anaphase the stage of mitosis during which sister interphase the period of the cell cycle leading up to
chromatids are separated from each other mitosis; includes G1, S, and G2 phases; the interim
binary fission the process of prokaryotic cell division between two consecutive cell divisions
cell cycle the ordered sequence of events that a cell kinetochore a protein structure in the centromere of
passes through between one cell division and the each sister chromatid that attracts and binds
next spindle microtubules during prometaphase
cell cycle checkpoints mechanisms that monitor the locus the position of a gene on a chromosome
preparedness of a eukaryotic cell to advance metaphase the stage of mitosis during which
through the various cell cycle stages chromosomes are lined up at the metaphase plate
cell plate a structure formed during plant-cell metaphase plate the equatorial plane midway
cytokinesis by Golgi vesicles fusing at the between two poles of a cell where the
metaphase plate; will ultimately lead to formation of chromosomes align during metaphase
a cell wall to separate the two daughter cells mitosis the period of the cell cycle at which the
centriole a paired rod-like structure constructed of duplicated chromosomes are separated into
microtubules at the center of each animal cell identical nuclei; includes prophase, prometaphase,
centrosome metaphase, anaphase, and telophase
cleavage furrow a constriction formed by the actin mitotic phase the period of the cell cycle when
ring during animal-cell cytokinesis that leads to duplicated chromosomes are distributed into two
cytoplasmic division nuclei and the cytoplasmic contents are divided;
cytokinesis the division of the cytoplasm following includes mitosis and cytokinesis
mitosis to form two daughter cells mitotic spindle the microtubule apparatus that
diploid describes a cell, nucleus, or organism orchestrates the movement of chromosomes during
containing two sets of chromosomes (2n) mitosis
FtsZ a tubulin-like protein component of the oncogene a mutated version of a proto-oncogene,
prokaryotic cytoskeleton that is important in which allows for uncontrolled progression of the cell
prokaryotic cytokinesis (name origin: Filamenting cycle, or uncontrolled cell reproduction
temperature-sensitive mutant Z) origin the region of the prokaryotic chromosome at
G0 phase a cell-cycle phase distinct from the G1 which replication begins
phase of interphase; a cell in G0 is not preparing to prometaphase the stage of mitosis during which
divide mitotic spindle fibers attach to kinetochores
G1 phase (also, first gap) a cell-cycle phase; first prophase the stage of mitosis during which
phase of interphase centered on cell growth during chromosomes condense and the mitotic spindle
mitosis begins to form
G2 phase (also, second gap) a cell-cycle phase; third proto-oncogene a normal gene that controls cell
phase of interphase where the cell undergoes the division by regulating the cell cycle that becomes an
final preparations for mitosis oncogene if it is mutated
gamete a haploid reproductive cell or sex cell (sperm quiescent describes a cell that is performing normal
or egg) cell functions and has not initiated preparations for
gene the physical and functional unit of heredity; a cell division
sequence of DNA that codes for a specific peptide or S phase the second, or synthesis phase, of
RNA molecule interphase during which DNA replication occurs
genome the entire genetic complement (DNA) of an septum a wall formed between bacterial daughter
organism cells as a precursor to cell separation
haploid describes a cell, nucleus, or organism telophase the stage of mitosis during which
containing one set of chromosomes (n) chromosomes arrive at opposite poles, decondense,
homologous chromosomes chromosomes of the and are surrounded by new nuclear envelopes
same length with genes in the same location; tumor suppressor gene a gene that codes for
diploid organisms have pairs of homologous regulator proteins that prevent the cell from
chromosomes, and the members of each pair come undergoing uncontrolled division
from different parents

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 6 • Chapter Summary 147

Chapter Summary
6.1 The Genome controls called checkpoints. There are three major
checkpoints in the cell cycle: one near the end of G1, a
Prokaryotes have a single loop chromosome, whereas
second at the G2–M transition, and the third during
eukaryotes have multiple, linear chromosomes
metaphase.
surrounded by a nuclear membrane. Human somatic
cells have 46 chromosomes consisting of two sets of 6.3 Cancer and the Cell Cycle
22 homologous chromosomes and a pair of
Cancer is the result of unchecked cell division caused
nonhomologous sex chromosomes. This is the 2n, or
by a breakdown of the mechanisms regulating the cell
diploid, state. Human gametes have 23 chromosomes
cycle. The loss of control begins with a change in the
or one complete set of chromosomes. This is the n, or
DNA sequence of a gene that codes for one of the
haploid, state. Genes are segments of DNA that code
regulatory molecules. Faulty instructions lead to a
for a specific protein or RNA molecule. An organism’s
protein that does not function as it should. Any
traits are determined in large part by the genes
disruption of the monitoring system can allow other
inherited from each parent, but also by the
mistakes to be passed on to the daughter cells. Each
environment that they experience. Genes are
successive cell division will give rise to daughter cells
expressed as characteristics of the organism and each
with even more accumulated damage. Eventually, all
characteristic may have different variants called traits
checkpoints become nonfunctional, and rapidly
that are caused by differences in the DNA sequence for
reproducing cells crowd out normal cells, resulting in
a gene.
tumorous growth.
6.2 The Cell Cycle
6.4 Prokaryotic Cell Division
The cell cycle is an orderly sequence of events. Cells on
In both prokaryotic and eukaryotic cell division, the
the path to cell division proceed through a series of
genomic DNA is replicated and each copy is allocated
precisely timed and carefully regulated stages. In
into a daughter cell. The cytoplasmic contents are also
eukaryotes, the cell cycle consists of a long
divided evenly to the new cells. However, there are
preparatory period, called interphase. Interphase is
many differences between prokaryotic and eukaryotic
divided into G1, S, and G2 phases. Mitosis consists of
cell division. Bacteria have a single, circular DNA
five stages: prophase, prometaphase, metaphase,
chromosome and no nucleus. Therefore, mitosis is not
anaphase, and telophase. Mitosis is usually
necessary in bacterial cell division. Bacterial
accompanied by cytokinesis, during which the
cytokinesis is directed by a ring composed of a protein
cytoplasmic components of the daughter cells are
called FtsZ. Ingrowth of membrane and cell-wall
separated either by an actin ring (animal cells) or by
material from the periphery of the cells results in a
cell plate formation (plant cells).
septum that eventually forms the separate cell walls of
Each step of the cell cycle is monitored by internal the daughter cells.
148 6 • Visual Connection Questions

Visual Connection Questions

1. Figure 6.4 Which of the following is the correct
order of events in mitosis?
a. 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.
b. 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.
c. 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.
d. 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.

Review Questions
2. A diploid cell has ________ the number of 6. The individual chromosomes become visible with a
chromosomes as a haploid cell. light microscope during which stage of mitosis?
a. one-fourth a. prophase
b. one-half b. prometaphase
c. twice c. metaphase
d. four times d. anaphase

3. An organism’s traits are determined by the specific 7. What is necessary for a cell to pass the G2
combination of inherited ________. checkpoint?
a. cells a. cell has reached a sufficient size
b. genes b. an adequate stockpile of nucleotides
c. proteins c. accurate and complete DNA replication
d. chromatids d. proper attachment of mitotic spindle fibers to
kinetochores
4. Chromosomes are duplicated during what portion
of the cell cycle? 8. ________ are changes to the nucleotides in a
a. G1 phase segment of DNA that codes for a protein.
b. S phase a. Proto-oncogenes
c. prophase b. Tumor suppressor genes
d. prometaphase c. Gene mutations
d. Negative regulators
5. Separation of the sister chromatids is a
characteristic of which stage of mitosis?
a. prometaphase
b. metaphase
c. anaphase
d. telophase

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 6 • Critical Thinking Questions 149

9. A gene that codes for a positive cell cycle regulator 11. FtsZ proteins direct the formation of a ________
is called a(n) ________. that will eventually form the new cell walls of the
a. kinase inhibitor daughter cells.
b. tumor suppressor gene a. contractile ring
c. proto-oncogene b. cell plate
d. oncogene c. cytoskeleton
d. septum
10. Which eukaryotic cell-cycle event is missing in
binary fission?
a. cell growth
b. DNA duplication
c. mitosis
d. cytokinesis

Critical Thinking Questions

12. Compare and contrast a human somatic cell to a 14. Outline the steps that lead to a cell becoming
human gamete. cancerous.

13. Describe the similarities and differences between 15. Explain the difference between a proto-oncogene
the cytokinesis mechanisms found in animal cells and a tumor suppressor gene.
versus those in plant cells.
16. Name the common components of eukaryotic cell
division and binary fission.
150 6 • Critical Thinking Questions

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CHAPTER 7
The Cellular Basis of Inheritance

FIGURE 7.1 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)

CHAPTER OUTLINE
7.1 Sexual Reproduction
7.2 Meiosis
7.3 Variations in Meiosis

INTRODUCTION 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.

Note that, in genetics, "parent" is often used to describe the individual organism(s) that contribute
genetic material to an offspring, usually in the form of gamete cells. The concept of a genetic
parent is distinct from social and legal concepts of parenthood, and may differ from those whom
people consider their parents. Even within the animal kingdom, characteristics that may often be
associated with sexual reproduction, such as parental care or sexual behavior, are not universal.

Sexual reproduction is the production of haploid cells and the fusion of a haploid cell from each
genetic 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.
152 7 • The Cellular Basis of Inheritance

7.1 Sexual Reproduction

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

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.

EVOLUTION CONNECTION

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
1
in 1973. 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

1 Leigh Van Valen, “A new evolutionary law,” Evolutionary Theory 1 (1973): 1–30.

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 7.1 • Sexual Reproduction 153

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 7.2a).
154 7 • The Cellular Basis of Inheritance

VISUAL CONNECTION

FIGURE 7.2 (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?

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 7.2 • Meiosis 155

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 7.2b).

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 7.2c).

7.2 Meiosis
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.
156 7 • The Cellular Basis of Inheritance

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 7.3).

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 7.3) 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.

FIGURE 7.3 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

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 7.2 • Meiosis 157

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 7.4).

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.

FIGURE 7.4 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
158 7 • The Cellular Basis of Inheritance

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 (Figure 7.5).

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.

LINK TO LEARNING
Review the process of meiosis, observing how chromosomes align and migrate, at this site (http://openstax.org/l/
animal_meiosis2).

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.

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 7.2 • Meiosis 159

FIGURE 7.5 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 (Figure 7.6).

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
160 7 • The Cellular Basis of Inheritance

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.

FIGURE 7.6 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.

LINK TO LEARNING
For an animation comparing mitosis and meiosis, go to this website (http://openstax.org/l/how_cells_dvid2).

7.3 Variations in Meiosis

LEARNING OBJECTIVES
By the end of this section, you will be able to:
• Explain how nondisjunction leads to differences 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.

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 7.3 • Variations in Meiosis 161

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 7.7).

FIGURE 7.7 This karyogram shows the chromosomes of a female human immune cell during mitosis. (credit: Andreas Bolzer, et al)

CAREER CONNECTION

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 (Figure 7.7).

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 7.8). 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
162 7 • The Cellular Basis of Inheritance

gamete that lacks that chromosome, two normal gametes with one copy of the chromosome, and one gamete with
two copies of the chromosome.

FIGURE 7.8 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 7.9).

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 7.3 • Variations in Meiosis 163

FIGURE 7.9 The incidence of having a fetus with trisomy 21 increases dramatically with the age of the birth parent.

LINK TO LEARNING
Visualize the addition of a chromosome that leads to Down syndrome in this video (https://www.youtube.com/
watch?v=ze_6VWwLtOE).

Humans display dramatic deleterious effects with autosomal trisomies and monosomies. Therefore, it may seem
counterintuitive that human females and males can function, 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 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 7.10). 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.
164 7 • The Cellular Basis of Inheritance

FIGURE 7.10 Embryonic inactivation of one of two different X chromosomes encoding different coat colors gives rise to the tortoiseshell
phenotype in cats. (credit: Michael Bodega)

In an individual carrying an abnormal number of X chromosomes, cellular mechanisms will inactivate all but one X in
each cell. As a result, X-chromosomal abnormalities are typically associated with mild intellectual and physical
disabilities, 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, are assigned 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 7.11). Infants with this genotype emit a characteristic high-pitched cry upon which
the disorder’s name is based.

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 7.3 • Variations in Meiosis 165

FIGURE 7.11 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 (Figure 7.12).
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 CONNECTION

The Chromosome 18 Inversion

Not 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.
166 7 • The Cellular Basis of Inheritance

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
2
in the divergence of humans from other primates.

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 7.12).

FIGURE 7.12 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)

2 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.

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 7 • Key Terms 167

Key Terms
alternation of generations a life-cycle type in which meiosis I the first round of meiotic cell division;
the diploid and haploid stages alternate referred to as reduction division because the
aneuploid an individual with an error in chromosome resulting cells are haploid
number; includes deletions and duplications of meiosis II the second round of meiotic cell division
chromosome segments following meiosis I; sister chromatids are separated
autosome any of the non-sex chromosomes from each other, and the result is four unique
chiasmata (singular = chiasma) the structure that haploid cells
forms at the crossover points after genetic material monosomy an otherwise diploid genotype in which
is exchanged one chromosome is missing
chromosome inversion the detachment, 180° nondisjunction the failure of synapsed homologs to
rotation, and reinsertion of a chromosome arm completely separate and migrate to separate poles
crossing over (also, recombination) the exchange of during the first cell division of meiosis
genetic material between homologous polyploid an individual with an incorrect number of
chromosomes resulting in chromosomes that chromosome sets
incorporate genes from both parents of the recombinant describing something composed of
organism forming reproductive cells genetic material from two sources, such as a
diploid-dominant a life-cycle type in which the chromosome with both maternal and paternal
multicellular diploid stage is prevalent segments of DNA
euploid an individual with the appropriate number of reduction division a nuclear division that produces
chromosomes for their species daughter nuclei each having one-half as many
fertilization the union of two haploid cells typically chromosome sets as the parental nucleus; meiosis I
from two individual organisms is a reduction division
gametophyte a multicellular haploid life-cycle stage somatic cell all the cells of a multicellular organism
that produces gametes except the gamete-forming cells
germ cell a specialized cell that produces gametes, sporophyte a multicellular diploid life-cycle stage
such as eggs or sperm that produces spores
haploid-dominant a life-cycle type in which the synapsis the formation of a close association
multicellular haploid stage is prevalent between homologous chromosomes during
interkinesis a period of rest that may occur between prophase I
meiosis I and meiosis II; there is no replication of tetrad two duplicated homologous chromosomes
DNA during interkinesis (four chromatids) bound together by chiasmata
karyogram the photographic image of a karyotype during prophase I
karyotype the number and appearance of an translocation the process by which one segment of a
individuals chromosomes, including the size, chromosome dissociates and reattaches to a
banding patterns, and centromere position different, nonhomologous chromosome
life cycle the sequence of events in the development trisomy an otherwise diploid genotype in which one
of an organism and the production of cells that entire chromosome is duplicated
produce offspring X inactivation the condensation of X chromosomes
meiosis a nuclear division process that results in four into Barr bodies during embryonic development in
haploid cells females to compensate for the double genetic dose

Chapter Summary
7.1 Sexual Reproduction Fertilization, the fusion of haploid gametes from two
individuals, restores the diploid condition. Thus,
Nearly all eukaryotes undergo sexual reproduction. The
sexually reproducing organisms alternate between
variation introduced into the reproductive cells by
haploid and diploid stages. However, the ways in which
meiosis appears to be one of the advantages of sexual
reproductive cells are produced and the timing
reproduction that has made it so successful. Meiosis
between meiosis and fertilization vary greatly. There
and fertilization alternate in sexual life cycles. The
are three main categories of life cycles: diploid-
process of meiosis produces genetically unique
dominant, demonstrated by most animals; haploid-
reproductive cells called gametes, which have half the
dominant, demonstrated by all fungi and some algae;
number of chromosomes as the parent cell.
and alternation of generations, demonstrated by plants
168 7 • Visual Connection Questions

and some algae. occur in the first division of meiosis. The homologous
chromosomes separate into different nuclei during
7.2 Meiosis meiosis I causing a reduction of ploidy level. The
Sexual reproduction requires that diploid organisms second division of meiosis is much more similar to a
produce haploid cells that can fuse during fertilization mitotic division.
to form diploid offspring. The process that results in
7.3 Variations in Meiosis
haploid cells is called meiosis. Meiosis is a series of
events that arrange and separate chromosomes into The number, size, shape, and banding pattern of
daughter cells. During the interphase of meiosis, each chromosomes make them easily identifiable in a
chromosome is duplicated. In meiosis, there are two karyogram and allow for the assessment of many
rounds of nuclear division resulting in four nuclei and chromosomal abnormalities. Disorders in chromosome
usually four haploid daughter cells, each with half the number, or aneuploidies, are typically lethal to the
number of chromosomes as the parent cell. During embryo, although a few trisomic genotypes are viable.
meiosis, variation in the daughter nuclei is introduced Because of X inactivation, aberrations in sex
because of crossover in prophase I and random chromosomes typically have milder effects on an
alignment at metaphase I. The cells that are produced individual. Aneuploidies also include instances in which
by meiosis are genetically unique. segments of a chromosome are duplicated or deleted.
Chromosome structures also may be rearranged, for
Meiosis and mitosis share similarities, but have distinct
example by inversion or translocation. Both of these
outcomes. Mitotic divisions are single nuclear divisions
aberrations can result in negative effects on
that produce daughter nuclei that are genetically
development, or death. Because they force
identical and have the same number of chromosome
chromosomes to assume contorted pairings during
sets as the original cell. Meiotic divisions are two
meiosis I, inversions and translocations are often
nuclear divisions that produce four daughter nuclei
associated with reduced fertility because of the
that are genetically different and have one
likelihood of nondisjunction.
chromosome set rather than the two sets the parent
cell had. The main differences between the processes

Visual Connection Questions

1. Figure 7.2 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?

Review Questions
2. What is a likely evolutionary advantage of sexual 4. Which event leads to a diploid cell in a life cycle?
reproduction over asexual reproduction? a. meiosis
a. sexual reproduction involves fewer steps b. fertilization
b. less chance of using up the resources in a given c. alternation of generations
environment d. mutation
c. sexual reproduction results in greater variation
in the offspring 5. Meiosis produces ________ daughter cells.
d. sexual reproduction is more cost-effective a. two haploid
b. two diploid
3. Which type of life cycle has both a haploid and c. four haploid
diploid multicellular stage? d. four diploid
a. an asexual life cycle
b. diploid-dominant 6. At which stage of meiosis are sister chromatids
c. haploid-dominant separated from each other?
d. alternation of generations a. prophase I
b. prophase II
c. anaphase I
d. anaphase II

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 7 • Critical Thinking Questions 169

7. The part of meiosis that is similar to mitosis is 10. Abnormalities in the number of X chromosomes
________. tend to be milder than the same abnormalities in
a. meiosis I autosomes because of ________.
b. anaphase I a. deletions
c. meiosis II b. nonhomologous recombination
d. interkinesis c. synapsis
d. X inactivation
8. If a muscle cell of a typical organism has 32
chromosomes, how many chromosomes will be in a 11. Aneuploidies are deleterious for the individual
gamete of that same organism? because of what phenomenon?
a. 8 a. nondisjunction
b. 16 b. gene dosage
c. 32 c. meiotic errors
d. 64 d. X inactivation

9. The genotype XXY corresponds to:

a. Klinefelter syndrome
b. Turner syndrome
c. Triplo-X
d. Jacob syndrome

Critical Thinking Questions

12. Explain the advantage that populations of sexually 15. In what ways is meiosis II similar to and different
reproducing organisms have over asexually from mitosis of a diploid cell?
reproducing organisms?
16. Individuals with trisomy 21 are more likely to
13. Describe the two events that are common to all survive to adulthood than individuals with trisomy
sexually reproducing organisms and how they fit 18. Based on what you know about aneuploidies
into the different life cycles of those organisms. from this module, what can you hypothesize about
chromosomes 21 and 18?
14. Explain how the random alignment of homologous
chromosomes during metaphase I contributes to
variation in gametes produced by meiosis.
170 7 • Critical Thinking Questions

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CHAPTER 8
Patterns of Inheritance

FIGURE 8.1 Experimenting with thousands of garden peas, Mendel uncovered the fundamentals of genetics. (credit:
modification of work by Jerry Kirkhart)

CHAPTER OUTLINE
8.1 Mendel’s Experiments
8.2 Laws of Inheritance
8.3 Extensions of the Laws of Inheritance

INTRODUCTION 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 traits
are transmitted from parents to offspring according to Mendelian genetics, but Mendel’s
experiments serve as an excellent starting point for thinking about inheritance.
172 8 • Patterns of Inheritance

8.1 Mendel’s Experiments

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

FIGURE 8.2 Johann Gregor Mendel set the framework for the study of genetics.

Johann Gregor Mendel (1822–1884) (Figure 8.2) 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
1
specific patterns. In 1866, he published his work, Experiments in Plant Hybridization, in the
proceedings of the Natural History Society of Brünn. As stated earlier, in genetics, "parent" is often
used to describe the individual organism(s) that contribute genetic material to an offspring,
usually in the form of gamete cells.

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

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]

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 8.1 • Mendel’s Experiments 173

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. Because every pea plant has
both male reproductive organs and female reproductive organs, each plant produces both types of gametes
required for reproduction—both pollen and ova. In plants, just as in animals, reproductive organs are classified by
the size of the gametes produced. The organs producing the smaller pollen are called male reproductive organs,
while the organs producing the larger ova are called female reproductive organs.

In garden peas, 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 8.3). 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.
174 8 • Patterns of Inheritance

FIGURE 8.3 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.

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 8.1 • Mendel’s Experiments 175

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 F2 generation 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. Mendel performed an additional experiment to ascertain differences in
inheritance of traits carried in the pollen versus the ovum. When Mendel transferred pollen from a plant with violet
flowers to fertilize the ova of a plant with white flowers and vice versa, he obtained approximately the same ratio
irrespective of which gamete 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 8.4).

FIGURE 8.4 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.
176 8 • Patterns of Inheritance

8.2 Laws of Inheritance

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 8.5). 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.

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 8.2 • Laws of Inheritance 177

FIGURE 8.5 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 traits of the recessive allele will only be observed in homozygous
recessive individuals (Table 8.1).

Correspondence between Genotype and Phenotype for a Dominant-Recessive Characteristic.

Homozygous Heterozygous Homozygous

Genotype YY Yy yy

Phenotype yellow yellow green

TABLE 8.1

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 8.6), and these offspring will breed true when self-crossed.
178 8 • Patterns of Inheritance

FIGURE 8.6 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 8.9 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

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 8.2 • Laws of Inheritance 179

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 8.7).

FIGURE 8.7 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 8.8). Alternatively, if the dominant-expressing organism is a heterozygote, the
F1 offspring will exhibit a 1:1 ratio of heterozygotes and recessive homozygotes (Figure 8.8). The test cross further
validates Mendel’s postulate that pairs of unit factors segregate equally.
180 8 • Patterns of Inheritance

FIGURE 8.8 A test cross can be performed to determine whether an organism expressing a dominant trait is a homozygote or a
heterozygote.

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 8.2 • Laws of Inheritance 181

VISUAL CONNECTION

FIGURE 8.9 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?

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 8.10).
182 8 • Patterns of Inheritance

VISUAL CONNECTION

FIGURE 8.10 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, round seed shape (R) is dominant to wrinkled seed shape (r) and yellow peas (Y) are dominant to
green peas (y). What are the possible genotypes and phenotypes for a cross between RrYY and rrYy pea plants? How
many squares do you need to do a Punnett square analysis of this cross?

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 (Figure 8.10) 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 (Figure 8.10). 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 8.11).

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 8.3 • Extensions of the Laws of Inheritance 183

FIGURE 8.11 The random segregation into daughter nuclei that happens during the first division in meiosis can lead to a variety of possible
genetic arrangements.

8.3 Extensions of the Laws of Inheritance

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

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
184 8 • Patterns of Inheritance

does appear to be intermediate between the two parents. For example, in the snapdragon, Antirrhinum majus
(Figure 8.12), 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.

FIGURE 8.12 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 8.13).

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 8.3 • Extensions of the Laws of Inheritance 185

FIGURE 8.13 This Punnet 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 8.14. 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.
186 8 • Patterns of Inheritance

FIGURE 8.14 Inheritance of the ABO blood system in humans is shown.

EVOLUTION CONNECTION

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. Ninety percent of malaria victims live in Africa, most of them
children under the age of five.

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
2
malaria burden.

n late 2021, R21/Matrix-M became the first vaccine to be recommended for widespread use by the World Health
Organization. At least ten other candidate vaccines are in development. The effort is an multinational one involving
governments, universities, nonprofits, philanthropists, and pharmaceutical companies. Much of the recent progress
can be credited to organizations within the most affected countries, such as the Malaria Research and Training
Center in Mali. Founded by Ogobara Duombo and Yeya Touré in the 1990s, the center has emerged as a primary
front-line research driver, including running many of the critical clinical trials that are so important to vaccine
development and approval.

2 Sumiti Vinayak et al., “Origin and Evolution of Sulfadoxine Resistant Plasmodium falciparum,” PLoS Pathogens 6 (2010): e1000830.

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 8.3 • Extensions of the Laws of Inheritance 187

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. Humans may identify as being male, female, neither of
these, both, or other gender(s) independently of these chromosomes, but the sex chromosomes can be associated
with certain traits. 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 8.15).
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.

FIGURE 8.15 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 8.16). 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).
188 8 • Patterns of Inheritance

VISUAL CONNECTION

FIGURE 8.16 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?

Discoveries in fruit fly genetics can be applied to human genetics. When a female parent is homozygous for a
recessive X-linked trait, the parent will pass the trait on to 100 percent of the 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
male offspring and will pass carrier status to half of their female offspring; 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.

LINK TO LEARNING
Watch this video (http://openstax.org/l/sex-linked_trts) 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

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 8.3 • Extensions of the Laws of Inheritance 189

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 8.17). 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.

FIGURE 8.17 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 pairs of 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.
190 8 • Patterns of Inheritance

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.

LINK TO LEARNING
Eye color in humans is determined by multiple alleles. Use the Eye Color Calculator (http://openstax.org/l/
eye_color_calc) 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 8.18). 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 8.18). In this case, the C gene is
epistatic to the A gene.

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 8.3 • Extensions of the Laws of Inheritance 191

FIGURE 8.18 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.
192 8 • Key Terms

Key Terms
allele one of two or more variants of a gene that into gametes; every possible combination of alleles
determines a particular trait for a characteristic is equally likely to occur
codominance in a heterozygote, complete and law of segregation paired unit factors (i.e., genes)
simultaneous expression of both alleles for the segregate equally into gametes such that offspring
same characteristic have an equal likelihood of inheriting any
continuous variation a variation in a characteristic in combination of factors
which individuals show a range of traits with small linkage a phenomenon in which alleles that are
differences between them located in close proximity to each other on the same
dihybrid the result of a cross between two true- chromosome are more likely to be inherited
breeding parents that express different traits for two together
characteristics model system a species or biological system used to
discontinuous variation a variation in a characteristic study a specific biological phenomenon to gain
in which individuals show two, or a few, traits with understanding that will be applied to other species
large differences between them monohybrid the result of a cross between two true-
dominant describes a trait that masks the expression breeding parents that express different traits for
of another trait when both versions of the gene are only one characteristic
present in an individual parental generation (P) the first generation in a cross
epistasis an interaction between genes such that one phenotype the observable traits expressed by an
gene masks or interferes with the expression of organism
another Punnett square a visual representation of a cross
F1 the first filial generation in a cross; the offspring of between two individuals in which the gametes of
the parental generation each individual are denoted along the top and side
F2 the second filial generation produced when F1 of a grid, respectively, and the possible zygotic
individuals are self-crossed or fertilized with each genotypes are recombined at each box in the grid
other recessive describes a trait whose expression is
genotype the underlying genetic makeup, consisting masked by another trait when the alleles for both
of both physically visible and non-expressed alleles, traits are present in an individual
of an organism reciprocal cross a paired cross in which the
hemizygous the presence of only one allele for a respective traits of the male and female in one cross
characteristic, as in X-linkage; hemizygosity makes become the respective traits of the female and male
descriptions of dominance and recessiveness in the other cross
irrelevant recombination the process during meiosis in which
heterozygous having two different alleles for a given homologous chromosomes exchange linear
gene on the homologous chromosomes segments of genetic material, thereby dramatically
homozygous having two identical alleles for a given increasing genetic variation in the offspring and
gene on the homologous chromosomes separating linked genes
hybridization the process of mating two individuals test cross a cross between a dominant expressing
that differ, with the goal of achieving a certain individual with an unknown genotype and a
characteristic in their offspring homozygous recessive individual; the offspring
incomplete dominance in a heterozygote, expression phenotypes indicate whether the unknown parent is
of two contrasting alleles such that the individual heterozygous or homozygous for the dominant trait
displays an intermediate phenotype trait a variation in an inherited characteristic
law of dominance in a heterozygote, one trait will wild type the most commonly occurring genotype or
conceal the presence of another trait for the same phenotype for a given characteristic found in a
characteristic population
law of independent assortment genes do not X-linked a gene present on the X chromosome, but
influence each other with regard to sorting of alleles not the Y chromosome

Chapter Summary
8.1 Mendel’s Experiments crosses between parents that differed for one trait
produced F1 offspring that all expressed one parent’s
Working with garden pea plants, Mendel found that
traits. The traits that were visible in the F1 generation

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 8 • Visual Connection Questions 193

are referred to as dominant, and traits that disappear in situations in which the heterozygote exhibits a
the F1 generation are described as recessive. When the phenotype that is intermediate between the
F1 plants in Mendel’s experiment were self-crossed, homozygous phenotypes. Codominance describes the
the F2 offspring exhibited the dominant trait or the simultaneous expression of both of the alleles in the
recessive trait in a 3:1 ratio, confirming that the heterozygote. Although diploid organisms can only
recessive trait had been transmitted faithfully from the have two alleles for any given gene, it is common for
original P parent. Reciprocal crosses generated more than two alleles for a gene to exist in a
identical F1 and F2 offspring ratios. By examining population. In humans, as in many animals and some
sample sizes, Mendel showed that traits were inherited plants, females have two X chromosomes and males
as independent events. have one X and one Y chromosome. Genes that are
present on the X but not the Y chromosome are said to
8.2 Laws of Inheritance be X-linked, such that males only inherit one allele for
When true-breeding, or homozygous, individuals that the gene, and females inherit two.
differ for a certain trait are crossed, all of the offspring
According to Mendel’s law of independent assortment,
will be heterozygous for that trait. If the traits are
genes sort independently of each other into gametes
inherited as dominant and recessive, the F1 offspring
during meiosis. This occurs because chromosomes, on
will all exhibit the same phenotype as the parent
which the genes reside, assort independently during
homozygous for the dominant trait. If these
meiosis and crossovers cause most genes on the same
heterozygous offspring are self-crossed, the resulting
chromosomes to also behave independently. When
F2 offspring will be equally likely to inherit gametes
genes are located in close proximity on the same
carrying the dominant or recessive trait, giving rise to
chromosome, their alleles tend to be inherited
offspring of which one quarter are homozygous
together. This results in offspring ratios that violate
dominant, half are heterozygous, and one quarter are
Mendel's law of independent assortment. However,
homozygous recessive. Because homozygous dominant
recombination serves to exchange genetic material on
and heterozygous individuals are phenotypically
homologous chromosomes such that maternal and
identical, the observed traits in the F2 offspring will
paternal alleles may be recombined on the same
exhibit a ratio of three dominant to one recessive.
chromosome. This is why alleles on a given
Mendel postulated that genes (characteristics) are chromosome are not always inherited together.
inherited as pairs of alleles (traits) that behave in a Recombination is a random event occurring anywhere
dominant and recessive pattern. Alleles segregate into on a chromosome. Therefore, genes that are far apart
gametes such that each gamete is equally likely to on the same chromosome are likely to still assort
receive either one of the two alleles present in a diploid independently because of recombination events that
individual. In addition, genes are assorted into occurred in the intervening chromosomal space.
gametes independently of one another. That is, in
Whether or not they are sorting independently, genes
general, alleles are not more likely to segregate into a
may interact at the level of gene products, such that
gamete with a particular allele of another gene.
the expression of an allele for one gene masks or
8.3 Extensions of the Laws of Inheritance modifies the expression of an allele for a different
gene. This is called epistasis.
Alleles do not always behave in dominant and
recessive patterns. Incomplete dominance describes

Visual Connection Questions

1. Figure 8.9 In pea plants, round peas (R) are 2. Figure 8.10 In pea plants, round seed shape (R) is
dominant to wrinkled peas (r). You do a test cross dominant to wrinkled seed shape (r) and yellow
between a pea plant with wrinkled peas (genotype peas (Y) are dominant to green peas (y). What are
rr) and a plant of unknown genotype that has round the possible genotypes and phenotypes for a cross
peas. You end up with three plants, all which have between RrYY and rrYy pea plants? How many
round peas. From this data, can you tell if the squares do you need to do a Punnett square
parent plant is homozygous dominant or analysis of this cross?
heterozygous?
3. Figure 8.16 What ratio of offspring would result
from a cross between a white-eyed male and a
female that is heterozygous for red eye color?
194 8 • Review Questions

Review Questions
4. Imagine that you are performing a cross involving 9. What is the reason for doing a test cross?
seed color in garden pea plants. What traits would a. to identify heterozygous individuals with the
you expect to observe in the F1 offspring if you dominant phenotype
cross true-breeding parents with green seeds and b. to determine which allele is dominant and
yellow seeds? Yellow seed color is dominant over which is recessive
green. c. to identify homozygous recessive individuals in
a. only yellow-green seeds the F2
b. only yellow seeds d. to determine if two genes assort independently
c. 1:1 yellow seeds:green seeds
d. 1:3 green seeds:yellow seeds 10. If black and white true-breeding mice are mated
and the result is all gray offspring, what
5. Imagine that you are performing a cross involving inheritance pattern would this be indicative of?
seed texture in garden pea plants. You cross true- a. dominance
breeding round and wrinkled parents to obtain F1 b. codominance
offspring. Which of the following experimental c. multiple alleles
results in terms of numbers of plants are closest to d. incomplete dominance
what you expect in the F2 progeny?
a. 810 round seeds 11. The ABO blood groups in humans are expressed
b. 810 wrinkled seeds as the IA, IB, and i alleles. The IA allele encodes
c. 405:395 round seeds:wrinkled seeds the A blood group antigen, IB encodes B, and i
d. 610:190 round seeds:wrinkled seeds encodes O. Both A and B are dominant to O. If a
heterozygous blood type A parent (IAi) and a
6. The observable traits expressed by an organism are heterozygous blood type B parent (IBi) mate, one
described as its ________. quarter of their offspring are expected to have the
a. phenotype AB blood type (IAIB) in which both antigens are
b. genotype expressed equally. Therefore, ABO blood groups
c. alleles are an example of:
d. zygote a. multiple alleles and incomplete dominance
b. codominance and incomplete dominance
7. A recessive trait will be observed in individuals that c. incomplete dominance only
are ________ for that trait. d. multiple alleles and codominance
a. heterozygous
b. homozygous or heterozygous 12. In a cross between a homozygous red-eyed
c. homozygous female fruit fly and a white-eyed male fruit fly,
d. diploid what is the expected outcome?
a. all white-eyed male offspring
8. What are the types of gametes that can be b. all white-eyed female offspring
produced by an individual with the genotype AaBb? c. all red-eyed offspring
a. Aa, Bb d. half white-eyed make offspring
b. AA, aa, BB, bb
c. AB, Ab, aB, ab 13. When a population has a gene with four alleles
d. AB, ab circulating, how many possible genotypes are
there?
a. 3
b. 6
c. 10
d. 16

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 8 • Critical Thinking Questions 195

Critical Thinking Questions

14. Describe one of the reasons that made the garden 16. Use a Punnett square to predict the offspring in a
pea an excellent choice of model system for cross between a tall pea plant (heterozygous) and
studying inheritance. a tall pea plant (heterozygous). What is the
genotypic ratio of the offspring?
15. Use a Punnett square to predict the offspring in a
cross between a dwarf pea plant (homozygous 17. Can a male be a carrier of red-green color
recessive) and a tall pea plant (heterozygous). blindness?
What is the phenotypic ratio of the offspring?
18. Could an individual with blood type O (genotype ii)
be a legitimate child of parents in which one
parent had blood type A and the other parent had
blood type B?
196 8 • Critical Thinking Questions

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CHAPTER 9
Molecular Biology

FIGURE 9.1 Dolly the sheep was the first cloned mammal.

CHAPTER OUTLINE
9.1 The Structure of DNA
9.2 DNA Replication
9.3 Transcription
9.4 Translation
9.5 How Genes Are Regulated

INTRODUCTION 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
198 9 • Molecular Biology

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.

9.1 The Structure of DNA

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 9.2). 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.

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 9.1 • The Structure of DNA 199

FIGURE 9.2 Scientist Rosalind Franklin discovered the X-ray diffraction pattern of DNA, which helped to elucidate its double helix structure.
(credit: 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 9.3). 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.
200 9 • Molecular Biology

FIGURE 9.3 (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.

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 9.4).

FIGURE 9.4 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

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 9.1 • The Structure of DNA 201

deoxyribose, which has only a hydrogen atom (Figure 9.5).

FIGURE 9.5 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 9.6).
Most prokaryotes contain a single, circular chromosome that is found in an area in the cytoplasm called the
nucleoid.

FIGURE 9.6 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 (Figure 9.7). Before the structure of DNA was even uncovered, Marie Maynard
Daly and Arthur E. Mirsky conducted extensive research in the 1940s and 1950s to understand the molecules and
structures in involved. 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”
202 9 • Molecular Biology

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.

FIGURE 9.7 These figures illustrate the compaction of the eukaryotic chromosome.

LINK TO LEARNING
Watch this animation (http://openstax.org/l/DNA_packaging) of DNA packaging.

9.2 DNA Replication

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

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 9.2 • DNA Replication 203

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 9.8).

FIGURE 9.8 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 9.9).
204 9 • Molecular Biology

FIGURE 9.9 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 9.10). 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:

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 9.2 • DNA Replication 205

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.

VISUAL CONNECTION

FIGURE 9.10 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 9.11) 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.
206 9 • Molecular Biology

FIGURE 9.11 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 9.12) received the Nobel Prize for Medicine and Physiology in
2009. Later research using HeLa cells (obtained from Henrietta Lacks) confirmed that telomerase is present in
human cells. And in 2001, researchers including Diane L. Wright found that telomerase is necessary for cells in
human embryos to rapidly proliferate.

FIGURE 9.12 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
1
medicine. 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

1 Mariella Jaskelioff, et al., “Telomerase reactivation reverses tissue degeneration in aged telomerase-deficient mice,” Nature, 469
(2011):102–7.

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 9.2 • DNA Replication 207

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. Table 9.1 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

TABLE 9.1

LINK TO LEARNING
Click through a tutorial (http://openstax.org/l/DNA_replicatio2) 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
9.13a). 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 9.13b). 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 9.13c). 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.
208 9 • Molecular Biology

FIGURE 9.13 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.

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 9.3 • Transcription 209

9.3 Transcription
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
9.14), which states that genes specify the sequences of mRNAs, which in turn specify the sequences of proteins.

FIGURE 9.14 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 9.15).
210 9 • Molecular Biology

FIGURE 9.15 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 9.16).

FIGURE 9.16 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 9.17). In contrast, the
presence of a nucleus in eukaryotic cells precludes simultaneous transcription and translation.

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 9.3 • Transcription 211

FIGURE 9.17 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 9.18). Introns are removed and degraded while the pre-mRNA is still in
the nucleus.

FIGURE 9.18 Eukaryotic mRNA contains introns that must be spliced out. A 5' cap and 3' tail are also added.
212 9 • Molecular Biology

9.4 Translation
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 9.19).

FIGURE 9.19 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.

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 9.4 • Translation 213

The Genetic Code

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 9.20).

FIGURE 9.20 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
214 9 • Molecular Biology

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 9.21).
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.

FIGURE 9.21 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.

LINK TO LEARNING
Transcribe a gene and translate it to protein using complementary pairing and the genetic code at this site
(http://openstax.org/l/create_protein2).

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 9.5 • How Genes Are Regulated 215

9.5 How Genes Are Regulated

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
216 9 • Molecular Biology

gene expression can occur at all stages of the process (Figure 9.22). 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).

FIGURE 9.22 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 Table
9.2.

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 9.5 • How Genes Are Regulated 217

Differences in the Regulation of Gene Expression of Prokaryotic and Eukaryotic Organisms

Prokaryotic organisms Eukaryotic organisms

Lack nucleus Contain nucleus

• RNA transcription occurs prior to protein translation, and it takes place

RNA transcription and protein in the nucleus. RNA translation to protein occurs in the cytoplasm.
translation occur almost • RNA post-processing includes addition of a 5' cap, poly-A tail, and
simultaneously excision of introns and splicing of exons.

Gene expression is regulated Gene expression is regulated at many levels (epigenetic, transcriptional,
primarily at the transcriptional level post-transcriptional, translational, and post-translational)

TABLE 9.2

EVOLUTION CONNECTION

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 9.23). 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.
218 9 • Molecular Biology

FIGURE 9.23 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.

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 9 • Key Terms 219

Key Terms
alternative RNA splicing a post-transcriptional gene nontemplate strand the strand of DNA that is not
regulation mechanism in eukaryotes in which used to transcribe mRNA; this strand is identical to
multiple protein products are produced by a single the mRNA except that T nucleotides in the DNA are
gene through alternative splicing combinations of replaced by U nucleotides in the mRNA
the RNA transcript nucleotide excision repair a form of DNA repair in
codon three consecutive nucleotides in mRNA that which the DNA molecule is unwound and separated
specify the addition of a specific amino acid or the in the region of the nucleotide damage, the
release of a polypeptide chain during translation damaged nucleotides are removed and replaced
deoxyribose a five-carbon sugar molecule with a with new nucleotides using the complementary
hydrogen atom rather than a hydroxyl group in the strand, and the DNA strand is resealed and allowed
2' position; the sugar component of DNA to rejoin its complement
nucleotides Okazaki fragments the DNA fragments that are
DNA ligase the enzyme that catalyzes the joining of synthesized in short stretches on the lagging strand
DNA fragments together phosphate group a molecular group consisting of a
DNA polymerase an enzyme that synthesizes a new central phosphorus atom bound to four oxygen
strand of DNA complementary to a template strand atoms
double helix the molecular shape of DNA in which post-transcriptional control of gene expression after
two strands of nucleotides wind around each other the RNA molecule has been created but before it is
in a spiral shape translated into protein
epigenetic describing non-genetic regulatory factors, post-translational control of gene expression after a
such as changes in modifications to histone proteins protein has been created
and DNA that control accessibility to genes in primer a short stretch of RNA nucleotides that is
chromosomes required to initiate replication and allow DNA
exon a sequence present in protein-coding mRNA polymerase to bind and begin replication
after completion of pre-mRNA splicing promoter a sequence on DNA to which RNA
gene expression processes that control whether a polymerase and associated factors bind and initiate
gene is expressed transcription
genetic code the amino acids that correspond to replication fork the Y-shaped structure formed
three-nucleotide codons of mRNA during the initiation of replication
helicase an enzyme that helps to open up the DNA RNA polymerase an enzyme that synthesizes an RNA
helix during DNA replication by breaking the strand from a DNA template strand
hydrogen bonds rRNA ribosomal RNA; molecules of RNA that combine
intron non–protein-coding intervening sequences to form part of the ribosome
that are spliced from mRNA during processing semiconservative replication the method used to
lagging strand during replication of the 3' to 5' replicate DNA in which the double-stranded
strand, the strand that is replicated in short molecule is separated and each strand acts as a
fragments and away from the replication fork template for a new strand to be synthesized, so the
leading strand the strand that is synthesized resulting DNA molecules are composed of one new
continuously in the 5' to 3' direction that is strand of nucleotides and one old strand of
synthesized in the direction of the replication fork nucleotides
mismatch repair a form of DNA repair in which non- splicing the process of removing introns and
complementary nucleotides are recognized, reconnecting exons in a pre-mRNA
excised, and replaced with correct nucleotides start codon the AUG (or, rarely GUG) on an mRNA
mRNA messenger RNA; a form of RNA that carries from which translation begins; always specifies
the nucleotide sequence code for a protein methionine
sequence that is translated into a polypeptide stop codon one of the three mRNA codons that
sequence specifies termination of translation
mutation a permanent variation in the nucleotide telomerase an enzyme that contains a catalytic part
sequence of a genome and an inbuilt RNA template; it functions to maintain
nitrogenous base a nitrogen-containing molecule telomeres at chromosome ends
that acts as a base; often referring to one of the telomere the DNA at the end of linear chromosomes
purine or pyrimidine components of nucleic acids template strand the strand of DNA that specifies the
220 9 • Chapter Summary

complementary mRNA molecule specific three-nucleotide anticodon sequence to

transcription bubble the region of locally unwound pair with the mRNA codon and also binds to a
DNA that allows for transcription of mRNA specific amino acid
tRNA transfer RNA; an RNA molecule that contains a

Chapter Summary
9.1 The Structure of DNA a single origin of replication. The DNA is opened with
enzymes, resulting in the formation of the replication
The model of the double-helix structure of DNA was
fork. Primase synthesizes an RNA primer to initiate
proposed by Watson and Crick. The DNA molecule is a
synthesis by DNA polymerase, which can add
polymer of nucleotides. Each nucleotide is composed
nucleotides in only one direction. One strand is
of a nitrogenous base, a five-carbon sugar
synthesized continuously in the direction of the
(deoxyribose), and a phosphate group. There are four
replication fork; this is called the leading strand. The
nitrogenous bases in DNA, two purines (adenine and
other strand is synthesized in a direction away from the
guanine) and two pyrimidines (cytosine and thymine).
replication fork, in short stretches of DNA known as
A DNA molecule is composed of two strands. Each
Okazaki fragments. This strand is known as the lagging
strand is composed of nucleotides bonded together
strand. Once replication is completed, the RNA primers
covalently between the phosphate group of one and
are replaced by DNA nucleotides and the DNA is sealed
the deoxyribose sugar of the next. From this backbone
with DNA ligase.
extend the bases. The bases of one strand bond to the
bases of the second strand with hydrogen bonds. The ends of eukaryotic chromosomes pose a problem,
Adenine always bonds with thymine, and cytosine as polymerase is unable to extend them without a
always bonds with guanine. The bonding causes the primer. Telomerase, an enzyme with an inbuilt RNA
two strands to spiral around each other in a shape template, extends the ends by copying the RNA
called a double helix. Ribonucleic acid (RNA) is a template and extending one end of the chromosome.
second nucleic acid found in cells. RNA is a single- DNA polymerase can then extend the DNA using the
stranded polymer of nucleotides. It also differs from primer. In this way, the ends of the chromosomes are
DNA in that it contains the sugar ribose, rather than protected. Cells have mechanisms for repairing DNA
deoxyribose, and the nucleotide uracil rather than when it becomes damaged or errors are made in
thymine. Various RNA molecules function in the replication. These mechanisms include mismatch
process of forming proteins from the genetic code in repair to replace nucleotides that are paired with a
DNA. non-complementary base and nucleotide excision
repair, which removes bases that are damaged such as
Prokaryotes contain a single, double-stranded circular
thymine dimers.
chromosome. Eukaryotes contain double-stranded
linear DNA molecules packaged into chromosomes. 9.3 Transcription
The DNA helix is wrapped around proteins to form
In prokaryotes, mRNA synthesis is initiated at a
nucleosomes. The protein coils are further coiled, and
promoter sequence on the DNA template. Elongation
during mitosis and meiosis, the chromosomes become
synthesizes new mRNA. Termination liberates the
even more greatly coiled to facilitate their movement.
mRNA and occurs by mechanisms that stall the RNA
Chromosomes have two distinct regions which can be
polymerase and cause it to fall off the DNA template.
distinguished by staining, reflecting different degrees
Newly transcribed eukaryotic mRNAs are modified with
of packaging and determined by whether the DNA in a
a cap and a poly-A tail. These structures protect the
region is being expressed (euchromatin) or not
mature mRNA from degradation and help export it from
(heterochromatin).
the nucleus. Eukaryotic mRNAs also undergo splicing,
9.2 DNA Replication in which introns are removed and exons are
reconnected with single-nucleotide accuracy. Only
DNA replicates by a semi-conservative method in
finished mRNAs are exported from the nucleus to the
which each of the two parental DNA strands act as a
cytoplasm.
template for new DNA to be synthesized. After
replication, each DNA has one parental or “old” strand, 9.4 Translation
and one daughter or “new” strand.
The central dogma describes the flow of genetic
Replication in eukaryotes starts at multiple origins of information in the cell from genes to mRNA to proteins.
replication, while replication in prokaryotes starts from Genes are used to make mRNA by the process of

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 9 • Visual Connection Questions 221

transcription; mRNA is used to synthesize proteins by dissociates the components and frees the new protein.
the process of translation. The genetic code is the
correspondence between the three-nucleotide mRNA
9.5 How Genes Are Regulated
codon and an amino acid. The genetic code is While all somatic cells within an organism contain the
“translated” by the tRNA molecules, which associate a same DNA, not all cells within that organism express
specific codon with a specific amino acid. The genetic the same proteins. Prokaryotic organisms express the
code is degenerate because 64 triplet codons in mRNA entire DNA they encode in every cell, but not
specify only 20 amino acids and three stop codons. necessarily all at the same time. Proteins are
This means that more than one codon corresponds to expressed only when they are needed. Eukaryotic
an amino acid. Almost every species on the planet uses organisms express a subset of the DNA that is encoded
the same genetic code. in any given cell. In each cell type, the type and amount
of protein is regulated by controlling gene expression.
The players in translation include the mRNA template,
To express a protein, the DNA is first transcribed into
ribosomes, tRNAs, and various enzymatic factors. The
RNA, which is then translated into proteins. In
small ribosomal subunit binds to the mRNA template.
prokaryotic cells, these processes occur almost
Translation begins at the initiating AUG on the mRNA.
simultaneously. In eukaryotic cells, transcription
The formation of bonds occurs between sequential
occurs in the nucleus and is separate from the
amino acids specified by the mRNA template according
translation that occurs in the cytoplasm. Gene
to the genetic code. The ribosome accepts charged
expression in prokaryotes is regulated only at the
tRNAs, and as it steps along the mRNA, it catalyzes
transcriptional level, whereas in eukaryotic cells, gene
bonding between the new amino acid and the end of
expression is regulated at the epigenetic,
the growing polypeptide. The entire mRNA is translated
transcriptional, post-transcriptional, translational, and
in three-nucleotide “steps” of the ribosome. When a
post-translational levels.
stop codon is encountered, a release factor binds and

Visual Connection Questions

1. Figure 9.10 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?

Review Questions
2. Which of the following does cytosine pair with? 5. The initial mechanism for repairing nucleotide
a. guanine errors in DNA is ________.
b. thymine a. mismatch repair
c. adenine b. DNA polymerase proofreading
d. a pyrimidine c. nucleotide excision repair
d. thymine dimers
3. Prokaryotes contain a ________chromosome, and
eukaryotes contain ________ chromosomes. 6. A promoter is ________.
a. single-stranded circular; single-stranded linear a. a specific sequence of DNA nucleotides
b. single-stranded linear; single-stranded circular b. a specific sequence of RNA nucleotides
c. double-stranded circular; double-stranded c. a protein that binds to DNA
linear d. an enzyme that synthesizes RNA
d. double-stranded linear; double-stranded
circular 7. Portions of eukaryotic mRNA sequence that are
removed during RNA processing are ________.
4. DNA replicates by which of the following models? a. exons
a. conservative b. caps
b. semiconservative c. poly-A tails
c. dispersive d. introns
d. none of the above
222 9 • Critical Thinking Questions

8. The RNA components of ribosomes are synthesized 10. Control of gene expression in eukaryotic cells
in the ________. occurs at which level(s)?
a. cytoplasm a. only the transcriptional level
b. nucleus b. epigenetic and transcriptional levels
c. nucleolus c. epigenetic, transcriptional, and translational
d. endoplasmic reticulum levels
d. epigenetic, transcriptional, post-
9. How long would the peptide be that is translated transcriptional, translational, and post-
from this MRNA sequence: 5'-AUGGGCUACCGA-3'? translational levels
a. 0
b. 2 11. Post-translational control refers to:
c. 3 a. regulation of gene expression after
d. 4 transcription
b. regulation of gene expression after translation
c. control of epigenetic activation
d. period between transcription and translation

Critical Thinking Questions

12. Describe the organization of the eukaryotic 15. Transcribe and translate the following DNA
chromosome. sequence (nontemplate strand): 5'-
ATGGCCGGTTATTAAGCA-3'
13. Describe the structure and complementary base
pairing of DNA. 16. Describe how controlling gene expression will
alter the overall protein levels in the cell.
14. How do the linear chromosomes in eukaryotes
ensure that its ends are replicated completely?

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CHAPTER 10
Biotechnology

FIGURE 10.1 (a) A thermal cycler, such as the one shown here, is a basic tool used to study DNA in a process called
the polymerase chain reaction (PCR). The polymerase enzyme most often used with PCR comes from a strain of
bacteria that lives in (b) the hot springs of Yellowstone National Park. (credit a: modification of work by Magnus
Manske; credit b: modification of work by Jon Sullivan)

CHAPTER OUTLINE
10.1 Cloning and Genetic Engineering
10.2 Biotechnology in Medicine and Agriculture
10.3 Genomics and Proteomics

INTRODUCTION The latter half of the twentieth century began with the discovery of the structure
of DNA, then progressed to the development of the basic tools used to study and manipulate DNA.
These advances, as well as advances in our understanding of and ability to manipulate cells, have
led some to refer to the twenty-first century as the biotechnology century. The rate of discovery
and of the development of new applications in medicine, agriculture, and energy is expected to
accelerate, bringing huge benefits to humankind and perhaps also significant risks. Many of these
developments are expected to raise significant ethical and social questions that human societies
have not yet had to consider.

10.1 Cloning and Genetic Engineering

LEARNING OBJECTIVES
By the end of this section, you will be able to:
• Explain the basic techniques used to manipulate genetic material
• Explain molecular and reproductive cloning

Biotechnology is the use of artificial methods to modify the genetic material of living organisms or
cells to produce novel compounds or to perform new functions. Biotechnology has been used for
improving livestock and crops since the beginning of agriculture through selective breeding. Since
the discovery of the structure of DNA in 1953, and particularly since the development of tools and
methods to manipulate DNA in the 1970s, biotechnology has become synonymous with the
manipulation of organisms’ DNA at the molecular level. The primary applications of this
technology are in medicine (for the production of vaccines and antibiotics) and in agriculture (for
224 10 • Biotechnology

the genetic modification of crops). Biotechnology also has many industrial applications, such as
fermentation, the treatment of oil spills, and the production of biofuels, as well as many
household applications such as the use of enzymes in laundry detergent.

Manipulating Genetic Material

To accomplish the applications described above, biotechnologists must be able to extract,
manipulate, and analyze nucleic acids.

Review of Nucleic Acid Structure

To understand the basic techniques used to work with nucleic acids, remember that nucleic acids
are macromolecules made of nucleotides (a sugar, a phosphate, and a nitrogenous base). The
phosphate groups on these molecules each have a net negative charge. An entire set of DNA
molecules in the nucleus of eukaryotic organisms is called the genome. DNA has two
complementary strands linked by hydrogen bonds between the paired bases.

Unlike DNA in eukaryotic cells, RNA molecules leave the nucleus. Messenger RNA (mRNA) is
analyzed most frequently because it represents the protein-coding genes that are being expressed
in the cell.

Isolation of Nucleic Acids

To study or manipulate nucleic acids, the DNA must first be extracted from cells. Various
techniques are used to extract different types of DNA (Figure 10.2). Most nucleic acid extraction
techniques involve steps to break open the cell, and then the use of enzymatic reactions to
destroy all undesired macromolecules. Cells are broken open using a detergent solution
containing buffering compounds. To prevent degradation and contamination, macromolecules
such as proteins and RNA are inactivated using enzymes. The DNA is then brought out of solution
using alcohol. The resulting DNA, because it is made up of long polymers, forms a gelatinous
mass.

FIGURE 10.2 This diagram shows the basic method used for the extraction of DNA.

RNA is studied to understand gene expression patterns in cells. RNA is naturally very unstable
because enzymes that break down RNA are commonly present in nature. Some are even secreted
by our own skin and are very difficult to inactivate. Similar to DNA extraction, RNA extraction
involves the use of various buffers and enzymes to inactivate other macromolecules and preserve
only the RNA.

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 10.1 • Cloning and Genetic Engineering 225

Gel Electrophoresis
Because nucleic acids are negatively charged ions at neutral or alkaline pH in an aqueous environment, they can be
moved by an electric field. Gel electrophoresis is a technique used to separate charged molecules on the basis of
size and charge. The nucleic acids can be separated as whole chromosomes or as fragments. The nucleic acids are
loaded into a slot at one end of a gel matrix, an electric current is applied, and negatively charged molecules are
pulled toward the opposite end of the gel (the end with the positive electrode). Smaller molecules move through the
pores in the gel faster than larger molecules; this difference in the rate of migration separates the fragments on the
basis of size. The nucleic acids in a gel matrix are invisible until they are stained with a compound that allows them
to be seen, such as a dye. Distinct fragments of nucleic acids appear as bands at specific distances from the top of
the gel (the negative electrode end) that are based on their size (Figure 10.3). A mixture of many fragments of
varying sizes appear as a long smear, whereas uncut genomic DNA is usually too large to run through the gel and
forms a single large band at the top of the gel.

FIGURE 10.3 Shown are DNA fragments from six samples run on a gel, stained with a fluorescent dye and viewed under UV light. (credit:
modification of work by James Jacob, Tompkins Cortland Community College)

Polymerase Chain Reaction

DNA analysis often requires focusing on one or more specific regions of the genome. It also frequently involves
situations in which only one or a few copies of a DNA molecule are available for further analysis. These amounts are
insufficient for most procedures, such as gel electrophoresis. Polymerase chain reaction (PCR) is a technique used
to rapidly increase the number of copies of specific regions of DNA for further analyses (Figure 10.4). PCR uses a
special form of DNA polymerase, the enzyme that replicates DNA, and other short nucleotide sequences called
primers that base pair to a specific portion of the DNA being replicated. PCR is used for many purposes in
laboratories. These include: 1) the identification of the owner of a DNA sample left at a crime scene; 2) paternity
analysis; 3) the comparison of small amounts of ancient DNA with modern organisms; and 4) determining the
sequence of nucleotides in a specific region.
226 10 • Biotechnology

FIGURE 10.4 Polymerase chain reaction, or PCR, is used to produce many copies of a specific sequence of DNA using a special form of DNA
polymerase.

Cloning
In general, cloning means the creation of a perfect replica. Typically, the word is used to describe the creation of a
genetically identical copy. In biology, the re-creation of a whole organism is referred to as “reproductive cloning.”
Long before attempts were made to clone an entire organism, researchers learned how to copy short stretches of
DNA—a process that is referred to as molecular cloning. The technique offered methods to create new medicines
and to overcome difficulties with existing ones. When Lydia Villa-Komaroff, working in the Gilbert Lab at Harvard,
published the first paper outlining the technique for producing synthetic insulin, diabetes researchers and patients
received new hope in fighting the disease. Insulin at that time was only produced using pig and cow pancreases, and
the life-saving substance was often in short supply. Synthetic insulin, once mass produced, would solve that
problem for many patients. These early discoveries led to the "BioTech Boom," and spurred continued research and
funding for newer and better ways to improve health.

Molecular Cloning
Cloning allows for the creation of multiple copies of genes, expression of genes, and study of specific genes. To get
the DNA fragment into a bacterial cell in a form that will be copied or expressed, the fragment is first inserted into a
plasmid. A plasmid (also called a vector in this context) is a small circular DNA molecule that replicates
independently of the chromosomal DNA in bacteria. In cloning, the plasmid molecules can be used to provide a

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 10.1 • Cloning and Genetic Engineering 227

"vehicle" in which to insert a desired DNA fragment. Modified plasmids are usually reintroduced into a bacterial host
for replication. As the bacteria divide, they copy their own DNA (including the plasmids). The inserted DNA fragment
is copied along with the rest of the bacterial DNA. In a bacterial cell, the fragment of DNA from the human genome
(or another organism that is being studied) is referred to as foreign DNA to differentiate it from the DNA of the
bacterium (the host DNA).

Plasmids occur naturally in bacterial populations (such as Escherichia coli) and have genes that can contribute
favorable traits to the organism, such as antibiotic resistance (the ability to be unaffected by antibiotics). Plasmids
have been highly engineered as vectors for molecular cloning and for the subsequent large-scale production of
important molecules, such as insulin. A valuable characteristic of plasmid vectors is the ease with which a foreign
DNA fragment can be introduced. These plasmid vectors contain many short DNA sequences that can be cut with
different commonly available restriction enzymes. Restriction enzymes (also called restriction endonucleases)
recognize specific DNA sequences and cut them in a predictable manner; they are naturally produced by bacteria as
a defense mechanism against foreign DNA. Many restriction enzymes make staggered cuts in the two strands of
DNA, such that the cut ends have a 2- to 4-nucleotide single-stranded overhang. The sequence that is recognized by
the restriction enzyme is a four- to eight-nucleotide sequence that is a palindrome. Like with a word palindrome, this
means the sequence reads the same forward and backward. In most cases, the sequence reads the same forward
on one strand and backward on the complementary strand. When a staggered cut is made in a sequence like this,
the overhangs are complementary (Figure 10.5).

FIGURE 10.5 In this (a) six-nucleotide restriction enzyme recognition site, notice that the sequence of six nucleotides reads the same in the
5' to 3' direction on one strand as it does in the 5' to 3' direction on the complementary strand. This is known as a palindrome. (b) The
restriction enzyme makes breaks in the DNA strands, and (c) the cut in the DNA results in “sticky ends”. Another piece of DNA cut on either
end by the same restriction enzyme could attach to these sticky ends and be inserted into the gap made by this cut.

Because these overhangs are capable of coming back together by hydrogen bonding with complementary overhangs
on a piece of DNA cut with the same restriction enzyme, these are called “sticky ends.” The process of forming
hydrogen bonds between complementary sequences on single strands to form double-stranded DNA is called
annealing. Addition of an enzyme called DNA ligase, which takes part in DNA replication in cells, permanently joins
the DNA fragments when the sticky ends come together. In this way, any DNA fragment can be spliced between the
two ends of a plasmid DNA that has been cut with the same restriction enzyme (Figure 10.6).
228 10 • Biotechnology

FIGURE 10.6 This diagram shows the steps involved in molecular cloning.

Plasmids with foreign DNA inserted into them are called recombinant DNA molecules because they contain new
combinations of genetic material. Proteins that are produced from recombinant DNA molecules are called
recombinant proteins. Not all recombinant plasmids are capable of expressing genes. Plasmids may also be
engineered to express proteins only when stimulated by certain environmental factors, so that scientists can control
the expression of the recombinant proteins.

Reproductive Cloning
Reproductive cloning is a method used to make a clone or an identical copy of an entire multicellular organism.
Most multicellular organisms undergo reproduction by sexual means, which involves the contribution of DNA from
two individuals (parents), making it impossible to generate an identical copy or a clone of either parent. Recent

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 10.1 • Cloning and Genetic Engineering 229

advances in biotechnology have made it possible to reproductively clone mammals in the laboratory.

Natural sexual reproduction involves the union, during fertilization, of a sperm and an egg. Each of these gametes is
haploid, meaning they contain one set of chromosomes in their nuclei. The resulting cell, or zygote, is then diploid
and contains two sets of chromosomes. This cell divides mitotically to produce a multicellular organism. However,
the union of just any two cells cannot produce a viable zygote; there are components in the cytoplasm of the egg cell
that are essential for the early development of the embryo during its first few cell divisions. Without these
provisions, there would be no subsequent development. Therefore, to produce a new individual, both a diploid
genetic complement and an egg cytoplasm are required. The approach to producing an artificially cloned individual
is to take the egg cell of one individual and to remove the haploid nucleus. Then a diploid nucleus from a body cell of
a second individual, the donor, is put into the egg cell. The egg is then stimulated to divide so that development
proceeds. This sounds simple, but in fact it takes many attempts before each of the steps is completed successfully.

The first cloned agricultural animal was Dolly, a sheep who was born in 1996. The success rate of reproductive
cloning at the time was very low. Dolly lived for six years and died of a lung tumor (Figure 10.7). There was
speculation that because the cell DNA that gave rise to Dolly came from an older individual, the age of the DNA may
have affected her life expectancy. Since Dolly, several species of animals (such as horses, bulls, and goats) have
been successfully cloned.

There have been attempts at producing cloned human embryos as sources of embryonic stem cells. In the
procedure, the DNA from an adult human is introduced into a human egg cell, which is then stimulated to divide. The
technology is similar to the technology that was used to produce Dolly, but the embryo is never implanted into a
surrogate carrier. The cells produced are called embryonic stem cells because they have the capacity to develop into
many different kinds of cells, such as muscle or nerve cells. The stem cells could be used to research and ultimately
provide therapeutic applications, such as replacing damaged tissues. The benefit of cloning in this instance is that
the cells used to regenerate new tissues would be a perfect match to the donor of the original DNA. For example, a
leukemia patient would not require a sibling with a tissue match for a bone-marrow transplant. Freda Miller and
Elaine Fuchs, working independently, discovered stem cells in different layers of the skin. These cells help the skin
repair itself, and their discovery may have applications in treatments of skin disease and potentially other
conditions, such as nerve damage.
230 10 • Biotechnology

VISUAL CONNECTION

FIGURE 10.7 Dolly the sheep was the first agricultural animal to be cloned. To create Dolly, the nucleus was removed from a donor egg cell.
The enucleated egg was placed next to the other cell, then they were shocked to fuse. They were shocked again to start division. The cells
were allowed to divide for several days until an early embryonic stage was reached, before being implanted in a surrogate mother.

Why was Dolly a Finn-Dorset and not a Scottish Blackface sheep?

Genetic Engineering
Using recombinant DNA technology to modify an organism’s DNA to achieve desirable traits is called genetic
engineering. Addition of foreign DNA in the form of recombinant DNA vectors that are generated by molecular
cloning is the most common method of genetic engineering. An organism that receives the recombinant DNA is
called a genetically modified organism (GMO). If the foreign DNA that is introduced comes from a different species,
the host organism is called transgenic. Bacteria, plants, and animals have been genetically modified since the early
1970s for academic, medical, agricultural, and industrial purposes. These applications will be examined in more
detail in the next module.

LINK TO LEARNING
Watch this short video (http://openstax.org/l/transgenic) explaining how scientists create a transgenic animal.

Although the classic methods of studying the function of genes began with a given phenotype and determined the
genetic basis of that phenotype, modern techniques allow researchers to start at the DNA sequence level and ask:
"What does this gene or DNA element do?" This technique, called reverse genetics, has resulted in reversing the
classical genetic methodology. One example of this method is analogous to damaging a body part to determine its
function. An insect that loses a wing cannot fly, which means that the wing’s function is flight. The classic genetic
method compares insects that cannot fly with insects that can fly, and observes that the non-flying insects have lost
wings. Similarly in a reverse genetics approach, mutating or deleting genes provides researchers with clues about
gene function. Alternately, reverse genetics can be used to cause a gene to overexpress itself to determine what
phenotypic effects may occur.

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 10.2 • Biotechnology in Medicine and Agriculture 231

10.2 Biotechnology in Medicine and Agriculture

LEARNING OBJECTIVES
By the end of this section, you will be able to:
• Describe uses of biotechnology in medicine
• Describe uses of biotechnology in agriculture

It is easy to see how biotechnology can be used for medicinal purposes. Knowledge of the genetic makeup of our
species, the genetic basis of heritable diseases, and the invention of technology to manipulate and fix mutant genes
provides methods to treat diseases. Biotechnology in agriculture can enhance resistance to disease, pests, and
environmental stress to improve both crop yield and quality.

Genetic Diagnosis and Gene Therapy

The process of testing for suspected genetic defects before administering treatment is called genetic diagnosis by
genetic testing. In some cases in which a genetic disease is present in an individual’s family, family members may
be advised to undergo genetic testing. For example, mutations in the BRCA genes may increase the likelihood of
developing breast, ovarian, and some other cancers. A person with breast cancer can be screened for these
mutations. If one of the high-risk mutations is found, relatives may also wish to be screened for that particular
mutation, or simply be more vigilant for the occurrence of cancers. Genetic testing is also offered for fetuses (or
embryos with in vitro fertilization) to determine the presence or absence of disease-causing genes in families with
specific debilitating diseases.

LINK TO LEARNING
See how human DNA is extracted (http://openstax.org/l/DNA_extraction) for uses such as genetic testing.

Gene therapy is a genetic engineering technique that may one day be used to cure certain genetic diseases. In its
simplest form, it involves the introduction of a non-mutated gene at a random location in the genome to cure a
disease by replacing a protein that may be absent in these individuals because of a genetic mutation. The non-
mutated gene is usually introduced into diseased cells as part of a vector transmitted by a virus, such as an
adenovirus, that can infect the host cell and deliver the foreign DNA into the genome of the targeted cell (Figure
10.8). To date, gene therapies have been primarily experimental procedures in humans. A few of these experimental
treatments have been successful, but the methods may be important in the future as the factors limiting its success
are resolved.
232 10 • Biotechnology

FIGURE 10.8 This diagram shows the steps involved in curing disease with gene therapy using an adenovirus vector. (credit: modification of
work by NIH)

Production of Vaccines, Antibiotics, and Hormones

Traditional vaccination strategies use weakened or inactive forms of microorganisms or viruses to stimulate the
immune system. Modern techniques use specific genes of microorganisms cloned into vectors and mass-produced
in bacteria to make large quantities of specific substances to stimulate the immune system. The substance is then
used as a vaccine. In some cases, such as the H1N1 flu vaccine, genes cloned from the virus have been used to
combat the constantly changing strains of this virus.

Antibiotics kill bacteria and are naturally produced by microorganisms such as fungi; penicillin is perhaps the most
well-known example. Antibiotics are produced on a large scale by cultivating and manipulating fungal cells. The
fungal cells have typically been genetically modified to improve the yields of the antibiotic compound.

Recombinant DNA technology was used to produce large-scale quantities of the human hormone insulin in E. coli as
early as 1978. Previously, it was only possible to treat diabetes with pig insulin, which caused allergic reactions in
many humans because of differences in the insulin molecule. In addition, human growth hormone (HGH) is used to
treat growth disorders in children. The HGH gene was cloned from a cDNA (complementary DNA) library and
inserted into E. coli cells by cloning it into a bacterial vector.

Transgenic Animals
Although several recombinant proteins used in medicine are successfully produced in bacteria, some proteins need
a eukaryotic animal host for proper processing. For this reason, genes have been cloned and expressed in animals
such as sheep, goats, chickens, and mice. Animals that have been modified to express recombinant DNA are called
transgenic animals (Figure 10.9).

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 10.2 • Biotechnology in Medicine and Agriculture 233

FIGURE 10.9 It can be seen that two of these mice are transgenic because they have a gene that causes them to fluoresce under a UV light.
The non-transgenic mouse does not have the gene that causes fluorescence. (credit: Ingrid Moen et al.)

Several human proteins are expressed in the milk of transgenic sheep and goats. In one commercial example, the
FDA has approved a blood anticoagulant protein that is produced in the milk of transgenic goats for use in humans.
Mice have been used extensively for expressing and studying the effects of recombinant genes and mutations.

Transgenic Plants
Manipulating the DNA of plants (creating genetically modified organisms, or GMOs) has helped to create desirable
traits such as disease resistance, herbicide, and pest resistance, better nutritional value, and better shelf life (Figure
10.10). Plants are the most important source of food for the human population. Farmers developed ways to select
for plant varieties with desirable traits long before modern-day biotechnology practices were established.

FIGURE 10.10 Corn, a major agricultural crop used to create products for a variety of industries, is often modified through plant
biotechnology. (credit: Keith Weller, USDA)

Transgenic plants have received DNA from other species. Because they contain unique combinations of genes and
are not restricted to the laboratory, transgenic plants and other GMOs are closely monitored by government
agencies to ensure that they are fit for human consumption and do not endanger other plant and animal life.
234 10 • Biotechnology

Because foreign genes can spread to other species in the environment, particularly in the pollen and seeds of plants,
extensive testing is required to ensure ecological stability. Staples like corn, potatoes, and tomatoes were the first
crop plants to be genetically engineered.

Transformation of Plants Using Agrobacterium tumefaciens

In plants, tumors caused by the bacterium Agrobacterium tumefaciens occur by transfer of DNA from the bacterium
to the plant. The artificial introduction of DNA into plant cells is more challenging than in animal cells because of the
thick plant cell wall. Researchers used the natural transfer of DNA from Agrobacterium to a plant host to introduce
DNA fragments of their choice into plant hosts. In nature, the disease-causing A. tumefaciens have a set of plasmids
that contain genes that integrate into the infected plant cell’s genome. Researchers manipulate the plasmids to
carry the desired DNA fragment and insert it into the plant genome.

The Organic Insecticide Bacillus thuringiensis

Bacillus thuringiensis (Bt) is a bacterium that produces protein crystals that are toxic to many insect species that
feed on plants. Insects that have eaten Bt toxin stop feeding on the plants within a few hours. After the toxin is
activated in the intestines of the insects, death occurs within a couple of days. The crystal toxin genes have been
cloned from the bacterium and introduced into plants, therefore allowing plants to produce their own crystal Bt
toxin that acts against insects. Bt toxin is safe for the environment and non-toxic to mammals (including humans).
As a result, it has been approved for use by organic farmers as a natural insecticide. There is some concern,
however, that insects may evolve resistance to the Bt toxin in the same way that bacteria evolve resistance to
antibiotics.

FlavrSavr Tomato
The first GM crop to be introduced into the market was the FlavrSavr Tomato produced in 1994. Molecular genetic
technology was used to slow down the process of softening and rotting caused by fungal infections, which led to
increased shelf life of the GM tomatoes. Additional genetic modification improved the flavor of this tomato. The
FlavrSavr tomato did not successfully stay in the market because of problems maintaining and shipping the crop.

10.3 Genomics and Proteomics

LEARNING OBJECTIVES
By the end of this section, you will be able to:
• Define genomics and proteomics
• Define whole genome sequencing
• Explain different applications of genomics and proteomics

The study of nucleic acids began with the discovery of DNA, progressed to the study of genes and small fragments,
and has now exploded to the field of genomics. Genomics is the study of entire genomes, including the complete set
of genes, their nucleotide sequence and organization, and their interactions within a species and with other species.
The advances in genomics have been made possible by DNA sequencing technology. Just as information technology
has led to Google Maps that enable us to get detailed information about locations around the globe, genomic
information is used to create similar maps of the DNA of different organisms.

Mapping Genomes
Genome mapping is the process of finding the location of genes on each chromosome. The maps that are created
are comparable to the maps that we use to navigate streets. A genetic map is an illustration that lists genes and
their location on a chromosome. Genetic maps provide the big picture (similar to a map of interstate highways) and
use genetic markers (similar to landmarks). A genetic marker is a gene or sequence on a chromosome that shows
genetic linkage with a trait of interest. The genetic marker tends to be inherited with the gene of interest, and one
measure of distance between them is the recombination frequency during meiosis. Early geneticists called this
linkage analysis.

Physical maps get into the intimate details of smaller regions of the chromosomes (similar to a detailed road map)
(Figure 10.11). A physical map is a representation of the physical distance, in nucleotides, between genes or genetic
markers. Both genetic linkage maps and physical maps are required to build a complete picture of the genome.
Having a complete map of the genome makes it easier for researchers to study individual genes. Human genome

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 10.3 • Genomics and Proteomics 235

maps help researchers in their efforts to identify human disease-causing genes related to illnesses such as cancer,
heart disease, and cystic fibrosis, to name a few. In addition, genome mapping can be used to help identify
organisms with beneficial traits, such as microbes with the ability to clean up pollutants or even prevent pollution.
Research involving plant genome mapping may lead to methods that produce higher crop yields or to the
development of plants that adapt better to climate change.

FIGURE 10.11 This is a physical map of the human X chromosome. (credit: modification of work by NCBI, NIH)

Genetic maps provide the outline, and physical maps provide the details. It is easy to understand why both types of
genome-mapping techniques are important to show the big picture. Information obtained from each technique is
used in combination to study the genome. Genomic mapping is used with different model organisms that are used
for research. Genome mapping is still an ongoing process, and as more advanced techniques are developed, more
advances are expected. Genome mapping is similar to completing a complicated puzzle using every piece of
available data. Mapping information generated in laboratories all over the world is entered into central databases,
such as the National Center for Biotechnology Information (NCBI). Efforts are made to make the information more
easily accessible to researchers and the general public. Just as we use global positioning systems instead of paper
maps to navigate through roadways, NCBI allows us to use a genome viewer tool to simplify the data mining
process.
236 10 • Biotechnology

LINK TO LEARNING
Online Mendelian Inheritance in Man (OMIM) (http://openstax.org/l/OMIM2) is a searchable online catalog of human
genes and genetic disorders. This website shows genome mapping, and also details the history and research of each
trait and disorder. Click the link to search for traits (such as handedness) and genetic disorders (such as diabetes).

Whole Genome Sequencing

Although there have been significant advances in the medical sciences in recent years, doctors are still confounded
by many diseases and researchers are using whole genome sequencing to get to the bottom of the problem. Whole
genome sequencing is a process that determines the DNA sequence of an entire genome. Whole genome
sequencing is a brute-force approach to problem solving when there is a genetic basis at the core of a disease.
Several laboratories now provide services to sequence, analyze, and interpret entire genomes.

In 2010, whole genome sequencing was used to save a young boy whose intestines had multiple mysterious
abscesses. The child had several colon operations with no relief. Finally, a whole genome sequence revealed a
defect in a pathway that controls apoptosis (programmed cell death). A bone marrow transplant was used to
overcome this genetic disorder, leading to a cure for the boy. He was the first person to be successfully diagnosed
using whole genome sequencing.

The first genomes to be sequenced, such as those belonging to viruses, bacteria, and yeast, were smaller in terms of
the number of nucleotides than the genomes of multicellular organisms. The genomes of other model organisms,
such as the mouse (Mus musculus), the fruit fly (Drosophila melanogaster), and the nematode (Caenorhabditis
elegans) are now known. A great deal of basic research is performed in model organisms because the information
can be applied to other organisms. A model organism is a species that is studied as a model to understand the
biological processes in other species that can be represented by the model organism. For example, fruit flies are
able to metabolize alcohol like humans, so the genes affecting sensitivity to alcohol have been studied in fruit flies in
an effort to understand the variation in sensitivity to alcohol in humans. Having entire genomes sequenced helps
with the research efforts in these model organisms (Figure 10.12).

FIGURE 10.12 Much basic research is done with model organisms, such as the mouse, Mus musculus; the fruit fly, Drosophila
melanogaster; the nematode Caenorhabditis elegans; the yeast Saccharomyces cerevisiae; and the common weed, Arabidopsis thaliana.
(credit "mouse": modification of work by Florean Fortescue; credit "nematodes": modification of work by "snickclunk"/Flickr; credit
"common weed": modification of work by Peggy Greb, USDA; scale-bar data from Matt Russell)

The first human genome sequence was published in 2003. The number of whole genomes that have been
sequenced steadily increases and now includes hundreds of species and thousands of individual human genomes.

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 10.3 • Genomics and Proteomics 237

Applying Genomics
The introduction of DNA sequencing and whole genome sequencing projects, particularly the Human Genome
Project, has expanded the applicability of DNA sequence information. Genomics is now being used in a wide variety
of fields, such as metagenomics, pharmacogenomics, and mitochondrial genomics. The most commonly known
application of genomics is to understand and find cures for diseases.

Predicting Disease Risk at the Individual Level

Predicting the risk of disease involves screening and identifying currently healthy individuals by genome analysis at
the individual level. Intervention with lifestyle changes and drugs can be recommended before disease onset.
However, this approach is most applicable when the problem arises from a single gene mutation. Such defects only
account for about 5 percent of diseases found in developed countries. Most of the common diseases, such as heart
disease, are multifactorial or polygenic, which refers to a phenotypic characteristic that is determined by two or
more genes, and also environmental factors such as diet. In April 2010, scientists at Stanford University published
the genome analysis of a healthy individual (Stephen Quake, a scientist at Stanford University, who had his genome
sequenced); the analysis predicted his propensity to acquire various diseases. A risk assessment was done to
analyze Quake’s percentage of risk for 55 different medical conditions. A rare genetic mutation was found that
showed him to be at risk for sudden heart attack. He was also predicted to have a 23 percent risk of developing
prostate cancer and a 1.4 percent risk of developing Alzheimer’s disease. The scientists used databases and several
publications to analyze the genomic data. Even though genomic sequencing is becoming more affordable and
analytical tools are becoming more reliable, ethical issues surrounding genomic analysis at a population level
remain to be addressed. For example, could such data be legitimately used to charge more or less for insurance or
to affect credit ratings?

Gene Editing
For thousands of years, humans have engaged in some level of control over genes and heredity regarding the plants
and animals we rely on. The technology now exists to exert that control more directly by precisely altering the DNA
of organisms. The technique is usually referred to as CRISPR, for the portions of DNA it targets: "Clustered Regularly
Interspaced Short Palindromic Repeats." In essence, DNA contains repetitive sequences with "spacers" between
them. CRISPR-associated nucleases (known as "Cas") are enzymes that can identify, attach to, and cut the strand at
precise locations. In 2012, Jennifer Doudna and Emmanuelle Charpentier developed a method to combine the Cas
nuclease with a synthetically produced "guide RNA" that leads the nuclease to selected locations on the DNA
strand. The discovery revolutionized gene editing. Researchers around the world have used CRISPR to manipulate
the actual DNA of plants, animals, laboratory cell lines, and (in trials) human patients. Doudna and Charpentier were
awarded the Nobel Prize for their work.

Gene editing is so promising because it can be used experimentally to understand disease or organismal limitations,
then be applied to overcome those issues. For example, in a human trial, cancerous cells were removed from a
person, edited to remove their cancerous properties at the DNA level, and reintroduced into the patient so that
those now edited cells could multiply and replace the cancerous ones. Using the person's own cells increases the
likelihood of acceptance and success.

Like other applications of genomics, the prospect of directly editing genes brings up a number of ethical issues. Both
Doudna and Chapentier, as well as many other genetic engineers, support only certain CRISPR applications. And
many governments and other entities place strict guidelines on the uses of the powerful technology.

Genome-wide Association Studies

Since 2005, it has been possible to conduct a type of study called a genome-wide association study, or GWAS. A
GWAS is a method that identifies differences between individuals in single nucleotide polymorphisms (SNPs) that
may be involved in causing diseases. The method is particularly suited to diseases that may be affected by one or
many genetic changes throughout the genome. It is very difficult to identify the genes involved in such a disease
using family history information. The GWAS method relies on a genetic database that has been in development since
2002 called the International HapMap Project. The HapMap Project sequenced the genomes of several hundred
individuals from around the world and identified groups of SNPs. The groups include SNPs that are located near to
each other on chromosomes so they tend to stay together through recombination. The fact that the group stays
together means that identifying one marker SNP is all that is needed to identify all the SNPs in the group. There are
238 10 • Biotechnology

several million SNPs identified, but identifying them in other individuals who have not had their complete genome
sequenced is much easier because only the marker SNPs need to be identified.

In a common design for a GWAS, two groups of individuals are chosen; one group has the disease, and the other
group does not. The individuals in each group are matched in other characteristics to reduce the effect of
confounding variables causing differences between the two groups. For example, the genotypes may differ because
the two groups are mostly taken from different parts of the world. Once the individuals are chosen, and typically
their numbers are a thousand or more for the study to work, samples of their DNA are obtained. The DNA is analyzed
using automated systems to identify large differences in the percentage of particular SNPs between the two groups.
Often the study examines a million or more SNPs in the DNA. The results of GWAS can be used in two ways: the
genetic differences may be used as markers for susceptibility to the disease in undiagnosed individuals, and the
particular genes identified can be targets for research into the molecular pathway of the disease and potential
therapies. An offshoot of the discovery of gene associations with disease has been the formation of companies that
provide so-called “personal genomics” that will identify risk levels for various diseases based on an individual’s SNP
complement. The science behind these services is controversial.

Because GWAS looks for associations between genes and disease, these studies provide data for other research into
causes, rather than answering specific questions themselves. An association between a gene difference and a
disease does not necessarily mean there is a cause-and-effect relationship. However, some studies have provided
useful information about the genetic causes of diseases. For example, three different studies in 2005 identified a
gene for a protein involved in regulating inflammation in the body that is associated with a disease-causing
blindness called age-related macular degeneration. This opened up new possibilities for research into the cause of
this disease. A large number of genes have been identified to be associated with Crohn’s disease using GWAS, and
some of these have suggested new hypothetical mechanisms for the cause of the disease.

Pharmacogenomics
Pharmacogenomics involves evaluating the effectiveness and safety of drugs on the basis of information from an
individual's genomic sequence. Personal genome sequence information can be used to prescribe medications that
will be most effective and least toxic on the basis of the individual patient’s genotype. Studying changes in gene
expression could provide information about the gene transcription profile in the presence of the drug, which can be
used as an early indicator of the potential for toxic effects. For example, genes involved in cellular growth and
controlled cell death, when disturbed, could lead to the growth of cancerous cells. Genome-wide studies can also
help to find new genes involved in drug toxicity. The gene signatures may not be completely accurate, but can be
tested further before pathologic symptoms arise.

Metagenomics
Traditionally, microbiology has been taught with the view that microorganisms are best studied under pure culture
conditions, which involves isolating a single type of cell and culturing it in the laboratory. Because microorganisms
can go through several generations in a matter of hours, their gene expression profiles adapt to the new laboratory
environment very quickly. On the other hand, many species resist being cultured in isolation. Most microorganisms
do not live as isolated entities, but in microbial communities known as biofilms. For all of these reasons, pure
culture is not always the best way to study microorganisms. Metagenomics is the study of the collective genomes of
multiple species that grow and interact in an environmental niche. Metagenomics can be used to identify new
species more rapidly and to analyze the effect of pollutants on the environment (Figure 10.13). Metagenomics
techniques can now also be applied to communities of higher eukaryotes, such as fish.

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 10.3 • Genomics and Proteomics 239

FIGURE 10.13 Metagenomics involves isolating DNA from multiple species within an environmental niche. The DNA is cut up and
sequenced, allowing entire genome sequences of multiple species to be reconstructed from the sequences of overlapping pieces.

Creation of New Biofuels

Knowledge of the genomics of microorganisms is being used to find better ways to harness biofuels from algae and
cyanobacteria. The primary sources of fuel today are coal, oil, wood, and other plant products such as ethanol.
Although plants are renewable resources, there is still a need to find more alternative renewable sources of energy
to meet our population’s energy demands. The microbial world is one of the largest resources for genes that encode
new enzymes and produce new organic compounds, and it remains largely untapped. This vast genetic resource
holds the potential to provide new sources of biofuels (Figure 10.14).

FIGURE 10.14 Renewable fuels were tested in Navy ships and aircraft at the first Naval Energy Forum. (credit: modification of work by John
F. Williams, US Navy)
240 10 • Biotechnology

Mitochondrial Genomics
Mitochondria are intracellular organelles that contain their own DNA. Mitochondrial DNA mutates at a rapid rate and
is often used to study evolutionary relationships. Another feature that makes studying the mitochondrial genome
interesting is that in most multicellular organisms, the mitochondrial DNA is passed on from the mother during the
process of fertilization. For this reason, mitochondrial genomics is often used to trace genealogy.

Genomics in Forensic Analysis

Information and clues obtained from DNA samples found at crime scenes have been used as evidence in court
cases, and genetic markers have been used in forensic analysis. Genomic analysis has also become useful in this
field. In 2001, the first use of genomics in forensics was published. It was a collaborative effort between academic
research institutions and the FBI to solve the mysterious cases of anthrax (Figure 10.15) that was transported by
the US Postal Service. Anthrax bacteria were made into an infectious powder and mailed to news media and two
U.S. Senators. The powder infected the administrative staff and postal workers who opened or handled the letters.
Five people died, and 17 were sickened from the bacteria. Using microbial genomics, researchers determined that a
specific strain of anthrax was used in all the mailings; eventually, the source was traced to a scientist at a national
biodefense laboratory in Maryland.

FIGURE 10.15 Bacillus anthracis is the organism that causes anthrax. (credit: modification of work by CDC; scale-bar data from Matt
Russell)

Genomics in Agriculture
Genomics can reduce the trials and failures involved in scientific research to a certain extent, which could improve
the quality and quantity of crop yields in agriculture (Figure 10.16). Linking traits to genes or gene signatures helps
to improve crop breeding to generate hybrids with the most desirable qualities. Scientists use genomic data to
identify desirable traits, and then transfer those traits to a different organism to create a new genetically modified
organism, as described in the previous module. Scientists are discovering how genomics can improve the quality
and quantity of agricultural production. For example, scientists could use desirable traits to create a useful product
or enhance an existing product, such as making a drought-sensitive crop more tolerant of the dry season.

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 10.3 • Genomics and Proteomics 241

FIGURE 10.16 Transgenic agricultural plants can be made to resist disease. These transgenic plums are resistant to the plum pox virus.
(credit: Scott Bauer, USDA ARS)

Proteomics
Proteins are the final products of genes that perform the function encoded by the gene. Proteins are composed of
amino acids and play important roles in the cell. All enzymes (except ribozymes) are proteins and act as catalysts
that affect the rate of reactions. Proteins are also regulatory molecules, and some are hormones. Transport proteins,
such as hemoglobin, help transport oxygen to various organs. Antibodies that defend against foreign particles are
also proteins. In the diseased state, protein function can be impaired because of changes at the genetic level or
because of direct impact on a specific protein.

A proteome is the entire set of proteins produced by a cell type. Proteomes can be studied using the knowledge of
genomes because genes code for mRNAs, and the mRNAs encode proteins. The study of the function of proteomes
is called proteomics. Proteomics complements genomics and is useful when scientists want to test their
hypotheses that were based on genes. Even though all cells in a multicellular organism have the same set of genes,
the set of proteins produced in different tissues is different and dependent on gene expression. Thus, the genome is
constant, but the proteome varies and is dynamic within an organism. In addition, RNAs can be alternatively spliced
(cut and pasted to create novel combinations and novel proteins), and many proteins are modified after translation.
Although the genome provides a blueprint, the final architecture depends on several factors that can change the
progression of events that generate the proteome.

Genomes and proteomes of patients suffering from specific diseases are being studied to understand the genetic
basis of the disease. The most prominent disease being studied with proteomic approaches is cancer (Figure 10.17).
Proteomic approaches are being used to improve the screening and early detection of cancer; this is achieved by
identifying proteins whose expression is affected by the disease process. An individual protein is called a
biomarker, whereas a set of proteins with altered expression levels is called a protein signature. For a biomarker or
protein signature to be useful as a candidate for early screening and detection of a cancer, it must be secreted in
body fluids such as sweat, blood, or urine, so that large-scale screenings can be performed in a noninvasive fashion.
The current problem with using biomarkers for the early detection of cancer is the high rate of false-negative results.
A false-negative result is a negative test result that should have been positive. In other words, many cases of cancer
go undetected, which makes biomarkers unreliable. Some examples of protein biomarkers used in cancer detection
are CA-125 for ovarian cancer and PSA for prostate cancer. Protein signatures may be more reliable than biomarkers
to detect cancer cells. Proteomics is also being used to develop individualized treatment plans, which involves the
prediction of whether or not an individual will respond to specific drugs and the side effects that the individual may
have. Proteomics is also being used to predict the possibility of disease recurrence.
242 10 • Biotechnology

FIGURE 10.17 This machine is preparing to do a proteomic pattern analysis to identify specific cancers so that an accurate cancer
prognosis can be made. (credit: Dorie Hightower, NCI, NIH)

The National Cancer Institute has developed programs to improve the detection and treatment of cancer. The
Clinical Proteomic Technologies for Cancer and the Early Detection Research Network are efforts to identify protein
signatures specific to different types of cancers. The Biomedical Proteomics Program is designed to identify protein
signatures and design effective therapies for cancer patients.

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 10 • Key Terms 243

Key Terms
anneal in molecular biology, the process by which a model to understand the biological processes in
two single strands of DNA hydrogen bond at other species represented by the model organism
complementary nucleotides to form a double- pharmacogenomics the study of drug interactions
stranded molecule with the genome or proteome; also called
biomarker an individual protein that is uniquely toxicogenomics
produced in a diseased state physical map a representation of the physical
biotechnology the use of artificial methods to modify distance between genes or genetic markers
the genetic material of living organisms or cells to plasmid a small circular molecule of DNA found in
produce novel compounds or to perform new bacteria that replicates independently of the main
functions bacterial chromosome; plasmids code for some
cloning the production of an exact copy—specifically, important traits for bacteria and can be used as
an exact genetic copy—of a gene, cell, or organism vectors to transport DNA into bacteria in genetic
gel electrophoresis a technique used to separate engineering applications
molecules on the basis of their ability to migrate polymerase chain reaction (PCR) a technique used
through a semisolid gel in response to an electric to make multiple copies of DNA
current protein signature a set of over- or under-expressed
gene therapy the technique used to cure heritable proteins characteristic of cells in a particular
diseases by replacing mutant genes with good diseased tissue
genes proteomics study of the function of proteomes
genetic engineering alteration of the genetic makeup recombinant DNA a combination of DNA fragments
of an organism using the molecular methods of generated by molecular cloning that does not exist
biotechnology in nature
genetic map an outline of genes and their location on recombinant protein a protein that is expressed from
a chromosome that is based on recombination recombinant DNA molecules
frequencies between markers reproductive cloning cloning of entire organisms
genetic testing identifying gene variants in an restriction enzyme an enzyme that recognizes a
individual that may lead to a genetic disease in that specific nucleotide sequence in DNA and cuts the
individual DNA double strand at that recognition site, often
genetically modified organism (GMO) an organism with a staggered cut leaving short single strands or
whose genome has been artificially changed “sticky” ends
genomics the study of entire genomes, including the reverse genetics a form of genetic analysis that
complete set of genes, their nucleotide sequence manipulates DNA to disrupt or affect the product of
and organization, and their interactions within a a gene to analyze the gene’s function
species and with other species transgenic describing an organism that receives DNA
metagenomics the study of the collective genomes of from a different species
multiple species that grow and interact in an whole genome sequencing a process that
environmental niche determines the nucleotide sequence of an entire
model organism a species that is studied and used as genome

Chapter Summary
10.1 Cloning and Genetic Engineering modifying them to achieve desirable traits.

Nucleic acids can be isolated from cells for the Cloning may involve cloning small DNA fragments
purposes of further analysis by breaking open the cells (molecular cloning), or cloning entire organisms
and enzymatically destroying all other major (reproductive cloning). In molecular cloning with
macromolecules. Fragmented or whole chromosomes bacteria, a desired DNA fragment is inserted into a
can be separated on the basis of size by gel bacterial plasmid using restriction enzymes and the
electrophoresis. Short stretches of DNA can be plasmid is taken up by a bacterium, which will then
amplified by PCR. DNA can be cut (and subsequently express the foreign DNA. Using other techniques,
re-spliced together) using restriction enzymes. The foreign genes can be inserted into eukaryotic
molecular and cellular techniques of biotechnology organisms. In each case, the organisms are called
allow researchers to genetically engineer organisms, transgenic organisms. In reproductive cloning, a donor
244 10 • Visual Connection Questions

nucleus is put into an enucleated egg cell, which is provide an outline for the location of genes within a
then stimulated to divide and develop into an genome, and they estimate the distance between
organism. genes and genetic markers on the basis of the
recombination frequency during meiosis. Physical
In reverse genetics methods, a gene is mutated or
maps provide detailed information about the physical
removed in some way to identify its effect on the
distance between the genes. The most detailed
phenotype of the whole organism as a way to
information is available through sequence mapping.
determine its function.
Information from all mapping and sequencing sources
10.2 Biotechnology in Medicine and is combined to study an entire genome.
Agriculture Whole genome sequencing is the latest available
Genetic testing is performed to identify disease- resource to treat genetic diseases. Some doctors are
causing genes, and can be used to benefit affected using whole genome sequencing to save lives.
individuals and their relatives who have not developed Genomics has many industrial applications, including
disease symptoms yet. Gene therapy—by which biofuel development, agriculture, pharmaceuticals, and
functioning genes are incorporated into the genomes of pollution control.
individuals with a non-functioning mutant gene—has Imagination is the only barrier to the applicability of
the potential to cure heritable diseases. Transgenic genomics. Genomics is being applied to most fields of
organisms possess DNA from a different species, biology; it can be used for personalized medicine,
usually generated by molecular cloning techniques. prediction of disease risks at an individual level, the
Vaccines, antibiotics, and hormones are examples of study of drug interactions before the conduction of
products obtained by recombinant DNA technology. clinical trials, and the study of microorganisms in the
Transgenic animals have been created for experimental environment as opposed to the laboratory. It is also
purposes and some are used to produce some human being applied to the generation of new biofuels,
proteins. genealogical assessment using mitochondria,
Genes are inserted into plants, using plasmids in the advances in forensic science, and improvements in
bacterium Agrobacterium tumefaciens, which infects agriculture.
plants. Transgenic plants have been created to improve Proteomics is the study of the entire set of proteins
the characteristics of crop plants—for example, by expressed by a given type of cell under certain
giving them insect resistance by inserting a gene for a environmental conditions. In a multicellular organism,
bacterial toxin. different cell types will have different proteomes, and
10.3 Genomics and Proteomics these will vary with changes in the environment. Unlike
a genome, a proteome is dynamic and under constant
Genome mapping is similar to solving a big, flux, which makes it more complicated and more useful
complicated puzzle with pieces of information coming than the knowledge of genomes alone.
from laboratories all over the world. Genetic maps

Visual Connection Questions

1. Figure 10.7 Why was Dolly a Finn-Dorset and not a
Scottish Blackface sheep?

Review Questions
2. In gel electrophoresis of DNA, the different bands in 3. In the reproductive cloning of an animal, the
the final gel form because the DNA molecules genome of the cloned individual comes from
________. ________.
a. are from different organisms a. a sperm cell
b. have different lengths b. an egg cell
c. have different nucleotide compositions c. any gamete cell
d. have different genes d. a body cell

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 10 • Critical Thinking Questions 245

4. What carries a gene from one organism into a 7. What is the most challenging issue facing genome
bacteria cell? sequencing?
a. a plasmid a. the inability to develop fast and accurate
b. an electrophoresis gel sequencing techniques
c. a restriction enzyme b. the ethics of using information from genomes
d. polymerase chain reaction at the individual level
c. the availability and stability of DNA
5. What is a genetically modified organism (GMO)? d. all of the above
a. a plant with certain genes removed
b. an organism with an artificially altered genome 8. Genomics can be used in agriculture to:
c. a hybrid organism a. generate new hybrid strains
d. any agricultural organism produced by b. improve disease resistance
breeding or biotechnology c. improve yield
d. all of the above
6. What is the role of Agrobacterium tumefaciens in
the production of transgenic plants? 9. What kind of diseases are studied using genome-
a. Genes from A. tumefaciens are inserted into wide association studies?
plant DNA to give the plant different traits. a. viral diseases
b. Transgenic plants have been given resistance b. single-gene inherited diseases
to the pest A. tumefaciens. c. diseases caused by multiple genes
c. A. tumefaciens is used as a vector to move d. diseases caused by environmental factors
genes into plant cells.
d. Plant genes are incorporated into the genome
of Agrobacterium tumefaciens.

Critical Thinking Questions

10. What is the purpose and benefit of the polymerase 12. Describe two of the applications for genome
chain reaction? mapping.

11. Today, it is possible for a diabetic patient to 13. Identify a possible advantage and a possible
purchase human insulin from a pharmacist. What disadvantage of a genetic test that would identify
technology makes this possible and why is it a genes in individuals that increase their probability
benefit over how things used to be? of having Alzheimer's disease later in life.
246 10 • Critical Thinking Questions

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CHAPTER 11
Evolution and Its Processes

FIGURE 11.1 The diversity of life on Earth is the result of evolution, a continuous process that is still occurring. (credit
“wolf”: modification of work by Gary Kramer, USFWS; credit “coral”: modification of work by William Harrigan, NOAA;
credit “river”: modification of work by Vojtěch Dostál; credit “protozoa”: modification of work by Sharon Franklin,
Stephen Ausmus, USDA ARS; credit “fish” modification of work by Christian Mehlführer; credit “mushroom”, “bee”:
modification of work by Cory Zanker; credit “tree”: modification of work by Joseph Kranak)

CHAPTER OUTLINE
11.1 Discovering How Populations Change
11.2 Mechanisms of Evolution
11.3 Evidence of Evolution
11.4 Speciation
11.5 Common Misconceptions about Evolution

INTRODUCTION All species of living organisms—from the bacteria on our skin, to the trees in our
yards, to the birds outside—evolved at some point from a different species. Although it may seem
that living things today stay much the same from generation to generation, that is not the case:
evolution is ongoing. Evolution is the process through which the characteristics of species change
and through which new species arise.
248 11 • Evolution and Its Processes

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 experiment after experiment. The Ukrainian-
born American geneticist Theodosius Dobzhansky famously wrote that “nothing makes sense in
1
biology except in the light of evolution.” He meant that the principle that all life has evolved and
diversified from a common ancestor is the foundation from which we understand all other
questions in biology. This chapter will explain some of the mechanisms for evolutionary change
and the kinds of questions that biologists can and have answered using evolutionary theory.

11.1 Discovering How Populations Change

LEARNING OBJECTIVES
By the end of this section, you will be able to:
• Explain how Darwin’s theory of evolution differed from the current view at the time
• Describe how the present-day theory of evolution was developed
• Describe how population genetics is used to study the evolution of populations

The theory of evolution by natural selection describes a mechanism for species change over time.
That species change had been suggested and debated well before Darwin. The view that species
were static and unchanging was grounded in the writings of Plato, yet there were also ancient
Greeks that expressed evolutionary ideas.

In the eighteenth century, ideas about the evolution of animals were reintroduced by the
naturalist Georges-Louis Leclerc, Comte de Buffon and even by Charles Darwin’s grandfather,
Erasmus Darwin. During this time, it was also accepted that there were extinct species. At the
same time, James Hutton, the Scottish naturalist, proposed that geological change occurred
gradually by the accumulation of small changes from processes (over long periods of time) just
like those happening today. This contrasted with the predominant view that the geology of the
planet was a consequence of catastrophic events occurring during a relatively brief past. Hutton’s
view was later popularized by the geologist Charles Lyell in the nineteenth century. Lyell became a
friend to Darwin and his ideas were very influential on Darwin’s thinking. Lyell argued that the
greater age of Earth gave more time for gradual change in species, and the process provided an
analogy for gradual change in species.

In the early nineteenth century, Jean-Baptiste Lamarck published a book that detailed a
mechanism for evolutionary change that is now referred to as inheritance of acquired
characteristics. In Lamarck’s theory, modifications in an individual caused by its environment, or
the use or disuse of a structure during its lifetime, could be inherited by its offspring and, thus,
bring about change in a species. While this mechanism for evolutionary change as described by
Lamarck was discredited, Lamarck’s ideas were an important influence on evolutionary thought.
The inscription on the statue of Lamarck that stands at the gates of the Jardin des Plantes in Paris
describes him as the “founder of the doctrine of evolution.”

1 Theodosius Dobzhansky. “Biology, Molecular and Organismic.” American Zoologist 4, no. 4 (1964): 449.

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 11.1 • Discovering How Populations Change 249

Charles Darwin and Natural Selection

The actual mechanism for evolution was independently conceived of and described by two naturalists, Charles
Darwin and Alfred Russell Wallace, in the mid-nineteenth century. Importantly, each 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,
visiting 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 in 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 that each had a unique beak shape (Figure 11.2). He observed both that these
finches closely resembled another finch species on the mainland of South America and that the group of species in
the Galápagos formed a graded series of beak sizes and shapes, with very small differences between the most
similar. Darwin imagined that the island species might be all species modified from one original mainland species. In
1860, he wrote, “Seeing this gradation and diversity of structure in one small, intimately related group of birds, one
might really fancy that from an original paucity of birds in this archipelago, one species had been taken and modified
2
for different ends.”

FIGURE 11.2 Darwin observed that beak shape varies among finch species. He postulated that the beak of an ancestral species had
adapted over time to equip the finches to acquire different food sources. This illustration shows the beak shapes for four species of ground
finch: 1. Geospiza magnirostris (the large ground finch), 2. G. fortis (the medium ground finch), 3. G. parvula (the small tree finch), and 4.
Certhidea olivacea (the green-warbler finch).

Wallace and Darwin both observed similar patterns in other organisms and independently conceived a mechanism
to explain how and why such changes could take place. Darwin called this mechanism natural selection. Natural
selection, Darwin argued, was an inevitable outcome of three principles that operated in nature. First, the
characteristics of organisms are inherited, or passed from parent to offspring. Second, more offspring are produced
than are able to survive; in other words, 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 a
competition for those resources in each generation. Both Darwin and Wallace’s understanding of this principle came
from reading an essay by the economist Thomas Malthus, who discussed this principle in relation to human
populations. Third, offspring vary among each other in regard to their characteristics and those variations are
inherited. Out of these three principles, Darwin and Wallace reasoned that offspring with inherited characteristics
that 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

2 Charles Darwin, Journal of Researches into the Natural History and Geology of the Countries Visited during the Voyage of H.M.S. Beagle
Round the World, under the Command of Capt. Fitz Roy, R.N, 2nd. ed. (London: John Murray, 1860), http://www.archive.org/details/
journalofresea00darw.
250 11 • Evolution and Its Processes

called “descent with modification.”

Papers by Darwin and Wallace (Figure 11.3) presenting the idea of natural selection were read together in 1858
before the Linnaean Society in London. The following year Darwin’s book, On the Origin of Species, was published,
which outlined in considerable detail his arguments for evolution by natural selection.

FIGURE 11.3 (a) Charles Darwin and (b) Alfred Wallace wrote scientific papers on natural selection that were presented together before the
Linnean Society in 1858.

Demonstrations of evolution by natural selection can be time consuming. One of the best demonstrations has been
in the very birds that helped to inspire the theory, the Galápagos finches. Peter and Rosemary Grant and their
colleagues have studied Galápagos finch populations every year since 1976 and have provided important
demonstrations of the operation of natural selection. The Grants found changes from one generation to the next in
the beak shapes of the medium ground finches on the Galápagos island of Daphne Major. The medium ground finch
feeds on seeds. The birds have inherited variation in the bill shape with some individuals having wide, deep bills and
others having thinner bills. Large-billed birds feed more efficiently on large, hard seeds, whereas smaller billed birds
feed more efficiently on small, soft seeds. During 1977, a drought period altered vegetation on the island. After this
period, the number of seeds declined dramatically: the decline in small, soft seeds was greater than the decline in
large, hard seeds. The large-billed birds were able to survive better than the small-billed birds the following year.
The year following the drought when the Grants measured beak sizes in the much-reduced population, they found
that the average bill size was larger (Figure 11.4). This was clear evidence for natural selection (differences in
survival) of bill size caused by the availability of seeds. The Grants had studied the inheritance of bill sizes and knew
that the surviving large-billed birds would tend to produce offspring with larger bills, so the selection would lead to
evolution of bill size. Subsequent studies by the Grants have demonstrated selection on and evolution of bill size in
this species in response to changing conditions on the island. The evolution has occurred both to larger bills, as in
this case, and to smaller bills when large seeds became rare.

FIGURE 11.4 A drought on the Galápagos island of Daphne Major in 1977 reduced the number of small seeds available to finches, causing
many of the small-beaked finches to die. This caused an increase in the finches’ average beak size between 1976 and 1978.

Variation and Adaptation

Natural selection can only take place if there is variation, or differences, among individuals in a population.

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 11.1 • Discovering How Populations Change 251

Importantly, these differences must have some genetic basis; otherwise, selection will not lead to change in the
next generation. This is critical because variation among individuals can be caused by non-genetic reasons, such as
an individual being taller because of better nutrition rather than different genes.

Genetic diversity in a population comes from two main sources: mutation and sexual reproduction. Mutation, a
change in DNA, is the ultimate source of new alleles or new genetic variation in any population. An individual that
has a mutated gene might have a different trait than other individuals in the population. However, this is not always
the case. A mutation can have one of three outcomes on the organisms’ appearance (or phenotype):

• A mutation may affect the phenotype of the organism in a way that gives it reduced fitness—lower likelihood of
survival, resulting in fewer offspring.
• A mutation may produce a phenotype with a beneficial effect on fitness.
• Many mutations, called neutral mutations, will have no effect on fitness.

Mutations may also have a whole range of effect sizes on the fitness of the organism that expresses them in their
phenotype, from a small effect to a great effect. Sexual reproduction and crossing over in meiosis also lead to
genetic diversity: when two parents reproduce, unique combinations of alleles assemble to produce unique
genotypes and, thus, phenotypes in each of the offspring.

A heritable trait that aids the survival and reproduction of an organism in its present environment is called an
adaptation. An adaptation is a “match” of the organism to the environment. Adaptation to an environment comes
about when a change in the range of genetic variation occurs over time that increases or maintains the match of the
population with its environment. The variations in finch beaks shifted from generation to generation providing
adaptation to food availability.

Whether or not a trait is favorable depends on the environment at the time. The same traits do not always have the
same relative benefit or disadvantage because environmental conditions can change. For example, finches with
large bills were benefited in one climate, while small bills were a disadvantage; in a different climate, the
relationship reversed.

Patterns of Evolution
The evolution of species has resulted in enormous variation in form and function. When two species evolve in
different directions from a common point, it is called divergent evolution. Such divergent evolution can be seen 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 11.5).

FIGURE 11.5 Flowering plants evolved from a common ancestor. Notice that the (a) dense blazing star and (b) purple coneflower vary in
appearance, yet both share a similar basic morphology. (credit a, b: modification of work by Cory Zanker)

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. The
wings of bats and insects, however, evolved from very different original structures. When similar structures arise
through evolution independently in different species it is called convergent evolution. The wings of bats and insects
are called analogous structures; they are similar in function and appearance, but do not share an origin in a
common ancestor. Instead they evolved independently in the two lineages. The wings of a hummingbird and an
252 11 • Evolution and Its Processes

ostrich are homologous structures, meaning they share similarities (despite their differences resulting from
evolutionary divergence). The wings of hummingbirds and ostriches did not evolve independently in the
hummingbird lineage and the ostrich lineage—they descended from a common ancestor with wings.

The Modern Synthesis

The mechanisms of inheritance, genetics, were not understood at the time Darwin and Wallace were developing
their idea of natural selection. This lack of understanding was a stumbling block to comprehending many aspects of
evolution. In fact, blending inheritance was the predominant (and incorrect) genetic theory of the time, which made
it difficult to understand how natural selection might operate. Darwin and Wallace were unaware of the genetics
work by Austrian monk Gregor Mendel, which was published in 1866, not long after publication of On the Origin of
Species. Mendel’s work was rediscovered in the early twentieth century at which time geneticists were rapidly
coming to an understanding of the basics of inheritance. Initially, the newly discovered particulate nature of genes
made it difficult for biologists to understand how gradual evolution could occur. But over the next few decades
genetics and evolution were integrated in what became known as the modern synthesis—the coherent
understanding of the relationship between natural selection and genetics that took shape by the 1940s and is
generally accepted today. In sum, the modern synthesis describes how evolutionary pressures, such as natural
selection, can affect a population’s genetic makeup, and, in turn, how this can result in the gradual evolution of
populations and species. The theory also connects this gradual change of a population over time, called
microevolution, with the processes that gave rise to new species and higher taxonomic groups with widely
divergent characters, called macroevolution.

Population Genetics
Recall that a gene for a particular character may have several variants, or alleles, that code for different traits
associated with that character. For example, in the ABO blood type system in humans, three alleles determine the
particular blood-type carbohydrate on the surface of red blood cells. Each individual in a population of diploid
organisms can only carry two alleles for a particular gene, but more than two may be present in the individuals that
make up the population. Mendel followed alleles as they were inherited from parent to offspring. In the early
twentieth century, biologists began to study what happens to all the alleles in a population in a field of study known
as population genetics.

Until now, we have defined evolution as a change in the characteristics of a population of organisms, but behind that
phenotypic change is genetic change. In population genetic terms, evolution is defined as a change in the frequency
of an allele in a population. Using the ABO system as an example, the frequency of one of the alleles, IA, is the
number of copies of that allele divided by all the copies of the ABO gene in the population. For example, a study in
3
Jordan found a frequency of IA to be 26.1 percent. The IB, I0 alleles made up 13.4 percent and 60.5 percent of the
alleles respectively, and all of the frequencies add up to 100 percent. A change in this frequency over time would
constitute evolution in the population.

There are several ways the allele frequencies of a population can change. One of those ways is natural selection. If a
given allele confers a phenotype that allows an individual to have more offspring that survive and reproduce, that
allele, by virtue of being inherited by those offspring, will be in greater frequency in the next generation. Since allele
frequencies always add up to 100 percent, an increase in the frequency of one allele always means a corresponding
decrease in one or more of the other alleles. Highly beneficial alleles may, over a very few generations, become
“fixed” in this way, meaning that every individual of the population will carry the allele. Similarly, detrimental alleles
may be swiftly eliminated from the gene pool, the sum of all the alleles in a population. Part of the study of
population genetics is tracking how selective forces change the allele frequencies in a population over time, which
can give scientists clues regarding the selective forces that may be operating on a given population. The studies of
changes in wing coloration in the peppered moth from mottled white to dark in response to soot-covered tree trunks
and then back to mottled white when factories stopped producing so much soot is a classic example of studying
evolution in natural populations (Figure 11.6).

3 Sahar S. Hanania, Dhia S. Hassawi, and Nidal M. Irshaid, “Allele Frequency and Molecular Genotypes of ABO Blood Group System in a
Jordanian Population,” Journal of Medical Sciences 7 (2007): 51-58, doi:10.3923/jms.2007.51.58

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 11.1 • Discovering How Populations Change 253

FIGURE 11.6 As the Industrial Revolution caused trees to darken from soot, darker colored peppered moths were better camouflaged than
the lighter colored ones, which caused there to be more of the darker colored moths in the population.

In the early twentieth century, English mathematician Godfrey Hardy and German physician Wilhelm Weinberg
independently provided an explanation for a somewhat counterintuitive concept. Hardy’s original explanation was in
response to a misunderstanding as to why a “dominant” allele, one that masks a recessive allele, should not
increase in frequency in a population until it eliminated all the other alleles. The question resulted from a common
confusion about what “dominant” means, but it forced Hardy, who was not even a biologist, to point out that if there
are no factors that affect an allele frequency those frequencies will remain constant from one generation to the
next. This principle is now known as the Hardy-Weinberg equilibrium. The theory states that a population’s allele
and genotype frequencies are inherently stable—unless some kind of evolutionary force is acting on the population,
the population would carry the same alleles in the same proportions generation after generation. Individuals would,
as a whole, look essentially the same and this would be unrelated to whether the alleles were dominant or
recessive. The four most important evolutionary forces, which will disrupt the equilibrium, are natural selection,
mutation, genetic drift, and migration into or out of a population. A fifth factor, nonrandom mating, will also disrupt
the Hardy-Weinberg equilibrium but only by shifting genotype frequencies, not allele frequencies (unless the allele
contributes toward increased or decreased reproductive potential). In nonrandom mating, individuals are more
likely to mate with individuals with specific phenotypes rather than at random. Since nonrandom mating does not
change allele frequencies, it does not cause evolution directly. Natural selection has been described. Mutation
creates one allele out of another one and changes an allele’s frequency by a small, but continuous amount each
generation. Each allele is generated by a low, constant mutation rate that will slowly increase the allele’s frequency
in a population if no other forces act on the allele. If natural selection acts against the allele, it will be removed from
the population at a low rate leading to a frequency that results from a balance between selection and mutation. This
is one reason that genetic diseases remain in the human population at very low frequencies. If the allele is favored
by selection, it will increase in frequency. Genetic drift causes random changes in allele frequencies when
populations are small. Genetic drift can often be important in evolution, as discussed in the next section. Finally, if
two populations of a species have different allele frequencies, migration of individuals between them will cause
frequency changes in both populations. As it happens, there is no population in which one or more of these
processes are not operating, so populations are always evolving, and the Hardy-Weinberg equilibrium will never be
exactly observed. However, the Hardy-Weinberg principle gives scientists a baseline expectation for allele
frequencies in a non-evolving population to which they can compare evolving populations and thereby infer what
evolutionary forces might be at play. The population is evolving if the frequencies of alleles or genotypes deviate
from the value expected from the Hardy-Weinberg principle.

Darwin identified a special case of natural selection that he called sexual selection. Sexual selection affects an
individual’s ability to mate and thus produce offspring, and it leads to the evolution of dramatic traits that often
appear maladaptive in terms of survival but persist because they give their owners greater reproductive success.
Sexual selection occurs in two ways: through intrasexual selection, as male–male or female–female competition for
mates, and through intersexual selection, as female or male selection of mates. Male–male competition takes the
form of conflicts between males, which are often ritualized, but may also pose significant threats to a male’s
survival. Sometimes the competition is for territory, with females more likely to mate with males with higher quality
territories. Female choice occurs when females choose a male based on a particular trait, such as feather colors, the
performance of a mating dance, or the building of an elaborate structure. In some cases male–male competition
and female choice combine in the mating process. In each of these cases, the traits selected for, such as fighting
ability or feather color and length, become enhanced in the males. In general, it is thought that sexual selection can
254 11 • Evolution and Its Processes

proceed to a point at which natural selection against a character’s further enhancement prevents its further
evolution because it negatively impacts the male’s ability to survive. For example, colorful feathers or an elaborate
display make the male more obvious to predators.

11.2 Mechanisms of Evolution

LEARNING OBJECTIVES
By the end of this section, you will be able to:
• Describe the four basic causes of evolution: natural selection, mutation, genetic drift, and gene flow
• Explain how each evolutionary force can influence the allele frequencies of a population

The Hardy-Weinberg equilibrium principle says that allele frequencies in a population will remain constant in the
absence of the four factors that could change them. Those factors are natural selection, mutation, genetic drift, and
migration (gene flow). In fact, we know they are probably always affecting populations.

Natural Selection
Natural selection has already been discussed. Alleles are expressed in a phenotype. Depending on the
environmental conditions, the phenotype confers an advantage or disadvantage to the individual with the phenotype
relative to the other phenotypes in the population. If it is an advantage, then that individual will likely have more
offspring than individuals with the other phenotypes, and this will mean that the allele behind the phenotype will
have greater representation in the next generation. If conditions remain the same, those offspring, which are
carrying the same allele, will also benefit. Over time, the allele will increase in frequency in the population.

Mutation
Mutation is a source of new alleles in a population. Mutation is a change in the DNA sequence of the gene. A
mutation can change one allele into another, but the net effect is a change in frequency. The change in frequency
resulting from mutation is small, so its effect on evolution is small unless it interacts with one of the other factors,
such as selection. A mutation may produce an allele that is selected against, selected for, or selectively neutral.
Harmful mutations are removed from the population by selection and will generally only be found in very low
frequencies equal to the mutation rate. Beneficial mutations will spread through the population through selection,
although that initial spread is slow. Whether or not a mutation is beneficial or harmful is determined by whether it
helps an organism survive to sexual maturity and reproduce. It should be noted that mutation is the ultimate source
of genetic variation in all populations—new alleles, and, therefore, new genetic variations arise through mutation.

Genetic Drift
Another way a population’s allele frequencies can change is genetic drift (Figure 11.7), which is simply the effect of
chance. Genetic drift is most important in small populations. Drift would be completely absent in a population with
infinite individuals, but, of course, no population is this large. Genetic drift occurs because the alleles in an offspring
generation are a random sample of the alleles in the parent generation. Alleles may or may not make it into the next
generation due to chance events including mortality of an individual, events affecting finding a mate, and even the
events affecting which gametes end up in fertilizations. If one individual in a population of ten individuals happens
to die before it leaves any offspring to the next generation, all of its genes—a tenth of the population’s gene
pool—will be suddenly lost. In a population of 100, that 1 individual represents only 1 percent of the overall gene
pool; therefore, it has much less impact on the population’s genetic structure and is unlikely to remove all copies of
even a relatively rare allele.

Imagine a population of ten individuals, half with allele A and half with allele a (the individuals are haploid). In a
stable population, the next generation will also have ten individuals. Choose that generation randomly by flipping a
coin ten times and let heads be A and tails be a. It is unlikely that the next generation will have exactly half of each
allele. There might be six of one and four of the other, or some different set of frequencies. Thus, the allele
frequencies have changed and evolution has occurred. A coin will no longer work to choose the next generation
(because the odds are no longer one half for each allele). The frequency in each generation will drift up and down on
what is known as a random walk until at one point either all A or all a are chosen and that allele is fixed from that
point on. This could take a very long time for a large population. This simplification is not very biological, but it can
be shown that real populations behave this way. The effect of drift on frequencies is greater the smaller a population

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 11.2 • Mechanisms of Evolution 255

is. Its effect is also greater on an allele with a frequency far from one half. Drift will influence every allele, even those
that are being naturally selected.

VISUAL CONNECTION

FIGURE 11.7 Genetic drift in a population can lead to the elimination of an allele from a population by chance. In each generation, a
random set of individuals reproduces to produce the next generation. The frequency of alleles in the next generation is equal to the
frequency of alleles among the individuals reproducing.

Do you think genetic drift would happen more quickly on an island or on the mainland?

Genetic drift can also be magnified by natural or human-caused events, such as a disaster that randomly kills a large
portion of the population, which is known as the bottleneck effect that results in a large portion of the gene pool
suddenly being wiped out (Figure 11.8). In one fell swoop, the genetic structure of the survivors becomes the
genetic structure of the entire population, which may be very different from the pre-disaster population. The
disaster must be one that kills for reasons unrelated to the organism’s traits, such as a hurricane or lava flow. A
mass killing caused by unusually cold temperatures at night, is likely to affect individuals differently depending on
the alleles they possess that confer cold hardiness.

FIGURE 11.8 A chance event or catastrophe can reduce the genetic variability within a population.
256 11 • Evolution and Its Processes

Another scenario in which populations might experience a strong influence of genetic drift is if some portion of the
population leaves to start a new population in a new location, or if a population gets divided by a physical barrier of
some kind. In this situation, those individuals are unlikely to be representative of the entire population which results
in the founder effect. The founder effect occurs when the genetic structure matches that of the new population’s
founding fathers and mothers. The founder effect is believed to have been a key factor in the genetic history of the
Afrikaner population of Dutch settlers in South Africa, as evidenced by mutations that are common in Afrikaners but
rare in most other populations. This is likely due to a higher-than-normal proportion of the founding colonists, which
were a small sample of the original population, carried these mutations. As a result, the population expresses
unusually high incidences of Huntington’s disease (HD) and Fanconi anemia (FA), a genetic disorder known to cause
4
bone marrow and congenital abnormalities, and even cancer.

LINK TO LEARNING
Visit this site (http://openstax.org/l/genetic_drift2) to learn more about genetic drift and to run simulations of allele
changes caused by drift.

Gene Flow
Another important evolutionary force is gene flow, or the flow of alleles in and out of a population resulting from the
migration of individuals or gametes (Figure 11.9). While some populations are fairly stable, others experience more
flux. Many plants, for example, send their seeds far and wide, by wind or in the guts of animals; these seeds may
introduce alleles common in the source population to a new population in which they are rare.

FIGURE 11.9 Gene flow can occur when an individual travels from one geographic location to another and joins a different population of the
species. In the example shown here, the brown allele is introduced into the green population.

11.3 Evidence of Evolution

LEARNING OBJECTIVES
By the end of this section, you will be able to:
• Explain sources of evidence for evolution
• Define homologous and vestigial structures

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, 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 found today; fossils show the
gradual evolutionary changes over time. Scientists determine the age of fossils and categorize them 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 11.10). For example, highly detailed fossil
4 A. J. Tipping et al., “Molecular and Genealogical Evidence for a Founder Effect in Fanconi Anemia Families of the Afrikaner Population of
South Africa,” PNAS 98, no. 10 (2001): 5734-5739, doi: 10.1073/pnas.091402398.

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 11.3 • Evidence of Evolution 257

records have been recovered for sequences of species in the evolution of whales and modern horses. The fossil
record of horses in North America is especially rich and many contain transition fossils: those showing intermediate
anatomy between earlier and later forms. The fossil record extends back to a dog-like ancestor some 55 million
years ago that gave rise to the first horse-like species 55 to 42 million years ago in the genus Eohippus. The series of
fossils tracks the change in anatomy resulting from a gradual drying trend that changed the landscape from a
forested one to a prairie. Successive fossils show the evolution of teeth shapes and foot and leg anatomy to a
grazing habit, with adaptations for escaping predators, for example in species of Mesohippus found from 40 to 30
million years ago. Later species showed gains in size, such as those of Hipparion, which existed from about 23 to 2
million years ago. The fossil record shows several adaptive radiations in the horse lineage, which is now much
reduced to only one genus, Equus, with several species.

FIGURE 11.10 This illustration shows an artist’s renderings of these species derived from fossils of the evolutionary history of the horse
and its ancestors. The species depicted are only four from a very diverse lineage that contains many branches, dead ends, and adaptive
radiations. One of the trends, depicted here is the evolutionary tracking of a drying climate and increase in prairie versus forest habitat
reflected in forms that are more adapted to grazing and predator escape through running. Przewalski's horse is one of a few living species
of horse.

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 the appendages of a human, dog, bird, and whale all share the same overall construction
(Figure 11.11). That similarity results from their origin in the appendages of a common ancestor. Over time,
evolution led to changes in the shapes and sizes of these bones in different species, but they have maintained the
same overall layout, evidence of descent from a common ancestor. Scientists call these synonymous parts
homologous structures. Some structures exist in organisms that have no apparent function at all, and appear to be
residual parts from a past ancestor. For example, some snakes have pelvic bones despite having no legs because
they descended from reptiles that did have legs. These unused structures without function are called vestigial
structures. Other examples of vestigial structures are wings on flightless birds (which may have other functions),
leaves on some cacti, traces of pelvic bones in whales, and the sightless eyes of cave animals.

FIGURE 11.11 The similar construction of these appendages indicates that these organisms share a common ancestor.
258 11 • Evolution and Its Processes

LINK TO LEARNING
Click through the activities at this interactive site (http://openstax.org/l/bone_structure2) to guess which bone
structures are homologous and which are analogous, and to see examples of all kinds of evolutionary adaptations
that illustrate these concepts.

Another piece of 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 (a bird), living in the arctic region have
temporary white coverings during winter to blend with the snow and ice (Figure 11.12). The similarity occurs not
because of common ancestry, indeed one covering is of fur and the other of feathers, but because of similar
selection pressures—the benefits of not being seen by predators.

FIGURE 11.12 The white winter coat of (a) the arctic fox and (b) the ptarmigan’s plumage are adaptations to their environments. (credit a:
modification of work by Keith Morehouse)

Embryology, the study of the development of the anatomy of an organism to its adult form also provides evidence of
relatedness between now widely divergent groups of organisms. Structures that are absent in some groups often
appear in their embryonic forms and disappear by the time the adult or juvenile form is reached. For example, all
vertebrate embryos, including humans, exhibit gill slits at some point in their early development. These disappear in
the adults of terrestrial groups, but are maintained in adult forms of aquatic groups such as fish and some
amphibians. Great ape embryos, including humans, have a tail structure during their development that is lost by the
time of birth. The reason embryos of unrelated species are often similar is that mutational changes that affect the
organism during embryonic development can cause amplified differences in the adult, even while the embryonic
similarities are preserved.

Biogeography
The geographic distribution of organisms on the planet follows patterns that are best explained by evolution in
conjunction with the movement of tectonic plates over geological time. Broad groups that evolved before the
breakup of the supercontinent Pangaea (about 200 million years ago) are distributed worldwide. Groups that
evolved since the breakup appear uniquely in regions of the planet, for example 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 Proteaceae in Australia, southern Africa, and South America is best
explained by the plant family’s presence there prior to the southern supercontinent Gondwana breaking up (Figure
11.13).

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 11.4 • Speciation 259

FIGURE 11.13 The Proteacea family of plants evolved before the supercontinent Gondwana broke up. Today, members of this plant family
are found throughout the southern hemisphere (shown in red). (credit “Proteacea flower”: modification of work by “dorofofoto”/Flickr)

The great diversification of the marsupials in Australia and the absence of other mammals reflects that island
continent’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 migration of species to other regions. Over time,
these species diverge evolutionarily into new species that look very different from their ancestors that may exist on
the mainland. The marsupials of Australia, the finches on the Galápagos, and many species on the Hawaiian Islands
are all found nowhere else but on their island, yet display distant relationships to ancestral species on mainlands.

Molecular Biology
Like anatomical structures, the structures of the molecules of life reflect descent with modification. Evidence of a
common ancestor for all of life is reflected in the universality of DNA as the genetic material and of the near
universality of the genetic code and the machinery of DNA replication and expression. Fundamental divisions in life
between the three domains are reflected in major structural differences in otherwise conservative structures such
as the components of ribosomes and the structures of membranes. In general, the relatedness of groups of
organisms is reflected in the similarity of their DNA sequences—exactly the pattern that would be expected 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. These duplications are a
kind of mutation in which an entire gene is added as an extra copy (or many copies) in the genome. These
duplications allow the free modification of one copy by mutation, selection, and drift, while the second copy
continues to produce a functional protein. This allows the original function for the protein to be kept, while
evolutionary forces tweak the copy until it functions in a new way.

11.4 Speciation
LEARNING OBJECTIVES
By the end of this section, you will be able to:
• Describe the definition of species and how species are identified as different
• Explain allopatric and sympatric speciation
• Describe adaptive radiation

The biological definition of species, which works for sexually reproducing organisms, is a group of actually or
potentially interbreeding individuals. According to this definition, one species is distinguished from another by the
possibility of matings between individuals from each species to produce fertile offspring. 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. In fact, the presence of hybrids between similar species suggests
260 11 • Evolution and Its Processes

that they may have descended from a single interbreeding species and that 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 found in On the Origin of Species (Figure 11.14a). For speciation to occur, two new
populations must be formed 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, meaning speciation in “other
homelands,” involves a geographic separation of populations from a parent species and subsequent evolution.
Sympatric speciation, meaning speciation in the “same homeland,” involves speciation occurring within a parent
species while 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 there might not be more than two species formed at one time except that it is less likely and such
multiple events can also be conceptualized as single splits occurring close in time.

FIGURE 11.14 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 are drawn today to illustrate the relationships of species. (b) Modern
elephants evolved from the Palaeomastodon, a species that lived in Egypt 35–50 million years ago.

Speciation through Geographic Separation

A geographically continuous population has a gene pool that is relatively homogeneous. Gene flow, the movement of
alleles across the range of the species, is relatively free because individuals can move and then mate with
individuals in their new location. Thus, the frequency of an allele at one end of a distribution will be similar to the
frequency of the allele at the other end. When populations become geographically discontinuous that free-flow of
alleles is prevented. 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 more and more
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. Different histories of genetic drift, enhanced because the populations
are smaller than the parent population, will also lead to divergence.

Given enough time, the genetic and phenotypic divergence between populations will likely affect characters that
influence reproduction enough that were individuals of the two populations brought together, mating would be less
likely, or if a mating occurred, offspring would be non-viable or infertile. Many types of diverging characters may
affect the reproductive isolation (inability to interbreed) of the two populations. These mechanisms of reproductive
isolation can be divided into prezygotic mechanisms (those that operate before fertilization) and postzygotic
mechanisms (those that operate after fertilization). Prezygotic mechanisms include traits that allow the individuals
to find each other, such as the timing of mating, sensitivity to pheromones, or choice of mating sites. If individuals

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 11.4 • Speciation 261

are able to encounter each other, character divergence may prevent courtship rituals from leading to a mating either
because female preferences have changed or male behaviors have changed. Physiological changes may interfere
with successful fertilization if mating is able to occur. Postzygotic mechanisms include genetic incompatibilities that
prevent proper development of the offspring, or if the offspring live, they may be unable to produce viable gametes
themselves as in the example of the mule, the infertile offspring of a female horse and a male donkey.

If the two isolated populations are brought back together and the hybrid offspring that formed from matings
between individuals of the two populations have lower survivorship or reduced fertility, then selection will favor
individuals that are able to discriminate between potential mates of their own population and the other population.
This selection will enhance the reproductive isolation.

Isolation of populations leading to allopatric speciation can occur in a variety of ways: from a river forming a new
branch, erosion forming a new valley, or a group of organisms traveling to a new location without the ability to
return, such as seeds floating over the ocean to an island. The nature of the geographic separation necessary to
isolate populations depends entirely on the biology of the organism and its potential for dispersal. If two flying
insect populations took up residence in separate nearby valleys, chances are that individuals from each population
would fly back and forth, continuing gene flow. However, if two rodent populations became divided by the formation
of a new lake, continued gene flow would be unlikely; therefore, speciation would be more likely.

Biologists group allopatric processes into two categories. If a few members of a species move to a new geographical
area, this is called dispersal. If a natural situation arises to physically divide organisms, this is called vicariance.

Scientists have documented numerous cases of allopatric speciation taking place. For example, along the west
coast of the United States, two separate subspecies of spotted owls exist. The northern spotted owl has genetic and
phenotypic differences from its close relative, the Mexican spotted owl, which lives in the south (Figure 11.15). The
cause of their initial separation is not clear, but it may have been caused by the glaciers of the ice age dividing an
5
initial population into two.

FIGURE 11.15 The northern spotted owl and the Mexican spotted owl inhabit geographically separate locations with different climates and
ecosystems. The owl is an example of incipient speciation. (credit “northern spotted owl”: modification of work by John and Karen
Hollingsworth, USFWS; credit “Mexican spotted owl”: modification of work by Bill Radke, USFWS)

5 Courtney, S.P., et al, “Scientific Evaluation of the Status of the Northern Spotted Owl,” Sustainable Ecosystems Institute (2004),
Portland, OR.
262 11 • Evolution and Its Processes

Additionally, scientists have found that the further the distance between two groups that once were the same
species, the more likely for speciation to take place. 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 other types of organisms in each ecosystem differ, as
do their behaviors and habits; also, the hunting habits and prey choices of the owls in the south vary from the
northern ones. These variances can lead to evolved differences in the owls, and over time speciation will likely occur
unless gene flow between the populations is restored.

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, which is called adaptive radiation. From one point of origin, many adaptations evolve 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 (Figure 11.16). The Hawaiian honeycreeper illustrates one example of adaptive radiation. From a single
species, called the founder species, numerous species have evolved, including the eight shown in Figure 11.16.

FIGURE 11.16 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 11.16. Change in the genetic variation for beaks 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 fruit and seed-eating birds have thicker, stronger beaks which are suited to break hard
nuts. The nectar-eating birds have long beaks to dip into flowers to reach their nectar. The insect-eating birds have
beaks like swords, appropriate for stabbing and impaling insects. Darwin’s finches are another well-studied example
of adaptive radiation in an archipelago.

LINK TO LEARNING
Click through this interactive site (http://openstax.org/l/bird_evolution) to see how island birds evolved; click to see
images of each species in evolutionary increments from five million years ago to today.

Access for free at openstax.org

 11.4 • Speciation 263

Speciation without Geographic Separation

Can divergence occur if no physical barriers are in place to separate individuals who continue to live and reproduce
in the same habitat? A number of mechanisms for sympatric speciation have been proposed and studied.

One form of sympatric speciation can begin with a chromosomal error during meiosis or the formation of a hybrid
individual with too many 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 polyploid state. In some cases a polyploid individual will have two or more complete sets of
chromosomes from its own species in a condition called autopolyploidy (Figure 11.17). 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.

FIGURE 11.17 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 produced by this plant species. But 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 called 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 called an
allopolyploid. The prefix “allo” means “other” (recall from allopatric); therefore, an allopolyploid occurs when
gametes from two different species combine. Figure 11.18 illustrates one possible way an allopolyploidy can form.
Notice how it takes two generations, or two reproductive acts, before the viable fertile hybrid results.

FIGURE 11.18 Alloploidy results when two species mate to produce viable offspring. In the example shown, a normal gamete from one
species fuses with a polyploid 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, most chromosomal abnormalities in animals are lethal; it takes place most commonly in
plants. Scientists have discovered more than 1/2 of all plant species studied relate back to a species evolved
through polyploidy.
264 11 • Evolution and Its Processes

Sympatric speciation may also take place in ways other than polyploidy. For example, imagine a species of fish that
lived in a lake. As the population grew, competition for food also grew. Under pressure to find food, suppose that a
group of these fish had the genetic flexibility to discover and feed off another resource that was unused by the other
fish. What if this new food source was found 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 and feed and live in the same area, keeping them
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 11.19 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; however, they have come to have different morphologies that allow
them to eat various food sources.

FIGURE 11.19 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 the lake was populated only 100 years ago by a single population of cichlid fish. 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.

Finally, a well-documented example of ongoing sympatric speciation occurred in the apple maggot fly, Rhagoletis
pomonella, which arose as an isolated population sometime after the introduction of the apple into North America.
The native population of flies fed on hawthorn species and is host-specific: it only infests hawthorn trees.
Importantly, it also uses the trees as a location to meet for mating. It is hypothesized that either through mutation
or a behavioral mistake, flies jumped hosts and met and mated in apple trees, subsequently laying their eggs in
apple fruit. The offspring matured and kept their preference for the apple trees effectively dividing the original
population into two new populations separated by host species, not by geography. The host jump took place in the
nineteenth century, but there are now measureable differences between the two populations of fly. It seems likely
that host specificity of parasites in general is a common cause of sympatric speciation.

11.5 Common Misconceptions about Evolution

LEARNING OBJECTIVES
By the end of this section, you will be able to:
• Identify common misconceptions about evolution
• Identify common criticisms of evolution

Although the theory of evolution initially generated some controversy, by 20 years after the publication of On the
Origin of Species it was almost universally accepted by biologists, particularly younger biologists. Nevertheless, the
theory of evolution is a difficult concept and misconceptions about how it works abound. In addition, there are those
that reject it as an explanation for the diversity of life.

LINK TO LEARNING
This website (http://openstax.org/l/misconception2) addresses some of the main misconceptions associated with
the theory of evolution.

Access for free at openstax.org

 11.5 • Common Misconceptions about Evolution 265

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, a “theory” is understood to be a concept that has been
extensively tested and supported over time. We have a theory of the atom, a theory of gravity, and the theory of
relativity, each of which describes what scientists understand to be 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, who are naturally skeptical. While theories can sometimes be overturned or
revised, this does not lessen their weight but simply reflects the constantly evolving state of scientific knowledge. In
contrast, a “theory” in common vernacular means a guess or suggested explanation for something. This meaning is
more akin to the concept of a “hypothesis” used by scientists, which is a tentative explanation for something that is
proposed to either be supported or disproved. When critics of evolution say evolution is “just a theory,” they are
implying that there is little evidence supporting it and that it is still in the process of being rigorously tested. This is a
mischaracterization. If this were the case, geneticist Theodosius Dobzhansky would not have said that “nothing in
6
biology makes sense, except in the light of evolution.”

Individuals Evolve
An individual is born with the genes it has—these do not change as the individual ages. Therefore, an individual
cannot evolve or adapt through natural selection. Evolution is the change in genetic composition of a population
over time, specifically over generations, resulting from differential reproduction of individuals with certain alleles.
Individuals do change over their lifetime, but this is called development; it 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 the average bill size in the population
several years later after there has been a strong selective pressure, this average value may be different as a result of
evolution. Although some individuals may survive from the first time to the second, those individuals will still have
the same bill size. However, there may be enough new individuals with different bill sizes to change the average bill
size.

Evolution Explains the Origin of Life

It is a common misunderstanding that evolution includes an explanation of life’s origins. Some of the theory’s critics
complain 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 is how life is defined. The mechanisms of
the origin of life on Earth are a particularly difficult problem because it occurred a very long time ago, over a very
long time, and presumably just occurred once. Importantly, biologists believe that the presence of life on Earth
precludes the possibility that the events that led to life on Earth can be repeated because the intermediate stages
would immediately become food for existing living things. The early stages of life included the formation of organic
molecules such as carbohydrates, amino acids, or nucleotides. If these were formed from inorganic precursors
today, they would simply be broken down by living things. The early stages of life also probably included more
complex aggregations of molecules into enclosed structures with an internal environment, a boundary layer of some
form, and the external environment. Such structures, if they were formed now, would be quickly consumed or
broken down by living organisms.

However, once a mechanism of inheritance was in place in the form of a molecule like DNA or RNA, either within a
cell or within a 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. So 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.

6 Theodosius Dobzhansky. “Biology, Molecular and Organismic.” American Zoologist 4, no. 4 (1964): 449.
266 11 • Evolution and Its Processes

Organisms Evolve on Purpose

Statements such as “organisms evolve in response to a change in an environment,” are quite common. There are
two easy misunderstandings possible with such a statement. First of all, the statement must not be understood to
mean that individual organisms evolve, as was discussed above. 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 characters 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 for a population of bacteria that are resistant to antibiotics. The resistance, which is caused by
a gene, did not arise by mutation because of the application of the antibiotic. The gene for resistance was already
present in the gene pool of the bacteria, likely at a low frequency. The antibiotic, which kills the bacterial cells
without the resistance gene, strongly selects for 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 application.

In a larger sense, evolution is also 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. This kind of
language is common in popular literature. Certain organisms, ourselves included, are described as the “pinnacle” of
evolution, or “perfected” by evolution. What characteristics evolve in a species are a function of the variation
present and the environment, both of which are constantly changing in a non-directional way. What trait is fit in one
environment at one time may well be fatal at some point in the future. This holds equally well for a species of insect
as it does the human species.

Evolution Is Controversial among Scientists

The theory of evolution was controversial when it was first proposed in 1859, yet within 20 years virtually every
working biologist had accepted evolution as the explanation for the diversity of life. The rate of acceptance was
extraordinarily rapid, partly because Darwin had amassed an impressive body of evidence. The early controversies
involved both scientific arguments against the theory and the arguments of religious leaders. It was the arguments
of the biologists that were resolved after a short time, while the arguments of religious leaders have persisted to this
day.

The theory of evolution replaced the predominant theory at the time that species had all been specially created
within relatively recent history. Despite the prevalence of this theory, it was becoming increasingly clear to
naturalists during the nineteenth century that it could no longer explain many observations of geology and the living
world. The persuasiveness of the theory of evolution to these naturalists lay in its ability to explain these
phenomena, and it continues to hold extraordinary explanatory power to this day. Its continued rejection by some
religious leaders results from its replacement of special creation, a tenet of their religious belief. These leaders
cannot accept the replacement of special creation by a mechanistic process that excludes the actions of a deity as
an explanation for the diversity of life including the origins of the human species. It should be noted, however, that
most of the major denominations in the United States have statements supporting the acceptance of evidence for
evolution as compatible with their theologies.

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 11.5 • Common Misconceptions about Evolution 267

The nature of the arguments against evolution by religious leaders has evolved over time. One current argument is
that the theory is still controversial among biologists. This claim is simply not true. The number of working scientists
who reject the theory of evolution, or question its validity and say so, is small. A Pew Research poll in 2009 found
7
that 97 percent of the 2500 scientists polled believe species evolve. The support for the theory is reflected in
signed statements from many scientific societies such as the American Association for the Advancement of Science,
which includes working scientists as members. Many of the scientists that reject or question the theory of evolution
are non-biologists, such as engineers, physicians, and chemists. There are no experimental results or research
programs that contradict the theory. There are no papers published in peer-reviewed scientific journals that appear
to refute the theory. The latter observation might be considered a consequence of suppression of dissent, but it
must be remembered that scientists are skeptics and that there is a long history of published reports that
challenged scientific orthodoxy in unpopular ways. Examples include the endosymbiotic theory of eukaryotic
origins, the theory of group selection, the microbial cause of stomach ulcers, the asteroid-impact theory of the
Cretaceous extinction, and the theory of plate tectonics. Research with evidence and ideas with scientific merit are
considered by the scientific community. Research that does not meet these standards is rejected.

Other Theories Should Be Taught

A common argument from some people is that alternative theories to evolution should be taught in public schools.
Critics of evolution use this strategy to create uncertainty about the validity of the theory without offering actual
evidence. In fact, there are no viable alternative scientific theories to evolution. The last such theory, proposed by
Lamarck in the nineteenth century, was replaced by the theory of natural selection. A single exception was a
research program in the Soviet Union based on Lamarck’s theory during the early twentieth century that set that
country’s agricultural research back decades. Special creation is not a viable alternative scientific theory because it
is not a scientific theory, since it relies on an untestable explanation. Intelligent design, despite the claims of its
proponents, is also not a scientific explanation. This is because intelligent design posits the existence of an
unknown designer of living organisms and their systems. Whether the designer is unknown or supernatural, it is a
cause that cannot be measured; therefore, it is not a scientific explanation. There are two reasons not to teach
nonscientific theories. First, these explanations for the diversity of life lack scientific usefulness because they do
not, and cannot, give rise to research programs that promote our understanding of the natural world. Experiments
cannot test non-material explanations for natural phenomena. For this reason, teaching these explanations as
science in public schools is not in the public interest. Second, in the United States, it is illegal to teach them as
science because the U.S. Supreme Court and lower courts have ruled that the teaching of religious belief, such as
special creation or intelligent design, violates the establishment clause of the First Amendment of the U.S.
Constitution, which prohibits government sponsorship of a particular religion.

The theory of evolution and science in general is, by definition, silent on the existence or non-existence of the
spiritual world. Science is only able to study and know the material world. Individual biologists have sometimes
been vocal atheists, but it is equally true that there are many deeply religious biologists. Nothing in biology
precludes the existence of a god or other supreme beings, indeed biology as a science has nothing to say about it.
Individual biologists are free to reconcile their personal and scientific knowledge as they see fit. The Voices for
Evolution project (http://ncse.com/voices), developed through the National Center for Science Education, works to
gather the diversity of perspectives on evolution to advocate it being taught in public schools.

7 Pew Research Center for the People & the Press, Public Praises Science; Scientists Fault Public, Media (Washington, DC, 2009), 37.
268 11 • Key Terms

Key Terms
adaptation a heritable trait or behavior in an proposed by Lamarck in which traits acquired by
organism that aids in its survival in its present individuals through use or disuse could be passed
environment on to their offspring thus leading to evolutionary
adaptive radiation a speciation when one species change in the population
radiates out to form several other species macroevolution a broader scale of evolutionary
allopatric speciation a speciation that occurs via a changes seen over paleontological time
geographic separation microevolution the changes in a population’s genetic
analogous structure a structure that is similar structure (i.e., allele frequency)
because of evolution in response to similar selection migration the movement of individuals of a
pressures resulting in convergent evolution, not population to a new location; in population genetics
similar because of descent from a common ancestor it refers to the movement of individuals and their
bottleneck effect the magnification of genetic drift as alleles from one population to another, potentially
a result of natural events or catastrophes changing allele frequencies in both the old and the
convergent evolution an evolution that results in new population
similar forms on different species modern synthesis the overarching evolutionary
dispersal an allopatric speciation that occurs when a paradigm that took shape by the 1940s and is
few members of a species move to a new generally accepted today
geographical area natural selection the greater relative survival and
divergent evolution an evolution that results in reproduction of individuals in a population that have
different forms in two species with a common favorable heritable traits, leading to evolutionary
ancestor change
founder effect a magnification of genetic drift in a population genetics the study of how selective
small population that migrates away from a large forces change the allele frequencies in a population
parent population carrying with it an over time
unrepresentative set of alleles speciation a formation of a new species
gene flow the flow of alleles in and out of a sympatric speciation a speciation that occurs in the
population due to the migration of individuals or same geographic space
gametes variation the variety of alleles in a population
gene pool all of the alleles carried by all of the vestigial structure a physical structure present in an
individuals in the population organism but that has no apparent function and
genetic drift the effect of chance on a population’s appears to be from a functional structure in a
gene pool distant ancestor
homologous structure a structure that is similar vicariance an allopatric speciation that occurs when
because of descent from a common ancestor something in the environment separates organisms
inheritance of acquired characteristics a phrase of the same species into separate groups
that describes the mechanism of evolution

Chapter Summary
11.1 Discovering How Populations Change The modern synthesis of evolutionary theory grew out
of the reconciliation of Darwin’s, Wallace’s, and
Evolution by natural selection arises from three
Mendel’s thoughts on evolution and heredity.
conditions: individuals within a species vary, some of
Population genetics is a theoretical framework for
those variations are heritable, and organisms have
describing evolutionary change in populations through
more offspring than resources can support. The
the change in allele frequencies. Population genetics
consequence is that individuals with relatively
defines evolution as a change in allele frequency over
advantageous variations will be more likely to survive
generations. In the absence of evolutionary forces
and have higher reproductive rates than those
allele frequencies will not change in a population; this
individuals with different traits. The advantageous
is known as Hardy-Weinberg equilibrium principle.
traits will be passed on to offspring in greater
However, in all populations, mutation, natural
proportion. Thus, the trait will have higher
selection, genetic drift, and migration act to change
representation in the next and subsequent generations
allele frequencies.
leading to genetic change in the population.

Access for free at openstax.org

 11 • Visual Connection Questions 269

11.2 Mechanisms of Evolution form gametes with extra chromosomes, called

polyploidy. Autopolyploidy occurs within a single
There are four factors that can change the allele
species, whereas allopolyploidy occurs because of a
frequencies of a population. Natural selection works by
mating between closely related species. Once the
selecting for alleles that confer beneficial traits or
populations are isolated, evolutionary divergence can
behaviors, while selecting against those for deleterious
take place leading to the evolution of reproductive
qualities. Mutations introduce new alleles into a
isolating traits that prevent interbreeding should the
population. Genetic drift stems from the chance
two populations come together again. The reduced
occurrence that some individuals have more offspring
viability of hybrid offspring after a period of isolation is
than others and results in changes in allele frequencies
expected to select for stronger inherent isolating
that are random in direction. When individuals leave or
mechanisms.
join the population, allele frequencies can change as a
result of gene flow. 11.5 Common Misconceptions about
Evolution
11.3 Evidence of Evolution
The theory of evolution is a difficult concept and
The evidence for evolution is found at all levels of
misconceptions abound. The factual nature of
organization in living things and in the extinct species
evolution is often challenged by wrongly associating
we know about through fossils. Fossils provide
the scientific meaning of a theory with the vernacular
evidence for the evolutionary change through now
meaning. Evolution is sometimes mistakenly
extinct forms that led to modern species. For example,
interpreted to mean that individuals evolve, when in
there is a rich fossil record that shows the evolutionary
fact only populations can evolve as their gene
transitions from horse ancestors to modern horses that
frequencies change over time. Evolution is often
document intermediate forms and a gradual adaptation
assumed to explain the origin of life, which it does not
o changing ecosystems. The anatomy of species and
speak to. It is often spoken in goal-directed terms by
the embryological development of that anatomy reveal
which organisms change through intention, and
common structures in divergent lineages that have
selection operates on mutations present in a
been modified over time by evolution. The geographical
population that have not arisen in response to a
distribution of living species reflects the origins of
particular environmental stress. Evolution is often
species in particular geographic locations and the
characterized as being controversial among scientists;
history of continental movements. The structures of
however, it is accepted by the vast majority of working
molecules, like anatomical structures, reflect the
scientists. Critics of evolution often argue that
relationships of living species and match patterns of
alternative theories to evolution should be taught in
similarity expected from descent with modification.
public schools; however, there are no viable alternative
11.4 Speciation scientific theories to evolution. The alternative religious
beliefs should not be taught as science because it
Speciation occurs along two main pathways:
cannot be proven, and in the United States it is
geographic separation (allopatric speciation) and
unconstitutional. Science is silent on the question of
through mechanisms that occur within a shared habitat
the existence of a god while scientists are able to
(sympatric speciation). Both pathways force
reconcile religious belief and scientific knowledge.
reproductive isolation between populations. Sympatric
speciation can occur through errors in meiosis that

Visual Connection Questions

1. Figure 11.7 Do you think genetic drift would happen
more quickly on an island or on the mainland?

Review Questions
2. Which scientific concept did Charles Darwin and
Alfred Wallace independently discover?
a. mutation
b. natural selection
c. overbreeding
d. sexual reproduction
270 11 • Review Questions

3. Which of the following situations will lead to natural 7. In which of the following pairs do both evolutionary
selection? processes introduce new genetic variation into a
a. The seeds of two plants land near each other population?
and one grows larger than the other. a. natural selection and genetic drift
b. Two types of fish eat the same kind of food, b. mutation and gene flow
and one is better able to gather food than the c. natural selection and gene flow
other. d. gene flow and genetic drift
c. Male lions compete for the right to mate with
females, with only one possible winner. 8. The wing of a bird and the arm of a human are
d. all of the above examples of ________.
a. vestigial structures
4. What is the difference between micro- and b. molecular structures
macroevolution? c. homologous structures
a. Microevolution describes the evolution of small d. analogous structures
organisms, such as insects, while
macroevolution describes the evolution of large 9. The fact that DNA sequences are more similar in
organisms, like people and elephants. more closely related organisms is evidence of
b. Microevolution describes the evolution of what?
microscopic entities, such as molecules and a. optimal design in organisms
proteins, while macroevolution describes the b. adaptation
evolution of whole organisms. c. mutation
c. Microevolution describes the evolution of d. descent with modification
populations, while macroevolution describes
the emergence of new species over long 10. Which situation would most likely lead to
periods of time. allopatric speciation?
d. Microevolution describes the evolution of a. A flood causes the formation of a new lake.
organisms over their lifetimes, while b. A storm causes several large trees to fall
macroevolution describes the evolution of down.
organisms over multiple generations. c. A mutation causes a new trait to develop.
d. An injury causes an organism to seek out a
5. Population genetics is the study of ________. new food source.
a. how allele frequencies in a population change
over time 11. What is the main difference between dispersal
b. populations of cells in an individual and vicariance?
c. the rate of population growth a. One leads to allopatric speciation, whereas
d. how genes affect embryological development the other leads to sympatric speciation.
b. One involves the movement of the organism,
6. Galápagos medium ground finches are found on whereas the other involves a change in the
Santa Cruz and San Cristóbal islands, which are environment.
separated by about 100 km of ocean. Occasionally, c. One depends on a genetic mutation occurring,
individuals from either island fly to the other island whereas the other does not.
to stay. This can alter the allele frequencies of the d. One involves closely related organisms,
population through which of the following whereas the other involves only individuals of
mechanisms? the same species.
a. natural selection
b. genetic drift 12. Which variable increases the likelihood of
c. gene flow allopatric speciation taking place more quickly?
d. mutation a. lower rate of mutation
b. longer distance between divided groups
c. increased instances of hybrid formation
d. equivalent numbers of individuals in each
population

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 11 • Critical Thinking Questions 271

13. The word “theory” in theory of evolution is best 14. Why are alternative scientific theories to evolution
replaced by ________. not taught in public school?
a. fact a. more theories would confuse students
b. hypothesis b. there are no viable scientific alternatives
c. idea c. it is against the law
d. alternate explanation d. alternative scientific theories are suppressed
by the science establishment

Critical Thinking Questions

15. If a person scatters a handful of plant seeds from 20. Two species of fish had recently undergone
one species in an area, how would natural sympatric speciation. The males of each species
selection work in this situation? had a different coloring through which females
could identify and choose a partner from her own
16. Explain the Hardy-Weinberg principle of
species. After some time, pollution made the lake
equilibrium.
so cloudy it was hard for females to distinguish
17. Describe natural selection and give an example of colors. What might take place in this situation?
natural selection at work in a population.
21. How does the scientific meaning of “theory” differ
18. Why do scientists consider vestigial structures from the common, everyday meaning of the word?
evidence for evolution?
22. Explain why the statement that a monkey is more
19. Why do island chains provide ideal conditions for evolved than a mouse is incorrect.
adaptive radiation to occur?
272 11 • Critical Thinking Questions

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CHAPTER 12
Diversity of Life

FIGURE 12.1 Although they look different, this bee and flower are distantly related. (credit: modification of work by
John Beetham)

CHAPTER OUTLINE
12.1 Organizing Life on Earth
12.2 Determining Evolutionary Relationships

INTRODUCTION This bee and Echinacea flower could not look more different, yet they are
related, as are all living organisms on Earth. By following pathways of similarities and
differences—both visible and genetic—scientists seek to map the history of evolution from single-
celled organisms to the tremendous diversity of creatures that have crawled, germinated, floated,
swam, flown, and walked on this planet.

12.1 Organizing Life on Earth

LEARNING OBJECTIVES
By the end of this section, you will be able to:
• Discuss the need for a comprehensive classification system
• List the different levels of the taxonomic classification system
• Describe how systematics and taxonomy relate to phylogeny

All life on Earth evolved from a common ancestor. Biologists map how organisms are related by
constructing phylogenetic trees. In other words, a “tree of life” can be constructed to illustrate
when different organisms evolved and to show the relationships among different organisms, as
shown in Figure 12.2. Notice that from a single point, the three domains of Archaea, Bacteria, and
274 12 • Diversity of Life

Eukarya diverge and then branch repeatedly. The small branch that plants and animals (including
humans) occupy in this diagram shows how recently these groups had their origin compared with
other groups.

FIGURE 12.2 In the evolution of life on Earth, the three domains of life—Archaea, Bacteria, and Eukarya—branch from
a single point. (credit: modification of work by Eric Gaba)

The phylogenetic tree in Figure 12.2 illustrates the pathway of evolutionary history. The pathway
can be traced from the origin of life to any individual species by navigating through the
evolutionary branches between the two points. Also, by starting with a single species and tracing
backward to any branch point, the organisms related to it by various degrees of closeness can be
identified.

A phylogeny is the evolutionary history and the relationships among a species or group of species.
The study of organisms with the purpose of deriving their relationships is called systematics.

Many disciplines within the study of biology contribute to understanding how past and present life
evolved over time, and together they contribute to building, updating, and maintaining the “tree of
life.” Information gathered may include data collected from fossils, from studying morphology,
from the structure of body parts, or from molecular structure, such as the sequence of amino
acids in proteins or DNA nucleotides. By considering the trees generated by different sets of data
scientists can put together the phylogeny of a species.

Scientists continue to discover new species of life on Earth as well as new character information,
thus trees change as new data arrive.

The Levels of Classification

Taxonomy (which literally means “arrangement law”) is the science of naming and grouping
species to construct an internationally shared classification system. The taxonomic classification
system (also called the Linnaean system after its inventor, Carl Linnaeus, a Swedish naturalist)
uses a hierarchical model. A hierarchical system has levels and each group at one of the levels
includes groups at the next lowest level, so that at the lowest level each member belongs to a
series of nested groups. An analogy is the nested series of directories on the main disk drive of a
computer. For example, in the most inclusive grouping, scientists divide organisms into three

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 12.1 • Organizing Life on Earth 275

domains: Bacteria, Archaea, and Eukarya. Within each domain is a second level called a kingdom. Each domain
contains several kingdoms. Within kingdoms, the subsequent categories of increasing specificity are: phylum, class,
order, family, genus, and species.

As an example, the classification levels for the domestic dog are shown in Figure 12.3. The group at each level is
called a taxon (plural: taxa). In other words, for the dog, Carnivora is the taxon at the order level, Canidae is the
taxon at the family level, and so forth. Organisms also have a common name that people typically use, such as
domestic dog, or wolf. Each taxon name is capitalized except for species, and the genus and species names are
italicized. Scientists refer to an organism by its genus and species names together, commonly called a scientific
name, or Latin name. This two-name system is called binomial nomenclature. The scientific name of the wolf is
therefore Canis lupus. Recent study of the DNA of domestic dogs and wolves suggest that the domestic dog is a
subspecies of the wolf, not its own species, thus it is given an extra name to indicate its subspecies status, Canis
lupus familiaris.

Figure 12.3 also shows how taxonomic levels move toward specificity. Notice how within the domain we find the dog
grouped with the widest diversity of organisms. These include plants and other organisms not pictured, such as
fungi and protists. At each sublevel, the organisms become more similar because they are more closely related.
Before Darwin’s theory of evolution was developed, naturalists sometimes classified organisms using arbitrary
similarities, but since the theory of evolution was proposed in the 19th century, biologists work to make the
classification system reflect evolutionary relationships. This means that all of the members of a taxon should have a
common ancestor and be more closely related to each other than to members of other taxa.

Recent genetic analysis and other advancements have found that some earlier taxonomic classifications do not
reflect actual evolutionary relationships, and therefore, changes and updates must be made as new discoveries take
place. One dramatic and recent example was the breaking apart of prokaryotic species, which until the 1970s were
all classified as bacteria. Their division into Archaea and Bacteria came about after the recognition that their large
genetic differences warranted their separation into two of three fundamental branches of life.
276 12 • Diversity of Life

VISUAL CONNECTION

FIGURE 12.3 At each sublevel in the taxonomic classification system, organisms become more similar. Dogs and wolves are the same
species because they can breed and produce viable offspring, but they are different enough to be classified as different subspecies. (credit
“plant”: modification of work by "berduchwal"/Flickr; credit “insect”: modification of work by Jon Sullivan; credit “fish”: modification of
work by Christian Mehlführer; credit “rabbit”: modification of work by Aidan Wojtas; credit “cat”: modification of work by Jonathan Lidbeck;
credit “fox”: modification of work by Kevin Bacher, NPS; credit “jackal”: modification of work by Thomas A. Hermann, NBII, USGS; credit
“wolf” modification of work by Robert Dewar; credit “dog”: modification of work by "digital_image_fan"/Flickr)

In what levels are cats and dogs considered to be part of the same group?

Classification and Phylogeny

Scientists use a tool called a phylogenetic tree to show the evolutionary pathways and relationships between
organisms. A phylogenetic tree is a diagram used to reflect evolutionary relationships among organisms or groups
of organisms. The hierarchical classification of groups nested within more inclusive groups is reflected in diagrams.
Scientists consider phylogenetic trees to be a hypothesis of the evolutionary past because one cannot go back
through time to confirm the proposed relationships.

Unlike with a taxonomic classification, a phylogenetic tree can be read like a map of evolutionary history, as shown
in Figure 12.4. Shared characteristics are used to construct phylogenetic trees. The point where a split occurs in a
tree, called a branch point, represents where a single lineage evolved into distinct new ones. Many phylogenetic
trees have a single branch point at the base representing a common ancestor of all the branches in the tree.
Scientists call such trees rooted, which means there is a single ancestral taxon at the base of a phylogenetic tree to

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 12.1 • Organizing Life on Earth 277

which all organisms represented in the diagram descend from. When two lineages stem from the same branch point,
they are called sister taxa, for example the two species of orangutans. A branch point with more than two groups
illustrates a situation for which scientists have not definitively determined relationships. An example is illustrated by
the three branches leading to the gorilla subspecies; their exact relationships are not yet understood. It is important
to note that sister taxa share an ancestor, which does not mean that one taxon evolved from the other. The branch
point, or split, represents a common ancestor that existed in the past, but that no longer exists. Humans did not
evolve from chimpanzees (nor did chimpanzees evolve from humans) although they are our closest living relatives.
Both humans and chimpanzees evolved from a common ancestor that lived, scientists believe, six million years ago
and looked different from both modern chimpanzees and modern humans.

FIGURE 12.4 A phylogenetic tree is rooted and shows how different organisms, in this case the species and subspecies of living apes,
evolved from a common ancestor.

The branch points and the branches in phylogenetic tree structure also imply evolutionary change. Sometimes the
significant character changes are identified on a branch or branch point. For example, in Figure 12.5, the branch
point that gives rise to the mammal and reptile lineage from the frog lineage shows the origin of the amniotic egg
character. Also the branch point that gives rise to organisms with legs is indicated at the common ancestor of
mammals, reptiles, amphibians, and jawed fishes.

FIGURE 12.5 This phylogenetic tree is rooted by an organism that lacked a vertebral column. At each branch point, organisms with different
characters are placed in different groups.

LINK TO LEARNING
This interactive exercise (http://openstax.org/l/tree_of_life3) allows you to explore the evolutionary relationships
among species.

Limitations of Phylogenetic Trees

It is easy to assume that more closely related organisms look more alike, and while this is often the case, it is not
always true. If two closely related lineages evolved under significantly different surroundings or after the evolution
of a major new adaptation, they may look quite different from each other, even more so than other groups that are
278 12 • Diversity of Life

not as closely related. For example, the phylogenetic tree in Figure 12.5 shows that lizards and rabbits both have
amniotic eggs, whereas salamanders (within the frog lineage) do not; yet on the surface, lizards and salamanders
appear more similar than the lizards and rabbits.

Another aspect of phylogenetic trees is that, unless otherwise indicated, the branches do not show length of time,
they show only the order in time of evolutionary events. In other words, a long branch does not necessarily mean
more time passed, nor does a short branch mean less time passed— unless specified on the diagram. For example,
in Figure 12.5, the tree does not indicate how much time passed between the evolution of amniotic eggs and hair.
What the tree does show is the order in which things took place. Again using Figure 12.5, the tree shows that the
oldest trait is the vertebral column, followed by hinged jaws, and so forth. Remember that any phylogenetic tree is a
part of the greater whole, and similar to a real tree, it does not grow in only one direction after a new branch
develops. So, for the organisms in Figure 12.5, just because a vertebral column evolved does not mean that
invertebrate evolution ceased, it only means that a new branch formed. Also, groups that are not closely related, but
evolve under similar conditions, may appear more similar to each other than to a close relative.

12.2 Determining Evolutionary Relationships

LEARNING OBJECTIVES
By the end of this section, you will be able to:
• Compare homologous and analogous traits
• Discuss the purpose of cladistics

Scientists collect information that allows them to make evolutionary connections between organisms. Similar to
detective work, scientists must use evidence to uncover the facts. In the case of phylogeny, evolutionary
investigations focus on two types of evidence: morphologic (form and function) and genetic.

Two Measures of Similarity

Organisms that share similar physical features and genetic sequences tend to be more closely related than those
that do not. Features that overlap both morphologically and genetically are referred to as homologous structures;
the similarities stem from common evolutionary paths. For example, as shown in Figure 12.6, the bones in the wings
of bats and birds, the arms of humans, and the foreleg of a horse are homologous structures. Notice the structure is
not simply a single bone, but rather a grouping of several bones arranged in a similar way in each organism even
though the elements of the structure may have changed shape and size.

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 12.2 • Determining Evolutionary Relationships 279

FIGURE 12.6 Bat and bird wings, the foreleg of a horse, the flipper of a whale, and the arm of a human are homologous structures,
indicating that bats, birds, horses, whales, and humans share a common evolutionary past. (credit a photo: modification of work by Steve
Hillebrand, USFWS; credit b photo: modification of work by U.S. BLM; credit c photo: modification of work by Virendra Kankariya; credit d
photo: modification of work by Russian Gov./Wikimedia Commons)

Misleading Appearances
Some organisms may be very closely related, even though a minor genetic change caused a major morphological
difference to make them look quite different. For example, chimpanzees and humans, the skulls of which are shown
1
in Figure 12.7 are very similar genetically, sharing 99 percent of their genes. However, chimpanzees and humans
show considerable anatomical differences, including the degree to which the jaw protrudes in the adult and the
relative lengths of our arms and legs.

1 Gibbons, A. (2012, June 13). Science Now. Retrieved from http://news.sciencemag.org/sciencenow/2012/06/bonobo-genome-

280 12 • Diversity of Life

FIGURE 12.7 (a) The chimpanzee jaw protrudes to a much greater degree than (b) the human jaw. (credit a: modification of work by
"Pastorius"/Wikimedia Commons)

However, unrelated organisms may be distantly related yet appear very much alike, usually because common
adaptations to similar environmental conditions evolved in both. An example is the streamlined body shapes, the
shapes of fins and appendages, and the shape of the tails in fishes and whales, which are mammals. These
structures bear superficial similarity because they are adaptations to moving and maneuvering in the same
environment—water. When a characteristic that is similar occurs by adaptive convergence (convergent evolution),
and not because of a close evolutionary relationship, it is called an analogous structure. In another example,
insects use wings to fly like bats and birds. We call them both wings because they perform the same function and
have a superficially similar form, but the embryonic origin of the two wings is completely different. The difference in
the development, or embryogenesis, of the wings in each case is a signal that insects and bats or birds do not share
a common ancestor that had a wing. The wing structures, shown in Figure 12.8 evolved independently in the two
lineages.

Similar traits can be either homologous or analogous. Homologous traits share an evolutionary path that led to the
development of that trait, and analogous traits do not. Scientists must determine which type of similarity a feature
exhibits to decipher the phylogeny of the organisms being studied.

sequenced.html

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 12.2 • Determining Evolutionary Relationships 281

FIGURE 12.8 The wing of a honey bee is similar in shape to a bird wing and a bat wing and serves the same function (flight). The bird and
bat wings are homologous structures. However, the honey bee wing has a different structure (it is made of a chitinous exoskeleton, not a
boney endoskeleton) and embryonic origin. The bee and bird or bat wing types illustrate an analogy—similar structures that do not share an
evolutionary history. (credit a photo: modification of work by U.S. BLM; credit b: modification of work by Steve Hillebrand, USFWS; credit c:
modification of work by Jon Sullivan)

LINK TO LEARNING
This website (https://openstax.org/l/relationships2) has several examples to show how appearances can be
misleading in understanding the phylogenetic relationships of organisms.

Molecular Comparisons
With the advancement of DNA technology, the area of molecular systematics, which describes the use of
information on the molecular level including DNA sequencing, has blossomed. New analysis of molecular characters
not only confirms many earlier classifications, but also uncovers previously made errors. Molecular characters can
include differences in the amino-acid sequence of a protein, differences in the individual nucleotide sequence of a
gene, or differences in the arrangements of genes. Phylogenies based on molecular characters assume that the
more similar the sequences are in two organisms, the more closely related they are. Different genes change
evolutionarily at different rates and this affects the level at which they are useful at identifying relationships. Rapidly
evolving sequences are useful for determining the relationships among closely related species. More slowly evolving
sequences are useful for determining the relationships between distantly related species. To determine the
relationships between very different species such as Eukarya and Archaea, the genes used must be very ancient,
slowly evolving genes that are present in both groups, such as the genes for ribosomal RNA. Comparing
phylogenetic trees using different sequences and finding them similar helps to build confidence in the inferred
relationships.
282 12 • Diversity of Life

Sometimes two segments of DNA in distantly related organisms randomly share a high percentage of bases in the
same locations, causing these organisms to appear closely related when they are not. For example, the fruit fly
2
shares 60 percent of its DNA with humans. In this situation, computer-based statistical algorithms have been
developed to help identify the actual relationships, and ultimately, the coupled use of both morphologic and
molecular information is more effective in determining phylogeny.

EVOLUTION CONNECTION

Why Does Phylogeny Matter?

In addition to enhancing our understanding of the evolutionary history of species, our own included, phylogenetic
analysis has numerous practical applications. Two of those applications include understanding the evolution and
3
transmission of disease and making decisions about conservation efforts. A 2010 study of MRSA (methicillin-
resistant Staphylococcus aureus), an antibiotic resistant pathogenic bacterium, traced the origin and spread of the
strain throughout the past 40 years. The study uncovered the timing and patterns in which the resistant strain
moved from its point of origin in Europe to centers of infection and evolution in South America, Asia, North America,
and Australasia. The study suggested that introductions of the bacteria to new populations occurred very few times,
perhaps only once, and then spread from that limited number of individuals. This is in contrast to the possibility that
many individuals had carried the bacteria from one place to another. This result suggests that public health officials
should concentrate on quickly identifying the contacts of individuals infected with a new strain of bacteria to control
its spread.

A second area of usefulness for phylogenetic analysis is in conservation. Biologists have argued that it is important
to protect species throughout a phylogenetic tree rather than just those from one branch of the tree. Doing this will
preserve more of the variation produced by evolution. For example, conservation efforts should focus on a single
species without sister species rather than another species that has a cluster of close sister species that recently
evolved. If the single evolutionarily distinct species goes extinct a disproportionate amount of variation from the tree
4
will be lost compared to one species in the cluster of closely related species. A study published in 2007 made
recommendations for conservation of mammal species worldwide based on how evolutionarily distinct and at risk of
extinction they are. The study found that their recommendations differed from priorities based on simply the level of
extinction threat to the species. The study recommended protecting some threatened and valued large mammals
such as the orangutans, the giant and lesser pandas, and the African and Asian elephants. But they also found that
some much lesser known species should be protected based on how evolutionary distinct they are. These include a
number of rodents, bats, shrews and hedgehogs. In addition there are some critically endangered species that did
not rate as very important in evolutionary distinctiveness including species of deer mice and gerbils. While many
criteria affect conservation decisions, preserving phylogenetic diversity provides an objective way to protect the full
range of diversity generated by evolution.

Building Phylogenetic Trees

How do scientists construct phylogenetic trees? Presently, the most accepted method for constructing phylogenetic
trees is a method called cladistics. This method sorts organisms into clades, groups of organisms that are most
closely related to each other and the ancestor from which they descended. For example, in Figure 12.9, all of the
organisms in the shaded region evolved from a single ancestor that had amniotic eggs. Consequently, all of these
organisms also have amniotic eggs and make a single clade, also called a monophyletic group. Clades must include
the ancestral species and all of the descendants from a branch point.

2 Background on comparative genomic analysis. (2002, December). Retrieved from http://www.genome.gov/10005835

3 Harris, S.R. et al. 2010. Evolution of MRSA during hospital transmission and intercontinental spread. Science 327:469–474.
4 Isaac NJ, Turvey ST, Collen B, Waterman C, Baillie JE (2007) Mammals on the EDGE: Conservation Priorities Based on Threat and
Phylogeny. PLoS ONE 2(3): e296. doi:10.1371/journal.pone.0000296

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 12.2 • Determining Evolutionary Relationships 283

VISUAL CONNECTION

FIGURE 12.9 Lizards, rabbits, and humans all descend from a common ancestor in which the amniotic egg evolved. Thus, lizards, rabbits,
and humans all belong to the clade Amniota. Vertebrata is a larger clade that also includes fish and lamprey.

Which animals in this figure belong to a clade that includes animals with hair? Which evolved first: hair or the
amniotic egg?

Clades can vary in size depending on which branch point is being referenced. The important factor is that all of the
organisms in the clade or monophyletic group stem from a single point on the tree. This can be remembered
because monophyletic breaks down into “mono,” meaning one, and “phyletic,” meaning evolutionary relationship.

Shared Characteristics
Cladistics rests on three assumptions. The first is that living things are related by descent from a common ancestor,
which is a general assumption of evolution. The second is that speciation occurs by splits of one species into two,
never more than two at a time, and essentially at one point in time. This is somewhat controversial, but is acceptable
to most biologists as a simplification. The third assumption is that traits change enough over time to be considered
to be in a different state .It is also assumed that one can identify the actual direction of change for a state. In other
words, we assume that an amniotic egg is a later character state than non-amniotic eggs. This is called the polarity
of the character change. We know this by reference to a group outside the clade: for example, insects have non-
amniotic eggs; therefore, this is the older or ancestral character state. Cladistics compares ingroups and outgroups.
An ingroup (lizard, rabbit and human in our example) is the group of taxa being analyzed. An outgroup (lancelet,
lamprey and fish in our example) is a species or group of species that diverged before the lineage containing the
group(s) of interest. By comparing ingroup members to each other and to the outgroup members, we can determine
which characteristics are evolutionary modifications determining the branch points of the ingroup’s phylogeny.

If a characteristic is found in all of the members of a group, it is a shared ancestral character because there has
been no change in the trait during the descent of each of the members of the clade. Although these traits appear
interesting because they unify the clade, in cladistics they are considered not helpful when we are trying to
determine the relationships of the members of the clade because every member is the same. In contrast, consider
the amniotic egg characteristic of Figure 12.9. Only some of the organisms have this trait, and to those that do, it is
called a shared derived character because this trait changed at some point during descent. This character does tell
us about the relationships among the members of the clade; it tells us that lizards, rabbits, and humans group more
closely together than any of these organisms do with fish, lampreys, and lancelets.

A sometimes confusing aspect of “ancestral” and “derived” characters is that these terms are relative. The same
trait could be either ancestral or derived depending on the diagram being used and the organisms being compared.
Scientists find these terms useful when distinguishing between clades during the building of phylogenetic trees, but
it is important to remember that their meaning depends on context.

Choosing the Right Relationships

Constructing a phylogenetic tree, or cladogram, from the character data is a monumental task that is usually left up
to a computer. The computer draws a tree such that all of the clades share the same list of derived characters. But
there are other decisions to be made, for example, what if a species presence in a clade is supported by all of the
284 12 • Diversity of Life

shared derived characters for that clade except one? One conclusion is that the trait evolved in the ancestor, but
then changed back in that one species. Also a character state that appears in two clades must be assumed to have
evolved independently in those clades. These inconsistencies are common in trees drawn from character data and
complicate the decision-making process about which tree most closely represents the real relationships among the
taxa.

To aid in the tremendous task of choosing the best tree, scientists often use a concept called maximum parsimony,
which means that events occurred in the simplest, most obvious way. This means that the “best” tree is the one
with the fewest number of character reversals, the fewest number of independent character changes, and the
fewest number of character changes throughout the tree. Computer programs search through all of the possible
trees to find the small number of trees with the simplest evolutionary pathways. Starting with all of the homologous
traits in a group of organisms, scientists can determine the order of evolutionary events of which those traits
occurred that is the most obvious and simple.

LINK TO LEARNING
Practice Parsimony: Go to this website (http://openstax.org/l/parsimony2) to learn how maximum parsimony is used
to create phylogenetic trees (be sure to continue to the second page).

These tools and concepts are only a few of the strategies scientists use to tackle the task of revealing the
evolutionary history of life on Earth. Recently, newer technologies have uncovered surprising discoveries with
unexpected relationships, such as the fact that people seem to be more closely related to fungi than fungi are to
plants. Sound unbelievable? As the information about DNA sequences grows, scientists will become closer to
mapping the evolutionary history of all life on Earth.

Access for free at openstax.org

 12 • Key Terms 285

Key Terms
analogous structure a character found in two taxa relationships
that looks similar because of convergent evolution, monophyletic group (also, clade) organisms that
not because of descent from a common ancestor share a single ancestor
binomial nomenclature a system of two-part order the category in the taxonomic classification
scientific names for an organism, which includes system that falls within class and includes families
genus and species names phylogenetic tree diagram used to reflect the
branch point a point on a phylogenetic tree where a evolutionary relationships between organisms or
single lineage splits to distinct new ones groups of organisms
clade a group of taxa with the same set of shared phylogeny evolutionary history and relationship of an
derived characters, including an ancestral species organism or group of organisms
and all its descendants phylum the category in the taxonomic classification
cladistics a method used to organize homologous system that falls within kingdom and includes
traits to describe phylogenies using common classes
descendent as the primary criterion used to classify rooted describing a phylogenetic tree with a single
organisms ancestral lineage to which all organisms
class the category in the taxonomic classification represented in the diagram relate
system that falls within phylum and includes orders shared ancestral character a character on a
domain the highest level category in the classification phylogenetic branch that is shared by a particular
system and that includes all taxonomic clade
classifications below it; it is the most inclusive taxon shared derived character a character on a
family the category in the taxonomic classification phylogenetic tree that is shared only by a certain
system that falls within order and includes genera clade of organisms
genus the category in the taxonomic classification sister taxa two lineages that diverged from the same
system that falls within family and includes species; branch point
the first part of the scientific name species the most specific category of classification
kingdom the category in the taxonomic classification systematics the science of determining the
system that falls within domain and includes phyla evolutionary relationships of organisms
maximum parsimony applying the simplest, most taxon a single level in the taxonomic classification
obvious way with the least number of steps system
molecular systematics the methods of using taxonomy the science of classifying organisms
molecular evidence to identify phylogenetic

Chapter Summary
12.1 Organizing Life on Earth character information that allows them to make
evolutionary connections between organisms. Using
Scientists continually obtain new information that
morphologic and molecular data, scientists work to
helps to understand the evolutionary history of life on
identify homologous characteristics and genes.
Earth. Each group of organisms went through its own
Similarities between organisms can stem either from
evolutionary journey, called its phylogeny. Each
shared evolutionary history (homologies) or from
organism shares relatedness with others, and based on
separate evolutionary paths (analogies). After
morphologic and genetic evidence scientists attempt to
homologous information is identified, scientists use
map the evolutionary pathways of all life on Earth.
cladistics to organize these events as a means to
Historically, organisms were organized into a
determine an evolutionary timeline. Scientists apply
taxonomic classification system. However, today many
the concept of maximum parsimony, which states that
scientists build phylogenetic trees to illustrate
the likeliest order of events is probably the simplest
evolutionary relationships and the taxonomic
shortest path. For evolutionary events, this would be
classification system is expected to reflect evolutionary
the path with the least number of major divergences
relationships.
that correlate with the evidence.
12.2 Determining Evolutionary
Relationships
To build phylogenetic trees, scientists must collect
286 12 • Visual Connection Questions

Visual Connection Questions

1. Figure 12.3 In what levels are cats and dogs 2. Figure 12.9 Which animals in this figure belong to a
considered to be part of the same group? clade that includes animals with hair? Which
evolved first: hair or the amniotic egg?

Review Questions
3. What is a phylogeny a description of? 8. Which statement about analogies is correct?
a. mutations a. They occur only as errors.
b. DNA b. They are synonymous with homologous traits.
c. evolutionary history c. They are derived by response to similar
d. organisms on Earth environmental pressures.
d. They are a form of mutation.
4. What do scientists in the field of systematics
accomplish? 9. What kind of trait is important to cladistics?
a. discover new fossil sites a. shared derived traits
b. organize and classify organisms b. shared ancestral traits
c. name new species c. analogous traits
d. communicate between field biologists d. parsimonious traits

5. Which statement about the taxonomic classification 10. What is true about organisms that are a part of the
system is correct? same clade?
a. There are more domains than kingdoms. a. They all share the same basic characteristics.
b. Kingdoms are the top category of classification. b. They evolved from a shared ancestor.
c. A phylum may be represented in more than one c. They all are on the same tree.
kingdom. d. They have identical phylogenies.
d. Species are the most specific category of
classification. 11. Which assumption of cladistics is stated
incorrectly?
6. Which best describes the relationship between a. Living things are related by descent from a
chimpanzees and humans? common ancestor.
a. chimpanzees evolved from humans b. Speciation can produce one, two, or three
b. humans evolved from chimpanzees new species.
c. chimpanzees and humans evolved from a c. Traits change from one state to another.
common ancestor d. The polarity of a character state change can
d. chimpanzees and humans belong to the same be determined.
species
12. A monophyletic group is a ________.
7. Which best describes a branch point in a a. phylogenetic tree
phylogenetic tree? b. shared derived trait
a. a hypothesis c. character state
b. new lineage d. clade
c. hybridization
d. a mating

Critical Thinking Questions

13. How does a phylogenetic tree indicate major 15. Dolphins and fish have similar body shapes. Is this
evolutionary events within a lineage? feature more likely a homologous or analogous
trait?
14. List the different levels of the taxonomic
classification system. 16. Describe maximum parsimony.

17. How does a biologist determine the polarity of a

character change?

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CHAPTER 13
Diversity of Microbes, Fungi, and
Protists

FIGURE 13.1 Living things are very diverse, from simple, single-celled bacteria to complex, multicellular organisms.
(credit "ringworm": modification of work by Dr. Lucille K. Georg, CDC; credit "Trypanosomes": modification of work by
Dr. Myron G. Schultz, CDC; credit “tree mold”: modification of work by Janice Haney Carr, Robert Simmons, CDC;
credit "coral fungus": modification of work by Cory Zanker; credit "bacterium": modification of work by Dr. David Cox,
CDC; credit "cup fungus": modification of work by "icelight"/Flickr; credit "MRSA": modification of work by Janice
Haney Carr, CDC; credit "moldy grapefruit": modification of work by Joseph Smilanick)

CHAPTER OUTLINE
13.1 Prokaryotic Diversity
13.2 Eukaryotic Origins
13.3 Protists
13.4 Fungi

INTRODUCTION Until the late twentieth century, scientists most commonly grouped living things
into five kingdoms—animals, plants, fungi, protists, and bacteria—based on several criteria, such
as absence or presence of a nucleus and other membrane-bound organelles, absence or presence
of cell walls, multicellularity, and mode of nutrition. In the late twentieth century, the pioneering
work of Carl Woese and others compared nucleotide sequences of small-subunit ribosomal RNA
(SSU rRNA), which resulted in a dramatically different way to group organisms on Earth. Based on
differences in the structure of cell membranes and in rRNA, Woese and his colleagues proposed
288 13 • Diversity of Microbes, Fungi, and Protists

that all life on Earth evolved along three lineages, called domains. The three domains are called
Bacteria, Archaea, and Eukarya.

Two of the three domains—Bacteria and Archaea—are prokaryotic, meaning that they lack both a
nucleus and true membrane-bound organelles. However, they are now considered, on the basis of
membrane structure and rRNA, to be as different from each other as they are from the third
domain, the Eukarya. Prokaryotes were the first inhabitants on Earth, perhaps appearing
approximately 3.9 billion years ago. Today they are ubiquitous—inhabiting the harshest
environments on the planet, from boiling hot springs to permanently frozen environments in
Antarctica, as well as more benign environments such as compost heaps, soils, ocean waters, and
the guts of animals (including humans). The Eukarya include the familiar kingdoms of animals,
plants, and fungi. They also include a diverse group of kingdoms formerly grouped together as
protists.

13.1 Prokaryotic Diversity

LEARNING OBJECTIVES
By the end of this section, you will be able to:
• Describe the evolutionary history of prokaryotes
• Describe the basic structure of a typical prokaryote
• Identify bacterial diseases that caused historically important plagues and epidemics
• Describe the uses of prokaryotes in food processing and bioremediation

Prokaryotes are present everywhere. They cover every imaginable surface where there is
sufficient moisture, and they live on and inside of other living things. There are more prokaryotes
inside and on the exterior of the human body than there are human cells in the body. Some
prokaryotes thrive in environments that are inhospitable for most other living things. Prokaryotes
recycle nutrients—essential substances (such as carbon and nitrogen)—and they drive the
evolution of new ecosystems, some of which are natural while others are man-made. Prokaryotes
have been on Earth since long before multicellular life appeared.

Prokaryotic Diversity
The advent of DNA sequencing provided immense insight into the relationships and origins of
prokaryotes that were not possible using traditional methods of classification. A major insight
identified two groups of prokaryotes that were found to be as different from each other as they
were from eukaryotes. This recognition of prokaryotic diversity forced a new understanding of the
classification of all life and brought us closer to understanding the fundamental relationships of all
living things, including ourselves.

Early Life on Earth

When and where did life begin? What were the conditions on Earth when life began? Prokaryotes
were the first forms of life on Earth, and they existed for billions of years before plants and animals
appeared. Earth is about 4.54 billion years old. This estimate is based on evidence from the dating
of meteorite material, since surface rocks on Earth are not as old as Earth itself. Most rocks
available on Earth have undergone geological changes that make them younger than Earth itself.
Some meteorites are made of the original material in the solar disk that formed the objects of the
solar system, and they have not been altered by the processes that altered rocks on Earth. Thus,
the age of meteorites is a good indicator of the age of the formation of Earth. The original estimate
of 4.54 billion years was obtained by Clair Patterson in 1956. His meticulous work has since been
corroborated by ages determined from other sources, all of which point to an Earth age of about
4.54 billion years.

Early Earth had a very different atmosphere than it does today. Evidence indicates that during the
first 2 billion years of Earth’s existence, the atmosphere was anoxic, meaning that there was no
oxygen. Therefore, only those organisms that can grow without oxygen—anaerobic
organisms—were able to live. Organisms that convert solar energy into chemical energy are called

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 13.1 • Prokaryotic Diversity 289

phototrophs. Phototrophic organisms that required an organic source of carbon appeared within one billion years of
the formation of Earth. Then, cyanobacteria, also known as blue-green algae, evolved from these simple
phototrophs one billion years later. Cyanobacteria are able to use carbon dioxide as a source of carbon.
Cyanobacteria (Figure 13.2) began the oxygenation of the atmosphere. The increase in oxygen concentration
allowed the evolution of other life forms.

FIGURE 13.2 This hot spring in Yellowstone National Park flows toward the foreground. Cyanobacteria in the spring are green, and as water
flows down the heat gradient, the intensity of the color increases because cell density increases. The water is cooler at the edges of the
stream than in the center, causing the edges to appear greener. (credit: Graciela Brelles-Mariño)

Before the atmosphere became oxygenated, the planet was subjected to strong radiation; thus, the first organisms
would have flourished where they were more protected, such as in ocean depths or beneath the surface of Earth. At
this time, too, strong volcanic activity was common on Earth, so it is likely that these first organisms—the first
prokaryotes—were adapted to very high temperatures. These are not the typical temperate environments in which
most life flourishes today; thus, we can conclude that the first organisms that appeared on Earth likely were able to
withstand harsh conditions.

Microbial mats may represent the earliest forms of life on Earth, and there is fossil evidence of their presence,
starting about 3.5 billion years ago. A microbial mat is a large biofilm, a multi-layered sheet of prokaryotes (Figure
13.3a), including mostly bacteria, but also archaea. Microbial mats are a few centimeters thick, and they typically
grow on moist surfaces. Their various types of prokaryotes carry out different metabolic pathways, and for this
reason, they reflect various colors. Prokaryotes in a microbial mat are held together by a gummy-like substance that
they secrete.

The first microbial mats likely obtained their energy from hydrothermal vents. A hydrothermal vent is a fissure in
Earth’s surface that releases geothermally heated water. With the evolution of photosynthesis about 3 billion years
ago, some prokaryotes in microbial mats came to use a more widely available energy source—sunlight—whereas
others were still dependent on chemicals from hydrothermal vents for food.

FIGURE 13.3 (a) This microbial mat grows over a hydrothermal vent in the Pacific Ocean. Chimneys such as the one indicated by the arrow
allow gases to escape. (b) This photo shows stromatolites that are nearly 1.5 billion years old, found in Glacier National Park, Montana.
(credit a: modification of work by Dr. Bob Embley, NOAA PMEL; credit b: modification of work by P. Carrara, NPS)
290 13 • Diversity of Microbes, Fungi, and Protists

Fossilized microbial mats represent the earliest record of life on Earth. A stromatolite is a sedimentary structure
formed when minerals are precipitated from water by prokaryotes in a microbial mat (Figure 13.3b). Stromatolites
form layered rocks made of carbonate or silicate. Although most stromatolites are artifacts from the past, there are
places on Earth where stromatolites are still forming. For example, living stromatolites have been found in the Anza-
Borrego Desert State Park in San Diego County, California. Efforts to understand the earliest microbial mats may also
have implications on the search for life elsewhere. Nora Noffke, who identified many of the features used in dating
and categorizing microbially produced sedimentary structures, emphasizes that similar formations could be used to
find evidence of life on Mars. When analyzing photos taken by the NASA Curiosity rover, Noffke showcased the
similarities between fossilized microbial mats found on the two planets.

Some prokaryotes are able to thrive and grow under conditions that would kill a plant or animal. Bacteria and
archaea that grow under extreme conditions are called extremophiles, meaning “lovers of extremes.”
Extremophiles have been found in extreme environments of all kinds, including the depths of the oceans, hot
springs, the Arctic and the Antarctic, very dry places, deep inside Earth, harsh chemical environments, and high
radiation environments. Extremophiles give us a better understanding of prokaryotic diversity and open up the
possibility of the discovery of new therapeutic drugs or industrial applications. They have also opened up the
possibility of finding life in other places in the solar system, which have harsher environments than those typically
found on Earth. Many of these extremophiles cannot survive in moderate environments.

LINK TO LEARNING
Read this transcript (https://openstax.org/l/extremophiles) of NASA scientist Richard Hoover discussing the
implications that the existence extremophiles on Earth have on the possibility of finding life on other planets in our
solar system, such as Mars.

Biofilms
Until a couple of decades ago, microbiologists thought of prokaryotes as isolated entities living apart. This model,
however, does not reflect the true ecology of prokaryotes, most of which prefer to live in communities where they
can interact. A biofilm is a microbial community held together in a gummy-textured matrix, consisting primarily of
polysaccharides secreted by the organisms, together with some proteins and nucleic acids. Biofilms grow attached
to surfaces. Some of the best-studied biofilms are composed of prokaryotes, although fungal biofilms have also
been described.

Biofilms are present almost everywhere. They cause the clogging of pipes and readily colonize surfaces in industrial
settings. They have played roles in recent, large-scale outbreaks of bacterial contamination of food. Biofilms also
colonize household surfaces, such as kitchen counters, cutting boards, sinks, and toilets.

Interactions among the organisms that populate a biofilm, together with their protective environment, make these
communities more robust than are free-living, or planktonic, prokaryotes. Overall, biofilms are very difficult to
destroy, because they are resistant to many of the common forms of sterilization.

Characteristics of Prokaryotes
There are many differences between prokaryotic and eukaryotic cells. However, all cells have four common
structures: a plasma membrane that functions as a barrier for the cell and separates the cell from its environment;
cytoplasm, a jelly-like substance inside the cell; genetic material (DNA and RNA); and ribosomes, where protein
synthesis takes place. Prokaryotes come in various shapes, but many fall into three categories: cocci (spherical),
bacilli (rod-shaped), and spirilla (spiral-shaped) (Figure 13.4).

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 13.1 • Prokaryotic Diversity 291

FIGURE 13.4 Many prokaryotes fall into three basic categories based on their shape: (a) cocci, or spherical; (b) bacilli, or rod-shaped; and
(c) spirilla, or spiral-shaped. (credit a: modification of work by Janice Haney Carr, Dr. Richard Facklam, CDC; credit c: modification of work
by Dr. David Cox, CDC; scale-bar data from Matt Russell)

The Prokaryotic Cell

Recall that prokaryotes (Figure 13.5) are unicellular organisms that lack organelles surrounded by membranes.
Therefore, they do not have a nucleus but instead have a single chromosome—a piece of circular DNA located in an
area of the cell called the nucleoid. Most prokaryotes have a cell wall lying outside the plasma membrane. The
composition of the cell wall differs significantly between the domains Bacteria and Archaea (and their cell walls also
differ from the eukaryotic cell walls found in plants and fungi.) The cell wall functions as a protective layer and is
responsible for the organism’s shape. Some other structures are present in some prokaryotic species, but not in
others. For example, the capsule found in some species enables the organism to attach to surfaces and protects it
from dehydration. Some species may also have flagella (singular, flagellum) used for locomotion, and pili (singular,
pilus) used for attachment to surfaces and to other bacteria for conjugation. Plasmids, which consist of small,
circular pieces of DNA outside of the main chromosome, are also present in many species of bacteria.

FIGURE 13.5 The features of a typical bacterium cell are shown.

Both Bacteria and Archaea are types of prokaryotic cells. They differ in the lipid composition of their cell membranes
and in the characteristics of their cell walls. Both types of prokaryotes have the same basic structures, but these are
built from different chemical components that are evidence of an ancient separation of their lineages. The archaeal
plasma membrane is chemically different from the bacterial membrane; some archaeal membranes are lipid
monolayers instead of phosopholipid bilayers.

The Cell Wall

The cell wall is a protective layer that surrounds some prokaryotic cells and gives them shape and rigidity. It is
located outside the cell membrane and prevents osmotic lysis (bursting caused by increasing volume). The chemical
compositions of the cell walls vary between Archaea and Bacteria, as well as between bacterial species. Bacterial
cell walls contain peptidoglycan, composed of polysaccharide chains cross-linked to peptides. Bacteria are divided
into two major groups: Gram-positive and Gram-negative, based on their reaction to a procedure called Gram
292 13 • Diversity of Microbes, Fungi, and Protists

staining. The different bacterial responses to the staining procedure are caused by cell wall structure. Gram-positive
organisms have a thick wall consisting of many layers of peptidoglycan. Gram-negative bacteria have a thinner cell
wall composed of a few layers of peptidoglycan and additional structures, surrounded by an outer membrane
(Figure 13.6).

VISUAL CONNECTION

FIGURE 13.6 Bacteria are divided into two major groups: Gram-positive and Gram-negative. Both groups have a cell wall composed of
peptidoglycans: In Gram-positive bacteria, the wall is thick, whereas in Gram-negative bacteria, the wall is thin. In Gram-negative bacteria,
the cell wall is surrounded by an outer membrane.

Which of the following statements is true?

a. Gram-positive bacteria have a single cell wall formed from peptidoglycan.

b. Gram-positive bacteria have an outer membrane.
c. The cell wall of Gram-negative bacteria is thick, and the cell wall of Gram-positive bacteria is thin.
d. Gram-negative bacteria have a cell wall made of peptidoglycan, while Gram-positive bacteria have a cell wall
made of phospholipids.

Archaeal cell walls do not contain peptidoglycan. There are four different types of archaeal cell walls. One type is
composed of pseudopeptidoglycan. The other three types of cell walls contain polysaccharides, glycoproteins, and
surface-layer proteins known as S-layers.

Reproduction
Reproduction in prokaryotes is primarily asexual and takes place by binary fission. Recall that the DNA of a
prokaryote exists usually as a single, circular chromosome. Prokaryotes do not undergo mitosis. Rather, the
chromosome loop is replicated, and the two resulting copies attached to the plasma membrane move apart as the
cell grows in a process called binary fission. The prokaryote, now enlarged, is pinched inward at its equator, and the
two resulting cells, which are clones, separate. Binary fission does not provide an opportunity for genetic
recombination, but prokaryotes can alter their genetic makeup in three ways.

Binary fission as a way of reproduction does not provide an opportunity for genetic recombination and increased
genetic variability. However, prokaryotes can alter their genetic makeup by three mechanisms of obtaining
exogenous DNA. In a process called transformation, the cell takes in DNA found in its environment that is shed by
other prokaryotes, alive or dead. A pathogen is an organism that causes a disease. If a nonpathogenic bacterium
takes up DNA from a pathogen and incorporates the new DNA in its own chromosome, it too may become
pathogenic. In transduction, bacteriophages, the viruses that infect bacteria, move DNA from one bacterium to
another. Archaea have a different set of viruses that infect them and translocate genetic material from one individual
to another. During conjugation, DNA is transferred from one prokaryote to another by means of a pilus that brings
the organisms into contact with one another. The DNA transferred is usually a plasmid, but parts of the chromosome
can also be moved.

Cycles of binary fission can be very rapid, on the order of minutes for some species. This short generation time
coupled with mechanisms of genetic recombination result in the rapid evolution of prokaryotes, allowing them to

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 13.1 • Prokaryotic Diversity 293

respond to environmental changes (such as the introduction of an antibiotic) very quickly.

How Prokaryotes Obtain Energy and Carbon

Prokaryotes are metabolically diverse organisms. Prokaryotes fill many niches on Earth, including being involved in
nutrient cycles such as the nitrogen and carbon cycles, decomposing dead organisms, and growing and multiplying
inside living organisms, including humans. Different prokaryotes can use different sources of energy to assemble
macromolecules from smaller molecules. Phototrophs obtain their energy from sunlight. Chemotrophs obtain their
energy from chemical compounds.

Bacterial Diseases in Humans

Devastating pathogen-borne diseases and plagues, both viral and bacterial in nature, have affected and continue to
affect humans. It is worth noting that all pathogenic prokaryotes are Bacteria; there are no known pathogenic
Archaea in humans or any other organism. Pathogenic organisms evolved alongside humans. In the past, the true
cause of these diseases was not understood, and some cultures thought that diseases were a spiritual punishment
or were mistaken about material causes. Over time, people came to realize that staying apart from afflicted persons,
improving sanitation, and properly disposing of the corpses and personal belongings of victims of illness reduced
their own chances of getting sick.

Historical Perspective
There are records of infectious diseases as far back as 3,000 B.C. A number of significant pandemics caused by
Bacteria have been documented over several hundred years. Some of the largest pandemics led to the decline of
cities and cultures. Many were zoonoses that appeared with the domestication of animals, as in the case of
tuberculosis. A zoonosis is a disease that infects animals but can be transmitted from animals to humans.

Infectious diseases remain among the leading causes of death worldwide. Their impact is less significant in many
developed countries, but they are important determiners of mortality in developing countries. The development of
antibiotics did much to lessen the mortality rates from bacterial infections, but access to antibiotics is not universal,
and the overuse of antibiotics has led to the development of resistant strains of bacteria. Public sanitation efforts
that dispose of sewage and provide clean drinking water have done as much or more than medical advances to
prevent deaths caused by bacterial infections.

In 430 B.C., the plague of Athens killed one-quarter of the Athenian troops that were fighting in the Great
Peloponnesian War. The disease killed a quarter of the population of Athens in over 4 years and weakened Athens’
dominance and power. The source of the plague may have been identified recently when researchers from the
University of Athens were able to analyze DNA from teeth recovered from a mass grave. The scientists identified
1
nucleotide sequences from a pathogenic bacterium that causes typhoid fever.

From 541 to 750 A.D., an outbreak called the plague of Justinian (likely a bubonic plague) eliminated, by some
estimates, one-quarter to one-half of the human population. The population in Europe declined by 50 percent
during this outbreak. Bubonic plague would decimate Europe more than once.

One of the most devastating pandemics was the Black Death (1346 to 1361), which is believed to have been
another outbreak of bubonic plague caused by the bacterium Yersinia pestis. This bacterium is carried by fleas living
on black rats. The Black Death reduced the world’s population from an estimated 450 million to about 350 to 375
million. Bubonic plague struck London hard again in the mid-1600s. There are still approximately 1,000 to 3,000
cases of plague globally each year. Although contracting bubonic plague before antibiotics meant almost certain
death, the bacterium responds to several types of modern antibiotics, and mortality rates from plague are now very
low.

LINK TO LEARNING
Watch a video (http://openstax.org/l/black_death2) on the modern understanding of the Black Death (bubonic

1 Papagrigorakis M. J., Synodinos P. N., Yapijakis C, “Ancient typhoid epidemic reveals possible ancestral strain of Salmonella enterica
serovar Typhi, Infect Genet Evol 7 (2007): 126-7.
294 13 • Diversity of Microbes, Fungi, and Protists

plague) in Europe during the fourteenth century.

Over the centuries, Europeans developed resistance to many infectious diseases. However, European conquerors
brought disease-causing bacteria and viruses with them when they reached the Western hemisphere, triggering
epidemics that completely devastated populations of Native Americans (who had no natural resistance to many
European diseases).

The Antibiotic Crisis

The word antibiotic comes from the Greek anti, meaning “against,” and bios, meaning “life.” An antibiotic is an
organism-produced chemical that is hostile to the growth of other organisms. Today’s news and media often
address concerns about an antibiotic crisis. Are antibiotics that were used to treat bacterial infections easily
treatable in the past becoming obsolete? Are there new “superbugs”—bacteria that have evolved to become more
resistant to our arsenal of antibiotics? Is this the beginning of the end of antibiotics? All of these questions challenge
the healthcare community.

One of the main reasons for resistant bacteria is the overuse and incorrect use of antibiotics, such as not completing
a full course of prescribed antibiotics. The incorrect use of an antibiotic results in the natural selection of resistant
forms of bacteria. The antibiotic kills most of the infecting bacteria, and therefore only the resistant forms remain.
These resistant forms reproduce, resulting in an increase in the proportion of resistant forms over non-resistant
ones.

Another problem is the excessive use of antibiotics in livestock. The routine use of antibiotics in animal feed
promotes bacterial resistance as well. In the United States, 70 percent of the antibiotics produced are fed to
animals. The antibiotics are not used to prevent disease, but to enhance production of their products.

LINK TO LEARNING
Watch an overview report (http://openstax.org/l/antibiotics2) on the problem of routine antibiotic administration to
livestock and antibiotic-resistant bacteria.

Staphylococcus aureus, often called “staph,” is a common bacterium that can live in and on the human body, which
usually is easily treatable with antibiotics. A very dangerous strain, however, has made the news over the past few
years (Figure 13.7). This strain, methicillin-resistant Staphylococcus aureus (MRSA), is resistant to many
commonly used antibiotics, including methicillin, amoxicillin, penicillin, and oxacillin. While MRSA infections have
been common among people in healthcare facilities, it is appearing more commonly in healthy people who live or
work in dense groups (like military personnel and prisoners). The Journal of the American Medical Association
reported that, among MRSA-afflicted persons in healthcare facilities, the average age is 68 years, while people with
2
“community-associated MRSA” (CA-MRSA) have an average age of 23 years.

FIGURE 13.7 This scanning electron micrograph shows methicillin-resistant Staphylococcus aureus bacteria, commonly known as MRSA.
(credit: modification of work by Janice Haney Carr, CDC; scale-bar data from Matt Russell)

2 Naimi, T. S., LeDell, K. H., Como-Sabetti, K., et al., “Comparison of community- and health care-associated methicillin-resistant
Staphylococcus aureus infection,” JAMA 290 (2003): 2976-2984, doi: 10.1001/jama.290.22.2976.

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 13.1 • Prokaryotic Diversity 295

In summary, society is facing an antibiotic crisis. Some scientists believe that after years of being protected from
bacterial infections by antibiotics, we may be returning to a time in which a simple bacterial infection could again
devastate the human population. Researchers are working on developing new antibiotics, but few are in the drug
development pipeline, and it takes many years to generate an effective and approved drug.

Foodborne Diseases
Prokaryotes are everywhere: They readily colonize the surface of any type of material, and food is not an exception.
Outbreaks of bacterial infection related to food consumption are common. A foodborne disease (colloquially called
“food poisoning”) is an illness resulting from the consumption of food contaminated with pathogenic bacteria,
viruses, or other parasites. Although the United States has one of the safest food supplies in the world, the Center
for Disease Control and Prevention (CDC) has reported that “76 million people get sick, more than 300,000 are
3
hospitalized, and 5,000 Americans die each year from foodborne illness.”

The characteristics of foodborne illnesses have changed over time. In the past, it was relatively common to hear
about sporadic cases of botulism, the potentially fatal disease produced by a toxin from the anaerobic bacterium
Clostridium botulinum. A can, jar, or package created a suitable anaerobic environment where Clostridium could
grow. Proper sterilization and canning procedures have reduced the incidence of this disease.

Most cases of foodborne illnesses are now linked to produce contaminated by animal waste. For example, there
have been serious, produce-related outbreaks associated with raw spinach in the United States and with vegetable
sprouts in Germany (Figure 13.8). The raw spinach outbreak in 2006 was produced by the bacterium E. coli strain
O157:H7. Most E. coli strains are not particularly dangerous to humans, (indeed, they live in our large intestine), but
O157:H7 is potentially fatal.

FIGURE 13.8 (a) Locally grown vegetable sprouts were the cause of a European E. coli outbreak that killed 31 people and sickened about
3,000 in 2010. (b) Escherichia coli are shown here in a scanning electron micrograph. The strain of E. coli that caused a deadly outbreak in
Germany is a new one not involved in any previous E. coli outbreaks. It has acquired several antibiotic resistance genes and specific genetic
sequences involved in aggregation ability and virulence. It has recently been sequenced. (credit b: Rocky Mountain Laboratories, NIAID,
NIH; scale-bar data from Matt Russell)

All types of food can potentially be contaminated with harmful bacteria of different species. Recent outbreaks of
Salmonella reported by the CDC occurred in foods as diverse as peanut butter, alfalfa sprouts, and eggs.

CAREER CONNECTION

Epidemiologist
Epidemiology is the study of the occurrence, distribution, and determinants of health and disease in a population. It
is, therefore, related to public health. An epidemiologist studies the frequency and distribution of diseases within
human populations and environments.

Epidemiologists collect data about a particular disease and track its spread to identify the original mode of

3 http://www.cdc.gov/ecoli/2006/september, Centers for Disease Control and Prevention, “Multi-state outbreak of E. coli O157:H7
infections from spinach,” September-October (2006).
296 13 • Diversity of Microbes, Fungi, and Protists

transmission. They sometimes work in close collaboration with historians to try to understand the way a disease
evolved geographically and over time, tracking the natural history of pathogens. They gather information from
clinical records, patient interviews, and any other available means. That information is used to develop strategies
and design public health policies to reduce the incidence of a disease or to prevent its spread. Epidemiologists also
conduct rapid investigations in case of an outbreak to recommend immediate measures to control it.

Epidemiologists typically have a graduate-level education. An epidemiologist often has a bachelor’s degree in some
field and a master’s degree in public health (MPH). Many epidemiologists are also physicians (and have an MD) or
they have a PhD in an associated field, such as biology or epidemiology.

Beneficial Prokaryotes
Not all prokaryotes are pathogenic. On the contrary, pathogens represent only a very small percentage of the
diversity of the microbial world. In fact, our life and all life on this planet would not be possible without prokaryotes.

Prokaryotes, and Food and Beverages

According to the United Nations Convention on Biological Diversity, biotechnology is “any technological application
that uses biological systems, living organisms, or derivatives thereof, to make or modify products or processes for
4
specific use.” The concept of “specific use” involves some sort of commercial application. Genetic engineering,
artificial selection, antibiotic production, and cell culture are current topics of study in biotechnology. However,
humans have used prokaryotes to create products before the term biotechnology was even coined. And some of the
goods and services are as simple as cheese, yogurt, sour cream, vinegar, cured sausage, sauerkraut, and fermented
seafood that contains both bacteria and archaea (Figure 13.9).

FIGURE 13.9 Some of the products derived from the use of prokaryotes in early biotechnology include (a) cheese, (b) salami, (c) yogurt,
and (d) fish sauce. (credit b: modification of work by Alisdair McDiarmid; credit c: modification of work by Kris Miller; credit d: modification
of work by Jane Whitney)

Cheese production began around 4,000 years ago when humans started to breed animals and process their milk.
Evidence suggests that cultured milk products, like yogurt, have existed for at least 4,000 years.

4 http://www.cbd.int/convention/articles/?a=cbd-02http://www.cbd.int/convention/articles/?a=cbd-02, United Nations Convention on

Biological Diversity, “Article 2: Use of Terms.”

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 13.1 • Prokaryotic Diversity 297

Using Prokaryotes to Clean up Our Planet: Bioremediation

Microbial bioremediation is the use of prokaryotes (or microbial metabolism) to remove pollutants. Bioremediation
has been used to remove agricultural chemicals (pesticides and fertilizers) that leach from soil into groundwater.
Certain toxic metals, such as selenium and arsenic compounds, can also be removed from water by bioremediation.
The reduction of to and to Se0 (metallic selenium) is a method used to remove selenium ions from
water. Mercury is an example of a toxic metal that can be removed from an environment by bioremediation. Mercury
is an active ingredient of some pesticides; it is used in industry and is also a byproduct of certain industries, such as
battery production. Mercury is usually present in very low concentrations in natural environments but it is highly
toxic because it accumulates in living tissues. Several species of bacteria can carry out the biotransformation of
toxic mercury into nontoxic forms. These bacteria, such as Pseudomonas aeruginosa, can convert Hg2+ to Hg0,
which is nontoxic to humans.

Probably one of the most useful and interesting examples of the use of prokaryotes for bioremediation purposes is
the cleanup of oil spills. The importance of prokaryotes to petroleum bioremediation has been demonstrated in
several oil spills in recent years, such as the Exxon Valdez spill in Alaska (1989) (Figure 13.10), the Prestige oil spill
in Spain (2002), the spill into the Mediterranean from a Lebanon power plant (2006,) and more recently, the BP oil
spill in the Gulf of Mexico (2010). To clean up these spills, bioremediation is promoted by adding inorganic nutrients
that help bacteria already present in the environment to grow. Hydrocarbon-degrading bacteria feed on the
hydrocarbons in the oil droplet, breaking them into inorganic compounds. Some species, such as Alcanivorax
borkumensis, produce surfactants that solubilize the oil, while other bacteria degrade the oil into carbon dioxide. In
the case of oil spills in the ocean, ongoing, natural bioremediation tends to occur, inasmuch as there are oil-
consuming bacteria in the ocean prior to the spill. Under ideal conditions, it has been reported that up to 80 percent
of the nonvolatile components in oil can be degraded within 1 year of the spill. Other oil fractions containing
aromatic and highly branched hydrocarbon chains are more difficult to remove and remain in the environment for
longer periods of time. Researchers have genetically engineered other bacteria to consume petroleum products;
indeed, the first patent application for a bioremediation application in the U.S. was for a genetically modified oil-
eating bacterium.

FIGURE 13.10 (a) Cleaning up oil after the Valdez spill in Alaska, the workers hosed oil from beaches and then used a floating boom to
corral the oil, which was finally skimmed from the water surface. Some species of bacteria are able to solubilize and degrade the oil. (b) One
of the most catastrophic consequences of oil spills is the damage to fauna. (credit a: modification of work by NOAA; credit b: modification of
work by GOLUBENKOV, NGO: Saving Taman)

Prokaryotes in and on the Body

Humans are no exception when it comes to forming symbiotic relationships with prokaryotes. We are accustomed to
thinking of ourselves as single organisms, but in reality, we are walking ecosystems. There are 10 to 100 times as
many bacterial and archaeal cells inhabiting our bodies as we have cells in our bodies. Some of these are in mutually
beneficial relationships with us, in which both the human host and the bacterium benefit, while some of the
relationships are classified as commensalism, a type of relationship in which the bacterium benefits and the human
host is neither benefited nor harmed.

Human gut flora lives in the large intestine and consists of hundreds of species of bacteria and archaea, with
different individuals containing different species mixes. The term “flora,” which is usually associated with plants, is
traditionally used in this context because bacteria were once classified as plants. The primary functions of these
prokaryotes for humans appear to be metabolism of food molecules that we cannot break down, assistance with the
298 13 • Diversity of Microbes, Fungi, and Protists

absorption of ions by the colon, synthesis of vitamin K, training of the infant immune system, maintenance of the
adult immune system, maintenance of the epithelium of the large intestine, and formation of a protective barrier
against pathogens.

The surface of the skin is also coated with prokaryotes. The different surfaces of the skin, such as the underarms,
the head, and the hands, provide different habitats for different communities of prokaryotes. Unlike with gut flora,
the possible beneficial roles of skin flora have not been well studied. However, the few studies conducted so far
have identified bacteria that produce antimicrobial compounds as probably responsible for preventing infections by
pathogenic bacteria.

As they would in any ecosystem, the organisms in the microbiome are subject to selection and evolution. Simply to
survive through changes in the human body requires a degree of adaptability and resistance. Because humans and
other animals (such as livestock) ingest more and more antibiotics, the bacteria within our bodies are becoming
resistant to those medicines. Abigail A. Salyers, who provided much of the foundational research on the human
microbiome, focused much of her early work on a type of bacteria (Bacteroides) that could not only become
resistant to antibiotics, but pass on that resistance to surrounding bacteria. Salyers was among the first researchers
to sound the alarm about the dangers of antibiotic resistance and its potential impact on health. Researchers are
actively studying the relationships between various diseases and alterations to the composition of human microbial
flora. Some of this work is being carried out by the Human Microbiome Project, funded in the United States by the
National Institutes of Health.

13.2 Eukaryotic Origins

LEARNING OBJECTIVES
By the end of this section, you will be able to:
• Describe the endosymbiotic theory
• Explain the origin of mitochondria and chloroplasts

The fossil record and genetic evidence suggest that prokaryotic cells were the first organisms on Earth. These cells
originated approximately 3.5 billion years ago, which was about 1 billion years after Earth’s formation, and were the
only life forms on the planet until eukaryotic cells emerged approximately 2.1 billion years ago. During the
prokaryotic reign, photosynthetic prokaryotes evolved that were capable of applying the energy from sunlight to
synthesize organic materials (like carbohydrates) from carbon dioxide and an electron source (such as hydrogen,
hydrogen sulfide, or water).

Photosynthesis using water as an electron donor consumes carbon dioxide and releases molecular oxygen (O2) as a
byproduct. The functioning of photosynthetic bacteria over millions of years progressively saturated Earth’s water
with oxygen and then oxygenated the atmosphere, which previously contained much greater concentrations of
carbon dioxide and much lower concentrations of oxygen. Older anaerobic prokaryotes of the era could not function
in their new, aerobic environment. Some species perished, while others survived in the remaining anaerobic
environments left on Earth. Still other early prokaryotes evolved mechanisms, such as aerobic respiration, to exploit
the oxygenated atmosphere by using oxygen to store energy contained within organic molecules. Aerobic respiration
is a more efficient way of obtaining energy from organic molecules, which contributed to the success of these
species (as evidenced by the number and diversity of aerobic organisms living on Earth today). The evolution of
aerobic prokaryotes was an important step toward the evolution of the first eukaryote, but several other
distinguishing features had to evolve as well.

Endosymbiosis
The origin of eukaryotic cells was largely a mystery until a revolutionary hypothesis was comprehensively examined
in the 1960s by Lynn Margulis. The endosymbiotic theory states that eukaryotes are a product of one prokaryotic
cell engulfing another, one living within another, and evolving together over time until the separate cells were no
longer recognizable as such. This once-revolutionary hypothesis had immediate persuasiveness and is now widely
accepted, with work progressing on uncovering the steps involved in this evolutionary process as well as the key
players. It has become clear that many nuclear eukaryotic genes and the molecular machinery responsible for
replicating and expressing those genes appear closely related to the Archaea. On the other hand, the metabolic
organelles and the genes responsible for many energy-harvesting processes had their origins in bacteria. Much

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 13.2 • Eukaryotic Origins 299

remains to be clarified about how this relationship occurred; this continues to be an exciting field of discovery in
biology. Several endosymbiotic events likely contributed to the origin of the eukaryotic cell.

Mitochondria
Eukaryotic cells may contain anywhere from one to several thousand mitochondria, depending on the cell’s level of
energy consumption. Each mitochondrion measures 1 to 10 micrometers in length and exists in the cell as a moving,
fusing, and dividing oblong spheroid (Figure 13.11). However, mitochondria cannot survive outside the cell. As the
atmosphere was oxygenated by photosynthesis, and as successful aerobic prokaryotes evolved, evidence suggests
that an ancestral cell engulfed and kept alive a free-living, aerobic prokaryote. This gave the host cell the ability to
use oxygen to release energy stored in nutrients. Several lines of evidence support that mitochondria are derived
from this endosymbiotic event. Most mitochondria are shaped like a specific group of bacteria and are surrounded
by two membranes. The mitochondrial inner membrane involves substantial infoldings or cristae that resemble the
textured outer surface of certain bacteria.

FIGURE 13.11 In this transmission electron micrograph of mitochondria in a mammalian lung cell, the cristae, infoldings of the
mitochondrial inner membrane, can be seen in cross-section. (credit: modification of work by Louisa Howard; scale-bar data from Matt
Russell)

Mitochondria divide on their own by a process that resembles binary fission in prokaryotes. Mitochondria have their
own circular DNA chromosome that carries genes similar to those expressed by bacteria. Mitochondria also have
special ribosomes and transfer RNAs that resemble these components in prokaryotes. These features all support
that mitochondria were once free-living prokaryotes.

Chloroplasts
Chloroplasts are one type of plastid, a group of related organelles in plant cells that are involved in the storage of
starches, fats, proteins, and pigments. Chloroplasts contain the green pigment chlorophyll and play a role in
photosynthesis. Genetic and morphological studies suggest that plastids evolved from the endosymbiosis of an
ancestral cell that engulfed a photosynthetic cyanobacterium. Plastids are similar in size and shape to cyanobacteria
and are enveloped by two or more membranes, corresponding to the inner and outer membranes of cyanobacteria.
Like mitochondria, plastids also contain circular genomes and divide by a process reminiscent of prokaryotic cell
division. The chloroplasts of red and green algae exhibit DNA sequences that are closely related to photosynthetic
cyanobacteria, suggesting that red and green algae are direct descendants of this endosymbiotic event.

Mitochondria likely evolved before plastids because all eukaryotes have either functional mitochondria or
mitochondria-like organelles. In contrast, plastids are only found in a subset of eukaryotes, such as terrestrial plants
and algae. One hypothesis of the evolutionary steps leading to the first eukaryote is summarized in Figure 13.12.
300 13 • Diversity of Microbes, Fungi, and Protists

FIGURE 13.12 The first eukaryote may have originated from an ancestral prokaryote that had undergone membrane proliferation,
compartmentalization of cellular function (into a nucleus, lysosomes, and an endoplasmic reticulum), and the establishment of
endosymbiotic relationships with an aerobic prokaryote and, in some cases, a photosynthetic prokaryote to form mitochondria and
chloroplasts, respectively.

The exact steps leading to the first eukaryotic cell can only be hypothesized, and some controversy exists regarding
which events actually took place and in what order. Spirochete bacteria have been hypothesized to have given rise
to microtubules, and a flagellated prokaryote may have contributed the raw materials for eukaryotic flagella and
cilia. Other scientists suggest that membrane proliferation and compartmentalization, not endosymbiotic events,
led to the development of mitochondria and plastids. However, the vast majority of studies support the
endosymbiotic hypothesis of eukaryotic evolution.

The early eukaryotes were unicellular like most protists are today, but as eukaryotes became more complex, the
evolution of multicellularity allowed cells to remain small while still exhibiting specialized functions. The ancestors
of today’s multicellular eukaryotes are thought to have evolved about 1.5 billion years ago.

13.3 Protists
LEARNING OBJECTIVES
By the end of this section, you will be able to:
• Describe the main characteristics of protists
• Describe important pathogenic species of protists
• Describe the roles of protists as food sources and as decomposers

FIGURE 13.13 Protists range from the microscopic, single-celled (a) Acanthocystis turfacea and the (b) ciliate Tetrahymena thermophila to
the enormous, multicellular (c) kelps (Chromalveolata) that extend for hundreds of feet in underwater “forests.” (credit a: modification of
work by Yuiuji Tsukii; credit b: modification of work by Richard Robinson, Public Library of Science; credit c: modification of work by Kip
Evans, NOAA; scale-bar data from Matt Russell)

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 13.3 • Protists 301

Eukaryotic organisms that did not fit the criteria for the kingdoms Animalia, Fungi, or Plantae historically were called
protists and were classified into the kingdom Protista. Protists include the single-celled eukaryotes living in pond
water (Figure 13.13), although protist species live in a variety of other aquatic and terrestrial environments, and
occupy many different niches. Not all protists are microscopic and single-celled; there exist some very large
multicellular species, such as the kelps. During the past two decades, the field of molecular genetics has
demonstrated that some protists are more related to animals, plants, or fungi than they are to other protists. For this
reason, protist lineages originally classified into the kingdom Protista have been reassigned into new kingdoms or
other existing kingdoms. The evolutionary lineages of the protists continue to be examined and debated. In the
meantime, the term “protist” still is used informally to describe this tremendously diverse group of eukaryotes. As a
collective group, protists display an astounding diversity of morphologies, physiologies, and ecologies.

Characteristics of Protists
There are over 100,000 described living species of protists, and it is unclear how many undescribed species may
exist. Since many protists live in symbiotic relationships with other organisms and these relationships are often
species specific, there is a huge potential for undescribed protist diversity that matches the diversity of the hosts. As
the catchall term for eukaryotic organisms that are not animals, plants, fungi, or any single phylogenetically related
group, it is not surprising that few characteristics are common to all protists.

Nearly all protists exist in some type of aquatic environment, including freshwater and marine environments, damp
soil, and even snow. Several protist species are parasites that infect animals or plants. A parasite is an organism
that lives on or in another organism and feeds on it, often without killing it. A few protist species live on dead
organisms or their wastes, and contribute to their decay.

Protist Structure
The cells of protists are among the most elaborate of all cells. Most protists are microscopic and unicellular, but
some true multicellular forms exist. A few protists live as colonies that behave in some ways as a group of free-living
cells and in other ways as a multicellular organism. Still other protists are composed of enormous, multinucleate,
single cells that look like amorphous blobs of slime or, in other cases, like ferns. In fact, many protist cells are
multinucleated; in some species, the nuclei are different sizes and have distinct roles in protist cell function.

Single protist cells range in size from less than a micrometer to the 3-meter lengths of the multinucleate cells of the
seaweed Caulerpa. Protist cells may be enveloped by animal-like cell membranes or plant-like cell walls. Others are
encased in glassy silica-based shells or wound with pellicles of interlocking protein strips. The pellicle functions like
a flexible coat of armor, preventing the protist from being torn or pierced without compromising its range of motion.

The majority of protists are motile, but different types of protists have evolved varied modes of movement. Some
protists have one or more flagella, which they rotate or whip. Others are covered in rows or tufts of tiny cilia that
they beat in coordination to swim. Still others send out lobe-like pseudopodia from anywhere on the cell, anchor the
pseudopodium to a substrate, and pull the rest of the cell toward the anchor point. Some protists can move toward
light by coupling their locomotion strategy with a light-sensing organ.

How Protists Obtain Energy

Protists exhibit many forms of nutrition and may be aerobic or anaerobic. Photosynthetic protists (photoautotrophs)
are characterized by the presence of chloroplasts. Other protists are heterotrophs and consume organic materials
(such as other organisms) to obtain nutrition. Amoebas and some other heterotrophic protist species ingest
particles by a process called phagocytosis, in which the cell membrane engulfs a food particle and brings it inward,
pinching off an intracellular membranous sac, or vesicle, called a food vacuole (Figure 13.14). This vesicle then
fuses with a lysosome, and the food particle is broken down into small molecules that can diffuse into the cytoplasm
and be used in cellular metabolism. Undigested remains ultimately are expelled from the cell through exocytosis.
302 13 • Diversity of Microbes, Fungi, and Protists

FIGURE 13.14 The stages of phagocytosis include the engulfment of a food particle, the digestion of the particle using hydrolytic enzymes
contained within a lysosome, and the expulsion of undigested material from the cell.

Some heterotrophs absorb nutrients from dead organisms or their organic wastes, and others are able to use
photosynthesis or feed on organic matter, depending on conditions.

Reproduction
Protists reproduce by a variety of mechanisms. Most are capable some form of asexual reproduction, such as binary
fission to produce two daughter cells, or multiple fission to divide simultaneously into many daughter cells. Others
produce tiny buds that go on to divide and grow to the size of the parental protist. Sexual reproduction, involving
meiosis and fertilization, is common among protists, and many protist species can switch from asexual to sexual
reproduction when necessary. Sexual reproduction is often associated with periods when nutrients are depleted or
environmental changes occur. Sexual reproduction may allow the protist to recombine genes and produce new
variations of progeny that may be better suited to surviving in the new environment. However, sexual reproduction is
also often associated with cysts that are a protective, resting stage. Depending on their habitat, the cysts may be
particularly resistant to temperature extremes, desiccation, or low pH. This strategy also allows certain protists to
“wait out” stressors until their environment becomes more favorable for survival or until they are carried (such as by
wind, water, or transport on a larger organism) to a different environment because cysts exhibit virtually no cellular
metabolism.

Protist Diversity
With the advent of DNA sequencing, the relationships among protist groups and between protist groups and other
eukaryotes are beginning to become clearer. Many relationships that were based on morphological similarities are
being replaced by new relationships based on genetic similarities. Protists that exhibit similar morphological
features may have evolved analogous structures because of similar selective pressures—rather than because of
recent common ancestry. This phenomenon is called convergent evolution. It is one reason why protist classification
is so challenging. The emerging classification scheme groups the entire domain Eukaryota into six “supergroups”
that contain all of the protists as well as animals, plants, and fungi (Figure 13.15); these include the Excavata,
Chromalveolata, Rhizaria, Archaeplastida, Amoebozoa, and Opisthokonta. The supergroups are believed to be
monophyletic; all organisms within each supergroup are believed to have evolved from a single common ancestor,
and thus all members are most closely related to each other than to organisms outside that group. There is still
evidence lacking for the monophyly of some groups.

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 13.3 • Protists 303

FIGURE 13.15 Protists appear in all six eukaryotic supergroups.

Human Pathogens
Many protists are pathogenic parasites that must infect other organisms to survive and propagate. Protist parasites
include the causative agents of malaria, African sleeping sickness, and waterborne gastroenteritis in humans. Other
protist pathogens prey on plants, effecting massive destruction of food crops.

Plasmodium Species
Members of the genus Plasmodium must infect a mosquito and a vertebrate to complete their life cycle. In
vertebrates, the parasite develops in liver cells and goes on to infect red blood cells, bursting from and destroying
the blood cells with each asexual replication cycle (Figure 13.16). Of the four Plasmodium species known to infect
humans, P. falciparum accounts for 50 percent of all malaria cases and is the primary cause of disease-related
fatalities in tropical regions of the world. In 2010, it was estimated that malaria caused between 0.5 and 1 million
deaths, mostly in African children. During the course of malaria, P. falciparum can infect and destroy more than one-
half of a human’s circulating blood cells, leading to severe anemia. In response to waste products released as the
parasites burst from infected blood cells, the host immune system mounts a massive inflammatory response with
delirium-inducing fever episodes, as parasites destroy red blood cells, spilling parasite waste into the blood stream.
P. falciparum is transmitted to humans by the African malaria mosquito, Anopheles gambiae. Techniques to kill,
304 13 • Diversity of Microbes, Fungi, and Protists

sterilize, or avoid exposure to this highly aggressive mosquito species are crucial to malaria control.

FIGURE 13.16 This light micrograph shows a 100× magnification of red blood cells infected with P. falciparum (seen as purple). (credit:
modification of work by Michael Zahniser; scale-bar data from Matt Russell)

LINK TO LEARNING
This movie (https://www.animalplanet.com/tv-shows/monsters-inside-me/videos/malaria-parasite ) depicts the
pathogenesis of Plasmodium falciparum, the causative agent of malaria.

Trypanosomes
T. brucei, the parasite that is responsible for African sleeping sickness, confounds the human immune system by
changing its thick layer of surface glycoproteins with each infectious cycle (Figure 13.17). The glycoproteins are
identified by the immune system as foreign matter, and a specific antibody defense is mounted against the parasite.
However, T. brucei has thousands of possible antigens, and with each subsequent generation, the protist switches
to a glycoprotein coating with a different molecular structure. In this way, T. brucei is capable of replicating
continuously without the immune system ever succeeding in clearing the parasite. Without treatment, African
sleeping sickness leads invariably to death because of damage it does to the nervous system. During epidemic
periods, mortality from the disease can be high. Greater surveillance and control measures have led to a reduction
in reported cases; some of the lowest numbers reported in 50 years (fewer than 10,000 cases in all of sub-Saharan
Africa) have happened since 2009.

In Latin America, another species in the genus, T. cruzi, is responsible for Chagas disease. T. cruzi infections are
mainly caused by a blood-sucking bug. The parasite inhabits heart and digestive system tissues in the chronic phase
of infection, leading to malnutrition and heart failure caused by abnormal heart rhythms. An estimated 10 million
people are infected with Chagas disease, which caused 10,000 deaths in 2008.

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 13.3 • Protists 305

FIGURE 13.17 Trypanosomes are shown in this light micrograph among red blood cells. (credit: modification of work by Myron G. Schultz,
CDC; scale-bar data from Matt Russell)

LINK TO LEARNING
This movie (https://www.animalplanet.com/tv-shows/monsters-inside-me/videos/african-sleeping-sickness)
discusses the pathogenesis of Trypanosoma brucei, the causative agent of African sleeping sickness.

Plant Parasites
Protist parasites of terrestrial plants include agents that destroy food crops. The oomycete Plasmopara viticola
parasitizes grape plants, causing a disease called downy mildew (Figure 13.18a). Grape plants infected with P.
viticola appear stunted and have discolored withered leaves. The spread of downy mildew caused the near collapse
of the French wine industry in the nineteenth century.

FIGURE 13.18 (a) The downy and powdery mildews on this grape leaf are caused by an infection of P. viticola. (b) This potato exhibits the
results of an infection with P. infestans, the potato late blight. (credit a: modification of work by David B. Langston, University of Georgia,
USDA ARS; credit b: USDA ARS)

Phytophthora infestans is an oomycete responsible for potato late blight, which causes potato stalks and stems to
decay into black slime (Figure 13.18b). Widespread potato blight caused by P. infestans precipitated the well-
known Irish potato famine in the nineteenth century that claimed the lives of approximately 1 million people and led
to the emigration from Ireland of at least 1 million more. Late blight continues to plague potato crops in certain parts
of the United States and Russia, wiping out as much as 70 percent of crops when no pesticides are applied.

Beneficial Protists
Protists play critically important ecological roles as producers particularly in the world’s oceans. They are equally
important on the other end of food webs as decomposers.

Protists as Food Sources

Protists are essential sources of nutrition for many other organisms. In some cases, as in plankton, protists are
consumed directly. Alternatively, photosynthetic protists serve as producers of nutrition for other organisms by
306 13 • Diversity of Microbes, Fungi, and Protists

carbon fixation. For instance, photosynthetic dinoflagellates called zooxanthellae pass on most of their energy to the
coral polyps that house them (Figure 13.19). In this mutually beneficial relationship, the polyps provide a protective
environment and nutrients for the zooxanthellae. The polyps secrete the calcium carbonate that builds coral reefs.
Without dinoflagellate symbionts, corals lose algal pigments in a process called coral bleaching, and they eventually
die. This explains why reef-building corals do not reside in waters deeper than 20 meters: Not enough light reaches
those depths for dinoflagellates to photosynthesize.

FIGURE 13.19 Coral polyps obtain nutrition through a symbiotic relationship with dinoflagellates.

Protists themselves and their products of photosynthesis are essential—directly or indirectly—to the survival of
organisms ranging from bacteria to mammals. As primary producers, protists feed a large proportion of the world’s
aquatic species. (On land, terrestrial plants serve as primary producers.) In fact, approximately one-quarter of the
world’s photosynthesis is conducted by protists, particularly dinoflagellates, diatoms, and multicellular algae.

Protists do not create food sources only for sea-dwelling organisms. For instance, certain anaerobic species exist in
the digestive tracts of termites and wood-eating cockroaches, where they contribute to digesting cellulose ingested
by these insects as they bore through wood. The actual enzyme used to digest the cellulose is actually produced by
bacteria living within the protist cells. The termite provides the food source to the protist and its bacteria, and the
protist and bacteria provide nutrients to the termite by breaking down the cellulose.

Agents of Decomposition
Many fungus-like protists are saprobes, organisms that feed on dead organisms or the waste matter produced by
organisms (saprophyte is an equivalent term), and are specialized to absorb nutrients from nonliving organic matter.
For instance, many types of oomycetes grow on dead animals or algae. Saprobic protists have the essential function
of returning inorganic nutrients to the soil and water. This process allows for new plant growth, which in turn
generates sustenance for other organisms along the food chain. Indeed, without saprobic species, such as protists,
fungi, and bacteria, life would cease to exist as all organic carbon became “tied up” in dead organisms.

13.4 Fungi
LEARNING OBJECTIVES
By the end of this section, you will be able to:
• List the characteristics of fungi
• Describe fungal parasites and pathogens of plants and infections in humans
• Describe the importance of fungi to the environment
• Summarize the beneficial role of fungi in food and beverage preparation and in the chemical and
pharmaceutical industry

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 13.4 • Fungi 307

FIGURE 13.20 The (a) familiar mushroom is only one type of fungus. The brightly colored fruiting bodies of this (b) coral fungus are
displayed. This (c) electron micrograph shows the spore-bearing structures of Aspergillus, a type of toxic fungi found mostly in soil and
plants. (credit a: modification of work by Chris Wee; credit b: modification of work by Cory Zanker; credit c: modification of work by Janice
Haney Carr, Robert Simmons, CDC; scale-bar data from Matt Russell)

The word fungus comes from the Latin word for mushroom. Indeed, the familiar mushrooms are fungi, but there are
many other types of fungi as well (Figure 13.20). The kingdom Fungi includes an enormous variety of living
organisms. While scientists have identified about 135,000 species of fungi, this is only a fraction of the more than
1.5 million species of fungus likely present on Earth. Edible mushrooms, yeasts, black mold, and Penicillium
notatum (the producer of the antibiotic penicillin) are all members of the kingdom Fungi, which belongs to the
domain Eukarya. As eukaryotes, a typical fungal cell contains a true nucleus and many membrane-bound organelles.

Fungi were once considered plant-like organisms; however, DNA comparisons have shown that fungi are more
closely related to animals than plants. Fungi are not capable of photosynthesis: They use complex organic
compounds as sources of energy and carbon. Some fungal organisms multiply only asexually, whereas others
undergo both asexual reproduction and sexual reproduction. Most fungi produce a large number of spores that are
disseminated by the wind. Like bacteria, fungi play an essential role in ecosystems, because they are decomposers
and participate in the cycling of nutrients by breaking down organic materials into simple molecules.

Fungi often interact with other organisms, forming mutually beneficial or mutualistic associations. Fungi also cause
serious infections in plants and animals. For example, Dutch elm disease is a particularly devastating fungal
infection that destroys many native species of elm (Ulmus spp.). The fungus infects the vascular system of the tree.
It was accidentally introduced to North America in the 1900s and decimated elm trees across the continent. Dutch
elm disease is caused by the fungus Ophiostoma ulmi. The elm bark beetle acts as a vector and transmits the
disease from tree to tree. Many European and Asiatic elms are less susceptible than American elms.

In humans, fungal infections are generally considered challenging to treat because, unlike bacteria, they do not
respond to traditional antibiotic therapy since they are also eukaryotes. These infections may prove deadly for
individuals with a compromised immune system.

Fungi have many commercial applications. The food industry uses yeasts in baking, brewing, and wine making. Many
industrial compounds are byproducts of fungal fermentation. Fungi are the source of many commercial enzymes and
antibiotics.

Cell Structure and Function

Fungi are eukaryotes and as such have a complex cellular organization. As eukaryotes, fungal cells contain a
membrane-bound nucleus. A few types of fungi have structures comparable to the plasmids (loops of DNA) seen in
bacteria. Fungal cells also contain mitochondria and a complex system of internal membranes, including the
endoplasmic reticulum and Golgi apparatus.

Fungal cells do not have chloroplasts. Although the photosynthetic pigment chlorophyll is absent, many fungi
display bright colors, ranging from red to green to black. The poisonous Amanita muscaria (fly agaric) is recognizable
by its bright red cap with white patches (Figure 13.21). Pigments in fungi are associated with the cell wall and play a
308 13 • Diversity of Microbes, Fungi, and Protists

protective role against ultraviolet radiation. Some pigments are toxic.

FIGURE 13.21 The poisonous Amanita muscaria is native to the temperate and boreal regions of North America. (credit: Christine Majul)

Like plant cells, fungal cells are surrounded by a thick cell wall; however, the rigid layers contain the complex
polysaccharides chitin and glucan and not cellulose that is used by plants. Chitin, also found in the exoskeleton of
insects, gives structural strength to the cell walls of fungi. The wall provides structural support and protects the cell
from desiccation and some predators. Fungi have plasma membranes similar to other eukaryotes, except that the
structure is stabilized by ergosterol, a steroid molecule that functions like the cholesterol found in animal cell
membranes. Most members of the kingdom Fungi are nonmotile. Flagella are produced only by the gametes in the
primitive division Chytridiomycota.

Growth and Reproduction

The vegetative body of a fungus is called a thallus and can be unicellular or multicellular. Some fungi are dimorphic
because they can go from being unicellular to multicellular depending on environmental conditions. Unicellular fungi
are generally referred to as yeasts.Saccharomyces cerevisiae (baker’s yeast) and Candida species (the agents of
thrush, a common fungal infection) are examples of unicellular fungi.

Most fungi are multicellular organisms. They display two distinct morphological stages: vegetative and reproductive.
The vegetative stage is characterized by a tangle of slender thread-like structures called hyphae (singular, hypha),
whereas the reproductive stage can be more conspicuous. A mass of hyphae is called a mycelium (Figure 13.22). It
can grow on a surface, in soil or decaying material, in a liquid, or even in or on living tissue. Although individual
hypha must be observed under a microscope, the mycelium of a fungus can be very large with some species truly
being “the fungus humongous.” The giant Armillaria ostoyae (honey mushroom) is considered the largest organism
on Earth, spreading across over 2,000 acres of underground soil in eastern Oregon; it is estimated to be at least
2,400 years old.

FIGURE 13.22 The mycelium of the fungus Neotestudina rosati can be pathogenic to humans. The fungus enters through a cut or scrape
and develops into a mycetoma, a chronic subcutaneous infection. (credit: CDC)

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 13.4 • Fungi 309

Most fungal hyphae are divided into separate cells by end walls called septa (singular, septum). In most divisions
(like plants, fungal phyla are called divisions by tradition) of fungi, tiny holes in the septa allow for the rapid flow of
nutrients and small molecules from cell to cell along the hyphae. They are described as perforated septa. The
hyphae in bread molds (which belong to the division Zygomycota) are not separated by septa. They are formed of
large cells containing many nuclei, an arrangement described as coenocytic hyphae.

Fungi thrive in environments that are moist and slightly acidic, and can grow in dark places or places exposed to
light. They vary in their oxygen requirements. Most fungi are obligate aerobes, requiring oxygen to survive. Other
species, such as the Chytridiomycota that reside in the rumen of cattle, are obligate anaerobes, meaning that they
cannot grow and reproduce in an environment with oxygen. Yeasts are intermediate: They grow best in the presence
of oxygen but can use fermentation in the absence of oxygen. The alcohol produced from yeast fermentation is used
in wine and beer production, and the carbon dioxide they produce carbonates beer and sparkling wine, and makes
bread rise.

The reproductive stage could be sexual or asexual. In both sexual and asexual reproduction, fungi produce spores
that disperse from the parent organism by either floating in the wind or hitching a ride on an animal. Fungal spores
are smaller and lighter than plant seeds, but they are not usually released as high in the air. The giant puffball
mushroom bursts open and releases trillions of spores: The huge number of spores released increases the
likelihood of spores landing in an environment that will support growth (Figure 13.23).

FIGURE 13.23 The (a) giant puffball mushroom releases (b) a cloud of spores when it reaches maturity. (credit a: modification of work by
Roger Griffith; credit b: modification of work by Pearson Scott Foresman, donated to the Wikimedia Foundation)

How Fungi Obtain Nutrition

Like animals, fungi are heterotrophs: They use complex organic compounds as a source of carbon rather than fixing
carbon dioxide from the atmosphere, as some bacteria and most plants do. In addition, fungi do not fix nitrogen
from the atmosphere. Like animals, they must obtain it from their diet. However, unlike most animals that ingest
food and then digest it internally in specialized organs, fungi perform these steps in the reverse order. Digestion
precedes ingestion. First, exoenzymes, enzymes that catalyze reactions on compounds outside of the cell, are
transported out of the hyphae where they break down nutrients in the environment. Then, the smaller molecules
produced by the external digestion are absorbed through the large surface areas of the mycelium. As with animal
cells, the fungal storage polysaccharide is glycogen rather than starch, as found in plants.

Fungi are mostly saprobes, organisms that derive nutrients from decaying organic matter. They obtain their nutrients
from dead or decomposing organic matter, mainly plant material. Fungal exoenzymes are able to break down
insoluble polysaccharides, such as the cellulose and lignin of dead wood, into readily absorbable glucose molecules.
Decomposers are important components of ecosystems, because they return nutrients locked in dead bodies to a
form that is usable for other organisms. This role is discussed in more detail later. Because of their varied metabolic
pathways, fungi fulfill an important ecological role and are being investigated as potential tools in bioremediation.
For example, some species of fungi can be used to break down diesel oil and polycyclic aromatic hydrocarbons.
Other species take up heavy metals such as cadmium and lead.

Fungal Diversity
The kingdom Fungi contains four major divisions that were established according to their mode of sexual
310 13 • Diversity of Microbes, Fungi, and Protists

reproduction. Polyphyletic, unrelated fungi that reproduce without a sexual cycle, are placed for convenience in a
fifth division, and a sixth major fungal group that does not fit well with any of the previous five has recently been
described. Not all mycologists agree with this scheme. Rapid advances in molecular biology and the sequencing of
18S rRNA (a component of ribosomes) continue to reveal new and different relationships between the various
categories of fungi.

The traditional divisions of Fungi are the Chytridiomycota (chytrids), the Zygomycota (conjugated fungi), the
Ascomycota (sac fungi), and the Basidiomycota (club fungi). An older classification scheme grouped fungi that
strictly use asexual reproduction into Deuteromycota, a group that is no longer in use. The Glomeromycota belong
to a newly described group (Figure 13.24).

FIGURE 13.24 Divisions of fungi include (a) chytrids, (b) conjugated fungi, (c) sac fungi, and (d) club fungi. (credit a: modification of work by
USDA APHIS PPQ; credit c: modification of work by "icelight"/Flickr; credit d: modification of work by Cory Zanker.)

Pathogenic Fungi
Many fungi have negative impacts on other species, including humans and the organisms they depend on for food.
Fungi may be parasites, pathogens, and, in a very few cases, predators.

Plant Parasites and Pathogens

The production of enough good-quality crops is essential to our existence. Plant diseases have ruined crops,
bringing widespread famine. Most plant pathogens are fungi that cause tissue decay and eventual death of the host
(Figure 13.25). In addition to destroying plant tissue directly, some plant pathogens spoil crops by producing potent
toxins. Fungi are also responsible for food spoilage and the rotting of stored crops. For example, the fungus
Claviceps purpurea causes ergot, a disease of cereal crops (especially of rye). Although the fungus reduces the yield
of cereals, the effects of the ergot’s alkaloid toxins on humans and animals are of much greater significance: In
animals, the disease is referred to as ergotism. The most common signs and symptoms are convulsions,
hallucination, gangrene, and loss of milk in cattle. The active ingredient of ergot is lysergic acid, which is a precursor
of the drug LSD. Smuts, rusts, and powdery or downy mildew are other examples of common fungal pathogens that
affect crops.

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 13.4 • Fungi 311

FIGURE 13.25 Some fungal pathogens include (a) green mold on grapefruit, (b) fungus on grapes, (c) powdery mildew on a zinnia, and (d)
stem rust on a sheaf of barley. Notice the brownish color of the fungus in (b) Botrytis cinerea, also referred to as the “noble rot,” which
grows on grapes and other fruit. Controlled infection of grapes by Botrytis is used to produce strong and much-prized dessert wines. (credit
a: modification of work by Scott Bauer, USDA ARS; credit b: modification of work by Stephen Ausmus, USDA ARS; credit c: modification of
work by David Marshall, USDA ARS; credit d: modification of work by Joseph Smilanick, USDA ARS)

Aflatoxins are toxic and carcinogenic compounds released by fungi of the genus Aspergillus. Periodically, harvests of
nuts and grains are tainted by aflatoxins, leading to massive recall of produce, sometimes ruining producers, and
causing food shortages in developing countries.

Animal and Human Parasites and Pathogens

Fungi can affect animals, including humans, in several ways. Fungi attack animals directly by colonizing and
destroying tissues. Humans and other animals can be poisoned by eating toxic mushrooms or foods contaminated
by fungi. In addition, individuals who display hypersensitivity to molds and spores develop strong and dangerous
allergic reactions. Fungal infections are generally very difficult to treat because, unlike bacteria, fungi are
eukaryotes. Antibiotics only target prokaryotic cells, whereas compounds that kill fungi also adversely affect the
eukaryotic animal host.

Many fungal infections (mycoses) are superficial and termed cutaneous (meaning “skin”) mycoses. They are usually
visible on the skin of the animal. Fungi that cause the superficial mycoses of the epidermis, hair, and nails rarely
spread to the underlying tissue (Figure 13.26). These fungi are often misnamed “dermatophytes” from the Greek
dermis skin and phyte plant, but they are not plants. Dermatophytes are also called “ringworms” because of the red
ring that they cause on skin (although the ring is caused by fungi, not a worm). These fungi secrete extracellular
enzymes that break down keratin (a protein found in hair, skin, and nails), causing a number of conditions such as
athlete’s foot, jock itch, and other cutaneous fungal infections. These conditions are usually treated with over-the-
counter topical creams and powders, and are easily cleared. More persistent, superficial mycoses may require
prescription oral medications.
312 13 • Diversity of Microbes, Fungi, and Protists

FIGURE 13.26 (a) Ringworm presents as a red ring on the skin. (b) Trichophyton violaceum is a fungus that causes superficial mycoses on
the scalp. (c) Histoplasma capsulatum, seen in this X-ray as speckling of light areas in the lung, is a species of Ascomycota that infects
airways and causes symptoms similar to the flu. (credit a, b: modification of work by Dr. Lucille K. Georg, CDC; credit c: modification of work
by M Renz, CDC; scale-bar data from Matt Russell)

Systemic mycoses spread to internal organs, most commonly entering the body through the respiratory system. For
example, coccidioidomycosis (valley fever) is commonly found in the southwestern United States, where the fungus
resides in the dust. Once inhaled, the spores develop in the lungs and cause signs and symptoms similar to those of
tuberculosis. Histoplasmosis (Figure 13.26c) is caused by the dimorphic fungus Histoplasma capsulatum; it causes
pulmonary infections and, in rare cases, swelling of the membranes of the brain and spinal cord. Treatment of many
fungal diseases requires the use of antifungal medications that have serious side effects.

Opportunistic mycoses are fungal infections that are either common in all environments or part of the normal biota.
They affect mainly individuals who have a compromised immune system. Patients in the late stages of AIDS suffer
from opportunistic mycoses, such as Pneumocystis, which can be life threatening. The yeast Candida spp., which is
a common member of the natural biota, can grow unchecked if the pH, the immune defenses, or the normal
population of bacteria is altered, causing yeast infections of the vagina or mouth (oral thrush).

Fungi may even take on a predatory lifestyle. In soil environments that are poor in nitrogen, some fungi resort to
predation of nematodes (small roundworms). Species of Arthrobotrys fungi have a number of mechanisms to trap
nematodes. For example, they have constricting rings within their network of hyphae. The rings swell when the
nematode touches it and closes around the body of the nematode, thus trapping it. The fungus extends specialized
hyphae that can penetrate the body of the worm and slowly digest the hapless prey.

Beneficial Fungi
Fungi play a crucial role in the balance of ecosystems. They colonize most habitats on Earth, preferring dark, moist
conditions. They can thrive in seemingly hostile environments, such as the tundra, thanks to a most successful
symbiosis with photosynthetic organisms, like lichens. Fungi are not obvious in the way that large animals or tall
trees are. Yet, like bacteria, they are major decomposers of nature. With their versatile metabolism, fungi break
down organic matter that is insoluble and would not be recycled otherwise.

Importance to Ecosystems
Food webs would be incomplete without organisms that decompose organic matter and fungi are key participants in
this process. Decomposition allows for cycling of nutrients such as carbon, nitrogen, and phosphorus back into the
environment so they are available to living things, rather than being trapped in dead organisms. Fungi are
particularly important because they have evolved enzymes to break down cellulose and lignin, components of plant
cell walls that few other organisms are able to digest, releasing their carbon content.

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 13.4 • Fungi 313

Fungi are also involved in ecologically important coevolved symbioses, both mutually beneficial and pathogenic with
organisms from the other kingdoms. Mycorrhiza, a term combining the Greek roots myco meaning fungus and rhizo
meaning root, refers to the association between vascular plant roots and their symbiotic fungi. Somewhere between
80–90 percent of all plant species have mycorrhizal partners. In a mycorrhizal association, the fungal mycelia use
their extensive network of hyphae and large surface area in contact with the soil to channel water and minerals from
the soil into the plant. In exchange, the plant supplies the products of photosynthesis to fuel the metabolism of the
fungus. Ectomycorrhizae (“outside” mycorrhiza) depend on fungi enveloping the roots in a sheath (called a mantle)
and a net of hyphae that extends into the roots between cells. In a second type, the Glomeromycota fungi form
arbuscular mycorrhiza. In these mycorrhiza, the fungi form arbuscles, a specialized highly branched hypha, which
penetrate root cells and are the sites of the metabolic exchanges between the fungus and the host plant. Orchids
rely on a third type of mycorrhiza. Orchids form small seeds without much storage to sustain germination and
growth. Their seeds will not germinate without a mycorrhizal partner (usually Basidiomycota). After nutrients in the
seed are depleted, fungal symbionts support the growth of the orchid by providing necessary carbohydrates and
minerals. Some orchids continue to be mycorrhizal throughout their lifecycle.

Lichens blanket many rocks and tree bark, displaying a range of colors and textures. Lichens are important pioneer
organisms that colonize rock surfaces in otherwise lifeless environments such as are created by glacial recession.
The lichen is able to leach nutrients from the rocks and break them down in the first step to creating soil. Lichens are
also present in mature habitats on rock surfaces or the trunks of trees. They are an important food source for
caribou. Lichens are not a single organism, but rather a fungus (usually an Ascomycota or Basidiomycota species)
living in close contact with a photosynthetic organism (an alga or cyanobacterium). The body of a lichen, referred to
as a thallus, is formed of hyphae wrapped around the green partner. The photosynthetic organism provides carbon
and energy in the form of carbohydrates and receives protection from the elements by the thallus of the fungal
partner. Some cyanobacteria fix nitrogen from the atmosphere, contributing nitrogenous compounds to the
association. In return, the fungus supplies minerals and protection from dryness and excessive light by encasing the
algae in its mycelium. The fungus also attaches the symbiotic organism to the substrate.

Fungi have evolved mutualistic associations with numerous arthropods. The association between species of
Basidiomycota and scale insects is one example. The fungal mycelium covers and protects the insect colonies. The
scale insects foster a flow of nutrients from the parasitized plant to the fungus. In a second example, leaf-cutting
ants of Central and South America literally farm fungi. They cut disks of leaves from plants and pile them up in
gardens. Fungi are cultivated in these gardens, digesting the cellulose that the ants cannot break down. Once
smaller sugar molecules are produced and consumed by the fungi, they in turn become a meal for the ants. The
insects also patrol their garden, preying on competing fungi. Both ants and fungi benefit from the association. The
fungus receives a steady supply of leaves and freedom from competition, while the ants feed on the fungi they
cultivate.

Importance to Humans
Although we often think of fungi as organisms that cause diseases and rot food, fungi are important to human life on
many levels. As we have seen, they influence the well-being of human populations on a large scale because they
help nutrients cycle in ecosystems. They have other ecosystem roles as well. For example, as animal pathogens,
fungi help to control the population of damaging pests. These fungi are very specific to the insects they attack and
do not infect other animals or plants. The potential to use fungi as microbial insecticides is being investigated, with
several species already on the market. For example, the fungus Beauveria bassiana is a pesticide that is currently
being tested as a possible biological control for the recent spread of emerald ash borer. It has been released in
Michigan, Illinois, Indiana, Ohio, West Virginia, and Maryland.

The mycorrhizal relationship between fungi and plant roots is essential for the productivity of farmland. Without the
fungal partner in the root systems, 80–90% of trees and grasses would not survive. Mycorrhizal fungal inoculants
are available as soil amendments from gardening supply stores and are promoted by supporters of organic
agriculture, but there is little evidence as to the effectiveness.

We also eat some types of fungi. Mushrooms figure prominently in the human diet. Morels, shiitake mushrooms,
chanterelles, and truffles are considered delicacies (Figure 13.27). The humble meadow mushroom, Agaricus
campestris, appears in many dishes. Molds of the genus Penicillium ripen many cheeses. They originate in the
natural environment such as the caves of Roquefort, France, where wheels of sheep milk cheese are stacked to
314 13 • Diversity of Microbes, Fungi, and Protists

capture the molds responsible for the blue veins and pungent taste of the cheese.

FIGURE 13.27 The morel mushroom is an ascomycete that is much appreciated for its delicate taste. (credit: Jason Hollinger)

Fermentation—of grains to produce beer, and of fruits to produce wine—is an ancient art that humans in most
cultures have practiced for millennia. Wild yeasts are acquired from the environment and used to ferment sugars
into CO2 and ethyl alcohol under anaerobic conditions. It is now possible to purchase isolated strains of wild yeasts
from different wine-making regions. Pasteur was instrumental in developing a reliable strain of brewer’s yeast,
Saccharomyces cerevisiae, for the French brewing industry in the late 1850s. It was one of the first examples of
biotechnology patenting. Yeast is also used to make breads that rise. The carbon dioxide they produce is
responsible for the bubbles produced in the dough that become the air pockets of the baked bread.

Many secondary metabolites of fungi are of great commercial importance. Antibiotics are naturally produced by
fungi to kill or inhibit the growth of bacteria, and limit competition in the natural environment. Valuable drugs
isolated from fungi include the immunosuppressant drug cyclosporine (which reduces the risk of rejection after
organ transplant), the precursors of steroid hormones, and ergot alkaloids used to stop bleeding. In addition, as
easily cultured eukaryotic organisms, some fungi are important model research organisms including the red bread
mold Neurospora crassa and the yeast, S. cerevisiae.

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 13 • Key Terms 315

Key Terms
Amoebozoa the eukaryotic supergroup that contains pathogenic bacteria, viruses, or other parasites that
the amoebas and slime molds contaminate food
anaerobic refers to organisms that grow without Glomeromycota a group of fungi that form symbiotic
oxygen relationships with the roots of trees
anoxic without oxygen Gram-negative describes a bacterium whose cell
Archaeplastida the eukaryotic supergroup that wall contains little peptidoglycan but has an outer
contains land plants, green algae, and red algae membrane
Ascomycota (sac fungi) a division of fungi that store Gram-positive describes a bacterium that contains
spores in a sac called ascus mainly peptidoglycan in its cell walls
basidiomycota (club fungi) a division of fungi that hydrothermal vent a fissure in Earth’s surface that
produce club shaped structures, basidia, which releases geothermally heated water
contain spores hypha a fungal filament composed of one or more
biofilm a microbial community that is held together cells
by a gummy-textured matrix lichen the close association of a fungus with a
bioremediation the use of microbial metabolism to photosynthetic alga or bacterium that benefits both
remove pollutants partners
Black Death a devastating pandemic that is believed microbial mat a multi-layered sheet of prokaryotes
to have been an outbreak of bubonic plague caused that may include bacteria and archaea
by the bacterium Yersinia pestis mold a tangle of visible mycelia with a fuzzy
botulism a disease produce by the toxin of the appearance
anaerobic bacterium Clostridium botulinum MRSA (methicillin-resistant Staphylococcus aureus) a
capsule an external structure that enables a very dangerous Staphylococcus aureus strain
prokaryote to attach to surfaces and protects it from resistant to antibiotics
dehydration mycelium a mass of fungal hyphae
Chromalveolata the eukaryotic supergroup that mycorrhiza a mutualistic association between fungi
contains the dinoflagellates, ciliates, the brown and vascular plant roots
algae, diatoms, and water molds mycosis a fungal infection
Chytridiomycota (chytrids) a primitive division of Opisthokonta the eukaryotic supergroup that
fungi that live in water and produce gametes with contains the fungi, animals, and choanoflagellates
flagella pandemic a widespread, usually worldwide, epidemic
commensalism a symbiotic relationship in which one disease
member benefits while the other member is not parasite an organism that lives on or in another
affected organism and feeds on it, often without killing it
conjugation the process by which prokaryotes move pathogen an organism, or infectious agent, that
DNA from one individual to another using a pilus causes a disease
cyanobacteria bacteria that evolved from early pellicle an outer cell covering composed of
phototrophs and oxygenated the atmosphere; also interlocking protein strips that function like a
known as blue-green algae flexible coat of armor, preventing cells from being
endosymbiosis the engulfment of one cell by another torn or pierced without compromising their range of
such that the engulfed cell survives and both cells motion
benefit; the process responsible for the evolution of peptidoglycan a material composed of
mitochondria and chloroplasts in eukaryotes polysaccharide chains cross-linked to unusual
epidemic a disease that occurs in an unusually high peptides
number of individuals in a population at the same phototroph an organism that uses energy from
time sunlight
Excavata the eukaryotic supergroup that contains plastid one of a group of related organelles in plant
flagellated single-celled organisms with a feeding cells that are involved in the storage of starches,
groove fats, proteins, and pigments
extremophile an organism that grows under extreme pseudopeptidoglycan a component of some cell
or harsh conditions walls of Archaea
foodborne disease any illness resulting from the Rhizaria the eukaryotic supergroup that contains
consumption of contaminated food, or of the organisms that move by amoeboid movement
316 13 • Chapter Summary

saprobe an organism that feeds on dead organic transformation a mechanism of genetic change in
material prokaryotes in which DNA present in the
septum the cell wall division between hyphae environment is taken into the cell and incorporated
stromatolite a layered sedimentary structure formed into the genome
by precipitation of minerals by prokaryotes in yeast a general term used to describe unicellular
microbial mats fungi
thallus a vegetative body of a fungus Zygomycota (conjugated fungi) the division of fungi
transduction the process by which a bacteriophage that form a zygote contained in a zygospore
moves DNA from one prokaryote to another

Chapter Summary
13.1 Prokaryotic Diversity immune system, nutrition, and protection from
pathogens.
Prokaryotes existed for billions of years before plants
and animals appeared. Microbial mats are thought to 13.2 Eukaryotic Origins
represent the earliest forms of life on Earth, and there
The first eukaryotes evolved from ancestral
is fossil evidence, called stromatolites, of their
prokaryotes by a process that involved membrane
presence about 3.5 billion years ago. During the first 2
proliferation, the loss of a cell wall, the evolution of a
billion years, the atmosphere was anoxic and only
cytoskeleton, and the acquisition and evolution of
anaerobic organisms were able to live. Cyanobacteria
organelles. Nuclear eukaryotic genes appear to have
began the oxygenation of the atmosphere. The
had an origin in the Archaea, whereas the energy
increase in oxygen concentration allowed the evolution
machinery of eukaryotic cells appears to be bacterial in
of other life forms.
origin. The mitochondria and plastids originated from
Prokaryotes (domains Archaea and Bacteria) are endosymbiotic events when ancestral cells engulfed an
single-celled organisms lacking a nucleus. They have a aerobic bacterium (in the case of mitochondria) and a
single piece of circular DNA in the nucleoid area of the photosynthetic bacterium (in the case of chloroplasts).
cell. Most prokaryotes have cell wall outside the The evolution of mitochondria likely preceded the
plasma membrane. Bacteria and Archaea differ in the evolution of chloroplasts. There is evidence of
compositions of their cell membranes and the secondary endosymbiotic events in which plastids
characteristics of their cell walls. appear to be the result of endosymbiosis after a
previous endosymbiotic event.
Bacterial cell walls contain peptidoglycan. Archaean
cell walls do not have peptidoglycan. Bacteria can be 13.3 Protists
divided into two major groups: Gram-positive and
Protists are extremely diverse in terms of biological
Gram-negative. Gram-positive organisms have a thick
and ecological characteristics due in large part to the
cell wall. Gram-negative organisms have a thin cell wall
fact that they are an artificial assemblage of
and an outer membrane. Prokaryotes use diverse
phylogenetically unrelated groups. Protists display
sources of energy to assemble macromolecules from
highly varied cell structures, several types of
smaller molecules. Phototrophs obtain their energy
reproductive strategies, virtually every possible type of
from sunlight, whereas chemotrophs obtain it from
nutrition, and varied habitats. Most single-celled
chemical compounds.
protists are motile, but these organisms use diverse
Infectious diseases caused by bacteria remain among structures for transportation.
the leading causes of death worldwide. The excessive
The process of classifying protists into meaningful
use of antibiotics to control bacterial infections has
groups is ongoing, but genetic data in the past 20 years
resulted in resistant forms of bacteria being selected.
have clarified many relationships that were previously
Foodborne diseases result from the consumption of
unclear or mistaken. The majority view at present is to
contaminated food, pathogenic bacteria, viruses, or
order all eukaryotes into six supergroups. The goal of
parasites that contaminate food. Prokaryotes are used
this classification scheme is to create clusters of
in human food products. Microbial bioremediation is
species that all are derived from a common ancestor.
the use of microbial metabolism to remove pollutants.
The human body contains a huge community of 13.4 Fungi
prokaryotes, many of which provide beneficial services
Fungi are eukaryotic organisms that appeared on land
such as the development and maintenance of the

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 13 • Visual Connection Questions 317

over 450 million years ago. They are heterotrophs and the body. Fungal infections are difficult to cure.
contain neither photosynthetic pigments such as
Fungi have colonized all environments on Earth but are
chlorophylls nor organelles such as chloroplasts.
most often found in cool, dark, moist places with a
Because they feed on decaying and dead matter, they
supply of decaying material. Fungi are important
are saprobes. Fungi are important decomposers and
decomposers because they are saprobes. Many
release essential elements into the environment.
successful mutualistic relationships involve a fungus
External enzymes digest nutrients that are absorbed by
and another organism. They establish complex
the body of the fungus called a thallus. A thick cell wall
mycorrhizal associations with the roots of plants.
made of chitin surrounds the cell. Fungi can be
Lichens are a symbiotic relationship between a fungus
unicellular as yeasts or develop a network of filaments
and a photosynthetic organism, usually an alga or
called a mycelium, often described as mold. Most
cyanobacterium.
species multiply by asexual and sexual reproductive
cycles, and display an alternation of generations. Fungi are important to everyday human life. Fungi are
important decomposers in most ecosystems.
The divisions of fungi are the Chytridiomycota,
Mycorrhizal fungi are essential for the growth of most
Zygomycota, Ascomycota, Basidiomycota, and
plants. Fungi, as food, play a role in human nutrition in
Glomeromycota.
the form of mushrooms and as agents of fermentation
Fungi establish parasitic relationships with plants and in the production of bread, cheeses, alcoholic
animals. Fungal diseases can decimate crops and spoil beverages, and numerous other food preparations.
food during storage. Compounds produced by fungi can Secondary metabolites of fungi are used in medicine as
be toxic to humans and other animals. Mycoses are antibiotics and anticoagulants. Fungi are used in
infections caused by fungi. Superficial mycoses affect research as model organisms for the study of
the skin, whereas systemic mycoses spread through eukaryotic genetics and metabolism.

Visual Connection Questions

1. Figure 13.6 Which of the following statements is
true?
a. Gram-positive bacteria have a single cell wall
formed from peptidoglycan.
b. Gram-positive bacteria have an outer
membrane.
c. The cell wall of Gram-negative bacteria is thick,
and the cell wall of Gram-positive bacteria is
thin.
d. Gram-negative bacteria have a cell wall made
of peptidoglycan, while Gram-positive bacteria
have a cell wall made of phospholipids.

Review Questions
2. The first forms of life on Earth were thought to 4. Which of the following consist of prokaryotic cells?
be_______. a. bacteria and fungi
a. single-celled plants b. archaea and fungi
b. prokaryotes c. protists and animals
c. insects d. bacteria and archaea
d. large animals such as dinosaurs
5. Prokaryotes stain as Gram-positive or Gram-
3. The first organisms that oxygenated the negative because of differences in the _______.
atmosphere were _______. a. cell wall
a. cyanobacteria b. cytoplasm
b. phototrophic organisms c. nucleus
c. anaerobic organisms d. chromosome
d. all of the above
318 13 • Critical Thinking Questions

6. Prokaryotes that obtain their energy from chemical 10. Protists with the capabilities to absorb nutrients
compounds are called _____. from dead organisms are called_____________.
a. phototrophs a. photoautotrophs
b. auxotrophs b. autotrophs
c. chemotrophs c. saprobes
d. lithotrophs d. heterotrophs

7. Bioremediation includes _____. 11. Which parasitic protist evades the host immune
a. the use of prokaryotes that can fix nitrogen system by altering its surface proteins with each
b. the use of prokaryotes to clean up pollutants generation?
c. the use of prokaryotes as natural fertilizers a. Paramecium caudatum
d. All of the above b. Trypanosoma brucei
c. Plasmodium falciparum
8. What event is thought to have contributed to the d. Phytophthora infestans
evolution of eukaryotes?
a. global warming 12. Which polysaccharide is usually found in the cell
b. glaciation walls of fungi?
c. volcanic activity a. starch
d. oxygenation of the atmosphere b. glycogen
c. chitin
9. Mitochondria most likely evolved from d. cellulose
_____________.
a. a photosynthetic cyanobacterium 13. What term describes the close association of a
b. cytoskeletal elements fungus with the root of a tree?
c. aerobic bacteria a. a rhizoid
d. membrane proliferation b. a lichen
c. a mycorrhiza
d. an endophyte

Critical Thinking Questions

14. Explain the reason why the imprudent and 17. How does killing Anopheles mosquitoes affect the
excessive use of antibiotics has resulted in a major Plasmodium protists?
global problem.
18. Without treatment, why does African sleeping
15. Your friend believes that prokaryotes are always sickness invariably lead to death?
detrimental and pathogenic. How would you
19. Why can superficial mycoses in humans lead to
explain to them that they are wrong?
bacterial infections?
16. Describe the hypothesized steps in the origin of
eukaryote cells.

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CHAPTER 14
Diversity of Plants

FIGURE 14.1 Plants dominate the landscape and play an integral role in human societies. (a) Palm trees grow in
tropical or subtropical climates; (b) wheat is a crop in most of the world; the flower of (c) the cotton plant produces
fibers that are woven into fabric; the potent alkaloids of (d) the beautiful opium poppy have influenced human life
both as a medicinal remedy and as a dangerously addictive drug. (credit a: modification of work by
“3BoysInSanDiego”/Wikimedia Commons”; credit b: modification of work by Stephen Ausmus, USDA ARS; credit c:
modification of work by David Nance, USDA ARS; credit d: modification of work by Jolly Janner)

CHAPTER OUTLINE
14.1 The Plant Kingdom
14.2 Seedless Plants
14.3 Seed Plants: Gymnosperms
14.4 Seed Plants: Angiosperms
320 14 • Diversity of Plants

INTRODUCTION Plants play an integral role in all aspects of life on the planet, shaping the
physical terrain, influencing the climate, and maintaining life as we know it. For millennia, human
societies have depended on plants for nutrition and medicinal compounds, and for many industrial
by-products, such as timber, paper, dyes, and textiles. Palms provide materials including rattans,
oils, and dates. Wheat is grown to feed both human and animal populations. The cotton boll flower
is harvested and its fibers transformed into clothing or pulp for paper. The showy opium poppy is
valued both as an ornamental flower and as a source of potent opiate compounds.

Current evolutionary thought holds that all plants are monophyletic: that is, descendants of a
single common ancestor. The evolutionary transition from water to land imposed severe
constraints on the ancestors of contemporary plants. Plants had to evolve strategies to avoid
drying out, to disperse reproductive cells in air, for structural support, and to filter sunlight. While
seed plants developed adaptations that allowed them to populate even the most arid habitats on
Earth, full independence from water did not happen in all plants, and most seedless plants still
require a moist environment.

14.1 The Plant Kingdom

LEARNING OBJECTIVES
By the end of this section, you will be able to:
• Describe the major characteristics of the plant kingdom
• Discuss the challenges to plant life on land
• Describe the adaptations that allowed plants to colonize land

Plants are a large and varied group of organisms. There are close to 300,000 species of
1
catalogued plants. Of these, about 260,000 are plants that produce seeds. Mosses, ferns,
conifers, and flowering plants are all members of the plant kingdom. The plant kingdom contains
mostly photosynthetic organisms; a few parasitic forms have lost the ability to photosynthesize.
The process of photosynthesis uses chlorophyll, which is located in organelles called chloroplasts.
Plants possess cell walls containing cellulose. Most plants reproduce sexually, but they also have
diverse methods of asexual reproduction. Plants exhibit indeterminate growth, meaning they do
not have a final body form, but continue to grow body mass until they die.

Plant sex cells and sex organs are classified using the same system as those of animals. Plants
reproduce through a union of two sex cells or gametes of different sizes. The larger gametes,
called eggs, are classified as female gametes; the organs that produce them, called pistils, are
classified as female organs. The smaller gametes, called sperm, are classified as male gametes;
the organs that produces them, called the stamens, are classified as male organs. In many plants,
pistils and stamens are found on the same plant body, making the plant capable of both self-
fertilization or cross-fertilization with another individual.

Plant Adaptations to Life on Land

As organisms adapt to life on land, they have to contend with several challenges in the terrestrial
environment. Water has been described as “the stuff of life.” The cell’s interior—the medium in
which most small molecules dissolve and diffuse, and in which the majority of the chemical
reactions of metabolism take place—is a watery soup. Desiccation, or drying out, is a constant
danger for an organism exposed to air. Even when parts of a plant are close to a source of water,
their aerial structures are likely to dry out. Water provides buoyancy to organisms that live in
aquatic habitats. On land, plants need to develop structural support in air—a medium that does
not give the same lift. Additionally, the male and female gametes must reach one another using
new strategies because swimming is no longer possible. Finally, both gametes and zygotes must
be protected from drying out. The successful land plants evolved strategies to deal with all of

1 A.D. Chapman (2009) Numbers of Living Species in Australia and the World. 2nd edition. A Report for the
Australian Biological Resources Study. Australian Biodiversity Information Services, Toowoomba, Australia. Available
online at http://www.environment.gov.au/biodiversity/abrs/publications/other/species-numbers/2009/
04-03-groups-plants.html.

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 14.1 • The Plant Kingdom 321

these challenges, although not all adaptations appeared at once. Some species did not move far from an aquatic
environment, whereas others left the water and went on to conquer the driest environments on Earth.

To balance these survival challenges, life on land offers several advantages. First, sunlight is abundant. On land, the
spectral quality of light absorbed by the photosynthetic pigment, chlorophyll, is not filtered out by water or
competing photosynthetic species in the water column above. Second, carbon dioxide is more readily available
because its concentration is higher in air than in water. Additionally, land plants evolved before land animals;
therefore, until dry land was colonized by animals, no predators threatened the well-being of plants. This situation
changed as animals emerged from the water and found abundant sources of nutrients in the established flora. In
turn, plants evolved strategies to deter predation: from spines and thorns to toxic chemicals.

The early land plants, like the early land animals, did not live far from an abundant source of water and developed
survival strategies to combat dryness. One of these strategies is drought tolerance. Mosses, for example, can dry out
to a brown and brittle mat, but as soon as rain makes water available, mosses will soak it up and regain their
healthy, green appearance. Another strategy is to colonize environments with high humidity where droughts are
uncommon. Ferns, an early lineage of plants, thrive in damp and cool places, such as the understory of temperate
forests. Later, plants moved away from aquatic environments using resistance to desiccation, rather than tolerance.
These plants, like the cactus, minimize water loss to such an extent they can survive in the driest environments on
Earth.

In addition to adaptations specific to life on land, land plants exhibit adaptations that were responsible for their
diversity and predominance in terrestrial ecosystems. Four major adaptations are found in many terrestrial plants:
the alternation of generations, a sporangium in which spores are formed, a gametangium that produces haploid
cells, and in vascular plants, apical meristem tissue in roots and shoots.

Alternation of Generations
Alternation of generations describes a life cycle in which an organism has both haploid and diploid multicellular
stages (Figure 14.2).

FIGURE 14.2 Alternation of generations between the haploid (1n) gametophyte and diploid (2n) sporophyte is shown. (credit: modification
of work by Peter Coxhead)

Haplontic refers to a life cycle in which there is a dominant haploid stage. Diplontic refers to a life cycle in which the
diploid stage is the dominant stage, and the haploid chromosome number is only seen for a brief time in the life
cycle during sexual reproduction. Humans are diplontic, for example. Most plants exhibit alternation of generations,
which is described as haplodiplontic: the haploid multicellular form known as a gametophyte is followed in the
development sequence by a multicellular diploid organism, the sporophyte. The gametophyte gives rise to the
gametes, or reproductive cells, by mitosis. It can be the most obvious phase of the life cycle of the plant, as in the
mosses, or it can occur in a microscopic structure, such as a pollen grain in the higher plants (the collective term for
the vascular plants). The sporophyte stage is barely noticeable in lower plants (the collective term for the plant
groups of mosses, liverworts, and hornworts). Towering trees are the diplontic phase in the lifecycles of plants such
as sequoias and pines.
322 14 • Diversity of Plants

Sporangia in the Seedless Plants

The sporophyte of seedless plants is diploid and results from syngamy or the fusion of two gametes (Figure 14.2).
The sporophyte bears the sporangia (singular, sporangium), organs that first appeared in the land plants. The term
“sporangia” literally means “spore in a vessel,” as it is a reproductive sac that contains spores. Inside the
multicellular sporangia, the diploid sporocytes, or mother cells, produce haploid spores by meiosis, which reduces
the 2n chromosome number to 1n. The spores are later released by the sporangia and disperse in the environment.
Two different types of spores are produced in land plants, resulting in the separation of sexes at different points in
the life cycle. Seedless nonvascular plants (more appropriately referred to as “seedless nonvascular plants with a
dominant gametophyte phase”) produce only one kind of spore, and are called homosporous. After germinating
from a spore, the gametophyte produces both male and female gametangia, usually on the same individual. In
contrast, heterosporous plants produce two morphologically different types of spores. The male spores are called
microspores because of their smaller size; the comparatively larger megaspores will develop into the female
gametophyte. Heterospory is observed in a few seedless vascular plants and in all seed plants.

When the haploid spore germinates, it generates a multicellular gametophyte by mitosis. The gametophyte supports
the zygote formed from the fusion of gametes and the resulting young sporophyte or vegetative form, and the cycle
begins anew (Figure 14.3 and Figure 14.4).

FIGURE 14.3 This life cycle of a fern shows alternation of generations with a dominant sporophyte stage. (credit "fern": modification of
work by Cory Zanker; credit "gametophyte": modification of work by "Vlmastra"/Wikimedia Commons)

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 14.1 • The Plant Kingdom 323

FIGURE 14.4 This life cycle of a moss shows alternation of generations with a dominant gametophyte stage. (credit: modification of work by
Mariana Ruiz Villareal)

The spores of seedless plants and the pollen of seed plants are surrounded by thick cell walls containing a tough
polymer known as sporopollenin. This substance is characterized by long chains of organic molecules related to
fatty acids and carotenoids, and gives most pollen its yellow color. Sporopollenin is unusually resistant to chemical
and biological degradation. Its toughness explains the existence of well-preserved fossils of pollen. Sporopollenin
was once thought to be an innovation of land plants; however, the green algae Coleochaetes is now known to form
spores that contain sporopollenin.

Protection of the embryo is a major requirement for land plants. The vulnerable embryo must be sheltered from
desiccation and other environmental hazards. In both seedless and seed plants, the female gametophyte provides
nutrition, and in seed plants, the embryo is also protected as it develops into the new generation of sporophyte.

Gametangia in the Seedless Plants

Gametangia (singular, gametangium) are structures on the gametophytes of seedless plants in which gametes are
produced by mitosis. The male gametangium, the antheridium, releases sperm. Many seedless plants produce
sperm equipped with flagella that enable them to swim in a moist environment to the archegonia, the female
gametangium. The embryo develops inside the archegonium as the sporophyte.

Apical Meristems
The shoots and roots of plants increase in length through rapid cell division within a tissue called the apical
meristem (Figure 14.5). The apical meristem is a cap of cells at the shoot tip or root tip made of undifferentiated
cells that continue to proliferate throughout the life of the plant. Meristematic cells give rise to all the specialized
tissues of the plant. Elongation of the shoots and roots allows a plant to access additional space and resources: light
in the case of the shoot, and water and minerals in the case of roots. A separate meristem, called the lateral
meristem, produces cells that increase the diameter of stems and tree trunks. Apical meristems are an adaptation
to allow vascular plants to grow in directions essential to their survival: upward to greater availability of sunlight,
and downward into the soil to obtain water and essential minerals.
324 14 • Diversity of Plants

FIGURE 14.5 This apple seedling is an example of a plant in which the apical meristem gives rise to new shoots and root growth.

Additional Land Plant Adaptations

As plants adapted to dry land and became independent of the constant presence of water in damp habitats, new
organs and structures made their appearance. Early land plants did not grow above a few inches off the ground, and
on these low mats, they competed for light. By evolving a shoot and growing taller, individual plants captured more
light. Because air offers substantially less support than water, land plants incorporated more rigid molecules in their
stems (and later, tree trunks). The evolution of vascular tissue for the distribution of water and solutes was a
necessary prerequisite for plants to evolve larger bodies. The vascular system contains xylem and phloem tissues.
Xylem conducts water and minerals taken from the soil up to the shoot; phloem transports food derived from
photosynthesis throughout the entire plant. The root system that evolved to take up water and minerals also
anchored the increasingly taller shoot in the soil.

In land plants, a waxy, waterproof cover called a cuticle coats the aerial parts of the plant: leaves and stems. The
cuticle also prevents intake of carbon dioxide needed for the synthesis of carbohydrates through photosynthesis.
Stomata, or pores, that open and close to regulate traffic of gases and water vapor therefore appeared in plants as
they moved into drier habitats.

Plants cannot avoid predatory animals. Instead, they synthesize a large range of poisonous secondary metabolites:
complex organic molecules such as alkaloids, whose noxious smells and unpleasant taste deter animals. These
toxic compounds can cause severe diseases and even death.

Additionally, as plants coevolved with animals, sweet and nutritious metabolites were developed to lure animals
into providing valuable assistance in dispersing pollen grains, fruit, or seeds. Plants have been coevolving with
animal associates for hundreds of millions of years (Figure 14.6).

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 14.1 • The Plant Kingdom 325

FIGURE 14.6 Plants have evolved various adaptations to life on land. (a) Early plants grew close to the ground, like this moss, to avoid
desiccation. (b) Later plants developed a waxy cuticle to prevent desiccation. (c) To grow taller, like these maple trees, plants had to evolve
new structural chemicals to strengthen their stems and vascular systems to transport water and minerals from the soil and nutrients from
the leaves. (d) Plants developed physical and chemical defenses to avoid being eaten by animals. (credit a, b: modification of work by Cory
Zanker; credit c: modification of work by Christine Cimala; credit d: modification of work by Jo Naylor)

EVOLUTION CONNECTION

Paleobotany
How organisms acquired traits that allow them to colonize new environments, and how the contemporary
ecosystem is shaped, are fundamental questions of evolution. Paleobotany addresses these questions by
specializing in the study of extinct plants. Paleobotanists analyze specimens retrieved from field studies,
reconstituting the morphology of organisms that have long disappeared. They trace the evolution of plants by
following the modifications in plant morphology, and shed light on the connection between existing plants by
identifying common ancestors that display the same traits. This field seeks to find transitional species that bridge
gaps in the path to the development of modern organisms. Fossils are formed when organisms are trapped in
sediments or environments where their shapes are preserved (Figure 14.7). Paleobotanists determine the
geological age of specimens and the nature of their environment using the geological sediments and fossil
organisms surrounding them. The activity requires great care to preserve the integrity of the delicate fossils and the
layers in which they are found.

One of the most exciting recent developments in paleobotany is the use of analytical chemistry and molecular
biology to study fossils. Preservation of molecular structures requires an environment free of oxygen, since
oxidation and degradation of material through the activity of microorganisms depend on the presence of oxygen.
One example of the use of analytical chemistry and molecular biology is in the identification of oleanane, a
compound that deters pests and which, up to this point, appears to be unique to flowering plants. Oleanane was
recovered from sediments dating from the Permian, much earlier than the current dates given for the appearance of
the first flowering plants. Fossilized nucleic acids—DNA and RNA—yield the most information. Their sequences are
analyzed and compared to those of living and related organisms. Through this analysis, evolutionary relationships
can be built for plant lineages.

Some paleobotanists are skeptical of the conclusions drawn from the analysis of molecular fossils. For one, the
chemical materials of interest degrade rapidly during initial isolation when exposed to air, as well as in further
326 14 • Diversity of Plants

manipulations. There is always a high risk of contaminating the specimens with extraneous material, mostly from
microorganisms. Nevertheless, as technology is refined, the analysis of DNA from fossilized plants will provide
invaluable information on the evolution of plants and their adaptation to an ever-changing environment.

FIGURE 14.7 This fossil of a palm leaf (Palmacites sp.) discovered in Wyoming dates to about 40 million years ago.

The Major Divisions of Land Plants

Land plants are classified into two major groups according to the absence or presence of vascular tissue, as detailed
in Figure 14.8. Plants that lack vascular tissue formed of specialized cells for the transport of water and nutrients
are referred to as nonvascular plants. The bryophytes, liverworts, mosses, and hornworts are seedless and
nonvascular, and likely appeared early in land plant evolution. Vascular plants developed a network of cells that
conduct water and solutes through the plant body. The first vascular plants appeared in the late Ordovician
(461–444 million years ago) and were probably similar to lycophytes, which include club mosses (not to be
confused with the mosses) and the pterophytes (ferns, horsetails, and whisk ferns). Lycophytes and pterophytes are
referred to as seedless vascular plants. They do not produce seeds, which are embryos with their stored food
reserves protected by a hard casing. The seed plants form the largest group of all existing plants and, hence,
dominate the landscape. Seed plants include gymnosperms, most notably conifers, which produce “naked seeds,”
and the most successful plants, the flowering plants, or angiosperms, which protect their seeds inside chambers at
the center of a flower. The walls of these chambers later develop into fruits.

FIGURE 14.8 This table shows the major divisions of plants.

14.2 Seedless Plants

LEARNING OBJECTIVES
By the end of this section, you will be able to:
• Describe the distinguishing traits of the three types of bryophytes
• Identify the new traits that first appear in seedless vascular plants
• Describe the major classes of seedless vascular plants

An incredible variety of seedless plants populates the terrestrial landscape. Mosses grow on tree trunks, and
horsetails (Figure 14.9) display their jointed stems and spindly leaves on the forest floor. Yet, seedless plants
represent only a small fraction of the plants in our environment. Three hundred million years ago, seedless plants
dominated the landscape and grew in the enormous swampy forests of the Carboniferous period. Their

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 14.2 • Seedless Plants 327

decomposing bodies created large deposits of coal that we mine today.

FIGURE 14.9 Seedless plants like these horsetails (Equisetum sp.) thrive in damp, shaded environments under the tree canopy where
dryness is a rare occurrence. (credit: Jerry Kirkhart)

Bryophytes
Bryophytes, an informal grouping of the nonvascular plants, are the closest extant relative of early terrestrial plants.
The first bryophytes most probably appeared in the Ordovician period, about 490 million years ago. Because of the
lack of lignin—the tough polymer in cell walls in the stems of vascular plants—and other resistant structures, the
likelihood of bryophytes forming fossils is rather small, though some spores made up of sporopollenin have been
discovered that have been attributed to early bryophytes. By the Silurian period (440 million years ago), however,
vascular plants had spread throughout the continents. This fact is used as evidence that nonvascular plants must
have preceded the Silurian period.

There are about 18,000 species of bryophytes, which thrive mostly in damp habitats, although some grow in
deserts. They constitute the major flora of inhospitable environments like the tundra, where their small size and
tolerance to desiccation offer distinct advantages. They do not have the specialized cells that conduct fluids found in
the vascular plants, and generally lack lignin. In bryophytes, water and nutrients circulate inside specialized
conducting cells. Although the name nontracheophyte is more accurate, bryophytes are commonly referred to as
nonvascular plants.

In a bryophyte, all the conspicuous vegetative organs belong to the haploid organism, or gametophyte. The diploid
sporophyte is barely noticeable. The gametes formed by bryophytes swim using flagella. The sporangium, the
multicellular sexual reproductive structure, is present in bryophytes. The embryo also remains attached to the
parent plant, which nourishes it. This is a characteristic of land plants.

The bryophytes are divided into three divisions (in plants, the taxonomic level “division” is used instead of phylum):
the liverworts, or Marchantiophyta; the hornworts, or Anthocerotophyta; and the mosses, or true Bryophyta.

Liverworts
Liverworts (Marchantiophyta) may be viewed as the plants most closely related to the ancestor that moved to land.
Liverworts have colonized many habitats on Earth and diversified to more than 6,000 existing species (Figure
14.10a). Some gametophytes form lobate green structures, as seen in Figure 14.10b. The shape is similar to the
lobes of the liver and, hence, provides the origin of the common name given to the division.
328 14 • Diversity of Plants

FIGURE 14.10 (a) A 1904 drawing of liverworts shows the variety of their forms. (b) A liverwort, Lunularia cruciata, displays its lobate, flat
thallus. The organism in the photograph is in the gametophyte stage.

Hornworts
The hornworts (Anthocerotophyta) have colonized a variety of habitats on land, although they are never far from a
source of moisture. There are about 100 described species of hornworts. The dominant phase of the life cycle of
hornworts is the short, blue-green gametophyte. The sporophyte is the defining characteristic of the group. It is a
long and narrow pipe-like structure that emerges from the parent gametophyte and maintains growth throughout
the life of the plant (Figure 14.11).

FIGURE 14.11 Hornworts grow a tall and slender sporophyte. (credit: modification of work by Jason Hollinger)

Mosses
More than 12,000 species of mosses have been catalogued. Their habitats vary from the tundra, where they are the
main vegetation, to the understory of tropical forests. In the tundra, their shallow rhizoids allow them to fasten to a
substrate without digging into the frozen soil. They slow down erosion, store moisture and soil nutrients, and
provide shelter for small animals and food for larger herbivores, such as the musk ox. Mosses are very sensitive to
air pollution and are used to monitor the quality of air. The sensitivity of mosses to copper salts makes these salts a
common ingredient of compounds marketed to eliminate mosses in lawns (Figure 14.12).

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 14.2 • Seedless Plants 329

FIGURE 14.12 This green feathery moss has reddish-brown sporophytes growing upward. (credit: "Lordgrunt"/Wikimedia Commons)

Vascular Plants
The vascular plants are the dominant and most conspicuous group of land plants. There are about 275,000 species
of vascular plants, which represent more than 90 percent of Earth’s vegetation. Several evolutionary innovations
explain their success and their spread to so many habitats.

Vascular Tissue: Xylem and Phloem

The first fossils that show the presence of vascular tissue are dated to the Silurian period, about 430 million years
ago. The simplest arrangement of conductive cells shows a pattern of xylem at the center surrounded by phloem.
Xylem is the tissue responsible for long-distance transport of water and minerals, the transfer of water-soluble
growth factors from the organs of synthesis to the target organs, and storage of water and nutrients.

A second type of vascular tissue is phloem, which transports sugars, proteins, and other solutes through the plant.
Phloem cells are divided into sieve elements, or conducting cells, and supportive tissue. Together, xylem and
phloem tissues form the vascular system of plants.

Roots: Support for the Plant

Roots are not well preserved in the fossil record; nevertheless, it seems that they did appear later in evolution than
vascular tissue. The development of an extensive network of roots represented a significant new feature of vascular
plants. Thin rhizoids attached the bryophytes to the substrate. Their rather flimsy filaments did not provide a strong
anchor for the plant; neither did they absorb water and nutrients. In contrast, roots, with their prominent vascular
tissue system, transfer water and minerals from the soil to the rest of the plant. The extensive network of roots that
penetrates deep in the ground to reach sources of water also stabilizes trees by acting as ballast and an anchor. The
majority of roots establish a symbiotic relationship with fungi, forming mycorrhizae. In the mycorrhizae, fungal
hyphae grow around the root and within the root around the cells, and in some instances within the cells. This
benefits the plant by greatly increasing the surface area for absorption.

Leaves, Sporophylls, and Strobili

A third adaptation marks seedless vascular plants. Accompanying the prominence of the sporophyte and the
development of vascular tissue, the appearance of true leaves improved photosynthetic efficiency. Leaves capture
more sunlight with their increased surface area.

In addition to photosynthesis, leaves play another role in the life of the plants. Pinecones, mature fronds of ferns,
and flowers are all sporophylls—leaves that were modified structurally to bear sporangia. Strobili are structures
that contain the sporangia. They are prominent in conifers and are known commonly as cones: for example, the pine
cones of pine trees.

Seedless Vascular Plants

By the Late Devonian period (385 million years ago), plants had evolved vascular tissue, well-defined leaves, and
root systems. With these advantages, plants increased in height and size. During the Carboniferous period (359–299
million years ago), swamp forests of club mosses and horsetails, with some specimens reaching more than 30
330 14 • Diversity of Plants

meters tall, covered most of the land. These forests gave rise to the extensive coal deposits that gave the
Carboniferous its name. In seedless vascular plants, the sporophyte became the dominant phase of the lifecycle.

Water is still required for fertilization of seedless vascular plants, and most favor a moist environment. Modern-day
seedless vascular plants include club mosses, horsetails, ferns, and whisk ferns.

Club Mosses
The club mosses, or Lycophyta, are the earliest group of seedless vascular plants. They dominated the landscape of
the Carboniferous period, growing into tall trees and forming large swamp forests. Today’s club mosses are
diminutive, evergreen plants consisting of a stem (which may be branched) and small leaves called microphylls
(Figure 14.13). The division Lycophyta consists of close to 1,000 species, including quillworts (Isoetales), club
mosses (Lycopodiales), and spike mosses (Selaginellales): none of which is a true moss.

FIGURE 14.13 Lycopodium clavatum is a club moss. (credit: Cory Zanker)

Horsetails
Ferns and whisk ferns belong to the division Pterophyta. A third group of plants in the Pterophyta, the horsetails, is
sometimes classified separately from ferns. Horsetails have a single genus, Equisetum. They are the survivors of a
large group of plants, known as Arthrophyta, which produced large trees and entire swamp forests in the
Carboniferous. The plants are usually found in damp environments and marshes (Figure 14.14).

FIGURE 14.14 Horsetails thrive in a marsh. (credit: Myriam Feldman)

The stem of a horsetail is characterized by the presence of joints, or nodes: hence the name Arthrophyta, which
means “jointed plant”. Leaves and branches come out as whorls from the evenly spaced rings. The needle-shaped
leaves do not contribute greatly to photosynthesis, the majority of which takes place in the green stem (Figure
14.15).

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 14.2 • Seedless Plants 331

FIGURE 14.15 Thin leaves originating at the joints are noticeable on the horsetail plant. (credit: Myriam Feldman)

Ferns and Whisk Ferns

Ferns are considered the most advanced seedless vascular plants and display characteristics commonly observed in
seed plants. Ferns form large leaves and branching roots. In contrast, whisk ferns, the psilophytes, lack both roots
and leaves, which were probably lost by evolutionary reduction. Evolutionary reduction is a process by which natural
selection reduces the size of a structure that is no longer favorable in a particular environment. Photosynthesis
takes place in the green stem of a whisk fern. Small yellow knobs form at the tip of the branch stem and contain the
sporangia. Whisk ferns have been classified outside the true ferns; however, recent comparative analysis of DNA
suggests that this group may have lost both vascular tissue and roots through evolution, and is actually closely
related to ferns.

With their large fronds, ferns are the most readily recognizable seedless vascular plants (Figure 14.16). About
12,000 species of ferns live in environments ranging from tropics to temperate forests. Although some species
survive in dry environments, most ferns are restricted to moist and shaded places. They made their appearance in
the fossil record during the Devonian period (416–359 million years ago) and expanded during the Carboniferous
period, 359–299 million years ago (Figure 14.17).

FIGURE 14.16 Some specimens of this short tree-fern species can grow very tall. (credit: Adrian Pingstone)
332 14 • Diversity of Plants

FIGURE 14.17 This chart shows the geological time scale, beginning with the Pre-Archean eon 3800 million years ago and ending with the
Quaternary period in present time. (credit: modification of work by USGS)

LINK TO LEARNING
Watch this video (https://www.youtube.com/watch?v=Fhk-Y0duNjg) illustrating the life cycle of a fern and assess
your knowledge.

CAREER CONNECTION

Landscape Designer
Looking at the well-laid gardens of flowers and fountains seen in royal castles and historic houses of Europe, it is
clear that the creators of those gardens knew more than art and design. They were also familiar with the biology of
the plants they chose. Landscape design also has strong roots in the United States’ tradition. A prime example of
early American classical design is Monticello, Thomas Jefferson’s private estate; among his many other interests,
Jefferson maintained a passion for botany. Landscape layout can encompass a small private space, like a backyard
garden; public gathering places, like Central Park in New York City; or an entire city plan, like Pierre L’Enfant’s design
for Washington, DC.

A landscape designer will plan traditional public spaces—such as botanical gardens, parks, college campuses,
gardens, and larger developments—as well as natural areas and private gardens (Figure 14.18). The restoration of
natural places encroached upon by human intervention, such as wetlands, also requires the expertise of a
landscape designer.

With such an array of required skills, a landscape designer’s education includes a solid background in botany, soil
science, plant pathology, entomology, and horticulture. Coursework in architecture and design software is also
required for the completion of the degree. The successful design of a landscape rests on an extensive knowledge of
plant growth requirements, such as light and shade, moisture levels, compatibility of different species, and
susceptibility to pathogens and pests. For example, mosses and ferns will thrive in a shaded area where fountains
provide moisture; cacti, on the other hand, would not fare well in that environment. The future growth of the
individual plants must be taken into account to avoid crowding and competition for light and nutrients. The
appearance of the space over time is also of concern. Shapes, colors, and biology must be balanced for a well-
maintained and sustainable green space. Art, architecture, and biology blend in a beautifully designed and

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 14.3 • Seed Plants: Gymnosperms 333

implemented landscape.

FIGURE 14.18 This campus garden was designed by students in the horticulture and landscaping department of the college. (credit:
Myriam Feldman)

14.3 Seed Plants: Gymnosperms

LEARNING OBJECTIVES
By the end of this section, you will be able to:
• Discuss the type of seeds produced by gymnosperms, as well as other characteristics of gymnosperms
• List the four groups of modern-day gymnosperms and provide examples of each

The first plants to colonize land were most likely closely related to modern-day mosses (bryophytes) and are
thought to have appeared about 500 million years ago. They were followed by liverworts (also bryophytes) and
primitive vascular plants, the pterophytes, from which modern ferns are derived. The life cycle of bryophytes and
pterophytes is characterized by the alternation of generations. The completion of the life cycle requires water, as the
male gametes must swim to the female gametes. The male gametophyte releases sperm, which must
swim—propelled by their flagella—to reach and fertilize the female gamete or egg. After fertilization, the zygote
matures and grows into a sporophyte, which in turn will form sporangia, or "spore vessels,” in which mother cells
undergo meiosis and produce haploid spores. The release of spores in a suitable environment will lead to
germination and a new generation of gametophytes.

The Evolution of Seed Plants

In seed plants, the evolutionary trend led to a dominant sporophyte generation, in which the larger and more
ecologically significant generation for a species is the diploid plant. At the same time, the trend led to a reduction in
the size of the gametophyte, from a conspicuous structure to a microscopic cluster of cells enclosed in the tissues of
the sporophyte. Lower vascular plants, such as club mosses and ferns, are mostly homosporous (produce only one
type of spore). In contrast, all seed plants, or spermatophytes, are heterosporous, forming two types of spores:
megaspores (female) and microspores (male). Megaspores develop into female gametophytes that produce eggs,
and microspores mature into male gametophytes that generate sperm. Because gametophyte maturation depends
on water and nutrient supply from the dominant sporophyte tissue, they are not free-living, as are the gametophytes
of seedless vascular plants. Heterosporous seedless plants are seen as the evolutionary forerunners of seed plants.

Seeds and pollen—two adaptations to drought—distinguish seed plants from other (seedless) vascular plants. Both
adaptations were critical to the colonization of land. Fossils place the earliest distinct seed plants at about 350
million years ago. The earliest reliable record of gymnosperms dates their appearance to the Carboniferous period
(359–299 million years ago). Gymnosperms were preceded by the progymnosperms (“first naked seed plants”).
This was a transitional group of plants that superficially resembled conifers (“cone bearers”) because they produced
wood from the secondary growth of the vascular tissues; however, they still reproduced like ferns, releasing spores
to the environment. In the Mesozoic era (251–65.5 million years ago), gymnosperms dominated the landscape.
Angiosperms took over by the middle of the Cretaceous period (145.5–65.5 million years ago) in the late Mesozoic
era, and have since become the most abundant plant group in most terrestrial biomes.
334 14 • Diversity of Plants

The two innovative structures of pollen and seed allowed seed plants to break their dependence on water for
reproduction and development of the embryo, and to conquer dry land. The pollen grains carry the male gametes of
the plant. The small haploid (1n) cells are encased in a protective coat that prevents desiccation (drying out) and
mechanical damage. Pollen can travel far from the sporophyte that bore it, spreading the plant’s genes and avoiding
competition with other plants. The seed offers the embryo protection, nourishment and a mechanism to maintain
dormancy for tens or even thousands of years, allowing it to survive in a harsh environment and ensuring
germination when growth conditions are optimal. Seeds allow plants to disperse the next generation through both
space and time. With such evolutionary advantages, seed plants have become the most successful and familiar
group of plants.

Gymnosperms
Gymnosperms (“naked seed”) are a diverse group of seed plants and are paraphyletic. Paraphyletic groups do not
include descendants of a single common ancestor. Gymnosperm characteristics include naked seeds, separate
female and male gametes, pollination by wind, and tracheids, which transport water and solutes in the vascular
system.

Life Cycle of a Conifer

Pine trees are conifers and carry both male and female sporophylls on the same plant. Like all gymnosperms, pines
are heterosporous and produce male microspores and female megaspores. In the male cones, or staminate cones,
the microsporocytes give rise to microspores by meiosis. The microspores then develop into pollen grains. Each
pollen grain contains two cells: one generative cell that will divide into two sperm, and a second cell that will
become the pollen tube cell. In the spring, pine trees release large amounts of yellow pollen, which is carried by the
wind. Some gametophytes will land on a female cone. The pollen tube grows from the pollen grain slowly, and the
generative cell in the pollen grain divides into two sperm cells by mitosis. One of the sperm cells will finally unite its
haploid nucleus with the haploid nucleus of an egg cell in the process of fertilization.

Female cones, or ovulate cones, contain two ovules per scale. One megasporocyte undergoes meiosis in each
ovule. Only a single surviving haploid cell will develop into a female multicellular gametophyte that encloses an egg.
On fertilization, the zygote will give rise to the embryo, which is enclosed in a seed coat of tissue from the parent
plant. Fertilization and seed development is a long process in pine trees—it may take up to two years after
pollination. The seed that is formed contains three generations of tissues: the seed coat that originates from the
parent plant tissue, the female gametophyte that will provide nutrients, and the embryo itself. Figure 14.19
illustrates the life cycle of a conifer.

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 14.3 • Seed Plants: Gymnosperms 335

VISUAL CONNECTION

FIGURE 14.19 This image shows the lifecycle of a conifer.

At what stage does the diploid zygote form?

a. when the female cone begins to bud from the tree

b. when the sperm nucleus and the egg nucleus fuse
c. when the seeds drop from the tree
d. when the pollen tube begins to grow

LINK TO LEARNING
Watch this video (http://openstax.org/l/gymnosperm) to see the process of seed production in gymnosperms.

Diversity of Gymnosperms
Modern gymnosperms are classified into four major divisions and comprise about 1,000 described species.
Coniferophyta, Cycadophyta, and Ginkgophyta are similar in their production of secondary cambium (cells that
generate the vascular system of the trunk or stem) and their pattern of seed development, but are not closely
related phylogenetically to each other. Gnetophyta are considered the closest group to angiosperms because they
produce true xylem tissue that contains both tracheids and vessel elements.

Conifers
Conifers are the dominant phylum of gymnosperms, with the most variety of species. Most are tall trees that usually
bear scale-like or needle-like leaves. The thin shape of the needles and their waxy cuticle limits water loss through
transpiration. Snow slides easily off needle-shaped leaves, keeping the load light and decreasing breaking of
branches. These adaptations to cold and dry weather explain the predominance of conifers at high altitudes and in
cold climates. Conifers include familiar evergreen trees, such as pines, spruces, firs, cedars, sequoias, and yews
(Figure 14.20). A few species are deciduous and lose their leaves all at once in fall. The European larch and the
tamarack are examples of deciduous conifers. Many coniferous trees are harvested for paper pulp and timber. The
wood of conifers is more primitive than the wood of angiosperms; it contains tracheids, but no vessel elements, and
336 14 • Diversity of Plants

is referred to as “soft wood.”

FIGURE 14.20 Conifers are the dominant form of vegetation in cold or arid environments and at high altitudes. Shown here are the (a)
evergreen spruce, (b) sequoia, (c) juniper, and (d) a deciduous gymnosperm: the tamarack Larix laricina. Notice the yellow leaves of the
tamarack. (credit b: modification of work by Alan Levine; credit c: modification of work by Wendy McCormac; credit d: modification of work
by Micky Zlimen)

Cycads
Cycads thrive in mild climates and are often mistaken for palms because of the shape of their large, compound
leaves. They bear large cones, and unusually for gymnosperms, may be pollinated by beetles, rather than wind. They
dominated the landscape during the age of dinosaurs in the Mesozoic era (251–65.5 million years ago). Only a
hundred or so cycad species persisted to modern times. They face possible extinction, and several species are
protected through international conventions. Because of their attractive shape, they are often used as ornamental
plants in gardens (Figure 14.21).

FIGURE 14.21 This Encephalartos ferox cycad exhibits large cones. (credit: Wendy Cutler)

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 14.3 • Seed Plants: Gymnosperms 337

Gingkophytes
The single surviving species of ginkgophyte is the Ginkgo biloba (Figure 14.22). Its fan-shaped leaves, unique
among seed plants because they feature a dichotomous venation pattern, turn yellow in autumn and fall from the
plant. For centuries, Buddhist monks cultivated Ginkgo biloba, ensuring its preservation. It is planted in public
spaces because it is unusually resistant to pollution. Male and female organs are found on separate plants. Usually,
only male trees are planted by gardeners because the seeds produced by the female plant have an off-putting smell
of rancid butter.

FIGURE 14.22 This plate from the 1870 book Flora Japonica, Sectio Prima (Tafelband) depicts the leaves and fruit of Gingko biloba, as
drawn by Philipp Franz von Siebold and Joseph Gerhard Zuccarini.

Gnetophytes
Gnetophytes are the closest relatives to modern angiosperms, and include three dissimilar genera of plants. Like
angiosperms, they have broad leaves. Gnetum species are mostly vines in tropical and subtropical zones. The single
species of Welwitschia is an unusual, low-growing plant found in the deserts of Namibia and Angola. It may live for
up to 2000 years. The genus Ephedra is represented in North America in dry areas of the southwestern United
States and Mexico (Figure 14.23). Ephedra’s small, scale-like leaves are the source of the compound ephedrine,
which is used in medicine as a potent decongestant. Because ephedrine is similar to amphetamines, both in
chemical structure and neurological effects, its use is restricted to prescription drugs. Like angiosperms, but unlike
other gymnosperms, all gnetophytes possess vessel elements in their xylem.
338 14 • Diversity of Plants

FIGURE 14.23 Ephedra viridis, known by the common name Mormon tea, grows in the western United States. (credit: US National Park
Service, USDA-NRCS PLANTS Database)

LINK TO LEARNING
Watch this BBC video (http://openstax.org/l/welwitschia) describing the amazing strangeness of Welwitschia.

14.4 Seed Plants: Angiosperms

LEARNING OBJECTIVES
By the end of this section, you will be able to:
• Describe the main parts of a flower and their purpose
• Detail the life cycle of an angiosperm
• Discuss the two main groups into which flower plants are divided, as well as explain how basal
angiosperms differ from others

From their humble and still obscure beginning during the early Jurassic period (202–145.5 MYA), the angiosperms,
or flowering plants, have successfully evolved to dominate most terrestrial ecosystems. Angiosperms include a
staggering number of genera and species; with more than 260,000 species, the division is second only to insects in
terms of diversification (Figure 14.24).

FIGURE 14.24 These flowers grow in a botanical garden border in Bellevue, WA. Flowering plants dominate terrestrial landscapes. The
vivid colors of flowers are an adaptation to pollination by insects and birds. (credit: Myriam Feldman)

Angiosperm success is a result of two novel structures that ensure reproductive success: flowers and fruit. Flowers
allowed plants to form cooperative evolutionary relationships with animals, in particular insects, to disperse their

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 14.4 • Seed Plants: Angiosperms 339

pollen to female gametophytes in a highly targeted way. Fruit protect the developing embryo and serve as an agent
of dispersal. Different structures on fruit reflect the dispersal strategies that help with the spreading of seeds.

Flowers
Flowers are modified leaves or sporophylls organized around a central stalk. Although they vary greatly in
appearance, all flowers contain the same structures: sepals, petals, pistils, and stamens. A whorl of sepals (the
calyx) is located at the base of the peduncle, or stem, and encloses the floral bud before it opens. Sepals are usually
photosynthetic organs, although there are some exceptions. For example, the corolla in lilies and tulips consists of
three sepals and three petals that look virtually identical—this led botanists to coin the word tepal. Petals
(collectively the corolla) are located inside the whorl of sepals and usually display vivid colors to attract pollinators.
Flowers pollinated by wind are usually small and dull. The sexual organs are located at the center of the flower.

As illustrated in Figure 14.25, the stigma, style, and ovary constitute the female organ, the carpel or pistil, which is
also referred to as the gynoecium. A gynoecium may contain one or more carpels within a single flower. The
megaspores and the female gametophytes are produced and protected by the thick tissues of the carpel. A long,
thin structure called a style leads from the sticky stigma, where pollen is deposited, to the ovary enclosed in the
carpel. The ovary houses one or more ovules that will each develop into a seed upon fertilization. The male
reproductive organs, the androecium or stamens, surround the central carpel. Stamens are composed of a thin stalk
called a filament and a sac-like structure, the anther, in which microspores are produced by meiosis and develop
into pollen grains. The filament supports the anther.

FIGURE 14.25 This image depicts the structure of a perfect and complete flower. Perfect flowers carry both male and female floral organs.
(credit: modification of work by Mariana Ruiz Villareal)

Fruit
The seed forms in an ovary, which enlarges as the seeds grow. As the seed develops, the walls of the ovary also
thicken and form the fruit. In botany, a fruit is a fertilized and fully grown, ripened ovary. Many foods commonly
called vegetables are actually fruit. Eggplants, zucchini, string beans, and bell peppers are all technically fruit
because they contain seeds and are derived from the thick ovary tissue. Acorns and winged maple keys, whose
scientific name is a samara, are also fruit.

Mature fruit can be described as fleshy or dry. Fleshy fruit include the familiar berries, peaches, apples, grapes, and
340 14 • Diversity of Plants

tomatoes. Rice, wheat, and nuts are examples of dry fruit. Another distinction is that not all fruits are derived from
the ovary. Some fruits are derived from separate ovaries in a single flower, such as the raspberry. Other fruits, such
as the pineapple, form from clusters of flowers. Additionally, some fruits, like watermelon and orange, have rinds.
Regardless of how they are formed, fruits are an agent of dispersal. The variety of shapes and characteristics reflect
the mode of dispersal. The light, dry fruits of trees and dandelions are carried by the wind. Floating coconuts are
transported by water. Some fruits are colored, perfumed, sweet, and nutritious to attract herbivores, which eat the
fruit and disperse the tough undigested seeds in their feces. Other fruits have burs and hooks that cling to fur and
hitch rides on animals.

The Life Cycle of an Angiosperm

The adult, or sporophyte, phase is the main phase in an angiosperm’s life cycle. Like gymnosperms, angiosperms are
heterosporous. They produce microspores, which develop into pollen grains (the male gametophytes), and
megaspores, which form an ovule containing the female gametophytes. Inside the anthers’ microsporangia (Figure
14.26), male microsporocytes divide by meiosis, generating haploid microspores that undergo mitosis and give rise
to pollen grains. Each pollen grain contains two cells: one generative cell that will divide into two sperm, and a
second cell that will become the pollen tube cell.

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 14.4 • Seed Plants: Angiosperms 341

VISUAL CONNECTION

FIGURE 14.26 This diagram shows the lifecycle of an angiosperm. Anthers and ovaries are structures that shelter the actual gametophytes:
the pollen grain and embryo sac. Double fertilization is a process unique to angiosperms. (credit: modification of work by Mariana Ruiz
Villareal)

If a flower lacked a megasporangium, what type of gamete would it not be able to form? If it lacked a
microsporangium, what type of gamete would not form?

In the ovules, the female gametophyte is produced when a megasporocyte undergoes meiosis to produce four
haploid megaspores. One of these is larger than the others and undergoes mitosis to form the female gametophyte
or embryo sac. Three mitotic divisions produce eight nuclei in seven cells. The egg and two cells move to one end of
the embryo sac (gametophyte) and three cells move to the other end. Two of the nuclei remain in a single cell and
fuse to form a 2n nucleus; this cell moves to the center of the embryo sac.

When a pollen grain reaches the stigma, a pollen tube extends from the grain, grows down the style, and enters
342 14 • Diversity of Plants

through an opening in the integuments of the ovule. The two sperm cells are deposited in the embryo sac.

What occurs next is called a double fertilization event (Figure 14.27) and is unique to angiosperms. One sperm and
the egg combine, forming a diploid zygote—the future embryo. The other sperm fuses with the diploid nucleus in the
center of the embryo sac, forming a triploid cell that will develop into the endosperm: a tissue that serves as a food
reserve. The zygote develops into an embryo with a radicle, or small root, and one or two leaf-like organs called
cotyledons. Seed food reserves are stored outside the embryo, and the cotyledons serve as conduits to transmit the
broken-down food reserves to the developing embryo. The seed consists of a toughened layer of integuments
forming the coat, the endosperm with food reserves and, at the center, the well-protected embryo.

FIGURE 14.27 Double fertilization occurs only in angiosperms. (credit: modification of work by Mariana Ruiz Villareal)

Most flowers carry both stamens and carpels; however, a few species self-pollinate. These are known as “perfect”
flowers because they contain both types of sex organs (Figure 14.25. Biochemical and anatomical barriers to self-
pollination promote cross-pollination. Self-pollination is a severe form of inbreeding, and can increase the number
of genetic defects in offspring.

A plant may have perfect flowers, and thus have multiple sexes in each flower; or, it may have imperfect flowers of
both kinds on one plant (Figure 14.28). In each case, such species are called monoecious plants, meaning “one
house.” Some botanists refer to plants with perfect flowers simply as hermaphroditic. (Note: hermaphrodite is a
scientific term for bodies containing two types of sex organs in plants and non-human animals.) Some plants are
dioecious, meaning “two houses,” and have male and female flowers (“imperfect flowers”) on different plants. In
these species, cross-pollination occurs all the time.

FIGURE 14.28 Monoecious plants have both male and female reproductive structures on the same flower or plant. In dioecious plants,
males and females reproductive structures are on separate plants. (credit a: modification of work by Liz West; credit c: modification of work
by Scott Zona)

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 14.4 • Seed Plants: Angiosperms 343

Diversity of Angiosperms
Angiosperms are classified in a single division, the Anthophyta. Modern angiosperms appear to be a monophyletic
group, which means that they originate from a single ancestor. Flowering plants are divided into two major groups,
according to the structure of the cotyledons, the pollen grains, and other features: monocots, which include grasses
and lilies, and eudicots or dicots, a polyphyletic group. Basal angiosperms are a group of plants that are believed to
have branched off before the separation into monocots and eudicots because they exhibit traits from both groups.
They are categorized separately in many classification schemes, and correspond to a grouping known as the
Magnoliidae. The Magnoliidae group is comprised of magnolia trees, laurels, water lilies, and the pepper family.

Basal Angiosperms
The Magnoliidae are represented by the magnolias: tall trees that bear large, fragrant flowers with many parts, and
are considered archaic (Figure 14.29d). Laurel trees produce fragrant leaves and small inconspicuous flowers. The
Laurales are small trees and shrubs that grow mostly in warmer climates. Familiar plants in this group include the
bay laurel, cinnamon, spice bush (Figure 14.29a), and the avocado tree. The Nymphaeales are comprised of the
water lilies, lotus (Figure 14.29c), and similar plants. All species of the Nymphaeales thrive in freshwater biomes,
and have leaves that float on the water surface or grow underwater. Water lilies are particularly prized by gardeners,
and have graced ponds and pools since antiquity. The Piperales are a group of herbs, shrubs, and small trees that
grow in tropical climates. They have small flowers without petals that are tightly arranged in long spikes. Many
species are the source of prized fragrances or spices; for example, the berries of Piper nigrum (Figure 14.29b) are
the familiar black pepper that is used to flavor many dishes.

FIGURE 14.29 The (a) southern spicebush belongs to the Laurales, the same family as cinnamon and bay laurel. The fruit of (b) the Piper
nigrum plant is black pepper, the main product that was traded along spice routes. Notice the small, unobtrusive clustered flowers. (c)
Lotus flowers, Nelumbo nucifera, have been cultivated since antiquity for their ornamental value; the root of the lotus flower is eaten as a
vegetable. The (d) red berries of a magnolia tree, characteristic of the final stage, are just starting to appear. (credit a: modification of work
by Cory Zanker; credit b: modification of work by Franz Eugen Köhler; credit c: modification of work by "berduchwal"/Flickr; credit d:
modification of work by "Coastside2"/Wikimedia Commons)

Monocots
Plants in the monocot group have a single cotyledon in the seedling, and also share other anatomical features. Veins
344 14 • Diversity of Plants

run parallel to the length of the leaves, and flower parts are arranged in a three- or six-fold symmetry. The pollen
from the first angiosperms was monosulcate (containing a single furrow or pore through the outer layer). This
feature is still seen in the modern monocots. True woody tissue is rarely found in monocots, and the vascular tissue
of the stem is not arranged in any particular pattern. The root system is mostly adventitious (unusually positioned)
with no major taproot. The monocots include familiar plants such as the true lilies (not to be confused with the
water lilies), orchids, grasses, and palms. Many important crops, such as rice and other cereals (Figure 14.30a),
corn, sugar cane, and tropical fruit, including bananas and pineapple, belong to the monocots.

FIGURE 14.30 The major crops in the world are flowering plants. One staple food, (a) rice, is a monocot, as are other cereals, while (b)
beans are eudicots. Some popular flowers, such as this (c) lily are monocots; while others, such as this (d) daisy are eudicots. (credit a:
modification of work by David Nance; credit b: modification of work by USDA, ARS; credit c: modification of work by “longhorndave”/Flickr;
credit d: modification of work by “Cellulaer”/NinjaPhoto)

Eudicots
Eudicots, or true dicots, are characterized by the presence of two cotyledons. Veins form a network in leaves. Flower
parts come in four, five, or many whorls. Vascular tissue forms a ring in the stem. (In monocots, vascular tissue is
scattered in the stem.) Eudicots can be herbaceous (like dandelions or violets), or produce woody tissues. Most
eudicots produce pollen that is trisulcate or triporate, with three furrows or pores. The root system is usually
anchored by one main root developed from the embryonic radicle. Eudicots comprise two-thirds of all flowering
plants. Many species seem to exhibit characteristics that belong to either group; therefore, the classification of a
plant as a monocot or a eudicot is not always clearly evident (Table 14.1).

Comparison of Structural Characteristics of Monocots and Eudicots

Characteristic Monocot Eudicot

Cotyledon One Two

Veins in leaves Parallel Network ( branched)

Vascular tissue Scattered Arranged in ring pattern

Roots Network of adventitious roots Tap root with many lateral roots
TABLE 14.1

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 14.4 • Seed Plants: Angiosperms 345

Characteristic Monocot Eudicot

Pollen Monosulcate Trisulcate

Flower parts Three or multiple of three Four, five, multiple of four or five and whorls

TABLE 14.1

LINK TO LEARNING
Explore this website (http://openstax.org/l/pollinators) for more information on pollinators.

The Role of Seed Plants

Without seed plants, life as we know it would not be possible. Plants play a key role in the maintenance of terrestrial
ecosystems through the stabilization of soils, cycling of carbon, and climate moderation. Large tropical forests
release oxygen and act as carbon dioxide “sinks.” Seed plants provide shelter to many life forms, as well as food for
herbivores, thereby indirectly feeding carnivores. Plant secondary metabolites are used for medicinal purposes and
industrial production. Virtually all animal life is dependent on plants for survival.

Animals and Plants: Herbivory

Coevolution of flowering plants and insects is a hypothesis that has received much attention and support, especially
because both angiosperms and insects diversified at about the same time in the middle Mesozoic. Many authors
have attributed the diversity of plants and insects to both pollination and herbivory, or the consumption of plants by
insects and other animals. Herbivory is believed to have been as much a driving force as pollination. Coevolution of
herbivores and plant defenses is easily and commonly observed in nature. Unlike animals, most plants cannot
outrun predators or use mimicry to hide from hungry animals (although mimicry has been used to entice
pollinators). A sort of arms race exists between plants and herbivores. To “combat” herbivores, some plant
seeds—such as acorn and unripened persimmon—are high in alkaloids and therefore unsavory to some animals.
Other plants are protected by bark, although some animals developed specialized mouth pieces to tear and chew
vegetal material. Spines and thorns deter most animals, except for mammals with thick fur, and some birds have
specialized beaks to get past such defenses.

Herbivory has been exploited by seed plants for their own benefit. The dispersal of fruits by herbivorous animals is a
striking example of mutualistic relationships. The plant offers to the herbivore a nutritious source of food in return
for spreading the plant’s genetic material to a wider area.

Animals and Plants: Pollination

More than 80 percent of angiosperms depend on animals for pollination (technically the transfer of pollen from the
anther to the stigma). Consequently, plants have developed many adaptations to attract pollinators. With over
200,000 different plants dependent on animal pollination, the plant needs to advertise to its pollinators with some
specificity. The specificity of specialized plant structures that target animals can be very surprising. It is possible, for
example, to determine the general type of pollinators favored by a plant by observing the flower’s physical
characteristics. Many bird or insect-pollinated flowers secrete nectar, which is a sugary liquid. They also produce
both fertile pollen, for reproduction, and sterile pollen rich in nutrients for birds and insects. Many butterflies and
bees can detect ultraviolet light, and flowers that attract these pollinators usually display a pattern of ultraviolet
reflectance that helps them quickly locate the flower's center. In this manner, pollinating insects collect nectar while
at the same time are dusted with pollen. Large, red flowers with little smell and a long funnel shape are preferred by
hummingbirds, who have good color perception, a poor sense of smell, and need a strong perch. White flowers that
open at night attract moths. Other animals—such as bats, lemurs, and lizards—can also act as pollinating agents.
Any disruption to these interactions, such as the disappearance of bees, for example as a consequence of colony
collapse disorders, can lead to disaster for agricultural industries that depend heavily on pollinated crops.

The Importance of Seed Plants in Human Life

Seed plants are the foundation of human diets across the world. Many societies eat almost exclusively vegetarian
346 14 • Diversity of Plants

fare and depend solely on seed plants for their nutritional needs. A few crops (rice, wheat, and potatoes) dominate
the agricultural landscape. Many crops were developed during the agricultural revolution, when human societies
made the transition from nomadic hunter–gatherers to horticulture and agriculture. Cereals, rich in carbohydrates,
provide the staple of many human diets. Beans and nuts supply proteins. Fats are derived from crushed seeds, as is
the case for peanut and rapeseed (canola) oils, or fruits

The medicinal properties of plants have been known to human societies since ancient times. There are references to
the use of plants’ curative properties in Egyptian, Babylonian, and Chinese writings from 5,000 years ago. Many
modern synthetic therapeutic drugs are derived or synthesized from plant secondary metabolites. Very often, the
raw form of the plant or plant-based substance may be unusable even if it demonstrates helpful properties. For
example, chaulmoogra oil was somewhat effective for treating leprosy, but it was difficult to apply and painful for
patients. In 1915, Alice Ball (at only 23 years old), created a method for extracting the active ester compounds from
the oil so that it could be absorbed by the body, creating a much more effective treatment without the negative side
effects. The "Ball Technique" remained the preferred method until synthetic medicines replaced it decades later. It
is important to note that the same plant extract can be a therapeutic remedy at low concentrations, become an
addictive drug at higher doses, and can potentially kill at high concentrations. Table 14.2 presents a few drugs, their
plants of origin, and their medicinal applications.

Plant Origin of Medicinal Compounds and Medical Applications

Plant Compound Application

Deadly nightshade (
Atropine Dilate eye pupils for eye exams
Atropa belladonna )

Foxglove ( Digitalis
Digitalis Heart disease, stimulates heart beat
purpurea )

Yam ( Dioscorea
Steroids Steroid hormones: contraceptive pill and cortisone
spp.)

Ephedra ( Ephedra
Ephedrine Decongestant and bronchiole dilator
spp.)

Pacific yew ( Taxus

Taxol Cancer chemotherapy; inhibits mitosis
brevifolia )

Opium poppy (
Analgesic (reduces pain without loss of consciousness) and narcotic
Papaver Opioids
(reduces pain with drowsiness and loss of consciousness) in higher doses
somniferum )

Quinine tree (
Quinine Antipyretic (lowers body temperature) and antimalarial
Cinchona spp.)

Salicylic
Willow ( Salix spp.) acid Analgesic and antipyretic
(aspirin)

TABLE 14.2

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 14 • Key Terms 347

Key Terms
anther a sac-like structure at the tip of the stamen in haplontic describes a life cycle in which the haploid
which pollen grains are produced stage is the dominant stage
Anthophyta the division to which angiosperms herbaceous describes a plant without woody tissue
belong heterosporous having two kinds of spores that give
apical meristem the growing point in a vascular plant rise to male and female gametophytes
at the tip of a shoot or root where cell division homosporous having one kind of spore that gives rise
occurs to gametophytes that give rise to both male and
basal angiosperms a group of plants that probably female gametes
branched off before the separation of monocots and hornwort a group of non-vascular plants in which
eudicots stomata appear
calyx the whorl of sepals horsetail a seedless vascular plant characterized by a
carpel the female reproductive part of a flower jointed stem
consisting of the stigma, style, and ovary liverwort the most primitive group of non-vascular
club moss the earliest group of seedless vascular plants
plants megasporocyte a megaspore mother cell; larger
cone the ovulate strobilus on gymnosperms that spore that germinates into a female gametophyte in
contains ovules a heterosporous plant
conifer the dominant division of gymnosperms with microsporocyte smaller spore that produces a male
the most variety of species gametophyte in a heterosporous plant
corolla the collection of petals monocot a related group of angiosperms that
cotyledon the one (monocot) or two (dicot) primitive produce embryos with one cotyledon and pollen
leaves present in a seed with a single ridge
cycad a division of gymnosperms that grow in tropical moss a group of plants in which a primitive
climates and resemble palm trees conductive system appears
dicot a group of angiosperms whose embryos nonvascular plant a plant that lacks vascular tissue
possess two cotyledons; also known as eudicot formed of specialized cells for the transport of water
diplontic describes a life cycle in which the diploid and nutrients
stage is the dominant stage ovary the chamber that contains and protects the
eudicots a group of angiosperms whose embryos ovule or female megasporangium
possess two cotyledons; also known as dicot petal a modified leaf interior to the sepal; colorful
fern a seedless vascular plant that produces large petals attract animal pollinator
fronds; the most advanced group of seedless phloem the vascular tissue responsible for transport
vascular plants of sugars, proteins, and other solutes
filament the thin stalk that links the anther to the pistil the group of structures that constitute the
base of the flower female reproductive organ; also called the carpel
gametangium (plural: gametangia) the structure sepal a modified leaf that encloses the bud;
within which gametes are produced outermost structure of a flower
gametophyte the haploid plant that produces sporangium (plural: sporangia) the organ within
gametes which spores are produced
gingkophyte a division of gymnosperm with one sporophyll a leaf modified structurally to bear
living species, the Gingko biloba, a tree with fan- sporangia
shaped leaves sporophyte the diploid plant that produces spores
gnetophyte a division of gymnosperms with varied stamen the group of structures that contain the male
morphological features that produce vessel reproductive organs
elements in their woody tissues stigma uppermost structure of the carpel where
gymnosperm a seed plant with naked seeds (seeds pollen is deposited
exposed on modified leaves or in cones) strobili cone-like structures that contain the
gynoecium the group of structures that constitute the sporangia
female reproductive organ; also called the pistil style the long thin structure that links the stigma to
haplodiplontic describes a life cycle in which the the ovary
haploid and diploid stages alternate; also known as syngamy the union of two gametes in fertilization
an alternation of generations life cycle vascular plant a plant in which there is a network of
348 14 • Chapter Summary

cells that conduct water and solutes through the and leaves by evolutionary reduction
organism xylem the vascular tissue responsible for long-
whisk fern a seedless vascular plant that lost roots distance transport of water and nutrients

Chapter Summary
14.1 The Plant Kingdom produce naked seeds. They appeared in the
Carboniferous period (359–299 million years ago) and
Land plants evolved traits that made it possible to
were the dominant plant life during the Mesozoic era
colonize land and survive out of water. Adaptations to
(251–65.5 million years ago). Modern-day
life on land include vascular tissues, roots, leaves,
gymnosperms belong to four divisions. The division
waxy cuticles, and a tough outer layer that protects the
Coniferophyta—the conifers—are the predominant
spores. Land plants include nonvascular plants and
woody plants at high altitudes and latitudes. Cycads
vascular plants. Vascular plants, which include
resemble palm trees and grow in tropical climates.
seedless plants and plants with seeds, have apical
Gingko biloba is the only species of the division
meristems, and embryos with nutritional stores. All
Gingkophyta. The last division, the Gnetophytes, is a
land plants share the following characteristics:
diverse group of species that produce vessel elements
alternation of generations, with the haploid plant called
in their wood.
a gametophyte and the diploid plant called a
sporophyte; formation of haploid spores in a 14.4 Seed Plants: Angiosperms
sporangium; and formation of gametes in a
Angiosperms are the dominant form of plant life in
gametangium.
most terrestrial ecosystems, comprising about 90
14.2 Seedless Plants percent of all plant species. Most crop and ornamental
plants are angiosperms. Their success results, in part,
Seedless nonvascular plants are small. The dominant
from two innovative structures: the flower and the fruit.
stage of the life cycle is the gametophyte. Without a
Flowers are derived evolutionarily from modified
vascular system and roots, they absorb water and
leaves. The main parts of a flower are the sepals and
nutrients through all of their exposed surfaces. There
petals, which protect the reproductive parts: the
are three main groups: the liverworts, the hornworts,
stamens and the carpels. The stamens produce the
and the mosses. They are collectively known as
male gametes, which are pollen grains. The carpels
bryophytes.
contain the female gametes, which are the eggs inside
Vascular systems consist of xylem tissue, which ovaries. The walls of the ovary thicken after
transports water and minerals, and phloem tissue, fertilization, ripening into fruit that can facilitate seed
which transports sugars and proteins. With the dispersal.
vascular system, there appeared leaves—large
Angiosperms’ life cycles are dominated by the
photosynthetic organs—and roots to absorb water from
sporophyte stage. Double fertilization is an event
the ground. The seedless vascular plants include club
unique to angiosperms. The flowering plants are
mosses, which are the most primitive; whisk ferns,
divided into two main groups—the monocots and
which lost leaves and roots by reductive evolution;
eudicots—according to the number of cotyledons in the
horsetails, and ferns.
seedlings. Basal angiosperms belong to a lineage older
14.3 Seed Plants: Gymnosperms than monocots and eudicots.

Gymnosperms are heterosporous seed plants that

Visual Connection Questions

1. Figure 14.19 At what stage does the diploid zygote 2. Figure 14.26 If a flower lacked a megasporangium,
form? what type of gamete would it not be able to form? If
a. When the female cone begins to bud from the it lacked a microsporangium, what type of gamete
tree would not form?
b. When the sperm nucleus and the egg nucleus
fuse
c. When the seeds drop from the tree
d. When the pollen tube begins to grow

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 14 • Review Questions 349

Review Questions
3. The land plants are probably descendants of which 8. Which group are vascular plants?
of these groups? a. liverworts
a. green algae b. mosses
b. red algae c. hornworts
c. brown algae d. ferns
d. angiosperms
9. Which of the following traits characterizes
4. The event that leads from the haploid stage to the gymnosperms?
diploid stage in alternation of generations is a. The plants carry exposed seeds on modified
________. leaves.
a. meiosis b. Reproductive structures are located in a flower.
b. mitosis c. After fertilization, the ovary thickens and forms
c. fertilization a fruit.
d. germination d. The gametophyte is longest phase of the life
cycle.
5. Moss is an example of which type of plant?
a. haplontic plant 10. What adaptation do seed plants have in addition
b. vascular plant to the seed that is not found in seedless plants?
c. diplontic plant a. gametophytes
d. seed plant b. vascular tissue
c. pollen
6. Why do mosses grow well in the Arctic tundra? d. chlorophyll
a. They grow better at cold temperatures.
b. They do not require moisture. 11. Pollen grains develop in which structure?
c. They do not have true roots and can grow on a. the anther
hard surfaces. b. the stigma
d. There are no herbivores in the tundra. c. the filament
d. the carpel
7. Which is the most diverse group of seedless
vascular plants? 12. Corn develops from a seedling with a single
a. the liverworts cotyledon, displays parallel veins on its leaves,
b. the horsetails and produces monosulcate pollen. It is most
c. the club mosses likely:
d. the ferns a. a gymnosperm
b. a monocot
c. a eudicot
d. a basal angiosperm

Critical Thinking Questions

13. What adaptations do plants have that allow them 17. Cycads are considered endangered species and
to survive on land? their trade is severely restricted. Customs officials
stop suspected smugglers, who claim that the
14. What are the three classes of bryophytes?
plants in their possession are palm trees and not
15. How did the development of a vascular system cycads. How would a botanist distinguish between
contribute to the increase in size of plants? the two types of plants?

16. What are the four modern-day groups of 18. What are the two structures that allow
gymnosperms? angiosperms to be the dominant form of plant life
in most terrestrial ecosystems?
350 14 • Critical Thinking Questions

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CHAPTER 15
Diversity of Animals

FIGURE 15.1 The leaf chameleon (Brookesia micra) was discovered in northern Madagascar in 2012. At just over one
inch long, it is the smallest known chameleon. (credit: modification of work by Frank Glaw, et al., PLOS)

CHAPTER OUTLINE
15.1 Features of the Animal Kingdom
15.2 Sponges and Cnidarians
15.3 Flatworms, Nematodes, and Arthropods
15.4 Mollusks and Annelids
15.5 Echinoderms and Chordates
15.6 Vertebrates

INTRODUCTION While we can easily identify dogs, lizards, fish, spiders, and worms as animals,
other animals, such as corals and sponges, might be easily mistaken as plants or some other form
of life. Yet scientists have recognized a set of common characteristics shared by all animals,
including sponges, jellyfish, sea urchins, and humans.

The kingdom Animalia is a group of multicellular Eukarya. Animal evolution began in the ocean
over 600 million years ago, with tiny creatures that probably do not resemble any living organism
today. Since then, animals have evolved into a highly diverse kingdom. Although over one million
currently living species of animals have been identified, scientists are continually discovering
more species. The number of described living animal species is estimated to be about 1.4
1
million, and there may be as many as 6.8 million.

Understanding and classifying the variety of living species helps us to better understand how to
conserve and benefit from this diversity. The animal classification system characterizes animals

1 “Number of Living Species in Australia and the World,” A.D. Chapman, Australia Biodiversity Information Services,
last modified August 26, 2010, http://www.environment.gov.au/biodiversity/abrs/publications/other/species-
numbers/2009/03-exec-summary.html.
352 15 • Diversity of Animals

based on their anatomy, features of embryological development, and genetic makeup. Scientists
are faced with the task of classifying animals within a system of taxonomy that reflects their
evolutionary history. Additionally, they must identify traits that are common to all animals as well
as traits that can be used to distinguish among related groups of animals. However, animals vary
in the complexity of their organization and exhibit a huge diversity of body forms, so the
classification scheme is constantly changing as new information about species is learned.

15.1 Features of the Animal Kingdom

LEARNING OBJECTIVES
By the end of this section, you will be able to:
• List the features that distinguish the animal kingdom from other kingdoms
• Explain the processes of animal reproduction and embryonic development
• Describe the hierarchy of basic animal classification
• Compare and contrast the embryonic development of protostomes and deuterostomes

Even though members of the animal kingdom are incredibly diverse, animals share common
features that distinguish them from organisms in other kingdoms. All animals are eukaryotic,
multicellular organisms, and almost all animals have specialized tissues. Most animals are motile,
at least during certain life stages. Animals require a source of food to grow and develop. All
animals are heterotrophic, ingesting living or dead organic matter. This form of obtaining energy
distinguishes them from autotrophic organisms, such as most plants, which make their own
nutrients through photosynthesis and from fungi that digest their food externally. Animals may be
carnivores, herbivores, omnivores, or parasites (Figure 15.2). Most animals reproduce sexually:
The offspring pass through a series of developmental stages that establish a determined body
plan, unlike plants, for example, in which the exact shape of the body is indeterminate. The body
plan refers to the shape of an animal.

FIGURE 15.2 All animals that derive energy from food are heterotrophs. The (a) black bear is an omnivore, eating both
plants and animals. The (b) heartworm Dirofilaria immitis is a parasite that derives energy from its hosts. It spends its
larval stage in mosquitos and its adult stage infesting the hearts of dogs and other mammals, as shown here. (credit a:
modification of work by USDA Forest Service; credit b: modification of work by Clyde Robinson)

Complex Tissue Structure

A hallmark trait of animals is specialized structures that are differentiated to perform unique
functions. As multicellular organisms, most animals develop specialized cells that group together
into tissues with specialized functions. A tissue is a collection of similar cells that had a common
embryonic origin. There are four main types of animal tissues: nervous, muscle, connective, and
epithelial. Nervous tissue contains neurons, or nerve cells, which transmit nerve impulses. Muscle
tissue contracts to cause all types of body movement from locomotion of the organism to

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 15.1 • Features of the Animal Kingdom 353

movements within the body itself. Animals also have specialized connective tissues that provide many functions,
including transport and structural support. Examples of connective tissues include blood and bone. Connective
tissue is comprised of cells separated by extracellular material made of organic and inorganic materials, such as the
protein and mineral deposits of bone. Epithelial tissue covers the internal and external surfaces of organs inside the
animal body and the external surface of the body of the organism.

LINK TO LEARNING
View this video (http://openstax.org/l/saving_life2) to watch a presentation by biologist E.O. Wilson on the
importance of animal diversity.

Animal Reproduction and Development

Most animals have diploid body (somatic) cells and a small number of haploid reproductive (gamete) cells produced
through meiosis. Some exceptions exist: For example, in bees, wasps, and ants, the male is haploid because it
develops from an unfertilized egg. Most animals undergo sexual reproduction, while many also have mechanisms of
asexual reproduction.

Sexual Reproduction and Embryonic Development

Almost all animal species are capable of reproducing sexually; for many, this is the only mode of reproduction
possible. This distinguishes animals from fungi, protists, and bacteria, where asexual reproduction is common or
exclusive. During sexual reproduction, the male and female gametes of a species combine in a process called
fertilization. Typically, the small, motile male sperm travels to the much larger, sessile female egg. Sperm form is
diverse and includes cells with flagella or amoeboid cells to facilitate motility. Fertilization and fusion of the gamete
nuclei produce a zygote. Fertilization may be internal, especially in land animals, or external, as is common in many
aquatic species.

After fertilization, a developmental sequence ensues as cells divide and differentiate. Many of the events in
development are shared in groups of related animal species, and these events are one of the main ways scientists
classify high-level groups of animals. During development, animal cells specialize and form tissues, determining
their future morphology and physiology. In many animals, such as mammals, the young resemble the adult. Other
animals, such as some insects and amphibians, undergo complete metamorphosis in which individuals enter one or
more larval stages. For these animals, the young and the adult have different diets and sometimes habitats. In other
species, a process of incomplete metamorphosis occurs in which the young somewhat resemble the adults and go
through a series of stages separated by molts (shedding of the skin) until they reach the final adult form.

Asexual Reproduction
Asexual reproduction, unlike sexual reproduction, produces offspring genetically identical to each other and to the
parent. A number of animal species—especially those without backbones, but even some fish, amphibians, and
reptiles—are capable of asexual reproduction. Asexual reproduction, except for occasional identical twinning, is
absent in birds and mammals. The most common forms of asexual reproduction for stationary aquatic animals
include budding and fragmentation, in which part of a parent individual can separate and grow into a new individual.
In contrast, a form of asexual reproduction found in certain invertebrates and rare vertebrates is called
parthenogenesis (or “virgin beginning”), in which unfertilized eggs develop into new offspring.

Classification Features of Animals

Animals are classified according to morphological and developmental characteristics, such as a body plan. With the
exception of sponges, the animal body plan is symmetrical. This means that their distribution of body parts is
balanced along an axis. Additional characteristics that contribute to animal classification include the number of
tissue layers formed during development, the presence or absence of an internal body cavity, and other features of
embryological development.
354 15 • Diversity of Animals

VISUAL CONNECTION

FIGURE 15.3 The phylogenetic tree of animals is based on morphological, fossil, and genetic evidence.

Which of the following statements is false?

a. Eumetazoa have specialized tissues and Parazoa do not.

b. Both acoelomates and pseudocoelomates have a body cavity.
c. Chordates are more closely related to echinoderms than to rotifers according to the figure.
d. Some animals have radial symmetry, and some animals have bilateral symmetry.

Body Symmetry
Animals may be asymmetrical, radial, or bilateral in form (Figure 15.4). Asymmetrical animals are animals with no
pattern or symmetry; an example of an asymmetrical animal is a sponge (Figure 15.4a). An organism with radial
symmetry (Figure 15.4b) has a longitudinal (up-and-down) orientation: Any plane cut along this up–down axis
produces roughly mirror-image halves. An example of an organism with radial symmetry is a sea anemone.

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 15.1 • Features of the Animal Kingdom 355

FIGURE 15.4 Animals exhibit different types of body symmetry. The (a) sponge is asymmetrical and has no planes of symmetry, the (b) sea
anemone has radial symmetry with multiple planes of symmetry, and the (c) goat has bilateral symmetry with one plane of symmetry.

Bilateral symmetry is illustrated in Figure 15.4c using a goat. The goat also has upper and lower sides to it, but they
are not symmetrical. A vertical plane cut from front to back separates the animal into roughly mirror-image right and
left sides. Animals with bilateral symmetry also have a “head” and “tail” (anterior versus posterior) and a back and
underside (dorsal versus ventral).

LINK TO LEARNING
Watch this video (http://openstax.org/l/symmetry2) to see a quick sketch of the different types of body symmetry.

Layers of Tissues
Most animal species undergo a layering of early tissues during embryonic development. These layers are called
germ layers. Each layer develops into a specific set of tissues and organs. Animals develop either two or three
embryonic germs layers (Figure 15.5). The animals that display radial symmetry develop two germ layers, an inner
layer (endoderm) and an outer layer (ectoderm). These animals are called diploblasts. Animals with bilateral
symmetry develop three germ layers: an inner layer (endoderm), an outer layer (ectoderm), and a middle layer
(mesoderm). Animals with three germ layers are called triploblasts.

FIGURE 15.5 During embryogenesis, diploblasts develop two embryonic germ layers: an ectoderm and an endoderm. Triploblasts develop
a third layer—the mesoderm—between the endoderm and ectoderm.

Presence or Absence of a Coelom

Triploblasts may develop an internal body cavity derived from mesoderm, called a coelom (pr. see-LŌM). This
epithelial-lined cavity is a space, usually filled with fluid, which lies between the digestive system and the body wall.
It houses organs such as the kidneys and spleen, and contains the circulatory system. Triploblasts that do not
develop a coelom are called acoelomates, and their mesoderm region is completely filled with tissue, although they
have a gut cavity. Examples of acoelomates include the flatworms. Animals with a true coelom are called
356 15 • Diversity of Animals

eucoelomates (or coelomates) (Figure 15.6). A true coelom arises entirely within the mesoderm germ layer.
Animals such as earthworms, snails, insects, starfish, and vertebrates are all eucoelomates. A third group of
triploblasts has a body cavity that is derived partly from mesoderm and partly from endoderm tissue. These animals
are called pseudocoelomates. Roundworms are examples of pseudocoelomates. New data on the relationships of
pseudocoelomates suggest that these phyla are not closely related and so the evolution of the pseudocoelom must
have occurred more than once (Figure 15.3). True coelomates can be further characterized based on features of
their early embryological development.

FIGURE 15.6 Triploblasts may be acoelomates, eucoelomates, or pseudocoelomates. Eucoelomates have a body cavity within the
mesoderm, called a coelom, which is lined with mesoderm tissue. Pseudocoelomates have a similar body cavity, but it is lined with
mesoderm and endoderm tissue. (credit a: modification of work by Jan Derk; credit b: modification of work by NOAA; credit c: modification
of work by USDA, ARS)

Protostomes and Deuterostomes

Bilaterally symmetrical, triploblastic eucoelomates can be divided into two groups based on differences in their
early embryonic development. Protostomes include phyla such as arthropods, mollusks, and annelids.
Deuterostomes include the chordates and echinoderms. These two groups are named from which opening of the
digestive cavity develops first: mouth or anus. The word protostome comes from Greek words meaning “mouth
first,” and deuterostome originates from words meaning “mouth second” (in this case, the anus develops first). This
difference reflects the fate of a structure called the blastopore (Figure 15.7), which becomes the mouth in
protostomes and the anus in deuterostomes. Other developmental characteristics differ between protostomes and
deuterostomes, including the mode of formation of the coelom and the early cell division of the embryo.

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 15.2 • Sponges and Cnidarians 357

FIGURE 15.7 Eucoelomates can be divided into two groups, protostomes and deuterostomes, based on their early embryonic
development. Two of these differences include the origin of the mouth opening and the way in which the coelom is formed.

15.2 Sponges and Cnidarians

LEARNING OBJECTIVES
By the end of this section, you will be able to:
• Describe the organizational features of the simplest animals
• Describe the organizational features of cnidarians

The kingdom of animals is informally divided into invertebrate animals, those without a backbone, and vertebrate
animals, those with a backbone. Although in general we are most familiar with vertebrate animals, the vast majority
of animal species, about 95 percent, are invertebrates. Invertebrates include a huge diversity of animals, millions of
species in about 32 phyla, which we can just begin to touch on here.

The sponges and the cnidarians represent the simplest of animals. Sponges appear to represent an early stage of
multicellularity in the animal clade. Although they have specialized cells for particular functions, they lack true
tissues in which specialized cells are organized into functional groups. Sponges are similar to what might have been
the ancestor of animals: colonial, flagellated protists. The cnidarians, or the jellyfish and their kin, are the simplest
animal group that displays true tissues, although they possess only two tissue layers.

Sponges
Animals in subkingdom Parazoa represent the simplest animals and include the sponges, or phylum Porifera (Figure
15.8). All sponges are aquatic and the majority of species are marine. Sponges live in intimate contact with water,
which plays a role in their feeding, gas exchange, and excretion. Much of the body structure of the sponge is
dedicated to moving water through the body so it can filter out food, absorb dissolved oxygen, and eliminate wastes.
358 15 • Diversity of Animals

FIGURE 15.8 Sponges are members of the phylum Porifera, which contains the simplest animals. (credit: Andrew Turner)

The body of the simplest sponges takes the shape of a cylinder with a large central cavity, the spongocoel. Water
enters the spongocoel from numerous pores in the body wall. Water flows out through a large opening called the
osculum (Figure 15.9). However, sponges exhibit a diversity of body forms, which vary in the size and branching of
the spongocoel, the number of osculi, and where the cells that filter food from the water are located.

Sponges consist of an outer layer of flattened cells and an inner layer of cells called choanocytes separated by a
jelly-like substance called mesohyl. The mesohyl contains embedded amoeboid cells that secrete tiny needles
called spicules or protein fibers that help give the sponge its structural strength. The cell body of the choanocyte is
embedded in mesohyl but protruding into the spongocoel is a mesh-like collar surrounding a single flagellum. The
beating of flagella from all choanocytes moves water through the sponge. Food particles are trapped in mucus
produced by the sieve-like collar of the choanocytes and are ingested by phagocytosis. This process is called
intracellular digestion. Amoebocytes take up nutrients repackaged in food vacuoles of the choanocytes and deliver
them to other cells within the sponge.

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 15.2 • Sponges and Cnidarians 359

FIGURE 15.9 The sponge’s basic body plan is shown.

Physiological Processes in Sponges

Despite their lack of complexity, sponges are clearly successful organisms, having persisted on Earth for more than
half a billion years. Lacking a true digestive system, sponges depend on the intracellular digestive processes of their
choanocytes for their energy intake. The limit of this type of digestion is that food particles must be smaller than
individual cells. Gas exchange, circulation, and excretion occur by diffusion between cells and the water.

Sponges reproduce both sexually and asexually. Asexual reproduction is either by fragmentation (in which a piece
of the sponge breaks off and develops into a new individual), or budding (an outgrowth from the parent that
eventually detaches). A type of asexual reproduction found only in freshwater sponges occurs through the formation
of gemmules, clusters of cells surrounded by a tough outer layer. Gemmules survive hostile environments and can
attach to a substrate and grow into a new sponge.

Sponges are monoecious (or hermaphroditic), meaning one individual can produce both eggs and sperm. Sponges
may be sequentially hermaphroditic, producing eggs first and sperm later. Eggs arise from amoebocytes and are
retained within the spongocoel, whereas sperm arise from choanocytes and are ejected through the osculum.
Sperm carried by water currents fertilize the eggs of other sponges. Early larval development occurs within the
sponge, and free-swimming larvae are then released through the osculum. This is the only time that sponges exhibit
mobility. Sponges are sessile as adults and spend their lives attached to a fixed substrate.

LINK TO LEARNING
Watch this video (http://openstax.org/l/sponge_feed) that demonstrates the feeding of sponges.

Cnidarians
The phylum Cnidaria includes animals that show radial or biradial symmetry and are diploblastic. Nearly all (about
99 percent) cnidarians are marine species. Cnidarians have specialized cells known as cnidocytes (“stinging cells”)
containing organelles called nematocysts. These cells are concentrated around the mouth and tentacles of the
animal and can immobilize prey with toxins. Nematocysts contain coiled threads that may bear barbs. The outer wall
of the cell has a hairlike projection that is sensitive to touch. When touched, the cells fire the toxin-containing coiled
threads that can penetrate and stun the predator or prey (see Figure 15.10).
360 15 • Diversity of Animals

FIGURE 15.10 Animals from the phylum Cnidaria have stinging cells called cnidocytes. Cnidocytes contain large organelles called (a)
nematocysts that store a coiled thread and barb. When hairlike projections on the cell surface are touched, (b) the thread, barb, and a toxin
are fired from the organelle.

Cnidarians display two distinct body plans: polyp or “stalk” and medusa or “bell” (Figure 15.11). Examples of the
polyp form are freshwater species of the genus Hydra; perhaps the best-known medusoid animals are the jellies
(jellyfish). Polyps are sessile as adults, with a single opening to the digestive system (the mouth) facing up with
tentacles surrounding it. Medusae are motile, with the mouth and tentacles hanging from the bell-shaped body. In
other cnidarians, both a polyp and medusa form exist, and the life cycle alternates between these forms.

FIGURE 15.11 Cnidarians have two distinct body plans, the (a) medusa and the (b) polyp. All cnidarians have two tissue layers, with a jelly-
like mesoglea between them.

Physiological Processes of Cnidarians

All cnidarians have two tissue layers. The outer layer is called the epidermis, whereas the inner layer is called the
gastrodermis and lines the digestive cavity. Between these two layers is a non-living, jelly-like mesoglea. There are
differentiated cell types in each tissue layer, such as nerve cells, enzyme-secreting cells, and nutrient-absorbing
cells, as well as intercellular connections between the cells. However, organs and organ systems are not present in
this phylum.

The nervous system is primitive, with nerve cells scattered across the body in a network. The function of the nerve

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 15.2 • Sponges and Cnidarians 361

cells is to carry signals from sensory cells and to contractile cells. Groups of cells in the nerve net form nerve cords
that may be essential for more rapid transmission. Cnidarians perform extracellular digestion, with digestion
completed by intracellular digestive processes. Food is taken into the gastrovascular cavity, enzymes are secreted
into the cavity, and the cells lining the cavity absorb the nutrient products of the extracellular digestive process. The
gastrovascular cavity has only one opening that serves as both a mouth and an anus (an incomplete digestive
system). Like the sponges, Cnidarian cells exchange oxygen, carbon dioxide, and nitrogenous wastes by diffusion
between cells in the epidermis and gastrodermis with water.

Cnidarian Diversity
The phylum Cnidaria contains about 10,000 described species divided into four classes: Anthozoa, Scyphozoa,
Cubozoa, and Hydrozoa.

The class Anthozoa includes all cnidarians that exhibit a sessile polyp body plan only; in other words, there is no
medusa stage within their life cycle. Examples include sea anemones, sea pens, and corals, with an estimated
number of 6,100 described species. Sea anemones are usually brightly colored and can attain a size of 1.8 to 10 cm
in diameter. These animals are usually cylindrical in shape and are attached to a substrate. A mouth opening is
surrounded by tentacles bearing cnidocytes (Figure 15.12).

FIGURE 15.12 Sea anemones are cnidarians of class Anthozoa. (credit: "Dancing With Ghosts"/Flickr)

Scyphozoans include all the jellies and are motile and exclusively marine with about 200 described species. The
medusa is the dominant stage in the life cycle, although there is also a polyp stage. Species range from 2 cm in
length to the largest scyphozoan species, Cyanea capillata, at 2 m across. Jellies display a characteristic bell-like
body shape (Figure 15.13).
362 15 • Diversity of Animals

FIGURE 15.13 Scyphozoans include the jellies. (credit: "Jimg944"/Flickr)

LINK TO LEARNING
Use this video (https://openstax.org/l/amazing_jelly2) to identify the life cycle stages of jellies.

The class Cubozoa includes jellies that are square in cross-section and so are known as “box jellyfish.” These
species may achieve sizes of 15–25 cm. Cubozoans are anatomically similar to the jellyfish. A prominent difference
between the two classes is the arrangement of tentacles. Cubozoans have muscular pads called pedalia at the
corners of the square bell canopy, with one or more tentacles attached to each pedalium. In some cases, the
digestive system may extend into the pedalia. Cubozoans typically exist in a polyp form that develops from a larva.
The polyps may bud to form more polyps and then transform into the medusoid forms.

LINK TO LEARNING
Watch this video (http://openstax.org/l/box_jellyfish) to learn more about the deadly toxins of the box jellyfish.

2
Hydrozoa includes nearly 3,500 species, most of which are marine. Most species in this class have both polyp and
medusa forms in their life cycle. Many hydrozoans form colonies composed of branches of specialized polyps that
share a gastrovascular cavity. Colonies may also be free-floating and contain both medusa and polyp individuals in
the colony, as in the Portuguese Man O’War (Physalia) or By-the-Wind Sailor (Velella). Other species are solitary
polyps or solitary medusae. The characteristic shared by all of these species is that their gonads are derived from
epidermal tissue, whereas in all other cnidarians, they are derived from gastrodermal tissue (Figure 15.14ab).

2 “The Hydrozoa Directory,” Peter Schuchert, Muséum Genève, last updated November 2012, http://www.ville-ge.ch/mhng/hydrozoa/
hydrozoa-directory.htm.

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 15.3 • Flatworms, Nematodes, and Arthropods 363

FIGURE 15.14 A (a) box jelly is an example from class Cubozoa. The (b) hydra is from class Hydrozoa. (credit b: scale-bar data from Matt
Russell)

15.3 Flatworms, Nematodes, and Arthropods

LEARNING OBJECTIVES
By the end of this section, you will be able to:
• Describe the structure and systems of flatworms
• Describe the structural organization of nematodes
• Compare the internal systems and the appendage specialization of arthropods

The animal phyla of this and subsequent modules are triploblastic and have an embryonic mesoderm sandwiched
between the ectoderm and endoderm. These phyla are also bilaterally symmetrical, meaning that a longitudinal
section will divide them into right and left sides that are mirror images of each other. Associated with bilateralism is
the beginning of cephalization, the evolution of a concentration of nervous tissues and sensory organs in the head of
the organism, which is where the organism first encounters its environment.

The flatworms are acoelomate organisms that include free-living and parasitic forms. The nematodes, or
roundworms, possess a pseudocoelom and consist of both free-living and parasitic forms. Finally, the arthropods,
one of the most successful taxonomic groups on the planet, are coelomate organisms with a hard exoskeleton and
jointed appendages. The nematodes and the arthropods belong to a clade with a common ancestor, called
Ecdysozoa. The name comes from the word ecdysis, which refers to the periodic shedding, or molting, of the
exoskeleton. The ecdysozoan phyla have a hard cuticle covering their bodies that must be periodically shed and
replaced for them to increase in size.

Flatworms
The relationships among flatworms, or phylum Platyhelminthes, is being revised and the description here will follow
the traditional groupings. Most flatworms are parasitic, including important parasites of humans. Flatworms have
three embryonic germ layers that give rise to surfaces covering tissues, internal tissues, and the lining of the
digestive system. The epidermal tissue is a single layer of cells or a layer of fused cells covering a layer of circular
muscle above a layer of longitudinal muscle. The mesodermal tissues include support cells and secretory cells that
secrete mucus and other materials to the surface. The flatworms are acoelomate, so their bodies contain no cavities
or spaces between the outer surface and the inner digestive tract.

Physiological Processes of Flatworms

Free-living species of flatworms are predators or scavengers, whereas parasitic forms feed from the tissues of their
hosts. Most flatworms have an incomplete digestive system with an opening, the “mouth,” that is also used to expel
digestive system wastes. Some species also have an anal opening. The gut may be a simple sac or highly branched.
364 15 • Diversity of Animals

Digestion is extracellular, with enzymes secreted into the space by cells lining the tract, and digested materials
taken into the same cells by phagocytosis. One group, the cestodes, does not have a digestive system, because their
parasitic lifestyle and the environment in which they live (suspended within the digestive cavity of their host) allows
them to absorb nutrients directly across their body wall. Flatworms have an excretory system with a network of
tubules throughout the body that open to the environment and nearby flame cells, whose cilia beat to direct waste
fluids concentrated in the tubules out of the body. The system is responsible for regulation of dissolved salts and
excretion of nitrogenous wastes. The nervous system consists of a pair of nerve cords running the length of the body
with connections between them and a large ganglion or concentration of nerve cells at the anterior end of the worm;
here, there may also be a concentration of photosensory and chemosensory cells (Figure 15.15).

FIGURE 15.15 This planarian is a free-living flatworm that has an incomplete digestive system, an excretory system with a network of
tubules throughout the body, and a nervous system made up of nerve cords running the length of the body with a concentration of nerves
and photosensory and chemosensory cells at the anterior end.

Since there is no circulatory or respiratory system, gas and nutrient exchange is dependent on diffusion and
intercellular junctions. This necessarily limits the thickness of the body in these organisms, constraining them to be
“flat” worms. Most flatworm species are monoecious (hermaphroditic, possessing both sets of sex organs), and
fertilization is typically internal. Asexual reproduction is common in some groups in which an entire organism can be
regenerated from just a part of itself.

Diversity of Flatworms
Flatworms are traditionally divided into four classes: Turbellaria, Monogenea, Trematoda, and Cestoda (Figure
15.16). The turbellarians include mainly free-living marine species, although some species live in freshwater or
moist terrestrial environments. The simple planarians found in freshwater ponds and aquaria are examples. The
epidermal layer of the underside of turbellarians is ciliated, and this helps them move. Some turbellarians are
capable of remarkable feats of regeneration in which they may regrow the body, even from a small fragment.

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 15.3 • Flatworms, Nematodes, and Arthropods 365

FIGURE 15.16 Phylum Platyhelminthes is divided into four classes: (a) Bedford’s Flatworm (Pseudobiceros bedfordi) and the (b) planarian
belong to class Turbellaria; (c) the Trematoda class includes about 20,000 species, most of which are parasitic; (d) class Cestoda includes
tapeworms such as this Taenia saginata; and the parasitic class Monogenea (not shown). (credit a: modification of work by Jan Derk; credit
c: modification of work by “Sahaquiel9102”/Wikimedia Commons; credit d: modification of work by CDC)

The monogeneans are external parasites mostly of fish with life cycles consisting of a free-swimming larva that
attaches to a fish to begin transformation to the parasitic adult form. They have only one host during their life,
typically of just one species. The worms may produce enzymes that digest the host tissues or graze on surface
mucus and skin particles. Most monogeneans are hermaphroditic, but the sperm develop first, and it is typical for
them to mate between individuals and not to self-fertilize.

The trematodes, or flukes, are internal parasites of mollusks and many other groups, including humans. Trematodes
have complex life cycles that involve a primary host in which sexual reproduction occurs and one or more secondary
hosts in which asexual reproduction occurs. The primary host is almost always a mollusk. Trematodes are
responsible for serious human diseases including schistosomiasis, caused by a blood fluke (Schistosoma). The
disease infects an estimated 200 million people in the tropics and leads to organ damage and chronic symptoms
including fatigue. Infection occurs when a human enters the water, and a larva, released from the primary snail host,
locates and penetrates the skin. The parasite infects various organs in the body and feeds on red blood cells before
reproducing. Many of the eggs are released in feces and find their way into a waterway where they are able to
reinfect the primary snail host.

The cestodes, or tapeworms, are also internal parasites, mainly of vertebrates. Tapeworms live in the intestinal tract
of the primary host and remain fixed using a sucker on the anterior end, or scolex, of the tapeworm body. The
remaining body of the tapeworm is made up of a long series of units called proglottids, each of which may contain an
excretory system with flame cells, but will contain reproductive structures, both male and female. Tapeworms do
not have a digestive system, they absorb nutrients from the food matter passing them in the host’s intestine.
Proglottids are produced at the scolex and are pushed to the end of the tapeworm as new proglottids form, at which
point, they are “mature” and all structures except fertilized eggs have degenerated. Most reproduction occurs by
cross-fertilization. The proglottid detaches and is released in the feces of the host. The fertilized eggs are eaten by
an intermediate host. The juvenile worms emerge and infect the intermediate host, taking up residence, usually in
muscle tissue. When the muscle tissue is eaten by the primary host, the cycle is completed. There are several
tapeworm parasites of humans that are acquired by eating uncooked or poorly cooked pork, beef, and fish.
366 15 • Diversity of Animals

Nematodes
The phylum Nematoda, or roundworms, includes more than 28,000 species with an estimated 16,000 parasitic
species. The name Nematoda is derived from the Greek word “nemos,” which means “thread.” Nematodes are
present in all habitats and are extremely common, although they are usually not visible (Figure 15.17).

FIGURE 15.17 (a) An scanning electron micrograph of the nematode Heterodera glycines and (b) a schematic representation of the
anatomy of a nematode are shown. (credit a: modification of work by USDA, ARS; scale-bar data from Matt Russell)

Most nematodes look similar to each other: slender tubes, tapered at each end (Figure 15.17). Nematodes are
pseudocoelomates and have a complete digestive system with a distinct mouth and anus.

The nematode body is encased in a cuticle, a flexible but tough exoskeleton, or external skeleton, which offers
protection and support. The cuticle contains a carbohydrate-protein polymer called chitin. The cuticle also lines the
pharynx and rectum. Although the exoskeleton provides protection, it restricts growth, and therefore must be
continually shed and replaced as the animal increases in size.

A nematode’s mouth opens at the anterior end with three or six lips and, in some species, teeth in the form of
cuticular extensions. There may also be a sharp stylet that can protrude from the mouth to stab prey or pierce plant
or animal cells. The mouth leads to a muscular pharynx and intestine, leading to the rectum and anal opening at the
posterior end.

Physiological Processes of Nematodes

In nematodes, the excretory system is not specialized. Nitrogenous wastes are removed by diffusion. In marine
nematodes, regulation of water and salt is achieved by specialized glands that remove unwanted ions while

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 15.3 • Flatworms, Nematodes, and Arthropods 367

maintaining internal body fluid concentrations.

Most nematodes have four nerve cords that run along the length of the body on the top, bottom, and sides. The
nerve cords fuse in a ring around the pharynx, to form a head ganglion or “brain” of the worm, as well as at the
posterior end to form the tail ganglion. Beneath the epidermis lies a layer of longitudinal muscles that permits only
side-to-side, wave-like undulation of the body.

LINK TO LEARNING
View this video (http://openstax.org/l/nematode) to see nematodes move about and feed on bacteria.

Nematodes employ a diversity of sexual reproductive strategies depending on the species; they may be
monoecious, dioecious (separate sexes), or may reproduce asexually by parthenogenesis. Caenorhabditis elegans is
nearly unique among animals in having both self-fertilizing hermaphrodites and a male sex that can mate with the
hermaphrodite.

Arthropoda
The name “arthropoda” means “jointed legs,” which aptly describes each of the enormous number of species
belonging to this phylum. Arthropoda dominate the animal kingdom with an estimated 85 percent of known
species, with many still undiscovered or undescribed. The principal characteristics of all the animals in this phylum
are functional segmentation of the body and the presence of jointed appendages (Figure 15.18). As members of
Ecdysozoa, arthropods also have an exoskeleton made principally of chitin. Arthropoda is the largest phylum in the
animal world in terms of numbers of species, and insects form the single largest group within this phylum.
Arthropods are true coelomate animals and exhibit prostostomic development.

FIGURE 15.18 Trilobites, like the one in this fossil, are an extinct group of arthropods. (credit: Kevin Walsh)

Physiological Processes of Arthropods

A unique feature of arthropods is the presence of a segmented body with fusion of certain sets of segments to give
rise to functional segments. Fused segments may form a head, thorax, and abdomen, or a cephalothorax and
abdomen, or a head and trunk. The coelom takes the form of a hemocoel (or blood cavity). The open circulatory
system, in which blood bathes the internal organs rather than circulating in vessels, is regulated by a two-
chambered heart. Respiratory systems vary, depending on the group of arthropod: Insects and myriapods use a
series of tubes (tracheae) that branch throughout the body, open to the outside through openings called spiracles,
and perform gas exchange directly between the cells and air in the tracheae. Aquatic crustaceans use gills,
arachnids employ “book lungs,” and aquatic chelicerates use “book gills.” The book lungs of arachnids are internal
stacks of alternating air pockets and hemocoel tissue shaped like the pages of a book. The book gills of crustaceans
are external structures similar to book lungs with stacks of leaf-like structures that exchange gases with the
surrounding water (Figure 15.19).
368 15 • Diversity of Animals

FIGURE 15.19 The book lungs of (a) arachnids are made up of alternating air pockets and hemocoel tissue shaped like a stack of books.
The book gills of (b) crustaceans are similar to book lungs but are external so that gas exchange can occur with the surrounding water.
(credit a: modification of work by Ryan Wilson based on original work by John Henry Comstock; credit b: modification of work by Angel
Schatz)

Arthropod Diversity
Phylum Arthropoda includes animals that have been successful in colonizing terrestrial, aquatic, and aerial habitats.
The phylum is further classified into five subphyla: Trilobitomorpha (trilobites), Hexapoda (insects and relatives),
Myriapoda (millipedes, centipedes, and relatives), Crustacea (crabs, lobsters, crayfish, isopods, barnacles, and
some zooplankton), and Chelicerata (horseshoe crabs, arachnids, scorpions, and daddy longlegs). Trilobites are an
extinct group of arthropods found from the Cambrian period (540–490 million years ago) until they became extinct
in the Permian (300–251 million years ago) that are probably most closely related to the Chelicerata. The 17,000
described species have been identified from fossils (Figure 15.18).

The Hexapoda have six legs (three pairs) as their name suggests. Hexapod segments are fused into a head, thorax,
and abdomen (Figure 15.20). The thorax bears the wings and three pairs of legs. The insects we encounter on a
daily basis—such as ants, cockroaches, butterflies, and bees—are examples of Hexapoda.

FIGURE 15.20 In this basic anatomy of a hexapod, note that insects have a developed digestive system (yellow), a respiratory system
(blue), a circulatory system (red), and a nervous system (purple).

Subphylum Myriapoda includes arthropods with legs that may vary in number from 10 to 750. This subphylum
includes 13,000 species; the most commonly found examples are millipedes and centipedes. All myriapods are
terrestrial animals and prefer a humid environment (Figure 15.21).

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 15.3 • Flatworms, Nematodes, and Arthropods 369

FIGURE 15.21 (a) The centipede Scutigera coleoptrata has up to 15 pairs of legs. (b) This North American millipede (Narceus americanus)
bears many legs, although not one thousand, as its name might suggest. (credit a: modification of work by Bruce Marlin; credit b:
modification of work by Cory Zanker)

Crustaceans, such as shrimp, lobsters, crabs, and crayfish, are the dominant aquatic arthropods. A few crustaceans
are terrestrial species like the pill bugs or sow bugs. The number of described crustacean species stands at about
3
47,000.

Although the basic body plan in crustaceans is similar to the Hexapoda—head, thorax, and abdomen—the head and
thorax may be fused in some species to form a cephalothorax, which is covered by a plate called the carapace
(Figure 15.22). The exoskeleton of many species is also infused with calcium carbonate, which makes it even
stronger than in other arthropods. Crustaceans have an open circulatory system in which blood is pumped into the
hemocoel by the dorsal heart. Most crustaceans typically have separate sexes, but some, like barnacles, may be
hermaphroditic. Serial hermaphroditism, in which the gonad can switch from producing sperm to ova, is also found
in some crustacean species. Larval stages are seen in the early development of many crustaceans. Most
crustaceans are carnivorous, but detritivores and filter feeders are also common.

FIGURE 15.22 The crayfish is an example of a crustacean. It has a carapace around the cephalothorax and the heart in the dorsal thorax
area. (credit: Jane Whitney)

Subphylum Chelicerata includes animals such as spiders, scorpions, horseshoe crabs, and sea spiders. This
4
subphylum is predominantly terrestrial, although some marine species also exist. An estimated 103,000 described
species are included in subphylum Chelicerata.

The body of chelicerates may be divided into two parts and a distinct “head” is not always discernible. The phylum
derives its name from the first pair of appendages: the chelicerae (Figure 15.23a), which are specialized
mouthparts. The chelicerae are mostly used for feeding, but in spiders, they are typically modified to inject venom
into their prey (Figure 15.23b). As in other members of Arthropoda, chelicerates also utilize an open circulatory
system, with a tube-like heart that pumps blood into the large hemocoel that bathes the internal organs. Aquatic
chelicerates utilize gill respiration, whereas terrestrial species use either tracheae or book lungs for gaseous
exchange.

3 “Number of Living Species in Australia and the World,” A.D. Chapman, Australia Biodiversity Information Services, last modified August
26, 2010, http://www.environment.gov.au/biodiversity/abrs/publications/other/species-numbers/2009/03-exec-summary.html.
4 “Number of Living Species in Australia and the World,” A.D. Chapman, Australia Biodiversity Information Services, last modified August
26, 2010, http://www.environment.gov.au/biodiversity/abrs/publications/other/species-numbers/2009/03-exec-summary.html.
370 15 • Diversity of Animals

FIGURE 15.23 (a) The chelicerae (first set of appendages, circled) are well developed in the Chelicerata, which includes scorpions (a) and
spiders (b). (credit a: modification of work by Kevin Walsh; credit b: modification of work by Marshal Hedin)

LINK TO LEARNING
Click through (http://openstax.org/l/arthropod2) this lesson on arthropods to explore interactive habitat maps and
more.

15.4 Mollusks and Annelids

LEARNING OBJECTIVES
By the end of this section, you will be able to:
• Describe the unique anatomical features of mollusks
• Describe the features of an animal classified in phylum Annelida

The mollusks are a diverse group (85,000 described species) of mostly marine species. They have a variety of forms,
ranging from large predatory squid and octopus, some of which show a high degree of intelligence, to small grazing
forms with elaborately sculpted and colored shells. The annelids traditionally include the oligochaetes, which
include the earthworms and leeches, the polychaetes, which are a marine group, and two other smaller classes.

The phyla Mollusca and Annelida belong to a clade called the Lophotrochozoa, which also includes the phylum
Nemertea, or ribbon worms (Figure 15.3). They are distinct from the Ecdysozoa (nematodes and arthropods) based
on evidence from analysis of their DNA, which has changed our views of the relationships among invertebrates.

Phylum Mollusca
Mollusca is the predominant phylum in marine environments, where it is estimated that 23 percent of all known
marine species belong to this phylum. It is the second most diverse phylum of animals with over 75,000 described
species. The name “mollusca” signifies a soft body, as the earliest descriptions of mollusks came from observations
of unshelled, soft-bodied cuttlefish (squid relatives). Although mollusk body forms vary, they share key
characteristics, such as a ventral, muscular foot that is typically used for locomotion; the visceral mass, which
contains most of the internal organs of the animal; and a dorsal mantle, which is a flap of tissue over the visceral
mass that creates a space called the mantle cavity. The mantle may or may not secrete a shell of calcium carbonate.
In addition, many mollusks have a scraping structure at the mouth, called a radula (Figure 15.24).

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 15.4 • Mollusks and Annelids 371

The muscular foot varies in shape and function, depending on the type of mollusk (described below in the section on
mollusk diversity). It is a retractable as well as extendable organ, used for locomotion and anchorage. Mollusks are
eucoelomates, but the coelomic cavity is restricted to a cavity around the heart in adult animals. The mantle cavity,
formed inside the mantle, develops independently of the coelomic cavity. It is a multi-purpose space, housing the
gills, the anus, organs for sensing food particles in the water, and an outlet for gametes. Most mollusks have an open
circulatory system with a heart that circulates the hemolymph in open spaces around the organs. The octopuses and
squid are an exception to this and have a closed circulatory system with two hearts that move blood through the
gills and a third, systemic heart that pumps blood through the rest of the body.

VISUAL CONNECTION

FIGURE 15.24 There are many species and variations of mollusks; the gastropod mollusk anatomy is shown here, which shares many
characteristics common with other groups.

Which of the following statements about the anatomy of a mollusk is false?

a. Mollusks have a radula for scraping food.

b. Mollusks have ventral nerve cords.
c. The tissue beneath the shell is called the mantle.
d. The mantle cavity contains hemolymph.

Mollusk Diversity
This phylum is comprised of seven classes: Aplacophora, Monoplacophora, Polyplacophora, Bivalvia, Gastropoda,
Cephalopoda, and Scaphopoda.

Class Aplacophora (“bearing no plates”) includes worm-like animals living mostly on deep ocean bottoms. These
animals lack a shell but have aragonite spicules on their skin. Members of class Monoplacophora (“bearing one
plate”) have a single, cap-like shell enclosing the body. The monoplacophorans were believed extinct and only
known as fossils until the discovery of Neopilina galatheae in 1952. Today, scientists have identified nearly two
dozen living species.

Animals in the class Polyplacophora (“bearing many plates”) are commonly known as “chitons” and bear an armor-
like, eight-plated shell (Figure 15.25). These animals have a broad, ventral foot that is adapted for attachment to
rocks and a mantle that extends beyond the shell in the form of a girdle. They breathe with ctenidia (gills) present
ventrally. These animals have a radula modified for scraping. A single pair of nephridia for excretion is present.
372 15 • Diversity of Animals

FIGURE 15.25 This chiton from the class Polyplacophora has the eight-plated shell indicative of its class. (credit: Jerry Kirkhart)

Class Bivalvia (“two shells”) includes clams, oysters, mussels, scallops, and geoducks. They are found in marine and
freshwater habitats. As the name suggests, bivalves are enclosed in a pair of shells (or valves) that are hinged at the
dorsal side. The body is flattened on the sides. They feed by filtering particles from water and a radula is absent.
They exchange gases using a pair of ctenidia, and excretion and osmoregulation are carried out by a pair of
nephridia. In some species, the posterior edges of the mantle may fuse to form two siphons that inhale and exhale
water. Some bivalves like oysters and mussels have the unique ability to secrete and deposit a calcareous nacre or
“mother of pearl” around foreign particles that enter the mantle cavity. This property is commercially exploited to
produce pearls.

LINK TO LEARNING
Watch animations of clams (http://openstax.org/l/clams2) and mussels (http://openstax.org/l/mussels2) feeding to
understand more about bivalves.

Gastropods (“stomach foot”) include well-known mollusks like snails, slugs, conchs, sea hares, and sea butterflies.
Gastropods include shell-bearing species as well as species with a reduced shell. These animals are asymmetrical
and usually present a coiled shell (Figure 15.26).

FIGURE 15.26 (a) Like many gastropods, this snail has a stomach foot and a coiled shell. (b) This slug, which is also a gastropod, lacks a
shell. (credit a: modification of work by Murray Stevenson; credit b: modification of work by Rosendahl)

The visceral mass in the shelled species is characteristically twisted and the foot is modified for crawling. Most
gastropods bear a head with tentacles that support eyes. A complex radula is used to scrape food particles from the
substrate. The mantle cavity encloses the ctenidia as well as a pair of nephridia.

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 15.4 • Mollusks and Annelids 373

The class Cephalopoda (“head foot” animals) includes octopuses, squids, cuttlefish, and nautilus. Cephalopods
include shelled and reduced-shell groups. They display vivid coloration, typically seen in squids and octopuses,
which is used for camouflage. The ability of some octopuses to rapidly adjust their colors to mimic a background
pattern or to startle a predator is one of the more awe-inspiring feats of these animals. All animals in this class are
predators and have beak-like jaws. All cephalopods have a well-developed nervous system, complex eyes, and a
closed circulatory system. The foot is lobed and developed into tentacles and a funnel, which is used for locomotion.
Suckers are present on the tentacles in octopuses and squid. Ctenidia are enclosed in a large mantle cavity and are
serviced by large blood vessels, each with its own heart.

Cephalopods (Figure 15.27) are able to move quickly via jet propulsion by contracting the mantle cavity to forcefully
eject a stream of water. Cephalopods have separate sexes, and the females of some species care for the eggs for an
extended period of time. Although the shell is much reduced and internal in squid and cuttlefish, and absent
altogether in octopus, nautilus live inside a spiral, multi-chambered shell that is filled with gas or water to regulate
buoyancy.

FIGURE 15.27 The (a) nautilus, (b) giant cuttlefish, (c) reef squid, and (d) blue-ring octopus are all members of the class Cephalopoda.
(credit a: modification of work by J. Baecker; credit b: modification of work by Adrian Mohedano; credit c: modification of work by Silke
Baron; credit d: modification of work by Angell Williams)

Members of the class Scaphopoda (“boat feet”) are known colloquially as “tusk shells” or “tooth shells.” Tooth
shells are open at both ends and usually lie buried in sand with the front opening exposed to water and the reduced
head end projecting from the back of the shell. Tooth shells have a radula and a foot modified into tentacles, each
with a bulbous end that catches and manipulates prey (Figure 15.28).
374 15 • Diversity of Animals

FIGURE 15.28 Antalis vulgaris shows the classic Dentaliidae shape that gives these animals their common name of “tusk shell.” (credit:
Georges Jansoone)

Annelida
Phylum Annelida are segmented worms found in marine, terrestrial, and freshwater habitats, but the presence of
water or humidity is a critical factor for their survival in terrestrial habitats. The name of the phylum is derived from
the Latin word annellus, which means a small ring. Approximately 16,500 species have been described. The phylum
includes earthworms, polychaete worms, and leeches. Like mollusks, annelids exhibit protostomic development.

Annelids are bilaterally symmetrical and have a worm-like appearance. Their particular segmented body plan results
in repetition of internal and external features in each body segment. This type of body plan is called metamerism.
The evolutionary benefit of such a body plan is thought to be the capacity it allows for the evolution of independent
modifications in different segments that perform different functions. The overall body can then be divided into head,
body, and tail.

Physiological Processes of Annelida

The skin of annelids is protected by a cuticle that is thinner than the cuticle of the ecdysozoans and does not need to
be molted for growth. Chitinous hairlike extensions, anchored in the skin and projecting from the cuticle, called
chaetae, are present in every segment in most groups. The chaetae are a defining character of annelids. Polychaete
worms have paired, unjointed limbs called parapodia on each segment used for locomotion and breathing. Beneath
the cuticle there are two layers of muscle, one running around its circumference (circular) and one running the
length of the worm (longitudinal). Annelids have a true coelom in which organs are distributed and bathed in
coelomic fluid. Annelids possess a well-developed complete digestive system with specialized organs: mouth,
muscular pharynx, esophagus, and crop. A cross-sectional view of a body segment of an earthworm is shown in
Figure 15.29; each segment is limited by a membrane that divides the body cavity into compartments.

Annelids have a closed circulatory system with muscular pumping “hearts” in the anterior segments, dorsal and
ventral blood vessels that run the length of the body with connections in each segment, and capillaries that service
individual tissues. Gas exchange occurs across the moist body surface. Excretion is carried out by pairs of primitive
“kidneys” called metanephridia that consist of a convoluted tubule and an open, ciliated funnel present in every
segment. Annelids have a well-developed nervous system with two ventral nerve cords and a nerve ring of fused
ganglia present around the pharynx.

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 15.4 • Mollusks and Annelids 375

FIGURE 15.29 In this schematic showing the basic anatomy of annelids, the digestive system is indicated in green, the nervous system is
indicated in yellow, and the circulatory system is indicated in red.

Annelids may be either monoecious with permanent gonads (as in earthworms and leeches) or dioecious with
temporary or seasonal gonads (as in polychaetes).

LINK TO LEARNING
This video and animation (http://openstax.org/l/annelid2) provides a close-up look at annelid anatomy.

Annelid Diversity
Phylum Annelida includes the classes Polychaeta and Clitellata (Figure 15.30); the latter contains subclasses
Oligochaeta, Hirudinoidea, and Branchiobdellida.

Earthworms are the most abundant members of the subclass Oligochaeta, distinguished by the presence of the
clitellum, a ring structure in the skin that secretes mucus to bind mating individuals and forms a protective cocoon
for the eggs. They also have a few, reduced chaetae (oligo- = “few”; -chaetae = “hairs”). The number and size of
chaetae is greatly diminished in oligochaetes as compared to the polychaetes (poly- = “many”; -chaetae = “hairs”).
The chaetae of polychaetes are also arranged within fleshy, flat, paired appendages on each segment called
parapodia.

The subclass Hirudinoidea includes leeches. Significant differences between leeches and other annelids include the
development of suckers at the anterior and posterior ends, and the absence of chaetae. Additionally, the
segmentation of the body wall may not correspond to internal segmentation of the coelomic cavity. This adaptation
may allow leeches to swell when ingesting blood from host vertebrates. The subclass Branchiobdellida includes
about 150 species that show similarity to leeches as well as oligochaetes. All species are obligate symbionts,
meaning that they can only survive associated with their host, mainly with freshwater crayfish. They feed on the
algae that grows on the carapace of the crayfish.
376 15 • Diversity of Animals

FIGURE 15.30 The (a) earthworm and (b) leech are both annelids. (credit a: modification of work by "schizoform"/Flickr; credit b:
modification of work by "Sarah G..."/Flickr)

15.5 Echinoderms and Chordates

LEARNING OBJECTIVES
By the end of this section, you will be able to:
• Describe the distinguishing characteristics of echinoderms
• Describe the distinguishing characteristics of chordates

Deuterostomes include the phyla Echinodermata and Chordata (which includes the vertebrates) and two smaller
phyla. Deuterostomes share similar patterns of early development.

Echinoderms
Echinodermata are named for their spiny skin (from the Greek “echinos” meaning “spiny” and “dermos” meaning
5
“skin”). The phylum includes about 7,000 described living species, such as sea stars, sea cucumbers, sea urchins,
sand dollars, and brittle stars. Echinodermata are exclusively marine.

Adult echinoderms exhibit pentaradial symmetry and have a calcareous endoskeleton made of ossicles (Figure
15.31), although the early larval stages of all echinoderms have bilateral symmetry. The endoskeleton is developed
by epidermal cells, which may also possess pigment cells, giving vivid colors to these animals, as well as cells laden
with toxins. These animals have a true coelom, a portion of which is modified into a unique circulatory system called
a water vascular system. An interesting feature of these animals is their power to regenerate, even when over 75
percent of their body mass is lost.

Physiological Processes of Echinoderms

Echinoderms have a unique system for gas exchange, nutrient circulation, and locomotion called the water vascular
system. The system consists of a central ring canal and radial canals extending along each arm. Water circulates
through these structures allowing for gas, nutrient, and waste exchange. A structure on top of the body, called the
madreporite, regulates the amount of water in the water vascular system. “Tube feet,” which protrude through
openings in the endoskeleton, may be expanded or contracted using the hydrostatic pressure in the system. The
system allows for slow movement, but a great deal of power, as witnessed when the tube feet latch on to opposite
halves of a bivalve mollusk, like a clam, and slowly, but surely pull the shells apart, exposing the flesh within.

5 “Number of Living Species in Australia and the World,” A.D. Chapman, Australia Biodiversity Information Services, last modified August
26, 2010, http://www.environment.gov.au/biodiversity/abrs/publications/other/species-numbers/2009/03-exec-summary.html.

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 15.5 • Echinoderms and Chordates 377

FIGURE 15.31 This diagram shows the anatomy of a sea star.

The echinoderm nervous system has a nerve ring at the center and five radial nerves extending outward along the
arms. There is no centralized nervous control. Echinoderms have separate sexes and release their gametes into the
water where fertilization takes place. Echinoderms may also reproduce asexually through regeneration from body
parts.

Echinoderm Diversity
This phylum is divided into five classes: Asteroidea (sea stars), Ophiuroidea (brittle stars), Echinoidea (sea urchins
and sand dollars), Crinoidea (sea lilies or feather stars), and Holothuroidea (sea cucumbers) (Figure 15.32).

Perhaps the best-known echinoderms are members of the class Asteroidea, or sea stars. They come in a large
variety of shapes, colors, and sizes, with more than 1,800 species known. The characteristics of sea stars that set
them apart from other echinoderm classes include thick arms that extend from a central disk where organs
penetrate into the arms. Sea stars use their tube feet not only for gripping surfaces but also for grasping prey. Sea
stars have two stomachs, one of which they can evert through their mouths to secrete digestive juices into or onto
prey before ingestion. This process can essentially liquefy the prey and make digestion easier.

LINK TO LEARNING
View this video (http://openstax.org/l/echinoderm2) to explore a sea star’s body plan up close, watch one move
across the sea floor, and see it devour a mussel.

Brittle stars have long, thin arms that do not contain any organs. Sea urchins and sand dollars do not have arms but
are hemispherical or flattened with five rows of tube feet, which help them in slow movement. Sea lilies and feather
stars are stalked suspension feeders. Sea cucumbers are soft-bodied and elongate with five rows of tube feet and a
series of tube feet around the mouth that are modified into tentacles used in feeding.
378 15 • Diversity of Animals

FIGURE 15.32 Different members of Echinodermata include the (a) sea star in class Asteroidea, (b) the brittle star in class Ophiuroidea, (c)
the sea urchins of class Echinoidea, (d) the sea lilies belonging to class Crinoidea, and (e) sea cucumbers representing class Holothuroidea.
(credit a: modification of work by Adrian Pingstone; credit b: modification of work by Joshua Ganderson; credit c: modification of work by
Samuel Chow; credit d: modification of work by Sarah Depper; credit e: modification of work by Ed Bierman)

Chordates
The majority of species in the phylum Chordata are found in the subphylum Vertebrata, which include many species
with which we are familiar. The vertebrates contain more than 60,000 described species, divided into major
groupings of the lampreys, fishes, amphibians, reptiles, birds, and mammals.

Animals in the phylum Chordata share four key features that appear at some stage of their development: a
notochord, a dorsal hollow nerve cord, pharyngeal slits, and a post-anal tail (Figure 15.33). In certain groups, some
of these traits are present only during embryonic development.

The chordates are named for the notochord, which is a flexible, rod-shaped structure that is found in the embryonic
stage of all chordates and in the adult stage of some chordate species. It is located between the digestive tube and
the nerve cord, and provides skeletal support through the length of the body. In some chordates, the notochord acts
as the primary axial support of the body throughout the animal’s lifetime. In vertebrates, the notochord is present
during embryonic development, at which time it induces the development of the neural tube and serves as a support
for the developing embryonic body. The notochord, however, is not found in the postnatal stage of vertebrates; at
this point, it has been replaced by the vertebral column (the spine).

The dorsal hollow nerve cord is derived from ectoderm that sinks below the surface of the skin and rolls into a
hollow tube during development. In chordates, it is located dorsally to the notochord. In contrast, other animal
phyla possess solid nerve cords that are located either ventrally or laterally. The nerve cord found in most chordate
embryos develops into the brain and spinal cord, which compose the central nervous system.

Pharyngeal slits are openings in the pharynx, the region just posterior to the mouth, that extend to the outside
environment. In organisms that live in aquatic environments, pharyngeal slits allow for the exit of water that enters
the mouth during feeding. Some invertebrate chordates use the pharyngeal slits to filter food from the water that
enters the mouth. In fishes, the pharyngeal slits are modified into gill supports, and in jawed fishes, jaw supports. In
tetrapods, the slits are further modified into components of the ear and tonsils, since there is no longer any need for
gill supports in these air-breathing animals. Tetrapod means “four-footed,” and this group includes amphibians,
reptiles, birds, and mammals. (Birds are considered tetrapods because they evolved from tetrapod ancestors.)

The post-anal tail is a posterior elongation of the body extending beyond the anus. The tail contains skeletal

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 15.5 • Echinoderms and Chordates 379

elements and muscles, which provide a source of locomotion in aquatic species, such as fishes. In some terrestrial
vertebrates, the tail may also function in balance, locomotion, courting, and signaling when danger is near. In many
species, the tail is absent or reduced; for example, in apes, including humans, it is present in the embryo, but
reduced in size and nonfunctional in adults.

VISUAL CONNECTION

FIGURE 15.33 In chordates, four common features appear at some point in development: a notochord, a dorsal hollow nerve cord,
pharyngeal slits, and a post-anal tail. The anatomy of a cephalochordate shown here illustrates all of these features.

Which of the following statements about common features of chordates is true?

a. The dorsal hollow nerve cord is part of the chordate central nervous system.
b. In vertebrate fishes, the pharyngeal slits become the gills.
c. Humans are not chordates because humans do not have a tail.
d. Vertebrates do not have a notochord at any point in their development; instead, they have a vertebral column.

Invertebrate Chordates
In addition to the vertebrates, the phylum Chordata contains two clades of invertebrates: Urochordata (tunicates)
and Cephalochordata (lancelets). Members of these groups possess the four distinctive features of chordates at
some point during their development.

The tunicates (Figure 15.34) are also called sea squirts. The name tunicate derives from the cellulose-like
carbohydrate material, called the tunic, which covers the outer body. Although tunicates are classified as chordates,
the adult forms are much modified in body plan and do not have a notochord, a dorsal hollow nerve cord, or a post-
anal tail, although they do have pharyngeal slits. The larval form possesses all four structures. Most tunicates are
hermaphrodites. Tunicate larvae hatch from eggs inside the adult tunicate’s body. After hatching, a tunicate larva
swims for a few days until it finds a suitable surface on which it can attach, usually in a dark or shaded location. It
then attaches by the head to the substrate and undergoes metamorphosis into the adult form, at which point the
notochord, nerve cord, and tail disappear.

FIGURE 15.34 (a) This photograph shows a colony of the tunicate Botrylloides violaceus. In the (b) larval stage, the tunicate can swim
freely until it attaches to a substrate to become (c) an adult. (credit a: modification of work by Dr. Dwayne Meadows, NOAA/NMFS/OPR)
380 15 • Diversity of Animals

Most tunicates live a sessile existence in shallow ocean waters and are suspension feeders. The primary foods of
tunicates are plankton and detritus. Seawater enters the tunicate’s body through its incurrent siphon. Suspended
material is filtered out of this water by a mucus net (pharyngeal slits) and is passed into the intestine through the
action of cilia. The anus empties into the excurrent siphon, which expels wastes and water.

Lancelets possess a notochord, dorsal hollow nerve cord, pharyngeal slits, and a post-anal tail in the adult stage
(Figure 15.35). The notochord extends into the head, which gives the subphylum its name (Cephalochordata).
Extinct fossils of this subphylum date to the middle of the Cambrian period (540–488 mya).The living forms, the
lancelets, are named for their blade-like shape. Lancelets are only a few centimeters long and are usually found
buried in sand at the bottom of warm temperate and tropical seas. Like tunicates, they are suspension feeders.

FIGURE 15.35 Adult lancelets retain the four key features of chordates: a notochord, a dorsal hollow nerve cord, pharyngeal slits, and a
post-anal tail.

15.6 Vertebrates
LEARNING OBJECTIVES
By the end of this section, you will be able to:
• Describe the difference between jawless and jawed fishes
• Explain the main characteristics of amphibians, reptiles, and birds
• Describe the derived characteristics in birds that facilitate flight
• Name and describe the distinguishing features of the three main groups of mammals
• Describe the derived features that distinguish primates from other animals

Vertebrates are among the most recognizable organisms of the animal kingdom (Figure 15.36). More than 62,000
vertebrate species have been identified. The vertebrate species now living represent only a small portion of the
vertebrates that have existed. The best-known extinct vertebrates are the dinosaurs, a unique group of reptiles,
reaching sizes not seen before or since in terrestrial animals. They were the dominant terrestrial animals for 150
million years, until they died out near the end of the Cretaceous period in a mass extinction. A great deal is known
about the anatomy of the dinosaurs, given the preservation of their skeletal elements in the fossil record.

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 15.6 • Vertebrates 381

FIGURE 15.36 Examples of critically endangered vertebrate species include (a) the Siberian tiger (Panthera tigris altaica), (b) the
Panamanian golden frog (Atelopus zeteki), and (c) the Philippine eagle (Pithecophaga jefferyi). (credit a: modification of work by Dave Pape;
credit b: modification of work by Brian Gratwicke; credit c: modification of work by "cuatrok77"/Flickr)

Fishes
Modern fishes include an estimated 31,000 species. Fishes were the earliest vertebrates, and jawless fishes were
the earliest of these. Jawless fishes—the present day hagfishes and lampreys—have a distinct cranium and complex
sense organs including eyes, distinguishing them from the invertebrate chordates. The jawed fishes evolved later
and are extraordinarily diverse today. Fishes are active feeders, rather than sessile, suspension feeders.

Jawless Fishes
Jawless fishes are craniates (which includes all the chordate groups except the tunicates and lancelets) that
represent an ancient vertebrate lineage that arose over one half-billion years ago. Some of the earliest jawless
fishes were the ostracoderms (which translates as “shell-skin”). Ostracoderms, now extinct, were vertebrate fishes
encased in bony armor, unlike present-day jawless fishes, which lack bone in their scales.

The clade Myxini includes 67 species of hagfishes. Hagfishes are eel-like scavengers that live on the ocean floor
and feed on dead invertebrates, other fishes, and marine mammals (Figure 15.37a). Hagfishes are entirely marine
and are found in oceans around the world except for the polar regions. A unique feature of these animals is the slime
glands beneath the skin that are able to release an extraordinary amount of mucus through surface pores. This
mucus may allow the hagfish to escape from the grip of predators. Hagfish are known to enter the bodies of dead or
dying organisms to devour them from the inside.

FIGURE 15.37 (a) Pacific hagfishes are scavengers that live on the ocean floor. (b) These parasitic sea lampreys attach to their lake trout
host by suction and use their rough tongues to rasp away flesh in order to feed on the trout’s blood. (credit a: modification of work by Linda
Snook, NOAA/CBNMS; credit b: modification of work by USGS)

The skeleton of a hagfish is composed of cartilage, which includes a cartilaginous notochord, which runs the length
of the body, and a skull. This notochord provides support to the fish’s body. Although they are craniates, hagfishes
are not vertebrates, since they do not replace the notochord with a vertebral column during development, as do the
vertebrates.

The clade Petromyzontidae includes approximately 40 species of lampreys. Lampreys are similar to hagfishes in
size and shape; however, lampreys have a brain case and incomplete vertebrae. Lampreys lack paired appendages
382 15 • Diversity of Animals

and bone, as do the hagfishes. As adults, lampreys are characterized by a toothed, funnel-like sucking mouth. Some
species are parasitic as adults, attaching to and feeding on the body fluids of fish (Figure 15.37b). Most species are
free-living.

Lampreys live primarily in coastal and fresh waters and have a worldwide temperate region distribution. All species
spawn in fresh waters. Eggs are fertilized externally, and the larvae are distinctly different from the adult form,
spending 3 to 15 years as suspension feeders. Once they attain sexual maturity, the adults reproduce and die within
days. Lampreys have a notochord as adults.

Jawed Fishes
Gnathostomes or “jaw-mouths” are vertebrates that have jaws and include both cartilaginous and bony fishes. One
of the most significant developments in early vertebrate evolution was the origin of the jaw, which is a hinged
structure attached to the cranium that allows an animal to grasp and tear its food. The evolution of jaws allowed
early gnathostomes to exploit food resources that were unavailable to jawless fishes.

The clade Chondrichthyes, the cartilaginous fishes, is diverse, consisting of sharks (Figure 15.38a), rays, and
skates, together with sawfishes and a few dozen species of fishes called chimaeras, or ghost sharks. Chondrichthyes
have paired fins and a skeleton made of cartilage. This clade arose approximately 370 million years ago in the
middle Devonian. They are thought to have descended from an extinct group that had a skeleton made of bone;
thus, the cartilaginous skeleton of Chondrichthyes is a later development. Parts of the shark skeleton are
strengthened by granules of calcium carbonate, but this is not the same as bone.

Most cartilaginous fishes live in marine habitats, with a few species living in fresh water for some or all of their lives.
Most sharks are carnivores that feed on live prey, either swallowing it whole or using their jaws and teeth to tear it
into smaller pieces. Shark teeth likely evolved from the jagged scales that cover their skin. Some species of sharks
and rays are suspension feeders that feed on plankton.

FIGURE 15.38 (a) This hammerhead shark is an example of a predatory cartilaginous fish. (b) This stingray blends into the sandy bottom of
the ocean floor when it is feeding or awaiting prey. (credit a: modification of work by Masashi Sugawara; credit b: modification of work by
"Sailn1"/Flickr)

Sharks have well-developed sense organs that aid them in locating prey, including a keen sense of smell and
electroreception, the latter being perhaps the most sensitive of any animal. Organs called ampullae of Lorenzini
allow sharks to detect the electromagnetic fields that are produced by all living things, including their prey.
Electroreception has only been observed in aquatic or amphibious animals. Sharks, together with most fishes, also
have a sense organ called the lateral line, which is used to detect movement and vibration in the surrounding water,
and a sense that is often considered homologous to “hearing” in terrestrial vertebrates. The lateral line is visible as
a darker stripe that runs along the length of the fish’s body.

Sharks reproduce sexually and eggs are fertilized internally. Most species are ovoviviparous, that is, the fertilized
egg is retained in the oviduct of the mother’s body, and the embryo is nourished by the egg yolk. The eggs hatch in
the uterus and young are born alive and fully functional. Some species of sharks are oviparous: They lay eggs that
hatch outside of the mother’s body. Embryos are protected by a shark egg case or “mermaid’s purse” that has the
consistency of leather. The shark egg case has tentacles that snag in seaweed and give the newborn shark cover. A
few species of sharks are viviparous, that is, the young develop within the mother’s body, and she gives live birth.

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 15.6 • Vertebrates 383

Rays and skates include more than 500 species and are closely related to sharks. They can be distinguished from
sharks by their flattened bodies, pectoral fins that are enlarged and fused to the head, and gill slits on their ventral
surface (Figure 15.38b). Like sharks, rays and skates have a cartilaginous skeleton. Most species are marine and live
on the sea floor, with nearly a worldwide distribution.

Bony Fishes
Members of the clade Osteichthyes, or bony fishes, are characterized by a bony skeleton. The vast majority of
present-day fishes belong to this group, which consists of approximately 30,000 species, making it the largest class
of vertebrates in existence today.

Nearly all bony fishes have an ossified skeleton with specialized bone cells (osteocytes) that produce and maintain a
calcium phosphate matrix. This characteristic has only reverted in a few groups of Osteichthyes, such as sturgeons
and paddlefish, which have primarily cartilaginous skeletons. The skin of bony fishes is often covered in overlapping
scales, and glands in the skin secrete mucus that reduces drag when swimming and aids the fish in osmoregulation.
Like sharks, bony fishes have a lateral line system that detects vibrations in water. Unlike sharks, some bony fish
depend on their eyesight to locate prey. Bony fish are also unusual in possessing taste cells in the head and trunk
region of the body that allow them to detect extremely small concentrations of molecules in the water.

All bony fishes, like the cartilaginous fishes, use gills to breathe. Water is drawn over gills that are located in
chambers covered and ventilated by a protective, muscular flap called the operculum. Unlike sharks, bony fishes
have a swim bladder, a gas-filled organ that helps to control the buoyancy of the fish. Bony fishes are further
divided into two clades with living members: Actinopterygii (ray-finned fishes) and Sarcopterygii (lobe-finned
fishes).

The ray-finned fishes include many familiar fishes—tuna, bass, trout, and salmon (Figure 15.39a), among others.
Ray-finned fishes are named for the form of their fins—webs of skin supported by bony spines called rays. In
contrast, the fins of lobe-finned fishes are fleshy and supported by bone (Figure 15.39b). Living members of lobe-
finned fishes include the less familiar lungfishes and coelacanth.

FIGURE 15.39 The (a) sockeye salmon and (b) coelacanth are both bony fishes of the Osteichthyes clade. The coelacanth, sometimes
called a lobe-finned fish, was thought to have gone extinct in the Late Cretaceous period 100 million years ago until one was discovered in
1938 between Africa and Madagascar. (credit a: modification of work by Timothy Knepp, USFWS; credit b: modification of work by Robbie
Cada)

Amphibians
Amphibians are vertebrate tetrapods. Amphibia includes frogs, salamanders, and caecilians. The term amphibian
means “dual life,” which is a reference to the metamorphosis that many frogs undergo from a tadpole to an adult
and the mixture of aquatic and terrestrial environments in their life cycle. Amphibians evolved in the Devonian
period and were the earliest terrestrial tetrapods.

As tetrapods, most amphibians are characterized by four well-developed limbs, although some species of
salamanders and all caecilians possess only vestigial limbs. An important characteristic of extant amphibians is a
moist, permeable skin, achieved by mucus glands. The moist skin allows oxygen and carbon dioxide exchange with
the environment, a process called cutaneous respiration. All living adult amphibian species are carnivorous, and
some terrestrial amphibians have a sticky tongue that is used to capture prey.

Amphibian Diversity
Amphibia comprise an estimated 6,500 extant species that inhabit tropical and temperate regions around the world.
Amphibians can be divided into three clades: Urodela (“tailed-ones”), the salamanders and newts; Anura (“tail-less
ones”), the frogs and toads; and Apoda (“legless ones”), the caecilians.

Living salamanders (Figure 15.40a) include approximately 500 species, some of which are aquatic, others
384 15 • Diversity of Animals

terrestrial, and some that live on land only as adults. Adult salamanders usually have a generalized tetrapod body
plan with four limbs and a tail. Some salamanders are lungless, and respiration occurs through the skin or external
gills. Some terrestrial salamanders have primitive lungs; a few species have both gills and lungs.

FIGURE 15.40 (a) Most salamanders have legs and a tail, but respiration varies among species. (b) The Australian green tree frog is a
nocturnal predator that lives in the canopies of trees near a water source. (credit a: modification of work by Valentina Storti; credit b:
modification of work by Evan Pickett)

LINK TO LEARNING
Watch this video (https://www.youtube.com/watch?v=P_kyeHZjRJ4) about an unusually large salamander species.

Frogs (Figure 15.40b) are the most diverse group of amphibians, with approximately 5,000 species that live on all
continents except Antarctica. Frogs have a body plan that is more specialized than the salamander body plan for
movement on land. Adult frogs use their hind limbs to jump many times their body length on land. Frogs have a
number of modifications that allow them to avoid predators, including skin that acts as camouflage and defensive
chemicals that are poisonous to predators secreted from glands in the skin.

Frog eggs are fertilized externally, as they are laid in moist environments. Frogs demonstrate a range of parental
behaviors, with some species exhibiting little care, to species that carry eggs and tadpoles on their hind legs or
backs. The life cycle consists of two stages: the larval stage followed by metamorphosis to an adult stage. The larval
stage of a frog, the tadpole, is often a filter-feeding herbivore. Tadpoles usually have gills, a lateral line system, long-
finned tails, but no limbs. At the end of the tadpole stage, frogs undergo a gradual metamorphosis into the adult
form. During this stage, the gills and lateral line system disappear, and four limbs develop. The jaws become larger
and are suited for carnivorous feeding, and the digestive system transforms into the typical short gut of a predator.
An eardrum and air-breathing lungs also develop. These changes during metamorphosis allow the larvae to move
onto land in the adult stage (Figure 15.41).

FIGURE 15.41 A frog begins as a (a) tadpole and undergoes metamorphosis to become (b) a juvenile and finally (c) an adult. (credit:
modification of work by Brian Gratwicke)

Caecilians comprise an estimated 185 species. They lack external limbs and resemble giant earthworms. They
inhabit soil and are found primarily in the tropics of South America, Africa, and southern Asia where they are
adapted for a soil-burrowing lifestyle and are nearly blind. Unlike most of the other amphibians that breed in or near
water, reproduction in a drier soil habitat means that caecilians must utilize internal fertilization, and most species
give birth to live young (Figure 15.42).

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 15.6 • Vertebrates 385

FIGURE 15.42 Caecilians lack external limbs and are well adapted for a soil-burrowing lifestyle. (credit: modification of work by
"cliff1066"/Flickr)

Reptiles and Birds

The amniotes—reptiles, birds, and mammals—are distinguished from amphibians by their terrestrially adapted
(shelled) egg and an embryo protected by amniotic membranes. The evolution of amniotic membranes meant that
the embryos of amniotes could develop within an aquatic environment inside the egg. This led to less dependence
on a water environment for development and allowed the amniotes to invade drier areas. This was a significant
evolutionary change that distinguished them from amphibians, which were restricted to moist environments due to
their shell-less eggs. Although the shells of various amniotic species vary significantly, they all allow retention of
water. The membranes of the amniotic egg also allowed gas exchange and sequestering of wastes within the
enclosure of an eggshell. The shells of bird eggs are composed of calcium carbonate and are hard and brittle, but
possess pores for gas and water exchange. The shells of reptile eggs are more leathery and pliable. Most mammals
do not lay eggs; however, even with internal gestation, amniotic membranes are still present.

In the past, the most common division of amniotes has been into classes Mammalia, Reptilia, and Aves. Birds are
descended, however, from dinosaurs, so this classical scheme results in groups that are not true clades. We will
discuss birds as a group distinct from reptiles with the understanding that this does not reflect evolutionary history.

Reptiles
Reptiles are tetrapods. Limbless reptiles—snakes—may have vestigial limbs and, like caecilians, are classified as
tetrapods because they are descended from four-limbed ancestors. Reptiles lay shelled eggs on land. Even aquatic
reptiles, like sea turtles, return to the land to lay eggs. They usually reproduce sexually with internal fertilization.
Some species display ovoviviparity, with the eggs remaining in the mother’s body until they are ready to hatch. Other
species are viviparous, with the offspring born alive.

One of the key adaptations that permitted reptiles to live on land was the development of their scaly skin, containing
the protein keratin and waxy lipids, which prevented water loss from the skin. This occlusive skin means that
reptiles cannot use their skin for respiration, like amphibians, and thus all must breathe with lungs. In addition,
reptiles conserve valuable body water by excreting nitrogen in the form of uric acid paste. These characteristics,
along with the shelled, amniotic egg, were the major reasons why reptiles became so successful in colonizing a
variety of terrestrial habitats far from water.

Reptiles are ectotherms, that is, animals whose main source of body heat comes from the environment. Behavioral
maneuvers, like basking to heat themselves, or seeking shade or burrows to cool off, help them regulate their body
temperature,

Class Reptilia includes diverse species classified into four living clades. These are the Crocodilia, Sphenodontia,
Squamata, and Testudines.

The Crocodilia (“small lizard”) arose approximately 84 million years ago, and living species include alligators,
crocodiles, and caimans. Crocodilians (Figure 15.43a) live throughout the tropics of Africa, South America, the
southeastern United States, Asia, and Australia. They are found in freshwater habitats, such as rivers and lakes, and
spend most of their time in water. Some species are able to move on land due to their semi-erect posture.
386 15 • Diversity of Animals

FIGURE 15.43 (a) Crocodilians, such as this Siamese crocodile, provide parental care for their offspring. (b) This Jackson’s chameleon
blends in with its surroundings. (c) The garter snake belongs to the genus Thamnophis, the most widely distributed reptile genus in North
America. (d) The African spurred tortoise lives at the southern edge of the Sahara Desert. It is the third largest tortoise in the world. (credit
a: modification of work by Keshav Mukund Kandhadai; credit c: modification of work by Steve Jurvetson; credit d: modification of work by
Jim Bowen)

The Sphenodontia (“wedge tooth”) arose in the Mesozoic Era and includes only one living genus, Tuatara, with two
species that are found in New Zealand. There are many fossil species extending back to the Triassic period
(250–200 million years ago). Although the tuataras resemble lizards, they are anatomically distinct and share
characteristics that are found in birds and turtles.

Squamata (“scaly”) arose in the late Permian; living species include lizards and snakes, which are the largest extant
clade of reptiles (Figure 15.43b). Lizards differ from snakes by having four limbs, eyelids, and external ears, which
are lacking in snakes. Lizard species range in size from chameleons and geckos that are a few centimeters in length
to the Komodo dragon, which is about 3 meters in length.

Snakes are thought to have descended from either burrowing lizards or aquatic lizards over 100 million years ago
(Figure 15.43c). Snakes comprise about 3,000 species and are found on every continent except Antarctica. They
range in size from 10 centimeter-long thread snakes to 7.5 meter-long pythons and anacondas. All snakes are
carnivorous and eat small animals, birds, eggs, fish, and insects.

Turtles are members of the clade Testudines (“having a shell”) (Figure 15.43d). Turtles are characterized by a bony
or cartilaginous shell, made up of the carapace on the back and the plastron on the ventral surface, which develops
from the ribs. Turtles arose approximately 200 million years ago, predating crocodiles, lizards, and snakes. Turtles
lay eggs on land, although many species live in or near water. Turtles range in size from the speckled padloper
tortoise at 8 centimeters (3.1 inches) to the leatherback sea turtle at 200 centimeters (over 6 feet). The term
“turtle” is sometimes used to describe only those species of Testudines that live in the sea, with the terms
“tortoise” and “terrapin” used to refer to species that live on land and in fresh water, respectively.

Birds
Data now suggest that birds belong within the reptile clade, but they display a number of unique adaptations that
set them apart. Unlike the reptiles, birds are endothermic, meaning they generate their own body heat through

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 15.6 • Vertebrates 387

metabolic processes. The most distinctive characteristic of birds is their feathers, which are modified reptilian
scales. Birds have several different types of feathers that are specialized for specific functions, like contour feathers
that streamline the bird’s exterior and loosely structured down feathers that insulate (Figure 15.44a).

Feathers not only permitted the earliest birds to glide, and ultimately engage in flapping flight, but they insulated the
bird’s body, assisting the maintenance of endothermy, even in cooler temperatures. Powering a flying animal
requires economizing on the amount of weight carried. As body weight increases, the muscle output and energetic
cost required for flying increase. Birds have made several modifications to reduce body weight, including hollow or
pneumatic bones (Figure 15.44b) with air spaces that may be connected to air sacs and cross-linked struts within
their bones to provide structural reinforcement. Parts of the vertebral skeleton and braincase are fused to increase
its strength while lightening its weight. Most species of bird only possess one ovary rather than two, and no living
birds have teeth in their jaw, further reducing body mass.

FIGURE 15.44 (a) Primary feathers are located at the wing tip and provide thrust; secondary feathers are located close to the body and
provide lift. (b) Many birds have hollow pneumatic bones, which make flight easier.

Birds possess a system of air sacs branching from their primary airway that divert the path of air so that it passes
unidirectionally through the lung, during both inspiration and expiration. Unlike mammalian lungs in which air flows
in two directions as it is breathed in and out, air flows continuously through the bird’s lung to provide a more
efficient system of gas exchange.

Mammals
Mammals are vertebrates that have hair and mammary glands used to provide nutrition for their young. Certain
features of the jaw, skeleton, skin, and internal anatomy are also unique to mammals. The presence of hair is one of
the key characteristics of a mammal. Although it is not very extensive in some groups, such as whales, hair has
many important functions for mammals. Mammals are endothermic, and hair provides insulation by trapping a layer
of air close to the body to retain metabolic heat. Hair also serves as a sensory mechanism through specialized hairs
called vibrissae, better known as whiskers. These attach to nerves that transmit touch information, which is
particularly useful to nocturnal or burrowing mammals. Hair can also provide protective coloration.

Mammalian skin includes secretory glands with various functions. Sebaceous glands produce a lipid mixture called
sebum that is secreted onto the hair and skin for water resistance and lubrication. Sebaceous glands are located
over most of the body. Sudoriferous glands produce sweat and scent, which function in thermoregulation and
communication, respectively. Mammary glands produce milk that is used to feed newborns. While male and female
monotremes and eutherians possess mammary glands, some male marsupials do not.

The skeletal system of mammals possesses unique features that differentiate them from other vertebrates. Most
mammals have heterodont teeth, meaning they have different types and shapes of teeth that allow them to feed on
388 15 • Diversity of Animals

different kinds of foods. These different types of teeth include the incisors, the canines, premolars, and molars. The
first two types are for cutting and tearing, whereas the latter two types are for crushing and grinding. Different
groups have different proportions of each type, depending on their diet. Most mammals are also diphyodonts,
meaning they have two sets of teeth in their lifetime: deciduous or “baby” teeth, and permanent teeth. In other
vertebrates, the teeth can be replaced throughout life.

Modern mammals are divided into three broad groups: monotremes, marsupials, and eutherians (or placental
mammals). The eutherians, or placental mammals, and the marsupials collectively are called therian mammals,
whereas monotremes are called prototherians.

There are three living species of monotremes: the platypus and two species of echidnas, or spiny anteaters (Figure
15.45). The platypus and one species of echidna are found in Australia, whereas the other species of echidna is
found in New Guinea. Monotremes are unique among mammals, as they lay leathery eggs, similar to those of
reptiles, rather than giving birth to live young. However, the eggs are retained within the mother’s reproductive tract
until they are almost ready to hatch. Once the young hatch, the female begins to secrete milk from pores in a ridge
of mammary tissue along the ventral side of her body. Like other mammals, monotremes are endothermic but
regulate body temperatures somewhat lower (90 °F, 32 °C) than placental mammals do (98 °F, 37 °C). Like reptiles,
monotremes have one posterior opening for urinary, fecal, and reproductive products, rather than three separate
openings like placental mammals do. Adult monotremes lack teeth.

FIGURE 15.45 The platypus (left), a monotreme, possesses a leathery beak and lays eggs rather than giving birth to live young. An echidna,
another monotreme, is shown in the right photo. (credit “echidna”: modification of work by Barry Thomas)

Marsupials are found primarily in Australia and nearby islands, although about 100 species of opossums and a few
species of two other families are found in the Americas. Australian marsupials number over 230 species and include
the kangaroo, koala, bandicoot, and Tasmanian devil (Figure 15.46). Most species of marsupials possess a pouch in
which the young reside after birth, receiving milk and continuing to develop. Before birth, marsupials have a less
complex placental connection, and the young are born much less developed than in placental mammals.

FIGURE 15.46 The Tasmanian devil is one of several marsupials native to Australia. (credit: Wayne McLean)

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 15.6 • Vertebrates 389

Eutherians are the most widespread of the mammals, occurring throughout the world. There are several groups of
eutherians, including Insectivora, the insect eaters; Edentata, the toothless anteaters; Rodentia, the rodents;
Chiroptera, the bats; Cetacea, the aquatic mammals including whales; Carnivora, carnivorous mammals including
dogs, cats, and bears; and Primates, which includes humans. Eutherian mammals are sometimes called placental
mammals, because all species have a complex placenta that connects a fetus to the mother, allowing for gas, fluid,
waste, and nutrient exchange. While other mammals may possess a less complex placenta or briefly have a
placenta, all eutherians have a complex placenta during gestation.

Primates
Order Primates of class Mammalia includes lemurs, tarsiers, monkeys, and the apes, which include humans. Non-
human primates live primarily in tropical or subtropical regions of South America, Africa, and Asia. They range in size
from the mouse lemur at 30 grams (1 ounce) to the mountain gorilla at 200 kilograms (441 pounds). The
characteristics and evolution of primates are of particular interest to us as they allow us to understand the evolution
of our own species.

All primate species have adaptations for climbing trees, as they all descended from tree-dwellers, although not all
species are arboreal. This arboreal heritage of primates resulted in hands and feet that are adapted for brachiation,
or climbing and swinging through trees. These adaptations include, but are not limited to 1) a rotating shoulder joint,
2) a big toe that is widely separated from the other toes and thumbs that are widely separated from fingers (except
humans), which allow for gripping branches, and 3) stereoscopic vision, two overlapping visual fields, which allows
for the depth perception necessary to gauge distance. Other characteristics of primates are brains that are larger
than those of many other mammals, claws that have been modified into flattened nails, typically only one offspring
per pregnancy, and a trend toward holding the body upright.

Order Primates is divided into two groups: prosimians and anthropoids. Prosimians include the bush babies of
Africa, the lemurs of Madagascar, and the lorises, pottos, and tarsiers of Southeast Asia. Anthropoids include
monkeys, lesser apes, and great apes (Figure 15.47). In general, prosimians tend to be nocturnal, smaller in size
than anthropoids, and have relatively smaller brains compared to anthropoids.

FIGURE 15.47 Primates can be divided into prosimians, such as the (a) lemur, and anthropoids. Anthropoids include monkeys, such as the
(b) howler monkey; lesser apes, such as the (c) gibbon; and great apes, such as the (d) chimpanzee, (e) bonobo, (f) gorilla, and (g)
orangutan. (credit a: modification of work by Frank Vassen; credit b: modification of work by Xavi Talleda; credit d: modification of work by
Aaron Logan; credit e: modification of work by Trisha Shears; credit f: modification of work by Dave Proffer; credit g: modification of work by
Julie Langford)
390 15 • Key Terms

Key Terms
acoelomate without a body cavity possession of a notochord, a dorsal hollow nerve
Actinopterygii ray-finned fishes cord, pharyngeal slits, and a post-anal tail at some
amniote a clade of animals that possesses an point during their development
amniotic egg; includes reptiles (including birds) and clitellum a specialized band of fused segments in
mammals some annelids, which aids in reproduction
amoebocyte an amoeba-like cell of sponges whose Cnidaria a phylum of animals that are diploblastic
functions include distribution of nutrients to other and have radial symmetry and stinging cells
cells in the sponge cnidocyte a specialized stinging cell found in Cnidaria
Amphibia frogs, salamanders, and caecilians coelom a lined body cavity derived from mesodermal
ampulla of Lorenzini a sensory organ that allows embryonic tissue
sharks to detect electromagnetic fields produced by complete digestive system a digestive system that
living things opens at one end, the mouth, and exits at the other
Annelida a phylum of worm-like animals with end, the anus, and through which food normally
metamerism moves in one direction
anthropoids a clade consisting of monkeys, apes, and craniate a proposed clade of chordates that includes
humans all groups except the tunicates and lancelets
Anura frogs Crocodilia crocodiles and alligators
Apoda caecilians ctenidia specialized gills in mollusks
Arthropoda a phylum of Ecdysozoa with jointed cutaneous respiration gas exchange through the skin
appendages and segmented bodies deuterostome describing an animal in which the
asymmetrical having no plane of symmetry blastopore develops into the anus, with the second
bilateral symmetry a type of symmetry in which opening developing into the mouth
there is only one plane of symmetry that creates dioecious having separate male and female sexes
two mirror-image sides diphyodont refers to the possession of two sets of
body plan the shape and symmetry of an organism teeth in a lifetime
brachiation swinging through trees diploblast an animal that develops from two
budding a form of asexual reproduction that occurs embryonic germ layers
through the growth of a new organism as a branch dorsal hollow nerve cord a hollow, tubular structure
on an adult organism that breaks off and becomes derived from ectoderm, which is located dorsal to
independent; found in plants, sponges, cnidarians, the notochord in chordates
and some other invertebrates down feather feather specialized for insulation
caecilian a legless amphibian that belongs to clade Echinodermata a phylum of deuterostomes with
Apoda spiny skin; exclusively marine organisms
Cephalochordata a chordate clade whose members epidermis the layer of cells that lines the outer
possess a notochord, dorsal hollow nerve cord, surface of an animal
pharyngeal slits, and a post-anal tail in the adult eucoelomate describing animals with a body cavity
stage completely lined with mesodermal tissue
cephalothorax a fused head and thorax eutherian mammal a mammal with a complex
chaeta a chitinous projection from the cuticle found placenta, which connects a fetus to the mother;
in annelids sometimes called placental mammals
chelicerae a modified first pair of appendages in extracellular digestion a form of digestion, the
subphylum Chelicerata breakdown of food, which occurs outside of cells
chitin a tough nitrogen-containing polysaccharide with the aid of enzymes released by cells
found in the cuticles of arthropods and the cell walls fragmentation a form of asexual reproduction in
of fungi which a portion of the body of an organism breaks
choanocyte a cell type unique to sponges with a off and develops into a living independent organism;
flagellum surrounded by a collar used to maintain found in plants, sponges, and some other
water flow through the sponge, and capture and invertebrates
digest food particles frog a tail-less amphibian that belongs to clade Anura
Chondrichthyes jawed fishes with paired fins and a gastrodermis the layer of cells that lines the
skeleton made of cartilage gastrovascular cavity of cnidarians
Chordata a phylum of animals distinguished by their gastrovascular cavity the central cavity bounded by

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 15 • Key Terms 391

the gastrodermis in cnidarians coat foreign particulate matter

gemmule a structure produced by asexual nematocyst the harpoon-like organelle within a
reproduction in freshwater sponges that is able to cnidocyte with a pointed projectile and poison to
survive harsh conditions stun and entangle prey
germ layer a collection of cells formed during Nematoda a phylum of worms in Ecdysozoa
embryogenesis that will give rise to future body commonly called roundworms containing both free-
tissues living and parasitic forms
gnathostome a jawed fish notochord a flexible, rod-shaped structure that is
hagfish an eel-like jawless fish that lives on the found in the embryonic stage of all chordates and in
ocean floor and is a scavenger the adult stage of some chordates
hemocoel the internal body cavity seen in arthropods osculum the large opening in a sponge body through
heterodont teeth different types of teeth modified by which water leaves
different purposes Osteichthyes bony fishes
intracellular digestion the digestion of matter ostracoderm one of the earliest jawless fishes
brought into a cell by phagocytosis covered in bone
lamprey a jawless fish characterized by a toothed, Petromyzontidae the clade of lampreys
funnel-like, sucking mouth pharyngeal slit an opening in the pharynx
lancelet a member of Cephalochordata; named for its pneumatic bone an air-filled bone
blade-like shape polyp the stalk-like, sessile life form of a cnidarians
lateral line the sense organ that runs the length of a with mouth and tentacles facing upward, usually
fish’s body, used to detect vibration in the water sessile but may be able to glide along a surface
Lophotrochozoa a clade of invertebrate organisms Porifera a phylum of animals with no true tissues, but
that is a sister group to the Ecdysozoa a porous body with a rudimentary endoskeleton
madreporite a pore for regulating entry and exit of post-anal tail a muscular, posterior elongation of the
water into the water vascular system body extending beyond the anus in chordates
mammal one of the groups of endothermic Primates includes lemurs, tarsiers, monkeys, apes,
vertebrates that possess hair and mammary glands and humans
mammary gland in female mammals, a gland that prosimians a group of primates that includes bush
produces milk for newborns babies of Africa, lemurs of Madagascar, and lorises,
mantle a specialized epidermis that encloses all pottos, and tarsiers of southeast Asia
visceral organs and secretes shells in mollusks protostome describing an animal in which the mouth
marsupial one of the groups of mammals that develops first during embryogenesis and a second
includes the kangaroo, koala, bandicoot, Tasmanian opening developing into the anus
devil, and several other species; young develop pseudocoelomate an animal with a coelom that is
within a pouch not completely lined with tissues derived from the
medusa a free-floating cnidarian body plan with a mesoderm as in eucoelomate animals
mouth on the underside and tentacles hanging radial symmetry a type of symmetry with multiple
down from a bell planes of symmetry all cross at an axis through the
mesoglea the non-living, gel-like matrix present in center of the organism
between ectoderm and endoderm in cnidarians radula a tongue-like scraping organ with chitinous
mesohyl the collagen-like gel containing suspended ornamentation found in most mollusks
cells that perform various functions in sponges salamander a tailed amphibian that belongs to the
metamerism having a series of body structures that clade Urodela
are similar internally and externally, such as Sarcopterygii lobe-finned fishes
segments sebaceous gland in mammals, a skin gland that
Mollusca a phylum of protostomes with soft bodies produce a lipid mixture called sebum
and no segmentation Sphenodontia the reptilian clade that includes the
monoecious having both sexes in one body, tuataras
hermaphroditic spicule a short sliver or spike-like structure, in
monotreme an egg-laying mammal sponges, they are formed of silicon dioxide, calcium
Myxini hagfishes carbonate, or protein, and are found in the mesohyl
nacre a calcareous secretion produced by bivalve spiracle a respiratory openings in insects that allow
mollusks to line the inner side of shells as well as to air into the tracheae
392 15 • Chapter Summary

spongocoel the central cavity within the body of trachea in some arthropods, such as insects, a
some sponges respiratory tube that conducts air from the spiracles
Squamata the reptilian clade of lizards and snakes to the tissues
stereoscopic vision two overlapping fields of vision triploblast an animal that develops from three germ
from the eyes that produces depth perception layers
sudoriferous gland a gland in mammals that tunicate a sessile chordate that is a member of
produces sweat and scent molecules Urochordata
swim bladder in fishes, a gas filled organ that helps Urochordata the clade composed of the tunicates
to control the buoyancy of the fish Urodela salamanders
tadpole the larval stage of a frog vertebral column a series of separate bones that
Testudines turtles surround the spinal cord in vertebrates
tetrapod a four-footed animal; includes amphibians, water vascular system a system in echinoderms in
reptiles, birds, and mammals which water is the circulatory fluid

Chapter Summary
15.1 Features of the Animal Kingdom cell for delivering toxins to prey and predators.
Cnidarians have separate sexes. They have a life cycle
Animals constitute a diverse kingdom of organisms.
that involves morphologically distinct forms—medusoid
Although animals range in complexity from simple sea
and polypoid—at various stages in their life cycle.
sponges to human beings, most members share
certain features. Animals are eukaryotic, multicellular, 15.3 Flatworms, Nematodes, and
heterotrophic organisms that ingest their food and Arthropods
usually develop into motile creatures with a fixed body
Flatworms are acoelomate, triploblastic animals. They
plan. Most members of the animal kingdom have
lack circulatory and respiratory systems, and have a
differentiated tissues of four main classes—nervous,
rudimentary excretory system. The digestive system is
muscular, connective, and epithelial—that are
incomplete in most species. There are four traditional
specialized to perform different functions. Most
classes of flatworms, the largely free-living
animals reproduce sexually, leading to a
turbellarians, the ectoparasitic monogeneans, and the
developmental sequence that is relatively similar
endoparasitic trematodes and cestodes. Trematodes
across the animal kingdom.
have complex life cycles involving a secondary mollusk
Organisms in the animal kingdom are classified based host and a primary host in which sexual reproduction
on their body morphology and development. True takes place. Cestodes, or tapeworms, infect the
animals are divided into those with radial versus digestive systems of primary vertebrate hosts.
bilateral symmetry. Animals with three germ layers,
Nematodes are pseudocoelomate members of the
called triploblasts, are further characterized by the
clade Ecdysozoa. They have a complete digestive
presence or absence of an internal body cavity called a
system and a pseudocoelomic body cavity. This phylum
coelom. Animals with a body cavity may be either
includes free-living as well as parasitic organisms.
coelomates or pseudocoelomates, depending on which
They include dioecious and hermaphroditic species.
tissue gives rise to the coelom. Coelomates are further
Nematodes have a poorly developed excretory system.
divided into two groups called protostomes and
Embryonic development is external and proceeds
deuterostomes, based on a number of developmental
through larval stages separated by molts.
characteristics.
Arthropods represent the most successful phylum of
15.2 Sponges and Cnidarians
animals on Earth, in terms of number of species as well
Animals included in phylum Porifera are parazoans and as the number of individuals. They are characterized by
do not possess true tissues. These organisms show a a segmented body and jointed appendages. In the
simple organization. Sponges have multiple cell types basic body plan, a pair of appendages is present per
that are geared toward executing various metabolic body segment. Within the phylum, classification is
functions. based on mouthparts, number of appendages, and
modifications of appendages. Arthropods bear a
Cnidarians have outer and inner tissue layers
chitinous exoskeleton. Gills, tracheae, and book lungs
sandwiching a noncellular mesoglea. Cnidarians
facilitate respiration. Embryonic development may
possess a well-formed digestive system and carry out
include multiple larval stages.
extracellular digestion. The cnidocyte is a specialized

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 15 • Chapter Summary 393

15.4 Mollusks and Annelids and some species are parasitic on other fishes.
Gnathostomes include the jawed fishes (cartilaginous
The phylum Mollusca is a large, mainly marine group of
and bony fishes) as well as all other tetrapods.
invertebrates. Mollusks show a variety of
Cartilaginous fishes include sharks, rays, skates, and
morphologies. Many mollusks secrete a calcareous
ghost sharks. Bony fishes can be further divided into
shell for protection, but in other species, the shell is
ray-finned and lobe-finned fishes.
reduced or absent. Mollusks are protostomes. The
dorsal epidermis in mollusks is modified to form the As tetrapods, most amphibians are characterized by
mantle, which encloses the mantle cavity and visceral four well-developed limbs, although some species of
organs. This cavity is distinct from the coelomic cavity, salamanders and all caecilians are limbless.
which the adult animal retains, surrounding the heart. Amphibians have a moist, permeable skin used for
Respiration is facilitated by gills known as ctenidia. A cutaneous respiration. Amphibia can be divided into
chitinous scraper called the radula is present in most three clades: salamanders (Urodela), frogs (Anura),
mollusks. Mollusks are mostly dioecious and are and caecilians (Apoda). The life cycle of amphibians
divided into seven classes. consists of two distinct stages: the larval stage and
metamorphosis to an adult stage.
The phylum Annelida includes worm-like, segmented
animals. Segmentation is both external and internal, The amniotes are distinguished from amphibians by
which is called metamerism. Annelids are the presence of a terrestrially adapted egg protected
protostomes. The presence of chitinous hairs called by amniotic membranes. The amniotes include
chaetae is characteristic of most members. These reptiles, birds, and mammals. A key adaptation that
animals have well-developed nervous and digestive permitted reptiles to live on land was the development
systems. Polychaete annelids have parapodia that of scaly skin. Reptilia includes four living clades:
participate in locomotion and respiration. Suckers are Crocodilia (crocodiles and alligators), Sphenodontia
seen in the order Hirudinea. Breeding systems include (tuataras), Squamata (lizards and snakes), and
separate sexes and hermaphroditism. Testudines (turtles).

15.5 Echinoderms and Chordates Birds are endothermic amniotes. Feathers act as
insulation and allow for flight. Birds have pneumatic
Echinoderms are deuterostome marine organisms. This bones that are hollow rather than tissue-filled. Airflow
phylum of animals bear a calcareous endoskeleton through bird lungs travels in one direction. Birds
composed of ossicles covered by a spiny skin. evolved from dinosaurs.
Echinoderms possess a water-based circulatory
system. The madreporite is the point of entry and exit Mammals have hair and mammary glands. Mammalian
for water for the water vascular system. skin includes various secretory glands. Mammals are
endothermic, like birds. There are three groups of
The characteristic features of Chordata are a mammals living today: monotremes, marsupials, and
notochord, a dorsal hollow nerve cord, pharyngeal slits, eutherians. Monotremes are unique among mammals
and a post-anal tail. Chordata contains two clades of as they lay eggs, rather than giving birth to live young.
invertebrates: Urochordata (tunicates) and Eutherian mammals have a complex placenta.
Cephalochordata (lancelets), together with the
vertebrates. Most tunicates live on the ocean floor and There are 16 extant (living) orders of eutherian
are suspension feeders. Lancelets are suspension mammals. Humans are most closely related to
feeders that feed on phytoplankton and other Primates, all of which have adaptations for climbing
microorganisms. trees, although not all species are arboreal. Other
characteristics of primates are brains that are larger
15.6 Vertebrates than those of other mammals, claws that have been
The earliest vertebrates that diverged from the modified into flattened nails, and typically one young
invertebrate chordates were the jawless fishes. per pregnancy, stereoscopic vision, and a trend toward
Hagfishes are eel-like scavengers that feed on dead holding the body upright. Primates are divided into two
invertebrates and other fishes. Lampreys are groups: prosimians and anthropoids.
characterized by a toothed, funnel-like sucking mouth,
394 15 • Visual Connection Questions

Visual Connection Questions

1. Figure 15.3 Which of the following statements is 3. Figure 15.33 Which of the following statements
false? about common features of chordates is true?
a. Eumetazoa have specialized tissues and a. The dorsal hollow nerve cord is part of the
Parazoa do not. chordate central nervous system.
b. Both acoelomates and pseudocoelomates have b. In vertebrate fishes, the pharyngeal slits
a body cavity. become the gills.
c. Chordates are more closely related to c. Humans are not chordates because humans do
echinoderms than to rotifers according to the not have a tail.
figure. d. Vertebrates do not have a notochord at any
d. Some animals have radial symmetry, and some point in their development; instead, they have
animals have bilateral symmetry. a vertebral column.

2. Figure 15.24 Which of the following statements

about the anatomy of a mollusk is false?
a. Mollusks have a radula for scraping food.
b. Mollusks have ventral nerve cords.
c. The tissue beneath the shell is called the
mantle.
d. The mantle cavity contains hemolymph.

Review Questions
4. Which of the following is not a feature common to 8. Cubozoans are ________.
most animals? a. polyps
a. development into a fixed body plan b. medusoids
b. asexual reproduction c. polymorphs
c. specialized tissues d. sponges
d. heterotrophic nutrient sourcing
9. Which group of flatworms are primarily external
5. Which of the following does not occur? parasites of fish?
a. radially symmetrical diploblast a. monogeneans
b. diploblastic eucoelomate b. trematodes
c. protostomic coelomate c. cestodes
d. bilaterally symmetrical deuterostome d. turbellarians

6. The large central opening in the poriferan body is 10. Crustaceans are _____.
called the _____. a. ecdysozoans
a. emmule b. nematodes
b. picule c. arachnids
c. stia d. parazoans
d. osculum
11. A mantle and mantle cavity are present in _____.
7. Cnidocytes are found in _____. a. class Oligochaeta
a. phylum Porifera b. class Bivalvia
b. phylum Nemertea c. class Polychaeta
c. phylum Nematoda d. class Hirudinea
d. phylum Cnidaria
12. Annelids have a _____.
a. pseudocoelom
b. a true coelom
c. no coelom
d. none of the above

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 15 • Critical Thinking Questions 395

13. Echinoderms in their larval state have _____. 16. Members of Chondrichthyes differ from members
a. triangular symmetry of Osteichthyes by having a ________.
b. radial symmetry a. jaw
c. hexagonal symmetry b. bony skeleton
d. bilateral symmetry c. cartilaginous skeleton
d. two sets of paired fins
14. The circulatory fluid in echinoderms is _____.
a. blood 17. Squamata includes _____.
b. mesohyl a. crocodiles and alligators
c. water b. turtles
d. saline c. tuataras
d. lizards and snakes
15. Which of the following is not a member of the
phylum Chordata? 18. Sudoriferous glands produce ________.
a. Cephalochordata a. sweat
b. Echinodermata b. lipids
c. Urochordata c. sebum
d. Vertebrata d. milk

19. Which of the following is a Monotreme?

a. kangaroo
b. koala
c. bandicoot
d. platypus

Critical Thinking Questions

20. How are specialized tissues important for animal 26. Describe the morphology and anatomy of
function and complexity? mollusks.

21. Using the following terms, explain what 27. Sessile adult tunicates lose the notochord; what
classifications and groups humans fall into, from does this suggest about one function of this
the most general to the most specific: symmetry, structure?
germ layers, coelom, embryological development.
28. During embryonic development, what features do
22. Describe the feeding mechanism of sponges and we share with tunicates or lancelets?
identify how it is different from other animals.
29. What can be inferred about the evolution of the
23. Compare the structural differences between cranium and the vertebral column from examining
Porifera and Cnidaria. hagfishes and lampreys?

24. Speculate as to what advantage(s) a complete 30. Explain why frogs are restricted to a moist
digestive system has over an incomplete digestive environment.
system?
31. Describe three adaptations that allow for flight in
25. Describe a potential advantage and disadvantage birds.
of the cuticle of ecdysozoans.
396 15 • Critical Thinking Questions

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CHAPTER 16
The Body’s Systems

FIGURE 16.1 An arctic fox is a complex animal, well adapted to its environment. (credit: Keith Morehouse, USFWS)

CHAPTER OUTLINE
16.1 Homeostasis and Osmoregulation
16.2 Digestive System
16.3 Circulatory and Respiratory Systems
16.4 Endocrine System
16.5 Musculoskeletal System
16.6 Nervous System

INTRODUCTION The arctic fox, a complex animal that has adapted to its environment, illustrates
the relationships between an animal’s form and function. The multicellular bodies of animals
consist of tissues that make up more complex organs and organ systems. The organ systems of an
animal maintain homeostasis within the multicellular body. These systems are adapted to obtain
the necessary nutrients and other resources needed by the cells of the body, to remove the
wastes those cells produce, to coordinate the activities of the cells, tissues, and organs
throughout the body, and to coordinate the many responses of the individual organism to its
environment.
398 16 • The Body’s Systems

16.1 Homeostasis and Osmoregulation

LEARNING OBJECTIVES
By the end of this section, you will be able to:
• Explain the concept of homeostasis
• Describe thermoregulation of endothermic and ectothermic animals
• Explain how the kidneys serve as the main osmoregulatory organs in the human body

Homeostasis refers to the relatively stable state inside the body of an animal. Animal organs and
organ systems constantly adjust to internal and external changes in order to maintain this steady
state. Examples of internal conditions maintained homeostatically are the level of blood glucose,
body temperature, blood calcium level. These conditions remain stable because of physiologic
processes that result in negative feedback relationships. If the blood glucose or calcium rises, this
sends a signal to organs responsible for lowering blood glucose or calcium. The signals that
restore the normal levels are examples of negative feedback. When homeostatic mechanisms fail,
the results can be unfavorable for the animal. Homeostatic mechanisms keep the body in dynamic
equilibrium by constantly adjusting to the changes that the body’s systems encounter. Even an
animal that is apparently inactive is maintaining this homeostatic equilibrium. Two examples of
factors that are regulated homeostatically are temperature and water content. The processes that
maintain homeostasis of these two factors are called thermoregulation and osmoregulation.

Homeostasis
The goal of homeostasis is the maintenance of equilibrium around a specific value of some aspect
of the body or its cells called a set point. While there are normal fluctuations from the set point,
the body’s systems will usually attempt to go back to this point. A change in the internal or
external environment is called a stimulus and is detected by a receptor; the response of the
system is to adjust the activities of the system so the value moves back toward the set point. For
instance, if the body becomes too warm, adjustments are made to cool the animal. If glucose
levels in the blood rise after a meal, adjustments are made to lower them and to get the nutrient
into tissues that need it or to store it for later use.

When a change occurs in an animal’s environment, an adjustment must be made so that the
internal environment of the body and cells remains stable. The receptor that senses the change in
the environment is part of a feedback mechanism. The stimulus—temperature, glucose, or calcium
levels—is detected by the receptor. The receptor sends information to a control center, often the
brain, which relays appropriate signals to an effector organ that is able to cause an appropriate
change, either up or down, depending on the information the sensor was sending.

Thermoregulation
Animals can be divided into two groups: those that maintain a constant body temperature in the
face of differing environmental temperatures, and those that have a body temperature that is the
same as their environment and thus varies with the environmental temperature. Animals that do
not have internal control of their body temperature are called ectotherms. The body temperature
of these organisms is generally similar to the temperature of the environment, although the
individual organisms may do things that keep their bodies slightly below or above the
environmental temperature. This can include burrowing underground on a hot day or resting in the
sunlight on a cold day. The ectotherms have been called cold-blooded, a term that may not apply
to an animal in the desert with a very warm body temperature.

An animal that maintains a constant body temperature in the face of environmental changes is
called an endotherm. These animals are able to maintain a level of activity that an ectothermic
animal cannot because they generate internal heat that keeps their cellular processes operating
optimally even when the environment is cold.

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 16.1 • Homeostasis and Osmoregulation 399

LINK TO LEARNING
Watch this Discovery Channel video (http://openstax.org/l/thermoregulate2) on thermoregulation to see illustrations
of the process in a variety of animals.

Animals conserve or dissipate heat in a variety of ways. Endothermic animals have some form of insulation. They
have fur, fat, or feathers. Animals with thick fur or feathers create an insulating layer of air between their skin and
internal organs. Polar bears and seals live and swim in a subfreezing environment and yet maintain a constant,
warm, body temperature. The arctic fox, for example, uses its fluffy tail as extra insulation when it curls up to sleep
in cold weather. Mammals can increase body heat production by shivering, which is an involuntary increase in
muscle activity. In addition, arrector pili muscles can contract causing individual hairs to stand up when the
individual is cold. This increases the insulating effect of the hair. Humans retain this reaction, which does not have
the intended effect on our relatively hairless bodies; it causes “goose bumps” instead. Mammals use layers of fat as
insulation also. Loss of significant amounts of body fat will compromise an individual’s ability to conserve heat.

Ectotherms and endotherms use their circulatory systems to help maintain body temperature. Vasodilation, the
opening up of arteries to the skin by relaxation of their smooth muscles, brings more blood and heat to the body
surface, facilitating radiation and evaporative heat loss, cooling the body. Vasoconstriction, the narrowing of blood
vessels to the skin by contraction of their smooth muscles, reduces blood flow in peripheral blood vessels, forcing
blood toward the core and vital organs, conserving heat. Some animals have adaptions to their circulatory system
that enable them to transfer heat from arteries to veins that are flowing next to each other, warming blood returning
to the heart. This is called a countercurrent heat exchange; it prevents the cold venous blood from cooling the heart
and other internal organs. The countercurrent adaptation is found in dolphins, sharks, bony fish, bees, and
hummingbirds.

Some ectothermic animals use changes in their behavior to help regulate body temperature. They simply seek
cooler areas during the hottest part of the day in the desert to keep from getting too warm. The same animals may
climb onto rocks in the evening to capture heat on a cold desert night before entering their burrows.

Thermoregulation is coordinated by the nervous system (Figure 16.2). The processes of temperature control are
centered in the hypothalamus of the advanced animal brain. The hypothalamus maintains the set point for body
temperature through reflexes that cause vasodilation or vasoconstriction and shivering or sweating. The
sympathetic nervous system under control of the hypothalamus directs the responses that effect the changes in
temperature loss or gain that return the body to the set point. The set point may be adjusted in some instances.
During an infection, compounds called pyrogens are produced and circulate to the hypothalamus resetting the
thermostat to a higher value. This allows the body’s temperature to increase to a new homeostatic equilibrium point
in what is commonly called a fever. The increase in body heat makes the body less optimal for bacterial growth and
increases the activities of cells so they are better able to fight the infection.
400 16 • The Body’s Systems

VISUAL CONNECTION

FIGURE 16.2 The body is able to regulate temperature in response to signals from the nervous system.

When bacteria are destroyed by leukocytes, pyrogens are released into the blood. Pyrogens reset the body’s
thermostat to a higher temperature, resulting in fever. How might pyrogens cause the body temperature to rise?

Osmoregulation
Osmoregulation is the process of maintaining salt and water balance (osmotic balance) across membranes within
the body. The fluids inside and surrounding cells are composed of water, electrolytes, and nonelectrolytes. An
electrolyte is a compound that dissociates into ions when dissolved in water. A nonelectrolyte, in contrast, does not
dissociate into ions in water. The body’s fluids include blood plasma, fluid that exists within cells, and the
interstitial fluid that exists in the spaces between cells and tissues of the body. The membranes of the body (both
the membranes around cells and the “membranes” made of cells lining body cavities) are semipermeable
membranes. Semipermeable membranes are permeable to certain types of solutes and to water, but typically cell
membranes are impermeable to solutes.

The body does not exist in isolation. There is a constant input of water and electrolytes into the system. Excess
water, electrolytes, and wastes are transported to the kidneys and excreted, helping to maintain osmotic balance.
Insufficient fluid intake results in fluid conservation by the kidneys. Biological systems constantly interact and
exchange water and nutrients with the environment by way of consumption of food and water and through excretion
in the form of sweat, urine, and feces. Without a mechanism to regulate osmotic pressure, or when a disease
damages this mechanism, there is a tendency to accumulate toxic waste and water, which can have dire
consequences.

Mammalian systems have evolved to regulate not only the overall osmotic pressure across membranes, but also
specific concentrations of important electrolytes in the three major fluid compartments: blood plasma, interstitial
fluid, and intracellular fluid. Since osmotic pressure is regulated by the movement of water across membranes, the
volume of the fluid compartments can also change temporarily. Since blood plasma is one of the fluid components,
osmotic pressures have a direct bearing on blood pressure.

Excretory System
The human excretory system functions to remove waste from the body through the skin as sweat, the lungs in the
form of exhaled carbon dioxide, and through the urinary system in the form of urine. All three of these systems
participate in osmoregulation and waste removal. Here we focus on the urinary system, which is comprised of the

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 16.1 • Homeostasis and Osmoregulation 401

paired kidneys, the ureter, urinary bladder and urethra (Figure 16.3). The kidneys are a pair of bean-shaped
structures that are located just below the liver in the body cavity. Each of the kidneys contains more than a million
tiny units called nephrons that filter blood containing the metabolic wastes from cells. All the blood in the human
body is filtered about 60 times a day by the kidneys. The nephrons remove wastes, concentrate them, and form
urine that is collected in the bladder.

Internally, the kidney has three regions—an outer cortex, a medulla in the middle, and the renal pelvis, which is the
expanded end of the ureter. The renal cortex contains the nephrons—the functional unit of the kidney. The renal
pelvis collects the urine and leads to the ureter on the outside of the kidney. The ureters are urine-bearing tubes
that exit the kidney and empty into the urinary bladder.

FIGURE 16.3 The human excretory system is made up of the kidneys, ureter, urinary bladder, and urethra. The kidneys filter blood and form
urine, which is stored in the bladder until it is eliminated through the urethra. On the right, the internal structure of the kidney is shown.
(credit: modification of work by NCI, NIH)

Blood enters each kidney from the aorta, the main artery supplying the body below the heart, through a renal
artery. It is distributed in smaller vessels until it reaches each nephron in capillaries. Within the nephron the blood
comes in intimate contact with the waste-collecting tubules in a structure called the glomerulus. Water and many
solutes present in the blood, including ions of sodium, calcium, magnesium, and others; as well as wastes and
valuable substances such as amino acids, glucose and vitamins, leave the blood and enter the tubule system of the
nephron. As materials pass through the tubule much of the water, required ions, and useful compounds are
reabsorbed back into the capillaries that surround the tubules leaving the wastes behind. Some of this reabsorption
requires active transport and consumes ATP. Some wastes, including ions and some drugs remaining in the blood,
diffuse out of the capillaries into the interstitial fluid and are taken up by the tubule cells. These wastes are then
actively secreted into the tubules. The blood then collects in larger and larger vessels and leaves the kidney in the
renal vein. The renal vein joins the inferior vena cava, the main vein that returns blood to the heart from the lower
body. The amounts of water and ions reabsorbed into the circulatory system are carefully regulated and this is an
important way the body regulates its water content and ion levels. The waste is collected in larger tubules and then
leaves the kidney in the ureter, which leads to the bladder where urine, the combination of waste materials and
water, is stored.

The bladder contains sensory nerves, stretch receptors that signal when it needs to be emptied. These signals
create the urge to urinate, which can be voluntarily suppressed up to a limit. The conscious decision to urinate sets
in play signals that open the sphincters, rings of smooth muscle that close off the opening, to the urethra that
allows urine to flow out of the bladder and the body.
402 16 • The Body’s Systems

CAREER CONNECTION

Dialysis Technician
Dialysis is a medical process of removing wastes and excess water from the blood by diffusion and ultrafiltration.
When kidney function fails, dialysis must be done to artificially rid the body of wastes and fluids. This is a vital
process to keep patients alive. In some cases, the patients undergo artificial dialysis until they are eligible for a
kidney transplant. In others who are not candidates for kidney transplants, dialysis is a lifelong necessity.

Dialysis technicians typically work in hospitals and clinics. While some roles in this field include equipment
development and maintenance, most dialysis technicians work in direct patient care. Their on-the-job duties, which
typically occur under the direct supervision of a registered nurse, focus on providing dialysis treatments. This can
include reviewing patient history and current condition, assessing and responding to patient needs before and
during treatment, and monitoring the dialysis process. Treatment may include taking and reporting a patient’s vital
signs, preparing solutions and equipment to ensure accurate and sterile procedures.

16.2 Digestive System

LEARNING OBJECTIVES
By the end of this section, you will be able to:
• Explain the processes of digestion and absorption
• Explain the specialized functions of the organs involved in processing food in the body
• Describe the ways in which organs work together to digest food and absorb nutrients
• Describe the essential nutrients required for cellular function that cannot be synthesized by the animal
body
• Describe how excess carbohydrates and energy are stored in the body

All living organisms need nutrients to survive. While plants can obtain nutrients from their roots and the energy
molecules required for cellular function through the process of photosynthesis, animals obtain their nutrients by the
consumption of other organisms. At the cellular level, the biological molecules necessary for animal function are
amino acids, lipid molecules, nucleotides, and simple sugars. However, the food consumed consists of protein, fat,
and complex carbohydrates. Animals must convert these macromolecules into the simple molecules required for
maintaining cellular function. The conversion of the food consumed to the nutrients required is a multistep process
involving digestion and absorption. During digestion, food particles are broken down to smaller components, which
are later absorbed by the body. This happens by both physical means, such as chewing, and by chemical means.

One of the challenges in human nutrition is maintaining a balance between food intake, storage, and energy
expenditure. Taking in more food energy than is used in activity leads to storage of the excess in the form of fat
deposits. The rise in obesity and the resulting diseases like type 2 diabetes makes understanding the role of diet
and nutrition in maintaining good health all the more important.

The Human Digestive System

The process of digestion begins in the mouth with the intake of food (Figure 16.4). The teeth play an important role
in masticating (chewing) or physically breaking food into smaller particles. The enzymes present in saliva also begin
to chemically break down food. The food is then swallowed and enters the esophagus—a long tube that connects
the mouth to the stomach. Using peristalsis, or wave-like smooth-muscle contractions, the muscles of the
esophagus push the food toward the stomach. The stomach contents are extremely acidic, with a pH between 1.5
and 2.5. This acidity kills microorganisms, breaks down food tissues, and activates digestive enzymes. Further
breakdown of food takes place in the small intestine where bile produced by the liver, and enzymes produced by the
small intestine and the pancreas, continue the process of digestion. The smaller molecules are absorbed into the
blood stream through the epithelial cells lining the walls of the small intestine. The waste material travels on to the
large intestine where water is absorbed and the drier waste material is compacted into feces; it is stored until it is
excreted through the anus.

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 16.2 • Digestive System 403

FIGURE 16.4 The components of the human digestive system are shown.

Oral Cavity
Both physical and chemical digestion begin in the mouth or oral cavity, which is the point of entry of food into the
digestive system. The food is broken into smaller particles by mastication, the chewing action of the teeth. All
mammals have teeth and can chew their food to begin the process of physically breaking it down into smaller
particles.

The chemical process of digestion begins during chewing as food mixes with saliva, produced by the salivary glands
(Figure 16.5). Saliva contains mucus that moistens food and buffers the pH of the food. Saliva also contains
lysozyme, which has antibacterial action. It also contains an enzyme called salivary amylase that begins the process
of converting starches in the food into a disaccharide called maltose. Another enzyme called lipase is produced by
cells in the tongue to break down fats. The chewing and wetting action provided by the teeth and saliva prepare the
food into a mass called the bolus for swallowing. The tongue helps in swallowing—moving the bolus from the mouth
into the pharynx. The pharynx opens to two passageways: the esophagus and the trachea. The esophagus leads to
the stomach and the trachea leads to the lungs. The epiglottis is a flap of tissue that covers the tracheal opening
during swallowing to prevent food from entering the lungs.
404 16 • The Body’s Systems

FIGURE 16.5 (a) Digestion of food begins in the mouth. (b) Food is masticated by teeth and moistened by saliva secreted from the salivary
glands. Enzymes in the saliva begin to digest starches and fats. With the help of the tongue, the resulting bolus is moved into the esophagus
by swallowing. (credit: modification of work by Mariana Ruiz Villareal)

Esophagus
The esophagus is a tubular organ that connects the mouth to the stomach. The chewed and softened food passes
through the esophagus after being swallowed. The smooth muscles of the esophagus undergo peristalsis that
pushes the food toward the stomach. The peristaltic wave is unidirectional—it moves food from the mouth the
stomach, and reverse movement is not possible, except in the case of the vomit reflex. The peristaltic movement of
the esophagus is an involuntary reflex; it takes place in response to the act of swallowing.

Ring-like muscles called sphincters form valves in the digestive system. The gastro-esophageal sphincter (or cardiac
sphincter) is located at the stomach end of the esophagus. In response to swallowing and the pressure exerted by
the bolus of food, this sphincter opens, and the bolus enters the stomach. When there is no swallowing action, this
sphincter is shut and prevents the contents of the stomach from traveling up the esophagus. Acid reflux or
“heartburn” occurs when the acidic digestive juices escape into the esophagus.

Stomach
A large part of protein digestion occurs in the stomach (Figure 16.7). The stomach is a saclike organ that secretes
gastric digestive juices.

Protein digestion is carried out by an enzyme called pepsin in the stomach chamber. The highly acidic environment
kills many microorganisms in the food and, combined with the action of the enzyme pepsin, results in the
catabolism of protein in the food. Chemical digestion is facilitated by the churning action of the stomach caused by
contraction and relaxation of smooth muscles. The partially digested food and gastric juice mixture is called chyme.
Gastric emptying occurs within two to six hours after a meal. Only a small amount of chyme is released into the
small intestine at a time. The movement of chyme from the stomach into the small intestine is regulated by
hormones, stomach distension and muscular reflexes that influence the pyloric sphincter.

The stomach lining is unaffected by pepsin and the acidity because pepsin is released in an inactive form and the
stomach has a thick mucus lining that protects the underlying tissue.

Small Intestine
Chyme moves from the stomach to the small intestine. The small intestine is the organ where the digestion of
protein, fats, and carbohydrates is completed. The small intestine is a long tube-like organ with a highly folded
surface containing finger-like projections called the villi. The top surface of each villus has many microscopic
projections called microvilli. The epithelial cells of these structures absorb nutrients from the digested food and
release them to the bloodstream on the other side. The villi and microvilli, with their many folds, increase the
surface area of the small intestine and increase absorption efficiency of the nutrients.

The human small intestine is over 6 m (19.6 ft) long and is divided into three parts: the duodenum, the jejunum and

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 16.2 • Digestive System 405

the ileum. The duodenum is separated from the stomach by the pyloric sphincter. The chyme is mixed with
pancreatic juices, an alkaline solution rich in bicarbonate that neutralizes the acidity of chyme from the stomach.
Pancreatic juices contain several digestive enzymes that break down starches, disaccharides, proteins, and fats.
Bile is produced in the liver and stored and concentrated in the gallbladder; it enters the duodenum through the bile
duct. Bile contains bile salts, which make lipids accessible to the water-soluble enzymes. The monosaccharides,
amino acids, bile salts, vitamins, and other nutrients are absorbed by the cells of the intestinal lining.

The undigested food is sent to the colon from the ileum via peristaltic movements. The ileum ends and the large
intestine begins at the ileocecal valve. The vermiform, “worm-like,” appendix is located at the ileocecal valve. The
appendix of humans has a minor role in immunity.

Large Intestine
The large intestine reabsorbs the water from indigestible food material and processes the waste material (Figure
16.6). The human large intestine is much smaller in length compared to the small intestine but larger in diameter. It
has three parts: the cecum, the colon, and the rectum. The cecum joins the ileum to the colon and is the receiving
pouch for the waste matter. The colon is home to many bacteria or “intestinal flora” that aid in the digestive
processes. The colon has four regions, the ascending colon, the transverse colon, the descending colon and the
sigmoid colon. The main functions of the colon are to extract the water and mineral salts from undigested food, and
to store waste material.

FIGURE 16.6 The large intestine reabsorbs water from undigested food and stores waste until it is eliminated. (credit: modification of work
by Mariana Ruiz Villareal)

The rectum (Figure 16.6) stores feces until defecation. The feces are propelled using peristaltic movements during
elimination. The anus is an opening at the far-end of the digestive tract and is the exit point for the waste material.
Two sphincters regulate the exit of feces, the inner sphincter is involuntary and the outer sphincter is voluntary.

Accessory Organs
The organs discussed above are the organs of the digestive tract through which food passes. Accessory organs add
secretions and enzymes that break down food into nutrients. Accessory organs include the salivary glands, the liver,
the pancreas, and the gall bladder. The secretions of the liver, pancreas, and gallbladder are regulated by hormones
in response to food consumption.

The liver is the largest internal organ in humans and it plays an important role in digestion of fats and detoxifying
blood. The liver produces bile, a digestive juice that is required for the breakdown of fats in the duodenum. The liver
also processes the absorbed vitamins and fatty acids and synthesizes many plasma proteins. The gallbladder is a
small organ that aids the liver by storing bile and concentrating bile salts.

The pancreas secretes bicarbonate that neutralizes the acidic chyme and a variety of enzymes for the digestion of
protein and carbohydrates.
406 16 • The Body’s Systems

VISUAL CONNECTION

FIGURE 16.7 The stomach has an extremely acidic environment where most of the protein gets digested. (credit: modification of work by
Mariana Ruiz Villareal)

Which of the following statements about the digestive system is false?

a. Chyme is a mixture of food and digestive juices that is produced in the stomach.
b. Food enters the large intestine before the small intestine.
c. In the small intestine, chyme mixes with bile, which emulsifies fats.
d. The stomach is separated from the small intestine by the pyloric sphincter.

Nutrition
The human diet should be well balanced to provide nutrients required for bodily function and the minerals and
vitamins required for maintaining structure and regulation necessary for good health and reproductive capability
(Figure 16.8).

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 16.2 • Digestive System 407

FIGURE 16.8 For humans, a balanced diet includes fruits, vegetables, grains, protein, and dairy. (credit: USDA)

LINK TO LEARNING
Explore this interactive United States Department of Agriculture website (http://openstax.org/l/food_groups2) to
learn more about each food group and the recommended daily amounts.

The organic molecules required for building cellular material and tissues must come from food. During digestion,
digestible carbohydrates are ultimately broken down into glucose and used to provide energy within the cells of the
body. Complex carbohydrates, including polysaccharides, can be broken down into glucose through biochemical
modification; however, humans do not produce the enzyme necessary to digest cellulose (fiber). The intestinal flora
in the human gut are able to extract some nutrition from these plant fibers. These plant fibers are known as dietary
fiber and are an important component of the diet. The excess sugars in the body are converted into glycogen and
stored for later use in the liver and muscle tissue. Glycogen stores are used to fuel prolonged exertions, such as
long-distance running, and to provide energy during food shortage. Fats are stored under the skin of mammals for
insulation and energy reserves.

Proteins in food are broken down during digestion and the resulting amino acids are absorbed. All of the proteins in
the body must be formed from these amino-acid constituents; no proteins are obtained directly from food.

Fats add flavor to food and promote a sense of satiety or fullness. Fatty foods are also significant sources of energy,
and fatty acids are required for the construction of lipid membranes. Fats are also required in the diet to aid the
absorption of fat-soluble vitamins and the production of fat-soluble hormones.

While the animal body can synthesize many of the molecules required for function from precursors, there are some
nutrients that must be obtained from food. These nutrients are termed essential nutrients, meaning they must be
eaten, because the body cannot produce them.

The fatty acids omega-3 alpha-linolenic acid and omega-6 linoleic acid are essential fatty acids needed to make
some membrane phospholipids. Vitamins are another class of essential organic molecules that are required in
small quantities. Many of these assist enzymes in their function and, for this reason, are called coenzymes. Absence
or low levels of vitamins can have a dramatic effect on health. Minerals are another set of inorganic essential
nutrients that must be obtained from food. Minerals perform many functions, from muscle and nerve function, to
acting as enzyme cofactors. Certain amino acids also must be procured from food and cannot be synthesized by the
body. These amino acids are the “essential” amino acids. The human body can synthesize only 11 of the 20 required
amino acids; the rest must be obtained from food.
408 16 • The Body’s Systems

EVERYDAY CONNECTION
Obesity
With obesity at high rates in the United States, there is a public health focus on reducing obesity and associated
health risks, which include diabetes, colon and breast cancer, and cardiovascular disease. How does the food
consumed contribute to obesity?

Fatty foods are calorie-dense, meaning that they have more calories per unit mass than carbohydrates or
proteins. One gram of carbohydrates has four calories, one gram of protein has four calories, and one gram of fat
has nine calories. Animals tend to seek lipid-rich food for their higher energy content. Greater amounts of food
energy taken in than the body’s requirements will result in storage of the excess in fat deposits.

Excess carbohydrate is used by the liver to synthesize glycogen. When glycogen stores are full, additional
glucose is converted into fatty acids. These fatty acids are stored in adipose tissue cells—the fat cells in the
mammalian body whose primary role is to store fat for later use.

The rate of obesity among children is rapidly rising in the United States. To combat childhood obesity and ensure
that children get a healthy start in life, in 2010 First Lady Michelle Obama launched the Let’s Move! campaign.
The goal of this campaign is to educate parents and caregivers on providing healthy nutrition and encouraging
active lifestyles in future generations. This program aims to involve the entire community, including parents,
teachers, and healthcare providers to ensure that children have access to healthy foods—more fruits,
vegetables, and whole grains—and consume fewer calories from processed foods. Another goal is to ensure that
children get physical activity. With the increase in television viewing and stationary pursuits such as video
games, sedentary lifestyles have become the norm. Visit https://letsmove.obamawhitehouse.archives.gov/ to
learn more.

16.3 Circulatory and Respiratory Systems

LEARNING OBJECTIVES
By the end of this section, you will be able to:
• Describe the passage of air from the outside environment to the lungs
• Describe the function of the circulatory system
• Describe the cardiac cycle
• Explain how blood flows through the body

Animals are complex multicellular organisms that require a mechanism for transporting nutrients throughout their
bodies and removing wastes. The human circulatory system has a complex network of blood vessels that reach all
parts of the body. This extensive network supplies the cells, tissues, and organs with oxygen and nutrients, and
removes carbon dioxide and waste compounds.

The medium for transport of gases and other molecules is the blood, which continually circulates through the
system. Pressure differences within the system cause the movement of the blood and are created by the pumping of
the heart.

Gas exchange between tissues and the blood is an essential function of the circulatory system. In humans, other
mammals, and birds, blood absorbs oxygen and releases carbon dioxide in the lungs. Thus the circulatory and
respiratory system, whose function is to obtain oxygen and discharge carbon dioxide, work in tandem.

The Respiratory System

Take a breath in and hold it. Wait several seconds and then let it out. Humans, when they are not exerting
themselves, breathe approximately 15 times per minute on average. This equates to about 900 breaths an hour or
21,600 breaths per day. With every inhalation, air fills the lungs, and with every exhalation, it rushes back out. That
air is doing more than just inflating and deflating the lungs in the chest cavity. The air contains oxygen that crosses
the lung tissue, enters the bloodstream, and travels to organs and tissues. There, oxygen is exchanged for carbon
dioxide, which is a cellular waste material. Carbon dioxide exits the cells, enters the bloodstream, travels back to the
lungs, and is expired out of the body during exhalation.

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 16.3 • Circulatory and Respiratory Systems 409

Breathing is both a voluntary and an involuntary event. How often a breath is taken and how much air is inhaled or
exhaled is regulated by the respiratory center in the brain in response to signals it receives about the carbon dioxide
content of the blood. However, it is possible to override this automatic regulation for activities such as speaking,
singing and swimming under water.

During inhalation the diaphragm descends creating a negative pressure around the lungs and they begin to inflate,
drawing in air from outside the body. The air enters the body through the nasal cavity located just inside the nose
(Figure 16.9). As the air passes through the nasal cavity, the air is warmed to body temperature and humidified by
moisture from mucous membranes. These processes help equilibrate the air to the body conditions, reducing any
damage that cold, dry air can cause. Particulate matter that is floating in the air is removed in the nasal passages by
hairs, mucus, and cilia. Air is also chemically sampled by the sense of smell.

From the nasal cavity, air passes through the pharynx (throat) and the larynx (voice box) as it makes its way to the
trachea (Figure 16.9). The main function of the trachea is to funnel the inhaled air to the lungs and the exhaled air
back out of the body. The human trachea is a cylinder, about 25 to 30 cm (9.8–11.8 in) long, which sits in front of the
esophagus and extends from the pharynx into the chest cavity to the lungs. It is made of incomplete rings of
cartilage and smooth muscle. The cartilage provides strength and support to the trachea to keep the passage open.
The trachea is lined with cells that have cilia and secrete mucus. The mucus catches particles that have been
inhaled, and the cilia move the particles toward the pharynx.

The end of the trachea divides into two bronchi that enter the right and left lung. Air enters the lungs through the
primary bronchi. The primary bronchus divides, creating smaller and smaller diameter bronchi until the passages
are under 1 mm (.03 in) in diameter when they are called bronchioles as they split and spread through the lung. Like
the trachea, the bronchus and bronchioles are made of cartilage and smooth muscle. Bronchi are innervated by
nerves of both the parasympathetic and sympathetic nervous systems that control muscle contraction
(parasympathetic) or relaxation (sympathetic) in the bronchi and bronchioles, depending on the nervous system’s
cues. The final bronchioles are the respiratory bronchioles. Alveolar ducts are attached to the end of each
respiratory bronchiole. At the end of each duct are alveolar sacs, each containing 20 to 30 alveoli. Gas exchange
occurs only in the alveoli. The alveoli are thin-walled and look like tiny bubbles within the sacs. The alveoli are in
direct contact with capillaries of the circulatory system. Such intimate contact ensures that oxygen will diffuse from
the alveoli into the blood. In addition, carbon dioxide will diffuse from the blood into the alveoli to be exhaled. The
anatomical arrangement of capillaries and alveoli emphasizes the structural and functional relationship of the
respiratory and circulatory systems. Estimates for the surface area of alveoli in the lungs vary around 100 m2. This
large area is about the area of half a tennis court. This large surface area, combined with the thin-walled nature of
the alveolar cells, allows gases to easily diffuse across the cells.
410 16 • The Body’s Systems

VISUAL CONNECTION

FIGURE 16.9 Air enters the respiratory system through the nasal cavity, and then passes through the pharynx and the trachea into the
lungs. (credit: modification of work by NCI)

Which of the following statements about the human respiratory system is false?

a. When we breathe in, air travels from the pharynx to the trachea.
b. The bronchioles branch into bronchi.
c. Alveolar ducts connect to alveolar sacs.
d. Gas exchange between the lungs and blood takes place in the alveolus.

LINK TO LEARNING
Watch this video (http://openstax.org/l/lungs_pulmonar2) for a review of the respiratory system.

The Circulatory System

The circulatory system is a network of vessels—the arteries, veins, and capillaries—and a pump, the heart. In all
vertebrate organisms this is a closed-loop system, in which the blood is largely separated from the body’s other

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 16.3 • Circulatory and Respiratory Systems 411

extracellular fluid compartment, the interstitial fluid, which is the fluid bathing the cells. Blood circulates inside
blood vessels and circulates unidirectionally from the heart around one of two circulatory routes, then returns to the
heart again; this is a closed circulatory system. Open circulatory systems are found in invertebrate animals in
which the circulatory fluid bathes the internal organs directly even though it may be moved about with a pumping
heart.

The Heart
The heart is a complex muscle that consists of two pumps: one that pumps blood through pulmonary circulation to
the lungs, and the other that pumps blood through systemic circulation to the rest of the body’s tissues (and the
heart itself).

The heart is asymmetrical, with the left side being larger than the right side, correlating with the different sizes of
the pulmonary and systemic circuits (Figure 16.10). In humans, the heart is about the size of a clenched fist; it is
divided into four chambers: two atria and two ventricles. There is one atrium and one ventricle on the right side and
one atrium and one ventricle on the left side. The right atrium receives deoxygenated blood from the systemic
circulation through the major veins: the superior vena cava, which drains blood from the head and from the veins
that come from the arms, as well as the inferior vena cava, which drains blood from the veins that come from the
lower organs and the legs. This deoxygenated blood then passes to the right ventricle through the tricuspid valve,
which prevents the backflow of blood. After it is filled, the right ventricle contracts, pumping the blood to the lungs
for reoxygenation. The left atrium receives the oxygen-rich blood from the lungs. This blood passes through the
bicuspid valve to the left ventricle where the blood is pumped into the aorta. The aorta is the major artery of the
body, taking oxygenated blood to the organs and muscles of the body. This pattern of pumping is referred to as
double circulation and is found in all mammals. (Figure 16.10).

VISUAL CONNECTION

FIGURE 16.10 The heart is divided into four chambers, two atria, and two ventricles. Each chamber is separated by one-way valves. The
right side of the heart receives deoxygenated blood from the body and pumps it to the lungs. The left side of the heart pumps blood to the
rest of the body.

Which of the following statements about the circulatory system is false?

412 16 • The Body’s Systems

a. Blood in the pulmonary vein is deoxygenated.

b. Blood in the inferior vena cava is deoxygenated.
c. Blood in the pulmonary artery is deoxygenated.
d. Blood in the aorta is oxygenated.

The Cardiac Cycle

The main purpose of the heart is to pump blood through the body; it does so in a repeating sequence called the
cardiac cycle. The cardiac cycle is the flow of blood through the heart coordinated by electrochemical signals that
cause the heart muscle to contract and relax. In each cardiac cycle, a sequence of contractions pushes out the
blood, pumping it through the body; this is followed by a relaxation phase, where the heart fills with blood. These
two phases are called the systole (contraction) and diastole (relaxation), respectively (Figure 16.11). The signal for
contraction begins at a location on the outside of the right atrium. The electrochemical signal moves from there
across the atria causing them to contract. The contraction of the atria forces blood through the valves into the
ventricles. Closing of these valves caused by the contraction of the ventricles produces a “lub” sound. The signal
has, by this time, passed down the walls of the heart, through a point between the right atrium and right ventricle.
The signal then causes the ventricles to contract. The ventricles contract together forcing blood into the aorta and
the pulmonary arteries. Closing of the valves to these arteries caused by blood being drawn back toward the heart
during ventricular relaxation produces a monosyllabic “dub” sound.

FIGURE 16.11 In each cardiac cycle, a series of contractions (systoles) and relaxations (diastoles) pumps blood through the heart and
through the body. (a) During cardiac diastole, blood flows into the heart while all chambers are relaxed. (b) Then the ventricles remain
relaxed while atrial systole pushes blood into the ventricles. (c) Once the atria relax again, ventricle systole pushes blood out of the heart.

The pumping of the heart is a function of the cardiac muscle cells, or cardiomyocytes, that make up the heart
muscle. Cardiomyocytes are distinctive muscle cells that are striated like skeletal muscle but pump rhythmically
and involuntarily like smooth muscle; adjacent cells are connected by intercalated disks found only in cardiac
muscle. These connections allow the electrical signal to travel directly to neighboring muscle cells.

The electrical impulses in the heart produce electrical currents that flow through the body and can be measured on
the skin using electrodes. This information can be observed as an electrocardiogram (ECG) a recording of the
electrical impulses of the cardiac muscle.

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 16.3 • Circulatory and Respiratory Systems 413

LINK TO LEARNING
Visit this site (http://openstax.org/l/electric_heart2) and select the dropdown “Your Heart’s Electrical System” to
see the heart’s pacemaker, or electrocardiogram system, in action.

Blood Vessels
The blood from the heart is carried through the body by a complex network of blood vessels (Figure 16.12). Arteries
take blood away from the heart. The main artery of the systemic circulation is the aorta; it branches into major
arteries that take blood to different limbs and organs. The aorta and arteries near the heart have heavy but elastic
walls that respond to and smooth out the pressure differences caused by the beating heart. Arteries farther away
from the heart have more muscle tissue in their walls that can constrict to affect flow rates of blood. The major
arteries diverge into minor arteries, and then smaller vessels called arterioles, to reach more deeply into the
muscles and organs of the body.

Arterioles diverge into capillary beds. Capillary beds contain a large number, 10’s to 100’s of capillaries that branch
among the cells of the body. Capillaries are narrow-diameter tubes that can fit single red blood cells and are the
sites for the exchange of nutrients, waste, and oxygen with tissues at the cellular level. Fluid also leaks from the
blood into the interstitial space from the capillaries. The capillaries converge again into venules that connect to
minor veins that finally connect to major veins. Veins are blood vessels that bring blood high in carbon dioxide back
to the heart. Veins are not as thick-walled as arteries, since pressure is lower, and they have valves along their
length that prevent backflow of blood away from the heart. The major veins drain blood from the same organs and
limbs that the major arteries supply.
414 16 • The Body’s Systems

FIGURE 16.12 The arteries of the body, indicated in red, start at the aortic arch and branch to supply the organs and muscles of the body
with oxygenated blood. The veins of the body, indicated in blue, return blood to the heart. The pulmonary arteries are blue to reflect the fact
that they are deoxygenated, and the pulmonary veins are red to reflect that they are oxygenated. (credit: modification of work by Mariana
Ruiz Villareal)

16.4 Endocrine System

LEARNING OBJECTIVES
By the end of this section, you will be able to:
• List the different types of hormones and explain their roles in maintaining homeostasis
• Explain how hormones work
• Explain how hormone production is regulated
• Describe the role of different glands in the endocrine system
• Explain how the different glands work together to maintain homeostasis

The endocrine system produces hormones that function to control and regulate many different body processes. The
endocrine system coordinates with the nervous system to control the functions of the other organ systems. Cells of
the endocrine system produce molecular signals called hormones. These cells may compose endocrine glands, may
be tissues or may be located in organs or tissues that have functions in addition to hormone production. Hormones
circulate throughout the body and stimulate a response in cells that have receptors able to bind with them. The
changes brought about in the receiving cells affect the functioning of the organ system to which they belong. Many
of the hormones are secreted in response to signals from the nervous system, thus the two systems act in concert to
effect changes in the body.

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 16.4 • Endocrine System 415

Hormones
Maintaining homeostasis within the body requires the coordination of many different systems and organs. One
mechanism of communication between neighboring cells, and between cells and tissues in distant parts of the body,
occurs through the release of chemicals called hormones. Hormones are released into body fluids, usually blood,
which carries them to their target cells where they elicit a response. The cells that secrete hormones are often
located in specific organs, called endocrine glands, and the cells, tissues, and organs that secrete hormones make
up the endocrine system. Examples of endocrine organs include the pancreas, which produces the hormones insulin
and glucagon to regulate blood-glucose levels, the adrenal glands, which produce hormones such as epinephrine
and norepinephrine that regulate responses to stress, and the thyroid gland, which produces thyroid hormones that
regulate metabolic rates.

The endocrine glands differ from the exocrine glands. Exocrine glands secrete chemicals through ducts that lead
outside the gland (not to the blood). For example, sweat produced by sweat glands is released into ducts that carry
sweat to the surface of the skin. The pancreas has both endocrine and exocrine functions because besides releasing
hormones into the blood. It also produces digestive juices, which are carried by ducts into the small intestine.

CAREER CONNECTION

Endocrinologist
An endocrinologist is a medical doctor who specializes in treating endocrine disorders. An endocrine surgeon
specializes in the surgical treatment of endocrine diseases and glands. Some of the diseases that are managed by
endocrinologists include disorders of the pancreas (diabetes mellitus), disorders of the pituitary (gigantism,
acromegaly, and pituitary dwarfism), disorders of the thyroid gland (goiter and Graves’ disease), and disorders of the
adrenal glands (Cushing’s disease and Addison’s disease).

Endocrinologists are required to assess patients and diagnose endocrine disorders through extensive use of
laboratory tests. Many endocrine diseases are diagnosed using tests that stimulate or suppress endocrine organ
functioning. Blood samples are then drawn to determine the effect of stimulating or suppressing an endocrine organ
on the production of hormones. For example, to diagnose diabetes mellitus, patients are required to fast for 12 to 24
hours. They are then given a sugary drink, which stimulates the pancreas to produce insulin to decrease blood-
glucose levels. A blood sample is taken one to two hours after the sugar drink is consumed. If the pancreas is
functioning properly, the blood-glucose level will be within a normal range. Another example is the A1C test, which
can be performed during blood screening. The A1C test measures average blood-glucose levels over the past two to
three months. The A1C test is an indicator of how well blood glucose is being managed over a long time.

Once a disease such as diabetes has been diagnosed, endocrinologists can prescribe lifestyle changes and
medications to treat the disease. Some cases of diabetes mellitus can be managed by exercise, weight loss, and a
healthy diet; in other cases, medications may be required to enhance insulin’s production or effect. If the disease
cannot be controlled by these means, the endocrinologist may prescribe insulin injections.

In addition to clinical practice, endocrinologists may also be involved in primary research and development
activities. For example, ongoing islet transplant research is investigating how healthy pancreas islet cells may be
transplanted into diabetic patients. Successful islet transplants may allow patients to stop taking insulin injections.

How Hormones Work

Hormones cause changes in target cells by binding to specific cell-surface or intracellular hormone receptors,
molecules embedded in the cell membrane or floating in the cytoplasm with a binding site that matches a binding
site on the hormone molecule. In this way, even though hormones circulate throughout the body and come into
contact with many different cell types, they only affect cells that possess the necessary receptors. Receptors for a
specific hormone may be found on or in many different cells or may be limited to a small number of specialized
cells. For example, thyroid hormones act on many different tissue types, stimulating metabolic activity throughout
the body. Cells can have many receptors for the same hormone but often also possess receptors for different types
of hormones. The number of receptors that respond to a hormone determines the cell’s sensitivity to that hormone,
416 16 • The Body’s Systems

and the resulting cellular response. Additionally, the number of receptors available to respond to a hormone can
change over time, resulting in increased or decreased cell sensitivity. In up-regulation, the number of receptors
increases in response to rising hormone levels, making the cell more sensitive to the hormone and allowing for more
cellular activity. When the number of receptors decreases in response to rising hormone levels, called down-
regulation, cellular activity is reduced.

Endocrine Glands
The endocrine glands secrete hormones into the surrounding interstitial fluid; those hormones then diffuse into
blood and are carried to various organs and tissues within the body. The endocrine glands include the pituitary,
thyroid, parathyroid, adrenal glands, gonads, pineal, and pancreas.

The pituitary gland, sometimes called the hypophysis, is located at the base of the brain (Figure 16.13a). It is
attached to the hypothalamus. The posterior lobe stores and releases oxytocin and antidiuretic hormone produced
by the hypothalamus. The anterior lobe responds to hormones produced by the hypothalamus by producing its own
hormones, most of which regulate other hormone-producing glands.

FIGURE 16.13 (a) The pituitary gland sits at the base of the brain, just above the brain stem. (b) The parathyroid glands are located on the
posterior of the thyroid gland. (c) The adrenal glands are on top of the kidneys. d) The pancreas is found between the stomach and the
small intestine. (credit: modification of work by NCI, NIH)

The anterior pituitary produces six hormones: growth hormone, prolactin, thyroid-stimulating hormone,
adrenocorticotropic hormone, follicle-stimulating hormone, and luteinizing hormone. Growth hormone stimulates
cellular activities like protein synthesis that promote growth. Prolactin stimulates the production of milk by the

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 16.4 • Endocrine System 417

mammary glands. The other hormones produced by the anterior pituitary regulate the production of hormones by
other endocrine tissues (Table 16.1). The posterior pituitary is significantly different in structure from the anterior
pituitary. It is a part of the brain, extending down from the hypothalamus, and contains mostly nerve fibers that
extend from the hypothalamus to the posterior pituitary.

The thyroid gland is located in the neck, just below the larynx and in front of the trachea (Figure 16.13b). It is a
butterfly-shaped gland with two lobes that are connected. The thyroid follicle cells synthesize the hormone
thyroxine, which is also known as T4 because it contains four atoms of iodine, and triiodothyronine, also known as T3
because it contains three atoms of iodine. T3 and T4 are released by the thyroid in response to thyroid-stimulating
hormone produced by the anterior pituitary, and both T3 and T4 have the effect of stimulating metabolic activity in
the body and increasing energy use. A third hormone, calcitonin, is also produced by the thyroid. Calcitonin is
released in response to rising calcium ion concentrations in the blood and has the effect of reducing those levels.

Most people have four parathyroid glands; however, the number can vary from two to six. These glands are located
on the posterior surface of the thyroid gland (Figure 16.13b).

The parathyroid glands produce parathyroid hormone. Parathyroid hormone increases blood calcium concentrations
when calcium ion levels fall below normal.

The adrenal glands are located on top of each kidney (Figure 16.13c). The adrenal glands consist of an outer
adrenal cortex and an inner adrenal medulla. These regions secrete different hormones.

The adrenal cortex produces mineralocorticoids, glucocorticoids, and androgens. The main mineralocorticoid is
aldosterone, which regulates the concentration of ions in urine, sweat, and saliva. Aldosterone release from the
adrenal cortex is stimulated by a decrease in blood concentrations of sodium ions, blood volume, or blood pressure,
or by an increase in blood potassium levels. The glucocorticoids maintain proper blood-glucose levels between
meals. They also control a response to stress by increasing glucose synthesis from fats and proteins and interact
with epinephrine to cause vasoconstriction.

The testes and the adrenal cortex both secrete androgens, and the testes produce a larger amount that mostly
drives development in a testicular reproductive system. When androgens are produced, some of them are later
converted to estrogens. Androgens and estrogens resemble one another in chemical structure and originate from
the same molecule. Minute amounts of estrogen occur in all humans through actions in adipose, brain, skin, and
bone, which convert testosterone to estrogen. The small amount of androgens produced in the adrenal cortex may
supplement hormones released from the gonads. The adrenal medulla contains two types of secretory cells: one
that produces epinephrine (adrenaline) and another that produces norepinephrine (noradrenaline). Epinephrine and
norepinephrine cause immediate, short-term changes in response to stressors, inducing the so-called fight-or-flight
response. The responses include increased heart rate, breathing rate, cardiac muscle contractions, and blood-
glucose levels. They also accelerate the breakdown of glucose in skeletal muscles and stored fats in adipose tissue,
and redirect blood flow toward skeletal muscles and away from skin and viscera. The release of epinephrine and
norepinephrine is stimulated by neural impulses from the sympathetic nervous system that originate from the
hypothalamus.

The pancreas is an elongated organ located between the stomach and the proximal portion of the small intestine
(Figure 16.13d). It contains both exocrine cells that excrete digestive enzymes and endocrine cells that release
hormones.

The endocrine cells of the pancreas form clusters called pancreatic islets or the islets of Langerhans. Among the cell
types in each pancreatic islet are the alpha cells, which produce the hormone glucagon, and the beta cells, which
produce the hormone insulin. These hormones regulate blood-glucose levels. Alpha cells release glucagon as blood-
glucose levels decline. When blood-glucose levels rise, beta cells release insulin. Glucagon causes the release of
glucose to the blood from the liver, and insulin facilitates the uptake of glucose by the body’s cells.

The gonads—the testes and ovaries—produce steroid hormones. The testes produce androgens, testosterone being
the most prominent, which trigger the production of sperm cells, growth and development of the testes and penis,
increased skeletal and muscular growth, enlargement of the larynx, and increased growth and redistribution of body
hair. The ovaries produce estrogen and progesterone, which, during puberty, cause the increased development of
breast tissue, redistribution of fat towards hips, legs, and breast, the maturation of the uterus and vagina, and
418 16 • The Body’s Systems

regulate the production of eggs. If pregnancy occurs, these hormones manage and prepare the body systems for
carrying and birthing the offspring.

There are several organs whose primary functions are non-endocrine but that also possess endocrine functions.
These include the heart, kidneys, intestines, thymus, and adipose tissue. The heart has endocrine cells in the walls
of the atria that release a hormone in response to increased blood volume. It causes a reduction in blood volume
and blood pressure, and reduces the concentration of Na+ in the blood.

The gastrointestinal tract produces several hormones that aid in digestion. The endocrine cells are located in the
mucosa of the GI tract throughout the stomach and small intestine. They trigger the release of gastric juices, which
help to break down and digest food in the GI tract.

The kidneys also possess endocrine function. Two of these hormones regulate ion concentrations and blood volume
or pressure. Erythropoietin (EPO) is released by kidneys in response to low oxygen levels. EPO triggers the formation
of red blood cells in the bone marrow. EPO has been used by athletes to improve performance. But EPO doping has
its risks, since it thickens the blood and increases strain on the heart; it also increases the risk of blood clots and
therefore heart attacks and stroke.

The thymus is found behind the sternum. The thymus produces hormones referred to as thymosins, which
contribute to the development of the immune response in infants. Adipose tissue, or fat tissue, produces the
hormone leptin in response to food intake. Leptin produces a feeling of satiety after eating, reducing the urge for
further eating.

Endocrine Glands and Their Associated Hormones

Endocrine Associated
Effect
Gland Hormones

growth hormone promotes growth of body tissues

prolactin promotes milk production

thyroid-stimulating
stimulates thyroid hormone release
hormone

Pituitary
adrenocorticotropic
(anterior) stimulates hormone release by adrenal cortex
hormone

follicle-stimulating
stimulates gamete production
hormone

stimulates androgen production in testes; stimulates ovulation and

luteinizing hormone
production of estrogen and progesterone in ovaries

antidiuretic
stimulates water reabsorption by kidneys
Pituitary hormone
(posterior)
oxytocin stimulates uterine contractions during childbirth

thyroxine,
stimulate metabolism
triiodothyronine
Thyroid

calcitonin reduces blood Ca2+ levels

TABLE 16.1

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 16.4 • Endocrine System 419

Endocrine Associated
Effect
Gland Hormones

parathyroid
Parathyroid increases blood Ca2+ levels
hormone

aldosterone increases blood Na+ levels

Adrenal
cortisol,
(cortex)
corticosterone, increase blood-glucose levels
cortisone

Adrenal epinephrine,
stimulate fight-or-flight response
(medulla) norepinephrine

insulin reduces blood-glucose levels

Pancreas
glucagon increases blood-glucose levels

TABLE 16.1

Regulation of Hormone Production

Hormone production and release are primarily controlled by negative feedback, as described in the discussion on
homeostasis. In this way, the concentration of hormones in blood is maintained within a narrow range. For example,
the anterior pituitary signals the thyroid to release thyroid hormones. Increasing levels of these hormones in the
blood then give feedback to the hypothalamus and anterior pituitary to inhibit further signaling to the thyroid gland
(Figure 16.14).
420 16 • The Body’s Systems

VISUAL CONNECTION

FIGURE 16.14 The anterior pituitary stimulates the thyroid gland to release thyroid hormones T3 and T4. Increasing levels of these
hormones in the blood result in feedback to the hypothalamus and anterior pituitary to inhibit further signaling to the thyroid gland. (credit:
modification of work by Mikael Häggström)

Goiter, a disease caused by iodine deficiency, results in the inability of the thyroid gland to form T3 and T4. The body
typically attempts to compensate by producing greater amounts of TSH. Which of the following symptoms would
you expect goiter to cause?

a. Hypothyroidism, resulting in weight gain, cold sensitivity, and reduced mental activity.
b. Hyperthyroidism, resulting in weight loss, profuse sweating, and increased heart rate.
c. Hyperthyroidism, resulting in weight gain, cold sensitivity, and reduced mental activity.
d. Hypothyroidism, resulting in weight loss, profuse sweating, and increased heart rate.

16.5 Musculoskeletal System

LEARNING OBJECTIVES
By the end of this section, you will be able to:
• Discuss the axial and appendicular parts of the skeletal system
• Explain the role of joints in skeletal movement
• Explain the role of muscles in locomotion

The muscular and skeletal systems provide support to the body and allow for movement. The bones of the skeleton
protect the body’s internal organs and support the weight of the body. The muscles of the muscular system contract

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 16.5 • Musculoskeletal System 421

and pull on the bones, allowing for movements as diverse as standing, walking, running, and grasping items.

Injury or disease affecting the musculoskeletal system can be very debilitating. The most common musculoskeletal
diseases worldwide are caused by malnutrition, which can negatively affect development and maintenance of bones
and muscles. Other diseases affect the joints, such as arthritis, which can make movement difficult and, in advanced
cases, completely impair mobility.

Progress in the science of prosthesis design has resulted in the development of artificial joints, with joint
replacement surgery in the hips and knees being the most common. Replacement joints for shoulders, elbows, and
fingers are also available.

Skeletal System
The human skeleton is an endoskeleton that consists of 206 bones in the adult. An endoskeleton develops within
the body rather than outside like the exoskeleton of insects. The skeleton has five main functions: providing support
to the body, storing minerals and lipids, producing blood cells, protecting internal organs, and allowing for
movement. The skeletal system in vertebrates is divided into the axial skeleton (which consists of the skull,
vertebral column, and rib cage), and the appendicular skeleton (which consists of limb bones, the pectoral or
shoulder girdle, and the pelvic girdle).

LINK TO LEARNING
Explore the human skeleton by viewing the following video (http://openstax.org/l/human_skeleton) with digital 3D
sculpturing.

The axial skeleton forms the central axis of the body and includes the bones of the skull, ossicles of the middle ear,
hyoid bone of the throat, vertebral column, and the thoracic cage (rib cage) (Figure 16.15).
422 16 • The Body’s Systems

FIGURE 16.15 The axial skeleton, shown in blue, consists of the bones of the skull, ossicles of the middle ear, hyoid bone, vertebral
column, and thoracic cage. The appendicular skeleton, shown in red, consists of the bones of the pectoral limbs, pectoral girdle, pelvic limb,
and pelvic girdle. (credit: modification of work by Mariana Ruiz Villareal)

The bones of the skull support the structures of the face and protect the brain. The skull consists of cranial bones
and facial bones. The cranial bones form the cranial cavity, which encloses the brain and serves as an attachment
site for muscles of the head and neck. In the adult they are tightly jointed with connective tissue and adjoining
bones do not move.

The auditory ossicles of the middle ear transmit sounds from the air as vibrations to the fluid-filled cochlea. The
auditory ossicles consist of two malleus (hammer) bones, two incus (anvil) bones, and two stapes (stirrups), one on
each side. Facial bones provide cavities for the sense organs (eyes, mouth, and nose), and serve as attachment
points for facial muscles.

The hyoid bone lies below the mandible in the front of the neck. It acts as a movable base for the tongue and is
connected to muscles of the jaw, larynx, and tongue. The mandible forms a joint with the base of the skull. The

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 16.5 • Musculoskeletal System 423

mandible controls the opening to the mouth and hence, the airway and gut.

The vertebral column, or spinal column, surrounds and protects the spinal cord, supports the head, and acts as an
attachment point for ribs and muscles of the back and neck. It consists of 26 bones: the 24 vertebrae, the sacrum,
and the coccyx. Each vertebral body has a large hole in the center through which the spinal cord passes down to the
level of the first lumbar vertebra. Below this level, the hole contains spinal nerves which exit between the vertebrae.
There is a notch on each side of the hole through which the spinal nerves, can exit from the spinal cord to serve
different regions of the body. The vertebral column is approximately 70 cm (28 in) in adults and is curved, which can
be seen from a side view.

Intervertebral discs composed of fibrous cartilage lie between adjacent vertebrae from the second cervical vertebra
to the sacrum. Each disc helps form a slightly moveable joint and acts as a cushion to absorb shocks from
movements such as walking and running.

The thoracic cage, also known as the rib cage consists of the ribs, sternum, thoracic vertebrae, and costal
cartilages. The thoracic cage encloses and protects the organs of the thoracic cavity including the heart and lungs. It
also provides support for the shoulder girdles and upper limbs and serves as the attachment point for the
diaphragm, muscles of the back, chest, neck, and shoulders. Changes in the volume of the thorax enable breathing.
The sternum, or breastbone, is a long flat bone located at the anterior of the chest. Like the skull, it is formed from
many bones in the embryo, which fuse in the adult. The ribs are 12 pairs of long curved bones that attach to the
thoracic vertebrae and curve toward the front of the body, forming the ribcage. Costal cartilages connect the anterior
ends of most ribs to the sternum.

The appendicular skeleton is composed of the bones of the upper and lower limbs. It also includes the pectoral, or
shoulder girdle, which attaches the upper limbs to the body, and the pelvic girdle, which attaches the lower limbs to
the body (Figure 16.15).

The pectoral girdle bones transfer force generated by muscles acting on the upper limb to the thorax. It consists of
the clavicles (or collarbones) in the anterior, and the scapulae (or shoulder blades) in the posterior.

The upper limb contains bones of the arm (shoulder to elbow), the forearm, and the hand. The humerus is the
largest and longest bone of the upper limb. It forms a joint with the shoulder and with the forearm at the elbow. The
forearm extends from the elbow to the wrist and consists of two bones. The hand includes the bones of the wrist,
the palm, and the bones of the fingers.

The pelvic girdle attaches to the lower limbs of the axial skeleton. Since it is responsible for bearing the weight of
the body and for locomotion, the pelvic girdle is securely attached to the axial skeleton by strong ligaments. It also
has deep sockets with robust ligaments that securely attach to the femur. The pelvic girdle is mainly composed of
two large hip bones. The hip bones join together in the anterior of the body at a joint called the pubic symphysis and
with the bones of the sacrum at the posterior of the body.

The lower limb consists of the thigh, the leg, and the foot. The bones of the lower limbs are thicker and stronger than
the bones of the upper limbs to support the entire weight of the body and the forces from locomotion. The femur, or
thighbone, is the longest, heaviest, and strongest bone in the body. The femur and pelvis form the hip joint. At its
other end, the femur, along with the shinbone and kneecap, form the knee joint.

Joints and Skeletal Movement

The point at which two or more bones meet is called a joint, or articulation. Joints are responsible for movement,
such as the movement of limbs, and stability, such as the stability found in the bones of the skull.

There are two ways to classify joints: based on their structure or based on their function. The structural
classification divides joints into fibrous, cartilaginous, and synovial joints depending on the material composing the
joint and the presence or absence of a cavity in the joint. The bones of fibrous joints are held together by fibrous
connective tissue. There is no cavity, or space, present between the bones, so most fibrous joints do not move at all,
or are only capable of minor movements. The joints between the bones in the skull and between the teeth and the
bone of their sockets are examples of fibrous joints (Figure 16.16a).

Cartilaginous joints are joints in which the bones are connected by cartilage (Figure 16.16b). An example is found
424 16 • The Body’s Systems

at the joints between vertebrae, the so-called “disks” of the backbone. Cartilaginous joints allow for very little
movement.

Synovial joints are the only joints that have a space between the adjoining bones (Figure 16.16c). This space is
referred to as the joint cavity and is filled with fluid. The fluid lubricates the joint, reducing friction between the
bones and allowing for greater movement. The ends of the bones are covered with cartilage and the entire joint is
surrounded by a capsule. Synovial joints are capable of the greatest movement of the joint types. Knees, elbows,
and shoulders are examples of synovial joints.

FIGURE 16.16 (a) Sutures are fibrous joints found only in the skull. (b) Cartilaginous joints are bones connected by cartilage, such as
between vertebrae. (c) Synovial joints are the only joints that have a space or “synovial cavity” in the joint.

The wide range of movement allowed by synovial joints produces different types of movements. Angular movements
are produced when the angle between the bones of a joint changes. Flexion, or bending, occurs when the angle
between the bones decreases. Moving the forearm upward at the elbow is an example of flexion. Extension is the
opposite of flexion in that the angle between the bones of a joint increases. Rotational movement is the movement
of a bone as it rotates around its own longitudinal axis. Movement of the head as in saying “no” is an example of
rotation.

CAREER CONNECTION

Rheumatologist
Rheumatologists are medical doctors who specialize in the diagnosis and treatment of disorders of the joints,
muscles, and bones. They diagnose and treat diseases such as arthritis, musculoskeletal disorders, osteoporosis,
plus autoimmune diseases like ankylosing spondylitis, a chronic spinal inflammatory disease and rheumatoid
arthritis.

Rheumatoid arthritis (RA) is an inflammatory disorder that primarily affects synovial joints of the hands, feet, and
cervical spine. Affected joints become swollen, stiff, and painful. Although it is known that RA is an autoimmune
disease in which the body’s immune system mistakenly attacks healthy tissue, the exact cause of RA remains
unknown. Immune cells from the blood enter joints and the joint capsule causing cartilage breakdown and swelling
of the joint lining. Breakdown of cartilage causes bones to rub against each other causing pain. RA is more common
people with declining estrogen levels, in particular post-menopausal people, and the age of onset is usually
between 40 to 50 years. Researchers are still exploring possible causes and studies that suggest an X-linked genetic
factor.

Rheumatologists can diagnose RA based on symptoms such as joint inflammation and pain, x-ray and MRI imaging,
and blood tests. Arthrography is a type of medical imaging of joints that uses a contrast agent, such as a dye that is
opaque to x-rays. This allows the soft tissue structures of joints—such as cartilage, tendons, and ligaments—to be
visualized. An arthrogram differs from a regular x-ray by showing the surface of soft tissues lining the joint in
addition to joint bones. An arthrogram allows early degenerative changes in joint cartilage to be detected before

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 16.5 • Musculoskeletal System 425

bones become affected.

There is currently no cure for RA; however, rheumatologists have a number of treatment options available.
Treatments are divided into those that reduce the symptoms of the disease and those that reduce the damage to
bone and cartilage caused by the disease. Early stages can be treated with rest of the affected joints through the use
of a cane, or with joint splints that minimize inflammation. When inflammation has decreased, exercise can be used
to strengthen muscles that surround the joint and to maintain joint flexibility. If joint damage is more extensive,
medications can be used to relieve pain and decrease inflammation. Anti-inflammatory drugs that may be used
include aspirin, topical pain relievers, and corticosteroid injections. Surgery may be required in cases where joint
damage is severe. Physicians are now using drugs that reduce the damage to bones and cartilage caused by the
disease to slow its development. These drugs are diverse in their mechanisms but they all act to reduce the impact
of the autoimmune response, for example by inhibiting the inflammatory response or reducing the number of T
lymphocytes, a cell of the immune system.

Muscles
Muscles allow for movement such as walking, and they also facilitate bodily processes such as respiration and
digestion. The body contains three types of muscle tissue: skeletal muscle, cardiac muscle, and smooth muscle
(Figure 16.17).

FIGURE 16.17 The body contains three types of muscle tissue: skeletal muscle, smooth muscle, and cardiac muscle. Notice that skeletal
muscle cells are long and cylindrical, they have multiple nuclei, and the small, dark nuclei are pushed to the periphery of the cell. Smooth
muscle cells are short, tapered at each end, and have only one nucleus each. Cardiac muscle cells are also cylindrical, but short. The
cytoplasm may branch, and they have one or two nuclei in the center of the cell. (credit: modification of work by NCI, NIH; scale-bar data
from Matt Russell)

Skeletal muscle tissue forms skeletal muscles, which attach to bones and sometimes the skin and control
locomotion and any other movement that can be consciously controlled. Because it can be controlled intentionally,
skeletal muscle is also called voluntary muscle. When viewed under a microscope, skeletal muscle tissue has a
striped or striated appearance. This appearance results from the arrangement of the proteins inside the cell that are
responsible for contraction. The cells of skeletal muscle are long and tapered and have multiple nuclei on the
periphery of each cell.

Smooth muscle tissue occurs in the walls of hollow organs such as the intestines, stomach, and urinary bladder,
and around passages such as in the respiratory tract and blood vessels. Smooth muscle has no striations, is not
under voluntary control, and is called involuntary muscle. Smooth muscle cells have a single nucleus.

Cardiac muscle tissue is only found in the heart. The contractions of cardiac muscle tissue pump blood throughout
the body and maintain blood pressure. Like skeletal muscle, cardiac muscle is striated, but unlike skeletal muscle,
cardiac muscle cannot be consciously controlled and is called involuntary muscle. The cells of cardiac muscle tissue
are connected to each other through intercalated disks and usually have just one nucleus per cell.

Skeletal Muscle Fiber Structure and Function

Each skeletal muscle fiber is a skeletal muscle cell. Within each muscle fiber are myofibrils, long cylindrical
structures that lie parallel to the muscle fiber. Myofibrils run the entire length of the muscle fiber. They attach to the
plasma membrane, called the sarcolemma, at their ends, so that as myofibrils shorten, the entire muscle cell
contracts (Figure 16.18).
426 16 • The Body’s Systems

FIGURE 16.18 A skeletal muscle fiber is surrounded by a plasma membrane called the sarcolemma, with a cytoplasm called the
sarcoplasm. A muscle fiber is composed of many fibrils packaged into orderly units. The orderly arrangement of the proteins in each unit,
shown as red and blue lines, gives the cell its striated appearance.

The striated appearance of skeletal muscle tissue is a result of repeating bands of the proteins actin and myosin that
occur along the length of myofibrils.

Myofibrils are composed of smaller structures called myofilaments. There are two main types of myofilaments:
thick filaments and thin filaments. Thick filaments are composed of the protein myosin. The primary component of
thin filaments is the protein actin.

The thick and thin filaments alternate with each other in a structure called a sarcomere. The sarcomere is the unit of
contraction in a muscle cell. Contraction is stimulated by an electrochemical signal from a nerve cell associated with
the muscle fiber. For a muscle cell to contract, the sarcomere must shorten. However, thick and thin filaments do
not shorten. Instead, they slide by one another, causing the sarcomere to shorten while the filaments remain the
same length. The sliding is accomplished when a molecular extension of myosin, called the myosin head,
temporarily binds to an actin filament next to it and through a change in conformation, bends, dragging the two
filaments in opposite directions. The myosin head then releases its actin filament, relaxes, and then repeats the
process, dragging the two filaments further along each other. The combined activity of many binding sites and
repeated movements within the sarcomere causes it to contract. The coordinated contractions of many sarcomeres
in a myofibril leads to contraction of the entire muscle cell and ultimately the muscle itself. The movement of the
myosin head requires ATP, which provides the energy for the contraction.

LINK TO LEARNING
View this animation (http://openstax.org/l/skeletal_muscl2) to see how muscle fibers are organized.

16.6 Nervous System

LEARNING OBJECTIVES
By the end of this section, you will be able to:
• Describe the form and function of a neuron
• Describe the basic parts and functions of the central nervous system
• Describe the basic parts and functions of the peripheral nervous system

As you read this, your nervous system is performing several functions simultaneously. The visual system is
processing what is seen on the page; the motor system controls your eye movements and the turn of the pages (or
click of the mouse); the prefrontal cortex maintains attention. Even fundamental functions, like breathing and
regulation of body temperature, are controlled by the nervous system. The nervous system is one of two systems
that exert control over all the organ systems of the body; the other is the endocrine system. The nervous system’s
control is much more specific and rapid than the hormonal system. It communicates signals through cells and the
tiny gaps between them rather than through the circulatory system as in the endocrine system. It uses a
combination of chemical and electrochemical signals, rather than purely chemical signals used by the endocrine

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 16.6 • Nervous System 427

system to cover long distances quickly. The nervous system acquires information from sensory organs, processes it
and then may initiate a response either through motor function, leading to movement, or in a change in the
organism’s physiological state.

Nervous systems throughout the animal kingdom vary in structure and complexity. Some organisms, like sea
sponges, lack a true nervous system. Others, like jellyfish, lack a true brain and instead have a system of separate
but connected nerve cells (neurons) called a “nerve net.” Flatworms have both a central nervous system (CNS),
made up of a ganglion (clusters of connected neurons) and two nerve cords, and a peripheral nervous system (PNS)
containing a system of nerves that extend throughout the body. The insect nervous system is more complex but also
fairly decentralized. It contains a brain, ventral nerve cord, and ganglia. These ganglia can control movements and
behaviors without input from the brain.

Compared to invertebrates, vertebrate nervous systems are more complex, centralized, and specialized. While there
is great diversity among different vertebrate nervous systems, they all share a basic structure: a CNS that contains a
brain and spinal cord and a PNS made up of peripheral sensory and motor nerves. One interesting difference
between the nervous systems of invertebrates and vertebrates is that the nerve cords of many invertebrates are
located ventrally (toward the stomach) whereas the vertebrate spinal cords are located dorsally (toward the back).
There is debate among evolutionary biologists as to whether these different nervous system plans evolved
separately or whether the invertebrate body plan arrangement somehow “flipped” during the evolution of
vertebrates.

The nervous system is made up of neurons, specialized cells that can receive and transmit chemical or electrical
signals, and glia, cells that provide support functions for the neurons. There is great diversity in the types of neurons
and glia that are present in different parts of the nervous system.

Neurons and Glial Cells

The nervous system of the common laboratory fly, Drosophila melanogaster, contains around 100,000 neurons, the
same number as a lobster. This number compares to 75 million in the mouse and 300 million in the octopus. A
human brain contains around 86 billion neurons. Despite these very different numbers, the nervous systems of
these animals control many of the same behaviors—from basic reflexes to more complicated behaviors like finding
food and courting mates. The ability of neurons to communicate with each other as well as with other types of cells
underlies all of these behaviors.

Most neurons share the same cellular components. But neurons are also highly specialized—different types of
neurons have different sizes and shapes that relate to their functional roles.

Like other cells, each neuron has a cell body (or soma) that contains a nucleus, smooth and rough endoplasmic
reticulum, Golgi apparatus, mitochondria, and other cellular components. Neurons also contain unique structures
for receiving and sending the electrical signals that make communication between neurons possible (Figure 16.19).
Dendrites are tree-like structures that extend away from the cell body to receive messages from other neurons at
specialized junctions called synapses. Although some neurons do not have any dendrites, most have one or many
dendrites.

The bilayer lipid membrane that surrounds a neuron is impermeable to ions. To enter or exit the neuron, ions must
pass through ion channels that span the membrane. Some ion channels need to be activated to open and allow ions
to pass into or out of the cell. These ion channels are sensitive to the environment and can change their shape
accordingly. Ion channels that change their structure in response to voltage changes are called voltage-gated ion
channels. The difference in total charge between the inside and outside of the cell is called the membrane potential.

A neuron at rest is negatively charged: the inside of a cell is approximately 70 millivolts more negative than the
outside (–70 mV). This voltage is called the resting membrane potential; it is caused by differences in the
concentrations of ions inside and outside the cell and the selective permeability created by ion channels. Sodium-
potassium pumps in the membrane produce the different ion concentrations inside and outside of the cell by
bringing in two K+ ions and removing three Na+ ions. The actions of this pump are costly: one molecule of ATP is
used up for each turn. Up to 50 percent of a neuron’s ATP is used in maintaining its membrane resting potential.
Potassium ions (K+), which are higher inside the cell, move fairly freely out of the neuron through potassium
channels; this loss of positive charge produces a net negative charge inside the cell. Sodium ions (Na+), which are
428 16 • The Body’s Systems

low inside, have a driving force to enter but move less freely. Their channels are voltage dependent and will open
when a slight change in the membrane potential triggers them.

A neuron can receive input from other neurons and, if this input is strong enough, send the signal to downstream
neurons. Transmission of a signal between neurons is generally carried by a chemical, called a neurotransmitter,
which diffuses from the axon of one neuron to the dendrite of a second neuron. When neurotransmitter molecules
bind to receptors located on a neuron’s dendrites, the neurotransmitter opens ion channels in the dendrite’s plasma
membrane. This opening allows sodium ions to enter the neuron and results in depolarization of the membrane—a
decrease in the voltage across the neuron membrane. Once a signal is received by the dendrite, it then travels
passively to the cell body. A large enough signal from neurotransmitters will reach the axon. If it is strong enough
(that is, if the threshold of excitation, a depolarization to around –60mV is reached), then depolarization creates a
positive feedback loop: as more Na+ ions enter the cell, the axon becomes further depolarized, opening even more
sodium channels at further distances from the cell body. This will cause voltage dependent Na+ channels further
down the axon to open and more positive ions to enter the cell. In the axon, this “signal” will become a self-
propagating brief reversal of the resting membrane potential called an action potential.

An action potential is an all-or-nothing event; it either happens or it does not. The threshold of excitation must be
reached for the neuron to “fire” an action potential. As sodium ions rush into the cell, depolarization actually
reverses the charge across the membrane form -70mv to +30mV. This change in the membrane potential causes
voltage-gated K+ channels to open, and K+ begins to leave the cell, repolarizing it. At the same time, Na+ channels
inactivate so no more Na+ enters the cell. K+ ions continue to leave the cell and the membrane potential returns to
the resting potential. At the resting potential, the K+ channels close and Na+ channels reset. The depolarization of
the membrane proceeds in a wave down the length of the axon. It travels in only one direction because the sodium
channels have been inactivated and unavailable until the membrane potential is near the resting potential again; at
this point they are reset to closed and can be opened again.

An axon is a tube-like structure that propagates the signal from the cell body to specialized endings called axon
terminals. These terminals in turn then synapse with other neurons, muscle, or target organs. When the action
potential reaches the axon terminal, this causes the release of neurotransmitter onto the dendrite of another
neuron. Neurotransmitters released at axon terminals allow signals to be communicated to these other cells, and
the process begins again. Neurons usually have one or two axons, but some neurons do not contain any axons.

Some axons are covered with a special structure called a myelin sheath, which acts as an insulator to keep the
electrical signal from dissipating as it travels down the axon. This insulation is important, as the axon from a human
motor neuron can be as long as a meter (3.2 ft)—from the base of the spine to the toes. The myelin sheath is
produced by glial cells. Along the axon there are periodic gaps in the myelin sheath. These gaps are called nodes of
Ranvier and are sites where the signal is “recharged” as it travels along the axon.

It is important to note that a single neuron does not act alone—neuronal communication depends on the
connections that neurons make with one another (as well as with other cells, like muscle cells). Dendrites from a
single neuron may receive synaptic contact from many other neurons. For example, dendrites from a Purkinje cell in
the cerebellum are thought to receive contact from as many as 200,000 other neurons.

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 16.6 • Nervous System 429

FIGURE 16.19 Neurons contain organelles common to other cells, such as a nucleus and mitochondria. They also have more specialized
structures, including dendrites and axons.

EVERYDAY CONNECTION
Neurogenesis
At one time, scientists believed that people were born with all the neurons they would ever have. Research
performed during the last few decades indicates that neurogenesis, the birth of new neurons, continues into
adulthood. Neurogenesis was first discovered in songbirds that produce new neurons while learning songs. For
mammals, new neurons also play an important role in learning: about 1,000 new neurons develop in the
hippocampus (a brain structure involved in learning and memory) each day. While most of the new neurons will
die, researchers found that an increase in the number of surviving new neurons in the hippocampus correlated
with how well rats learned a new task. Interestingly, both exercise and some antidepressant medications also
promote neurogenesis in the hippocampus. Stress has the opposite effect. While neurogenesis is quite limited
compared to regeneration in other tissues, research in this area may lead to new treatments for disorders such
as Alzheimer’s, stroke, and epilepsy.

How do scientists identify new neurons? A researcher can inject a compound called bromodeoxyuridine (BrdU)
into the brain of an animal. While all cells will be exposed to BrdU, BrdU will only be incorporated into the DNA of
newly generated cells that are in S phase. A technique called immunohistochemistry can be used to attach a
fluorescent label to the incorporated BrdU, and a researcher can use fluorescent microscopy to visualize the
presence of BrdU, and thus new neurons, in brain tissue (Figure 16.20).
430 16 • The Body’s Systems

FIGURE 16.20 This image shows new neurons in a rat hippocampus. New neurons tagged with BrdU glow red in this micrograph.
(credit: modification of work by Dr. Maryam Faiz, University of Barcelona)

LINK TO LEARNING
Visit this link interactive lab (http://openstax.org/l/neurogenesis2) to see more information about neurogenesis,
including an interactive laboratory simulation and a video that explains how BrdU labels new cells.

While glial cells are often thought of as the supporting cast of the nervous system, the number of glial cells in the
brain actually outnumbers the number of neurons by a factor of 10. Neurons would be unable to function without
the vital roles that are fulfilled by these glial cells. Glia guide developing neurons to their destinations, buffer ions
and chemicals that would otherwise harm neurons, and provide myelin sheaths around axons. When glia do not
function properly, the result can be disastrous—most brain tumors are caused by mutations in glia.

How Neurons Communicate

All functions performed by the nervous system—from a simple motor reflex to more advanced functions like making
a memory or a decision—require neurons to communicate with one another. Neurons communicate between the
axon of one neuron and the dendrites, and sometimes the cell body, of another neuron across the gap between
them, known as the synaptic cleft. When an action potential reaches the end of an axon it stimulates the release of
neurotransmitter molecules into the synaptic cleft between the synaptic knob of the axon and the post-synaptic
membrane of the dendrite or soma of the next cell. The neurotransmitter is released through exocytosis of vesicles
containing the neurotransmitter molecules. The neurotransmitter diffuses across the synaptic cleft and binds to
receptors in the post-synaptic membrane. These receptor molecules are chemically regulated ion channels and will
open, allowing sodium to enter the cell. If sufficient neurotransmitter has been released an action potential may be
initiated in the next cell, but this is not guaranteed. If insufficient neurotransmitter is released the nerve signal will
die at this point. There are a number of different neurotransmitters that are specific to neuron types that have
specific functions.

The Central Nervous System

The central nervous system (CNS) is made up of the brain and spinal cord and is covered with three layers of
protective coverings called meninges (“meninges” is derived from the Greek and means “membranes”) (Figure
16.21). The outermost layer is the dura mater, the middle layer is the web-like arachnoid mater, and the inner layer
is the pia mater, which directly contacts and covers the brain and spinal cord. The space between the arachnoid and
pia maters is filled with cerebrospinal fluid (CSF). The brain floats in CSF, which acts as a cushion and shock
absorber.

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 16.6 • Nervous System 431

FIGURE 16.21 The cerebral cortex is covered by three layers of meninges: the dura, arachnoid, and pia maters. (credit: modification of work
by Gray's Anatomy)

The Brain
The brain is the part of the central nervous system that is contained in the cranial cavity of the skull. It includes the
cerebral cortex, limbic system, basal ganglia, thalamus, hypothalamus, cerebellum, brainstem, and retinas. The
outermost part of the brain is a thick piece of nervous system tissue called the cerebral cortex. The cerebral cortex,
limbic system, and basal ganglia make up the two cerebral hemispheres. A thick fiber bundle called the corpus
callosum (corpus = “body”; callosum = “tough”) connects the two hemispheres. Although there are some brain
functions that are localized more to one hemisphere than the other, the functions of the two hemispheres are largely
redundant. In fact, sometimes (very rarely) an entire hemisphere is removed to treat severe epilepsy. While patients
do suffer some deficits following the surgery, they can have surprisingly few problems, especially when the surgery
is performed on children who have very immature nervous systems.

In other surgeries to treat severe epilepsy, the corpus callosum is cut instead of removing an entire hemisphere.
This causes a condition called split-brain, which gives insights into unique functions of the two hemispheres. For
example, when an object is presented to patients’ left visual field, they may be unable to verbally name the object
(and may claim to not have seen an object at all). This is because the visual input from the left visual field crosses
and enters the right hemisphere and cannot then signal to the speech center, which generally is found in the left
side of the brain. Remarkably, if a split-brain patient is asked to pick up a specific object out of a group of objects
with the left hand, the patient will be able to do so but will still be unable to verbally identify it.

LINK TO LEARNING
Visit the following website (http://openstax.org/l/split-brain2) to learn more about split-brain patients and to play a
game where you can model split-brain experiments yourself.

Each hemisphere contains regions called lobes that are involved in different functions. Each hemisphere of the
mammalian cerebral cortex can be broken down into four functionally and spatially defined lobes: frontal, parietal,
temporal, and occipital (Figure 16.22).
432 16 • The Body’s Systems

FIGURE 16.22 The human cerebral cortex includes the frontal, parietal, temporal, and occipital lobes.

The frontal lobe is located at the front of the brain, over the eyes. This lobe contains the olfactory bulb, which
processes smells. The frontal lobe also contains the motor cortex, which is important for planning and implementing
movement. Areas within the motor cortex map to different muscle groups. Neurons in the frontal lobe also control
cognitive functions like maintaining attention, speech, and decision-making. Studies of humans who have damaged
their frontal lobes show that parts of this area are involved in personality, socialization, and assessing risk. The
parietal lobe is located at the top of the brain. Neurons in the parietal lobe are involved in speech and also reading.
Two of the parietal lobe’s main functions are processing somatosensation—touch sensations like pressure, pain,
heat, cold—and processing proprioception—the sense of how parts of the body are oriented in space. The parietal
lobe contains a somatosensory map of the body similar to the motor cortex. The occipital lobe is located at the
back of the brain. It is primarily involved in vision—seeing, recognizing, and identifying the visual world. The
temporal lobe is located at the base of the brain and is primarily involved in processing and interpreting sounds. It
also contains the hippocampus (named from the Greek for “seahorse,” which it resembles in shape) a structure that
processes memory formation. The role of the hippocampus in memory was partially determined by studying one
famous epileptic patient, HM, who had both sides of his hippocampus removed in an attempt to cure his epilepsy.
His seizures went away, but he could no longer form new memories (although he could remember some facts from
before his surgery and could learn new motor tasks).

Interconnected brain areas called the basal ganglia play important roles in movement control and posture. The
basal ganglia also regulate motivation.

The thalamus acts as a gateway to and from the cortex. It receives sensory and motor inputs from the body and
also receives feedback from the cortex. This feedback mechanism can modulate conscious awareness of sensory
and motor inputs depending on the attention and arousal state of the animal. The thalamus helps regulate
consciousness, arousal, and sleep states.

Below the thalamus is the hypothalamus. The hypothalamus controls the endocrine system by sending signals to
the pituitary gland. Among other functions, the hypothalamus is the body’s thermostat—it makes sure the body
temperature is kept at appropriate levels. Neurons within the hypothalamus also regulate circadian rhythms,
sometimes called sleep cycles.

The limbic system is a connected set of structures that regulates emotion, as well as behaviors related to fear and
motivation. It plays a role in memory formation and includes parts of the thalamus and hypothalamus as well as the
hippocampus. One important structure within the limbic system is a temporal lobe structure called the amygdala.
The two amygdala (one on each side) are important both for the sensation of fear and for recognizing fearful faces.

The cerebellum (cerebellum = “little brain”) sits at the base of the brain on top of the brainstem. The cerebellum
controls balance and aids in coordinating movement and learning new motor tasks. The cerebellum of birds is large
compared to other vertebrates because of the coordination required by flight.

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 16.6 • Nervous System 433

The brainstem connects the rest of the brain with the spinal cord and regulates some of the most important and
basic functions of the nervous system including breathing, swallowing, digestion, sleeping, walking, and sensory and
motor information integration.

Spinal cord
Connecting to the brainstem and extending down the body through the spinal column is the spinal cord. The spinal
cord is a thick bundle of nerve tissue that carries information about the body to the brain and from the brain to the
body. The spinal cord is contained within the meninges and the bones of the vertebral column but is able to
communicate signals to and from the body through its connections with spinal nerves (part of the peripheral
nervous system). A cross-section of the spinal cord looks like a white oval containing a gray butterfly-shape (Figure
16.23). Axons make up the “white matter” and neuron and glia cell bodies (and interneurons) make up the “gray
matter.” Axons and cell bodies in the dorsa spinal cord convey mostly sensory information from the body to the
brain. Axons and cell bodies in the spinal cord primarily transmit signals controlling movement from the brain to the
body.

The spinal cord also controls motor reflexes. These reflexes are quick, unconscious movements—like automatically
removing a hand from a hot object. Reflexes are so fast because they involve local synaptic connections. For
example, the knee reflex that a doctor tests during a routine physical is controlled by a single synapse between a
sensory neuron and a motor neuron. While a reflex may only require the involvement of one or two synapses,
synapses with interneurons in the spinal column transmit information to the brain to convey what happened (the
knee jerked, or the hand was hot).

FIGURE 16.23 A cross-section of the spinal cord shows gray matter (containing cell bodies and interneurons) and white matter (containing
myelinated axons).

The Peripheral Nervous System

The peripheral nervous system (PNS) is the connection between the central nervous system and the rest of the
body. The PNS can be broken down into the autonomic nervous system, which controls bodily functions without
conscious control, and the sensory-somatic nervous system, which transmits sensory information from the skin,
muscles, and sensory organs to the CNS and sends motor commands from the CNS to the muscles.
434 16 • The Body’s Systems

FIGURE 16.24 In the autonomic nervous system, a preganglionic neuron (originating in the CNS) synapses to a neuron in a ganglion that, in
turn, synapses on a target organ. Activation of the sympathetic nervous system causes release of norepinephrine on the target organ.
Activation of the parasympathetic nervous system causes release of acetylcholine on the target organ.

The autonomic nervous system serves as the relay between the CNS and the internal organs. It controls the lungs,
the heart, smooth muscle, and exocrine and endocrine glands. The autonomic nervous system controls these organs
largely without conscious control; it can continuously monitor the conditions of these different systems and
implement changes as needed. Signaling to the target tissue usually involves two synapses: a preganglionic neuron
(originating in the CNS) synapses to a neuron in a ganglion that, in turn, synapses on the target organ (Figure 16.24).
There are two divisions of the autonomic nervous system that often have opposing effects: the sympathetic nervous
system and the parasympathetic nervous system.

The sympathetic nervous system is responsible for the immediate responses an animal makes when it encounters
a dangerous situation. One way to remember this is to think of the “fight-or-flight” response a person feels when
encountering a snake (“snake” and “sympathetic” both begin with “s”). Examples of functions controlled by the
sympathetic nervous system include an accelerated heart rate and inhibited digestion. These functions help prepare
an organism’s body for the physical strain required to escape a potentially dangerous situation or to fend off a
predator.

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 16.6 • Nervous System 435

FIGURE 16.25 The sympathetic and parasympathetic nervous systems often have opposing effects on target organs.

While the sympathetic nervous system is activated in stressful situations, the parasympathetic nervous system
allows an animal to “rest and digest.” One way to remember this is to think that during a restful situation like a
picnic, the parasympathetic nervous system is in control (“picnic” and “parasympathetic” both start with “p”).
Parasympathetic preganglionic neurons have cell bodies located in the brainstem and in the sacral (toward the
bottom) spinal cord (Figure 16.25). The parasympathetic nervous system resets organ function after the
sympathetic nervous system is activated including slowing of heart rate, lowered blood pressure, and stimulation of
digestion.

The sensory-somatic nervous system is made up of cranial and spinal nerves and contains both sensory and motor
neurons. Sensory neurons transmit sensory information from the skin, skeletal muscle, and sensory organs to the
CNS. Motor neurons transmit messages about desired movement from the CNS to the muscles to make them
contract. Without its sensory-somatic nervous system, an animal would be unable to process any information about
its environment (what it sees, feels, hears, and so on) and could not control motor movements. Unlike the
autonomic nervous system, which usually has two synapses between the CNS and the target organ, sensory and
motor neurons usually have only one synapse—one ending of the neuron is at the organ and the other directly
contacts a CNS neuron.
436 16 • Key Terms

Key Terms
action potential a momentary change in the gas exchange occurs in the alveoli
electrical potential of a neuron (or muscle) bronchiole an airway that extends from the main
membrane bronchus to the alveolar sac
adrenal gland the endocrine gland associated with capillary the smallest blood vessel that allows the
the kidneys passage of individual blood cells and the site of
alveolus (plural: alveoli) (also, air sacs) the terminal diffusion of oxygen and nutrient exchange
structure of the lung passage where gas exchange cardiac cycle the filling and emptying the heart of
occurs blood caused by electrical signals that cause the
amygdala a structure within the limbic system that heart muscles to contract and relax
processes fear cardiac muscle tissue the muscle tissue found only
amylase an enzyme found in saliva and secreted by in the heart; cardiac contractions pump blood
the pancreas that converts carbohydrates to throughout the body and maintain blood pressure
maltose cartilaginous joint a joint in which the bones are
anus the exit point of the digestive system for waste connected by cartilage
material central nervous system (CNS) the nervous system
aorta the major artery that takes blood away from the made up of the brain and spinal cord; covered with
heart to the systemic circulatory system three layers of protective meninges
appendicular skeleton the skeleton composed of the cerebellum the brain structure involved in posture,
bones of the upper limbs, which function to grasp motor coordination, and learning new motor actions
and manipulate objects, and the lower limbs, which cerebral cortex the outermost sheet of brain tissue;
permit locomotion involved in many higher-order functions
artery a blood vessel that takes blood away from the cerebrospinal fluid (CSF) a clear liquid that
heart surrounds the brain and fills its ventricles and acts
atrium (plural: atria) a chamber of the heart that as a shock absorber
receives blood from the veins chyme a mixture of partially digested food and
auditory ossicles (also, middle ear bones) the bones stomach juices
that transduce sounds from the air into vibrations in closed circulatory system a system that has the
the fluid-filled cochlea blood separated from the bodily interstitial fluid and
autonomic nervous system the part of the peripheral contained in blood vessels
nervous system that controls bodily functions colon the largest portion of the large intestine
axial skeleton skeleton that forms the central axis of consisting of the ascending colon, transverse colon,
the body and includes the bones of the skull, the and descending colon
ossicles of the middle ear, the hyoid bone of the corpus callosum a thick nerve bundle that connects
throat, the vertebral column, and the thoracic cage the cerebral hemispheres
(ribcage) dendrite a structure that extends away from the cell
axon a tube-like structure that propagates a signal body to receive messages from other neurons
from a neuron’s cell body to axon terminals depolarization a change in the membrane potential
basal ganglia an interconnected collections of cells to a less negative value
in the brain that are involved in movement and diaphragm a skeletal muscle located under lungs
motivation that encloses the lungs in the thorax
bicuspid valve a one-way opening between the diastole the relaxation phase of the cardiac cycle
atrium and the ventricle in the left side of the heart when the heart is relaxed and the ventricles are
bile a digestive juice produced by the liver; important filling with blood
for digestion of lipids down-regulation a decrease in the number of
bolus a mass of food resulting from chewing action hormone receptors in response to increased
and wetting by saliva hormone levels
brainstem a portion of brain that connects with the ectotherm an organism that relies primarily on
spinal cord; controls basic nervous system functions environmental heat sources to maintain its body
like breathing and swallowing temperature
bronchi (singular: bronchus) smaller branches of electrocardiogram (ECG) a recording of the electrical
cartilaginous tissue that stem off of the trachea; air impulses of the cardiac muscle
is funneled through the bronchi to the region where endocrine gland the gland that secretes hormones

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 16 • Key Terms 437

into the surrounding interstitial fluid, which then meninges (singular: meninx) the membranes that
diffuse into blood and are carried to various organs cover and protect the central nervous system
and tissues within the body mineral an inorganic, elemental molecule that carries
endotherm an organism that relies primarily on out important roles in the body
internal heat sources to maintain its body myelin sheath a cellular extension containing a fatty
temperature substance produced by glia that surrounds and
esophagus a tubular organ that connects the mouth insulates axons
to the stomach myofibril the long cylindrical structures that lie
essential nutrient a nutrient that cannot be parallel to the muscle fiber
synthesized by the body; it must be obtained from myofilament the small structures that make up
food myofibrils
exocrine gland the gland that secretes chemicals nasal cavity an opening of the respiratory system to
through ducts that lead to skin surfaces, body the outside environment
cavities, and organ cavities. nephron the functional unit of the kidney
fibrous joint a joint held together by fibrous neuron a specialized cell that can receive and
connective tissue transmit electrical and chemical signals
frontal lobe the part of the cerebral cortex that occipital lobe the part of the cerebral cortex that
contains the motor cortex and areas involved in contains visual cortex and processes visual stimuli
planning, attention, and language open circulatory system a circulatory system that
gallbladder the organ that stores and concentrates has the blood mixed with interstitial fluid in the
bile body cavity and directly bathes the organs
glia (also, glial cells) the cells that provide support oral cavity the point of entry of food into the digestive
functions for neurons system
hippocampus the brain structure in the temporal osmoregulation the mechanism by which water and
lobe involved in processing memories solute concentrations are maintained at desired
hormone a chemical released by cells in one area of levels
the body that affects cells in other parts of the body osmotic balance the appropriate values of water and
hyoid bone the bone that lies below the mandible in solute concentrations for a healthy organism
the front of the neck pancreas a gland that secretes digestive juices
hypothalamus the brain structure that controls pancreas the organ located between the stomach
hormone release and body homeostasis and the small intestine that contains exocrine and
inferior vena cava the major vein of the body endocrine cells
returning blood from the lower parts of the body to parasympathetic nervous system the division of
the right atrium autonomic nervous system that regulates visceral
interstitial fluid the fluid found between cells in the functions during relaxation
body, similar in constitution to the fluid component parathyroid gland the gland located on the surface of
of blood, but without the high concentrations of the thyroid that produces parathyroid hormone
proteins parietal lobe the part of the cerebral cortex involved
intracellular hormone receptor a hormone receptor in processing touch and the sense of the body in
in the cytoplasm or nucleus of a cell space
joint the point at which two or more bones meet pectoral girdle the bones that transmit the force
kidney the organ that performs excretory and generated by the upper limbs to the axial skeleton
osmoregulatory functions pelvic girdle the bones that transmit the force
large intestine a digestive system organ that generated by the lower limbs to the axial skeleton
reabsorbs water from undigested material and pepsin an enzyme found in the stomach whose main
processes waste matter role is protein digestion
larynx the voice box, located within the throat peripheral nervous system (PNS) the nervous
limbic system a connected brain area that processes system that serves as the connection between the
emotion and motivation central nervous system and the rest of the body;
liver an organ that produces bile for digestion and consists of the autonomic nervous system and the
processes vitamins and lipids sensory-somatic nervous system
membrane potential a difference in electrical peristalsis wave-like movements of muscle tissue
potential between the inside and outside of a cell pharynx the throat
438 16 • Chapter Summary

pituitary gland the endocrine gland located at the synaptic cleft a space between the presynaptic and
base of the brain composed of an anterior and postsynaptic membranes
posterior region; also called hypophysis synovial joints the only joints that have a space
primary bronchus (also, main bronchus) a region of between the adjoining bones
the airway within the lung that attaches to the systemic circulation the flow of blood away from the
trachea and bifurcates to form the bronchioles heart to the brain, liver, kidneys, stomach, and other
pulmonary circulation the flow of blood away from organs, the limbs, and the muscles of the body, and
the heart through the lungs where oxygenation then back to the heart
occurs and then back to the heart systole the contraction phase of cardiac cycle when
rectum the area of the body where feces is stored the ventricles are pumping blood into the arteries
until elimination temporal lobe the part of the cerebral cortex that
renal artery the artery that delivers blood to the processes auditory input; parts of the temporal lobe
kidney are involved in speech, memory, and emotion
renal vein the vein that drains blood from the kidney processing
salivary gland one of three pairs of exocrine glands in thalamus the brain area that relays sensory
the mammalian mouth that secretes saliva, a mix of information to the cortex
watery mucus and enzymes thoracic cage (also, ribcage) the skeleton of the
sarcolemma the plasma membrane of a skeletal chest, which consists of the ribs, thoracic vertebrae,
muscle fiber sternum, and costal cartilages
sarcomere the functional unit of skeletal muscle threshold of excitation the level of depolarization
sensory-somatic nervous system the system of needed for an action potential to fire
sensory and motor nerves thymus the gland located behind the sternum that
set point the target value of a physiological state in produces thymosin hormones that contribute to the
homeostasis development of the immune system
skeletal muscle tissue forms skeletal muscles, thyroid gland an endocrine gland located in the neck
which attach to bones and control locomotion and that produces thyroid hormones thyroxine and
any movement that can be consciously controlled triiodothyronine
skull the bone that supports the structures of the trachea the cartilaginous tube that transports air
face and protects the brain from the throat to the lungs
small intestine the organ where digestion of protein, tricuspid valve a one-way opening between the
fats, and carbohydrates is completed atrium and the ventricle in the right side of the heart
smooth muscle tissue the muscle that occurs in the up-regulation an increase in the number of hormone
walls of hollow organs such as the intestines, receptors in response to increased hormone levels
stomach, and urinary bladder, and around passages ureter the urine-bearing tubes coming out of the
such as the respiratory tract and blood vessels kidney
spinal cord a thick fiber bundle that connects the urethra the tube that conducts urine from the urinary
brain with peripheral nerves; transmits sensory and bladder to the external environment
motor information; contains neurons that control urinary bladder the structure that the ureters empty
motor reflexes the urine into
stomach a saclike organ containing acidic digestive vein a blood vessel that brings blood back to the
juices heart
superior vena cava the major vein of the body ventricle (of the heart) a large chamber of the heart
returning blood from the upper part of the body to that pumps blood into arteries
the right atrium vertebral column (also, spine) the column that
sympathetic nervous system the division of surrounds and protects the spinal cord, supports
autonomic nervous system activated during the head, and acts as an attachment point for ribs
stressful "fight-or-flight” situations and muscles of the back and neck
synapse a junction between two neurons where vitamin an organic substance necessary in small
neuronal signals are communicated amounts to sustain life

Chapter Summary
16.1 Homeostasis and Osmoregulation maintained in body tissues and organs. It is dynamic
because it is constantly adjusting to the changes that
Homeostasis is a dynamic equilibrium that is

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 16 • Chapter Summary 439

the systems encounter. It is an equilibrium because the body. It consists of a network of vessels containing
body functions are kept within a normal range, with blood that circulates because of pressure differences
some fluctuations around a set point. The kidneys are generated by the heart.
the main osmoregulatory organs in mammalian
The heart contains two pumps that move blood
systems; they function to filter blood and maintain the
through the pulmonary and systemic circulations.
dissolved ion concentrations of body fluids. They are
There is one atrium and one ventricle on the right side
made up internally of three distinct regions—the cortex,
and one atrium and one ventricle on the left side. The
medulla, and pelvis. The blood vessels that transport
pumping of the heart is a function of cardiomyocytes,
blood into and out of the kidneys arise from and merge
distinctive muscle cells that are striated like skeletal
with the aorta and inferior vena cava, respectively. The
muscle but pump rhythmically and involuntarily like
nephron is the functional unit of the kidney, which
smooth muscle. The signal for contraction begins in the
actively filters blood and generates urine. The urine
wall of the right atrium. The electrochemical signal
leaves the kidney through the ureter and is stored in
causes the two atria to contract in unison; then the
the urinary bladder. Urine is voided from the body
signal causes the ventricles to contract. The blood from
through the urethra.
the heart is carried through the body by a complex
16.2 Digestive System network of blood vessels; arteries take blood away
from the heart, and veins bring blood back to the heart.
There are many organs that work together to digest
food and absorb nutrients. The mouth is the point of 16.4 Endocrine System
ingestion and the location where both mechanical and
Hormones cause cellular changes by binding to
chemical breakdown of food begins. Saliva contains an
receptors on or in target cells. The number of receptors
enzyme called amylase that breaks down
on a target cell can increase or decrease in response to
carbohydrates. The food bolus travels through the
hormone activity.
esophagus by peristaltic movements to the stomach.
The stomach has an extremely acidic environment. The Hormone levels are primarily controlled through
enzyme pepsin digests protein in the stomach. Further negative feedback, in which rising levels of a hormone
digestion and absorption take place in the small inhibit its further release.
intestine. The large intestine reabsorbs water from the
The pituitary gland is located at the base of the brain.
undigested food and stores waste until elimination.
The anterior pituitary receives signals from the
Carbohydrates, proteins, and fats are the primary hypothalamus and produces six hormones. The
components of food. Some essential nutrients are posterior pituitary is an extension of the brain and
required for cellular function but cannot be produced releases hormones (antidiuretic hormone and oxytocin)
by the animal body. These include vitamins, minerals, produced by the hypothalamus. The thyroid gland is
some fatty acids, and some amino acids. Food intake in located in the neck and is composed of two lobes. The
more than necessary amounts is stored as glycogen in thyroid produces the hormones thyroxine and
the liver and muscle cells, and in adipose tissue. triiodothyronine. The thyroid also produces calcitonin.
Excess adipose storage can lead to obesity and serious The parathyroid glands lie on the posterior surface of
health problems. the thyroid gland and produce parathyroid hormone.

16.3 Circulatory and Respiratory Systems The adrenal glands are located on top of the kidneys
and consist of the adrenal cortex and adrenal medulla.
Animal respiratory systems are designed to facilitate
The adrenal cortex produces the corticosteroids,
gas exchange. In mammals, air is warmed and
glucocorticoids and mineralocorticoids. The adrenal
humidified in the nasal cavity. Air then travels down the
medulla is the inner part of the adrenal gland and
pharynx and larynx, through the trachea, and into the
produces epinephrine and norepinephrine.
lungs. In the lungs, air passes through the branching
bronchi, reaching the respiratory bronchioles. The The pancreas lies in the abdomen between the
respiratory bronchioles open up into the alveolar ducts, stomach and the small intestine. Clusters of endocrine
alveolar sacs, and alveoli. Because there are so many cells in the pancreas form the islets of Langerhans,
alveoli and alveolar sacs in the lung, the surface area which contain alpha cells that release glucagon and
for gas exchange is very large. beta cells that release insulin. Some organs possess
endocrine activity as a secondary function but have
The mammalian circulatory system is a closed system
another primary function. The heart produces the
with double circulation passing through the lungs and
hormone atrial natriuretic peptide, which functions to
440 16 • Chapter Summary

reduce blood volume, pressure, and Na+ concentration. 16.6 Nervous System
The gastrointestinal tract produces various hormones
The nervous system is made up of neurons and glia.
that aid in digestion. The kidneys produce
Neurons are specialized cells that are capable of
erythropoietin. The thymus produces hormones that
sending electrical as well as chemical signals. Most
aid in the development of the immune system. The
neurons contain dendrites, which receive these signals,
gonads produce large amounts of steroid hormones,
and axons that send signals to other neurons or
including testosterone in testes and estrogen and
tissues. Glia are non-neuronal cells in the nervous
progesterone in ovaries. Adipose tissue produces
system that support neuronal development and
leptin, which promotes satiety signals in the brain.
signaling. There are several types of glia that serve
16.5 Musculoskeletal System different functions.

The human skeleton is an endoskeleton that is Neurons have a resting potential across their
composed of the axial and appendicular skeleton. The membranes and when they are stimulated by a strong
axial skeleton is composed of the bones of the skull, enough signal from another neuron an action potential
ossicles of the ear, hyoid bone, vertebral column, and may carry an electrochemical signal along the neuron
ribcage. The skull consists of eight cranial bones and to a synapse with another neuron. Neurotransmitters
14 facial bones. Six bones make up the ossicles of the carry signals across synapses to initiate a response in
middle ear, while the hyoid bone is located in the neck another neuron.
under the mandible. The vertebral column contains 26
The vertebrate central nervous system contains the
bones and surrounds and protects the spinal cord. The
brain and the spinal cord, which are covered and
thoracic cage consists of the sternum, ribs, thoracic
protected by three meninges. The brain contains
vertebrae, and costal cartilages. The appendicular
structurally and functionally defined regions. In
skeleton is made up of the upper and lower limbs. The
mammals, these include the cortex (which can be
pectoral girdle is composed of the clavicles and the
broken down into four primary functional lobes: frontal,
scapulae. The upper limb contains 30 bones in the
temporal, occipital, and parietal), basal ganglia,
arm, the forearm, and the hand. The pelvic girdle
thalamus, hypothalamus, limbic system, cerebellum,
attaches the lower limbs to the axial skeleton. The
and brainstem—although structures in some of these
lower limb includes the bones of the thigh, the leg, and
designations overlap. While functions may be primarily
the foot.
localized to one structure in the brain, most complex
The structural classification of joints divides them into functions, like language and sleep, involve neurons in
fibrous, cartilaginous, and synovial joints. The bones of multiple brain regions. The spinal cord is the
fibrous joints are held together by fibrous connective information superhighway that connects the brain with
tissue. Cartilaginous joints are joints in which the bones the rest of the body through its connections with
are connected by cartilage. Synovial joints are joints peripheral nerves. It transmits sensory and motor input
that have a space between the adjoining bones. The and also controls motor reflexes.
movement of synovial joints includes angular and
The peripheral nervous system contains both the
rotational. Angular movements are produced when the
autonomic and sensory-somatic nervous systems. The
angle between the bones of a joint changes. Rotational
autonomic nervous system provides unconscious
movement is the movement of a bone as it rotates
control over visceral functions and has two divisions:
around its own longitudinal axis.
the sympathetic and parasympathetic nervous
The body contains three types of muscle tissue: systems. The sympathetic nervous system is activated
skeletal muscle, cardiac muscle, and smooth muscle. in stressful situations to prepare the animal for a “fight-
Muscles are composed of individual cells called muscle or-flight” response. The parasympathetic nervous
fibers. Muscle fibers consist of myofilaments system is active during restful periods. The sensory-
composed of the proteins actin and myosin arranged in somatic nervous system is made of cranial and spinal
units called sarcomeres. Contraction of the muscle nerves that transmit sensory information from skin and
occurs by the combined action of myosin and actin muscle to the CNS and motor commands from the CNS
fibers sliding past each other when the myosin heads to the muscles.
bind to the actin fiber, bend, disengage, and then
repeat the process.

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 16 • Visual Connection Questions 441

Visual Connection Questions

1. Figure 16.2 When bacteria are destroyed by 4. Figure 16.10 Which of the following statements
leukocytes, pyrogens are released into the blood. about the circulatory system is false?
Pyrogens reset the body’s thermostat to a higher a. Blood in the pulmonary vein is deoxygenated.
temperature, resulting in fever. How might pyrogens b. Blood in the inferior vena cava is
cause the body temperature to rise? deoxygenated.
c. Blood in the pulmonary artery is deoxygenated.
2. Figure 16.7 Which of the following statements
d. Blood in the aorta is oxygenated.
about the digestive system is false?
a. Chyme is a mixture of food and digestive juices
5. Figure 16.14 Goiter, a disease caused by iodine
that is produced in the stomach.
deficiency, results in the inability of the thyroid
b. Food enters the large intestine before the small
gland to form T3 and T4. The body typically
intestine.
attempts to compensate by producing greater
c. In the small intestine, chyme mixes with bile,
amounts of TSH. Which of the following symptoms
which emulsifies fats.
would you expect goiter to cause?
d. The stomach is separated from the small
a. Hypothyroidism, resulting in weight gain, cold
intestine by the pyloric sphincter.
sensitivity, and reduced mental activity.
b. Hyperthyroidism, resulting in weight loss,
3. Figure 16.9 Which of the following statements
profuse sweating and increased heart rate.
about the human respiratory system is false?
c. Hyperthyroidism, resulting in weight gain, cold
a. When we breathe in, air travels from the
sensitivity, and reduced mental activity.
pharynx to the trachea.
d. Hypothyroidism, resulting in weight loss,
b. The bronchioles branch into bronchi.
profuse sweating and increased heart rate.
c. Alveolar ducts connect to alveolar sacs.
d. Gas exchange between the lungs and blood
takes place in the alveolus.

Review Questions
6. When faced with a sudden drop in environmental 9. Where does the majority of fat digestion take place?
temperature, an endothermic animal will ________. a. mouth
a. experience a drop in its body temperature b. stomach
b. wait to see if it goes lower c. small intestine
c. increase muscle activity to generate heat d. large intestine
d. add fur or fat to increase insulation
10. The bile from the liver is delivered to the
7. How are wastes carried to the kidney for removal? ________.
a. in cells a. stomach
b. in the urine b. liver
c. in blood c. small intestine
d. in interstitial fluid d. colon

8. What is the cause of a fever of 38.3 °C (101 °F)? 11. Which of the following statements is not true?
a. too much heat produced by the body a. Essential nutrients can be synthesized by the
b. upward adjustment of the body temperature body.
set point b. Vitamins are required in small quantities for
c. inadequate cooling mechanisms in the body bodily function.
d. the heat caused by a viral or bacterial infection c. Some amino acids can be synthesized by the
body, while others need to be obtained from
diet.
d. Vitamins come in two categories: fat-soluble
and water-soluble.
442 16 • Review Questions

12. The respiratory system ________. 18. What is the function of the hormone
a. provides body tissues with oxygen erythropoietin?
b. provides body tissues with oxygen and carbon a. stimulates production of red blood cells
dioxide b. stimulates muscle growth
c. establishes how many breaths are taken per c. causes the fight-or-flight response
minute d. causes testosterone production
d. provides the body with carbon dioxide
19. Which endocrine glands are associated with the
13. Which is the order of airflow during inhalation? kidneys?
a. nasal cavity, trachea, larynx, bronchi, a. thyroid glands
bronchioles, alveoli b. pituitary glands
b. nasal cavity, larynx, trachea, bronchi, c. adrenal glands
bronchioles, alveoli d. gonads
c. nasal cavity, larynx, trachea, bronchioles,
bronchi, alveoli 20. Among other bones, the axial skeleton includes
d. nasal cavity, trachea, larynx, bronchi, the ________.
bronchioles, alveoli a. thoracic cage and vertebral column
b. thoracic cage and pectoral girdle
14. Where does the right ventricle send blood? c. skull and pelvic girdle
a. the head d. pectoral and pelvic girdles
b. the upper body
c. the lungs 21. The pectoral girdle supports the ________.
d. the lower body a. arms
b. legs
15. During the systolic phase of the cardiac cycle, the c. skull
heart is ________. d. thoracic cage
a. contracting
b. relaxing 22. Which component is responsible for initially
c. contracting and relaxing stimulating a muscle contraction?
d. filling with blood a. proteins
b. electrochemical signals
16. How do arteries differ from veins? c. plasma membranes
a. Arteries have thicker wall layers to d. striations
accommodate the changes in pressure from
the heart. 23. What kind of muscle tissue is found surrounding
b. Arteries carry blood. the urinary bladder?
c. Arteries have thinner wall layers and valves a. cardiac
and move blood by the action of skeletal b. skeletal
muscle. c. striated
d. Arteries are thin walled and are used for gas d. smooth
exchange.
24. Neurons contain _________, which can receive
17. Most of the hormones produced by the anterior signals from other neurons.
pituitary perform what function? a. axons
a. regulate growth b. mitochondria
b. regulate the sleep cycle c. dendrites
c. regulate production of other hormones d. Golgi bodies
d. regulate blood volume and blood pressure

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 16 • Critical Thinking Questions 443

25. The part of the brain that is responsible for 26. Which part of the nervous system directly controls
coordination during movement is the ______. the digestive system?
a. limbic system a. parasympathetic nervous system
b. thalamus b. central nervous system
c. cerebellum c. spinal cord
d. parietal lobe d. sensory-somatic nervous system

Critical Thinking Questions

27. Describe how the body’s mechanisms maintain 36. Describe how hormone receptors can play a role in
homeostasis? affecting the size of the responses of tissues to
hormones.
28. Why is excretion important in order to achieve
osmotic balance? 37. Many hormone systems regulate body functions
through opposing hormone actions. Describe how
29. What is the role of the accessory organs in
opposing hormone actions regulate blood-glucose
digestion?
levels?
30. What is the role of minerals in maintaining good
38. What movements occur at the hip joint and knees
health?
as you bend down to pick something up?
31. Discuss why obesity is a growing epidemic.
39. How are neurons similar to other cells? How are
32. Describe the function of these terms and describe they unique?
where they are located: main bronchus, trachea,
40. What are the main functions of the spinal cord?
alveoli.
41. What are the main differences between the
33. How does the structure of alveoli maximize gas
sympathetic and parasympathetic branches of the
exchange?
autonomic nervous system?
34. Describe the cardiac cycle.
42. What are the main functions of the sensory-
35. What is a similarity and a difference between an somatic nervous system?
exocrine gland and an endocrine gland?
444 16 • Critical Thinking Questions

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CHAPTER 17
The Immune System and Disease

FIGURE 17.1 (a) This smallpox (variola) vaccine is derived from calves exposed to cowpox virus. Vaccines provoke a
reaction in the immune system that prepares it for a subsequent infection by smallpox. (b) Viewed under a
transmission electron microscope, you can see the variola’s dumbbell-shaped structure that contains the viral DNA.
(credit a: modification of work by James Gathany, CDC; credit b: modification of work by Dr. Fred Murphy; Sylvia
Whitfield, CDC; scale-bar data from Matt Russell)

CHAPTER OUTLINE
17.1 Viruses
17.2 Innate Immunity
17.3 Adaptive Immunity
17.4 Disruptions in the Immune System

INTRODUCTION Organisms have a wide array of adaptations for preventing attacks of parasites
and diseases. The vertebrate defense systems, including those of humans, are complex and
multilayered, with defenses unique to vertebrates. These unique vertebrate defenses interact with
other defense systems inherited from ancestral lineages, and include complex and specific
pathogen recognition and memory mechanisms. Research continues to unravel the complexities
and vulnerabilities of the immune system.

Despite a poor understanding of the workings of the body in the early 18th century in Europe, the
practice of inoculation as a method to prevent the often-deadly effects of smallpox was
introduced from the courts of the Ottoman Empire. The method involved causing limited infection
with the smallpox virus by introducing the pus of an affected individual to a scratch in an
uninfected person. The resulting infection was milder than if it had been caught naturally and
mortality rates were shown to be about two percent rather than 30 percent from natural
infections. Moreover, the inoculation gave the individual immunity to the disease. It was from
these early experiences with inoculation that the methods of vaccination were developed, in
which a weakened or relatively harmless (killed) derivative of a pathogen is introduced into the
446 17 • The Immune System and Disease

individual. The vaccination induces immunity to the disease with few of the risks of being infected.
A modern understanding of the causes of the infectious disease and the mechanisms of the
immune system began in the late 19th century and continues to grow today.

17.1 Viruses
LEARNING OBJECTIVES
By the end of this section, you will be able to:
• Describe how viruses were first discovered and how they are detected
• Explain the detailed steps of viral replication
• Describe how vaccines are used in prevention and treatment of viral diseases

FIGURE 17.2 (a) The tobacco mosaic virus, seen by transmission electron microscopy, was the first virus to be
discovered. (b) The leaves of an infected plant are shown. (credit a: scale-bar data from Matt Russell; credit b:
modification of work by USDA, Department of Plant Pathology Archive, North Carolina State University)

No one knows exactly when viruses emerged or from where they came, since viruses do not leave
historical footprints such as fossils. Modern viruses are thought to be a mosaic of bits and pieces
of nucleic acids picked up from various sources along their respective evolutionary paths. Viruses
are acellular, parasitic entities that are not classified within any domain because they are not
considered alive. They have no plasma membrane, internal organelles, or metabolic processes,
and they do not divide. Instead, they infect a host cell and use the host’s replication processes to
produce progeny virus particles. Viruses infect all forms of organisms including bacteria, archaea,
fungi, plants, and animals. Living things grow, metabolize, and reproduce. Viruses replicate, but to
do so, they are entirely dependent on their host cells. They do not metabolize or grow, but are
assembled in their mature form.

Viruses are diverse. They vary in their structure, their replication methods, and in their target hosts
or even host cells. While most biological diversity can be understood through evolutionary history,
such as how species have adapted to conditions and environments, much about virus origins and
evolution remains unknown.

How Viruses Replicate

Viruses were first discovered after the development of a porcelain filter, called the Chamberland-
Pasteur filter, which could remove all bacteria visible under the microscope from any liquid
sample. In 1886, Adolph Meyer demonstrated that a disease of tobacco plants, tobacco mosaic
disease, could be transferred from a diseased plant to a healthy one through liquid plant extracts.
In 1892, Dmitri Ivanowski showed that this disease could be transmitted in this way even after the
Chamberland-Pasteur filter had removed all viable bacteria from the extract. Still, it was many
years before it was proven that these “filterable” infectious agents were not simply very small
bacteria but were a new type of tiny, disease-causing particle.

Virions, single virus particles, are very small, about 20–250 nanometers (1 nanometer = 1/
1,000,000 mm). These individual virus particles are the infectious form of a virus outside the host
cell. Unlike bacteria (which are about 100 times larger), we cannot see viruses with a light
microscope, with the exception of some large virions of the poxvirus family (Figure 17.3).

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 17.1 • Viruses 447

FIGURE 17.3 The size of a virus is very small relative to the size of cells and organelles.

It was not until the development of the electron microscope in the 1940s that scientists got their first good view of
the structure of the tobacco mosaic virus (Figure 17.2) and others. The surface structure of virions can be observed
by both scanning and transmission electron microscopy, whereas the internal structures of the virus can only be
observed in images from a transmission electron microscope (Figure 17.4).

FIGURE 17.4 The ebola virus is shown here as visualized through (a) a scanning electron micrograph and (b) a transmission electron
micrograph. (credit a: modification of work by Cynthia Goldsmith, CDC; credit b: modification of work by Thomas W. Geisbert, Boston
University School of Medicine; scale-bar data from Matt Russell)

The use of this technology has allowed for the discovery of many viruses of all types of living organisms. They were
initially grouped by shared morphology, meaning their size, shape, and distinguishing structures. Later, groups of
viruses were classified by the type of nucleic acid they contained, DNA or RNA, and whether their nucleic acid was
single- or double-stranded. More recently, molecular analysis of viral replication cycles has further refined their
classification.

A virion consists of a nucleic-acid core, an outer protein coating, and sometimes an outer envelope made of protein
and phospholipid membranes derived from the host cell. The most visible difference between members of viral
families is their morphology, which is quite diverse. An interesting feature of viral complexity is that the complexity
of the host does not correlate to the complexity of the virion. Some of the most complex virion structures are
observed in bacteriophages, viruses that infect the simplest living organisms, bacteria.

Viruses come in many shapes and sizes, but these are consistent and distinct for each viral family (Figure 17.5). All
virions have a nucleic-acid genome covered by a protective layer of protein, called a capsid. The capsid is made of
protein subunits called capsomeres. Some viral capsids are simple polyhedral “spheres,” whereas others are quite
448 17 • The Immune System and Disease

complex in structure. The outer structure surrounding the capsid of some viruses is called the viral envelope. All
viruses use some sort of glycoprotein to attach to their host cells at molecules on the cell called viral receptors. The
virus exploits these cell-surface molecules, which the cell uses for some other purpose, as a way to recognize and
infect specific cell types. For example, the measles virus uses a cell-surface glycoprotein in humans that normally
functions in immune reactions and possibly in the sperm-egg interaction at fertilization. Attachment is a
requirement for viruses to later penetrate the cell membrane, inject the viral genome, and complete their replication
inside the cell.

The T4 bacteriophage, which infects the E. coli bacterium, is among the most complex virion known; T4 has a
protein tail structure that the virus uses to attach to the host cell and a head structure that houses its DNA.

Adenovirus, a nonenveloped animal virus that causes respiratory illnesses in humans, uses protein spikes
protruding from its capsomeres to attach to the host cell. Nonenveloped viruses also include those that cause polio
(poliovirus), plantar warts (papillomavirus), and hepatitis A (hepatitis A virus). Nonenveloped viruses tend to be
more robust and more likely to survive under harsh conditions, such as the gut.

Enveloped virions like HIV (human immunodeficiency virus), the causative agent in AIDS (acquired immune
deficiency syndrome), consist of nucleic acid (RNA in the case of HIV) and capsid proteins surrounded by a
phospholipid bilayer envelope and its associated proteins (Figure 17.5). Chicken pox, influenza, and mumps are
examples of diseases caused by viruses with envelopes. Because of the fragility of the envelope, nonenveloped
viruses are more resistant to changes in temperature, pH, and some disinfectants than enveloped viruses.

Overall, the shape of the virion and the presence or absence of an envelope tells us little about what diseases the
viruses may cause or what species they might infect, but is still a useful means to begin viral classification.

VISUAL CONNECTION

FIGURE 17.5 Viruses can be complex in shape or relatively simple. This figure shows three relatively complex virions: the bacteriophage
T4, with its DNA-containing head group and tail fibers that attach to host cells; adenovirus, which uses spikes from its capsid to bind to the
host cells; and HIV, which uses glycoproteins embedded in its envelope to do so. Notice that HIV has proteins called matrix proteins,
internal to the envelope, which help stabilize virion shape. HIV is a retrovirus, which means it reverse transcribes its RNA genome into DNA,
which is then spliced into the host’s DNA. (credit “bacteriophage, adenovirus”: modification of work by NCBI, NIH; credit “HIV retrovirus”:
modification of work by NIAID, NIH)

Which of the following statements about virus structure is true?

a. All viruses are encased in a viral membrane.

b. The capsomere is made up of small protein subunits called capsids.
c. DNA is the genetic material in all viruses.
d. Glycoproteins help the virus attach to the host cell.

Unlike all living organisms that use DNA as their genetic material, viruses may use either DNA or RNA as theirs. The

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 17.1 • Viruses 449

virus core contains the genome or total genetic content of the virus. Viral genomes tend to be small compared to
bacteria or eukaryotes, containing only those genes that code for proteins the virus cannot get from the host cell.
This genetic material may be single-stranded or double-stranded. It may also be linear or circular. While most
viruses contain a single segment of nucleic acid, others have genomes that consist of several segments.

DNA viruses have a DNA core. The viral DNA directs the host cell’s replication proteins to synthesize new copies of
the viral genome and to transcribe and translate that genome into viral proteins. DNA viruses cause human diseases
such as chickenpox, hepatitis B, and some venereal diseases like herpes and genital warts.

RNA viruses contain only RNA in their cores. To replicate their genomes in the host cell, the genomes of RNA viruses
encode enzymes not found in host cells. RNA polymerase enzymes are not as stable as DNA polymerases and often
make mistakes during transcription. For this reason, mutations, changes in the nucleotide sequence, in RNA viruses
occur more frequently than in DNA viruses. This leads to more rapid evolution and change in RNA viruses. For
example, the fact that influenza is an RNA virus is one reason a new flu vaccine is needed every year. Human
diseases caused by RNA viruses include hepatitis C, measles, and rabies.

Viruses can be seen as obligate intracellular parasites. The virus must attach to a living cell, be taken inside,
manufacture its proteins and copy its genome, and find a way to escape the cell so the virus can infect other cells
and ultimately other individuals. Viruses can infect only certain species of hosts and only certain cells within that
host. The molecular basis for this specificity is that a particular surface molecule, known as the viral receptor, must
be found on the host cell surface for the virus to attach. Also, metabolic differences seen in different cell types
based on differential gene expression are a likely factor in which cells a virus may use to replicate. The cell must be
making the substances the virus needs, such as enzymes the virus genome itself does not have genes for, or the
virus will not be able to replicate using that cell.

Steps of Virus Infections

A virus must “take over” a cell to replicate. The viral replication cycle can produce dramatic biochemical and
structural changes in the host cell, which may cause cell damage. These changes, called cytopathic effects, can
change cell functions or even destroy the cell. Some infected cells, such as those infected by the common cold virus
(rhinovirus), die through lysis (bursting) or apoptosis (programmed cell death or “cell suicide”), releasing all the
progeny virions at once. The symptoms of viral diseases result from the immune response to the virus, which
attempts to control and eliminate the virus from the body, and from cell damage caused by the virus. Many animal
viruses, such as HIV (human immunodeficiency virus), leave the infected cells of the immune system by a process
known as budding, where virions leave the cell individually. During the budding process, the cell does not undergo
lysis and is not immediately killed. However, the damage to the cells that HIV infects may make it impossible for the
cells to function as mediators of immunity, even though the cells remain alive for a period of time. Most productive
viral infections follow similar steps in the virus replication cycle: attachment, penetration, uncoating, replication,
assembly, and release.

A virus attaches to a specific receptor site on the host-cell membrane through attachment proteins in the capsid or
proteins embedded in its envelope. The attachment is specific, and typically a virus will only attach to cells of one or
a few species and only certain cell types within those species with the appropriate receptors.

LINK TO LEARNING
View this video (http://openstax.org/l/influenza2) for a visual explanation of how influenza attacks the body.

Unlike animal viruses, the nucleic acid of bacteriophages is injected into the host cell naked, leaving the capsid
outside the cell. Plant and animal viruses can enter their cells through endocytosis, in which the cell membrane
surrounds and engulfs the entire virus. Some enveloped viruses enter the cell when the viral envelope fuses directly
with the cell membrane. Once inside the cell, the viral capsid is degraded and the viral nucleic acid is released,
which then becomes available for replication and transcription.

The replication mechanism depends on the viral genome. DNA viruses usually use host cell proteins and enzymes to
make additional DNA that is used to copy the genome or be transcribed to messenger RNA (mRNA), which is then
used in protein synthesis. RNA viruses, such as the influenza virus, usually use the RNA core as a template for
450 17 • The Immune System and Disease

synthesis of viral genomic RNA and mRNA. The viral mRNA is translated into viral enzymes and capsid proteins to
assemble new virions (Figure 17.6). Of course, there are exceptions to this pattern. If a host cell does not provide
the enzymes necessary for viral replication, viral genes supply the information to direct synthesis of the missing
proteins. Retroviruses, such as HIV, have an RNA genome that must be reverse transcribed to make DNA, which
then is inserted into the host’s DNA. To convert RNA into DNA, retroviruses contain genes that encode the virus-
specific enzyme reverse transcriptase that transcribes an RNA template to DNA. The fact that HIV produces some of
its own enzymes, which are not found in the host, has allowed researchers to develop drugs that inhibit these
enzymes. These drugs, including the reverse transcriptase inhibitor AZT, inhibit HIV replication by reducing the
activity of the enzyme without affecting the host’s metabolism.

The last stage of viral replication is the release of the new virions into the host organism, where they are able to
infect adjacent cells and repeat the replication cycle. Some viruses are released when the host cell dies and other
viruses can leave infected cells by budding through the membrane without directly killing the cell.

VISUAL CONNECTION

FIGURE 17.6 In influenza virus infection, glycoproteins attach to a host epithelial cell. As a result, the virus is engulfed. RNA and proteins
are made and assembled into new virions.

Influenza virus is packaged in a viral envelope, which fuses with the plasma membrane. This way, the virus can exit
the host cell without killing it. What advantage does the virus gain by keeping the host cell alive?

LINK TO LEARNING
Click through this tutorial (http://openstax.org/l/viruses2) on viruses to identify structures, modes of transmission,
replication, and more.

Viruses and Disease

Viruses cause a variety of diseases in animals, including humans, ranging from the common cold to potentially fatal
illnesses like meningitis (Figure 17.7). These diseases can be treated by antiviral drugs or by vaccines, but some
viruses, such as HIV, are capable of avoiding the immune response and mutating so as to become resistant to
antiviral drugs.

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 17.1 • Viruses 451

FIGURE 17.7 Viruses are the cause of dozens of ailments in humans, ranging from mild illnesses to serious diseases. (credit: modification
of work by Mikael Häggström)

Vaccines for Prevention

While we do have limited numbers of effective antiviral drugs, such as those used to treat HIV and influenza, the
primary method of controlling viral disease is by vaccination, which is intended to prevent outbreaks by building
immunity to a virus or virus family. A vaccine may be prepared using weakened live viruses, killed viruses, or
molecular subunits of the virus. In general, live viruses lead to better immunity, but have the possibility of causing
disease at some low frequency. Killed viral vaccine and the subunit viruses are both incapable of causing disease,
but in general lead to less effective or long-lasting immunity.

Weakened live viral vaccines are designed in the laboratory to cause few symptoms in recipients while giving them
immunity against future infections. Polio was one disease that represented a milestone in the use of vaccines. Polio
epidemics occurred with increasing frequency and impact as the twentieth century progressed, becoming a
terrifying and tragic event each summer. Tens of thousands of people died and many more were paralyzed; children
made up a large portion of the victims. Using killed virus tested on the HeLa cell line (originally obtained from
Henrietta Lacks and then mass produced to meet the need), Jonas Salk developed a successful vaccine. Mass
immunization campaigns in the U.S. in the 1950s (killed vaccine) and 1960s (live vaccine) essentially eradicated the
disease. The success of the polio vaccine paved the way for the routine dispensation of childhood vaccines against
measles, mumps, rubella, chickenpox, and other diseases.

Live vaccines are usually made by attenuation (weakening) of the “wild-type” (disease-causing) virus by growing it
in the laboratory in tissues or at temperatures different from what the virus is accustomed to in the host. For
example, the virus may be grown in cells in a test tube, in bird embryos, or in live animals. The adaptation to these
new cells or temperature induces mutations in the virus’ genomes, allowing them to grow better in the laboratory
while inhibiting their ability to cause disease when reintroduced into the conditions found in the host. These
attenuated viruses thus still cause an infection, but they do not grow very well, allowing the immune response to
develop in time to prevent major disease. The danger of using live vaccines, which are usually more effective than
killed vaccines, is the low but significant risk that these viruses will revert back to their disease-causing form by
back mutations. Back mutations occur when the vaccine undergoes mutations in the host such that it readapts to
the host and can again cause disease, which can then be spread to other humans in an epidemic. This happened as
recently as 2007 in Nigeria where mutations in a polio vaccine led to an epidemic of polio in that country.
452 17 • The Immune System and Disease

Some vaccines are in continuous development because certain viruses, such as influenza and HIV, have a high
mutation rate compared to other viruses or host cells. With influenza, mutation in genes for the surface molecules
helps the virus evade the protective immunity that may have been obtained in a previous influenza season, making it
necessary for individuals to get vaccinated every year. Other viruses, such as those that cause the childhood
diseases measles, mumps, and rubella, mutate so little that the same vaccine is used year after year.

Other vaccines are developed because of a new mutation of a well known type of virus. Coronaviruses are very
common in nature and various diseases, but a specific mutation of a particular coronavirus led to the COVID-19
pandemic. The rapid development of successful vaccines was due in part to scientists who had been working with
other coronaviruses prior to the pandemic. Kizzmekia S. Corbett, a research fellow and scientific lead, had deep
experience and knowledge of coronaviruses, which was instrumental in developing one of the first vaccines
(Moderna). She is now applying that experience to other respiratory diseases and vaccine development processes.

Vaccines and Antiviral Drugs for Treatment

In some cases, vaccines can be used to treat an active viral infection. In the case of rabies, a fatal neurological
disease transmitted in the saliva of rabies virus-infected animals, the progression of the disease from the time of the
animal bite to the time it enters the central nervous system may be two weeks or longer. This is enough time to
vaccinate an individual who suspects being bitten by a rabid animal, and the boosted immune response from the
vaccination is enough to prevent the virus from entering nervous tissue. Thus, the fatal neurological consequences
of the disease are averted and the individual only has to recover from the infected bite. This approach is also being
used for the treatment of Ebola, one of the fastest and most deadly viruses affecting humans, though usually
infecting limited populations. Ebola is also a leading cause of death in gorillas. Transmitted by bats and great apes,
this virus can cause death in 70–90 percent of the infected within two weeks. Using newly developed vaccines that
boost the immune response, there is hope that immune systems of affected individuals will be better able to control
the virus, potentially reducing mortality rates.

Another way of treating viral infections is the use of antiviral drugs. These drugs often have limited ability to cure
viral disease but have been used to control and reduce symptoms for a wide variety of viral diseases. For most
viruses, these drugs inhibit the virus by blocking the actions of one or more of its proteins. It is important that the
targeted proteins be encoded for by viral genes and that these molecules are not present in a healthy host cell. In
fact, for many years, scientists thought that drugs capable of impacting viruses would be too toxic for the body to
endure. To meet this challenge, researcher Gertrude Elion sought to develop drugs that would target only the virus
through processes such as inhibiting only viral DNA replication. For example, some of her medicines focused on
purines, while others affected DNA polymerase. There are large numbers of antiviral drugs available to treat
infections, some specific for a particular virus and others that can affect multiple viruses.

Antivirals have been developed to treat genital herpes (herpes simplex II) and influenza. For genital herpes, drugs
such as acyclovir, developed by Elion, can reduce the number and duration of the episodes of active viral disease
during which patients develop viral lesions in their skins cells. As the virus remains latent in nervous tissue of the
body for life, this drug is not a cure but can make the symptoms of the disease more manageable. For influenza,
drugs like Tamiflu can reduce the duration of “flu” symptoms by one or two days, but the drug does not prevent
symptoms entirely. Other antiviral drugs, such as Ribavirin, have been used to treat a variety of viral infections.

By far the most successful use of antivirals has been in the treatment of the retrovirus HIV, which causes a disease
that, if untreated, is usually fatal within 10–12 years after being infected. Anti-HIV drugs have been able to control
viral replication to the point that individuals receiving these drugs survive for a significantly longer time than the
untreated.

A particular challenge with HIV is its tendency to mutate quickly within the body of an individual patient. This leads
to individual drug resistance, and requires a different treatment strategy than many other diseases. David Ho was
among the first to propose and develop a method to treat multiple mutations of HIV at the same time. Ho's efforts
were a turning point in fighting AIDS. Anti-HIV drugs inhibit viral replication at many different phases of the HIV
replicative cycle. Drugs have been developed that inhibit the fusion of the HIV viral envelope with the plasma
membrane of the host cell (fusion inhibitors), the conversion of its RNA genome to double-stranded DNA (reverse
transcriptase inhibitors), the integration of the viral DNA into the host genome (integrase inhibitors), and the
processing of viral proteins (protease inhibitors).

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 17.2 • Innate Immunity 453

When any of these drugs are used individually, the virus’ high mutation rate allows the virus to rapidly evolve
resistance to the drug. The breakthrough in the treatment of HIV was the development of highly active anti-
retroviral therapy (HAART), which involves a mixture of different drugs, sometimes called a drug “cocktail.” By
attacking the virus at different stages of its replication cycle, it is difficult for the virus to develop resistance to
multiple drugs at the same time. Still, even with the use of combination HAART therapy, there is concern that, over
time, the virus will evolve resistance to this therapy. Thus, new anti-HIV drugs are constantly being developed with
the hope of continuing the battle against this highly fatal virus.

17.2 Innate Immunity

LEARNING OBJECTIVES
By the end of this section, you will be able to:
• Describe the body’s innate physical and chemical defenses
• Explain the inflammatory response
• Describe the complement system

The vertebrate, including human, immune system is a complex multilayered system for defending against external
and internal threats to the integrity of the body. The system can be divided into two types of defense systems: the
innate immune system, which is nonspecific toward a particular kind of pathogen, and the adaptive immune system,
which is specific (Figure 17.8). Innate immunity is not caused by an infection or vaccination and depends initially on
physical and chemical barriers that work on all pathogens, sometimes called the first line of defense. The second
line of defense of the innate system includes chemical signals that produce inflammation and fever responses as
well as mobilizing protective cells and other chemical defenses. The adaptive immune system mounts a highly
specific response to substances and organisms that do not belong in the body. The adaptive system takes longer to
respond and has a memory system that allows it to respond with greater intensity should the body reencounter a
pathogen even years later.

FIGURE 17.8 There are two main parts to the vertebrate immune system. The innate immune system, which is made up of physical barriers
and internal defenses, responds to all pathogens. The adaptive immune system is highly specific.

External and Chemical Barriers

The body has significant physical barriers to potential pathogens. The skin contains the protein keratin, which
resists physical entry into cells. Other body surfaces, particularly those associated with body openings, are
protected by the mucous membranes. The sticky mucus provides a physical trap for pathogens, preventing their
movement deeper into the body. The openings of the body, such as the nose and ears, are protected by hairs that
catch pathogens, and the mucous membranes of the upper respiratory tract have cilia that constantly move
pathogens trapped in the mucus coat up to the mouth.

The skin and mucous membranes also create a chemical environment that is hostile to many microorganisms. The
surface of the skin is acidic, which prevents bacterial growth. Saliva, mucus, and the tears of the eye contain an
enzyme that breaks down bacterial cell walls. The stomach secretions create a highly acidic environment, which kills
many pathogens entering the digestive system.

Finally, the surface of the body and the lower digestive system have a community of microorganisms such as
bacteria, archaea, and fungi that coexist without harming the body. There is evidence that these organisms are
454 17 • The Immune System and Disease

highly beneficial to their host, combating disease-causing organisms and outcompeting them for nutritional
resources provided by the host body. Despite these defenses, pathogens may enter the body through skin abrasions
or punctures, or by collecting on mucosal surfaces in large numbers that overcome the protections of mucus or cilia.

Internal Defenses
When pathogens enter the body, the innate immune system responds with a variety of internal defenses. These
include the inflammatory response, phagocytosis, natural killer cells, and the complement system. White blood cells
in the blood and lymph recognize pathogens as foreign to the body. A white blood cell is larger than a red blood cell,
is nucleated, and is typically able to move using amoeboid locomotion. Because they can move on their own, white
blood cells can leave the blood to go to infected tissues. For example, a monocyte is a type of white blood cell that
circulates in the blood and lymph and develops into a macrophage after it moves into infected tissue. A macrophage
is a large cell that engulfs foreign particles and pathogens. Mast cells are produced in the same way as white blood
cells, but unlike circulating white blood cells, mast cells take up residence in connective tissues and especially
mucosal tissues. They are responsible for releasing chemicals in response to physical injury. They also play a role in
the allergic response, which will be discussed later in the chapter.

When a pathogen is recognized as foreign, chemicals called cytokines are released. A cytokine is a chemical
messenger that regulates cell differentiation (form and function), proliferation (production), and gene expression to
produce a variety of immune responses. Approximately 40 types of cytokines exist in humans. In addition to being
released from white blood cells after pathogen recognition, cytokines are also released by the infected cells and
bind to nearby uninfected cells, inducing those cells to release cytokines. This positive feedback loop results in a
burst of cytokine production.

One class of early-acting cytokines is the interferons, which are released by infected cells as a warning to nearby
uninfected cells. An interferon is a small protein that signals a viral infection to other cells. The interferons
stimulate uninfected cells to produce compounds that interfere with viral replication. Interferons also activate
macrophages and other cells.

The Inflammatory Response and Phagocytosis

The first cytokines to be produced encourage inflammation, a localized redness, swelling, heat, and pain.
Inflammation is a response to physical trauma, such as a cut or a blow, chemical irritation, and infection by
pathogens (viruses, bacteria, or fungi). The chemical signals that trigger an inflammatory response enter the
extracellular fluid and cause capillaries to dilate (expand) and capillary walls to become more permeable, or leaky.
The serum and other compounds leaking from capillaries cause swelling of the area, which in turn causes pain.
Various kinds of white blood cells are attracted to the area of inflammation. The types of white blood cells that arrive
at an inflamed site depend on the nature of the injury or infecting pathogen. For example, a neutrophil is an early
arriving white blood cell that engulfs and digests pathogens. Neutrophils are the most abundant white blood cells of
the immune system (Figure 17.9). Macrophages follow neutrophils and take over the phagocytosis function and are
involved in the resolution of an inflamed site, cleaning up cell debris and pathogens.

FIGURE 17.9 White blood cells (leukocytes) release chemicals to stimulate the inflammatory response following a cut in the skin.

Cytokines also send feedback to cells of the nervous system to bring about the overall symptoms of feeling sick,
which include lethargy, muscle pain, and nausea. Cytokines also increase the core body temperature, causing a

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 17.2 • Innate Immunity 455

fever. The elevated temperatures of a fever inhibit the growth of pathogens and speed up cellular repair processes.
For these reasons, suppression of fevers should be limited to those that are dangerously high.

LINK TO LEARNING
Check out this 23-second, stop-motion video (https://commons.wikimedia.org/wiki/
File:S1-Polymorphonuclear_Cells_with_Conidia_in_Liquid_Media.ogv) showing a neutrophil that searches and
engulfs fungus spores during an elapsed time of 79 minutes.

Natural Killer Cells

A lymphocyte is a white blood cell that contains a large nucleus (Figure 17.10). Most lymphocytes are associated
with the adaptive immune response, but infected cells are identified and destroyed by natural killer cells, the only
lymphocytes of the innate immune system. A natural killer (NK) cell is a lymphocyte that can kill cells infected with
viruses (or cancerous cells). NK cells identify intracellular infections, especially from viruses, by the altered
expression of major histocompatibility complex (MHC) I molecules on the surface of infected cells. MHC class I
molecules are proteins on the surfaces of all nucleated cells that provide a sample of the cell’s internal environment
at any given time. Unhealthy cells, whether infected or cancerous, display an altered MHC class I complement on
their cell surfaces.

FIGURE 17.10 Lymphocytes, such as NK cells, are characterized by their large nuclei that actively absorb Wright stain and therefore appear
dark colored under a microscope. (credit: scale-bar data from Matt Russell)

After the NK cell detects an infected or tumor cell, it induces programmed cell death, or apoptosis. Phagocytic cells
then come along and digest the cell debris left behind. NK cells are constantly patrolling the body and are an
effective mechanism for controlling potential infections and preventing cancer progression. The various types of
immune cells are shown in Figure 17.11.

FIGURE 17.11 Cells involved in the innate immune response include mast cells, natural killer cells, and white blood cells, such as
monocytes, macrophages and neutrophils.

Complement
An array of approximately 20 types of proteins, called a complement system, is also activated by infection or the
activity of the cells of the adaptive immune system and functions to destroy extracellular pathogens. Liver cells and
macrophages synthesize inactive forms of complement proteins continuously; these proteins are abundant in the
blood serum and are capable of responding immediately to infecting microorganisms. The complement system is so
named because it is complementary to the innate and adaptive immune system. Complement proteins bind to the
456 17 • The Immune System and Disease

surfaces of microorganisms and are particularly attracted to pathogens that are already tagged by the adaptive
immune system. This “tagging” involves the attachment of specific proteins called antibodies (discussed in detail
later) to the pathogen. When they attach, the antibodies change shape providing a binding site for one of the
complement proteins. After the first few complement proteins bind, a cascade of binding in a specific sequence of
proteins follows in which the pathogen rapidly becomes coated in complement proteins.

Complement proteins perform several functions, one of which is to serve as a marker to indicate the presence of a
pathogen to phagocytic cells and enhance engulfment. Certain complement proteins can combine to open pores in
microbial cell membranes and cause lysis of the cells.

17.3 Adaptive Immunity

LEARNING OBJECTIVES
By the end of this section, you will be able to:
• Explain adaptive immunity
• Describe cell-mediated immune response and humoral immune response
• Describe immune tolerance

The adaptive, or acquired, immune response takes days or even weeks to become established—much longer than
the innate response; however, adaptive immunity is more specific to an invading pathogen. Adaptive immunity is an
immunity that occurs after exposure to an antigen either from a pathogen or a vaccination. An antigen is a molecule
that stimulates a response in the immune system. This part of the immune system is activated when the innate
immune response is insufficient to control an infection. In fact, without information from the innate immune system,
the adaptive response could not be mobilized. There are two types of adaptive responses: the cell-mediated
immune response, which is controlled by activated T cells, and the humoral immune response, which is controlled
by activated B cells and antibodies. Activated T and B cells whose surface binding sites are specific to the
molecules on the pathogen greatly increase in numbers and attack the invading pathogen. Their attack can kill
pathogens directly or they can secrete antibodies that enhance the phagocytosis of pathogens and disrupt the
infection. Adaptive immunity also involves a memory to give the host long-term protection from reinfection with the
same type of pathogen; on reexposure, this host memory will facilitate a rapid and powerful response.

B and T Cells
Lymphocytes, which are white blood cells, are formed with other blood cells in the red bone marrow found in many
flat bones, such as the shoulder or pelvic bones. The two types of lymphocytes of the adaptive immune response
are B and T cells (Figure 17.12). Whether an immature lymphocyte becomes a B cell or T cell depends on where in
the body it matures. The B cells remain in the bone marrow to mature (hence the name “B” for “bone marrow”),
while T cells migrate to the thymus, where they mature (hence the name “T” for “thymus”).

Maturation of a B or T cell involves becoming immunocompetent, meaning that it can recognize, by binding, a
specific molecule or antigen (discussed below). During the maturation process, B and T cells that bind too strongly
to the body’s own cells are eliminated in order to minimize an immune response against the body’s own tissues.
Those cells that react weakly to the body’s own cells, but have highly specific receptors on their cell surfaces that
allow them to recognize a foreign molecule, or antigen, remain. This process occurs during fetal development and
continues throughout life. The specificity of this receptor is determined by the genetics of the individual and is
present before a foreign molecule is introduced to the body or encountered. Thus, it is genetics and not experience
that initially provides a vast array of cells, each capable of binding to a different specific foreign molecule. Once they
are immunocompetent, the T and B cells will migrate to the spleen and lymph nodes where they will remain until
they are called on during an infection. B cells are involved in the humoral immune response, which targets
pathogens loose in blood and lymph, and T cells are involved in the cell-mediated immune response, which targets
infected cells.

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 17.3 • Adaptive Immunity 457

FIGURE 17.12 This scanning electron micrograph shows a T lymphocyte. T and B cells are indistinguishable by light microscopy but can be
differentiated experimentally by probing their surface receptors. (credit: modification of work by NCI; scale-bar data from Matt Russell)

Humoral Immune Response

As mentioned, an antigen is a molecule that stimulates a response in the immune system. Not every molecule is
antigenic. B cells participate in a chemical response to antigens present in the body by producing specific antibodies
that circulate throughout the body and bind with the antigen whenever it is encountered. This is known as the
humoral immune response. As discussed, during maturation of B cells, a set of highly specific B cells are produced
that have many antigen receptor molecules in their membrane (Figure 17.13).

FIGURE 17.13 B cell receptors are embedded in the membranes of B cells and bind a variety of antigens through their variable regions.

Each B cell has only one kind of antigen receptor, which makes every B cell different. Once the B cells mature in the
bone marrow, they migrate to lymph nodes or other lymphatic organs. When a B cell encounters the antigen that
binds to its receptor, the antigen molecule is brought into the cell by endocytosis and reappears on the surface of
the cell bound to an MHC class II molecule. When this process is complete, the B cell is sensitized. In most cases,
the sensitized B cell must then encounter a specific kind of T cell, called a helper T cell, before it is activated. The
helper T cell must already have been activated through an encounter with the antigen (discussed below).

The helper T cell binds to the antigen-MHC class II complex and is induced to release cytokines that induce the B
cell to divide rapidly, which makes thousands of identical (clonal) cells. These daughter cells become either plasma
cells or memory B cells. The memory B cells remain inactive at this point, until another later encounter with the
antigen, caused by a reinfection by the same bacteria or virus, results in them dividing into a new population of
plasma cells. The plasma cells, on the other hand, produce and secrete large quantities, up to 100 million molecules
per hour, of antibody molecules. An antibody, also known as an immunoglobulin (Ig), is a protein that is produced
by plasma cells after stimulation by an antigen. Antibodies are the agents of humoral immunity. Antibodies occur in
the blood, in gastric and mucus secretions, and in breast milk. Antibodies in these bodily fluids can bind pathogens
458 17 • The Immune System and Disease

and mark them for destruction by phagocytes before they can infect cells.

These antibodies circulate in the blood stream and lymphatic system and bind with the antigen whenever it is
encountered. The binding can fight infection in several ways. Antibodies can bind to viruses or bacteria and interfere
with the chemical interactions required for them to infect or bind to other cells. The antibodies may create bridges
between different particles containing antigenic sites clumping them all together and preventing their proper
functioning. The antigen-antibody complex stimulates the complement system described previously, destroying the
cell bearing the antigen. Phagocytic cells, such as those already described, are attracted by the antigen-antibody
complexes, and phagocytosis is enhanced when the complexes are present. Finally, antibodies stimulate
inflammation, and their presence in mucus and on the skin prevents pathogen attack.

Antibodies coat extracellular pathogens and neutralize them by blocking key sites on the pathogen that enhance
their infectivity (such as receptors that “dock” pathogens on host cells) (Figure 17.14). Antibody neutralization can
prevent pathogens from entering and infecting host cells. The neutralized antibody-coated pathogens can then be
filtered by the spleen and eliminated in urine or feces.

Antibodies also mark pathogens for destruction by phagocytic cells, such as macrophages or neutrophils, in a
process called opsonization. In a process called complement fixation, some antibodies provide a place for
complement proteins to bind. The combination of antibodies and complement promotes rapid clearing of
pathogens.

The production of antibodies by plasma cells in response to an antigen is called active immunity and describes the
host’s active response of the immune system to an infection or to a vaccination. There is also a passive immune
response where antibodies come from an outside source, instead of the individual’s own plasma cells, and are
introduced into the host. For example, antibodies circulating in a pregnant person’s body move across the placenta
into the developing fetus. The child benefits from the presence of these antibodies for up to several months after
birth. In addition, a passive immune response is possible by injecting antibodies into an individual in the form of an
antivenom to a snake-bite toxin or antibodies in blood serum to help fight a hepatitis infection. This gives immediate
protection since the body does not need the time required to mount its own response.

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 17.3 • Adaptive Immunity 459

FIGURE 17.14 Antibodies may inhibit infection by (a) preventing the antigen from binding its target, (b) tagging a pathogen for destruction
by macrophages or neutrophils, or (c) activating the complement cascade.

The availability and reliability of antibodies makes them ideally suited for use in medical tests and investigations.
Radioimmunossays, for example, rely on the antigen-antibody interaction. Usually, a specific antigen is made
radioactive, allowed to bind to its antibody, and then introduced into a sample substance, such as a patient's blood.
By measuring eventual changes in the quantity of the bound and unbound antigen, analysts can detect the presence
and/or concentration of certain substances. Developed by Rosalyn Sussman Yalow and Solomon Berson in the
1950s, the technique is known for extreme sensitivity, meaning that it can detect and measure very small quantities
of a substance. It is used in narcotics detection, blood bank screening, early cancer screening, hormone
measurement, and allergy diagnosis. Based on her significant contribution to the field, Yalow received a Nobel Prize,
making her the second woman to be awarded the prize for medicine.

Cell-Mediated Immunity
Unlike B cells, T lymphocytes are unable to recognize pathogens without assistance. Instead, dendritic cells and
macrophages first engulf and digest pathogens into hundreds or thousands of antigens. Then, an antigen-
presenting cell (APC) detects, engulfs, and informs the adaptive immune response about an infection. When a
pathogen is detected, these APCs will engulf and break it down through phagocytosis. Antigen fragments will then
be transported to the surface of the APC, where they will serve as an indicator to other immune cells. A dendritic
cell is an immune cell that mops up antigenic materials in its surroundings and presents them on its surface.
Dendritic cells are located in the skin, the linings of the nose, lungs, stomach, and intestines. These positions are
ideal locations to encounter invading pathogens. Once they are activated by pathogens and mature to become APCs
they migrate to the spleen or a lymph node. Macrophages also function as APCs. After phagocytosis by a
macrophage, the phagocytic vesicle fuses with an intracellular lysosome. Within the resulting phagolysosome, the
components are broken down into fragments; the fragments are then loaded onto MHC class II molecules and are
460 17 • The Immune System and Disease

transported to the cell surface for antigen presentation (Figure 17.15). Helper T cells cannot properly respond to an
antigen unless it is processed and embedded in an MHC class II molecule. The APCs express MHC class II on their
surfaces, and when combined with a foreign antigen, these complexes signal an invader.

FIGURE 17.15 An antigen-presenting cell (APC), such as a macrophage, engulfs a foreign antigen, partially digests it in a lysosome, and
then embeds it in an MHC class II molecule for presentation at the cell surface. Lymphocytes of the adaptive immune response must
interact with antigen-embedded MHC class II molecules to mature into functional immune cells.

LINK TO LEARNING
View this animation from Rockefeller University (http://openstax.org/l/immune_system2) to see how dendritic cells
act as sentinels in the body’s immune system.

T cells have many functions. Some respond to APCs of the innate immune system and indirectly induce immune
responses by releasing cytokines. Others stimulate B cells to start the humoral response as described previously.
Another type of T cell detects APC signals and directly kills the infected cells, while some are involved in
suppressing inappropriate immune reactions to harmless or “self” antigens.

There are two main types of T cells: helper T lymphocytes (TH) and the cytotoxic T lymphocytes (TC). The TH
lymphocytes function indirectly to tell other immune cells about potential pathogens. TH lymphocytes recognize
specific antigens presented by the MHC class II complexes of APCs. There are two populations of TH cells: TH1 and
TH2. TH1 cells secrete cytokines to enhance the activities of macrophages and other T cells. TH2 cells stimulate
naïve B cells to secrete antibodies. Whether a TH1 or a TH2 immune response develops depends on the specific
types of cytokines secreted by cells of the innate immune system, which in turn depends on the nature of the
invading pathogen.

Cytotoxic T cells (TC) are the key component of the cell-mediated part of the adaptive immune system and attack
and destroy infected cells. TC cells are particularly important in protecting against viral infections; this is because
viruses replicate within cells where they are shielded from extracellular contact with circulating antibodies. Once
activated, the TC creates a large clone of cells with one specific set of cell-surface receptors, as in the case with
proliferation of activated B cells. As with B cells, the clone includes active TC cells and inactive memory TC cells. The
resulting active TC cells then identify infected host cells. Because of the time required to generate a population of
clonal T and B cells, there is a delay in the adaptive immune response compared to the innate immune response.

TC cells attempt to identify and destroy infected cells before the pathogen can replicate and escape, thereby halting
the progression of intracellular infections. TC cells also support NK lymphocytes to destroy early cancers. Cytokines
secreted by the TH1 response that stimulates macrophages also stimulate TC cells and enhance their ability to
identify and destroy infected cells and tumors. A summary of how the humoral and cell-mediated immune
responses are activated appears in Figure 17.16.

B plasma cells and TC cells are collectively called effector cells because they are involved in “effecting” (bringing

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 17.3 • Adaptive Immunity 461

about) the immune response of killing pathogens and infected host cells.

FIGURE 17.16 A helper T cell becomes activated by binding to an antigen presented by an APC via the MHCII receptor, causing it to release
cytokines. Depending on the cytokines released, this activates either the humoral or the cell-mediated immune response.

Immunological Memory
The adaptive immune system has a memory component that allows for a rapid and large response upon reinvasion
of the same pathogen. During the adaptive immune response to a pathogen that has not been encountered before,
known as the primary immune response, plasma cells secreting antibodies and differentiated T cells increase, then
plateau over time. As B and T cells mature into effector cells, a subset of the naïve populations differentiates into B
and T memory cells with the same antigen specificities (Figure 17.17). A memory cell is an antigen-specific B or T
lymphocyte that does not differentiate into an effector cell during the primary immune response, but that can
immediately become an effector cell on reexposure to the same pathogen. As the infection is cleared and
pathogenic stimuli subside, the effectors are no longer needed and they undergo apoptosis. In contrast, the memory
cells persist in the circulation.
462 17 • The Immune System and Disease

VISUAL CONNECTION

FIGURE 17.17 After initially binding an antigen to the B cell receptor, a B cell internalizes the antigen and presents it on MHC class II. A
helper T cell recognizes the MHC class II- antigen complex and activates the B cell. As a result, memory B cells and plasma cells are made.

The Rh antigen is found on Rh-positive red blood cells. An Rh-negative person can usually carry an Rh-positive fetus
to term without difficulty. However, having a second Rh-positive fetus may launch an immune attack that causes
hemolytic disease of the newborn. Why do you think hemolytic disease is only a problem during the second or
subsequent pregnancies?

If the pathogen is never encountered again during the individual’s lifetime, B and T memory cells will circulate for a
few years or even several decades and will gradually die off, having never functioned as effector cells. However, if
the host is re-exposed to the same pathogen type, circulating memory cells will immediately differentiate into
plasma cells and TC cells without input from APCs or TH cells. This is known as the secondary immune response.
One reason why the adaptive immune response is delayed is because it takes time for naïve B and T cells with the
appropriate antigen specificities to be identified, activated, and proliferate. On reinfection, this step is skipped, and
the result is a more rapid production of immune defenses. Memory B cells that differentiate into plasma cells output
tens to hundreds-fold greater antibody amounts than were secreted during the primary response (Figure 17.18).
This rapid and dramatic antibody response may stop the infection before it can even become established, and the
individual may not realize they had been exposed.

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 17.3 • Adaptive Immunity 463

FIGURE 17.18 In the primary response to infection, antibodies are secreted first from plasma cells. Upon re-exposure to the same
pathogen, memory cells differentiate into antibody-secreting plasma cells that output a greater amount of antibody for a longer period of
time.

Vaccination is based on the knowledge that exposure to noninfectious antigens, derived from known pathogens,
generates a mild primary immune response. The immune response to vaccination may not be perceived by the host
as illness but still confers immune memory. When exposed to the corresponding pathogen to which an individual
was vaccinated, the reaction is similar to a secondary exposure. Because each reinfection generates more memory
cells and increased resistance to the pathogen, some vaccine courses involve one or more booster vaccinations to
mimic repeat exposures.

The Lymphatic System

Lymph is the watery fluid that bathes tissues and organs and contains protective white blood cells but does not
contain erythrocytes. Lymph moves about the body through the lymphatic system, which is made up of vessels,
lymph ducts, lymph glands, and organs, such as tonsils, adenoids, thymus, and spleen.

Although the immune system is characterized by circulating cells throughout the body, the regulation, maturation,
and intercommunication of immune factors occur at specific sites. The blood circulates immune cells, proteins, and
other factors through the body. Approximately 0.1 percent of all cells in the blood are leukocytes, which include
monocytes (the precursor of macrophages) and lymphocytes. Most cells in the blood are red blood cells. Cells of the
immune system can travel between the distinct lymphatic and blood circulatory systems, which are separated by
interstitial space, by a process called extravasation (passing through to surrounding tissue).

Recall that cells of the immune system originate from stem cells in the bone marrow. B cell maturation occurs in the
bone marrow, whereas progenitor cells migrate from the bone marrow and develop and mature into naïve T cells in
the organ called the thymus.

On maturation, T and B lymphocytes circulate to various destinations. Lymph nodes scattered throughout the body
house large populations of T and B cells, dendritic cells, and macrophages (Figure 17.19). Lymph gathers antigens
as it drains from tissues. These antigens then are filtered through lymph nodes before the lymph is returned to
circulation. APCs in the lymph nodes capture and process antigens and inform nearby lymphocytes about potential
pathogens.
464 17 • The Immune System and Disease

FIGURE 17.19 (a) Lymphatic vessels carry a clear fluid called lymph throughout the body. The liquid passes through (b) lymph nodes that
filter the lymph that enters the node through afferent vessels and leaves through efferent vessels; lymph nodes are filled with lymphocytes
that purge infecting cells. (credit a: modification of work by NIH; credit b: modification of work by NCI, NIH)

The spleen houses B and T cells, macrophages, dendritic cells, and NK cells (Figure 17.20). The spleen is the site
where APCs that have trapped foreign particles in the blood can communicate with lymphocytes. Antibodies are
synthesized and secreted by activated plasma cells in the spleen, and the spleen filters foreign substances and
antibody-complexed pathogens from the blood. Functionally, the spleen is to the blood as lymph nodes are to the
lymph.

FIGURE 17.20 The spleen functions to immunologically filter the blood and allow for communication between cells corresponding to the
innate and adaptive immune responses. (credit: modification of work by NCI, NIH)

Mucosal Immune System

The innate and adaptive immune responses compose the systemic immune system (affecting the whole body),
which is distinct from the mucosal immune system. Mucosa associated lymphoid tissue (MALT) is a crucial
component of a functional immune system because mucosal surfaces, such as the nasal passages, are the first
tissues onto which inhaled or ingested pathogens are deposited. The mucosal tissue includes the mouth, pharynx,
and esophagus, and the gastrointestinal, respiratory, and urogenital tracts.

Mucosal immunity is formed by MALT, which functions independently of the systemic immune system, and which
has its own innate and adaptive components. MALT is a collection of lymphatic tissue that combines with epithelial
tissue lining the mucosa throughout the body. This tissue functions as the immune barrier and response in areas of
the body with direct contact to the external environment. The systemic and mucosal immune systems use many of
the same cell types. Foreign particles that make their way to MALT are taken up by absorptive epithelial cells and
delivered to APCs located directly below the mucosal tissue. APCs of the mucosal immune system are primarily

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 17.4 • Disruptions in the Immune System 465

dendritic cells, with B cells and macrophages having minor roles. Processed antigens displayed on APCs are
detected by T cells in the MALT and at the tonsils, adenoids, appendix, or the mesenteric lymph nodes of the
intestine. Activated T cells then migrate through the lymphatic system and into the circulatory system to mucosal
sites of infection.

Immune Tolerance
The immune system has to be regulated to prevent wasteful, unnecessary responses to harmless substances, and
more importantly, so that it does not attack “self.” The acquired ability to prevent an unnecessary or harmful
immune response to a detected foreign substance known not to cause disease, or self-antigens, is described as
immune tolerance. The primary mechanism for developing immune tolerance to self-antigens occurs during the
selection for weakly self-binding cells during T and B lymphocyte maturation. There are populations of T cells that
suppress the immune response to self-antigens and that suppress the immune response after the infection has
cleared to minimize host cell damage induced by inflammation and cell lysis. Immune tolerance is especially well
developed in the mucosa of the upper digestive system because of the tremendous number of foreign substances
(such as food proteins) that APCs of the oral cavity, pharynx, and gastrointestinal mucosa encounter. Immune
tolerance is brought about by specialized APCs in the liver, lymph nodes, small intestine, and lung that present
harmless antigens to a diverse population of regulatory T (Treg) cells, specialized lymphocytes that suppress local
inflammation and inhibit the secretion of stimulatory immune factors. The combined result of Treg cells is to prevent
immunologic activation and inflammation in undesired tissue compartments and to allow the immune system to
focus on pathogens instead.

17.4 Disruptions in the Immune System

LEARNING OBJECTIVES
By the end of this section, you will be able to:
• Describe hypersensitivity
• Define autoimmunity

A functioning immune system is essential for survival, but even the sophisticated cellular and molecular defenses of
the mammalian immune response can be defeated by pathogens at virtually every step. In the competition between
immune protection and pathogen evasion, pathogens have the advantage of more rapid evolution because of their
shorter generation time, large population sizes and often higher mutation rates. Thus pathogens have evolved a
diverse array of immune escape mechanisms. For instance, Streptococcus pneumoniae (the bacterium that causes
pneumonia and meningitis) surrounds itself with a capsule that inhibits phagocytes from engulfing it and displaying
antigens to the adaptive immune system. Staphylococcus aureus (the bacterium that can cause skin infections,
abscesses, and meningitis) synthesizes a toxin called leukocidin that kills phagocytes after they engulf the
bacterium. Other pathogens can also hinder the adaptive immune system. HIV infects TH cells using their CD4
surface molecules, gradually depleting the number of TH cells in the body (Figure 17.21); this inhibits the adaptive
immune system’s capacity to generate sufficient responses to infection or tumors. As a result, HIV-infected
individuals often suffer from infections that would not cause illness in people with healthy immune systems but
which can cause devastating illness to immune-compromised individuals.

FIGURE 17.21 HIV (green) is shown budding from a lymphocyte cell (red) in culture. (credit: modification of work by C. Goldsmith, CDC;
scale-bar data from Matt Russell)

Inappropriate responses of immune cells and molecules themselves can also disrupt the proper functioning of the
466 17 • The Immune System and Disease

entire system, leading to host-cell damage that can become fatal.

Immunodeficiency
Immunodeficiency is a failure, insufficiency, or delay in the response of the immune system, which may be acquired
or inherited. Immunodeficiency can allow pathogens or tumor cells to gain a foothold and replicate or proliferate to
high enough levels so that the immune system becomes overwhelmed. Immunodeficiency can be acquired as a
result of infection with certain pathogens that attack the cells of the immune system itself (such as HIV), chemical
exposure (including certain medical treatments such as chemotherapy), malnutrition, or extreme stress. For
instance, radiation exposure can destroy populations of lymphocytes and elevate an individual’s susceptibility to
infections and cancer. Rarely, primary immunodeficiencies that are present from birth may also occur. For example,
severe combined immunodeficiency disease (SCID) is a condition in which children are born without functioning B or
T cells.

Hypersensitivities
A maladaptive immune response toward harmless foreign substances or self-antigens that occur after tissue
sensitization is termed a hypersensitivity. Types of hypersensitivities include immediate, delayed, and
autoimmune. A large proportion of the human population is affected by one or more types of hypersensitivity.

Allergies
The immune reaction that results from immediate hypersensitivities in which an antibody-mediated immune
response occurs within minutes of exposure to a usually harmless antigen is called an allergy. In the United States,
20 percent of the population exhibits symptoms of allergy or asthma, whereas 55 percent test positive against one
or more allergens. On initial exposure to a potential allergen, an allergic individual synthesizes antibodies through
the typical process of APCs presenting processed antigen to TH cells that stimulate B cells to produce the
antibodies. The antibody molecules interact with mast cells embedded in connective tissues. This process primes,
or sensitizes, the tissue. On subsequent exposure to the same allergen, antibody molecules on mast cells bind the
antigen and stimulate the mast cell to release histamine and other inflammatory chemicals; these chemical
mediators then recruit eosinophils (a type of white blood cell), which also appear to be adapted to responding to
parasitic worms (Figure 17.22). Eosinophils release factors that enhance the inflammatory response and the
secretions of mast cells. The effects of an allergic reaction range from mild symptoms like sneezing and itchy,
watery eyes to more severe or even life-threatening reactions involving intensely itchy welts or hives, airway
constriction with severe respiratory distress, and plummeting blood pressure caused by dilating blood vessels and
fluid loss from the circulatory system. This extreme reaction, typically in response to an allergen introduced to the
circulatory system, is known as anaphylactic shock. Antihistamines are an insufficient counter to anaphylactic shock
and if not treated with epinephrine to counter the blood pressure and breathing effects, this condition can be fatal.

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 17.4 • Disruptions in the Immune System 467

FIGURE 17.22 On first exposure to an allergen, an antibody is synthesized by plasma cells in response to a harmless antigen. The
antibodies bind to mast cells, and on secondary exposure, the mast cells release histamines and other modulators that cause the
symptoms of allergy. (credit: modification of work by NIH)

Delayed hypersensitivity is a cell-mediated immune response that takes approximately one to two days after
secondary exposure for a maximal reaction. This type of hypersensitivity involves the TH1 cytokine-mediated
inflammatory response and may cause local tissue lesions or contact dermatitis (rash or skin irritation). Delayed
hypersensitivity occurs in some individuals in response to contact with certain types of jewelry or cosmetics.
Delayed hypersensitivity facilitates the immune response to poison ivy and is also the reason why the skin test for
tuberculosis results in a small region of inflammation on individuals who were previously exposed to Mycobacterium
tuberculosis, the organism that causes tuberculosis.

LINK TO LEARNING
Try your hand at diagnosing an allergic reaction by selecting one of the interactive case studies (http://openstax.org/
l/world_allergy) at the World Allergy Organization website.

Autoimmunity
Autoimmunity is a type of hypersensitivity to self-antigens that affects approximately five percent of the
population. Most types of autoimmunity involve the humoral immune response. An antibody that inappropriately
marks self-components as foreign is termed an autoantibody. In patients with myasthenia gravis, an autoimmune
disease, muscle-cell receptors that induce contraction in response to acetylcholine are targeted by antibodies. The
result is muscle weakness that may include marked difficultly with fine or gross motor functions. In systemic lupus
erythematosus, a diffuse autoantibody response to the individual’s own DNA and proteins results in various
systemic diseases (Figure 17.23). Systemic lupus erythematosus may affect the heart, joints, lungs, skin, kidneys,
central nervous system, or other tissues, causing tissue damage through antibody binding, complement
recruitment, lysis, and inflammation.
468 17 • The Immune System and Disease

FIGURE 17.23 Systemic lupus erythematosus is characterized by autoimmunity to the individual’s own DNA and/or proteins, which leads to
varied dysfunction of the organs. (credit: modification of work by Mikael Häggström)

Autoimmunity can develop with time and its causes may be rooted in molecular mimicry, a situation in which one
molecule is similar enough in shape to another molecule that it binds the same immune receptors. Antibodies and
T-cell receptors may bind self-antigens that are structurally similar to pathogen antigens. As an example, infection
with Streptococcus pyogenes (the bacterium that causes strep throat) may generate antibodies or T cells that react
with heart muscle, which has a similar structure to the surface of S. pyogenes. These antibodies can damage heart
muscle with autoimmune attacks, leading to rheumatic fever. Insulin-dependent (Type 1) diabetes mellitus arises
from a destructive inflammatory TH1 response against insulin-producing cells of the pancreas. Patients with this
autoimmunity must be treated with regular insulin injections.

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 17 • Key Terms 469

Key Terms
acellular lacking cells response in other cells
active immunity an immunity that occurs as a result effector cell a lymphocyte that has differentiated,
of the activity of the body’s own cells rather than such as a B cell, plasma cell, or cytotoxic T cell
from antibodies acquired from an external source glycoprotein a protein molecule with attached
adaptive immunity a specific immune response that carbohydrate molecules
occurs after exposure to an antigen either from a helper T lymphocyte (TH) a cell of the adaptive
pathogen or a vaccination immune system that binds APCs via MHC class II
allergy an immune reaction that results from molecules and stimulates B cells or secretes
immediate hypersensitivities in which an antibody- cytokines to initiate the immune response
mediated immune response occurs within minutes humoral immune response the adaptive immune
of exposure to a harmless antigen response that is controlled by activated B cells and
antibody a protein that is produced by plasma cells antibodies
after stimulation by an antigen; also known as an hypersensitivity a spectrum of inappropriate
immunoglobulin immune responses toward harmless foreign
antigen a macromolecule that reacts with cells of the particles or self-antigens; occurs after tissue
immune system and which may or may not have a sensitization and includes immediate-type (allergy),
stimulatory effect delayed-type, and autoimmunity
antigen-presenting cell (APC) an immune cell that immune tolerance an acquired ability to prevent an
detects, engulfs, and informs the adaptive immune unnecessary or harmful immune response to a
response about an infection by presenting the detected foreign body known not to cause disease
processed antigen on its cell surface immunodeficiency a failure, insufficiency, or delay at
apoptosis the cell death caused by induction of a any level of the immune system, which may be
cell’s own internal mechanisms either as a natural acquired or inherited
step in the development of a multicellular organism inflammation the localized redness, swelling, heat,
or by other environmental factors such as signals and pain that results from the movement of
from cells of the immune system leukocytes through opened capillaries to a site of
attenuation the weakening of a virus during vaccine infection
development innate immunity an immunity that occurs naturally
autoantibody an antibody that incorrectly marks because of genetic factors or physiology, and is not
“self” components as foreign and stimulates the caused by infection or vaccination
immune response interferon a cytokine that inhibits viral replication
autoimmunity a type of hypersensitivity to self- lymph the watery fluid present in the lymphatic
antigens circulatory system that bathes tissues and organs
B cell a lymphocyte that matures in the bone marrow with protective white blood cells and does not
capsid the protein coating of the viral core contain erythrocytes
cell-mediated immune response an adaptive lymphocyte a type of white blood cell that includes
immune response that is controlled by T cells natural killer cells of the innate immune system and
complement system an array of approximately 20 B and T cells of the adaptive immune system
soluble proteins of the innate immune system that macrophage a large phagocytic cell that engulfs
enhance phagocytosis, bore holes in pathogens, and foreign particles and pathogens
recruit lymphocytes major histocompatibility complex (MHC) I a group
cytokine a chemical messenger that regulates cell of proteins found on the surface of all nucleated
differentiation, proliferation, and gene expression to cells that signals to immune cells whether the cell is
effect immune responses normal or is infected or cancerous; it also provides
cytopathic causing cell damage the appropriate sites into which antigens can be
cytotoxic T lymphocyte (TC) an adaptive immune cell loaded for recognition by lymphocytes
that directly kills infected cells via enzymes, and major histocompatibility complex (MHC) II
that releases cytokines to enhance the immune molecule a protein found on the surface of
response antigen-presenting cells that signals to immune
dendritic cell an immune cell that processes antigen cells whether the cell is normal or is infected or
material and presents it on the surface of its cell in cancerous; it provides the appropriate template into
MHC class II molecules and induces an immune which antigens can be loaded for recognition by
470 17 • Chapter Summary

lymphocytes by transfer of antibodies from one individual to

mast cell a leukocyte that produces inflammatory another
molecules, such as histamine, in response to large primary immune response the response of the
pathogens adaptive immune system to the first exposure to an
memory cell an antigen-specific B or T lymphocyte antigen
that does not differentiate into an effector cell secondary immune response the response of the
during the primary immune response but that can adaptive immune system to a second or later
immediately become an effector cell on reexposure exposure to an antigen mediated by memory cells
to the same pathogen T cell a lymphocyte that matures in the thymus gland
monocyte a type of white blood cell that circulates in vaccine a weakened solution of virus components,
the blood and lymph and differentiates into a viruses, or other agents that produce an immune
macrophage after it moves into infected tissue response
natural killer (NK) cell a lymphocyte that can kill viral envelope a lipid bilayer that envelops some
cells infected with viruses or tumor cells viruses
neutrophil a phagocytic leukocyte that engulfs and virion an individual virus particle outside a host cell
digests pathogens white blood cell a nucleated cell found in the blood
passive immunity an immunity that does not result that is a part of the immune system; also called
from the activity of the body’s own immune cells but leukocytes

Chapter Summary
17.1 Viruses and mucous membranes and their secretions, ciliated
surfaces, and body hairs. The second line of defense is
Viruses are acellular entities that can usually only be
an internal defense system designed to counter
seen with an electron microscope. Their genomes
pathogenic threats that bypass the physical and
contain either DNA or RNA, and they replicate using the
chemical barriers of the body. Using a combination of
replication proteins of a host cell. Viruses are diverse,
cellular and molecular responses, the innate immune
infecting archaea, bacteria, fungi, plants, and animals.
system identifies the nature of a pathogen and
Viruses consist of a nucleic-acid core surrounded by a
responds with inflammation, phagocytosis, cytokine
protein capsid with or without an outer lipid envelope.
release, destruction by NK cells, or the complement
Viral replication within a living cell always produces system.
changes in the cell, sometimes resulting in cell death
17.3 Adaptive Immunity
and sometimes slowly killing the infected cells. There
are six basic stages in the virus replication cycle: The adaptive immune response is a slower-acting,
attachment, penetration, uncoating, replication, longer-lasting, and more specific response than the
assembly, and release. A viral infection may be innate response. However, the adaptive response
productive, resulting in new virions, or nonproductive, requires information from the innate immune system to
meaning the virus remains inside the cell without function. APCs display antigens on MHC molecules to
producing new virions. naïve T cells. T cells with cell-surface receptors that
bind a specific antigen will bind to that APC. In
Viruses cause a variety of diseases in humans. Many of
response, the T cells differentiate and proliferate,
these diseases can be prevented by the use of viral
becoming TH cells or TC cells. TH cells stimulate B cells
vaccines, which stimulate protective immunity against
that have engulfed and presented pathogen-derived
the virus without causing major disease. Viral vaccines
antigens. B cells differentiate into plasma cells that
may also be used in active viral infections, boosting the
secrete antibodies, whereas TC cells destroy infected
ability of the immune system to control or destroy the
or cancerous cells. Memory cells are produced by
virus. Antiviral drugs that target enzymes and other
activated and proliferating B and T cells and persist
protein products of viral genes have been developed
after a primary exposure to a pathogen. If re-exposure
and used with mixed success. Combinations of anti-
occurs, memory cells differentiate into effector cells
HIV drugs have been used to effectively control the
without input from the innate immune system. The
virus, extending the lifespan of infected individuals.
mucosal immune system is largely independent of the
17.2 Innate Immunity systemic immune system but functions in parallel to
protect the extensive mucosal surfaces of the body.
The innate immune system consists first of physical
Immune tolerance is brought about by Treg cells to
and chemical barriers to infection including the skin

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 17 • Visual Connection Questions 471

limit reactions to harmless antigens and the body’s susceptibility to infections and cancers.
own molecules. Hypersensitivities are misdirected responses either to
harmless foreign particles, as in the case of allergies, or
17.4 Disruptions in the Immune System to the individual’s own tissues, as in the case of
Immune disruptions may involve insufficient immune autoimmunity. Reactions to self-components may be
responses or inappropriate immune responses. the result of molecular mimicry.
Immunodeficiency increases an individual's

Visual Connection Questions

1. Figure 17.5 Which of the following statements 3. Figure 17.17 The Rh antigen is found on Rh-positive
about virus structure is true? red blood cells. An Rh-negative person can usually
a. All viruses are encased in a viral membrane. carry an Rh-positive fetus to term without difficulty.
b. The capsomere is made up of small protein However, having a second Rh-positive fetus may
subunits called capsids. launch an immune attack that causes hemolytic
c. DNA is the genetic material in all viruses. disease of the newborn. Why do you think
d. Glycoproteins help the virus attach to the host hemolytic disease is only a problem during the
cell. second or subsequent pregnancies?

2. Figure 17.6 Influenza virus is packaged in a viral

envelope, which fuses with the plasma membrane.
This way, the virus can exit the host cell without
killing it. What advantage does the virus gain by
keeping the host cell alive?

Review Questions
4. Which statement is true? 7. Which of the following is a barrier against
a. A virion contains DNA and RNA. pathogens provided by the skin?
b. Viruses are acellular. a. low pH
c. Viruses replicate outside of the cell. b. mucus
d. Most viruses are easily visualized with a light c. tears
microscope. d. cilia

5. The viral ________ plays a role in attaching a virion 8. Although interferons have several effects, they are
to the host cell. particularly useful against infections with which
a. core type of pathogen?
b. capsid a. bacteria
c. envelope b. viruses
d. both b and c c. fungi
d. helminths
6. Which statement is true of viral replication?
a. In the process of apoptosis, the cell survives. 9. Which innate immune system component uses MHC
b. During attachment, the virus attaches at class I molecules directly in its defense strategy?
specific sites on the cell surface. a. macrophages
c. The viral capsid helps the host cell produce b. neutrophils
more copies of the viral genome. c. NK cells
d. mRNA works outside of the host cell to d. interferon
produce enzymes and proteins.
10. The humoral immune response depends on which
cells?
a. TC cells
b. B cells
c. B and TH cells
d. TC and TH cells
472 17 • Critical Thinking Questions

11. The fact that the body does not normally mount an 13. Allergy to pollen is classified as ________.
immune response to the molecules in food is an a. an autoimmune reaction
example of _______. b. immunodeficiency
a. secondary immune response c. delayed hypersensitivity
b. immunological memory d. immediate hypersensitivity
c. immune tolerance
d. passive immunity 14. A potential cause of acquired autoimmunity is
________.
12. Foreign particles circulating in the blood are a. tissue hypersensitivity
filtered by the ____________. b. molecular mimicry
a. spleen c. histamine release
b. lymph nodes d. radiation exposure
c. MALT
d. lymph 15. Autoantibodies are probably involved in
________.
a. reactions to poison ivy
b. pollen allergies
c. systemic lupus erythematosus
d. HIV/AIDS

Critical Thinking Questions

16. Why can’t dogs catch the measles? 20. How do B and T cells differ with respect to
antigens that they bind?
17. Why is immunization after being bitten by a rabid
animal so effective? 21. Why is the immune response after reinfection
much faster than the adaptive immune response
18. Different MHC class I molecules between donor
after the initial infection?
and recipient cells can lead to rejection of a
transplanted organ or tissue. Suggest a reason for 22. Some photographers develop a sensitivity to
this. certain film developing chemicals leading to
severe rashes on their hands such that they are
19. If a series of genetic mutations prevented some,
unable to work with them. Explain what is
but not all, of the complement proteins from
probably happening.
binding antibodies or pathogens, would the entire
complement system be compromised?

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CHAPTER 18
Animal Reproduction and Development

FIGURE 18.1 Female seahorses produce eggs that are then fertilized by the male. Unlike with almost all other
animals, the young then develop in a pouch of the male seahorse until birth. (credit: "cliff1066"/Flickr)

CHAPTER OUTLINE
18.1 How Animals Reproduce
18.2 Development and Organogenesis
18.3 Human Reproduction

INTRODUCTION In the animal kingdom, each species has its unique adaptations for
reproduction. Asexual reproduction produces genetically identical offspring (clones), whereas in
sexual reproduction, the genetic material of two individuals combines to produce offspring that
are genetically different from their parents. Although animal species vary widely in sex-specific
morphology and behavior, there is almost always one type of body that produces smaller gametes,
and one type of body that produces larger gametes. The individuals who produce smaller gametes
are classified with a male sex, while those who produce larger gametes are classified with a
female sex. During sexual reproduction the male gamete (sperm) may be placed inside the
female’s body for internal fertilization, the sperm may be left in the environment for the female to
pick up and place in their own body, or both sperm and eggs may be released into the
environment for external fertilization. Seahorses provide an example of the latter, but with a twist
474 18 • Animal Reproduction and Development

(Figure 18.1). Following a mating dance, the female releases eggs into the male seahorse’s
abdominal brood pouch and the male releases sperm into the water, which then find their way into
the brood pouch to fertilize the eggs. The fertilized eggs develop in the pouch for several weeks.

18.1 How Animals Reproduce

LEARNING OBJECTIVES
By the end of this section, you will be able to:
• Describe advantages and disadvantages of asexual and sexual reproduction
• Discuss asexual reproduction methods
• Discuss sexual reproduction methods
• Discuss internal and external methods of fertilization

Some animals produce offspring through asexual reproduction while other animals produce
offspring through sexual reproduction. Both methods have advantages and disadvantages.
Asexual reproduction produces offspring that are genetically identical to the parent because the
offspring are all clones of the original parent. A single individual can produce offspring asexually
and large numbers of offspring can be produced quickly; these are two advantages that asexually
reproducing organisms have over sexually reproducing organisms. In a stable or predictable
environment, asexual reproduction is an effective means of reproduction because all the offspring
will be adapted to that environment. In an unstable or unpredictable environment, species that
reproduce asexually may be at a disadvantage because all the offspring are genetically identical
and may not be adapted to different conditions.

During sexual reproduction, the genetic material of two individuals is combined to produce
genetically diverse offspring that differ from their parents. The genetic diversity of sexually
produced offspring is thought to give sexually reproducing individuals greater fitness because
more of their offspring may survive and reproduce in an unpredictable or changing environment.
Species that reproduce sexually (and have separate sexes) must maintain two different types of
individuals, males and females. Only half the population (females) can produce the offspring, so
fewer offspring will be produced when compared to asexual reproduction. This is a disadvantage
of sexual reproduction compared to asexual reproduction.

Asexual Reproduction
Asexual reproduction occurs in prokaryotic microorganisms (bacteria and archaea) and in many
eukaryotic, single-celled and multi-celled organisms. There are several ways that animals
reproduce asexually, the details of which vary among individual species.

Fission
Fission, also called binary fission, occurs in some invertebrate, multi-celled organisms. It is in
some ways analogous to the process of binary fission of single-celled prokaryotic organisms. The
term fission is applied to instances in which an organism appears to split itself into two parts and,
if necessary, regenerate the missing parts of each new organism. For example, species of
turbellarian flatworms commonly called the planarians, such as Dugesia dorotocephala, are able
to separate their bodies into head and tail regions and then regenerate the missing half in each of
the two new organisms. Sea anemones (Cnidaria), such as species of the genus Anthopleura
(Figure 18.2), will divide along the oral-aboral axis, and sea cucumbers (Echinodermata) of the
genus Holothuria, will divide into two halves across the oral-aboral axis and regenerate the other
half in each of the resulting individuals.

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 18.1 • How Animals Reproduce 475

FIGURE 18.2 The Anthopleura artemisia sea anemone can reproduce through fission.

Budding
Budding is a form of asexual reproduction that results from the outgrowth of a part of the body leading to a
separation of the “bud” from the original organism and the formation of two individuals, one smaller than the other.
Budding occurs commonly in some invertebrate animals such as hydras and corals. In hydras, a bud forms that
develops into an adult and breaks away from the main body (Figure 18.3).

FIGURE 18.3 (a) Hydra reproduce asexually through budding: a bud forms on the tubular body of an adult hydra, develops a mouth and
tentacles, and then detaches from its parent. The new hydra is fully developed and will find its own location for attachment. (b) Some coral,
such as the Lophelia pertusa shown here, can reproduce through budding. (credit b: modification of work by Ed Bowlby, NOAA/Olympic
Coast NMS; NOAA/OAR/Office of Ocean Exploration)

LINK TO LEARNING
View this video (http://openstax.org/l/budding_hydra2) to see a hydra budding.

Fragmentation
Fragmentation is the breaking of an individual into parts followed by regeneration. If the animal is capable of
fragmentation, and the parts are big enough, a separate individual will regrow from each part. Fragmentation may
occur through accidental damage, damage from predators, or as a natural form of reproduction. Reproduction
through fragmentation is observed in sponges, some cnidarians, turbellarians, echinoderms, and annelids. In some
sea stars, a new individual can be regenerated from a broken arm and a piece of the central disc. This sea star
(Figure 18.4) is in the process of growing a complete sea star from an arm that has been cut off. Fisheries workers
have been known to try to kill the sea stars eating their clam or oyster beds by cutting them in half and throwing
them back into the ocean. Unfortunately for the workers, the two parts can each regenerate a new half, resulting in
twice as many sea stars to prey upon the oysters and clams.
476 18 • Animal Reproduction and Development

FIGURE 18.4 (a) Linckia multifora is a species of sea star that can reproduce asexually via fragmentation. In this process, (b) an arm that
has been shed grows into a new sea star. (credit a: modification of work by Dwayne Meadows, NOAA/NMFS/OPR)

Parthenogenesis
Parthenogenesis is a form of asexual reproduction in which an egg develops into an individual without being
fertilized. The resulting offspring can be either haploid or diploid, depending on the process in the species.
Parthenogenesis occurs in invertebrates such as water fleas, rotifers, aphids, stick insects, and ants, wasps, and
bees. Ants, bees, and wasps use parthenogenesis to produce haploid males (drones). The diploid females (workers
and queens) are the result of a fertilized egg.

Some vertebrate animals—such as certain reptiles, amphibians, and fish—also reproduce through parthenogenesis.
Parthenogenesis has been observed in species in which the sexes were separated in terrestrial or marine zoos. Two
female Komodo dragons, a hammerhead shark, and a blacktop shark have produced parthenogenic young when the
females have been isolated from males. It is possible that the asexual reproduction observed occurred in response
to unusual circumstances and would normally not occur.

Sexual Reproduction
Sexual reproduction is the combination of reproductive cells from two individuals to form genetically unique
offspring. The nature of the individuals that produce the two kinds of gametes can vary, having for example separate
sexes or multiple sexes in each individual. Sex determination, the mechanism that determines which sex an
individual develops into, also can vary.

Hermaphroditism
Hermaphroditism occurs in animals in which one individual has both male and female reproductive systems.
Invertebrates such as earthworms, slugs, tapeworms, and snails (Figure 18.5) are often hermaphroditic.
Hermaphrodites may self-fertilize, but typically they will mate with another of their species, fertilizing each other
and both producing offspring. Many species have specific mechanisms in place to prevent self-fertilization, because
it is an extreme form of inbreeding and usually produces less fit offspring. Hermaphrodite is not an accepted term
for humans, and does not describe differences in their sexual development. Intersex people are those whose sex
traits or reproductive anatomy develops differently from the typical ways humans develop, and can include
hormonal, chromosomal, or anatomical differences.

FIGURE 18.5 Many (a) snails are hermaphrodites. When two individuals (b) mate, they can produce up to 100 eggs each. (credit a:

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 18.1 • How Animals Reproduce 477

modification of work by Assaf Shtilman; credit b: modification of work by "Schristia"/Flickr)

Sex Determination
Pioneering scientist Nettie Stevens was the first to observe chromosomal differences between the different sexes of
organisms. Using a microscope to observe mealworm cells, she noted that one chromosome was notably different
between females and males, and she concluded that those chromosomes were the most likely determinants of the
worms' sex. She later studied other insects, and her discoveries were confirmed by other scientists. (Stevens was
initially denied credit due to her gender, but later publications acknowledged her critical role.) Mammalian sex is
determined genetically by the combination of X and Y chromosomes. Individuals homozygous for X (XX) are female
and heterozygous individuals (XY) are male. In mammals, the presence of a Y chromosome causes the development
of male characteristics and its absence results in female characteristics. The XY system is also found in some
insects and plants.

Bird sex determination is dependent on the combination of Z and W chromosomes. Homozygous for Z (ZZ) results
in a male and heterozygous (ZW) results in a female. Notice that this system is the opposite of the mammalian
system because in birds the female is the sex with the different sex chromosomes. The W appears to be essential in
determining the sex of the individual, similar to the Y chromosome in mammals. Some fish, crustaceans, insects
(such as butterflies and moths), and reptiles use the ZW system.

More complicated chromosomal sex determining systems also exist. For example, some swordtail fish have three
sex chromosomes in a population.

The sex of some other species is not determined by chromosomes, but by some aspect of the environment. Sex
determination in alligators, some turtles, and tuataras, for example, is dependent on the temperature during the
middle third of egg development. This is referred to as environmental sex determination, or more specifically, as
temperature-dependent sex determination. In many turtles, cooler temperatures during egg incubation produce
males and warm temperatures produce females, while in many other species of turtles, the reverse is true. In some
crocodiles and some turtles, moderate temperatures produce males and both warm and cool temperatures produce
females.

Individuals of some species change their entire set of reproductive organs during their lives, switching from one to
the other. If the individual is born with an ovarian system of organs first, it is termed protogyny or “first female,” if it
is born with a testicular system of organs first, it is termed protandry or “first male.” Oysters are born with male
morphology, grow in size, and change body parts and lay eggs. The wrasses, a family of reef fishes, are all sequential
hermaphrodites. Some of these species live in closely coordinated schools with a dominant male and a large
number of smaller females. If the male dies, a female increases in size, changes sex, and becomes the new
dominant male.

Fertilization
The fusion of a sperm and an egg is a process called fertilization. This can occur either inside (internal fertilization)
or outside (external fertilization) the body of the female. Humans provide an example of the former, whereas frog
reproduction is an example of the latter.

External Fertilization
External fertilization usually occurs in aquatic environments where both eggs and sperm are released into the water.
After the sperm reaches the egg, fertilization takes place. Most external fertilization happens during the process of
spawning where one or several females release their eggs and the male(s) release sperm in the same area, at the
same time. The spawning may be triggered by environmental signals, such as water temperature or the length of
daylight. Nearly all fish spawn, as do crustaceans (such as crabs and shrimp), mollusks (such as oysters), squid, and
echinoderms (such as sea urchins and sea cucumbers). Frogs, corals, squid, and octopuses also spawn (Figure
18.6).
478 18 • Animal Reproduction and Development

FIGURE 18.6 During sexual reproduction in toads, the male grasps the female from behind and externally fertilizes the eggs as they are
deposited. (credit: Bernie Kohl)

Internal Fertilization
Internal fertilization occurs most often in terrestrial animals, although some aquatic animals also use this method.
Internal fertilization may occur by the male directly depositing sperm in the female during mating. It may also occur
by the male depositing sperm in the environment, usually in a protective structure, which a female picks up to
deposit the sperm in the reproductive tract. There are three ways that offspring are produced following internal
fertilization. In oviparity, fertilized eggs are laid outside the parent’s body and develop there, receiving nourishment
from the yolk that is a part of the egg (Figure 18.7a). This occurs in some bony fish, some reptiles, a few
cartilaginous fish, some amphibians, a few mammals, and all birds. Most non-avian reptiles and insects produce
leathery eggs, while birds and some turtles produce eggs with high concentrations of calcium carbonate in the shell,
making them hard. Chicken eggs are an example of a hard shell. The eggs of the egg-laying mammals such as the
platypus and echidna are leathery.

In ovoviparity, fertilized eggs are retained in the female, and the embryo obtains its nourishment from the egg’s
yolk. The eggs are retained in the female’s body until they hatch inside the body, or the female lays the eggs right
before they hatch. This process helps protect the eggs until hatching. This occurs in some bony fish (like the
platyfish Xiphophorus maculatus, Figure 18.7b), some sharks, lizards, some snakes (garter snake Thamnophis
sirtalis), some vipers, and some invertebrate animals (Madagascar hissing cockroach Gromphadorhina portentosa).

In viviparity the young are born alive. They obtain their nourishment from the female and are born in varying states
of maturity. This occurs in most mammals (Figure 18.7c), some cartilaginous fish, and a few reptiles.

FIGURE 18.7 In (a) oviparity, young develop in eggs outside the female body, as with these Harmonia axydridis beetles hatching. Some
aquatic animals, like this (b) pregnant Xiphophorus maculatus are ovoviparous, with the egg developing inside the female and nutrition
supplied primarily from the yolk. In mammals, nutrition is supported by the placenta, as was the case with this (c) newborn squirrel. (credit
b: modification of work by Gourami Watcher; credit c: modification of work by "audreyjm529"/Flickr)

18.2 Development and Organogenesis

LEARNING OBJECTIVES
By the end of this section, you will be able to:
• Explain how the embryo forms from the zygote
• Discuss the role of cleavage and gastrulation in animal development
• Describe organogenesis

The process by which an organism develops from a single-celled zygote to a multi-cellular organism is complex and
well regulated. The regulation occurs through signaling between cells and tissues and responses in the form of

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 18.2 • Development and Organogenesis 479

differential gene expression.

Early Embryonic Development

Fertilization is the process in which gametes (an egg and sperm) fuse to form a zygote (Figure 18.8). To ensure that
the offspring has only one complete diploid set of chromosomes, only one sperm must fuse with one egg. In
mammals, a layer called the zona pellucida protects the egg. At the tip of the head of a sperm cell is a structure like
a lysosome called the acrosome, which contains enzymes. When a sperm binds to the zona pellucida, a series of
events, called the acrosomal reactions, take place. These reactions, involving enzymes from the acrosome, allow the
sperm plasma membrane to fuse with the egg plasma membrane and permit the sperm nucleus to transfer into the
ovum. The nuclear membranes of the egg and sperm break down and the two haploid nuclei fuse to form a diploid
nucleus or genome.

FIGURE 18.8 Fertilization is the process in which sperm and egg fuse to form a zygote. (credit: scale-bar data from Matt Russell)

To ensure successful development, organisms must ensure that that no more than one sperm fertilizes the egg.
Ernest Everett Just demonstrated several mechanisms at work at different rates. The fast reaction included what
Just called a "wave of negativity," in which the membrane potential of the egg cell altered quickly. Then, the slow
block involved changing the membrane structure itself. The acrosomal reactions take place at one location of the
egg membrane, the egg releases proteins in other locations to prevent other sperm from fusing with the egg.

The development of multi-cellular organisms begins from this single-celled zygote, which undergoes rapid cell
division, called cleavage (Figure 18.9a), to form a hollow ball of cells called a blastula (Figure 18.9b).

FIGURE 18.9 (a) During cleavage, the zygote rapidly divides into multiple cells. (b) The cells rearrange themselves to form a hollow ball
called the blastula. (credit a: modification of work by Gray's Anatomy; credit b: modification of work by Pearson Scott Foresman; donated to
the Wikimedia Foundation)

In mammals, the blastula forms the blastocyst in the next stage of development. Here the cells in the blastula
arrange themselves in two layers: the inner cell mass, and an outer layer called the trophoblast. The inner cell
480 18 • Animal Reproduction and Development

mass will go on to form the embryo. The trophoblast secretes enzymes that allow implantation of the blastocyst into
the endometrium of the uterus. The trophoblast will contribute to the placenta and nourish the embryo.

LINK TO LEARNING
Visit the Virtual Human Embryo project (http://openstax.org/l/human_embryo2) at the Endowment for Human
Development site to click through an interactive of the stages of embryo development, including micrographs and
rotating 3-D images.

The cells in the blastula then rearrange themselves spatially to form three layers of cells. This process is called
gastrulation. During gastrulation, the blastula folds in on itself and cells migrate to form the three layers of cells
(Figure 18.10) in a structure, the gastrula, with a hollow space that will become the digestive tract. Each of the
layers of cells is called a germ layer and will differentiate into different organ systems.

FIGURE 18.10 Gastrulation is the process wherein the cells in the blastula rearrange themselves to form the germ layers. (credit:
modification of work by Abigail Pyne)

The three germ layers are the endoderm, the ectoderm, and the mesoderm. Cells in each germ layer differentiate
into tissues and embryonic organs. The ectoderm gives rise to the nervous system and the epidermis, among other
tissues. The mesoderm gives rise to the muscle cells and connective tissue in the body. The endoderm gives rise to
the gut and many internal organs.

Organogenesis
Gastrulation leads to the formation of the three germ layers that give rise during further development to the
different organs in the animal body. This process is called organogenesis.

Organs develop from the germ layers through the process of differentiation. During differentiation, the embryonic
stem cells express specific sets of genes that will determine their ultimate cell type. For example, some cells in the
ectoderm will express the genes specific to skin cells. As a result, these cells will take on the shape and
characteristics of epidermal cells. The process of differentiation is regulated by location-specific chemical signals
from the cell’s embryonic environment that sets in play a cascade of events that regulates gene expression.

18.3 Human Reproduction

LEARNING OBJECTIVES
By the end of this section, you will be able to:
• Describe human testicular and ovarian reproductive anatomies
• Describe spermatogenesis and oogenesis and discuss their differences and similarities
• Describe the role of hormones in human reproduction
• Describe the roles of reproductive hormones

As in all animals, the adaptations for reproduction in humans are complex. They involve specialized and different
anatomies in the two sexes, a hormone regulation system, and specialized behaviors regulated by the brain and
endocrine system.

Human Reproductive Anatomy

The reproductive tissues of male and female humans develop similarly in utero until about the seventh week of
gestation when, in some cases, a low level of the hormone testosterone is released from the gonads. Testosterone

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 18.3 • Human Reproduction 481

causes the primitive gonads to differentiate into sexual organs, such as the scrotum and penis. When testosterone is
absent, the primitive gonads develop into ovaries. Tissues that produce a penis in males produce a clitoris in
females. The tissue that will become the scrotum in a male becomes the labia in a female. Thus the male and
female anatomies arise from a divergence in the development of what were once common embryonic structures.

Male Reproductive Anatomy

Sperm are immobile at body temperature; therefore, the testes are external to the body so that a correct
temperature is maintained for motility. In land mammals, including humans, the pair of testes must be suspended
outside the body so the environment of the sperm is about 2 °C lower than body temperature to produce viable
sperm. If the testes do not descend through the abdominal cavity during fetal development, the individual has
reduced fertility.

The scrotum houses the testicles or testes (singular: testis), and provides passage for blood vessels, nerves, and
muscles related to testicular function. The testes are a pair of male gonads that produce sperm and reproductive
hormones. Each testis is approximately 2.5 by 3.8 cm (1.5 by 1 inch) in size and divided into wedge-shaped lobes by
septa. Coiled in each wedge are seminiferous tubules that produce sperm.

The penis drains urine from the urinary bladder and is a copulatory organ during intercourse (Figure 18.12; Table
18.1). The penis contains three tubes of erectile tissue that become engorged with blood, making the penis erect, in
preparation for intercourse. The organ is inserted into the vagina culminating with an ejaculation. During orgasm, the
accessory organs and glands connected to the testes contract and empty the semen (containing sperm) into the
urethra and the fluid is expelled from the body by muscular contractions causing ejaculation. After intercourse, the
blood drains from the erectile tissue and the penis becomes flaccid.

Semen is a mixture of sperm (about five percent of the total) and fluids from accessory glands that contribute most
of the semen’s volume. Sperm are haploid cells, consisting of a flagellum for motility, a neck that contains the cell’s
energy-producing mitochondria, and a head that contains the genetic material (Figure 18.11). An acrosome
(acrosomal vesicle) is found at the top of the head of the sperm. This structure contains enzymes that can digest the
protective coverings that surround the egg and allow the sperm to fuse with the egg. An ejaculate will contain from
two to five milliliters of fluid and from 50–120 million sperm per milliliter.

FIGURE 18.11 As seen in this scanning electron micrograph, human sperm has a flagellum, neck, and head. (credit: scale-bar data from
Matt Russell)

Sperm form in the walls of seminiferous tubules that are coiled inside the testes (Figure 18.12; Table 18.1). The
walls of the seminiferous tubules are made up of the developing sperm cells, with the least developed sperm at the
periphery of the tubule and the fully developed sperm next to the lumen. The sperm cells are associated with
Sertoli cells that nourish and promote the development of the sperm. Other cells present between the walls of the
tubules are the interstitial cells of Leydig, which produce testosterone once the male reaches adolescence.

When the sperm have developed flagella they leave the seminiferous tubules and enter the epididymis (Figure
18.12; Table 18.1). This structure lies along the top and posterior of the testes and is the site of sperm maturation.
The sperm leave the epididymis and enter the vas deferens, which carries the sperm behind the bladder, and forms
the ejaculatory duct with the duct from the seminal vesicles. During a vasectomy, a section of the vas deferens is
482 18 • Animal Reproduction and Development

removed, preventing sperm (but not the secretions of the accessory glands) from being passed out of the body
during ejaculation and preventing fertilization.

The bulk of the semen comes from the accessory glands associated with the male reproductive system. These are
the seminal vesicles, the prostate gland, and the bulbourethral gland (Figure 18.12; Table 18.1). The secretions
from the accessory glands provide important compounds for the sperm including nutrients, electrolytes, and pH
buffering. There are also coagulation factors that affect sperm delivery and motility.

VISUAL CONNECTION

FIGURE 18.12 The testicular reproductive system structures are shown.

Which of the following statements about the testicular reproductive system is false?

a. The vas deferens carries sperm from the testes to the seminal vesicles.
b. The ejaculatory duct joins the urethra.
c. Both the prostate and the bulbourethral glands produce components of the semen.
d. The prostate gland is located in the testes.

Testicular Reproductive System Anatomy

Organ Location Function

Scrotum External Supports testes and regulates their temperature

Penis External Delivers urine, copulating organ

Testes Internal Produce sperm and male hormones

Seminal Vesicles Internal Contribute to semen production

Prostate Gland Internal Contributes to semen production

Bulbourethtral Glands Internal Neutralize urine in urethra

TABLE 18.1

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 18.3 • Human Reproduction 483

Female Reproductive Anatomy

A number of female reproductive structures are exterior to the body. These include the breasts and the vulva, which
consists of the mons pubis, clitoris, labia majora, labia minora, and the vestibular glands (Figure 18.13; Table
18.2).

FIGURE 18.13 The structures of the human ovarian reproductive system are shown. (credit a: modification of work by Gray's Anatomy;
credit b: modification of work by CDC)

The breasts consist of mammary glands and fat. Each gland consists of 15 to 25 lobes that have ducts that empty at
the nipple and that supply the nursing child with nutrient- and antibody-rich milk to aid development and protect
the child.

Internal female reproductive structures include ovaries, oviducts, the uterus, and the vagina (Figure 18.13; Table
18.2). The pair of ovaries is held in place in the abdominal cavity by a system of ligaments. The outermost layer of
the ovary is made up of follicles, each consisting of one or more follicular cells that surround, nourish, and protect a
single egg. During the menstrual period, a batch of follicular cells develops and prepares their eggs for release. At
ovulation, one follicle ruptures and one egg is released. Following ovulation, the follicular tissue that surrounded the
ovulated egg stays within the ovary and grows to form a solid mass called the corpus luteum. The corpus luteum
secretes additional estrogen and the hormone progesterone that helps maintain the uterine lining during pregnancy.
The ovaries also produce hormones, such as estrogen.

The oviducts, or fallopian tubes, extend from the uterus in the lower abdominal cavity to the ovaries, but they are
not in contact with the ovaries. The lateral ends of the oviducts flare out into a trumpet-like structure and have a
fringe of finger-like projections called fimbrae. When an egg is released at ovulation, the fimbrae help the nonmotile
egg enter into the tube. The walls of the oviducts have a ciliated epithelium over smooth muscle. The cilia beat, and
the smooth muscle contracts, moving the egg toward the uterus. Fertilization usually takes place within the oviduct
and the developing embryo is moved toward the uterus. It usually takes the egg or embryo a week to travel through
the oviduct.

Sterilization in females is called a tubal ligation; it is analogous to a vasectomy in males in that the oviducts are
severed and sealed, preventing sperm from reaching the egg.

The uterus is a structure about the size of a person’s fist. The uterus has a thick muscular wall and is lined with an
endometrium rich in blood vessels and mucus glands that develop and thicken during the female cycle. Thickening
of the endometrium prepares the uterus to receive the fertilized egg or zygote, which will then implant itself in the
endometrium. The uterus supports the developing embryo and fetus during gestation. Contractions of the smooth
484 18 • Animal Reproduction and Development

muscle in the uterus aid in forcing the baby through the vagina during labor. If fertilization does not occur, a portion
of the lining of the uterus sloughs off during each menstrual period. The endometrium builds up again in preparation
for implantation. Part of the uterus, called the cervix, protrudes into the top of the vagina.

The vagina is a muscular tube that serves several purposes. It allows menstrual flow to leave the body. It is the
receptacle for the penis during intercourse and the pathway for the delivery of offspring.

Ovarian Reproductive System Anatomy

Organ Location Function

Clitoris External Sensory organ

Mons pubis External Fatty area overlying pubic bone

Labia majora External Covers labia minora; contains sweat and sebaceous glands

Labia minora External Covers vestibule

Greater vestibular glands External Secrete mucus; lubricate vagina

Breast External Produces and delivers milk

Ovaries Internal Produce and develop eggs

Oviducts Internal Transport egg to uterus; site of fertilization

Uterus Internal Supports developing embryo

Vagina Internal Common tube for intercourse, birth canal, passing menstrual flow

TABLE 18.2

Gametogenesis (Spermatogenesis and Oogenesis)

Gametogenesis, the production of sperm and eggs, involves the process of meiosis. During meiosis, two nuclear
divisions separate the paired chromosomes in the nucleus and then separate the chromatids that were made during
an earlier stage of the cell’s life cycle. Meiosis and its associated cell divisions produces haploid cells with half of
each pair of chromosomes normally found in diploid cells. The production of sperm is called spermatogenesis and
the production of eggs is called oogenesis.

Spermatogenesis
Spermatogenesis occurs in the wall of the seminiferous tubules, with the most primitive cells at the periphery of the
tube and the most mature sperm at the lumen of the tube (Figure 18.14). Immediately under the capsule of the
tubule are diploid, undifferentiated cells. These stem cells, each called a spermatogonium (pl. spermatogonia), go
through mitosis to produce one cell that remains as a stem cell and a second cell called a primary spermatocyte that
will undergo meiosis to produce sperm.

The diploid primary spermatocyte goes through meiosis I to produce two haploid cells called secondary
spermatocytes. Each secondary spermatocyte divides after meiosis II to produce two cells called spermatids. The
spermatids eventually reach the lumen of the tubule and grow a flagellum, becoming sperm cells. Four sperm result
from each primary spermatocyte that goes through meiosis.

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 18.3 • Human Reproduction 485

FIGURE 18.14 During spermatogenesis, four sperm result from each primary spermatocyte. The process also maps onto the physical
structure of the wall of the seminiferous tubule, with the spermatogonia on the outer side of the tubule, and the sperm with their
developing tails extended into the lumen of the tubule.

LINK TO LEARNING
Visit this site (http://openstax.org/l/spermatogenes2) to see the process of spermatogenesis.

Oogenesis
Oogenesis occurs in the outermost layers of the ovaries. As with sperm production, oogenesis starts with a germ
cell. In oogenesis, this germ cell is called an oogonium and forms during the embryological development of the
individual. The oogonium undergoes mitosis to produce about one to two million oocytes by the time of birth.
486 18 • Animal Reproduction and Development

FIGURE 18.15 The process of oogenesis occurs in the ovary’s outermost layer.

The primary oocytes begin meiosis before birth (Figure 18.15). However, the meiotic division is arrested in its
progress in the first prophase stage. At the time of birth, all future eggs are in prophase I. This situation is in contrast
with the testicular reproductive system in which sperm are produced continuously throughout the life of the
individual. Starting at adolescence, anterior pituitary hormones cause the development of a few follicles in an ovary
each month. This results in a primary oocyte finishing the first meiotic division. The cell divides unequally, with most
of the cytoplasm and organelles going to one cell, called a secondary oocyte, and only one set of chromosomes and
a small amount of cytoplasm going to the other cell. This second cell is called a polar body and usually dies. Cell
division is again arrested, this time at metaphase II. At ovulation, this secondary oocyte is released and travels
toward the uterus through the oviduct. If the secondary oocyte is fertilized, the cell continues through meiosis II,
producing a second polar body and haploid egg, which fuses with the haploid sperm to form a fertilized egg (zygote)
containing all 46 chromosomes.

Hormonal Control of Reproduction

The human reproductive cycles are controlled by the interaction of hormones from the hypothalamus and anterior
pituitary with hormones from reproductive tissues and organs. The hypothalamus monitors and causes the release
of hormones from the anterior pituitary gland. When the reproductive hormone is required, the hypothalamus sends
a gonadotropin-releasing hormone (GnRH) to the anterior pituitary. This causes the release of follicle stimulating
hormone (FSH) and luteinizing hormone (LH) from the anterior pituitary into the blood. Although these hormones
are named after their functions in female reproduction, they are produced in both sexes and play important roles in
controlling reproduction. Other hormones have specific functions in the male and female reproductive systems.

Male Hormones
At the onset of puberty, the hypothalamus causes the release of FSH and LH into the male system for the first time.
FSH enters the testes and stimulates the Sertoli cells located in the walls of the seminiferous tubules to begin
promoting spermatogenesis (Figure 18.16). LH also enters the testes and stimulates the interstitial cells of Leydig,
located in between the walls of the seminiferous tubules, to make and release testosterone into the testes and the
blood.

Testosterone stimulates spermatogenesis. During adolescence, this hormone is also responsible for a deepening of
the voice, the growth of facial, axillary, and pubic hair, an increase in muscle bulk, and the beginnings of the sex
drive.

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 18.3 • Human Reproduction 487

FIGURE 18.16 Hormones control sperm production in a negative feedback system.

A negative feedback system occurs in the male with rising levels of testosterone acting on the hypothalamus and
anterior pituitary to inhibit the release of GnRH, FSH, and LH. In addition, the Sertoli cells produce the hormone
inhibin, which is released into the blood when the sperm count is too high. This inhibits the release of GnRH and
FSH, which will cause spermatogenesis to slow down. If the sperm count reaches a low of 20 million/mL, the Sertoli
cells cease the release of inhibin, and the sperm count increases.

Female Hormones
The control of reproduction in females is more complex. The female reproductive cycle is divided into the ovarian
cycle and the menstrual cycle. The ovarian cycle governs the preparation of endocrine tissues and release of eggs,
while the menstrual cycle governs the preparation and maintenance of the uterine lining (Figure 18.17). These
cycles are coordinated over a 22–32 day cycle, with an average length of 28 days.

As with the male, the GnRH from the hypothalamus causes the release of the hormones FSH and LH from the
anterior pituitary. In addition, estrogen and progesterone are released from the developing follicles. As with
testosterone in males, estrogen is responsible for the secondary sexual characteristics of females. These include
breast development, flaring of the hips, and a shorter period for bone growth.

The Ovarian Cycle and the Menstrual Cycle

The ovarian and menstrual cycles are regulated by hormones of the hypothalamus, pituitary, and ovaries (Figure
18.17). The ebb and flow of the hormones causes the ovarian and menstrual cycles to advance. The ovarian and
menstrual cycles occur concurrently. The first half of the ovarian cycle is the follicular phase. Slowly rising levels of
FSH cause the growth of follicles on the surface of the ovary. This process prepares the egg for ovulation. As the
follicles grow, they begin releasing estrogen. The first few days of this cycle coincide with menstruation or the
sloughing off of the functional layer of the endometrium in the uterus. After about five days, estrogen levels rise and
the menstrual cycle enters the proliferative phase. The endometrium begins to regrow, replacing the blood vessels
and glands that deteriorated during the end of the last cycle.
488 18 • Animal Reproduction and Development

VISUAL CONNECTION

FIGURE 18.17 The ovarian and menstrual cycles of reproduction are regulated by hormones produced by the hypothalamus, pituitary, and
ovaries.

Which of the following statements about hormone regulation of the ovarian and menstrual cycle is false?

a. LH and FSH are produced in the pituitary, and estrogen and progesterone are produced in the ovaries.
b. Estradiol and progesterone secreted from the corpus luteum cause the endometrium to thicken.
c. Both progesterone and estrogen are produced by the follicles.
d. Secretion of GnRH by the hypothalamus is inhibited by low levels of estrogen but stimulated by high levels of
estrogen.

Just prior to the middle of the cycle (approximately day 14), the high level of estrogen causes FSH and especially LH
to rise rapidly then fall. The spike in LH causes the most mature follicle to rupture and release its egg. This is
ovulation. The follicles that did not rupture degenerate and their eggs are lost. The level of estrogen decreases
when the extra follicles degenerate.

Following ovulation, the ovarian cycle enters its luteal phase and the menstrual cycle enters its secretory phase,
both of which run from about day 15 to 28. The luteal and secretory phases refer to changes in the ruptured follicle.
The cells in the follicle undergo physical changes and produce a structure called a corpus luteum. The corpus
luteum produces estrogen and progesterone. The progesterone facilitates the regrowth of the uterine lining and

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 18.3 • Human Reproduction 489

inhibits the release of further FSH and LH. The uterus is being prepared to accept a fertilized egg, should it occur
during this cycle. The inhibition of FSH and LH prevents any further eggs and follicles from developing, while the
progesterone is elevated. The level of estrogen produced by the corpus luteum increases to a steady level for the
next few days.

If no fertilized egg is implanted into the uterus, the corpus luteum degenerates and the levels of estrogen and
progesterone decrease. The endometrium begins to degenerate as the progesterone levels drop, initiating the next
menstrual cycle. The decrease in progesterone also allows the hypothalamus to send GnRH to the anterior pituitary,
releasing FSH and LH and starting the cycles again.

CAREER CONNECTION

Reproductive Endocrinologist
A reproductive endocrinologist is a physician who treats a variety of hormonal disorders related to reproduction and
infertility in people of any gender. The disorders include menstrual problems, infertility, pregnancy loss, sexual
dysfunction, and menopause. Doctors may use fertility drugs, surgery, or assisted reproductive techniques (ART) in
their therapy. ART involves the use of procedures to manipulate the egg or sperm to facilitate reproduction, such as
in vitro fertilization.

Reproductive endocrinologists undergo extensive medical training, first in a four-year residency in obstetrics and
gynecology, then in a three-year fellowship in reproductive endocrinology. To be board certified in this area, the
physician must pass written and oral exams in both areas.

Gestation
Pregnancy begins with the fertilization of an egg and continues through to the birth of the individual. The length of
time of gestation, or the gestation period, in humans is 266 days and is similar in other great apes.

Within 24 hours of fertilization, the egg nucleus has finished meiosis and the egg and sperm nuclei fuse. With fusion,
the cell is known as a zygote. The zygote initiates cleavage and the developing embryo travels through the oviduct to
the uterus. The developing embryo must implant into the wall of the uterus within seven days, or it will deteriorate
and die. The outer layers of the developing embryo or blastocyst grow into the endometrium by digesting the
endometrial cells, and healing of the endometrium closes up the blastocyst into the tissue. Another layer of the
blastocyst, the chorion, begins releasing a hormone called human beta chorionic gonadotropin (β-HCG), which
makes its way to the corpus luteum and keeps that structure active. This ensures adequate levels of progesterone
that will maintain the endometrium of the uterus for the support of the developing embryo. Pregnancy tests
determine the level of β-HCG in urine or serum. If the hormone is present, the test is positive.

The gestation period is divided into three equal periods or trimesters. During the first two-to-four weeks of the first
trimester, nutrition and waste are handled by the endometrial lining through diffusion. As the trimester progresses,
the outer layer of the embryo begins to merge with the endometrium, and the placenta forms. The placenta takes
over the nutrient and waste requirements of the embryo and fetus, with the gestational parent’s blood passing
nutrients to the placenta and removing waste from it. Chemicals from the fetus, such as bilirubin, are processed by
the gestational parent’s liver for elimination. Some of the pregnant person’s immunoglobulins will pass through the
placenta, providing passive immunity against some potential infections.

Internal organs and body structures begin to develop during the first trimester. By five weeks, limb buds, eyes, the
heart, and liver have been basically formed. By eight weeks, the term fetus applies, and the body is essentially
formed (Figure 18.18a). The individual is about five centimeters (two inches) in length and many of the organs, such
as the lungs and liver, are not yet functioning. Exposure to any toxins is especially dangerous during the first
trimester, as all of the body’s organs and structures are going through initial development. Anything that interferes
with chemical signaling during that development can have a severe effect on the fetus’ survival.
490 18 • Animal Reproduction and Development

FIGURE 18.18 (a) Fetal development is shown at nine weeks gestation. (b) This fetus is just entering the second trimester, when the
placenta takes over more of the functions performed as the baby develops. (c) There is rapid fetal growth during the third trimester. (credit
a: modification of work by Ed Uthman; credit b: modification of work by National Museum of Health and Medicine; credit c: modification of
work by Gray’s Anatomy)

During the second trimester, the fetus grows to about 30 cm (about 12 inches) (Figure 18.18b). It becomes active
and the pregnant person usually feels the first movements. All organs and structures continue to develop. The
placenta has taken over the functions of nutrition and waste elimination and the production of estrogen and
progesterone from the corpus luteum, which has degenerated. The placenta will continue functioning up through
the delivery of the baby. During the third trimester, the fetus grows to 3 to 4 kg (6.5–8.5 lbs.) and about 50 cm
(19–20 inches) long (Figure 18.18c). This is the period of the most rapid growth during the pregnancy as all organ
systems continue to grow and develop.

LINK TO LEARNING
Visit this website (http://openstax.org/l/embryo_fetus2) to see the stages of human fetal development.

Labor is the muscular contractions to expel the fetus and placenta from the uterus. Toward the end of the third
trimester, estrogen causes receptors on the uterine wall to develop and bind the hormone oxytocin. At this time, the
baby reorients, facing forward and down with the back or crown of the head engaging the cervix (uterine opening).
This causes the cervix to stretch and nerve impulses are sent to the hypothalamus, which signals the release of
oxytocin from the posterior pituitary. Oxytocin causes smooth muscle in the uterine wall to contract. At the same
time, the placenta releases prostaglandins into the uterus, increasing the contractions. A positive feedback relay
occurs between the uterus, hypothalamus, and the posterior pituitary to assure an adequate supply of oxytocin. As
more smooth muscle cells are recruited, the contractions increase in intensity and force.

There are three stages to labor. During stage one, the cervix thins and dilates. This is necessary for the baby and
placenta to be expelled during birth. The cervix will eventually dilate to about 10 cm. During stage two, the baby is
expelled from the uterus. The uterus contracts and, in most cases, the person giving birth pushes as they compress
the abdominal muscles to aid the delivery. The last stage is the passage of the placenta after the baby has been
born and the organ has completely disengaged from the uterine wall. If labor should stop before stage two is
reached, synthetic oxytocin, known as Pitocin, can be administered to restart and maintain labor.

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 18 • Key Terms 491

Key Terms
asexual reproduction a mechanism that produces inhibin a hormone made by Sertoli cells, provides
offspring that are genetically identical to the parent negative feedback to hypothalamus in control of
blastocyst the structure formed when cells in the FSH and GnRH release
mammalian blastula separate into an inner and inner cell mass the inner layer of cells in the
outer layer blastocyst, which becomes the embryo
budding a form of asexual reproduction that results internal fertilization the fertilization of eggs by
from the outgrowth of a part of an organism leading sperm inside the body of the female
to a separation from the original animal into two interstitial cell of Leydig a cell type found next to the
individuals seminiferous tubules that makes testosterone
bulbourethral gland the paired glands in the human labia majora the large folds of tissue covering
male that produce a secretion that cleanses the inguinal area
urethra prior to ejaculation labia minora the smaller folds of tissue within labia
clitoris a sensory and erectile structure in female majora
mammals, homologous to the male penis, luteinizing hormone (LH) a reproductive hormone
stimulated during sexual arousal that causes testosterone production in males and
corpus luteum the endocrine tissue that develops ovulation and lactation in females
from an ovarian follicle after ovulation; secretes menstrual cycle the cycle of the degradation and re-
progesterone and estrogen during pregnancy growth of the endometrium
estrogen a reproductive hormone, usually present in oogenesis the process of producing haploid eggs
animals of any sex, which in females assists in organogenesis the process of organ formation during
endometrial regrowth, ovulation, and calcium development
absorption ovarian cycle the cycle of preparation of egg for
external fertilization the fertilization of eggs by ovulation and the conversion of the follicle to the
sperm outside an animal’s body, often during corpus luteum
spawning oviduct (also, fallopian tube) the muscular tube
fission (also, binary fission) a form of asexual connecting uterus with ovary area
reproduction in which an organism splits into two oviparity a process by which fertilized eggs are laid
separate organisms or two parts that regenerate the outside the female’s body and develop there,
missing portions of the body receiving nourishment from the yolk that is a part of
follicle stimulating hormone (FSH) a reproductive the egg
hormone that causes sperm production in males ovoviparity a process by which fertilized eggs are
and follicle development in females retained within the female; the embryo obtains its
fragmentation the breaking of an organism into parts nourishment from the egg’s yolk, and the young are
and the growth of a separate individual from each fully developed when they are hatched
part ovulation the release of an oocyte from a mature
gastrulation the process in which the blastula folds follicle in the ovary of a vertebrate
over itself to form the three germ layers parthenogenesis a form of asexual reproduction in
gestation the development before birth of a which an egg develops into a complete individual
viviparous animal without being fertilized
gestation period the length of time of development, penis the male reproductive structure for urine
from conception to birth, of the young of a elimination and copulation
viviparous animal placenta the organ that supports the transport of
gonadotropin-releasing hormone (GnRH) a hormone nutrients and waste between the mothers and fetus’
from the hypothalamus that causes the release of blood in eutherian mammals
FSH and LH from the anterior pituitary progesterone a reproductive hormone in usually
hermaphroditism the state of having both male and present in animals of any sex; in human females it
female reproductive structures within the same assists in endometrial regrowth and inhibition of
individual FSH and LH release
human beta chorionic gonadotropin (β-HCG) a prostate gland a structure that is a mixture of
hormone produced by the chorion of the zygote that smooth muscle and glandular material and that
helps to maintain the corpus luteum and elevated contributes to semen
levels of progesterone scrotum a sac containing testes, exterior to body
492 18 • Chapter Summary

semen a fluid mixture of sperm and supporting testes a pair of male reproductive organs
materials testosterone a reproductive hormone usually present
seminal vesicle a secretory accessory gland in male; in animals of any sex, and that assists in sperm
contributes to semen production and promoting secondary sexual
seminiferous tubule the structures within which characteristics
sperm production occurs in the testes trophoblast the outer layer of cells in the blastocyst,
Sertoli cell a cell in the walls of the seminiferous which gives rise to the embryo’s contribution to the
tubules that assists developing sperm and secretes placenta
inhibin uterus a female reproductive structure in which an
sex determination the mechanism by which the sex embryo develops
of individuals in sexually reproducing organisms is vagina a muscular tube for the passage of menstrual
initially established flow, copulation, and birth of offspring
sexual reproduction a form of reproduction in which viviparity a process in which the young develop
cells containing genetic material from two within the female and are born in a nonembryonic
individuals combines to produce genetically unique state
offspring zona pellucida the protective layer around the
spermatogenesis the process of producing haploid mammalian egg
sperm

Chapter Summary
18.1 How Animals Reproduce process called gastrulation, during which the three
germ layers form. The ectoderm gives rise to the
Reproduction may be asexual when one individual
nervous system and the epidermal skin cells, the
produces genetically identical offspring, or sexual
mesoderm gives rise to the muscle cells and
when the genetic material from two individuals is
connective tissue in the body, and the endoderm gives
combined to produce genetically diverse offspring.
rise to the digestive system and other internal organs.
Asexual reproduction in animals occurs through fission,
Organogenesis is the formation of organs from the
budding, fragmentation, and parthenogenesis. Sexual
germ layers. Each germ layer gives rise to specific
reproduction may involve fertilization inside the body
tissue types.
or in the external environment. A species may have
separate sexes or combined sexes; when the sexes are 18.3 Human Reproduction
combined they may be expressed at different times in
The reproductive structures that evolved in land
the life cycle. The sex of an individual may be
animals allow them to mate, fertilize internally, and
determined by various chromosomal systems or
support the growth and development of offspring.
environmental factors such as temperature.
Gametogenesis, the production of sperm
Sexual reproduction starts with the combination of a (spermatogenesis) and eggs (oogenesis), takes place
sperm and an egg in a process called fertilization. This through the process of meiosis.
can occur either outside the bodies or inside the
The reproductive cycles are controlled by hormones
female. The method of fertilization varies among
released from the hypothalamus and anterior pituitary
animals. Some species release the egg and sperm into
and hormones from reproductive tissues and organs.
the environment, some species retain the egg and
The hypothalamus monitors the need for FSH and LH
receive the sperm into the female body and then expel
production and release from the anterior pituitary. FSH
the developing embryo covered with shell, while still
and LH affect reproductive structures to cause the
other species retain the developing offspring
formation of sperm and the preparation of eggs for
throughout the gestation period.
release and possible fertilization. In the male, FSH and
18.2 Development and Organogenesis LH stimulate Sertoli cells and interstitial cells of Leydig
in the testes to facilitate sperm production. The Leydig
The early stages of embryonic development begin with
cells produce testosterone, which in human males is
fertilization. The process of fertilization is tightly
also responsible for a deepening of the voice, the
controlled to ensure that only one sperm fuses with
growth of facial, axillary, and pubic hair, and an
one egg. After fertilization, the zygote undergoes
increase in muscle bulk. In females, FSH and LH cause
cleavage to form the blastula. The blastula, which in
estrogen and progesterone to be produced. They
some species is a hollow ball of cells, undergoes a
regulate the female reproductive cycle, which is

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 18 • Visual Connection Questions 493

divided into the ovarian cycle and the menstrual cycle. of all of the organs and systems. The third trimester
exhibits the greatest growth of the fetus and
Human pregnancy begins with fertilization of an egg
culminates in labor and delivery. The labor process has
and proceeds through the three trimesters of gestation.
three stages (contractions, delivery of the fetus, and
The first trimester lays down the basic structures of the
expulsion of the placenta), each propelled by
body, including the limb buds, heart, eyes, and the
hormones.
liver. The second trimester continues the development

Visual Connection Questions

1. Figure 18.12 Which of the following statements 2. Figure 18.17 Which of the following statements
about the testicular reproductive system is false? about hormone regulation of the ovarian and
a. The vas deferens carries sperm from the testes menstrual reproductive cycles is false?
to the seminal vesicles. a. LH and FSH are produced in the pituitary, and
b. The ejaculatory duct joins the urethra. estrogen and progesterone are produced in the
c. Both the prostate and the bulbourethral glands ovaries.
produce components of the semen. b. Estradiol and progesterone secreted from the
d. The prostate gland is located in the testes. corpus luteum cause the endometrium to
thicken.
c. Both progesterone and estrogen are produced
by the follicles.
d. Secretion of GnRH by the hypothalamus is
inhibited by low levels of estrogen but
stimulated by high levels of estrogen.

Review Questions
3. In which group is parthenogenesis a normal event? 7. Which of the following gives rise to the skin cells?
a. chickens a. ectoderm
b. bees b. endoderm
c. rabbits c. mesoderm
d. sea stars d. none of the above

4. Genetically unique individuals are produced 8. Sperm are produced in the ________.
through ________. a. scrotum
a. sexual reproduction b. seminal vesicles
b. parthenogenesis c. seminiferous tubules
c. budding d. prostate gland
d. fragmentation
9. Which organ has an endometrial lining that will
5. External fertilization occurs in which type of support a developing baby?
environment? a. labia minora
a. aquatic b. breast
b. forested c. ovaries
c. savanna d. uterus
d. steppe
10. Which hormone causes FSH and LH to be
6. The process of gastrulation forms the _______. released?
a. blastula a. testosterone
b. zygote b. estrogen
c. organs c. GnRH
d. germ layers d. progesterone
494 18 • Critical Thinking Questions

11. Nutrient and waste requirements for the 12. Which hormone is primarily responsible for the
developing fetus are handled during the first few contractions during labor?
weeks by ________. a. oxytocin
a. the placenta b. estrogen
b. diffusion through the endometrium c. β-HCG
c. the chorion d. progesterone
d. the blastocyst

Critical Thinking Questions

13. What might be a disadvantage to temperature- 16. Compare spermatogenesis and oogenesis as to
dependent sex determination? timing of the processes, and the number and type
of cells finally produced.
14. Compared to separate sexes and assuming self-
fertilizing is not possible, what might be one 17. Describe the events in the ovarian cycle leading up
advantage and one disadvantage to to ovulation.
hermaphroditism?
18. Describe the stages of labor.
15. What do you think would happen if multiple sperm
fused with one egg?

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CHAPTER 19
Population and Community Ecology

FIGURE 19.1 Asian carp jump out of the water in response to electrofishing. The Asian carp in the inset photograph
were harvested from the Little Calumet River in Illinois in May, 2010, using rotenone, a toxin often used as an
insecticide, in an effort to learn more about the population of the species. (credit main image: modification of work by
USGS; credit inset: modification of work by Lt. David French, USCG)

CHAPTER OUTLINE
19.1 Population Demographics and Dynamics
19.2 Population Growth and Regulation
19.3 The Human Population
19.4 Community Ecology

INTRODUCTION Imagine sailing down a river in a small motorboat on a weekend afternoon; the
water is smooth, and you are enjoying the sunshine and cool breeze when suddenly you are hit in
the head by a 20-pound silver carp. This is a risk now on many rivers and canal systems in Illinois
and Missouri because of the presence of Asian carp.

This fish—actually a group of species including the silver, black, grass, and big head carp—has
been farmed and eaten in China for over 1,000 years. It is one of the most important aquaculture
food resources worldwide. In the United States, however, Asian carp is considered a dangerous
invasive species that disrupts ecological community structure to the point of threatening native
species.

The effects of invasive species (such as the Asian carp, kudzu vine, predatory snakehead fish, and
zebra mussel) are just one aspect of what ecologists study to understand how populations interact
within ecological communities, and what impact natural and human-induced disturbances have
on the characteristics of communities.
496 19 • Population and Community Ecology

19.1 Population Demographics and Dynamics

LEARNING OBJECTIVES
By the end of this section, you will be able to:
• Describe how ecologists measure population size and density
• Describe three different patterns of population distribution
• Use life tables to calculate mortality rates
• Describe the three types of survivorship curves and relate them to specific populations

Populations are dynamic entities. Their size and composition fluctuate in response to numerous
factors, including seasonal and yearly changes in the environment, natural disasters such as forest
fires and volcanic eruptions, and competition for resources between and within species. The
statistical study of populations is called demography: a set of mathematical tools designed to
describe populations and investigate how they change. Many of these tools were actually designed
to study human populations. For example, life tables, which detail the life expectancy of
individuals within a population, were initially developed by life insurance companies to set
insurance rates. In fact, while the term “demographics” is sometimes assumed to mean a study of
human populations, all living populations can be studied using this approach.

Population Size and Density

Populations are characterized by their population size (total number of individuals) and their
population density (number of individuals per unit area). A population may have a large number
of individuals that are distributed densely, or sparsely. There are also populations with small
numbers of individuals that may be dense or very sparsely distributed in a local area. Population
size can affect potential for adaptation because it affects the amount of genetic variation present
in the population. Density can have effects on interactions within a population such as competition
for food and the ability of individuals to find a mate. Smaller organisms tend to be more densely
distributed than larger organisms (Figure 19.2).

VISUAL CONNECTION

FIGURE 19.2 Australian mammals show a typical inverse relationship between population density and body size.

As this graph shows, population density typically decreases with increasing body size. Why do you
think this is the case?

Estimating Population Size

The most accurate way to determine population size is to count all of the individuals within the

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 19.1 • Population Demographics and Dynamics 497

area. However, this method is usually not logistically or economically feasible, especially when studying large areas.
Thus, scientists usually study populations by sampling a representative portion of each habitat and use this sample
to make inferences about the population as a whole. The methods used to sample populations to determine their
size and density are typically tailored to the characteristics of the organism being studied. For immobile organisms
such as plants, or for very small and slow-moving organisms, a quadrat may be used. A quadrat is a wood, plastic,
or metal square that is randomly located on the ground and used to count the number of individuals that lie within
its boundaries. To obtain an accurate count using this method, the square must be placed at random locations
within the habitat enough times to produce an accurate estimate. This counting method will provide an estimate of
both population size and density. The number and size of quadrat samples depends on the type of organisms and
the nature of their distribution.

For smaller mobile organisms, such as mammals, a technique called mark and recapture is often used. This
method involves marking a sample of captured animals in some way and releasing them back into the environment
to mix with the rest of the population; then, a new sample is captured and scientists determine how many of the
marked animals are in the new sample. This method assumes that the larger the population, the lower the
percentage of marked organisms that will be recaptured since they will have mixed with more unmarked individuals.
For example, if 80 field mice are captured, marked, and released into the forest, then a second trapping 100 field
mice are captured and 20 of them are marked, the population size (N) can be determined using the following
equation:

Using our example, the population size would be 400.

These results give us an estimate of 400 total individuals in the original population. The true number usually will be
a bit different from this because of chance errors and possible bias caused by the sampling methods.

Species Distribution
In addition to measuring density, further information about a population can be obtained by looking at the
distribution of the individuals throughout their range. A species distribution pattern is the distribution of individuals
within a habitat at a particular point in time—broad categories of patterns are used to describe them.

Individuals within a population can be distributed at random, in groups, or equally spaced apart (more or less).
These are known as random, clumped, and uniform distribution patterns, respectively (Figure 19.3). Different
distributions reflect important aspects of the biology of the species; they also affect the mathematical methods
required to estimate population sizes. An example of random distribution occurs with dandelion and other plants
that have wind-dispersed seeds that germinate wherever they happen to fall in favorable environments. A clumped
distribution, may be seen in plants that drop their seeds straight to the ground, such as oak trees; it can also be seen
in animals that live in social groups (schools of fish or herds of elephants). Uniform distribution is observed in plants
that secrete substances inhibiting the growth of nearby individuals (such as the release of toxic chemicals by sage
plants). It is also seen in territorial animal species, such as penguins that maintain a defined territory for nesting.
The territorial defensive behaviors of each individual create a regular pattern of distribution of similar-sized
territories and individuals within those territories. Thus, the distribution of the individuals within a population
provides more information about how they interact with each other than does a simple density measurement. Just
as lower density species might have more difficulty finding a mate, solitary species with a random distribution might
have a similar difficulty when compared to social species clumped together in groups.
498 19 • Population and Community Ecology

FIGURE 19.3 Species may have a random, clumped, or uniform distribution. Plants such as (a) dandelions with wind-dispersed seeds tend
to be randomly distributed. Animals such as (b) elephants that travel in groups exhibit a clumped distribution. Territorial birds such as (c)
penguins tend to have a uniform distribution. (credit a: modification of work by Rosendahl; credit b: modification of work by Rebecca Wood;
credit c: modification of work by Ben Tubby)

Demography
While population size and density describe a population at one particular point in time, scientists must use
demography to study the dynamics of a population. Demography is the statistical study of population changes over
time: birth rates, death rates, and life expectancies. These population characteristics are often displayed in a life
table.

Life Tables
Life tables provide important information about the life history of an organism and the life expectancy of individuals
at each age. They are modeled after actuarial tables used by the insurance industry for estimating human life
expectancy. Life tables may include the probability of each age group dying before their next birthday, the
percentage of surviving individuals dying at a particular age interval (their mortality rate, and their life expectancy
at each interval. An example of a life table is shown in Table 19.1 from a study of Dall mountain sheep, a species
native to northwestern North America. Notice that the population is divided into age intervals (column A). The
mortality rate (per 1000) shown in column D is based on the number of individuals dying during the age interval
(column B), divided by the number of individuals surviving at the beginning of the interval (Column C) multiplied by
1000.

For example, between ages three and four, 12 individuals die out of the 776 that were remaining from the original
1000 sheep. This number is then multiplied by 1000 to give the mortality rate per thousand.

As can be seen from the mortality rate data (column D), a high death rate occurred when the sheep were between
six months and a year old, and then increased even more from 8 to 12 years old, after which there were few
survivors. The data indicate that if a sheep in this population were to survive to age one, it could be expected to live
another 7.7 years on average, as shown by the life-expectancy numbers in column E.

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 19.1 • Population Demographics and Dynamics 499

1
Life Table of Dall Mountain Sheep

A B C D E

Number dying Number surviving at Mortality rate per

Age Life expectancy or mean
in age interval beginning of age 1000 alive at
interval lifetime remaining to those
out of 1000 interval out of 1000 beginning of age
(years) attaining age interval
born born interval

0–0.5 54 1000 54.0 7.06

0.5–1 145 946 153.3 —

1–2 12 801 15.0 7.7

2–3 13 789 16.5 6.8

3–4 12 776 15.5 5.9

4–5 30 764 39.3 5.0

5–6 46 734 62.7 4.2

6–7 48 688 69.8 3.4

7–8 69 640 107.8 2.6

8–9 132 571 231.2 1.9

9–10 187 439 426.0 1.3

10–11 156 252 619.0 0.9

11–12 90 96 937.5 0.6

12–13 3 6 500.0 1.2

13–14 3 3 1000 0.7

TABLE 19.1 This life table of Ovis dalli shows the number of deaths, number of survivors, mortality rate, and life expectancy at each age
interval for Dall mountain sheep.

Survivorship Curves
Another tool used by population ecologists is a survivorship curve, which is a graph of the number of individuals
surviving at each age interval versus time. These curves allow us to compare the life histories of different
populations (Figure 19.4). There are three types of survivorship curves. In a type I curve, mortality is low in the early
and middle years and occurs mostly in older individuals. Organisms exhibiting a type I survivorship typically produce
few offspring and provide good care to the offspring increasing the likelihood of their survival. Humans and most
mammals exhibit a type I survivorship curve. In type II curves, mortality is relatively constant throughout the entire
life span, and mortality is equally likely to occur at any point in the life span. Many bird populations provide
examples of an intermediate or type II survivorship curve. In type III survivorship curves, early ages experience the
highest mortality with much lower mortality rates for organisms that make it to advanced years. Type III organisms

1 Data Adapted from Edward S. Deevey, Jr., “Life Tables for Natural Populations of Animals,” The Quarterly Review of Biology 22, no. 4
(December 1947): 283-314.
500 19 • Population and Community Ecology

typically produce large numbers of offspring, but provide very little or no care for them. Trees and marine
invertebrates exhibit a type III survivorship curve because very few of these organisms survive their younger years,
but those that do make it to an old age are more likely to survive for a relatively long period of time.

FIGURE 19.4 Survivorship curves show the distribution of individuals in a population according to age. Humans and most mammals have a
Type I survivorship curve, because death primarily occurs in the older years. Birds have a Type II survivorship curve, as death at any age is
equally probable. Trees have a Type III survivorship curve because very few survive the younger years, but after a certain age, individuals
are much more likely to survive.

19.2 Population Growth and Regulation

LEARNING OBJECTIVES
By the end of this section, you will be able to:
• Explain the characteristics of and differences between exponential and logistic growth patterns
• Give examples of exponential and logistic growth in natural populations
• Give examples of how the carrying capacity of a habitat may change
• Compare and contrast density-dependent growth regulation and density-independent growth regulation
giving examples

Population ecologists make use of a variety of methods to model population dynamics. An accurate model should be
able to describe the changes occurring in a population and predict future changes.

Population Growth
The two simplest models of population growth use deterministic equations (equations that do not account for
random events) to describe the rate of change in the size of a population over time. The first of these models,
exponential growth, describes theoretical populations that increase in numbers without any limits to their growth.
The second model, logistic growth, introduces limits to reproductive growth that become more intense as the
population size increases. Neither model adequately describes natural populations, but they provide points of
comparison.

Exponential Growth
Charles Darwin, in his theory of natural selection, was greatly influenced by the English clergyman Thomas Malthus.
Malthus published a book in 1798 stating that populations with unlimited natural resources grow very rapidly, which
represents an exponential growth, and then population growth decreases as resources become depleted,
indicating a logistic growth.

The best example of exponential growth in organisms is seen in bacteria. Bacteria are prokaryotes that reproduce
largely by binary fission. This division takes about an hour for many bacterial species. If 1000 bacteria are placed in
a large flask with an abundant supply of nutrients (so the nutrients will not become quickly depleted), the number of
bacteria will have doubled from 1000 to 2000 after just an hour. In another hour, each of the 2000 bacteria will

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 19.2 • Population Growth and Regulation 501

divide, producing 4000 bacteria. After the third hour, there should be 8000 bacteria in the flask. The important
concept of exponential growth is that the growth rate—the number of organisms added in each reproductive
generation—is itself increasing; that is, the population size is increasing at a greater and greater rate. After 24 of
these cycles, the population would have increased from 1000 to more than 16 billion bacteria. When the population
size, N, is plotted over time, a J-shaped growth curve is produced (Figure 19.5a).

The bacteria-in-a-flask example is not truly representative of the real world where resources are usually limited.
However, when a species is introduced into a new habitat that it finds suitable, it may show exponential growth for a
while. In the case of the bacteria in the flask, some bacteria will die during the experiment and thus not reproduce;
therefore, the growth rate is lowered from a maximal rate in which there is no mortality. The growth rate of a
population is largely determined by subtracting the death rate, D, (number organisms that die during an interval)
from the birth rate, B, (number organisms that are born during an interval). The growth rate can be expressed in a
simple equation that combines the birth and death rates into a single factor: r. This is shown in the following
formula:

The value of r can be positive, meaning the population is increasing in size (the rate of change is positive); or
negative, meaning the population is decreasing in size; or zero, in which case the population size is unchanging, a
condition known as zero population growth.

Logistic Growth
Extended exponential growth is possible only when infinite natural resources are available; this is not the case in the
real world. Charles Darwin recognized this fact in his description of the “struggle for existence,” which states that
individuals will compete (with members of their own or other species) for limited resources. The successful ones are
more likely to survive and pass on the traits that made them successful to the next generation at a greater rate
(natural selection). To model the reality of limited resources, population ecologists developed the logistic growth
model.

Carrying Capacity and the Logistic Model

In the real world, with its limited resources, exponential growth cannot continue indefinitely. Exponential growth
may occur in environments where there are few individuals and plentiful resources, but when the number of
individuals gets large enough, resources will be depleted and the growth rate will slow down. Eventually, the growth
rate will plateau or level off (Figure 19.5b). This population size, which is determined by the maximum population
size that a particular environment can sustain, is called the carrying capacity, or K. In real populations, a growing
population often overshoots its carrying capacity, and the death rate increases beyond the birth rate causing the
population size to decline back to the carrying capacity or below it. Most populations usually fluctuate around the
carrying capacity in an undulating fashion rather than existing right at it.

The formula used to calculate logistic growth adds the carrying capacity as a moderating force in the growth rate.
The expression “K – N” is equal to the number of individuals that may be added to a population at a given time, and
“K – N” divided by “K” is the fraction of the carrying capacity available for further growth. Thus, the exponential
growth model is restricted by this factor to generate the logistic growth equation:

Notice that when N is almost zero the quantity in brackets is almost equal to 1 (or K/K) and growth is close to
exponential. When the population size is equal to the carrying capacity, or N = K, the quantity in brackets is equal to
zero and growth is equal to zero. A graph of this equation (logistic growth) yields the S-shaped curve (Figure 19.5b).
It is a more realistic model of population growth than exponential growth. There are three different sections to an S-
shaped curve. Initially, growth is exponential because there are few individuals and ample resources available.
Then, as resources begin to become limited, the growth rate decreases. Finally, the growth rate levels off at the
carrying capacity of the environment, with little change in population number over time.
502 19 • Population and Community Ecology

FIGURE 19.5 When resources are unlimited, populations exhibit (a) exponential growth, shown in a J-shaped curve. When resources are
limited, populations exhibit (b) logistic growth. In logistic growth, population expansion decreases as resources become scarce, and it
levels off when the carrying capacity of the environment is reached. The logistic growth curve is S-shaped.

Role of Intraspecific Competition

The logistic model assumes that every individual within a population will have equal access to resources and, thus,
an equal chance for survival. For plants, the amount of water, sunlight, nutrients, and space to grow are the
important resources, whereas in animals, important resources include food, water, shelter, nesting space, and
mates.

In the real world, phenotypic variation among individuals within a population means that some individuals will be
better adapted to their environment than others. The resulting competition for resources among population
members of the same species is termed intraspecific competition. Intraspecific competition may not affect
populations that are well below their carrying capacity, as resources are plentiful and all individuals can obtain what
they need. However, as population size increases, this competition intensifies. In addition, the accumulation of
waste products can reduce carrying capacity in an environment.

Examples of Logistic Growth

Yeast, a microscopic fungus used to make bread and alcoholic beverages, exhibits the classical S-shaped curve
when grown in a test tube (Figure 19.6a). Its growth levels off as the population depletes the nutrients that are
necessary for its growth. In the real world, however, there are variations to this idealized curve. Examples in wild
populations include sheep and harbor seals (Figure 19.6b). In both examples, the population size exceeds the
carrying capacity for short periods of time and then falls below the carrying capacity afterwards. This fluctuation in
population size continues to occur as the population oscillates around its carrying capacity. Still, even with this
oscillation, the logistic model is confirmed.

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 19.2 • Population Growth and Regulation 503

VISUAL CONNECTION

FIGURE 19.6 (a) Yeast grown in ideal conditions in a test tube shows a classical S-shaped logistic growth curve, whereas (b) a natural
population of seals shows real-world fluctuation. The yeast is visualized using differential interference contrast light micrography. (credit a:
scale-bar data from Matt Russell)

If the major food source of seals declines due to pollution or overfishing, which of the following would likely occur?

a. The carrying capacity of seals would decrease, as would the seal population.
b. The carrying capacity of seals would decrease, but the seal population would remain the same.
c. The number of seal deaths would increase, but the number of births would also increase, so the population size
would remain the same.
d. The carrying capacity of seals would remain the same, but the population of seals would decrease.

Population Dynamics and Regulation

The logistic model of population growth, while valid in many natural populations and a useful model, is a
simplification of real-world population dynamics. Implicit in the model is that the carrying capacity of the
environment does not change, which is not the case. The carrying capacity varies annually. For example, some
summers are hot and dry whereas others are cold and wet; in many areas, the carrying capacity during the winter is
much lower than it is during the summer. Also, natural events such as earthquakes, volcanoes, and fires can alter an
environment and hence its carrying capacity. Additionally, populations do not usually exist in isolation. They share
the environment with other species, competing with them for the same resources (interspecific competition). These
factors are also important to understanding how a specific population will grow.
504 19 • Population and Community Ecology

Population growth is regulated in a variety of ways. These are grouped into density-dependent factors, in which the
density of the population affects growth rate and mortality, and density-independent factors, which cause mortality
in a population regardless of population density. Wildlife biologists, in particular, want to understand both types
because this helps them manage populations and prevent extinction or overpopulation.

Density-dependent Regulation
Most density-dependent factors are biological in nature and include predation, inter- and intraspecific competition,
and parasites. Usually, the denser a population is, the greater its mortality rate. For example, during intra- and
interspecific competition, the reproductive rates of the species will usually be lower, reducing their populations’ rate
of growth. In addition, low prey density increases the mortality of its predator because it has more difficulty locating
its food source. Also, when the population is denser, diseases spread more rapidly among the members of the
population, which affect the mortality rate.

Density dependent regulation was studied in a natural experiment with wild donkey populations on two sites in
2
Australia. On one site the population was reduced by a population control program; the population on the other
site received no interference. The high-density plot was twice as dense as the low-density plot. From 1986 to 1987
the high-density plot saw no change in donkey density, while the low-density plot saw an increase in donkey density.
The difference in the growth rates of the two populations was caused by mortality, not by a difference in birth rates.
The researchers found that numbers of offspring birthed by each mother was unaffected by density. Growth rates in
the two populations were different mostly because of juvenile mortality caused by the mother’s malnutrition due to
scarce high-quality food in the dense population. Figure 19.7 shows the difference in age-specific mortalities in the
two populations.

FIGURE 19.7 This graph shows the age-specific mortality rates for wild donkeys from high- and low-density populations. The juvenile
mortality is much higher in the high-density population because of maternal malnutrition caused by a shortage of high-quality food.

Density-independent Regulation and Interaction with Density-dependent Factors

Many factors that are typically physical in nature cause mortality of a population regardless of its density. These
factors include weather, natural disasters, and pollution. An individual deer will be killed in a forest fire regardless of
how many deer happen to be in that area. Its chances of survival are the same whether the population density is
high or low. The same holds true for cold winter weather.

In real-life situations, population regulation is very complicated and density-dependent and independent factors
can interact. A dense population that suffers mortality from a density-independent cause will be able to recover
differently than a sparse population. For example, a population of deer affected by a harsh winter will recover faster
if there are more deer remaining to reproduce.

2 David Choquenot, “Density-Dependent Growth, Body Condition, and Demography in Feral Donkeys: Testing the Food Hypothesis,”
Ecology 72, no. 3 (June 1991):805–813.

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 19.2 • Population Growth and Regulation 505

EVOLUTION CONNECTION

Why Did the Woolly Mammoth Go Extinct?

FIGURE 19.8 The three images include: (a) 1916 mural of a mammoth herd from the American Museum of Natural History, (b) the only
stuffed mammoth in the world is in the Museum of Zoology located in St. Petersburg, Russia, and (c) a one-month-old baby mammoth,
named Lyuba, discovered in Siberia in 2007. (credit a: modification of work by Charles R. Knight; credit b: modification of work by
“Tanapon”/Flickr; credit c: modification of work by Matt Howry)

Woolly mammoths began to go extinct about 10,000 years ago, soon after paleontologists believe humans able to
hunt them began to colonize North America and northern Eurasia (Figure 19.8). A mammoth population survived on
Wrangel Island, in the East Siberian Sea, and was isolated from human contact until as recently as 1700 BC. We
know a lot about these animals from carcasses found frozen in the ice of Siberia and other northern regions.

It is commonly thought that climate change and human hunting led to their extinction. A 2008 study estimated that
climate change reduced the mammoth’s range from 3,000,000 square miles 42,000 years ago to 310,000
3
square miles 6,000 years ago. Through archaeological evidence of kill sites, it is also well documented that
humans hunted these animals. A 2012 study concluded that no single factor was exclusively responsible for the
4
extinction of these magnificent creatures. In addition to climate change and reduction of habitat, scientists
demonstrated another important factor in the mammoth’s extinction was the migration of human hunters across the
Bering Strait to North America during the last ice age 20,000 years ago.

The maintenance of stable populations was and is very complex, with many interacting factors determining the
outcome. It is important to remember that humans are also part of nature. Once we contributed to a species’
decline using primitive hunting technology only.

Demographic-Based Population Models

Population ecologists have hypothesized that suites of characteristics may evolve in species that lead to particular
adaptations to their environments. These adaptations impact the kind of population growth their species

3 David Nogués-Bravo et al., “Climate Change, Humans, and the Extinction of the Woolly Mammoth.” PLoS Biol 6 (April 2008): e79,
doi:10.1371/journal.pbio.0060079.
4 G.M. MacDonald et al., “Pattern of Extinction of the Woolly Mammoth in Beringia.” Nature Communications 3, no. 893 (June 2012),
doi:10.1038/ncomms1881.
506 19 • Population and Community Ecology

experience. Life history characteristics such as birth rates, age at first reproduction, the numbers of offspring, and
even death rates evolve just like anatomy or behavior, leading to adaptations that affect population growth.
Population ecologists have described a continuum of life-history “strategies” with K-selected species on one end
and r-selected species on the other. K-selected species are adapted to stable, predictable environments.
Populations of K-selected species tend to exist close to their carrying capacity. These species tend to have larger,
but fewer, offspring and contribute large amounts of resources to each offspring. Elephants would be an example of
a K-selected species. r-selected species are adapted to unstable and unpredictable environments. They have large
numbers of small offspring. Animals that are r-selected do not provide a lot of resources or parental care to
offspring, and the offspring are relatively self-sufficient at birth. Examples of r-selected species are marine
invertebrates such as jellyfish and plants such as the dandelion. The two extreme strategies are at two ends of a
continuum on which real species life histories will exist. In addition, life history strategies do not need to evolve as
suites, but can evolve independently of each other, so each species may have some characteristics that trend
toward one extreme or the other.

19.3 The Human Population

LEARNING OBJECTIVES
By the end of this section, you will be able to:
• Discuss how human population growth can be exponential
• Explain how humans have expanded the carrying capacity of their habitat
• Relate population growth and age structure to the level of economic development in different countries
• Discuss the long-term implications of unchecked human population growth

Concepts of animal population dynamics can be applied to human population growth. Humans are not unique in
their ability to alter their environment. For example, beaver dams alter the stream environment where they are built.
Humans, however, have the ability to alter their environment to increase its carrying capacity, sometimes to the
detriment of other species. Earth’s human population and their use of resources are growing rapidly, to the extent
that some worry about the ability of Earth’s environment to sustain its human population. Long-term exponential
growth carries with it the potential risks of famine, disease, and large-scale death, as well as social consequences of
crowding such as increased crime.

Human technology and particularly our harnessing of the energy contained in fossil fuels have caused
unprecedented changes to Earth’s environment, altering ecosystems to the point where some may be in danger of
collapse. Changes on a global scale including depletion of the ozone layer, desertification and topsoil loss, and
global climate change are caused by human activities.

The world’s human population is presently growing exponentially (Figure 19.9).

FIGURE 19.9 Human population growth since 1000 AD is exponential.

A consequence of exponential growth rate is that the time that it takes to add a particular number of humans to the
population is becoming shorter. Figure 19.10 shows that 123 years were necessary to add 1 billion humans

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 19.3 • The Human Population 507

between 1804 and 1930, but it only took 24 years to add the two billion people between 1975 and 1999. This
acceleration in growth rate will likely begin to decrease in the coming decades. Despite this, the population will
continue to increase and the threat of overpopulation remains, particularly because the damage caused to
ecosystems and biodiversity is lowering the human carrying capacity of the planet.

FIGURE 19.10 The time between the addition of each billion human beings to Earth decreases over time. (credit: modification of work by
Ryan T. Cragun)

LINK TO LEARNING
Click through this video (http://openstax.org/l/human_growth2) of how human populations have changed over time.

Overcoming Density-Dependent Regulation

Humans are unique in their ability to alter their environment in myriad ways. This ability is responsible for human
population growth because it resets the carrying capacity and overcomes density-dependent growth regulation.
Much of this ability is related to human intelligence, society, and communication. Humans construct shelters to
protect themselves from the elements and have developed agriculture and domesticated animals to increase their
food supplies. In addition, humans use language to communicate this technology to new generations, allowing them
to improve upon previous accomplishments.

Other factors in human population growth are migration and public health. Humans originated in Africa, but we have
since migrated to nearly all inhabitable land on Earth, thus, increasing the area that we have colonized. Public
health, sanitation, and the use of antibiotics and vaccines have decreased the ability of infectious disease to limit
human population growth in developed countries. In the past, diseases such as the bubonic plaque of the
fourteenth century killed between 30 and 60 percent of Europe’s population and reduced the overall world
population by as many as one hundred million people. Infectious disease continues to have an impact on human
population growth. For example, life expectancy in sub-Saharan Africa, which was increasing from 1950 to 1990,
began to decline after 1985 largely as a result of HIV/AIDS mortality. The reduction in life expectancy caused by
5
HIV/AIDS was estimated to be 7 years for 2005.

Declining life expectancy is an indicator of higher mortality rates and leads to lower birth rates.

The fundamental cause of the acceleration of growth rate for humans in the past 200 years has been the reduced
death rate due to a development of the technological advances of the industrial age, urbanization that supported
those technologies, and especially the exploitation of the energy in fossil fuels. Fossil fuels are responsible for
dramatically increasing the resources available for human population growth through agriculture (mechanization,
pesticides, and fertilizers) and harvesting wild populations.

5 Danny Dorling, Mary Shaw, and George Davey Smith, “Global Inequality of Life Expectancy due to AIDS,” BMJ 332, no. 7542 (March
2006): 662-664, doi: 10.1136/bmj.332.7542.662.
508 19 • Population and Community Ecology

Age Structure, Population Growth, and Economic Development

The age structure of a population is an important factor in population dynamics. Age structure is the proportion of a
population in different age classes. Models that incorporate age structure allow better prediction of population
growth, plus the ability to associate this growth with the level of economic development in a region. Countries with
rapid growth have a pyramidal shape in their age structure diagrams, showing a preponderance of younger
individuals, many of whom are of reproductive age (Figure 19.11). This pattern is most often observed in
underdeveloped countries where individuals do not live to old age because of less-than-optimal living conditions,
and there is a high birth rate. Age structures of areas with slow growth, including developed countries such as the
United States, still have a pyramidal structure, but with many fewer young and reproductive-aged individuals and a
greater proportion of older individuals. Other developed countries, such as Italy, have zero population growth. The
age structure of these populations is more conical, with an even greater percentage of middle-aged and older
individuals. The actual growth rates in different countries are shown in Figure 19.12, with the highest rates tending
to be in the less economically developed countries of Africa and Asia.

VISUAL CONNECTION

FIGURE 19.11 Typical age structure diagrams are shown. The rapid growth diagram narrows to a point, indicating that the number of
individuals decreases rapidly with age. In the slow growth model, the number of individuals decreases steadily with age. Stable population
diagrams are rounded on the top, showing that the number of individuals per age group decreases gradually, and then increases for the
older part of the population.

Age structure diagrams for rapidly growing, slow growing, and stable populations are shown in stages 1 through 3.
What type of population change do you think stage 4 represents?

FIGURE 19.12 The percent growth rate of population in different countries is shown. Notice that the highest growth is occurring in less
economically developed countries in Africa and Asia.

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 19.4 • Community Ecology 509

Long-Term Consequences of Exponential Human Population Growth

Many dire predictions have been made about the world’s population leading to a major crisis called the “population
explosion.” In the 1968 book The Population Bomb, biologist Dr. Paul R. Ehrlich wrote, “The battle to feed all of
humanity is over. In the 1970s hundreds of millions of people will starve to death in spite of any crash programs
6
embarked upon now. At this late date nothing can prevent a substantial increase in the world death rate.” While
many critics view this statement as an exaggeration, the laws of exponential population growth are still in effect,
and unchecked human population growth cannot continue indefinitely.

Efforts to moderate population control led to the one-child policy in China, which imposes fines on urban couples
who have more than one child. Due to the fact that some couples wish to have a male heir, many Chinese couples
continue to have more than one child. The effectiveness of the policy in limiting overall population growth is
controversial, as is the policy itself. Moreover, there are stories of female infanticide having occurred in some of the
more rural areas of the country. Family planning education programs in other countries have had highly positive
effects on limiting population growth rates and increasing standards of living. In spite of population control policies,
the human population continues to grow. Because of the subsequent need to produce more and more food to feed
our population, inequalities in access to food and other resources will continue to widen. The United Nations
estimates the future world population size could vary from 6 billion (a decrease) to 16 billion people by the year
2100. There is no way to know whether human population growth will moderate to the point where the crisis
described by Dr. Ehrlich will be averted.

Another consequence of population growth is the change and degradation of the natural environment. Many
countries have attempted to reduce the human impact on climate change by limiting their emission of greenhouse
gases. However, a global climate change treaty remains elusive, and many underdeveloped countries trying to
improve their economic condition may be less likely to agree with such provisions without compensation if it means
slowing their economic development. Furthermore, the role of human activity in causing climate change has become
a hotly debated socio-political issue in some developed countries, including the United States. Thus, we enter the
future with considerable uncertainty about our ability to curb human population growth and protect our
environment to maintain the carrying capacity for the human species.

LINK TO LEARNING
Visit this website (http://openstax.org/l/populations2) and select “Launch the movie” for an animation discussing
the global impacts of human population growth.

19.4 Community Ecology

LEARNING OBJECTIVES
By the end of this section, you will be able to:
• Discuss the predator-prey cycle
• Give examples of defenses against predation and herbivory
• Describe the competitive exclusion principle
• Give examples of symbiotic relationships between species
• Describe community structure and succession

In general, populations of one species never live in isolation from populations of other species. The interacting
populations occupying a given habitat form an ecological community. The number of species occupying the same
habitat and their relative abundance is known as the diversity of the community. Areas with low species diversity,
such as the glaciers of Antarctica, still contain a wide variety of living organisms, whereas the diversity of tropical
rainforests is so great that it cannot be accurately assessed. Scientists study ecology at the community level to
understand how species interact with each other and compete for the same resources.

Predation and Herbivory

Perhaps the classical example of species interaction is the predator-prey relationship. The narrowest definition of

6 Paul R. Erlich, prologue to The Population Bomb, (1968; repr., New York: Ballantine, 1970).
510 19 • Population and Community Ecology

the predator-prey interaction describes individuals of one population that kill and then consume the individuals of
another population. Population sizes of predators and prey in a community are not constant over time, and they may
vary in cycles that appear to be related. The most often cited example of predator-prey population dynamics is seen
in the cycling of the lynx (predator) and the snowshoe hare (prey), using 100 years of trapping data from North
America (Figure 19.13). This cycling of predator and prey population sizes has a period of approximately ten years,
with the predator population lagging one to two years behind the prey population. An apparent explanation for this
pattern is that as the hare numbers increase, there is more food available for the lynx, allowing the lynx population
to increase as well. When the lynx population grows to a threshold level, however, they kill so many hares that hare
numbers begin to decline, followed by a decline in the lynx population because of scarcity of food. When the lynx
population is low, the hare population size begins to increase due, in part, to low predation pressure, starting the
cycle anew.

FIGURE 19.13 The cycling of snowshoe hare and lynx populations in Northern Ontario is an example of predator-prey dynamics.

Defense Mechanisms against Predation and Herbivory

Predation and predator avoidance are strong selective agents. Any heritable character that allows an individual of a
prey population to better evade its predators will be represented in greater numbers in later generations. Likewise,
traits that allow a predator to more efficiently locate and capture its prey will lead to a greater number of offspring
and an increase in the commonness of the trait within the population. Such ecological relationships between
specific populations lead to adaptations that are driven by reciprocal evolutionary responses in those populations.
Species have evolved numerous mechanisms to escape predation and herbivory (the consumption of plants for
food). Defenses may be mechanical, chemical, physical, or behavioral.

Mechanical defenses, such as the presence of armor in animals or thorns in plants, discourage predation and
herbivory by discouraging physical contact (Figure 19.14a). Many animals produce or obtain chemical defenses
from plants and store them to prevent predation. Many plant species produce secondary plant compounds that
serve no function for the plant except that they are toxic to animals and discourage consumption. For example, the
foxglove produces several compounds, including digitalis, that are extremely toxic when eaten (Figure 19.14b).
(Biomedical scientists have purposed the chemical produced by foxglove as a heart medication, which has saved
lives for many decades.)

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 19.4 • Community Ecology 511

FIGURE 19.14 The (a) honey locust tree uses thorns, a mechanical defense, against herbivores, while the (b) foxglove uses a chemical
defense: toxins produces by the plant can cause nausea, vomiting, hallucinations, convulsions, or death when consumed. (credit a:
modification of work by Huw Williams; credit b: modification of work by Philip Jägenstedt)

Many species use physical appearance, such as body shape and coloration, to avoid being detected by predators.
The tropical walking stick is an insect with the coloration and body shape of a twig, which makes it very hard to see
when it is stationary against a background of real twigs (Figure 19.15a). In another example, the chameleon can,
within limitations, change its color to match its surroundings (Figure 19.15b). There are many behavioral
adaptations to avoid or confuse predators. Playing dead and traveling in large groups, like schools of fish or flocks of
birds, are both behaviors that reduce the risk of being eaten.

FIGURE 19.15 (a) The tropical walking stick and (b) the chameleon use their body shape and/or coloration to prevent detection by
predators. (credit a: modification of work by Linda Tanner; credit b: modification of work by Frank Vassen)

Some species use coloration as a way of warning predators that they are distasteful or poisonous. For example, the
monarch butterfly caterpillar sequesters poisons from its food (plants and milkweeds) to make itself poisonous or
distasteful to potential predators. The caterpillar is bright yellow and black to advertise its toxicity. The caterpillar is
also able to pass the sequestered toxins on to the adult monarch, which is also dramatically colored black and red
as a warning to potential predators. Fire-bellied toads produce toxins that make them distasteful to their potential
predators. They have bright red or orange coloration on their bellies, which they display to a potential predator to
advertise their poisonous nature and discourage an attack. These are only two examples of warning coloration,
which is a relatively common adaptation. Warning coloration only works if a predator uses eyesight to locate prey
and can learn—a naïve predator must experience the negative consequences of eating one before it will avoid other
similarly colored individuals (Figure 19.16).
512 19 • Population and Community Ecology

FIGURE 19.16 The fire-bellied toad has bright coloration on its belly that serves to warn potential predators that it is toxic. (credit:
modification of work by Roberto Verzo)

While some predators learn to avoid eating certain potential prey because of their coloration, other species have
evolved mechanisms to mimic this coloration to avoid being eaten, even though they themselves may not be
unpleasant to eat or contain toxic chemicals. In some cases of mimicry, a harmless species imitates the warning
coloration of a harmful species. Assuming they share the same predators, this coloration then protects the harmless
ones. Many insect species mimic the coloration of wasps, which are stinging, venomous insects, thereby
discouraging predation (Figure 19.17).

FIGURE 19.17 One form of mimicry is when a harmless species mimics the coloration of a harmful species, as is seen with the (a) wasp
(Polistes sp.) and the (b) hoverfly (Syrphus sp.). (credit: modification of work by Tom Ings)

In other cases of mimicry, multiple species share the same warning coloration, but all of them actually have
defenses. The commonness of the signal improves the compliance of all the potential predators. Figure 19.18
shows a variety of foul-tasting butterflies with similar coloration.

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 19.4 • Community Ecology 513

FIGURE 19.18 Several unpleasant-tasting Heliconius butterfly species share a similar color pattern with better-tasting varieties, an
example of mimicry. (credit: Joron M, Papa R, Beltrán M, Chamberlain N, Mavárez J, et al.)

LINK TO LEARNING
Go to this website (http://openstax.org/l/find_the_mimic2) to view stunning examples of mimicry.

Competitive Exclusion Principle

Resources are often limited within a habitat and multiple species may compete to obtain them. Ecologists have
come to understand that all species have an ecological niche. A niche is the unique set of resources used by a
species, which includes its interactions with other species. The competitive exclusion principle states that two
species cannot occupy the same niche in a habitat: in other words, different species cannot coexist in a community
if they are competing for all the same resources. This principle works because if there is an overlap in resource use
and therefore competition between two species, then traits that lessen reliance on the shared resource will be
selected for leading to evolution that reduces the overlap. If either species is unable to evolve to reduce
competition, then the species that most efficiently exploits the resource will drive the other species to extinction. An
experimental example of this principle is shown in Figure 19.19 with two protozoan species: Paramecium aurelia
and Paramecium caudatum. When grown individually in the laboratory, they both thrive. But when they are placed
together in the same test tube (habitat), P. aurelia outcompetes P. caudatum for food, leading to the latter’s eventual
extinction.

FIGURE 19.19 Paramecium aurelia and Paramecium caudatum grow well individually, but when they compete for the same resources, the
P. aurelia outcompetes the P. caudatum.
514 19 • Population and Community Ecology

Symbiosis
Symbiotic relationships are close, long-term interactions between individuals of different species. Symbioses may
be commensal, in which one species benefits while the other is neither harmed nor benefited; mutualistic, in which
both species benefit; or parasitic, in which the interaction harms one species and benefits the other.

Commensalism
A commensal relationship occurs when one species benefits from a close prolonged interaction, while the other
neither benefits nor is harmed. Birds nesting in trees provide an example of a commensal relationship (Figure
19.20). The tree is not harmed by the presence of the nest among its branches. The nests are light and produce little
strain on the structural integrity of the branch, and most of the leaves, which the tree uses to get energy by
photosynthesis, are above the nest so they are unaffected. The bird, on the other hand, benefits greatly. If the bird
had to nest in the open, its eggs and young would be vulnerable to predators. Many potential commensal
relationships are difficult to identify because it is difficult to prove that one partner does not derive some benefit
from the presence of the other.

FIGURE 19.20 The southern masked-weaver is starting to make a nest in a tree in Zambezi Valley, Zambia. This is an example of a
commensal relationship, in which one species (the bird) benefits, while the other (the tree) neither benefits nor is harmed. (credit:
“Hanay”/Wikimedia Commons)

Mutualism
A second type of symbiotic relationship is called mutualism, in which two species benefit from their interaction. For
example, termites have a mutualistic relationship with protists that live in the insect’s gut (Figure 19.21a). The
termite benefits from the ability of the protists to digest cellulose. However, the protists are able to digest cellulose
only because of the presence of symbiotic bacteria within their cells that produce the cellulase enzyme. The termite
itself cannot do this: without the protozoa, it would not be able to obtain energy from its food (cellulose from the
wood it chews and eats). The protozoa benefit by having a protective environment and a constant supply of food
from the wood chewing actions of the termite. In turn, the protists benefit from the enzymes provided by their
bacterial endosymbionts, while the bacteria benefit from a doubly protective environment and a constant source of
nutrients from two hosts. Lichen are a mutualistic relationship between a fungus and photosynthetic algae or
cyanobacteria (Figure 19.21b). The glucose produced by the algae provides nourishment for both organisms,
whereas the physical structure of the lichen protects the algae from the elements and makes certain nutrients in the
atmosphere more available to the algae. The algae of lichens can live independently given the right environment, but
many of the fungal partners are unable to live on their own.

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 19.4 • Community Ecology 515

FIGURE 19.21 (a) Termites form a mutualistic relationship with symbiotic protozoa in their guts, which allow both organisms to obtain
energy from the cellulose the termite consumes. (b) Lichen is a fungus that has symbiotic photosynthetic algae living in close association.
(credit a: modification of work by Scott Bauer, USDA; credit b: modification of work by Cory Zanker)

Parasitism
A parasite is an organism that feeds off another without immediately killing the organism it is feeding on. In this
relationship, the parasite benefits, but the organism being fed upon, the host, is harmed. The host is usually
weakened by the parasite as it siphons resources the host would normally use to maintain itself. Parasites may kill
their hosts, but there is usually selection to slow down this process to allow the parasite time to complete its
reproductive cycle before it or its offspring are able to spread to another host.

The reproductive cycles of parasites are often very complex, sometimes requiring more than one host species. A
tapeworm causes disease in humans when contaminated, undercooked meat such as pork, fish, or beef is
consumed (Figure 19.22). The tapeworm can live inside the intestine of the host for several years, benefiting from
the host’s food, and it may grow to be over 50 feet long by adding segments. The parasite moves from one host
species to a second host species in order to complete its life cycle. Plasmodium falciparum is another parasite: the
protists that cause malaria, a significant disease in many parts of the world. Living inside human liver and red blood
cells, the organism reproduces asexually in the human host and then sexually in the gut of blood-feeding
mosquitoes to complete its life cycle. Thus malaria is spread from human to mosquito and back to human, one of
many arthropod-borne infectious diseases of humans.

FIGURE 19.22 This diagram shows the life cycle of the tapeworm, a human worm parasite. (credit: modification of work by CDC)
516 19 • Population and Community Ecology

LINK TO LEARNING
To learn more about “Symbiosis in the Sea,” watch this webisode (http://openstax.org/l/symbiosis) of Jonathan
Bird’s Blue World.

Characteristics of Communities
Communities are complex systems that can be characterized by their structure (the number and size of populations
and their interactions) and dynamics (how the members and their interactions change over time). Understanding
community structure and dynamics allows us to minimize impacts on ecosystems and manage ecological
communities we benefit from.

Biodiversity
Ecologists have extensively studied one of the fundamental characteristics of communities: biodiversity. One
measure of biodiversity used by ecologists is the number of different species in a particular area and their relative
abundance. The area in question could be a habitat, a biome, or the entire biosphere. Species richness is the term
used to describe the number of species living in a habitat or other unit. Species richness varies across the globe
(Figure 19.23). Ecologists have struggled to understand the determinants of biodiversity. Species richness is related
to latitude: the greatest species richness occurs near the equator and the lowest richness occurs near the poles.
Other factors influence species richness as well. Island biogeography attempts to explain the great species
richness found in isolated islands, and has found relationships between species richness, island size, and distance
from the mainland.

Relative species abundance is the number individuals in a species relative to the total number of individuals in all
species within a system. Foundation species, described below, often have the highest relative abundance of species.

FIGURE 19.23 The greatest species richness for mammals in North America is associated in the equatorial latitudes. (credit: modification
of work by NASA, CIESIN, Columbia University)

Foundation Species
Foundation species are considered the “base” or “bedrock” of a community, having the greatest influence on its
overall structure. They are often primary producers, and they are typically an abundant organism. For example, kelp,
a species of brown algae, is a foundation species that forms the basis of the kelp forests off the coast of California.

Foundation species may physically modify the environment to produce and maintain habitats that benefit the other
organisms that use them. Examples include the kelp described above or tree species found in a forest. The

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 19.4 • Community Ecology 517

photosynthetic corals of the coral reef also provide structure by physically modifying the environment (Figure
19.24). The exoskeletons of living and dead coral make up most of the reef structure, which protects many other
species from waves and ocean currents.

FIGURE 19.24 Coral is the foundation species of coral reef ecosystems. (credit: Jim E. Maragos, USFWS)

Keystone Species
A keystone species is one whose presence has inordinate influence in maintaining the prevalence of various
species in an ecosystem, the ecological community’s structure, and sometimes its biodiversity. Pisaster ochraceus,
the intertidal sea star, is a keystone species in the northwestern portion of the United States (Figure 19.25). Studies
have shown that when this organism is removed from communities, mussel populations (their natural prey)
increase, which completely alters the species composition and reduces biodiversity. Another keystone species is the
banded tetra, a fish in tropical streams, which supplies nearly all of the phosphorus, a necessary inorganic nutrient,
to the rest of the community. The banded tetra feeds largely on insects from the terrestrial ecosystem and then
excretes phosphorus into the aquatic ecosystem. The relationships between populations in the community, and
possibly the biodiversity, would change dramatically if these fish were to become extinct.

FIGURE 19.25 The Pisaster ochraceus sea star is a keystone species. (credit: Jerry Kirkhart)

EVERYDAY CONNECTION
Invasive Species
Invasive species are non-native organisms that, when introduced to an area out of its native range, alter the
community they invade. In the United States, invasive species like the purple loosestrife (Lythrum salicaria) and
the zebra mussel (Dreissena polymorpha) have altered aquatic ecosystems, and some forests are threatened by
the spread of common buckthorn (Rhamnus cathartica) and garlic mustard (Alliaria petiolata). Some well-known
invasive animals include the emerald ash borer (Agrilus planipennis) and the European starling (Sturnus
vulgaris). Whether enjoying a forest hike, taking a summer boat trip, or simply walking down an urban street, you
518 19 • Population and Community Ecology

have likely encountered an invasive species.

One of the many recent proliferations of an invasive species concerns the Asian carp in the United States. Asian
carp were introduced to the United States in the 1970s by fisheries (commercial catfish ponds) and by sewage
treatment facilities that used the fish’s excellent filter feeding abilities to clean their ponds of excess plankton.
Some of the fish escaped, and by the 1980s they had colonized many waterways of the Mississippi River basin,
including the Illinois and Missouri Rivers.

Voracious feeders and rapid reproducers, Asian carp may outcompete native species for food and could lead to
their extinction. One species, the grass carp, feeds on phytoplankton and aquatic plants. It competes with native
species for these resources and alters nursery habitats for other fish by removing aquatic plants. Another
species, the silver carp, competes with native fish that feed on zooplankton. In some parts of the Illinois River,
Asian carp constitute 95 percent of the community's biomass. Although edible, the fish is bony and not desired
in the United States. Moreover, their presence now threatens the native fish and fisheries of the Great Lakes,
which are important to local economies and recreational anglers. Asian carp have even injured humans. The fish,
frightened by the sound of approaching motorboats, thrust themselves into the air, often landing in the boat or
directly hitting boaters.

The Great Lakes and their prized salmon and lake trout fisheries are being threatened by Asian carp. The carp
are not yet present in the Great Lakes, and attempts are being made to prevent its access to the lakes through
the Chicago Ship and Sanitary Canal, which is the only connection between the Mississippi River and Great Lakes
basins. To prevent the Asian carp from leaving the canal, a series of electric barriers have been used to
discourage their migration; however, the threat is significant enough that several states and Canada have sued to
have the Chicago channel permanently cut off from Lake Michigan. Local and national politicians have weighed
in on how to solve the problem. In general, governments have been ineffective in preventing or slowing the
introduction of invasive species.

The issues associated with Asian carp show how population and community ecology, fisheries management, and
politics intersect on issues of vital importance to the human food supply and economy. Socio-political issues like
the Asian carp make extensive use of the sciences of population ecology, the study of members of a particular
species occupying a habitat; and community ecology, the study of the interaction of all species within a habitat.

Community Dynamics
Community dynamics are the changes in community structure and composition over time, often following
environmental disturbances such as volcanoes, earthquakes, storms, fires, and climate change. Communities with
a relatively constant number of species are said to be at equilibrium. The equilibrium is dynamic with species
identities and relationships changing over time, but maintaining relatively constant numbers. Following a
disturbance, the community may or may not return to the equilibrium state.

Succession describes the sequential appearance and disappearance of species in a community over time after a
severe disturbance. In primary succession, newly exposed or newly formed rock is colonized by living organisms; in
secondary succession, a part of an ecosystem is disturbed and remnants of the previous community remain. In
both cases, there is a sequential change in species until a more or less permanent community develops.

Primary Succession and Pioneer Species

Primary succession occurs when new land is formed, for example, following the eruption of volcanoes, such as those
on the Big Island of Hawaii. As lava flows into the ocean, new land is continually being formed. On the Big Island,
approximately 32 acres of land is added to it its size each year. Weathering and other natural forces break down the
rock enough for the establishment of hearty species such as lichens and some plants, known as pioneer species
(Figure 19.26). These species help to further break down the mineral-rich lava into soil where other, less hardy but
more competitive species, such as grasses, shrubs, and trees, will grow and eventually replace the pioneer species.
Over time the area will reach an equilibrium state, with a set of organisms quite different from the pioneer species.

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 19.4 • Community Ecology 519

FIGURE 19.26 During primary succession in lava on Maui, Hawaii, succulent plants are the pioneer species. (credit: Forest and Kim Starr)

Secondary succession
A classic example of secondary succession occurs in oak and hickory forests cleared by wildfire (Figure 19.27).
Wildfires will burn most vegetation, and unless the animals can flee the area, they are killed. Their nutrients,
however, are returned to the ground in the form of ash. Thus, although the community has been dramatically
altered, there is a soil ecosystem present that provides a foundation for rapid recolonization.

Before the fire, the vegetation was dominated by tall trees with access to the major plant energy resource: sunlight.
Their height gave them access to sunlight while also shading the ground and other low-lying species. After the fire,
though, these trees are no longer dominant. Thus, the first plants to grow back are usually annual plants followed
within a few years by quickly growing and spreading grasses and other pioneer species. Due, at least in part, to
changes in the environment brought on by the growth of grasses and forbs, over many years, shrubs emerge along
with small pine, oak, and hickory trees. These organisms are called intermediate species. Eventually, over 150
years, the forest will reach its equilibrium point and resemble the community before the fire. This equilibrium state
is referred to as the climax community, which will remain until the next disturbance. The climax community is
typically characteristic of a given climate and geology. Although the community in equilibrium looks the same once it
is attained, the equilibrium is a dynamic one with constant changes in abundance and sometimes species identities.
The return of a natural ecosystem after agricultural activities is also a well-documented secondary succession
process.

FIGURE 19.27 Secondary succession is seen in an oak and hickory forest after a forest fire. A sequence of the community present at three
successive times at the same location is depicted.
520 19 • Key Terms

Key Terms
age structure the distribution of the proportion of due to limiting resources
population members in each age class mark and recapture a method used to determine
birth rate the number of births within a population at population size in mobile organisms
a specific point in time mimicry an adaptation in which an organism looks
carrying capacity the maximum number of like another organism that is dangerous, toxic, or
individuals of a population that can be supported by distasteful to its predators
the limited resources of a habitat mortality rate the proportion of population surviving
climax community the final stage of succession, to the beginning of an age interval that dies during
where a stable community is formed by a that age interval
characteristic assortment of plant and animal mutualism a symbiotic relationship between two
species species where both species benefit
competitive exclusion principle no two species one-child policy a policy in China to limit population
within a habitat can coexist indefinitely when they growth by limiting urban couples to have only one
compete for the same resources at the same time child or face a penalty of a fine
and place parasite an organism that uses resources from
death rate the number of deaths within a population another species: the host
at a specific point in time pioneer species the first species to appear in primary
demography the statistical study of changes in and secondary succession
populations over time population density the number of population
density-dependent regulation the regulation of members divided by the area being measured
population in which birth and death rates are population size the number of individuals in a
dependent on population size population
density-independent regulation the regulation of primary succession the succession on land that
population in which the death rate is independent of previously has had no life
the population size quadrat a square within which a count of individuals
environmental disturbance a change in the is made that is combined with other such counts to
environment caused by natural disasters or human determine population size and density in slow
activities moving or stationary organisms
exponential growth an accelerating growth pattern r-selected species a species suited to changing
seen in populations where resources are not limiting environments that produce many offspring and
foundation species a species which often forms the provide little or no parental care
major structural portion of the habitat relative species abundance the absolute population
host an organism a parasite lives on size of a particular species relative to the population
intraspecific competition the competition among size of other species within the community
members of the same species S-shaped growth curve the shape of a logistic
island biogeography the study of life on island chains growth curve
and how their geography interacts with the diversity secondary succession the succession in response to
of species found there environmental disturbances that move a community
J-shaped growth curve the shape of an exponential away from its equilibrium
growth curve species distribution pattern the distribution of
K-selected species a species suited to stable individuals within a habitat at a given point in time
environments that produce a few, relatively large species richness the number of different species in a
offspring and provide parental care community
keystone species a species whose presence is key to survivorship curve a graph of the number of
maintaining biodiversity in an ecosystem and to surviving population members versus the relative
upholding an ecological community’s structure age of the member
life table a table showing the life expectancy of a zero population growth the steady population size
population member based on its age where birth rates and death rates are equal
logistic growth the leveling off of exponential growth

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 19 • Chapter Summary 521

Chapter Summary
19.1 Population Demographics and adaptations somewhere on a continuum between
Dynamics these two extremes.

Populations are individuals of a species that live in a 19.3 The Human Population
particular habitat. Ecologists measure characteristics
Earth’s human population is growing exponentially.
of populations: size, density, and distribution pattern.
Humans have increased their carrying capacity through
Life tables are useful to calculate life expectancies of
technology, urbanization, and harnessing the energy of
individual population members. Survivorship curves
fossil fuels. The age structure of a population allows us
show the number of individuals surviving at each age
to predict population growth. Unchecked human
interval plotted versus time.
population growth could have dire long-term effects on
19.2 Population Growth and Regulation human welfare and Earth’s ecosystems.

Populations with unlimited resources grow 19.4 Community Ecology

exponentially—with an accelerating growth rate. When
Communities include all the different species living in a
resources become limiting, populations follow a
given area. The variety of these species is referred to
logistic growth curve in which population size will level
as biodiversity. Many organisms have developed
off at the carrying capacity.
defenses against predation and herbivory, including
Populations are regulated by a variety of density- mechanical defenses, warning coloration, and mimicry.
dependent and density-independent factors. Life- Two species cannot exist indefinitely in the same
history characteristics, such as age at first reproduction habitat competing directly for the same resources.
or numbers of offspring, are characteristics that evolve Species may form symbiotic relationships such as
in populations just as anatomy or behavior can evolve commensalism, mutualism, or parasitism. Community
over time. The model of r- and K-selection suggests structure is described by its foundation and keystone
that characters, and possibly suites of characters, may species. Communities respond to environmental
evolve adaptations to population stability near the disturbances by succession: the predictable
carrying capacity (K-selection) or rapid population appearance of different types of plant species, until a
growth and collapse (r-selection). Species will exhibit stable community structure is established.

Visual Connection Questions

1. Figure 19.2 As this graph shows, population density 3. Figure 19.11 Age structure diagrams for rapidly
typically decreases with increasing body size. Why growing, slow growing, and stable populations are
do you think this is the case? shown in stages 1 through 3. What type of
population change do you think stage 4 represents?
2. Figure 19.6 If the major food source of seals
declines due to pollution or overfishing, which of
the following would likely occur?
a. The carrying capacity of seals would decrease,
as would the seal population.
b. The carrying capacity of seals would decrease,
but the seal population would remain the
same.
c. The number of seal deaths would increase, but
the number of births would also increase, so
the population size would remain the same.
d. The carrying capacity of seals would remain
the same, but the population of seals would
decrease.
522 19 • Review Questions

Review Questions
4. Which of the following methods will provide 11. A forest fire is an example of ________ regulation.
information to an ecologist about both the size and a. density-dependent
density of a population? b. density-independent
a. mark and recapture c. r-selected
b. mark and release d. K-selected
c. quadrat
d. life table 12. A country with zero population growth is likely to
be ________.
5. Which of the following is best at showing the life a. in Africa
expectancy of an individual within a population? b. in Asia
a. quadrat c. economically developed
b. mark and recapture d. economically underdeveloped
c. survivorship curve
d. life table 13. Which type of country has the greatest proportion
of young individuals?
6. Human populations have which type of survivorship a. economically developed
curve? b. economically underdeveloped
a. Type I c. countries with zero population growth
b. Type II d. countries in Europe
c. Type III
d. Type IV 14. Which of the following is underline
notend
a way
underline
that humans
have increased the carrying capacity of the
7. Species with limited resources usually exhibit a(n) environment?
________ growth curve. a. agriculture
a. logistic b. using large amounts of natural resources
b. logical c. domestication of animals
c. experimental d. use of language
d. exponential
15. The first species to live on new land, such as that
8. The maximum growth rate characteristic of a formed from volcanic lava, are called________.
species is called its ________. a. climax community
a. limit b. keystone species
b. carrying capacity c. foundation species
c. biotic potential d. pioneer species
d. exponential growth pattern
16. A symbiotic relationship where both of the co-
9. The population size of a species capable of being existing species benefit from the interaction is
supported by the environment is called its called ________.
________. a. commensalism
a. limit b. parasitism
b. carrying capacity c. mutualism
c. biotic potential d. communism
d. logistic growth pattern
17. When an invasive species alters the community
10. Species that have many offspring at one time are structure it is introduced to, what can the
usually: consequence be?
a. r-selected a. extinction of economically important species
b. K-selected b. reduced predation on some native species
c. both r- and K-selected c. increased predation on some native species
d. not selected d. all of the above

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 19 • Critical Thinking Questions 523

Critical Thinking Questions

18. Describe how a researcher would determine the 21. Describe the age structures in rapidly growing
size of a penguin population in Antarctica using countries, slowly growing countries, and countries
the mark and release method. with zero population growth.

19. Describe the growth at various parts of the S- 22. Describe the competitive exclusion principle and
shaped curve of logistic growth. its effects on competing species.

20. Give an example of how density-dependent and 23. Describe the potential effects when a keystone
density-independent factors might interact. species is removed from a community.
524 19 • Critical Thinking Questions

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CHAPTER 20
Ecosystems and the Biosphere

FIGURE 20.1 The (a) Karner blue butterfly and (b) wild lupine live in oak-pine barren habitats in North America. (credit
a: modification of work by John & Karen Hollingsworth, USFWS)

CHAPTER OUTLINE
20.1 Waterford's Energy Flow through Ecosystems
20.2 Biogeochemical Cycles
20.3 Terrestrial Biomes
20.4 Aquatic and Marine Biomes

INTRODUCTION Ecosystem ecology is an extension of organismal, population, and community

ecology. The ecosystem comprises all the biotic components (living things) and abiotic
components (non-living things) in a particular geographic area. Some of the abiotic components
include air, water, soil, and climate. Ecosystem biologists study how nutrients and energy are
stored and moved among organisms and the surrounding atmosphere, soil, and water.

Wild lupine and Karner blue butterflies live in an oak-pine barren habitat in portions of Indiana,
Michigan, Minnesota, Wisconsin, and New York (Figure 20.1). This habitat is characterized by
natural disturbance in the form of fire and nutrient-poor soils that are low in nitrogen—important
factors in the distribution of the plants that live in this habitat. Researchers interested in
ecosystem ecology study the importance of limited resources in this ecosystem and the
526 20 • Ecosystems and the Biosphere

movement of resources (such as nutrients) through the biotic and abiotic portions of the
ecosystem. Researchers also examine how organisms have adapted to their ecosystem.

20.1 Waterford's Energy Flow through Ecosystems

LEARNING OBJECTIVES
By the end of this section, you will be able to:
• Describe the basic types of ecosystems on Earth
• Differentiate between food chains and food webs and recognize the importance of each
• Describe how organisms acquire energy in a food web and in associated food chains
• Explain how the efficiency of energy transfers between trophic levels affects ecosystems

An ecosystem is a community of living organisms and their abiotic (non-living) environment.

Ecosystems can be small, such as the tide pools found near the rocky shores of many oceans, or
large, such as those found in the tropical rainforest of the Amazon in Brazil (Figure 20.2).

FIGURE 20.2 A (a) tidal pool ecosystem in Matinicus Island, Maine, is a small ecosystem, while the (b) Amazon
rainforest in Brazil is a large ecosystem. (credit a: modification of work by Jim Kuhn; credit b: modification of work by
Ivan Mlinaric)

There are three broad categories of ecosystems based on their general environment: freshwater,
marine, and terrestrial. Within these three categories are individual ecosystem types based on the
environmental habitat and organisms present.

Ecology of Ecosystems
Life in an ecosystem often involves competition for limited resources, which occurs both within a
single species and between different species. Organisms compete for food, water, sunlight, space,
and mineral nutrients. These resources provide the energy for metabolic processes and the matter
to make up organisms’ physical structures. Other critical factors influencing community dynamics
are the components of its physical environment: a habitat’s climate (seasons, sunlight, and
rainfall), elevation, and geology. These can all be important environmental variables that
determine which organisms can exist within a particular area.

Freshwater ecosystems are the least common, occurring on only 1.8 percent of Earth's surface.
These systems comprise lakes, rivers, streams, and springs; they are quite diverse, and support a
variety of animals, plants, fungi, protists and prokaryotes.

Marine ecosystems are the most common, comprising 75 percent of Earth's surface and consisting
of three basic types: shallow ocean, deep ocean water, and deep ocean bottom. Shallow ocean
ecosystems include extremely biodiverse coral reef ecosystems, yet the deep ocean water is
known for large numbers of plankton and krill (small crustaceans) that support it. These two
environments are especially important to aerobic respirators worldwide, as the phytoplankton
perform 40 percent of all photosynthesis on Earth. Although not as diverse as the other two, deep

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 20.1 • Waterford's Energy Flow through Ecosystems 527

ocean bottom ecosystems contain a wide variety of marine organisms. Such ecosystems exist even at depths where
light is unable to penetrate through the water.

Terrestrial ecosystems, also known for their diversity, are grouped into large categories called biomes. A biome is a
large-scale community of organisms, primarily defined on land by the dominant plant types that exist in geographic
regions of the planet with similar climatic conditions. Examples of biomes include tropical rainforests, savannas,
deserts, grasslands, temperate forests, and tundras. Grouping these ecosystems into just a few biome categories
obscures the great diversity of the individual ecosystems within them. For example, the saguaro cacti (Carnegiea
gigantean) and other plant life in the Sonoran Desert, in the United States, are relatively diverse compared with the
desolate rocky desert of Boa Vista, an island off the coast of Western Africa (Figure 20.3).

FIGURE 20.3 Desert ecosystems, like all ecosystems, can vary greatly. The desert in (a) Saguaro National Park, Arizona, has abundant plant
life, while the rocky desert of (b) Boa Vista island, Cape Verde, Africa, is devoid of plant life. (credit a: modification of work by Jay Galvin;
credit b: modification of work by Ingo Wölbern)

Ecosystems and Disturbance

Ecosystems are complex with many interacting parts. They are routinely exposed to various disturbances: changes
in the environment that affect their compositions, such as yearly variations in rainfall and temperature. Many
disturbances are a result of natural processes. For example, when lightning causes a forest fire and destroys part of
a forest ecosystem, the ground is eventually populated with grasses, followed by bushes and shrubs, and later
mature trees: thus, the forest is restored to its former state. This process is so universal that ecologists have given it
a name—succession. The impact of environmental disturbances caused by human activities is now as significant as
the changes wrought by natural processes. Human agricultural practices, air pollution, acid rain, global
deforestation, overfishing, oil spills, and illegal dumping on land and into the ocean all have impacts on ecosystems.

Equilibrium is a dynamic state of an ecosystem in which, despite changes in species numbers and occurrence,
biodiversity remains somewhat constant. In ecology, two parameters are used to measure changes in ecosystems:
resistance and resilience. The ability of an ecosystem to remain at equilibrium in spite of disturbances is called
resistance. The speed at which an ecosystem recovers equilibrium after being disturbed is called resilience.
Ecosystem resistance and resilience are especially important when considering human impact. The nature of an
ecosystem may change to such a degree that it can lose its resilience entirely. This process can lead to the complete
destruction or irreversible altering of the ecosystem.

Food Chains and Food Webs

A food chain is a linear sequence of organisms through which nutrients and energy pass as one organism eats
another; the levels in the food chain are producers, primary consumers, higher-level consumers, and finally
decomposers. These levels are used to describe ecosystem structure and dynamics. There is a single path through a
food chain. Each organism in a food chain occupies a specific trophic level (energy level), its position in the food
chain or food web.

In many ecosystems, the base, or foundation, of the food chain consists of photosynthetic organisms (plants or
phytoplankton), which are called producers. The organisms that consume the producers are herbivores: the
primary consumers. Secondary consumers are usually carnivores that eat the primary consumers. Tertiary
consumers are carnivores that eat other carnivores. Higher-level consumers feed on the next lower trophic levels,
528 20 • Ecosystems and the Biosphere

and so on, up to the organisms at the top of the food chain: the apex consumers. In the Lake Ontario food chain,
shown in Figure 20.4, the Chinook salmon is the apex consumer at the top of this food chain.

FIGURE 20.4 These are the trophic levels of a food chain in Lake Ontario at the United States–Canada border. Energy and nutrients flow
from photosynthetic green algae at the base to the top of the food chain: the Chinook salmon. (credit: modification of work by National
Oceanic and Atmospheric Administration/NOAA)

One major factor that limits the number of steps in a food chain is energy. Energy is lost at each trophic level and
between trophic levels as heat and in the transfer to decomposers (Figure 20.5). Thus, after a limited number of
trophic energy transfers, the amount of energy remaining in the food chain may not be great enough to support
viable populations at yet a higher trophic level.

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 20.1 • Waterford's Energy Flow through Ecosystems 529

FIGURE 20.5 The relative energy in trophic levels in a Silver Springs, Florida, ecosystem is shown. Each trophic level has less energy
available, and usually, but not always, supports a smaller mass of organisms at the next level.

There is a one problem when using food chains to describe most ecosystems. Even when all organisms are grouped
into appropriate trophic levels, some of these organisms can feed on more than one trophic level; likewise, some of
these organisms can also be fed on from multiple trophic levels. In addition, species feed on and are eaten by more
than one species. In other words, the linear model of ecosystems, the food chain, is a hypothetical, overly simplistic
representation of ecosystem structure. A holistic model—which includes all the interactions between different
species and their complex interconnected relationships with each other and with the environment—is a more
accurate and descriptive model for ecosystems. A food web is a concept that accounts for the multiple trophic
(feeding) interactions between each species and the many species it may feed on, or that feed on it. In a food web,
the several trophic connections between each species and the other species that interact with it may cross multiple
trophic levels. The matter and energy movements of virtually all ecosystems are more accurately described by food
webs (Figure 20.6).
530 20 • Ecosystems and the Biosphere

FIGURE 20.6 This food web shows the interactions between organisms across trophic levels. Arrows point from an organism that is
consumed to the organism that consumes it. All the producers and consumers eventually become nourishment for the decomposers (fungi,
mold, earthworms, and bacteria in the soil). (credit "fox": modification of work by Kevin Bacher, NPS; credit "owl": modification of work by
John and Karen Hollingsworth, USFWS; credit "snake": modification of work by Steve Jurvetson; credit "robin": modification of work by Alan
Vernon; credit "frog": modification of work by Alessandro Catenazzi; credit "spider": modification of work by "Sanba38"/Wikimedia
Commons; credit "centipede": modification of work by “Bauerph”/Wikimedia Commons; credit "squirrel": modification of work by Dawn
Huczek; credit "mouse": modification of work by NIGMS, NIH; credit "sparrow": modification of work by David Friel; credit "beetle":
modification of work by Scott Bauer, USDA Agricultural Research Service; credit "mushrooms": modification of work by Chris Wee; credit
"mold": modification of work by Dr. Lucille Georg, CDC; credit "earthworm": modification of work by Rob Hille; credit "bacteria":
modification of work by Don Stalons, CDC)

LINK TO LEARNING
Head to this online interactive simulator (http://openstax.org/l/food_web) to investigate food web function. In the
Interactive Labs box, under underline
Food Web,end
click
underline
Step 1. Read the instructions first, and then click Step 2 for additional
instructions. When you are ready to create a simulation, in the upper-right corner of the Interactive Labs box, click
OPEN SIMULATOR.

Two general types of food webs are often shown interacting within a single ecosystem. A grazing food web has
plants or other photosynthetic organisms at its base, followed by herbivores and various carnivores. A detrital food
web consists of a base of organisms that feed on decaying organic matter (dead organisms), including decomposers
(which break down dead and decaying organisms) and detritivores (which consume organic detritus). These
organisms are usually bacteria, fungi, and invertebrate animals that recycle organic material back into the biotic part
of the ecosystem as they themselves are consumed by other organisms. As ecosystems require a method to recycle
material from dead organisms, grazing food webs have an associated detrital food web. For example, in a meadow
ecosystem, plants may support a grazing food web of different organisms, primary and other levels of consumers,
while at the same time supporting a detrital food web of bacteria and fungi feeding off dead plants and animals.
Simultaneously, a detrital food web can contribute energy to a grazing food web, as when a robin eats an earthworm.

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 20.1 • Waterford's Energy Flow through Ecosystems 531

How Organisms Acquire Energy in a Food Web

All living things require energy in one form or another. Energy is used by most complex metabolic pathways (usually
in the form of ATP), especially those responsible for building large molecules from smaller compounds. Living
organisms would not be able to assemble macromolecules (proteins, lipids, nucleic acids, and complex
carbohydrates) from their monomers without a constant energy input.

Food-web diagrams illustrate how energy flows directionally through ecosystems. They can also indicate how
efficiently organisms acquire energy, use it, and how much remains for use by other organisms of the food web.
Energy is acquired by living things in two ways: autotrophs harness light or chemical energy and heterotrophs
acquire energy through the consumption and digestion of other living or previously living organisms.

Photosynthetic and chemosynthetic organisms are autotrophs, which are organisms capable of synthesizing their
own food (more specifically, capable of using inorganic carbon as a carbon source). Photosynthetic autotrophs
(photoautotrophs) use sunlight as an energy source, and chemosynthetic autotrophs (chemoautotrophs) use
inorganic molecules as an energy source. Autotrophs are critical for most ecosystems: they are the producer trophic
level. Without these organisms, energy would not be available to other living organisms, and life itself would not be
possible.

Photoautotrophs, such as plants, algae, and photosynthetic bacteria, are the energy source for a majority of the
world’s ecosystems. These ecosystems are often described by grazing and detrital food webs. Photoautotrophs
harness the Sun’s solar energy by converting it to chemical energy in the form of ATP (and NADP). The energy stored
in ATP is used to synthesize complex organic molecules, such as glucose. The rate at which photosynthetic
producers incorporate energy from the Sun is called gross primary productivity. However, not all of the energy
incorporated by producers is available to the other organisms in the food web because producers must also grow
and reproduce, which consumes energy. Net primary productivity is the energy that remains in the producers after
accounting for these organisms’ respiration and heat loss. The net productivity is then available to the primary
consumers at the next trophic level.

Chemoautotrophs are primarily bacteria and archaea that are found in rare ecosystems where sunlight is not
available, such as those associated with dark caves or hydrothermal vents at the bottom of the ocean (Figure 20.7).
Many chemoautotrophs in hydrothermal vents use hydrogen sulfide (H2S), which is released from the vents as a
source of chemical energy; this allows them to synthesize complex organic molecules, such as glucose, for their own
energy and, in turn, supplies energy to the rest of the ecosystem.

FIGURE 20.7 Swimming shrimp, a few squat lobsters, and hundreds of vent mussels are seen at a hydrothermal vent at the bottom of the
ocean. As no sunlight penetrates to this depth, the ecosystem is supported by chemoautotrophic bacteria and organic material that sinks
from the ocean’s surface. This picture was taken in 2006 at the submerged NW Eifuku volcano off the coast of Japan by the National
Oceanic and Atmospheric Administration (NOAA). The summit of this highly active volcano lies 1535 m below the surface.
532 20 • Ecosystems and the Biosphere

Consequences of Food Webs: Biological Magnification

One of the most important consequences of ecosystem dynamics in terms of human impact is biomagnification.
Biomagnification is the increasing concentration of persistent, toxic substances in organisms at each successive
trophic level. These are substances that are fat soluble, not water soluble, and are stored in the fat reserves of each
organism. Many substances have been shown to biomagnify, including classical studies with the pesticide
dichlorodiphenyltrichloroethane (DDT), which were described in the 1960s bestseller, Silent Spring by Rachel
Carson. DDT was a commonly used pesticide before its dangers to apex consumers, such as the bald eagle, became
known. In aquatic ecosystems, organisms from each trophic level consumed many organisms in the lower level,
which caused DDT to increase in birds (apex consumers) that ate fish. Thus, the birds accumulated sufficient
amounts of DDT to cause fragility in their eggshells. This effect increased egg breakage during nesting and was
shown to have devastating effects on these bird populations. The use of DDT was banned in the United States in the
1970s.

Other substances that biomagnify are polychlorinated biphenyls (PCB), which were used as coolant liquids in the
United States until their use was banned in 1979, and heavy metals, such as mercury, lead, and cadmium. These
substances are best studied in aquatic ecosystems, where predatory fish species accumulate very high
concentrations of toxic substances that are at quite low concentrations in the environment and in producers. As
illustrated in a study performed by the NOAA in the Saginaw Bay of Lake Huron of the North American Great Lakes
(Figure 20.8), PCB concentrations increased from the producers of the ecosystem (phytoplankton) through the
different trophic levels of fish species. The apex consumer, the walleye, has more than four times the amount of
PCBs compared to phytoplankton. Also, based on results from other studies, birds that eat these fish may have PCB
levels at least one order of magnitude higher than those found in the lake fish.

FIGURE 20.8 This chart shows the PCB concentrations found at the various trophic levels in the Saginaw Bay ecosystem of Lake Huron.
Notice that the fish in the higher trophic levels accumulate more PCBs than those in lower trophic levels. (credit: Patricia Van Hoof, NOAA)

Other concerns have been raised by the biomagnification of heavy metals, such as mercury and cadmium, in certain
types of seafood. The United States Environmental Protection Agency recommends that pregnant people and young
children should not consume any swordfish, shark, king mackerel, or tilefish because of their high mercury content.
These individuals are advised to eat fish low in mercury: salmon, shrimp, pollock, and catfish. Biomagnification is a
good example of how ecosystem dynamics can affect our everyday lives, even influencing the food we eat.

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 20.2 • Biogeochemical Cycles 533

20.2 Biogeochemical Cycles

LEARNING OBJECTIVES
By the end of this section, you will be able to:
• Discuss the biogeochemical cycles of water, carbon, nitrogen, phosphorus, and sulfur
• Explain how human activities have impacted these cycles and the resulting potential consequences for
Earth

Energy flows directionally through ecosystems, entering as sunlight (or inorganic molecules for chemoautotrophs)
and leaving as heat during the transfers between trophic levels. Rather than flowing through an ecosystem, the
matter that makes up living organisms is conserved and recycled. The six most common elements associated with
organic molecules—carbon, nitrogen, hydrogen, oxygen, phosphorus, and sulfur—take a variety of chemical forms
and may exist for long periods in the atmosphere, on land, in water, or beneath Earth’s surface. Geologic processes,
such as weathering, erosion, water drainage, and the subduction of the continental plates, all play a role in the
cycling of elements on Earth. Because geology and chemistry have major roles in the study of this process, the
recycling of inorganic matter between living organisms and their nonliving environment is called a biogeochemical
cycle.

Water, which contains hydrogen and oxygen, is essential to all living processes. The hydrosphere is the area of Earth
where water movement and storage occurs: as liquid water on the surface (rivers, lakes, oceans) and beneath the
surface (groundwater) or ice, (polar ice caps and glaciers), and as water vapor in the atmosphere. Carbon is found in
all organic macromolecules and is an important constituent of fossil fuels. Nitrogen is a major component of our
nucleic acids and proteins and is critical to human agriculture. Phosphorus, a major component of nucleic acids, is
one of the main ingredients (along with nitrogen) in artificial fertilizers used in agriculture, which has environmental
impacts on our surface water. Sulfur, critical to the three-dimensional folding of proteins (as in disulfide binding), is
released into the atmosphere by the burning of fossil fuels.

The cycling of these elements is interconnected. For example, the movement of water is critical for the leaching of
nitrogen and phosphate into rivers, lakes, and oceans. The ocean is also a major reservoir for carbon. Thus, mineral
nutrients are cycled, either rapidly or slowly, through the entire biosphere between the biotic and abiotic world and
from one living organism to another.

LINK TO LEARNING
Head to this website (http://openstax.org/l/biogeochemical) to learn more about biogeochemical cycles.

The Water Cycle

Water is essential for all living processes. The human body is more than one-half water and human cells are more
than 70 percent water. Thus, most land animals need a supply of fresh water to survive. Of the stores of water on
Earth, 97.5 percent is salt water (Figure 20.9). Of the remaining water, 99 percent is locked as underground water or
ice. Thus, less than one percent of fresh water is present in lakes and rivers. Many living things are dependent on
this small amount of surface fresh water supply, a lack of which can have important effects on ecosystem dynamics.
Humans, of course, have developed technologies to increase water availability, such as digging wells to harvest
groundwater, storing rainwater, and using desalination to obtain drinkable water from the ocean. Although this
pursuit of drinkable water has been ongoing throughout human history, the supply of fresh water continues to be a
major issue in modern times.
534 20 • Ecosystems and the Biosphere

FIGURE 20.9 Only 2.5 percent of water on Earth is fresh water, and less than 1 percent of fresh water is easily accessible to living things.

The various processes that occur during the cycling of water are illustrated in Figure 20.10. The processes include
the following:

• evaporation and sublimation

• condensation and precipitation
• subsurface water flow
• surface runoff and snowmelt
• streamflow

The water cycle is driven by the Sun’s energy as it warms the oceans and other surface waters. This leads to
evaporation (water to water vapor) of liquid surface water and sublimation (ice to water vapor) of frozen water, thus
moving large amounts of water into the atmosphere as water vapor. Over time, this water vapor condenses into
clouds as liquid or frozen droplets and eventually leads to precipitation (rain or snow), which returns water to Earth’s
surface. Rain reaching Earth’s surface may evaporate again, flow over the surface, or percolate into the ground. Most
easily observed is surface runoff: the flow of fresh water either from rain or melting ice. Runoff can make its way
through streams and lakes to the oceans or flow directly to the oceans themselves.

In most natural terrestrial environments rain encounters vegetation before it reaches the soil surface. A significant
percentage of water evaporates immediately from the surfaces of plants. What is left reaches the soil and begins to
move down. Surface runoff will occur only if the soil becomes saturated with water in a heavy rainfall. Most water in
the soil will be taken up by plant roots. The plant will use some of this water for its own metabolism, and some of
that will find its way into animals that eat the plants, but much of it will be lost back to the atmosphere through a
process known as evapotranspiration. Water enters the vascular system of the plant through the roots and
evaporates, or transpires, through the stomata of the leaves. Water in the soil that is not taken up by a plant and that
does not evaporate is able to percolate into the subsoil and bedrock. Here it forms groundwater.

Groundwater is a significant reservoir of fresh water. It exists in the pores between particles in sand and gravel, or in
the fissures in rocks. Shallow groundwater flows slowly through these pores and fissures and eventually finds its
way to a stream or lake where it becomes a part of the surface water again. Streams do not flow because they are
replenished from rainwater directly; they flow because there is a constant inflow from groundwater below. Some
groundwater is found very deep in the bedrock and can persist there for millennia. Most groundwater reservoirs, or
aquifers, are the source of drinking or irrigation water drawn up through wells. In many cases these aquifers are
being depleted faster than they are being replenished by water percolating down from above.

Rain and surface runoff are major ways in which minerals, including carbon, nitrogen, phosphorus, and sulfur, are
cycled from land to water. The environmental effects of runoff will be discussed later as these cycles are described.

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 20.2 • Biogeochemical Cycles 535

FIGURE 20.10 Water from the land and oceans enters the atmosphere by evaporation or sublimation, where it condenses into clouds and
falls as rain or snow. Precipitated water may enter freshwater bodies or infiltrate the soil. The cycle is complete when surface or
groundwater reenters the ocean. (credit: modification of work by John M. Evans and Howard Perlman, USGS)

The Carbon Cycle

Carbon is the fourth most abundant element in living organisms. Carbon is present in all organic molecules, and its
role in the structure of macromolecules is of primary importance to living organisms. Carbon compounds contain
energy, and many of these compounds from plants and algae have remained stored as fossilized carbon, which
humans use as fuel. Since the 1800s, the use of fossil fuels has accelerated. As global demand for Earth’s limited
fossil fuel supplies has risen since the beginning of the Industrial Revolution, the amount of carbon dioxide in our
atmosphere has increased as the fuels are burned. This increase in carbon dioxide has been associated with climate
change and is a major environmental concern worldwide.

The carbon cycle is most easily studied as two interconnected subcycles: one dealing with rapid carbon exchange
among living organisms and the other dealing with the long-term cycling of carbon through geologic processes. The
entire carbon cycle is shown in Figure 20.11.
536 20 • Ecosystems and the Biosphere

FIGURE 20.11 Carbon dioxide gas exists in the atmosphere and is dissolved in water. Photosynthesis converts carbon dioxide gas to
organic carbon, and respiration cycles the organic carbon back into carbon dioxide gas. Long-term storage of organic carbon occurs when
matter from living organisms is buried deep underground and becomes fossilized. Volcanic activity and, more recently, human emissions
bring this stored carbon back into the carbon cycle. (credit: modification of work by John M. Evans and Howard Perlman, USGS)

The Biological Carbon Cycle

Living organisms are connected in many ways, even between ecosystems. A good example of this connection is the
exchange of carbon between heterotrophs and autotrophs within and between ecosystems by way of atmospheric
carbon dioxide. Carbon dioxide is the basic building block that autotrophs use to build multi-carbon, high-energy
compounds, such as glucose. The energy harnessed from the Sun is used by these organisms to form the covalent
bonds that link carbon atoms together. These chemical bonds store this energy for later use in the process of
respiration. Most terrestrial autotrophs obtain their carbon dioxide directly from the atmosphere, while marine
autotrophs acquire it in the dissolved form (carbonic acid, HCO3–). However the carbon dioxide is acquired, a
byproduct of fixing carbon in organic compounds is oxygen. Photosynthetic organisms are responsible for
maintaining approximately 21 percent of the oxygen content of the atmosphere that we observe today.

The partners in biological carbon exchange are the heterotrophs (especially the primary consumers, largely
herbivores). Heterotrophs acquire the high-energy carbon compounds from the autotrophs by consuming them and
breaking them down by respiration to obtain cellular energy, such as ATP. The most efficient type of respiration,
aerobic respiration, requires oxygen obtained from the atmosphere or dissolved in water. Thus, there is a constant
exchange of oxygen and carbon dioxide between the autotrophs (which need the carbon) and the heterotrophs
(which need the oxygen). Autotrophs also respire and consume the organic molecules they form: using oxygen and
releasing carbon dioxide. They release more oxygen gas as a waste product of photosynthesis than they use for their
own respiration; therefore, there is excess available for the respiration of other aerobic organisms. Gas exchange
through the atmosphere and water is one way that the carbon cycle connects all living organisms on Earth.

The Biogeochemical Carbon Cycle

The movement of carbon through land, water, and air is complex, and, in many cases, it occurs much more slowly
geologically than the movement between living organisms. Carbon is stored for long periods in what are known as
carbon reservoirs, which include the atmosphere, bodies of liquid water (mostly oceans), ocean sediment, soil,
rocks (including fossil fuels), and Earth’s interior.

As stated, the atmosphere is a major reservoir of carbon in the form of carbon dioxide that is essential to the

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 20.2 • Biogeochemical Cycles 537

process of photosynthesis. The level of carbon dioxide in the atmosphere is greatly influenced by the reservoir of
carbon in the oceans. The exchange of carbon between the atmosphere and water reservoirs influences how much
carbon is found in each, and each one affects the other reciprocally. Carbon dioxide (CO2) from the atmosphere
dissolves in water and, unlike oxygen and nitrogen gas, reacts with water molecules to form ionic compounds. Some
of these ions combine with calcium ions in the seawater to form calcium carbonate (CaCO3), a major component of
the shells of marine organisms. These organisms eventually form sediments on the ocean floor. Over geologic time,
the calcium carbonate forms limestone, which comprises the largest carbon reservoir on Earth.

On land, carbon is stored in soil as organic carbon as a result of the decomposition of living organisms or from
weathering of terrestrial rock and minerals. Deeper under the ground, at land and at sea, are fossil fuels, the
anaerobically decomposed remains of plants that take millions of years to form. Fossil fuels are considered a non-
renewable resource because their use far exceeds their rate of formation. A non-renewable resource is either
regenerated very slowly or not at all. Another way for carbon to enter the atmosphere is from land (including land
beneath the surface of the ocean) by the eruption of volcanoes and other geothermal systems. Carbon sediments
from the ocean floor are taken deep within Earth by the process of subduction: the movement of one tectonic plate
beneath another. Carbon is released as carbon dioxide when a volcano erupts or from volcanic hydrothermal vents.

Carbon dioxide is also added to the atmosphere by the animal husbandry practices of humans. The large number of
land animals raised to feed Earth’s growing human population results in increased carbon-dioxide levels in the
atmosphere caused by their respiration. This is another example of how human activity indirectly affects
biogeochemical cycles in a significant way. Although much of the debate about the future effects of increasing
atmospheric carbon on climate change focuses on fossils fuels, scientists take natural processes, such as
volcanoes, plant growth, soil carbon levels, and respiration, into account as they model and predict the future
impact of this increase.

The Nitrogen Cycle

Getting nitrogen into the living world is difficult. Plants and phytoplankton are not equipped to incorporate nitrogen
from the atmosphere (which exists as tightly bonded, triple covalent N2) even though this molecule comprises
approximately 78 percent of the atmosphere. Nitrogen enters the living world via free-living and symbiotic bacteria,
which incorporate nitrogen into their macromolecules through nitrogen fixation (conversion of N2). Cyanobacteria
live in most aquatic ecosystems where sunlight is present; they play a key role in nitrogen fixation. Cyanobacteria
are able to use inorganic sources of nitrogen to “fix” nitrogen. Rhizobium bacteria live symbiotically in the root
nodules of legumes (such as peas, beans, and peanuts) and provide them with the organic nitrogen they need. Free-
living bacteria, such as Azotobacter, are also important nitrogen fixers.

Organic nitrogen is especially important to the study of ecosystem dynamics since many ecosystem processes, such
as primary production and decomposition, are limited by the available supply of nitrogen. As shown in Figure 20.12,
the nitrogen that enters living systems by nitrogen fixation is eventually converted from organic nitrogen back into
nitrogen gas by bacteria. This process occurs in three steps in terrestrial systems: ammonification, nitrification, and
denitrification. First, the ammonification process converts nitrogenous waste from living animals or from the
remains of dead animals into ammonium (NH4+ ) by certain bacteria and fungi. Second, this ammonium is then
converted to nitrites (NO2−) by nitrifying bacteria, such as Nitrosomonas, through nitrification. Subsequently, nitrites
are converted to nitrates (NO3−) by similar organisms. Lastly, the process of denitrification occurs, whereby bacteria,
such as Pseudomonas and Clostridium, convert the nitrates into nitrogen gas, thus allowing it to re-enter the
atmosphere.
538 20 • Ecosystems and the Biosphere

VISUAL CONNECTION

FIGURE 20.12 Nitrogen enters the living world from the atmosphere through nitrogen-fixing bacteria. This nitrogen and nitrogenous waste
from animals is then processed back into gaseous nitrogen by soil bacteria, which also supply terrestrial food webs with the organic
nitrogen they need. (credit: modification of work by John M. Evans and Howard Perlman, USGS)

Which of the following statements about the nitrogen cycle is false?

a. Ammonification converts organic nitrogenous matter from living organisms into ammonium (NH4+).
b. Denitrification by bacteria converts nitrates (NO3−)to nitrogen gas (N2).
c. Nitrification by bacteria converts nitrates (NO3−)to nitrites (NO2−)
d. Nitrogen fixing bacteria convert nitrogen gas (N2) into organic compounds.

Human activity can release nitrogen into the environment by two primary means: the combustion of fossil fuels,
which releases different nitrogen oxides, and by the use of artificial fertilizers (which contain nitrogen and
phosphorus compounds) in agriculture, which are then washed into lakes, streams, and rivers by surface runoff.
Atmospheric nitrogen (other than N2) is associated with several effects on Earth’s ecosystems including the
production of acid rain (as nitric acid, HNO3) and greenhouse gas effects (as nitrous oxide, N2O), potentially causing
climate change. A major effect from fertilizer runoff is saltwater and freshwater eutrophication, a process whereby
nutrient runoff causes the overgrowth of algae and a number of consequential problems.

A similar process occurs in the marine nitrogen cycle, where the ammonification, nitrification, and denitrification
processes are performed by marine bacteria and archaea. Some of this nitrogen falls to the ocean floor as sediment,
which can then be moved to land in geologic time by uplift of Earth’s surface, and thereby incorporated into
terrestrial rock. Although the movement of nitrogen from rock directly into living systems has been traditionally seen
as insignificant compared with nitrogen fixed from the atmosphere, a recent study showed that this process may
1
indeed be significant and should be included in any study of the global nitrogen cycle.

The Phosphorus Cycle

Phosphorus is an essential nutrient for living processes; it is a major component of nucleic acids and phospholipids,

1 Scott L. Morford, Benjamin Z. Houlton, and Randy A. Dahlgren, “Increased Forest Ecosystem Carbon and Nitrogen Storage from Nitrogen
Rich Bedrock,” Nature 477, no. 7362 (2011): 78–81.

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 20.2 • Biogeochemical Cycles 539

and, as calcium phosphate, makes up the supportive components of our bones. Phosphorus is often the limiting
nutrient (necessary for growth) in aquatic, particularly freshwater, ecosystems.

Phosphorus occurs in nature as the phosphate ion (PO43-). In addition to phosphate runoff as a result of human
activity, natural surface runoff occurs when it is leached from phosphate-containing rock by weathering, thus
sending phosphates into rivers, lakes, and the ocean. This rock has its origins in the ocean. Phosphate-containing
ocean sediments form primarily from the bodies of ocean organisms and from their excretions. However, volcanic
ash, aerosols, and mineral dust may also be significant phosphate sources. This sediment then is moved to land
over geologic time by the uplifting of Earth’s surface. (Figure 20.13)

Phosphorus is also reciprocally exchanged between phosphate dissolved in the ocean and marine organisms. The
movement of phosphate from the ocean to the land and through the soil is extremely slow, with the average
phosphate ion having an oceanic residence time between 20,000 and 100,000 years.

FIGURE 20.13 In nature, phosphorus exists as the phosphate ion (PO43-). Weathering of rocks and volcanic activity releases phosphate
into the soil, water, and air, where it becomes available to terrestrial food webs. Phosphate enters the oceans in surface runoff,
groundwater flow, and river flow. Phosphate dissolved in ocean water cycles into marine food webs. Some phosphate from the marine food
webs falls to the ocean floor, where it forms sediment. (credit: modification of work by John M. Evans and Howard Perlman, USGS)

Excess phosphorus and nitrogen that enter these ecosystems from fertilizer runoff and from sewage cause
excessive growth of algae. The subsequent death and decay of these organisms depletes dissolved oxygen, which
leads to the death of aquatic organisms, such as shellfish and finfish. This process is responsible for dead zones in
lakes and at the mouths of many major rivers and for massive fish kills, which often occur during the summer
months (see Figure 20.14).
540 20 • Ecosystems and the Biosphere

FIGURE 20.14 Dead zones occur when phosphorus and nitrogen from fertilizers cause excessive growth of microorganisms, which depletes
oxygen and kills fauna. Worldwide, large dead zones are found in areas of high population density. (credit: Robert Simmon, Jesse Allen,
NASA Earth Observatory)

A dead zone is an area in lakes and oceans near the mouths of rivers where large areas are periodically depleted of
their normal flora and fauna; these zones can be caused by eutrophication, oil spills, dumping toxic chemicals, and
other human activities. The number of dead zones has increased for several years, and more than 400 of these
zones were present as of 2008. One of the worst dead zones is off the coast of the United States in the Gulf of
Mexico: fertilizer runoff from the Mississippi River basin created a dead zone of over 8,463 square miles. Phosphate
and nitrate runoff from fertilizers also negatively affect several lake and bay ecosystems including the Chesapeake
Bay in the eastern United States.

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 20.2 • Biogeochemical Cycles 541

CAREER CONNECTION

Chesapeake Bay

FIGURE 20.15 This (a) satellite image shows the Chesapeake Bay, an ecosystem affected by phosphate and nitrate runoff. A (b) member of
the Army Corps of Engineers holds a clump of oysters being used as a part of the oyster restoration effort in the bay. (credit a: modification
of work by NASA/MODIS; credit b: modification of work by U.S. Army)

The Chesapeake Bay (Figure 20.15a) is one of the most scenic areas on Earth; it is now in distress and is recognized
as a case study of a declining ecosystem. In the 1970s, the Chesapeake Bay was one of the first aquatic ecosystems
to have identified dead zones, which continue to kill many fish and bottom-dwelling species such as clams, oysters,
and worms. Several species have declined in the Chesapeake Bay because surface water runoff contains excess
nutrients from artificial fertilizer use on land. The source of the fertilizers (with high nitrogen and phosphate content)
is not limited to agricultural practices. There are many nearby urban areas and more than 150 rivers and streams
empty into the bay that are carrying fertilizer runoff from lawns and gardens. Thus, the decline of the Chesapeake
Bay is a complex issue and requires the cooperation of industry, agriculture, and individual homeowners.

Of particular interest to conservationists is the oyster population (Figure 20.15b); it is estimated that more than
200,000 acres of oyster reefs existed in the bay in the 1700s, but that number has now declined to only 36,000
acres. Oyster harvesting was once a major industry for Chesapeake Bay, but it declined 88 percent between 1982
and 2007. This decline was caused not only by fertilizer runoff and dead zones, but also because of overharvesting.
Oysters require a certain minimum population density because they must be in close proximity to reproduce.
Human activity has altered the oyster population and locations, thus greatly disrupting the ecosystem.

The restoration of the oyster population in the Chesapeake Bay has been ongoing for several years with mixed
success. Not only do many people find oysters good to eat, but the oysters also clean up the bay. They are filter
feeders, and as they eat, they clean the water around them. Filter feeders eat by pumping a continuous stream of
water over finely divided appendages (gills in the case of oysters) and capturing prokaryotes, plankton, and fine
organic particles in their mucus. In the 1700s, it was estimated that it took only a few days for the oyster population
to filter the entire volume of the bay. Today, with the changed water conditions, it is estimated that the present
population would take nearly a year to do the same job.

Restoration efforts have been ongoing for several years by non-profit organizations such as the Chesapeake Bay
Foundation. The restoration goal is to find a way to increase population density so the oysters can reproduce more
efficiently. Many disease-resistant varieties (developed at the Virginia Institute of Marine Science for the College of
542 20 • Ecosystems and the Biosphere

William and Mary) are now available and have been used in the construction of experimental oyster reefs. Efforts by
Virginia and Delaware to clean and restore the bay have been hampered because much of the pollution entering the
bay comes from other states, which emphasizes the need for interstate cooperation to gain successful restoration.

The new, hearty oyster strains have also spawned a new and economically viable industry—oyster
aquaculture—which not only supplies oysters for food and profit, but also has the added benefit of cleaning the bay.

The Sulfur Cycle

Sulfur is an essential element for the macromolecules of living things. As part of the amino acid cysteine, it is
involved in the formation of proteins. As shown in Figure 20.16, sulfur cycles between the oceans, land, and
atmosphere. Atmospheric sulfur is found in the form of sulfur dioxide (SO2), which enters the atmosphere in three
ways: first, from the decomposition of organic molecules; second, from volcanic activity and geothermal vents; and,
third, from the burning of fossil fuels by humans.

FIGURE 20.16 Sulfur dioxide from the atmosphere becomes available to terrestrial and marine ecosystems when it is dissolved in
precipitation as weak sulfurous acid or when it falls directly to Earth as fallout. Weathering of rocks also makes sulfates available to
terrestrial ecosystems. Decomposition of living organisms returns sulfates to the ocean, soil, and atmosphere. (credit: modification of work
by John M. Evans and Howard Perlman, USGS)

On land, sulfur is deposited in four major ways: precipitation, direct fallout from the atmosphere, rock weathering,
and geothermal vents (Figure 20.17). Atmospheric sulfur is found in the form of sulfur dioxide (SO2), and as rain falls
through the atmosphere, sulfur is dissolved in the form of weak sulfurous acid (H2SO3). Sulfur can also fall directly
from the atmosphere in a process called fallout. Also, as sulfur-containing rocks weather, sulfur is released into the
soil. These rocks originate from ocean sediments that are moved to land by the geologic uplifting of ocean
sediments. Terrestrial ecosystems can then make use of these soil sulfates (SO42-), which enter the food web by
being taken up by plant roots. When these plants decompose and die, sulfur is released back into the atmosphere as
hydrogen sulfide (H2S) gas.

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 20.3 • Terrestrial Biomes 543

FIGURE 20.17 At this sulfur vent in Lassen Volcanic National Park in northeastern California, the yellowish sulfur deposits are visible near
the mouth of the vent. (credit: “Calbear22”/Wikimedia Commons)

Sulfur enters the ocean in runoff from land, from atmospheric fallout, and from underwater geothermal vents. Some
ecosystems rely on chemoautotrophs using sulfur as a biological energy source. This sulfur then supports marine
ecosystems in the form of sulfates.

Human activities have played a major role in altering the balance of the global sulfur cycle. The burning of large
quantities of fossil fuels, especially from coal, releases larger amounts of hydrogen sulfide gas into the atmosphere.
As rain falls through this gas, it creates the phenomenon known as acid rain, which damages the natural
environment by lowering the pH of lakes, thus killing many of the resident plants and animals. Acid rain is corrosive
rain caused by rainwater falling to the ground through sulfur dioxide gas, turning it into weak sulfuric acid, which
causes damage to aquatic ecosystems. Acid rain also affects the man-made environment through the chemical
degradation of buildings. For example, many marble monuments, such as the Lincoln Memorial in Washington, DC,
have suffered significant damage from acid rain over the years. These examples show the wide-ranging effects of
human activities on our environment and the challenges that remain for our future.

20.3 Terrestrial Biomes

LEARNING OBJECTIVES
By the end of this section, you will be able to:
• Identify the two major abiotic factors that determine the type of terrestrial biome in an area
• Recognize distinguishing characteristics of each of the eight major terrestrial biomes

Earth’s biomes can be either terrestrial or aquatic. Terrestrial biomes are based on land, while aquatic biomes
include both ocean and freshwater biomes. The eight major terrestrial biomes on Earth are each distinguished by
characteristic temperatures and amount of precipitation. Annual totals and fluctuations of precipitation affect the
kinds of vegetation and animal life that can exist in broad geographical regions. Temperature variation on a daily and
seasonal basis is also important for predicting the geographic distribution of a biome. Since a biome is defined by
climate, the same biome can occur in geographically distinct areas with similar climates (Figure 20.18). There are
also large areas on Antarctica, Greenland, and in mountain ranges that are covered by permanent glaciers and
support very little life. Strictly speaking, these are not considered biomes and in addition to extremes of cold, they
are also often deserts with very low precipitation.
544 20 • Ecosystems and the Biosphere

FIGURE 20.18 Each of the world’s eight major biomes is distinguished by characteristic temperatures and amount of precipitation. Polar ice
caps and mountains are also shown.

Tropical Forest
Tropical rainforests are also referred to as tropical wet forests. This biome is found in equatorial regions (Figure
20.18). Tropical rainforests are the most diverse terrestrial biome. This biodiversity is still largely unknown to
science and is under extraordinary threat primarily through logging and deforestation for agriculture. Tropical
rainforests have also been described as nature’s pharmacy because of the potential for new drugs that is largely
hidden in the chemicals produced by the huge diversity of plants, animals, and other organisms. The vegetation is
characterized by plants with spreading roots and broad leaves that fall off throughout the year, unlike the trees of
deciduous forests that lose their leaves in one season. These forests are “evergreen,” year-round.

The temperature and sunlight profiles of tropical rainforests are stable in comparison to that of other terrestrial
biomes, with average temperatures ranging from 20oC to 34oC (68oF to 93oF). Month-to-month temperatures are
relatively constant in tropical rainforests, in contrast to forests further from the equator. This lack of temperature
seasonality leads to year-round plant growth, rather than the seasonal growth seen in other biomes. In contrast to
other ecosystems, a more constant daily amount of sunlight (11–12 hours per day) provides more solar radiation,
thereby a longer period of time for plant growth.

The annual rainfall in tropical rainforests ranges from 250 cm to more than 450 cm (8.2–14.8 ft) with considerable
seasonal variation. Tropical rainforests have wet months in which there can be more than 30 cm (11–12 in) of
precipitation, as well as dry months in which there are fewer than 10 cm (3.5 in) of rainfall. However, the driest
month of a tropical rainforest can still exceed the annual rainfall of some other biomes, such as deserts.

Tropical rainforests have high net primary productivity because the annual temperatures and precipitation values
support rapid plant growth (Figure 20.19). However, the high rainfall quickly leaches nutrients from the soils of
these forests, which are typically low in nutrients. Tropical rainforests are characterized by vertical layering of
vegetation and the formation of distinct habitats for animals within each layer. On the forest floor is a sparse layer of
plants and decaying plant matter. Above that is an understory of short, shrubby foliage. A layer of trees rises above
this understory and is topped by a closed upper canopy—the uppermost overhead layer of branches and leaves.
Some additional trees emerge through this closed upper canopy. These layers provide diverse and complex habitats
for the variety of plants, animals, and other organisms within the tropical wet forests. Many species of animals use
the variety of plants and the complex structure of the tropical wet forests for food and shelter. Some organisms live
several meters above ground rarely ever descending to the forest floor.

Rainforests are not the only forest biome in the tropics; there are also tropical dry forests, which are characterized
by a dry season of varying lengths. These forests commonly experience leaf loss during the dry season to one
degree or another. The loss of leaves from taller trees during the dry season opens up the canopy and allows
sunlight to the forest floor that allows the growth of thick ground-level brush, which is absent in tropical rainforests.
Extensive tropical dry forests occur in Africa (including Madagascar), India, southern Mexico, and South America.

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 20.3 • Terrestrial Biomes 545

FIGURE 20.19 Species diversity is very high in tropical wet forests, such as these forests of Madre de Dios, Peru, near the Amazon River.
(credit: Roosevelt Garcia)

Savannas
Savannas are grasslands with scattered trees, and they are found in Africa, South America, and northern Australia
(Figure 20.18). Savannas are hot, tropical areas with temperatures averaging from 24oC –29oC (75oF –84oF) and an
annual rainfall of 51–127 cm (20–50 in). Savannas have an extensive dry season and consequent fires. As a result,
scattered in the grasses and forbs (herbaceous flowering plants) that dominate the savanna, there are relatively few
trees (Figure 20.20). Since fire is an important source of disturbance in this biome, plants have evolved well-
developed root systems that allow them to quickly re-sprout after a fire.

FIGURE 20.20 Although savannas are dominated by grasses, small woodlands, such as this one in Mount Archer National Park in
Queensland, Australia, may dot the landscape. (credit: "Ethel Aardvark"/Wikimedia Commons)

Deserts
Subtropical deserts exist between 15o and 30o north and south latitude and are centered on the Tropic of Cancer
and the Tropic of Capricorn (Figure 20.18). Deserts are frequently located on the downwind or lee side of mountain
ranges, which create a rain shadow after prevailing winds drop their water content on the mountains. This is typical
of the North American deserts, such as the Mohave and Sonoran deserts. Deserts in other regions, such as the
546 20 • Ecosystems and the Biosphere

Sahara Desert in northern Africa or the Namib Desert in southwestern Africa are dry because of the high-pressure,
dry air descending at those latitudes. Subtropical deserts are very dry; evaporation typically exceeds precipitation.
Subtropical hot deserts can have daytime soil surface temperatures above 60oC (140oF) and nighttime
temperatures approaching 0oC (32oF). The temperature drops so far because there is little water vapor in the air to
prevent radiative cooling of the land surface. Subtropical deserts are characterized by low annual precipitation of
fewer than 30 cm (12 in) with little monthly variation and lack of predictability in rainfall. Some years may receive
tiny amounts of rainfall, while others receive more. In some cases, the annual rainfall can be as low as 2 cm (0.8 in)
in subtropical deserts located in central Australia (“the Outback”) and northern Africa.

The low species diversity of this biome is closely related to its low and unpredictable precipitation. Despite the
relatively low diversity, desert species exhibit fascinating adaptations to the harshness of their environment. Very
dry deserts lack perennial vegetation that lives from one year to the next; instead, many plants are annuals that
grow quickly and reproduce when rainfall does occur, then they die. Perennial plants in deserts are characterized by
adaptations that conserve water: deep roots, reduced foliage, and water-storing stems (Figure 20.21). Seed plants
in the desert produce seeds that can lie dormant for extended periods between rains. Most animal life in subtropical
deserts has adapted to a nocturnal life, spending the hot daytime hours beneath the ground. The Namib Desert is
the oldest on the planet, and has probably been dry for more than 55 million years. It supports a number of endemic
species (species found only there) because of this great age. For example, the unusual gymnosperm Welwitschia
mirabilis is the only extant species of an entire order of plants. There are also five species of reptiles considered
endemic to the Namib.

In addition to subtropical deserts there are cold deserts that experience freezing temperatures during the winter
and any precipitation is in the form of snowfall. The largest of these deserts are the Gobi Desert in northern China
and southern Mongolia, the Taklimakan Desert in western China, the Turkestan Desert, and the Great Basin Desert
of the United States.

FIGURE 20.21 Many desert plants have tiny leaves or no leaves at all to reduce water loss. The leaves of ocotillo, shown here in the
Chihuahuan Desert in Big Bend National Park, Texas, appear only after rainfall and then are shed. (credit “bare ocotillo”:
"Leaflet"/Wikimedia Commons)

Chaparral
The chaparral is also called scrub forest and is found in California, along the Mediterranean Sea, and along the
southern coast of Australia (Figure 20.18). The annual rainfall in this biome ranges from 65 cm to 75 cm (25.6–29.5
in) and the majority of the rain falls in the winter. Summers are very dry and many chaparral plants are dormant
during the summertime. The chaparral vegetation is dominated by shrubs and is adapted to periodic fires, with
some plants producing seeds that germinate only after a hot fire. The ashes left behind after a fire are rich in
nutrients like nitrogen that fertilize the soil and promote plant regrowth. Fire is a natural part of the maintenance of
this biome and frequently threatens human habitation in this biome in the U.S. (Figure 20.22).

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 20.3 • Terrestrial Biomes 547

FIGURE 20.22 The chaparral is dominated by shrubs. (credit: Miguel Vieira)

Temperate Grasslands
Temperate grasslands are found throughout central North America, where they are also known as prairies, and in
Eurasia, where they are known as steppes (Figure 20.18). Temperate grasslands have pronounced annual
fluctuations in temperature with hot summers and cold winters. The annual temperature variation produces specific
growing seasons for plants. Plant growth is possible when temperatures are warm enough to sustain plant growth,
which occurs in the spring, summer, and fall.

Annual precipitation ranges from 25.4 cm to 88.9 cm (10–35 in). Temperate grasslands have few trees except for
those found growing along rivers or streams. The dominant vegetation tends to consist of grasses. The treeless
condition is maintained by low precipitation, frequent fires, and grazing (Figure 20.23). The vegetation is very dense
and the soils are fertile because the subsurface of the soil is packed with the roots and rhizomes (underground
stems) of these grasses. The roots and rhizomes act to anchor plants into the ground and replenish the organic
material (humus) in the soil when they die and decay.

FIGURE 20.23 The American bison (Bison bison), more commonly called the buffalo, is a grazing mammal that once populated American
prairies in huge numbers. (credit: Jack Dykinga, USDA ARS)

Fires, which are a natural disturbance in temperate grasslands, can be ignited by lightning strikes. It also appears
that the lightning-caused fire regime in North American grasslands was enhanced by intentional burning by humans.
When fire is suppressed in temperate grasslands, the vegetation eventually converts to scrub and dense forests.
548 20 • Ecosystems and the Biosphere

Often, the restoration or management of temperate grasslands requires the use of controlled burns to suppress the
growth of trees and maintain the grasses.

Temperate Forests
Temperate forests are the most common biome in eastern North America, Western Europe, Eastern Asia, Chile, and
New Zealand (Figure 20.18). This biome is found throughout mid-latitude regions. Temperatures range between
–30oC and 30oC (–22oF to 86oF) and drop to below freezing on an annual basis. These temperatures mean that
temperate forests have defined growing seasons during the spring, summer, and early fall. Precipitation is relatively
constant throughout the year and ranges between 75 cm and 150 cm (29.5–59 in).

Deciduous trees are the dominant plant in this biome with fewer evergreen conifers. Deciduous trees lose their
leaves each fall and remain leafless in the winter. Thus, little photosynthesis occurs during the dormant winter
period. Each spring, new leaves appear as temperature increases. Because of the dormant period, the net primary
productivity of temperate forests is less than that of tropical rainforests. In addition, temperate forests show far less
diversity of tree species than tropical rainforest biomes.

The trees of the temperate forests leaf out and shade much of the ground; however, more sunlight reaches the
ground in this biome than in tropical rainforests because trees in temperate forests do not grow as tall as the trees
in tropical rainforests. The soils of the temperate forests are rich in inorganic and organic nutrients compared to
tropical rainforests. This is because of the thick layer of leaf litter on forest floors and reduced leaching of nutrients
by rainfall. As this leaf litter decays, nutrients are returned to the soil. The leaf litter also protects soil from erosion,
insulates the ground, and provides habitats for invertebrates and their predators (Figure 20.24).

FIGURE 20.24 Deciduous trees are the dominant plant in the temperate forest. (credit: Oliver Herold)

Boreal Forests
The boreal forest, also known as taiga or coniferous forest, is found roughly between 50o and 60o north latitude
across most of Canada, Alaska, Russia, and northern Europe (Figure 20.18). Boreal forests are also found above a
certain elevation (and below high elevations where trees cannot grow) in mountain ranges throughout the Northern
Hemisphere. This biome has cold, dry winters and short, cool, wet summers. The annual precipitation is from 40 cm
to 100 cm (15.7–39 in) and usually takes the form of snow; little evaporation occurs because of the cold
temperatures.

The long and cold winters in the boreal forest have led to the predominance of cold-tolerant cone-bearing plants.
These are evergreen coniferous trees like pines, spruce, and fir, which retain their needle-shaped leaves year-round.
Evergreen trees can photosynthesize earlier in the spring than deciduous trees because less energy from the Sun is

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 20.3 • Terrestrial Biomes 549

required to warm a needle-like leaf than a broad leaf. Evergreen trees grow faster than deciduous trees in the boreal
forest. In addition, soils in boreal forest regions tend to be acidic with little available nitrogen. Leaves are a nitrogen-
rich structure and deciduous trees must produce a new set of these nitrogen-rich structures each year. Therefore,
coniferous trees that retain nitrogen-rich needles in a nitrogen limiting environment may have had a competitive
advantage over the broad-leafed deciduous trees.

The net primary productivity of boreal forests is lower than that of temperate forests and tropical wet forests. The
aboveground biomass of boreal forests is high because these slow-growing tree species are long-lived and
accumulate standing biomass over time. Species diversity is less than that seen in temperate forests and tropical
rainforests. Boreal forests lack the layered forest structure seen in tropical rainforests or, to a lesser degree,
temperate forests. The structure of a boreal forest is often only a tree layer and a ground layer. When conifer
needles are dropped, they decompose more slowly than broad leaves; therefore, fewer nutrients are returned to the
soil to fuel plant growth (Figure 20.25).

FIGURE 20.25 The boreal forest (taiga) has low lying plants and conifer trees. (credit: L.B. Brubaker, NOAA)

Arctic Tundra
The Arctic tundra lies north of the subarctic boreal forests and is located throughout the Arctic regions of the
Northern Hemisphere (Figure 20.18). Tundra also exists at elevations above the tree line on mountains. The average
winter temperature is –34°C (–29.2°F) and the average summer temperature is 3°C–12°C (37°F –52°F). Plants in
the Arctic tundra have a short growing season of approximately 50–60 days. However, during this time, there are
almost 24 hours of daylight and plant growth is rapid. The annual precipitation of the Arctic tundra is low (15–25 cm
or 6–10 in) with little annual variation in precipitation. And, as in the boreal forests, there is little evaporation
because of the cold temperatures.

Plants in the Arctic tundra are generally low to the ground and include low shrubs, grasses, lichens, and small
flowering plants (Figure 20.26). There is little species diversity, low net primary productivity, and low aboveground
biomass. The soils of the Arctic tundra may remain in a perennially frozen state referred to as permafrost. The
permafrost makes it impossible for roots to penetrate far into the soil and slows the decay of organic matter, which
inhibits the release of nutrients from organic matter. The melting of the permafrost in the brief summer provides
water for a burst of productivity while temperatures and long days permit it. During the growing season, the ground
of the Arctic tundra can be completely covered with plants or lichens.
550 20 • Ecosystems and the Biosphere

FIGURE 20.26 Low-growing plants such as shrub willow dominate the tundra landscape during the summer, shown here in the Arctic
National Wildlife Refuge. (credit: Arctic National Wildlife Refuge, USFWS)

LINK TO LEARNING
Watch this Assignment Discovery: Biomes (http://openstax.org/l/biomes)video for an overview of biomes. To explore
further, select one of the biomes on the extended playlist: desert, savanna, temperate forest, temperate grassland,
tropic, tundra.

20.4 Aquatic and Marine Biomes

LEARNING OBJECTIVES
By the end of this section, you will be able to:
• Describe the effects of abiotic factors on the composition of plant and animal communities in aquatic
biomes
• Compare the characteristics of the ocean zones
• Summarize the characteristics of standing water and flowing water in freshwater biomes

Like terrestrial biomes, aquatic biomes are influenced by abiotic factors. In the case of aquatic biomes the abiotic
factors include light, temperature, flow regime, and dissolved solids. The aquatic medium—water— has different
physical and chemical properties than air. Even if the water in a pond or other body of water is perfectly clear (there
are no suspended particles), water, on its own, absorbs light. As one descends deep enough into a body of water,
eventually there will be a depth at which the sunlight cannot reach. While there are some abiotic and biotic factors
in a terrestrial ecosystem that shade light (like fog, dust, or insect swarms), these are not usually permanent
features of the environment. The importance of light in aquatic biomes is central to the communities of organisms
found in both freshwater and marine ecosystems because it controls productivity through photosynthesis.

In addition to light, solar radiation warms bodies of water and many exhibit distinct layers of water at differing
temperatures. The water temperature affects the organisms’ rates of growth and the amount of dissolved oxygen
available for respiration.

The movement of water is also important in many aquatic biomes. In rivers, the organisms must obviously be
adapted to the constant movement of the water around them, but even in larger bodies of water such as the oceans,
regular currents and tides impact availability of nutrients, food resources, and the presence of the water itself.

Finally, all natural water contains dissolved solids, or salts. Fresh water contains low levels of such dissolved
substances because the water is rapidly recycled through evaporation and precipitation. The oceans have a
relatively constant high salt content. Aquatic habitats at the interface of marine and freshwater ecosystems have
complex and variable salt environments that range between freshwater and marine levels. These are known as
brackish water environments. Lakes located in closed drainage basins concentrate salt in their waters and can have

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 20.4 • Aquatic and Marine Biomes 551

extremely high salt content that only a few and highly specialized species are able to inhabit.

Marine Biomes
The ocean is a continuous body of salt water that is relatively uniform in chemical composition. It is a weak solution
of mineral salts and decayed biological matter. Within the ocean, coral reefs are a second type of marine biome.
Estuaries, coastal areas where salt water and fresh water mix, form a third unique marine biome.

The ocean is categorized by several zones (Figure 20.28). All of the ocean’s open water is referred to as the pelagic
realm (or zone). The benthic realm (or zone) extends along the ocean bottom from the shoreline to the deepest
parts of the ocean floor. From the surface to the bottom or the limit to which photosynthesis occurs is the photic
zone (approximately 200 m or 650 ft). At depths greater than 200 m, light cannot penetrate; thus, this is referred to
as the aphotic zone. The majority of the ocean is aphotic and lacks sufficient light for photosynthesis. The deepest
part of the ocean, the Challenger Deep (in the Mariana Trench, located in the western Pacific Ocean), is about
11,000 m (about 6.8 mi) deep. To give some perspective on the depth of this trench, the ocean is, on average, 4267
m or 14,000 ft deep.

Ocean
The physical diversity of the ocean has a significant influence on the diversity of organisms that live within it. The
ocean is categorized into different zones based on how far light reaches into the water. Each zone has a distinct
group of species adapted to the biotic and abiotic conditions particular to that zone.

The intertidal zone (Figure 20.28) is the oceanic region that is closest to land. With each tidal cycle, the intertidal
zone alternates between being inundated with water and left high and dry. Generally, most people think of this
portion of the ocean as a sandy beach. In some cases, the intertidal zone is indeed a sandy beach, but it can also be
rocky, muddy, or dense with tangled roots in mangrove forests. The intertidal zone is an extremely variable
environment because of tides. Organisms may be exposed to air at low tide and are underwater during high tide.
Therefore, living things that thrive in the intertidal zone are often adapted to being dry for long periods of time. The
shore of the intertidal zone is also repeatedly struck by waves and the organisms found there are adapted to
withstand damage from the pounding action of the waves (Figure 20.27). The exoskeletons of shoreline crustaceans
(such as the shore crab, Carcinus maenas) are tough and protect them from desiccation (drying out) and wave
damage. Another consequence of the pounding waves is that few algae and plants establish themselves in
constantly moving sand or mud.

FIGURE 20.27 Sea stars, sea urchins, and mussel shells are often found in the intertidal zone, shown here in Kachemak Bay, Alaska. (credit:
NOAA)

The neritic zone (Figure 20.28) extends from the margin of the intertidal zone to depths of about 200 m (or 650 ft)
at the edge of the continental shelf. When the water is relatively clear, photosynthesis can occur in the neritic zone.
552 20 • Ecosystems and the Biosphere

The water contains silt and is well-oxygenated, low in pressure, and stable in temperature. These factors all
contribute to the neritic zone having the highest productivity and biodiversity of the ocean. Phytoplankton, including
photosynthetic bacteria and larger species of algae, are responsible for the bulk of this primary productivity.
Zooplankton, protists, small fishes, and shrimp feed on the producers and are the primary food source for most of
the world’s fisheries. The majority of these fisheries exist within the neritic zone.

Beyond the neritic zone is the open ocean area known as the oceanic zone (Figure 20.28). Within the oceanic zone
there is thermal stratification. Abundant phytoplankton and zooplankton support populations of fish and whales.
Nutrients are scarce and this is a relatively less productive part of the marine biome. When photosynthetic
organisms and the organisms that feed on them die, their bodies fall to the bottom of the ocean where they remain;
the open ocean lacks a process for bringing the organic nutrients back up to the surface.

Beneath the pelagic zone is the benthic realm, the deepwater region beyond the continental shelf (Figure 20.28).
The bottom of the benthic realm is comprised of sand, silt, and dead organisms. Temperature decreases as water
depth increases. This is a nutrient-rich portion of the ocean because of the dead organisms that fall from the upper
layers of the ocean. Because of this high level of nutrients, a diversity of fungi, sponges, sea anemones, marine
worms, sea stars, fishes, and bacteria exists.

The deepest part of the ocean is the abyssal zone, which is at depths of 4000 m or greater. The abyssal zone (Figure
20.28) is very cold and has very high pressure, very low or no oxygen content, and high nutrient content as the dead
and decomposing material that drifts down from the layers above. There are a variety of invertebrates and fishes
found in this zone, but the abyssal zone does not have photosynthetic organisms. Chemosynthetic bacteria use the
hydrogen sulfide and other minerals emitted from deep hydrothermal vents. These chemosynthetic bacteria use the
hydrogen sulfide as an energy source and serve as the base of the food chain found around the vents.

VISUAL CONNECTION

FIGURE 20.28 The ocean is divided into different zones based on water depth, distance from the shoreline, and light penetration.

In which of the following regions would you expect to find photosynthetic organisms?

a. The aphotic zone, the neritic zone, the oceanic zone, and the benthic realm.
b. The photic zone, the intertidal zone, the neritic zone, and the oceanic zone.
c. The photic zone, the abyssal zone, the neritic zone, and the oceanic zone.
d. The pelagic realm, the aphotic zone, the neritic zone, and the oceanic zone.

Coral Reefs
Coral reefs are ocean ridges formed by marine invertebrates living in warm shallow waters within the photic zone of
the ocean. They are found within 30˚ north and south of the equator. The Great Barrier Reef is a well-known reef

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 20.4 • Aquatic and Marine Biomes 553

system located several miles off the northeastern coast of Australia. Other coral reefs are fringing islands, which are
directly adjacent to land, or atolls, which are circular reefs surrounding a former island that is now underwater. The
coral-forming colonies of organisms (members of phylum Cnidaria) secrete a calcium carbonate skeleton. These
calcium-rich skeletons slowly accumulate, thus forming the underwater reef (Figure 20.29). Corals found in
shallower waters (at a depth of approximately 60 m or about 200 ft) have a mutualistic relationship with
photosynthetic unicellular protists. The relationship provides corals with the majority of the nutrition and the energy
they require. The waters in which these corals live are nutritionally poor and, without this mutualism, it would not be
possible for large corals to grow because there are few planktonic organisms for them to feed on. Some corals living
in deeper and colder water do not have a mutualistic relationship with protists; these corals must obtain their
energy exclusively by feeding on plankton using stinging cells on their tentacles.

LINK TO LEARNING
In this National Oceanic and Atmospheric Administration (NOAA) video (http://openstax.org/l/coral_organisms),
marine ecologist Dr. Peter Etnoyer discusses his research on coral organisms.

Coral reefs are one of the most diverse biomes. It is estimated that more than 4000 fish species inhabit coral reefs.
These fishes can feed on coral, the cryptofauna (invertebrates found within the calcium carbonate structures of the
coral reefs), or the seaweed and algae that are associated with the coral. These species include predators,
herbivores, or planktivores. Predators are animal species that hunt and are carnivores or “flesh eaters.” Herbivores
eat plant material, and planktivores eat plankton.

FIGURE 20.29 Coral reefs are formed by the calcium carbonate skeletons of coral organisms, which are marine invertebrates in the phylum
Cnidaria. (credit: Terry Hughes)
554 20 • Ecosystems and the Biosphere

EVOLUTION CONNECTION

Global Decline of Coral Reefs

It takes a long time to build a coral reef. The animals that create coral reefs do so over thousands of years,
continuing to slowly deposit the calcium carbonate that forms their characteristic ocean homes. Bathed in warm
tropical waters, the coral animals and their symbiotic protist partners evolved to survive at the upper limit of ocean
water temperature.

Together, climate change and human activity pose dual threats to the long-term survival of the world’s coral reefs.
The main cause of killing of coral reefs is warmer-than-usual surface water. As global warming raises ocean
temperatures, coral reefs are suffering. The excessive warmth causes the coral organisms to expel their
endosymbiotic, food-producing protists, resulting in a phenomenon known as bleaching. The colors of corals are a
result of the particular protist endosymbiont, and when the protists leave, the corals lose their color and turn white,
hence the term “bleaching.”

Rising levels of atmospheric carbon dioxide further threaten the corals in other ways; as carbon dioxide dissolves in
ocean waters, it lowers pH, thus increasing ocean acidity. As acidity increases, it interferes with the calcification that
normally occurs as coral animals build their calcium carbonate homes.

When a coral reef begins to die, species diversity plummets as animals lose food and shelter. Coral reefs are also
economically important tourist destinations, so the decline of coral reefs poses a serious threat to coastal
economies.

Human population growth has damaged corals in other ways, too. As human coastal populations increase, the runoff
of sediment and agricultural chemicals has increased, causing some of the once-clear tropical waters to become
cloudy. At the same time, overfishing of popular fish species has allowed the predator species that eat corals to go
unchecked.

Although a rise in global temperatures of 1°C–2°C (a conservative scientific projection) in the coming decades may
not seem large, it is very significant to this biome. When change occurs rapidly, species can become extinct before
evolution leads to newly adapted species. Many scientists believe that global warming, with its rapid (in terms of
evolutionary time) and inexorable increases in temperature, is tipping the balance beyond the point at which many
of the world’s coral reefs can recover.

Estuaries: Where the Ocean Meets Fresh Water

Estuaries are biomes that occur where a river, a source of fresh water, meets the ocean. Therefore, both fresh water
and salt water are found in the same vicinity; mixing results in a diluted (brackish) salt water. Estuaries form
protected areas where many of the offspring of crustaceans, mollusks, and fish begin their lives. Salinity is an
important factor that influences the organisms and the adaptations of the organisms found in estuaries. The salinity
of estuaries varies and is based on the rate of flow of its freshwater sources. Once or twice a day, high tides bring
salt water into the estuary. Low tides occurring at the same frequency reverse the current of salt water (Figure
20.30).

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 20.4 • Aquatic and Marine Biomes 555

FIGURE 20.30 As estuary is where fresh water and salt water meet, such as the mouth of the Klamath River in California, shown here.
(credit: U.S. Army Corps of Engineers)

The daily mixing of fresh water and salt water is a physiological challenge for the plants and animals that inhabit
estuaries. Many estuarine plant species are halophytes, plants that can tolerate salty conditions. Halophytic plants
are adapted to deal with salt water spray and salt water on their roots. In some halophytes, filters in the roots
remove the salt from the water that the plant absorbs. Animals, such as mussels and clams (phylum Mollusca), have
developed behavioral adaptations that expend a lot of energy to function in this rapidly changing environment. When
these animals are exposed to low salinity, they stop feeding, close their shells, and switch from aerobic respiration
(in which they use gills) to anaerobic respiration (a process that does not require oxygen). When high tide returns to
the estuary, the salinity and oxygen content of the water increases, and these animals open their shells, begin
feeding, and return to aerobic respiration.

Freshwater Biomes
Freshwater biomes include lakes, ponds, and wetlands (standing water) as well as rivers and streams (flowing
water). Humans rely on freshwater biomes to provide aquatic resources for drinking water, crop irrigation,
sanitation, recreation, and industry. These various roles and human benefits are referred to as ecosystem services.
Lakes and ponds are found in terrestrial landscapes and are therefore connected with abiotic and biotic factors
influencing these terrestrial biomes.

Lakes and Ponds

Lakes and ponds can range in area from a few square meters to thousands of square kilometers. Temperature is an
important abiotic factor affecting living things found in lakes and ponds. During the summer in temperate regions,
thermal stratification of deep lakes occurs when the upper layer of water is warmed by the Sun and does not mix
with deeper, cooler water. The process produces a sharp transition between the warm water above and cold water
beneath. The two layers do not mix until cooling temperatures and winds break down the stratification and the
water in the lake mixes from top to bottom. During the period of stratification, most of the productivity occurs in the
warm, well-illuminated, upper layer, while dead organisms slowly rain down into the cold, dark layer below where
decomposing bacteria and cold-adapted species such as lake trout exist. Like the ocean, lakes and ponds have a
photic layer in which photosynthesis can occur. Phytoplankton (algae and cyanobacteria) are found here and provide
the base of the food web of lakes and ponds. Zooplankton, such as rotifers and small crustaceans, consume these
phytoplankton. At the bottom of lakes and ponds, bacteria in the aphotic zone break down dead organisms that sink
to the bottom.

Nitrogen and particularly phosphorus are important limiting nutrients in lakes and ponds. Therefore, they are
determining factors in the amount of phytoplankton growth in lakes and ponds. When there is a large input of
nitrogen and phosphorus (e.g., from sewage and runoff from fertilized lawns and farms), the growth of algae
skyrockets, resulting in a large accumulation of algae called an algal bloom. Algal blooms (Figure 20.31) can
become so extensive that they reduce light penetration in water. As a result, the lake or pond becomes aphotic and
photosynthetic plants cannot survive. When the algae die and decompose, severe oxygen depletion of the water
occurs. Fishes and other organisms that require oxygen are then more likely to die.
556 20 • Ecosystems and the Biosphere

FIGURE 20.31 The uncontrolled growth of algae in this waterway has resulted in an algal bloom.

Rivers and Streams

Rivers and the narrower streams that feed into the rivers are continuously moving bodies of water that carry water
from the source or headwater to the mouth at a lake or ocean. The largest rivers include the Nile River in Africa, the
Amazon River in South America, and the Mississippi River in North America (Figure 20.32).

FIGURE 20.32 Rivers range from (a) narrow and shallow to (b) wide and slow moving. (credit a: modification of work by Cory Zanker; credit
b: modification of work by David DeHetre)

Abiotic features of rivers and streams vary along the length of the river or stream. Streams begin at a point of origin
referred to as source water. The source water is usually cold, low in nutrients, and clear. The channel (the width of
the river or stream) is narrower here than at any other place along the length of the river or stream. Headwater
streams are of necessity at a higher elevation than the mouth of the river and often originate in regions with steep
grades leading to higher flow rates than lower elevation stretches of the river.

Faster-moving water and the short distance from its origin results in minimal silt levels in headwater streams;
therefore, the water is clear. Photosynthesis here is mostly attributed to algae that are growing on rocks; the swift
current inhibits the growth of phytoplankton. Photosynthesis may be further reduced by tree cover reaching over the
narrow stream. This shading also keeps temperatures lower. An additional input of energy can come from leaves or
other organic material that falls into a river or stream from the trees and other plants that border the water. When
the leaves decompose, the organic material and nutrients in the leaves are returned to the water. The leaves also
support a food chain of invertebrates that eat them and are in turn eaten by predatory invertebrates and fish. Plants
and animals have adapted to this fast-moving water. For instance, some species of mayfly (phylum Arthropoda) have

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 20.4 • Aquatic and Marine Biomes 557

flattened bodies and legs with modified claws to help them cling to the underside of submerged rocks. This body
form reduces drag and allows these species to benefit from the high oxygen concentrations in fast-moving currents
without being dislodged. Freshwater trout species (phylum Chordata) are an important predator in these fast-
moving rivers and streams.

As the river or stream flows away from the source, the width of the channel gradually widens, the current slows, and
the temperature characteristically increases. The increasing width results from the increased volume of water from
more and more tributaries. Gradients are typically lower farther along the river, which accounts for the slowing flow.
With increasing volume can come increased silt, and as the flow rate slows, the silt may settle, thus increasing the
deposition of sediment. Phytoplankton can also be suspended in slow-moving water. Therefore, the water will not
be as clear as it is near the source. The water is also warmer as a result of longer exposure to sunlight and the
absence of tree cover over wider expanses between banks. Worms (phylum Annelida) and insects (phylum
Arthropoda) can be found burrowing into the mud. Predatory vertebrates (phylum Chordata) include waterfowl,
frogs, and fishes. In heavily silt-laden rivers, these predators must find food in the murky waters, and, unlike the
trout in the clear waters at the source, these vertebrates cannot use vision as their primary sense to find food.
Instead, they are more likely to use taste or chemical cues to find prey.

When a river reaches the ocean or a large lake, the water typically slows dramatically and any silt in the river water
will settle. Rivers with high silt content discharging into oceans with minimal currents and wave action will build
deltas, low-elevation areas of sand and mud, as the silt settles onto the ocean bottom. Rivers with low silt content or
in areas where ocean currents or wave action are high create estuarine areas where the fresh water and salt water
mix.

Wetlands
Wetlands are environments in which the soil is either permanently or periodically saturated with water. Wetlands
are different from lakes and ponds because wetlands exhibit a near continuous cover of emergent vegetation.
Emergent vegetation consists of wetland plants that are rooted in the soil but have portions of leaves, stems, and
flowers extending above the water’s surface. There are several types of wetlands including marshes, swamps, bogs,
mudflats, and salt marshes (Figure 20.33).

FIGURE 20.33 Located in southern Florida, Everglades National Park is vast array of wetland environments, including sawgrass marshes,
cypress swamps, and estuarine mangrove forests. Here, a great egret walks among cypress trees. (credit: NPS)

Freshwater marshes and swamps are characterized by slow and steady water flow. Bogs develop in depressions
where water flow is low or nonexistent. Bogs usually occur in areas where there is a clay bottom with poor
percolation. Percolation is the movement of water through the pores in the soil or rocks. The water found in a bog is
stagnant and oxygen depleted because the oxygen that is used during the decomposition of organic matter is not
replaced. As the oxygen in the water is depleted, decomposition slows. This leads to organic acids and other acids
558 20 • Ecosystems and the Biosphere

building up and lowering the pH of the water. At a lower pH, nitrogen becomes unavailable to plants. This creates a
challenge for plants because nitrogen is an important limiting resource. Some types of bog plants (such as sundews,
pitcher plants, and Venus flytraps) capture insects and extract the nitrogen from their bodies. Bogs have low net
primary productivity because the water found in bogs has low levels of nitrogen and oxygen.

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 20 • Key Terms 559

Key Terms
abyssal zone the deepest part of the ocean at depths dead zone an area in a lake and ocean near the
of 4000 m or greater mouths of rivers where large areas are depleted of
acid rain a corrosive rain caused by rainwater mixing their normal flora and fauna; these zones can be
with sulfur dioxide gas as it fall through the caused by eutrophication, oil spills, dumping of toxic
atmosphere, turning it into weak sulfuric acid, chemicals, and other human activities
causing damage to aquatic ecosystems detrital food web a type of food web that is
algal bloom a rapid increase of algae in an aquatic supported by dead or decaying organisms rather
system than by living autotrophs; these are often associated
apex consumer an organism at the top of the food with grazing food webs within the same ecosystem
chain ecosystem a community of living organisms and their
aphotic zone the part of the ocean where interactions with their abiotic environment
photosynthesis cannot occur ecosystem services the human benefits provided by
arctic tundra a biome characterized by low average natural ecosystems
temperatures, brief growing seasons, the presence emergent vegetation the plants living in bodies of
of permafrost, and limited precipitation largely in water that are rooted in the soil but have portions of
the form of snow in which the dominant vegetation leaves, stems, and flowers extending above the
are low shrubs, lichens, mosses, and small water’s surface
herbaceous plants equilibrium the steady state of a system in which the
autotroph an organism capable of synthesizing its relationships between elements of the system do
own food molecules from smaller inorganic not change
molecules estuary a region where fresh water and salt water
benthic realm (also, benthic zone) the part of the mix where a river discharges into an ocean or sea
ocean that extends along the ocean bottom from the eutrophication the process whereby nutrient runoff
shoreline to the deepest parts of the ocean floor causes the excess growth of microorganisms and
biogeochemical cycle the cycling of minerals and plants in aquatic systems
nutrients through the biotic and abiotic world fallout the direct deposition of solid minerals on land
biomagnification an increasing concentration of or in the ocean from the atmosphere
persistent, toxic substances in organisms at each food chain a linear sequence of trophic (feeding)
trophic level, from the producers to the apex relationships of producers, primary consumers, and
consumers higher level consumers
biome a large-scale community of organisms, food web a web of trophic (feeding) relationships
primarily defined on land by the dominant plant among producers, primary consumers, and higher
types that exist in geographic regions of the planet level consumers in an ecosystem
with similar climatic conditions grazing food web a type of food web in which the
boreal forest a biome found in temperate and producers are either plants on land or
subarctic regions characterized by short growing phytoplankton in the water; often associated with a
seasons and dominated structurally by coniferous detrital food web within the same ecosystem
trees gross primary productivity the rate at which
canopy the branches and foliage of trees that form a photosynthetic producers incorporate energy from
layer of overhead coverage in a forest the Sun
channel the bed and banks of a river or stream hydrosphere the region of the planet in which water
chaparral a biome found in temperate coastal exists, including the atmosphere that contains water
regions characterized by low trees and dry-adapted vapor and the region beneath the ground that
shrubs and forbs contains groundwater
chemoautotroph an organism capable of intertidal zone the part of the ocean that is closest to
synthesizing its own food using energy from land; parts extend above the water at low tide
inorganic molecules neritic zone the part of the ocean that extends from
coral reef an ocean ridge formed by marine low tide to the edge of the continental shelf
invertebrates living in warm shallow waters within net primary productivity the energy that remains in
the photic zone the producers after accounting for the organisms’
cryptofauna the invertebrates found within the respiration and heat loss
calcium carbonate substrate of coral reefs non-renewable resource a resource, such as a fossil
560 20 • Chapter Summary

fuel, that is either regenerated very slowly or not at grassland with sparsely distributed trees
all secondary consumer a trophic level in an ecosystem,
oceanic zone the part of the ocean that begins usually a carnivore that eats a primary consumer
offshore where the water measures 200 m deep or source water the point of origin of a river or stream
deeper subduction the movement of one tectonic plate
pelagic realm (also, pelagic zone) the open ocean beneath another
waters that are not close to the bottom or near the subtropical desert a biome found in the subtropics
shore with hot daily temperatures, very low and
permafrost a perennially frozen portion of the Arctic unpredictable precipitation, and characterized by a
tundra soil limited dry-adapted vegetation
photic zone the upper layer of ocean water in which temperate forest a biome found in temperate regions
photosynthesis is able to take place with moderate rainfall and dominated structurally
photoautotroph an organism that uses sunlight as an by deciduous trees
energy source to synthesize its own food molecules temperate grassland a biome dominated by grasses
planktivore an animal that eats plankton and herbaceous plants due to low precipitation,
primary consumer the trophic level that obtains its periodic fires, and grazing
energy from the producers of an ecosystem tertiary consumer a trophic level in an ecosystem,
producer the trophic level that obtains its energy usually carnivores that eat other carnivores
from sunlight, inorganic chemicals, or dead or trophic level the position of a species or group of
decaying organic material species in a food chain or a food web
resilience (ecological) the speed at which an tropical rainforest a biome found near the equator
ecosystem recovers equilibrium after being characterized by stable temperatures with abundant
disturbed and seasonal rainfall in which trees form the
resistance (ecological) the ability of an ecosystem to structurally important vegetation
remain at equilibrium in spite of disturbances wetland environment in which the soil is either
savanna a biome located in the tropics with an permanently or periodically saturated with water
extended dry season and characterized by a

Chapter Summary
20.1 Waterford's Energy Flow through damaged by a variety of human activities that alter the
Ecosystems natural biogeochemical cycles due to pollution, oil
spills, and events causing global climate change. The
Ecosystems exist underground, on land, at sea, and in health of the biosphere depends on understanding
the air. Organisms in an ecosystem acquire energy in a these cycles and how to protect the environment from
variety of ways, which is transferred between trophic irreversible damage.
levels as the energy flows from the base to the top of
the food web, with energy being lost at each transfer. 20.3 Terrestrial Biomes
There is energy lost at each trophic level, so the
Earth has terrestrial and aquatic biomes. Aquatic
lengths of food chains are limited because there is a
biomes include both freshwater and marine
point where not enough energy remains to support a
environments. There are eight major terrestrial biomes:
population of consumers. Fat soluble compounds
tropical rainforests, savannas, subtropical deserts,
biomagnify up a food chain causing damage to top
chaparral, temperate grasslands, temperate forests,
consumers. even when environmental concentrations
boreal forests, and Arctic tundra. The same biome can
of a toxin are low.
occur in different geographic locations with similar
20.2 Biogeochemical Cycles climates. Temperature and precipitation, and variations
in both, are key abiotic factors that shape the
Mineral nutrients are cycled through ecosystems and composition of animal and plant communities in
their environment. Of particular importance are water, terrestrial biomes. Some biomes, such as temperate
carbon, nitrogen, phosphorus, and sulfur. All of these grasslands and temperate forests, have distinct
cycles have major impacts on ecosystem structure and seasons with cold and hot weather alternating
function. As human activities have caused major throughout the year. In warm, moist biomes, such as
disturbances to these cycles, their study and modeling the tropical rainforest, net primary productivity is high
is especially important. Ecosystems have been as warm temperatures, abundant water, and a year-

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 20 • Visual Connection Questions 561

round growing season fuel plant growth. Other biomes, movement, and salt content. Oceans may be thought of
such as deserts and tundra, have low primary as consisting of different zones based on water depth,
productivity due to extreme temperatures and a distance from the shoreline, and light penetrance.
shortage of water. Different kinds of organisms are adapted to the
conditions found in each zone. Coral reefs are unique
20.4 Aquatic and Marine Biomes marine ecosystems that are home to a wide variety of
Aquatic biomes include both saltwater and freshwater species. Estuaries are found where rivers meet the
biomes. The abiotic factors important for the ocean; their shallow waters provide nourishment and
structuring of aquatic biomes can be different than shelter for young crustaceans, mollusks, fishes, and
those seen in terrestrial biomes. Sunlight is an many other species. Freshwater biomes include lakes,
important factor in bodies of water, especially those ponds, rivers, streams, and wetlands. Bogs are an
that are very deep, because of the role of interesting type of wetland characterized by standing
photosynthesis in sustaining certain organisms. Other water, a lower pH, and a lack of nitrogen.
important factors include temperature, water

Visual Connection Questions

1. Figure 20.12 Which of the following statements 2. Figure 20.28 In which of the following regions
about the nitrogen cycle is false? would you expect to find photosynthetic organisms?
a. Ammonification converts organic nitrogenous a. The aphotic zone, the neritic zone, the oceanic
matter from living organisms into ammonium zone, and the benthic realm.
(NH4+). b. The photic zone, the intertidal zone, the neritic
b. Denitrification by bacteria converts nitrates zone, and the oceanic zone.
(NO3-) to nitrogen gas (N2). c. The photic zone, the abyssal zone, the neritic
c. Nitrification by bacteria converts nitrates zone, and the oceanic zone.
(NO3-) to nitrites (NO2-). d. The pelagic realm, the aphotic zone, the neritic
d. Nitrogen fixing bacteria convert nitrogen gas zone, and the oceanic zone.
(N2) into organic compounds.

Review Questions
3. Decomposers are associated with which class of 6. The majority of the water found on Earth is:
food web? a. ice
a. grazing b. water vapor
b. detrital c. fresh water
c. inverted d. salt water
d. aquatic
7. The process whereby oxygen is depleted by the
4. The producer in an ocean grazing food web is growth of microorganisms due to excess nutrients
usually a ________. in aquatic systems is called ________.
a. plant a. dead zoning
b. animal b. eutrophication
c. fungi c. retrophication
d. plankton d. depletion

5. Which term describes the process whereby toxic 8. Which of the following biomes is characterized by
substances increase along trophic levels of an abundant water resources?
ecosystem? a. deserts
a. biomassification b. boreal forests
b. biomagnification c. savanna
c. bioentropy d. tropical wet forests
d. heterotrophy
562 20 • Critical Thinking Questions

9. Which of the following biomes is characterized by 11. Where would you expect to find the most
short growing seasons? photosynthesis in an ocean biome?
a. deserts a. aphotic zone
b. tropical wet forests b. abyssal zone
c. Arctic tundra c. benthic realm
d. savanna d. intertidal zone

10. Why is the tundra treeless? 12. A key feature of estuaries is

a. lack of sufficient water a. low light conditions and high productivity
b. permanently frozen ground b. salt water and fresh water
c. winters too harsh c. frequent algal blooms
d. too many fires d. little or no vegetation

Critical Thinking Questions

13. Compare grazing and detrital food webs. Why 15. The extremely low precipitation of subtropical
would they both be present in the same desert biomes might lead one to expect fire to be
ecosystem? a major disturbance factor; however, fire is more
common in the temperate grassland biome than in
14. Why are drinking water supplies still a major
the subtropical desert biome. Why is this?
concern for many countries?
16. In what ways are the subtropical desert and the
Arctic tundra similar?

17. Describe the conditions and challenges facing

organisms living in the intertidal zone.

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CHAPTER 21
Conservation and Biodiversity

FIGURE 21.1 Habitat destruction through deforestation, especially of tropical rainforests as seen in this satellite view
of Amazon rainforests in Brazil, is a major cause of the current decline in biodiversity. (credit: modification of work by
Jesse Allen and Robert Simmon, NASA Earth Observatory)

CHAPTER OUTLINE
21.1 Importance of Biodiversity
21.2 Threats to Biodiversity
21.3 Preserving Biodiversity

INTRODUCTION Biologists estimate that species extinctions are currently 500–1000 times the
rate seen previously in Earth’s history when there were no unusual geological or climatic events
occurring. Biologists call the previous rate the “background” rate of extinction. The current high
rates will cause a precipitous decline in the biodiversity (the diversity of species) of the planet in
the next century or two. The losses will include many species we know today. Although it is
sometimes difficult to predict which species will become extinct, many are listed as endangered
(at great risk of extinction). However, the majority of extinctions will be of species that science has
not yet even described.

Most of these “invisible” species that will become extinct currently live in tropical rainforests like
those of the Amazon basin. These rainforests are the most diverse ecosystems on the planet and
are being destroyed rapidly by deforestation, which biologists believe is driving many rare species
with limited distributions extinct. Between 1970 and 2011, almost 20 percent of the Amazon
rainforest was lost. Rates are higher in other tropical rainforests. What we are likely to notice on a
day-to-day basis as a result of biodiversity loss is that food will be more difficult to produce, clean
water will be more difficult to find, and the rate of development of new medicines will become
slower, as we depend upon other species for much of these services. This increased loss of
biodiversity is almost entirely a result of human activities as we destroy species’ habitats,
564 21 • Conservation and Biodiversity

introduce disruptive species into ecosystems, hunt some species to extinction, continue to warm
the planet with greenhouse gases, and influence nature in other ways. Slowing the loss of
biodiversity is within our abilities if we make dramatic changes in our consumptive behavior and
identify and protect the elements of our ecosystems that we depend on for our lives and welfare.

21.1 Importance of Biodiversity

LEARNING OBJECTIVES
By the end of this section, you will be able to:
• Describe biodiversity as the equilibrium of naturally fluctuating rates of extinction and
speciation
• Identify benefits of biodiversity to humans

FIGURE 21.2 This tropical lowland rainforest in Madagascar is an example of a high biodiversity habitat. This
particular location is protected within a national forest, yet only 10 percent of the original coastal lowland forest
remains, and research suggests half the original biodiversity has been lost. (credit: Frank Vassen)

Biodiversity is a broad term for biological variety, and it can be measured at a number of
organizational levels. Traditionally, ecologists have measured biodiversity by taking into account
both the number of species and the number of individuals in each of those species. However,
biologists are using measures of biodiversity at several levels of biological organization (including
genes, populations, and ecosystems) to help focus efforts to preserve the biologically and
technologically important elements of biodiversity.

When biodiversity loss through extinction is thought of as the loss of the passenger pigeon, the
dodo, or, even, the woolly mammoth there seems to be no reason to care about it because these
events happened long ago. How is the loss practically important for the welfare of the human
species? Would these species have made our lives any better? From the perspective of evolution
and ecology, the loss of a particular individual species, with some exceptions, may seem
unimportant, but the current accelerated extinction rate means the loss of tens of thousands of
species within our lifetimes. Much of this loss is occurring in tropical rainforests like the one
pictured in Figure 21.2, which are especially high-diversity ecosystems that are being cleared for
timber and agriculture. This is likely to have dramatic effects on human welfare through the
collapse of ecosystems and in added costs to maintain food production, clean air and water, and
improve human health.

Biologists recognize that human populations are embedded in ecosystems and are dependent on
them, just as is every other species on the planet. Agriculture began after early hunter-gatherer
societies first settled in one place and heavily modified their immediate environment: the
ecosystem in which they existed. This cultural transition has made it difficult for humans to
recognize their dependence on living things other than crops and domesticated animals on the
planet. Today our technology smoothes out the extremes of existence and allows many of us to

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 21.1 • Importance of Biodiversity 565

live longer, more comfortable lives, but ultimately the human species cannot exist without its surrounding
ecosystems. Our ecosystems provide our food. This includes living plants that grow in soil ecosystems and the
animals that eat these plants (or other animals) as well as photosynthetic organisms in the oceans and the other
organisms that eat them. Our ecosystems have provided and will provide many of the medications that maintain our
health, which are commonly made from compounds found in living organisms. Ecosystems provide our clean water,
which is held in lake and river ecosystems or passes through terrestrial ecosystems on its way into groundwater.

Types of Biodiversity
A common meaning of biodiversity is simply the number of species in a location or on Earth; for example, the
American Ornithologists’ Union lists 2078 species of birds in North and Central America. This is one measure of the
bird biodiversity on the continent. More sophisticated measures of diversity take into account the relative
abundances of species. For example, a forest with 10 equally common species of trees is more diverse than a forest
that has 10 species of trees wherein just one of those species makes up 95 percent of the trees rather than them
being equally distributed. Biologists have also identified alternate measures of biodiversity, some of which are
important in planning how to preserve biodiversity.

Genetic and Chemical Biodiversity

Genetic diversity is one alternate concept of biodiversity. Genetic diversity (or variation) is the raw material for
adaptation in a species. A species’ future potential for adaptation depends on the genetic diversity held in the
genomes of the individuals in populations that make up the species. The same is true for higher taxonomic
categories. A genus with very different types of species will have more genetic diversity than a genus with species
that look alike and have similar ecologies. The genus with the greatest potential for subsequent evolution is the
most genetically diverse one.

Most genes code for proteins, which in turn carry out the metabolic processes that keep organisms alive and
reproducing. Genetic diversity can also be conceived of as chemical diversity in that species with different genetic
makeups produce different assortments of chemicals in their cells (proteins as well as the products and byproducts
of metabolism). This chemical diversity is important for humans because of the potential uses for these chemicals,
such as medications. For example, the drug eptifibatide is derived from rattlesnake venom and is used to prevent
heart attacks in individuals with certain heart conditions.

At present, it is far cheaper to discover compounds made by an organism than to imagine them and then synthesize
them in a laboratory. Chemical diversity is one way to measure diversity that is important to human health and
welfare. Through selective breeding, humans have domesticated animals, plants, and fungi, but even this diversity is
suffering losses because of market forces and increasing globalism in human agriculture and migration. For
example, international seed companies produce only a very few varieties of a given crop and provide incentives
around the world for farmers to buy these few varieties while abandoning their traditional varieties, which are far
more diverse. The human population depends on crop diversity directly as a stable food source and its decline is
troubling to biologists and agricultural scientists.

Ecosystems Diversity
It is also useful to define ecosystem diversity: the number of different ecosystems on Earth or in a geographical
area. Whole ecosystems can disappear even if some of the species might survive by adapting to other ecosystems.
The loss of an ecosystem means the loss of the interactions between species, the loss of unique features of
coadaptation, and the loss of biological productivity that an ecosystem is able to create. An example of a largely
extinct ecosystem in North America is the prairie ecosystem (Figure 21.3). Prairies once spanned central North
America from the boreal forest in northern Canada down into Mexico. They are now all but gone, replaced by crop
fields, pasture lands, and suburban sprawl. Many of the species survive, but the hugely productive ecosystem that
was responsible for creating our most productive agricultural soils is now gone. As a consequence, their soils are
now being depleted unless they are maintained artificially at greater expense. The decline in soil productivity occurs
because the interactions in the original ecosystem have been lost; this was a far more important loss than the
relatively few species that were driven extinct when the prairie ecosystem was destroyed.
566 21 • Conservation and Biodiversity

FIGURE 21.3 The variety of ecosystems on Earth—from coral reef to prairie—enables a great diversity of species to exist. (credit “coral
reef”: modification of work by Jim Maragos, USFWS; credit: “prairie”: modification of work by Jim Minnerath, USFWS)

Current Species Diversity

Despite considerable effort, knowledge of the species that inhabit the planet is limited. A recent estimate suggests
that the eukaryote species for which science has names, about 1.5 million species, account for less than 20 percent
of the total number of eukaryote species present on the planet (8.7 million species, by one estimate). Estimates of
numbers of prokaryotic species are largely guesses, but biologists agree that science has only just begun to catalog
their diversity. Even with what is known, there is no centralized repository of names or samples of the described
species; therefore, there is no way to be sure that the 1.5 million descriptions is an accurate number. It is a best
guess based on the opinions of experts on different taxonomic groups. Given that Earth is losing species at an
accelerating pace, science knows little about what is being lost. Table 21.1 presents recent estimates of biodiversity
in different groups.

Estimated Numbers of Described and Predicted species

Source: Groombridge and

Source: Mora et al 2011 Source: Chapman 2009
Jenkins 2002

Described Predicted Described Predicted Described Predicted

Animals 1,124,516 9,920,000 1,424,153 6,836,330 1,225,500 10,820,000

Photosynthetic
17,892 34,900 25,044 200,500 — —
protists

Fungi 44,368 616,320 98,998 1,500,000 72,000 1,500,000

Plants 224,244 314,600 310,129 390,800 270,000 320,000

Non-photosynthetic
16,236 72,800 28,871 1,000,000 80,000 600,000
protists

Prokaryotes — — 10,307 1,000,000 10,175 —

Total 1,438,769 10,960,000 1,897,502 10,897,630 1,657,675 13,240,000

TABLE 21.1 This table shows the estimated number of species by taxonomic group—including both described (named and studied) and
predicted (yet to be named) species.

There are various initiatives to catalog described species in accessible and more organized ways, and the internet is
facilitating that effort. Nevertheless, at the current rate of species description, which according to the State of
1
Observed Species reports is 17,000–20,000 new species a year, it would take close to 500 years to describe all of
the species currently in existence. The task, however, is becoming increasingly impossible over time as extinction
removes species from Earth faster than they can be described.

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 21.1 • Importance of Biodiversity 567

Naming and counting species may seem an unimportant pursuit given the other needs of humanity, but it is not
simply an accounting. Describing species is a complex process by which biologists determine an organism’s unique
characteristics and whether or not that organism belongs to any other described species. It allows biologists to find
and recognize the species after the initial discovery to follow up on questions about its biology. That subsequent
research will produce the discoveries that make the species valuable to humans and to our ecosystems. Without a
name and description, a species cannot be studied in depth and in a coordinated way by multiple scientists.

Patterns of Biodiversity
Biodiversity is not evenly distributed on the planet. Lake Victoria contained almost 500 species of cichlids (only one
family of fishes present in the lake) before the introduction of an exotic species in the 1980s and 1990s caused a
mass extinction. All of these species were found only in Lake Victoria, which is to say they were endemic. Endemic
species are found in only one location. For example, the blue jay is endemic to North America, while the Barton
Springs salamander is endemic to the mouth of one spring in Austin, Texas. Endemics with highly restricted
distributions, like the Barton Springs salamander, are particularly vulnerable to extinction. Higher taxonomic levels,
such as genera and families, can also be endemic.

Lake Huron contains about 79 species of fish, all of which are found in many other lakes in North America. What
accounts for the difference in diversity between Lake Victoria and Lake Huron? Lake Victoria is a tropical lake, while
Lake Huron is a temperate lake. Lake Huron in its present form is only about 7,000 years old, while Lake Victoria in
its present form is about 15,000 years old. These two factors, latitude and age, are two of several hypotheses
biogeographers have suggested to explain biodiversity patterns on Earth.

CAREER CONNECTION

Biogeography
Biogeography is the study of the distribution of the world’s species both in the past and in the present. The work of
biogeographers is critical to understanding our physical environment, how the environment affects species, and how
changes in environment impact the distribution of a species.

There are three main fields of study under the heading of biogeography: ecological biogeography, historical
biogeography (called paleobiogeography), and conservation biogeography. Ecological biogeography studies the
current factors affecting the distribution of plants and animals. Historical biogeography, as the name implies, studies
the past distribution of species. Conservation biogeography, on the other hand, is focused on the protection and
restoration of species based upon the known historical and current ecological information. Each of these fields
considers both zoogeography and phytogeography—the past and present distribution of animals and plants.

One of the oldest observed patterns in ecology is that biodiversity in almost every taxonomic group of organism
increases as latitude declines. In other words, biodiversity increases closer to the equator (Figure 21.4).

1 International Institute for Species Exploration (IISE), 2011 State of Observed Species (SOS). Tempe, AZ: IISE, 2011. Accessed May, 20,
2012. http://species.asu.edu/SOS.
568 21 • Conservation and Biodiversity

FIGURE 21.4 This map illustrates the number of amphibian species across the globe and shows the trend toward higher biodiversity at
lower latitudes. A similar pattern is observed for most taxonomic groups.

It is not yet clear why biodiversity increases closer to the equator, but hypotheses include the greater age of the
ecosystems in the tropics versus temperate regions, which were largely devoid of life or drastically impoverished
during the last ice age. The greater age provides more time for speciation. Another possible explanation is the
greater energy the tropics receive from the sun versus the lesser energy input in temperate and polar regions. But
scientists have not been able to explain how greater energy input could translate into more species. The complexity
of tropical ecosystems may promote speciation by increasing the habitat heterogeneity, or number of ecological
niches, in the tropics relative to higher latitudes. The greater heterogeneity provides more opportunities for
coevolution, specialization, and perhaps greater selection pressures leading to population differentiation. However,
this hypothesis suffers from some circularity—ecosystems with more species encourage speciation, but how did
they get more species to begin with? The tropics have been perceived as being more stable than temperate regions,
which have a pronounced climate and day-length seasonality. The tropics have their own forms of seasonality, such
as rainfall, but they are generally assumed to be more stable environments and this stability might promote
speciation.

Regardless of the mechanisms, it is certainly true that biodiversity is greatest in the tropics. The number of endemic
species is higher in the tropics. The tropics also contain more biodiversity hotspots. At the same time, our
knowledge of the species living in the tropics is lowest and because of recent, heavy human activity the potential for
biodiversity loss is greatest.

Importance of Biodiversity
Loss of biodiversity eventually threatens other species we do not impact directly because of their
interconnectedness; as species disappear from an ecosystem other species are threatened by the changes in
available resources. Biodiversity is important to the survival and welfare of human populations because it has
impacts on our health and our ability to feed ourselves through agriculture and harvesting populations of wild
animals.

Human Health
Many medications are derived from natural chemicals made by a diverse group of organisms. For example, many
plants produce secondary plant compounds, which are toxins used to protect the plant from insects and other
animals that eat them. Some of these secondary plant compounds also work as human medicines. Contemporary
societies that live close to the land often have a broad knowledge of the medicinal uses of plants growing in their
area. For centuries in Europe, older knowledge about the medical uses of plants was compiled in herbals—books
that identified the plants and their uses. Humans are not the only animals to use plants for medicinal reasons. The
other great apes, orangutans, chimpanzees, bonobos, and gorillas have all been observed self-medicating with
plants.

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 21.1 • Importance of Biodiversity 569

Modern pharmaceutical science also recognizes the importance of these plant compounds. Examples of significant
medicines derived from plant compounds include aspirin, codeine, digoxin, atropine, and vincristine (Figure 21.5).
Many medications were once derived from plant extracts but are now synthesized. It is estimated that, at one time,
25 percent of modern drugs contained at least one plant extract. That number has probably decreased to about 10
percent as natural plant ingredients are replaced by synthetic versions of the plant compounds. Antibiotics, which
are responsible for extraordinary improvements in health and lifespans in developed countries, are compounds
largely derived from fungi and bacteria.

FIGURE 21.5 Catharanthus roseus, the Madagascar periwinkle, has various medicinal properties. Among other uses, it is a source of
vincristine, a drug used in the treatment of lymphomas. (credit: Forest and Kim Starr)

In recent years, animal venoms and poisons have excited intense research for their medicinal potential. By 2007,
the FDA had approved five drugs based on animal toxins to treat diseases such as hypertension, chronic pain, and
diabetes. Another five drugs are undergoing clinical trials and at least six drugs are being used in other countries.
Other toxins under investigation come from mammals, snakes, lizards, various amphibians, fish, snails, octopuses,
and scorpions.

Aside from representing billions of dollars in profits, these medications improve people’s lives. Pharmaceutical
companies are actively looking for new natural compounds that can function as medicines. It is estimated that one
third of pharmaceutical research and development is spent on natural compounds and that about 35 percent of new
drugs brought to market between 1981 and 2002 were from natural compounds.

Finally, it has been argued that humans benefit psychologically from living in a biodiverse world. The chief proponent
of this idea is entomologist E. O. Wilson. He argues that human evolutionary history has adapted us to living in a
natural environment and that built environments generate stresses that affect human health and well-being. There
is considerable research into the psychologically regenerative benefits of natural landscapes that suggest the
hypothesis may hold some truth.

Agricultural
Since the beginning of human agriculture more than 10,000 years ago, human groups have been breeding and
selecting crop varieties. This crop diversity matched the cultural diversity of highly subdivided populations of
humans. For example, potatoes were domesticated beginning around 7,000 years ago in the central Andes of Peru
and Bolivia. The people in this region traditionally lived in relatively isolated settlements separated by mountains.
The potatoes grown in that region belong to seven species and the number of varieties likely is in the thousands.
Each variety has been bred to thrive at particular elevations and soil and climate conditions. The diversity is driven
by the diverse demands of the dramatic elevation changes, the limited movement of people, and the demands
created by crop rotation for different varieties that will do well in different fields.

Potatoes are only one example of agricultural diversity. Every plant, animal, and fungus that has been cultivated by
humans has been bred from original wild ancestor species into diverse varieties arising from the demands for food
value, adaptation to growing conditions, and resistance to pests. The potato demonstrates a well-known example of
the risks of low crop diversity: during the tragic Irish potato famine (1845–1852 AD), the single potato variety grown
in Ireland became susceptible to a potato blight—wiping out the crop. The loss of the crop led to famine, death, and
mass emigration. Resistance to disease is a chief benefit to maintaining crop biodiversity and lack of diversity in
570 21 • Conservation and Biodiversity

contemporary crop species carries similar risks. Seed companies, which are the source of most crop varieties in
developed countries, must continually breed new varieties to keep up with evolving pest organisms. These same
seed companies, however, have participated in the decline of the number of varieties available as they focus on
selling fewer varieties in more areas of the world replacing traditional local varieties.

The ability to create new crop varieties relies on the diversity of varieties available and the availability of wild forms
related to the crop plant. These wild forms are often the source of new gene variants that can be bred with existing
varieties to create varieties with new attributes. Loss of wild species related to a crop will mean the loss of potential
in crop improvement. Maintaining the genetic diversity of wild species related to domesticated species ensures our
continued supply of food.

Since the 1920s, government agriculture departments have maintained seed banks of crop varieties as a way to
maintain crop diversity. This system has flaws because over time seed varieties are lost through accidents and there
is no way to replace them. In 2008, the Svalbard Global seed Vault, located on Spitsbergen island, Norway, (Figure
21.6) began storing seeds from around the world as a backup system to the regional seed banks. If a regional seed
bank stores varieties in Svalbard, losses can be replaced from Svalbard should something happen to the regional
seeds. The Svalbard seed vault is deep into the rock of the arctic island. Conditions within the vault are maintained
at ideal temperature and humidity for seed survival, but the deep underground location of the vault in the arctic
means that failure of the vault’s systems will not compromise the climatic conditions inside the vault.

VISUAL CONNECTION

FIGURE 21.6 The Svalbard Global Seed Vault is a storage facility for seeds of Earth’s diverse crops. (credit: Mari Tefre, Svalbard Global Seed
Vault)

The Svalbard seed vault is located on Spitsbergen island in Norway, which has an arctic climate. Why might an arctic
climate be good for seed storage?

Although crops are largely under our control, our ability to grow them is dependent on the biodiversity of the
ecosystems in which they are grown. That biodiversity creates the conditions under which crops are able to grow
through what are known as ecosystem services—valuable conditions or processes that are carried out by an
ecosystem. Crops are not grown, for the most part, in built environments. They are grown in soil. Although some
agricultural soils are rendered sterile using controversial pesticide treatments, most contain a huge diversity of
organisms that maintain nutrient cycles—breaking down organic matter into nutrient compounds that crops need for
growth. These organisms also maintain soil texture that affects water and oxygen dynamics in the soil that are
necessary for plant growth. Replacing the work of these organisms in forming arable soil is not practically possible.
These kinds of processes are called ecosystem services. They occur within ecosystems, such as soil ecosystems, as
a result of the diverse metabolic activities of the organisms living there, but they provide benefits to human food
production, drinking water availability, and breathable air.

Other key ecosystem services related to food production are plant pollination and crop pest control. It is estimated
that honeybee pollination within the United States brings in $1.6 billion per year; other pollinators contribute up to

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 21.2 • Threats to Biodiversity 571

$6.7 billion. Over 150 crops in the United States require pollination to produce. Many honeybee populations are
managed by beekeepers who rent out their hives’ services to farmers. Honeybee populations in North America have
been suffering large losses caused by a syndrome known as colony collapse disorder, a new phenomenon with an
unclear cause. Other pollinators include a diverse array of other bee species and various insects and birds. Loss of
these species would make growing crops requiring pollination impossible, increasing dependence on other crops.

Finally, humans compete for their food with crop pests, most of which are insects. Pesticides control these
competitors, but these are costly and lose their effectiveness over time as pest populations adapt. They also lead to
collateral damage by killing non-pest species as well as beneficial insects like honeybees, and risking the health of
agricultural workers and consumers. Moreover, these pesticides may migrate from the fields where they are applied
and do damage to other ecosystems like streams, lakes, and even the ocean. Ecologists believe that the bulk of the
work in removing pests is actually done by predators and parasites of those pests, but the impact has not been well
studied. A review found that in 74 percent of studies that looked for an effect of landscape complexity (forests and
fallow fields near to crop fields) on natural enemies of pests, the greater the complexity, the greater the effect of
pest-suppressing organisms. Another experimental study found that introducing multiple enemies of pea aphids (an
important alfalfa pest) increased the yield of alfalfa significantly. This study shows that a diversity of pests is more
effective at control than one single pest. Loss of diversity in pest enemies will inevitably make it more difficult and
costly to grow food. The world’s growing human population faces significant challenges in the increasing costs and
other difficulties associated with producing food.

Wild Food Sources

In addition to growing crops and raising food animals, humans obtain food resources from wild populations,
primarily wild fish populations. For about one billion people, aquatic resources provide the main source of animal
protein. But since 1990, production from global fisheries has declined. Despite considerable effort, few fisheries on
Earth are managed sustainability.

Fishery extinctions rarely lead to complete extinction of the harvested species, but rather to a radical restructuring
of the marine ecosystem in which a dominant species is so over-harvested that it becomes a minor player,
ecologically. In addition to humans losing the food source, these alterations affect many other species in ways that
are difficult or impossible to predict. The collapse of fisheries has dramatic and long-lasting effects on local human
populations that work in the fishery. In addition, the loss of an inexpensive protein source to populations that cannot
afford to replace it will increase the cost of living and limit societies in other ways. In general, the fish taken from
fisheries have shifted to smaller species and the larger species are overfished. The ultimate outcome could clearly
be the loss of aquatic systems as food sources.

LINK TO LEARNING
Visit this website (http://openstax.org/l/decliningfish2) to view a brief video discussing a study of declining fisheries.

21.2 Threats to Biodiversity

LEARNING OBJECTIVES
By the end of this section, you will be able to:
• Identify significant threats to biodiversity
• Explain the effects of habitat loss, exotic species, and hunting on biodiversity
• Identify the early and predicted effects of climate change on biodiversity

The core threat to biodiversity on the planet, and therefore a threat to human welfare, is the combination of human
population growth and the resources used by that population. The human population requires resources to survive
and grow, and those resources are being removed unsustainably from the environment. The three greatest
proximate threats to biodiversity are habitat loss, overharvesting, and introduction of exotic species. The first two of
these are a direct result of human population growth and resource use. The third results from increased mobility
and trade. A fourth major cause of extinction, anthropogenic (human-caused) climate change, has not yet had a
large impact, but it is predicted to become significant during this century. Global climate change is also a
consequence of human population needs for energy and the use of fossil fuels to meet those needs (Figure 21.7).
572 21 • Conservation and Biodiversity

Environmental issues, such as toxic pollution, have specific targeted effects on species, but are not generally seen
as threats at the magnitude of the others.

FIGURE 21.7 Atmospheric carbon dioxide levels fluctuate in a cyclical manner. However, the burning of fossil fuels in recent history has
caused a dramatic increase in the levels of carbon dioxide in the Earth’s atmosphere, which have now reached levels never before seen on
Earth. Scientists predict that the addition of this “greenhouse gas” to the atmosphere is resulting in climate change that will significantly
impact biodiversity in the coming century.

Habitat Loss
Humans rely on technology to modify their environment and replace certain functions that were once performed by
the natural ecosystem. Other species cannot do this. Elimination of their habitat—whether it is a forest, coral reef,
grassland, or flowing river—will kill the individuals in the species. Remove the entire habitat within the range of a
species and, unless they are one of the few species that do well in human-built environments, the species will
become extinct. Human destruction of habitats (habitats generally refer to the part of the ecosystem required by a
particular species) accelerated in the latter half of the twentieth century. Consider the exceptional biodiversity of
Sumatra: it is home to one species of orangutan, a species of critically endangered elephant, and the Sumatran tiger,
but half of Sumatra’s forest is now gone. The neighboring island of Borneo, home to the other species of orangutan,
has lost a similar area of forest. Forest loss continues in protected areas of Borneo. The orangutan in Borneo is listed
as endangered by the International Union for Conservation of Nature (IUCN), but it is simply the most visible of
thousands of species that will not survive the disappearance of the forests of Borneo. The forests are removed for
timber and to plant palm oil plantations (Figure 21.8). Palm oil is used in many products including food products,
cosmetics, and biodiesel in Europe. A 5-year estimate of global forest cover loss for the years from 2000 to 2005
was 3.1 percent. Much loss (2.4 percent) occurred in the humid tropics where forest loss is primarily from timber
extraction. These losses certainly also represent the extinction of species unique to those areas.

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 21.2 • Threats to Biodiversity 573

FIGURE 21.8 An oil palm plantation in Sabah province Borneo, Malaysia, replaces native forest habitat that a variety of species depended
on to live. (credit: Lian Pin Koh)

EVERYDAY CONNECTION
Preventing Habitat Destruction with Wise Wood Choices
Most consumers do not imagine that the home improvement products they buy might be contributing to habitat
loss and species extinctions. Yet the market for illegally harvested tropical timber is huge, and the wood
products often find themselves in building supply stores in the United States. One estimate is that 10 percent of
the imported timber stream in the United States, which is the world’s largest consumer of wood products, is
potentially illegally logged. In 2006, this amounted to $3.6 billion in wood products. Most of the illegal products
are imported from countries that act as intermediaries and are not the originators of the wood.

How is it possible to determine if a wood product, such as flooring, was harvested sustainably or even legally?
The Forest Stewardship Council (FSC) certifies sustainably harvested forest products; therefore, looking for their
certification on flooring and other hardwood products is one way to ensure that the wood has not been taken
illegally from a tropical forest. Certification applies to specific products, not to a producer; some producers’
products may not have certification while other products are certified. There are certifications other than the
FSC, but these are run by timber companies creating a conflict of interest. Another approach is to buy domestic
wood species. While it would be great if there was a list of legal versus illegal woods, it is not that simple.
Logging and forest management laws vary from country to country; what is illegal in one country may be legal in
another. Where and how a product is harvested and whether the forest from which it comes is being sustainably
maintained all factor into whether a wood product will be certified by the FSC. It is always a good idea to ask
questions about where a wood product came from and how the supplier knows that it was harvested legally.

Habitat destruction can affect ecosystems other than forests. Rivers and streams are important ecosystems and are
frequently the target of habitat modification through building and from damming or water removal. Damming of
rivers affects flows and access to all parts of a river. Altering a flow regime can reduce or eliminate populations that
are adapted to seasonal changes in flow. For example, an estimated 91 percent of river lengths in the United States
have been modified with damming or bank modifications. Many fish species in the United States, especially rare
species or species with restricted distributions, have seen declines caused by river damming and habitat loss.
Research has confirmed that species of amphibians that must carry out parts of their life cycles in both aquatic and
terrestrial habitats are at greater risk of population declines and extinction because of the increased likelihood that
one of their habitats or access between them will be lost. This is of particular concern because amphibians have
been declining in numbers and going extinct more rapidly than many other groups for a variety of possible reasons.
Habitat destruction, even when undertaken on behalf of humans, can lead to negative effects for us as well.
Excessive soil erosion after forest removal, for example, can remove fertile soil and make river water toxic.
Scientists and conservationists such as Wangari Maathai, who founded the Green Belt movement in Kenya, focus on
replanting trees to repair habitats and prevent damage from deforestation. Maathai was awarded a Nobel Prize for
574 21 • Conservation and Biodiversity

her work, but unfortunately passed away in 2011.

Overharvesting
Overharvesting is a serious threat to many species, but particularly to aquatic species. There are many examples of
regulated fisheries (including hunting of marine mammals and harvesting of crustaceans and other species)
monitored by fisheries scientists that have nevertheless collapsed. The western Atlantic cod fishery is the most
spectacular recent collapse. While it was a hugely productive fishery for 400 years, the introduction of modern
factory trawlers in the 1980s and the pressure on the fishery led to it becoming unsustainable. The causes of fishery
collapse are both economic and political in nature. Most fisheries are managed as a common resource, available to
anyone willing to fish, even when the fishing territory lies within a country’s territorial waters. Common resources
are subject to an economic pressure known as the tragedy of the commons, in which fishers have little motivation
to exercise restraint in harvesting a fishery when they do not own the fishery. The general outcome of harvests of
resources held in common is their overexploitation. While large fisheries are regulated to attempt to avoid this
pressure, it still exists in the background. This overexploitation is exacerbated when access to the fishery is open
and unregulated and when technology gives fishers the ability to overfish. In a few fisheries, the biological growth of
the resource is less than the potential growth of the profits made from fishing if that time and money were invested
elsewhere. In these cases—whales are an example—economic forces will drive toward fishing the population to
extinction.

LINK TO LEARNING
Explore a U.S. Fish & Wildlife Service interactive map (http://openstax.org/l/habitat_map2) of critical habitat for
endangered and threatened species in the United States. To begin, select “Visit the online mapper.”

For the most part, fishery extinction is not equivalent to biological extinction—the last fish of a species is rarely
fished out of the ocean. But there are some instances in which true extinction is a possibility. Whales have slow-
growing populations and are at risk of complete extinction through hunting. Also, there are some species of sharks
with restricted distributions that are at risk of extinction. The groupers are another population of generally slow-
growing fishes that, in the Caribbean, includes a number of species that are at risk of extinction from overfishing.

Coral reefs are extremely diverse marine ecosystems that face peril from several processes. Reefs are home to 1/3
of the world’s marine fish species—about 4000 species—despite making up only one percent of marine habitat. Most
home marine aquaria house coral reef species that are wild-caught organisms—not cultured organisms. Although no
marine species is known to have been driven extinct by the pet trade, there are studies showing that populations of
some species have declined in response to harvesting, indicating that the harvest is not sustainable at those levels.
There are also concerns about the effect of the pet trade on some terrestrial species such as turtles, amphibians,
birds, plants, and even the orangutans.

LINK TO LEARNING
View a brief video (http://openstax.org/l/ocean_matters2) discussing the role of marine ecosystems in supporting
human welfare and the decline of ocean ecosystems.

Bush meat is the generic term used for wild animals killed for food. Hunting is practiced throughout the world, but
hunting practices, particularly in equatorial Africa and parts of Asia, are believed to threaten several species with
extinction. Traditionally, bush meat in Africa was hunted to feed families directly; however, recent commercialization
of the practice now has bush meat available in grocery stores, which has increased harvest rates to the level of
unsustainability. Additionally, human population growth has increased the need for protein foods that are not being
met from agriculture. Species threatened by the bush meat trade are mostly mammals including many monkeys and
the great apes living in the Congo basin.

Exotic Species
Exotic species are species that have been intentionally or unintentionally introduced by humans into an ecosystem

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 21.2 • Threats to Biodiversity 575

in which they did not evolve. Human transportation of people and goods, including the intentional transport of
organisms for trade, has dramatically increased the introduction of species into new ecosystems. These new
introductions are sometimes at distances that are well beyond the capacity of the species to ever travel itself and
outside the range of the species’ natural predators.

Most exotic species introductions probably fail because of the low number of individuals introduced or poor
adaptation to the ecosystem they enter. Some species, however, have characteristics that can make them especially
successful in a new ecosystem. These exotic species often undergo dramatic population increases in their new
habitat and reset the ecological conditions in the new environment, threatening the species that exist there. When
this happens, the exotic species also becomes an invasive species. Invasive species can threaten other species
through competition for resources, predation, or disease.

LINK TO LEARNING
Explore this interactive global database (http://openstax.org/l/exotic_invasiv2) of exotic or invasive species.

Lakes and islands are particularly vulnerable to extinction threats from introduced species. In Lake Victoria, the
intentional introduction of the Nile perch was largely responsible for the extinction of about 200 species of cichlids.
The accidental introduction of the brown tree snake via aircraft (Figure 21.9) from the Solomon Islands to Guam in
1950 has led to the extinction of three species of birds and three to five species of reptiles endemic to the island.
Several other species are still threatened. The brown tree snake is adept at exploiting human transportation as a
means to migrate; one was even found on an aircraft arriving in Corpus Christi, Texas. Constant vigilance on the part
of airport, military, and commercial aircraft personnel is required to prevent the snake from moving from Guam to
other islands in the Pacific, especially Hawaii. Islands do not make up a large area of land on the globe, but they do
contain a disproportionate number of endemic species because of their isolation from mainland ancestors.

FIGURE 21.9 The brown tree snake, Boiga irregularis, is an exotic species that has caused numerous extinctions on the island of Guam
since its accidental introduction in 1950. (credit: NPS)

Many introductions of aquatic species, both marine and freshwater, have occurred when ships have dumped ballast
water taken on at a port of origin into waters at a destination port. Water from the port of origin is pumped into tanks
on a ship empty of cargo to increase stability. The water is drawn from the ocean or estuary of the port and typically
contains living organisms such as plant parts, microorganisms, eggs, larvae, or aquatic animals. The water is then
pumped out before the ship takes on cargo at the destination port, which may be on a different continent. The zebra
mussel was introduced to the Great Lakes from Europe prior to 1988 in ship ballast. The zebra mussels in the Great
Lakes have cost the industry millions of dollars in clean up costs to maintain water intakes and other facilities. The
mussels have also altered the ecology of the lakes dramatically. They threaten native mollusk populations, but have
also benefited some species, such as smallmouth bass. The mussels are filter feeders and have dramatically
improved water clarity, which in turn has allowed aquatic plants to grow along shorelines, providing shelter for
young fish where it did not exist before. The European green crab, Carcinus maenas, was introduced to San
576 21 • Conservation and Biodiversity

Francisco Bay in the late 1990s, likely in ship ballast water, and has spread north along the coast to Washington. The
crabs have been found to dramatically reduce the abundance of native clams and crabs with resulting increases in
the prey of native crabs.

Invading exotic species can also be disease organisms. It now appears that the global decline in amphibian species
recognized in the 1990s is, in some part, caused by the fungus Batrachochytrium dendrobatidis, which causes the
disease chytridiomycosis (Figure 21.10). There is evidence that the fungus is native to Africa and may have been
spread throughout the world by transport of a commonly used laboratory and pet species: the African clawed frog,
Xenopus laevis. It may well be that biologists themselves are responsible for spreading this disease worldwide. The
North American bullfrog, Rana catesbeiana, which has also been widely introduced as a food animal but which
easily escapes captivity, survives most infections of B. dendrobatidis and can act as a reservoir for the disease.

FIGURE 21.10 This Limosa harlequin frog (Atelopus limosus), an endangered species from Panama, died from a fungal disease called
chytridiomycosis. The red lesions are symptomatic of the disease. (credit: Brian Gratwicke)

Early evidence suggests that another fungal pathogen, Geomyces destructans, introduced from Europe is
responsible for white-nose syndrome, which infects cave-hibernating bats in eastern North America and has
spread from a point of origin in western New York State (Figure 21.11). The disease has decimated bat populations
and threatens extinction of species already listed as endangered: the Indiana bat, Myotis sodalis, and potentially the
Virginia big-eared bat, Corynorhinus townsendii virginianus. How the fungus was introduced is unknown, but one
logical presumption would be that recreational cavers unintentionally brought the fungus on clothes or equipment
from Europe.

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 21.2 • Threats to Biodiversity 577

FIGURE 21.11 This little brown bat in Greeley Mine, Vermont, March 26, 2009, was found to have white-nose syndrome. (credit:
modification of work by Marvin Moriarty, USFWS)

Climate Change
Climate change, and specifically the anthropogenic warming trend presently underway, is recognized as a major
extinction threat, particularly when combined with other threats such as habitat loss. Anthropogenic warming of the
planet has been observed and is hypothesized to continue due to past and continuing emission of greenhouse
gases, primarily carbon dioxide and methane, into the atmosphere caused by the burning of fossil fuels and
deforestation. These gases decrease the degree to which Earth is able to radiate heat energy created by the sunlight
that enters the atmosphere. The changes in climate and energy balance caused by increasing greenhouse gases are
complex and our understanding of them depends on predictions generated from detailed computer models.
Scientists generally agree the present warming trend is caused by humans and some of the likely effects include
dramatic and dangerous climate changes in the coming decades. However, there is still debate and a lack of
understanding about specific outcomes. Scientists disagree about the likely magnitude of the effects on extinction
rates, with estimates ranging from 15 to 40 percent of species committed to extinction by 2050. Scientists do agree
that climate change will alter regional climates, including rainfall and snowfall patterns, making habitats less
hospitable to the species living in them. The warming trend will shift colder climates toward the north and south
poles, forcing species to move with their adapted climate norms, but also to face habitat gaps along the way. The
shifting ranges will impose new competitive regimes on species as they find themselves in contact with other
species not present in their historic range. One such unexpected species contact is between polar bears and grizzly
bears. Previously, these two species had separate ranges. Now, their ranges are overlapping and there are
documented cases of these two species mating and producing viable offspring. Changing climates also throw off the
delicate timing adaptations that species have to seasonal food resources and breeding times. Scientists have
already documented many contemporary mismatches to shifts in resource availability and timing.

Range shifts are already being observed: for example, on average, European bird species ranges have moved 91 km
(56.5 mi) northward. The same study suggested that the optimal shift based on warming trends was double that
distance, suggesting that the populations are not moving quickly enough. Range shifts have also been observed in
plants, butterflies, other insects, freshwater fishes, reptiles, amphibians, and mammals.

Climate gradients will also move up mountains, eventually crowding species higher in altitude and eliminating the
habitat for those species adapted to the highest elevations. Some climates will completely disappear. The rate of
warming appears to be accelerated in the arctic, which is recognized as a serious threat to polar bear populations
that require sea ice to hunt seals during the winter months: seals are the only source of protein available to polar
bears. A trend to decreasing sea ice coverage has occurred since observations began in the mid-twentieth century.
The rate of decline observed in recent years is far greater than previously predicted by climate models (Figure
21.12).
578 21 • Conservation and Biodiversity

FIGURE 21.12 The effect of global warming can be seen in the continuing retreat of Grinnell Glacier. The mean annual temperature in
Glacier National Park has increased 1.33°C since 1900. The loss of a glacier results in the loss of summer meltwaters, sharply reducing
seasonal water supplies and severely affecting local ecosystems. (credit: USGS, GNP Archives)

Finally, global warming will raise ocean levels due to meltwater from glaciers and the greater volume occupied by
warmer water. Shorelines will be inundated, reducing island size, which will have an effect on some species, and a
number of islands will disappear entirely. Additionally, the gradual melting and subsequent refreezing of the poles,
glaciers, and higher elevation mountains—a cycle that has provided freshwater to environments for centuries—will
be altered. This could result in an overabundance of salt water and a shortage of fresh water.

21.3 Preserving Biodiversity

LEARNING OBJECTIVES
By the end of this section, you will be able to:
• Describe biodiversity as the equilibrium of naturally fluctuating rates of extinction and speciation
• Explain the legislative framework for conservation
• Identify the factors important in conservation preserve design
• Identify examples of the effects of habitat restoration
• Identify the role of zoos in biodiversity conservation

Preserving biodiversity is an extraordinary challenge that must be met by greater understanding of biodiversity
itself, changes in human behavior and beliefs, and various preservation strategies.

Change in Biodiversity through Time

The number of species on the planet, or in any geographical area, is the result of an equilibrium of two evolutionary
processes that are ongoing: speciation and extinction. Both are natural “birth” and “death” processes of
macroevolution. When speciation rates begin to outstrip extinction rates, the number of species will increase;
likewise, the reverse is true when extinction rates begin to overtake speciation rates. Throughout the history of life
on Earth, as reflected in the fossil record, these two processes have fluctuated to a greater or lesser extent,
sometimes leading to dramatic changes in the number of species on the planet as reflected in the fossil record
(Figure 21.13).

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 21.3 • Preserving Biodiversity 579

FIGURE 21.13 Extinction intensity as reflected in the fossil record has fluctuated throughout Earth’s history. Sudden and dramatic losses of
biodiversity, called mass extinctions, have occurred five times.

Paleontologists have identified five strata in the fossil record that appear to show sudden and dramatic (greater than
half of all extant species disappearing from the fossil record) losses in biodiversity. These are called mass
extinctions. There are many lesser, yet still dramatic, extinction events, but the five mass extinctions have attracted
the most research into their causes. An argument can be made that the five mass extinctions are only the five most
extreme events in a continuous series of large extinction events throughout the fossil record (since 542 million years
ago). In most cases, the hypothesized causes are still controversial; in one, the most recent, the cause seems clear.
The most recent extinction in geological time, about 65 million years ago, saw the disappearance of the dinosaurs
and many other species. Most scientists now agree the cause of this extinction was the impact of a large asteroid in
the present-day Yucatán Peninsula and the subsequent energy release and global climate changes caused by dust
ejected into the atmosphere.

Recent and Current Extinction Rates

A sixth, or Holocene, mass extinction has mostly to do with the activities of Homo sapiens. There are numerous
recent extinctions of individual species that are recorded in human writings. Most of these are coincident with the
expansion of the European colonies since the 1500s.

One of the earlier and popularly known examples is the dodo bird. The dodo bird lived in the forests of Mauritius, an
island in the Indian Ocean. The dodo bird became extinct around 1662. It was hunted for its meat by sailors and
was easy prey because the dodo, which did not evolve with humans, would approach people without fear.
Introduced pigs, rats, and dogs brought to the island by European ships also killed dodo young and eggs (Figure
21.14).

FIGURE 21.14 The dodo bird was hunted to extinction around 1662. (credit: Ed Uthman, taken in Natural History Museum, London,
580 21 • Conservation and Biodiversity

England)

Steller’s sea cow became extinct in 1768; it was related to the manatee and probably once lived along the
northwest coast of North America. Steller’s sea cow was discovered by Europeans in 1741, and it was hunted for
meat and oil. A total of 27 years elapsed between the sea cow’s first contact with Europeans and extinction of the
species. The last Steller’s sea cow was killed in 1768. In another example, the last living passenger pigeon died in a
zoo in Cincinnati, Ohio, in 1914. This species had once migrated in the millions but declined in numbers because of
overhunting and loss of habitat through the clearing of forests for farmland.

These are only a few of the recorded extinctions in the past 500 years. The International Union for Conservation of
Nature (IUCN) keeps a list of extinct and endangered species called the Red List. The list is not complete, but it
describes 380 vertebrates that became extinct after 1500 AD, 86 of which were driven extinct by overhunting or
overfishing.

Estimates of Present-day Extinction Rates

Estimates of extinction rates are hampered by the fact that most extinctions are probably happening without being
observed. The extinction of a bird or mammal is often noticed by humans, especially if it has been hunted or used in
some other way. But there are many organisms that are less noticeable to humans (not necessarily of less value)
and many that are undescribed.

The background extinction rate is estimated to be about 1 per million species years (E/MSY). One “species year” is
one species in existence for one year. One million species years could be one species persisting for one million
years, or a million species persisting for one year. If it is the latter, then one extinction per million species years
would be one of those million species becoming extinct in that year. For example, if there are 10 million species in
existence, then we would expect 10 of those species to become extinct in a year. This is the background rate.

One contemporary extinction-rate estimate uses the extinctions in the written record since the year 1500. For birds
alone, this method yields an estimate of 26 E/MSY, almost thirty times the background rate. However, this value may
be underestimated for three reasons. First, many existing species would not have been described until much later in
the time period and so their loss would have gone unnoticed. Second, we know the number is higher than the
written record suggests because now extinct species are being described from skeletal remains that were never
mentioned in written history. And third, some species are probably already extinct even though conservationists are
reluctant to name them as such. Taking these factors into account raises the estimated extinction rate to nearer 100
E/MSY. The predicted rate by the end of the century is 1500 E/MSY.

A second approach to estimating present-time extinction rates is to correlate species loss with habitat loss, and it is
based on measuring forest-area loss and understanding species–area relationships. The species-area relationship
is the rate at which new species are seen when the area surveyed is increased (Figure 21.15). Likewise, if the habitat
area is reduced, the number of species seen will also decline. This kind of relationship is also seen in the
relationship between an island’s area and the number of species present on the island: as one increases, so does
the other, though not in a straight line. Estimates of extinction rates based on habitat loss and species–area
relationships have suggested that with about 90 percent of habitat loss an expected 50 percent of species would
become extinct. Figure 21.15 shows that reducing forest area from 100 km2 to 10 km2, a decline of 90 percent,
reduces the number of species by about 50 percent. Species–area estimates have led to estimates of present-day
species extinction rates of about 1000 E/MSY and higher. In general, actual observations do not show this amount
of loss and one explanation put forward is that there is a delay in extinction. According to this explanation, it takes
some time for species to fully suffer the effects of habitat loss and they linger on for some time after their habitat is
destroyed, but eventually they will become extinct. Recent work has also called into question the applicability of the
species-area relationship when estimating the loss of species. This work argues that the species–area relationship
leads to an overestimate of extinction rates. Using an alternate method would bring estimates down to around 500
E/MSY in the coming century. Note that this value is still 500 times the background rate.

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 21.3 • Preserving Biodiversity 581

FIGURE 21.15 A typical species-area curve shows the cumulative number of species found as more and more area is sampled. The curve
has also been interpreted to show the effect on species numbers of destroying habitat; a reduction in habitat of 90 percent from 100 km2
to 10 km2 reduces the number of species supported by about 50 percent.

LINK TO LEARNING
Go to this website (http://openstax.org/l/whats_missing2) for an interactive exploration of endangered and extinct
species, their ecosystems, and the causes of their endangerment or extinction.

Conservation of Biodiversity
The threats to biodiversity at the genetic, species, and ecosystem levels have been recognized for some time. In the
United States, the first national park with land set aside to remain in a wilderness state was Yellowstone Park in
1890. However, attempts to preserve nature for various reasons have occurred for centuries. Today, the main efforts
to preserve biodiversity involve legislative approaches to regulate human and corporate behavior, setting aside
protected areas, and habitat restoration.

Changing Human Behavior

Legislation has been enacted to protect species throughout the world. The legislation includes international treaties
as well as national and state laws. The Convention on International Trade in Endangered Species of Wild Fauna and
Flora (CITES) treaty came into force in 1975. The treaty, and the national legislation that supports it, provides a legal
framework for preventing “listed” species from being transported across nations’ borders, thus protecting them
from being caught or killed in the first place when the purpose involves international trade. The listed species that
are protected to one degree or another by the treaty number some 33,000. The treaty is limited in its reach because
it only deals with international movement of organisms or their parts. It is also limited by various countries’ ability or
willingness to enforce the treaty and supporting legislation. The illegal trade in organisms and their parts is probably
a market in the hundreds of millions of dollars.

Within many countries there are laws that protect endangered species and that regulate hunting and fishing. In the
United States, the Endangered Species Act was enacted in 1973. When an at-risk species is listed by the Act, the
U.S. Fish & Wildlife Service is required by law to develop a management plan to protect the species and bring it back
to sustainable numbers. The Act, and others like it in other countries, is a useful tool, but it suffers because it is
often difficult to get a species listed, or to get an effective management plan in place once a species is listed.
Additionally, species may be controversially taken off the list without necessarily having had a change in their
situation. More fundamentally, the approach to protecting individual species rather than entire ecosystems
(although the management plans commonly involve protection of the individual species’ habitat) is both inefficient
and focuses efforts on a few highly visible and often charismatic species, perhaps at the expense of other species
that go unprotected.

The Migratory Bird Treaty Act (MBTA) is an agreement between the United States and Canada that was signed into
582 21 • Conservation and Biodiversity

law in 1918 in response to declines in North American bird species caused by hunting. The Act now lists over 800
protected species. It makes it illegal to disturb or kill the protected species or distribute their parts (much of the
hunting of birds in the past was for their feathers). Examples of protected species include northern cardinals, the
red-tailed hawk, and the American black vulture.

Global warming is expected to be a major driver of biodiversity loss. Many governments are concerned about the
effects of anthropogenic global warming, primarily on their economies and food resources. Since greenhouse gas
emissions do not respect national boundaries, the effort to curb them is an international one. The international
response to global warming has been mixed. The Kyoto Protocol, an international agreement that came out of the
United Nations Framework Convention on Climate Change that committed countries to reducing greenhouse gas
emissions by 2012, was ratified by some countries, but spurned by others. Two countries that were especially
important in terms of their potential impact that did not ratify the Kyoto protocol were the United States and China.
Some goals for reduction in greenhouse gasses were met and exceeded by individual countries, but, worldwide, the
effort to limit greenhouse gas production is not succeeding. The intended replacement for the Kyoto Protocol has
not materialized because governments cannot agree on timelines and benchmarks. Meanwhile, the resulting costs
to human societies and biodiversity predicted by a majority of climate scientists will be high.

As already mentioned, the non-profit, non-governmental sector plays a large role in conservation effort both in
North America and around the world. The approaches range from species-specific organizations to the broadly
focused IUCN and Trade Records Analysis of Flora and Fauna in Commerce (TRAFFIC). The Nature Conservancy
takes a novel approach. It purchases land and protects it in an attempt to set up preserves for ecosystems.
Ultimately, human behavior will change when human values change. At present, the growing urbanization of the
human population is a force that mitigates against valuing biodiversity, because many people no longer come in
contact with natural environments and the species that inhabit them.

Conservation in Preserves
Establishment of wildlife and ecosystem preserves is one of the key tools in conservation efforts (Figure 21.16). A
preserve is an area of land set aside with varying degrees of protection for the organisms that exist within the
boundaries of the preserve. Preserves can be effective for protecting both species and ecosystems, but they have
some serious drawbacks.

FIGURE 21.16 National parks, such as Grand Teton National Park in Wyoming, help conserve biodiversity. (credit: Don DeBold)

A simple measure of success in setting aside preserves for biodiversity protection is to set a target percentage of
land or marine habitat to protect. However, a more detailed preserve design and choice of location is usually
necessary because of the way protected lands are allocated and how biodiversity is distributed: protected lands
tend to contain less economically valuable resources rather than being set aside specifically for the species or
ecosystems at risk. In 2003, the IUCN World Parks Congress estimated that 11.5 percent of Earth’s land surface
was covered by preserves of various kinds. This area is greater than previous goals; however, it only represents 9 out
of 14 recognized major biomes and research has shown that 12 percent of all species live outside preserves; these
percentages are much higher when threatened species are considered and when only high quality preserves are
considered. For example, high quality preserves include only about 50 percent of threatened amphibian species.
The conclusion must be that either the percentage of area protected must be increased, the percentage of high
quality preserves must be increased, or preserves must be targeted with greater attention to biodiversity protection.
Researchers argue that more attention to the latter solution is required.

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 21.3 • Preserving Biodiversity 583

A biodiversity hotspot is a conservation concept developed by Norman Myers in 1988. Hotspots are geographical
areas that contain high numbers of endemic species. The purpose of the concept was to identify important locations
on the planet for conservation efforts, a kind of conservation triage. By protecting hotspots, governments are able to
protect a larger number of species. The original criteria for a hotspot included the presence of 1500 or more species
of endemic plants and 70 percent of the area disturbed by human activity. There are now 34 biodiversity hotspots
(Figure 21.17) that contain large numbers of endemic species, which include half of Earth’s endemic plants.

FIGURE 21.17 Conservation International has identified 34 biodiversity hotspots. Although these cover only 2.3 percent of the Earth’s
surface, 42 percent of the terrestrial vertebrate species and 50 percent of the world’s plants are endemic to those hotspots.

There has been extensive research into optimal preserve designs for maintaining biodiversity. The fundamental
principles behind much of the research have come from the seminal theoretical work of Robert H. MacArthur and
2
Edward O. Wilson published in 1967 on island biogeography. This work sought to understand the factors affecting
biodiversity on islands. Conservation preserves can be seen as “islands” of habitat within “an ocean” of non-habitat.
In general, large preserves are better because they support more species, including species with large home ranges;
they have more core area of optimal habitat for individual species; they have more niches to support more species;
and they attract more species because they can be found and reached more easily.

Preserves perform better when there are partially protected buffer zones around them of suboptimal habitat. The
buffer allows organisms to exit the boundaries of the preserve without immediate negative consequences from
hunting or lack of resources. One large preserve is better than the same area of several smaller preserves because
there is more core habitat unaffected by less hospitable ecosystems outside the preserve boundary. For this same
reason, preserves in the shape of a square or circle will be better than a preserve with many thin “arms.” If
preserves must be smaller, then providing wildlife corridors between them so that species and their genes can move
between the preserves; for example, preserves along rivers and streams will make the smaller preserves behave
more like a large one. All of these factors are taken into consideration when planning the nature of a preserve before
the land is set aside.

In addition to the physical specifications of a preserve, there are a variety of regulations related to the use of a
preserve. These can include anything from timber extraction, mineral extraction, regulated hunting, human
habitation, and nondestructive human recreation. Many of the decisions to include these other uses are made based
on political pressures rather than conservation considerations. On the other hand, in some cases, wildlife protection
policies have been so strict that subsistence-living indigenous populations have been forced from ancestral lands
that fell within a preserve. In other cases, even if a preserve is designed to protect wildlife, if the protections are not
or cannot be enforced, the preserve status will have little meaning in the face of illegal poaching and timber

2 Robert H. MacArthur and Edward O. Wilson, E. O., The Theory of Island Biogeography (Princeton, N.J.: Princeton University Press, 1967).
584 21 • Conservation and Biodiversity

extraction. This is a widespread problem with preserves in the tropics.

Some of the limitations on preserves as conservation tools are evident from the discussion of preserve design.
Political and economic pressures typically make preserves smaller, never larger, so setting aside areas that are large
enough is difficult. Enforcement of protections is also a significant issue in countries without the resources or
political will to prevent poaching and illegal resource extraction.

Climate change will create inevitable problems with the location of preserves as the species within them migrate to
higher latitudes as the habitat of the preserve becomes less favorable. Planning for the effects of global warming on
future preserves, or adding new preserves to accommodate the changes expected from global warming is in
progress, but will only be as effective as the accuracy of the predictions of the effects of global warming on future
habitats.

Finally, an argument can be made that conservation preserves reinforce the cultural perception that humans are
separate from nature, can exist outside of it, and can only operate in ways that do damage to biodiversity. Creating
preserves reduces the pressure on human activities outside the preserves to be sustainable and non-damaging to
biodiversity. Ultimately, the political, economic, and human demographic pressures will degrade and reduce the size
of conservation preserves if the activities outside them are not altered to be less damaging to biodiversity.

LINK TO LEARNING
Check out this interactive global data system (http://openstax.org/l/protected_area2) of protected areas. Review
data about specific protected areas by location or study statistics on protected areas by country or region.

Habitat Restoration
Habitat restoration holds considerable promise as a mechanism for maintaining or restoring biodiversity. Of course
once a species has become extinct, its restoration is impossible. However, restoration can improve the biodiversity
of degraded ecosystems. Reintroducing wolves, a top predator, to Yellowstone National Park in 1995 led to dramatic
changes in the ecosystem that increased biodiversity. The wolves (Figure 21.18) function to suppress elk and coyote
populations and provide more abundant resources to the guild of carrion eaters. Reducing elk populations has
allowed revegetation of riparian (the areas along the banks of a stream or river) areas, which has increased the
diversity of species in that habitat. Suppression of coyotes has increased the species previously suppressed by this
predator. The number of species of carrion eaters has increased because of the predatory activities of the wolves. In
this habitat, the wolf is a keystone species, meaning a species that is instrumental in maintaining diversity within an
ecosystem. Removing a keystone species from an ecological community causes a collapse in diversity. The results
from the Yellowstone experiment suggest that restoring a keystone species effectively can have the effect of
restoring biodiversity in the community. Ecologists have argued for the identification of keystone species where
possible and for focusing protection efforts on these species. It makes sense to return the keystone species to the
ecosystems where they have been removed.

FIGURE 21.18 This photograph shows the Gibbon wolf pack in Yellowstone National Park, March 1, 2007. Wolves have been identified as a
keystone species. (credit: Doug Smith, NPS)

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 21.3 • Preserving Biodiversity 585

Other large-scale restoration experiments underway involve dam removal. In the United States, since the
mid-1980s, many aging dams are being considered for removal rather than replacement because of shifting beliefs
about the ecological value of free-flowing rivers. The measured benefits of dam removal include restoration of
naturally fluctuating water levels (often the purpose of dams is to reduce variation in river flows), which leads to
increased fish diversity and improved water quality. In the Pacific Northwest, dam removal projects are expected to
increase populations of salmon, which is considered a keystone species because it transports nutrients to inland
ecosystems during its annual spawning migrations. In other regions, such as the Atlantic coast, dam removal has
allowed the return of other spawning anadromous fish species (species that are born in fresh water, live most of
their lives in salt water, and return to fresh water to spawn). Some of the largest dam removal projects have yet to
occur or have happened too recently for the consequences to be measured. The large-scale ecological experiments
that these removal projects constitute will provide valuable data for other dam projects slated either for removal or
construction.

The Role of Zoos and Captive Breeding

Zoos have sought to play a role in conservation efforts both through captive breeding programs and education
(Figure 21.19). The transformation of the missions of zoos from collection and exhibition facilities to organizations
that are dedicated to conservation is ongoing. In general, it has been recognized that, except in some specific
targeted cases, captive breeding programs for endangered species are inefficient and often prone to failure when
the species are reintroduced to the wild. Zoo facilities are far too limited to contemplate captive breeding programs
for the numbers of species that are now at risk. Education, on the other hand, is a potential positive impact of zoos
on conservation efforts, particularly given the global trend to urbanization and the consequent reduction in contacts
between people and wildlife. A number of studies have been performed to look at the effectiveness of zoos on
people’s attitudes and actions regarding conservation; at present, the results tend to be mixed.

FIGURE 21.19 Zoos and captive breeding programs help preserve many endangered species, such as this golden lion tamarin. (credit:
Garrett Ziegler)
586 21 • Key Terms

Key Terms
biodiversity the variety of a biological system, extinction rate the number of species becoming
typically conceived as the number of species, but extinct over time, sometimes defined as extinctions
also applying to genes, biochemistry, and per million species–years to make numbers
ecosystems manageable (E/MSY)
biodiversity hotspot a concept originated by Norman genetic diversity the variety of genes and alleles in a
Myers to describe a geographical region with a large species or other taxonomic group or ecosystem; the
number of endemic species and a large percentage term can refer to allelic diversity or genome-wide
of degraded habitat diversity
bush meat a wild-caught animal used as food habitat heterogeneity the number of ecological
(typically mammals, birds, and reptiles); usually niches
referring to hunting in the tropics of sub-Saharan secondary plant compound a compound produced
Africa, Asia, and the Americas as a byproduct of plant metabolic processes that is
chemical diversity the variety of metabolic typically toxic, but is sequestered by the plant to
compounds in an ecosystem defend against herbivores
chytridiomycosis a disease of amphibians caused by species-area relationship the relationship between
the fungus Batrachochytrium dendrobatidis; area surveyed and number of species encountered;
thought to be a major cause of the global amphibian typically measured by incrementally increasing the
decline area of a survey and determining the cumulative
ecosystem diversity the variety of ecosystems numbers of species
endemic species a species native to one place tragedy of the commons an economic principle that
exotic species (also, invasive species) a species that resources held in common will inevitably be over-
has been introduced to an ecosystem in which it did exploited
not evolve white-nose syndrome a disease of cave-hibernating
extinction the disappearance of a species from Earth; bats in the eastern United States and Canada
local extinction is the disappearance of a species associated with the fungus Geomyces destructans
from a region

Chapter Summary
21.1 Importance of Biodiversity Crop diversity is a requirement for food security, and it
is being lost. The loss of wild relatives to crops also
Biodiversity exists at multiple levels of organization,
threatens breeders’ abilities to create new varieties.
and is measured in different ways depending on the
Ecosystems provide ecosystem services that support
goals of those taking the measurements. These include
human agriculture: pollination, nutrient cycling, pest
numbers of species, genetic diversity, chemical
control, and soil development and maintenance. Loss
diversity, and ecosystem diversity. The number of
of biodiversity threatens these ecosystem services and
described species is estimated to be 1.5 million with
risks making food production more expensive or
about 17,000 new species being described each year.
impossible. Wild food sources are mainly aquatic, but
Estimates for the total number of eukaryotic species on
few are being managed for sustainability. Fisheries’
Earth vary but are on the order of 10 million.
ability to provide protein to human populations is
Biodiversity is negatively correlated with latitude for
threatened when extinction occurs.
most taxa, meaning that biodiversity is higher in the
tropics. The mechanism for this pattern is not known 21.2 Threats to Biodiversity
with certainty, but several plausible hypotheses have
The core threats to biodiversity are human population
been advanced.
growth and unsustainable resource use. To date, the
Humans use many compounds that were first most significant causes of extinction are habitat loss,
discovered or derived from living organisms as introduction of exotic species, and overharvesting.
medicines: secondary plant compounds, animal toxins, Climate change is predicted to be a significant cause of
and antibiotics produced by bacteria and fungi. More extinction in the coming century. Habitat loss occurs
medicines are expected to be discovered in nature. through deforestation, damming of rivers, and other
Loss of biodiversity will impact the number of activities. Overharvesting is a threat particularly to
pharmaceuticals available to humans. Biodiversity may aquatic species, but the taking of bush meat in the
provide important psychological benefits to humans. humid tropics threatens many species in Asia, Africa,

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 21 • Visual Connection Questions 587

and the Americas. Exotic species have been the cause individual countries protecting species and agreements
of a number of extinctions and are especially damaging on global warming have had limited success; there is at
to islands and lakes. Exotic species’ introductions are present no international agreement on targets for
increasing because of the increased mobility of human greenhouse gas emissions. In the United States, the
populations and growing global trade and Endangered Species Act protects listed species but is
transportation. Climate change is forcing range hampered by procedural difficulties and a focus on
changes that may lead to extinction. It is also affecting individual species. The Migratory Bird Act is an
adaptations to the timing of resource availability that agreement between Canada and the United States to
negatively affects species in seasonal environments. protect migratory birds. The non-profit sector is also
The impacts of climate change are currently greatest in very active in conservation efforts in a variety of ways.
the arctic. Global warming will also raise sea levels,
Conservation preserves are a major tool in biodiversity
eliminating some islands and reducing the area of all
protection. Presently, 11 percent of Earth’s land
others.
surface is protected in some way. The science of island
21.3 Preserving Biodiversity biogeography has informed the optimal design of
preserves; however, preserves have limitations
Five mass extinctions with losses of more than 50
imposed by political and economic forces. In addition,
percent of extant species are observable in the fossil
climate change will limit the effectiveness of present
record. Recent extinctions are recorded in written
preserves in the future. A downside of preserves is that
history and are the basis for one method of estimating
they may lessen the pressure on human societies to
contemporary extinction rates. The other method uses
function more sustainably outside the preserves.
measures of habitat loss and species-area
relationships. Estimates of contemporary extinction Habitat restoration has the potential to restore
rates vary but are as high as 500 times the background ecosystems to previous biodiversity levels before
rate, as determined from the fossil record, and are species become extinct. Examples of restoration
predicted to rise. include reintroduction of keystone species and removal
of dams on rivers. Zoos have attempted to take a more
There is a legislative framework for biodiversity
active role in conservation and can have a limited role
protection. International treaties such as CITES
in captive breeding programs. Zoos also have a useful
regulate the transportation of endangered species
role in education.
across international borders. Legislation within

Visual Connection Questions

1. Figure 21.6 The Svalbard seed vault is located on
Spitsbergen island in Norway, which has an arctic
climate. Why might an arctic climate be good for
seed storage?

Review Questions
2. The number of currently described species on the 4. Pollination is an example of ________.
planet is about ________. a. a possible source of new drugs
a. 17,000 b. chemical diversity
b. 150,000 c. an ecosystem service
c. 1.5 million d. crop pest control
d. 10 million
5. Converting a prairie to a farm field is an example of
3. A secondary plant compound might be used for ________.
which of the following? a. overharvesting
a. a new crop variety b. habitat loss
b. a new drug c. exotic species
c. a soil nutrient d. climate change
d. a crop pest
588 21 • Critical Thinking Questions

6. Which two extinction risks may be a direct result of 8. Certain species of parrot cannot be brought to the
the pet trade? United States to be sold as pets. What is the name
a. climate change and exotic species introduction of the legislation that makes this illegal?
b. habitat loss and overharvesting a. Red List
c. overharvesting and exotic species introduction b. Migratory Bird Act
d. habitat loss and climate change c. CITES
d. Endangered Species Act (ESA)
7. What kind of ecosystem are exotic species
especially threatening to? 9. Which measures can protect biodiversity?
a. deserts a. legal protections
b. marine ecosystems b. conservation efforts
c. islands c. restoration efforts
d. tropical forests d. all of the above

Critical Thinking Questions

10. Explain how biodiversity loss can impact crop 13. Explain what extinction threats a frog living on a
diversity. mountainside in Costa Rica might face.

11. Describe two types of compounds from living 14. Describe two considerations in conservation
things that are used as medications. preserve design.

12. Describe the mechanisms by which human 15. Describe what happens to an ecosystem when a
population growth and resource use causes keystone species is removed.
increased extinction rates.

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 A • The Periodic Table of Elements 589

APPENDIX A

The Periodic Table of Elements

FIGURE A1
590 A • The Periodic Table of Elements

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 B • Geological Time 591

APPENDIX B

Geological Time

FIGURE B1 Geological Time Clock

592 B • Geological Time

FIGURE B2 Geological Time Chart

(credit: Richard S. Murphy, Jr.)

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 C • Measurements and the Metric System 593

APPENDIX C

Measurements and the Metric System

Measurements and the Metric System
Measurements and the Metric System

Approximate Standard
Measurement Unit Abbreviation Metric Equivalent
Equivalent

nanometer nm 1 nm = 10−9 m

micrometer µm 1 µm = 10−6 m

1 mm = 0.039 inch
millimeter mm 1 mm = 0.001 m
1 cm = 0.394 inch
1 m = 39.37 inches
Length centimeter cm 1 cm = 0.01 m
1 m = 3.28 feet
1 m = 1.093 yards
1 m = 100 cm
1 km = 0.621 miles
meter m 1 m = 1000
mm

kilometer km 1 km = 1000 m

microgram µg 1 µg = 10−6 g

milligram mg 1 mg = 10−3 g 1 g = 0.035 ounce

Mass 1 kg = 2.205 pounds
gram g 1 g = 1000 mg

kilogram kg 1 kg = 1000 g

microliter µl 1 µl = 10−6 l

milliliter ml 1 ml = 10−3 l 1 ml = 0.034 fluid ounce

Volume 1 l = 1.057 quarts
liter l 1 l = 1000 ml 1 kl = 264.172 gallons

kiloliter kl 1 kl = 1000 l

square 1 cm2 = 0.155 square inch

cm2 1 cm2 = 100 mm2
centimeter 1 m2 = 10.764 square feet
Area 1 m2 = 1.196 square yards
1 m2 = 10,000 1 ha = 2.471 acres
square meter m2
cm2
TABLE C1
594 C • Measurements and the Metric System

Approximate Standard
Measurement Unit Abbreviation Metric Equivalent
Equivalent

hectare ha 1 ha = 10,000 m2

Temperature Celsius °C — 1 °C = 5/9 × (°F − 32)

TABLE C1

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 Index 595

INDEX

A Annelida 374 basal ganglia 432

absorption spectrum 122 anoxic 288 bases 38
abyssal zone 552 anther 339 Basic science 22
acellular 446 Anthophyta 343 Basidiomycota 310
acetyl CoA 102 Anthropoids 389 benthic realm 551
Acid rain 543 antibody 457 bicuspid valve 411
Acids 38 antigen 456 Bilateral symmetry 355
acoelomates 355 antigen-presenting cell (APC) Bile 405
Actinopterygii 383 459 binary fission 143
action potential 428 Anura 383 binomial nomenclature 275
activation energy 95 anus 405 biodiversity 564
active immunity 458 aorta 411 biodiversity hotspot 583
active site 96 apex consumers 528 bioenergetics 90
Active transport 80 aphotic zone 551 biofilm 290
adaptation 251 apical meristem 323 biogeochemical cycle 533
Adaptive immunity 456 Apoda 383 Biology 5
adaptive radiation 262 apoptosis 449 Biomagnification 532
adhesion 37 appendicular skeleton 423 biomarker 241
adrenal glands 417 applied science 22 biome 527
Age structure 508 Archaeplastida 302 bioremediation 297
algal bloom 555 Arctic tundra 549 biosphere 12
alleles 176 Arteries 413 Biotechnology 223
allergy 466 Arthropoda 367 birth rate 501
Allopatric speciation 260 Ascomycota 310 Black Death 293
allosteric inhibition 97 Asexual reproduction 474 blastocyst 479
alternation of generations 153 Asymmetrical 354 body plan 352
alternative RNA splicing 217 atom 9 bolus 403
alveoli 409 atomic number 29 bones 387
Amino acids 46 ATP 100 boreal forest 548
amniotes 385 ATP synthase 104 bottleneck effect 255
Amoebocytes 358 atrium 411 botulism 295
Amoebozoa 302 attenuation 451 brachiation 389
Amphibia 383 auditory ossicles 422 brainstem 433
ampullae of Lorenzini 382 autoantibody 467 branch point 276
amygdala 432 Autoimmunity 467 bronchi 409
amylase 403 autonomic nervous system 433 bronchioles 409
anabolic 91 autosomes 162 budding 359, 475
anaerobic 288 autotroph 116 Buffers 38
analogous structure 280 autotrophs 531 bulbourethral gland 482
analogous structures 251 axial skeleton 421 Bush meat 574
anaphase 138 axon 428
C
aneuploid 162
B Caecilians 384
anions 32
B cells 456 Calvin cycle 125
annealing 227
Basal angiosperms 343 calyx 339
596 Index

canopy 544 chromatin 65 ctenidia 371

capillaries 413 chromosome 65 cutaneous respiration 383
capsid 447 chromosome inversion 165 cyanobacteria 289
capsule 291 chyme 404 Cycads 336
Carbohydrates 40 chytridiomycosis 576 cytokine 454
carbon fixation 125 Chytridiomycota 310 Cytokinesis 138
cardiac cycle 412 cilia 64 cytopathic 449
Cardiac muscle tissue 425 citric acid cycle 102 cytoplasm 63
carpel 339 clades 282 cytoskeleton 63
carrying capacity 501 cladistics 282 cytosol 63
Cartilaginous joints 423 class 275
catabolic 91 cleavage furrow 138
D
dead zone 540
cations 32 climax community 519
death rate 501
cell 10 clitellum 375
Deductive reasoning 19
cell cycle 135 clitoris 483
demography 496
cell cycle checkpoints 140 cloning 226
denaturation 46
cell plate 138 closed circulatory system 411
Dendrites 427
cell wall 69 club mosses 330
dendritic cell 459
cell-mediated immune response Cnidaria 359
density-dependent 504
456 cnidocytes 359
density-independent 504
Cellulose 41 codominance 184
deoxyribonucleic acid (DNA) 49
central nervous system (CNS) codon 213
deoxyribose 199
430 coelom 355
depolarization 428
central vacuole 70 cohesion 37
Descriptive 19
centrioles 136 colon 405
desmosomes 72
Cephalochordata 379 commensalism 297
detrital food web 530
cephalothorax 369 community 12
Deuterostomes 356
cerebellum 432 competitive exclusion principle
diaphragm 409
cerebral cortex 431 513
diastole 412
cerebrospinal fluid (CSF) 430 competitive inhibition 97
dicots 343
chaetae 374 complement system 455
Diffusion 77
channel 556 complete digestive system 366
dihybrid 181
chaparral 546 concentration gradient 77
dioecious 367
chelicerae 369 cones 334
diphyodonts 388
chemical bonds 31 Conifers 335
diploblasts 355
chemical diversity 565 conjugation 292
diploid 134
chemiosmosis 104 Continuous variation 172
diploid-dominant 153
chemoautotrophs 531 control 20
Diplontic 321
chiasmata 156 convergent evolution 251
Disaccharides 41
chitin 42, 366 Coral reefs 552
discontinuous variation 172
chlorophyll 118 corolla 339
dispersal 261
chlorophyll a 122 corpus callosum 431
divergent evolution 251
chlorophyll b 122 corpus luteum 483
DNA ligase 204
chloroplast 118 cotyledons 342
DNA polymerase 204
Chloroplasts 69 covalent bond 32
domains 275
choanocyte 358 craniates 381
Dominant 175
Chondrichthyes 382 Crocodilia 385
dorsal hollow nerve cord 378
Chordata 378 crossing over 156
double helix 200
Chromalveolata 302 cryptofauna 553
down feathers 387

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 Index 597

down-regulation 416 Exotic species 574 gastrulation 480

exponential growth 500 Gel electrophoresis 225
E external fertilization 477 gemmules 359
Echinodermata 376
extinction 566 gene expression 215
ecosystem 12, 526
extinction rates 580 gene flow 256
ecosystem diversity 565
extracellular digestion 361 gene pool 252
ecosystem services 555
extracellular matrix 71 Gene therapy 231
ectotherms 398
extremophiles 290 genes 134
effector cells 460
genetic code 213
electrocardiogram (ECG) 412 F Genetic diversity 565
electrochemical gradient 81 F1 173
genetic drift 253
electromagnetic spectrum 121 F2 173
genetic engineering 230
electron 28 facilitated transport 78
genetic map 234
electron transfer 32 fallout 542
genetically modified organism
electron transport chain 102 falsifiable 20
230
elements 28 family 275
genome 133
Emergent vegetation 557 fat 43
genomics 234
Endemic species 567 Feedback inhibition 99
genotype 176
endergonic reactions 94 fermentation 105
genus 275
endocrine glands 415 ferns 331
germ cells 153
Endocytosis 82 fertilization 155
germ layers 355
endomembrane system 65 fibrous joints 423
gestation 489
endoplasmic reticulum (ER) 65 filament 339
gestation period 489
endosymbiotic theory 298 Fission 474
ginkgophyte 337
endotherm 398 Flagella 64
glia 427
environmental disturbances 518 fluid mosaic model 74
Glomeromycota 310
Enzymes 45, 95 follicle stimulating hormone
Glycogen 41
epidemics 294 (FSH) 486
Glycolysis 101
epidermis 360 food chain 527
glycoprotein 448
epigenetic 216 food web 529
Gnathostomes 382
epistasis 190 foodborne disease 295
Gnetophytes 337
Equilibrium 527 Foundation species 516
Golgi apparatus 66
esophagus 402 founder effect 256
gonadotropin-releasing hormone
essential nutrients 407 fragmentation 359, 475
(GnRH) 486
estrogen 487 Frogs 384
Gram-negative 291
Estuaries 554 frontal lobe 432
Gram-positive 291
eucoelomates 356 FtsZ 144
granum 119
eudicots 343
eukaryotes 10
G grazing food web 530
G0 phase 139 gross primary productivity 531
eukaryotic cell 60
G1 phase 135 Gymnosperms 334
euploid 162
G2 phase 136 gynoecium 339
Eutherian mammals 389
gallbladder 405
eutrophication 538 H
gametangia 322
evaporation 35 habitat heterogeneity 568
gametes 134
evolution 12 Hagfishes 381
gametophyte 321
Excavata 302 haplodiplontic 321
gametophytes 155
exergonic reactions 94 haploid 134
Gap junctions 72
Exocrine glands 415 haploid-dominant 153
gastrodermis 360
Exocytosis 83 Haplontic 321
gastrovascular cavity 361
exons 211 heat energy 93
598 Index

helicase 204 interferon 454 line 382

hemizygous 187 interkinesis 158 linkage 189
hemocoel 367 internal fertilization 477 Lipids 42
herbaceous 344 interphase 135 litmus 37
Hermaphroditism 476 interstitial cells of Leydig 481 liver 405
heterodont teeth 387 interstitial fluid 400 Liverworts 327
heterosporous 322 intertidal zone 551 locus 134
Heterotrophs 116 intracellular 415 logistic growth 501
heterozygous 176 intracellular digestion 358 Lophotrochozoa 370
hippocampus 432 intraspecific competition 502 luteinizing hormone (LH) 486
Homeostasis 8 introns 211 Lymph 463
homologous chromosomes 134 ion 32 lymphocyte 455
homologous structures 252 ionic bond 32 lysosomes 66
homosporous 322 Island biogeography 516
homozygous 176 isotonic 79
M
macroevolution 252
hormone receptors 415 Isotopes 29
macromolecules 9, 39
Hormones 45, 415
hornworts 328
J macrophage 454
J-shaped growth curve 501 madreporite 376
Horsetails 330
joint 423 major histocompatibility complex
host 515
(MHC) I molecules 455
human beta chorionic K Mammals 387
gonadotropin (β-HCG) 489 K-selected species 506
Mammary glands 387
humoral immune response 456 karyogram 161
mantle 371
hybridizations 173 karyotype 161
mark and recapture 497
hydrogen bond 33 keystone species 517
Marsupials 388
hydrophilic 35 kidneys 401
mass number 29
hydrophobic 35 kinetic energy 93
Mast cells 454
hydrosphere 533 kinetochore 138
Matter 28
hydrothermal vent 289 kingdom 275
maximum parsimony 284
hyoid bone 422
hypersensitivity 466 L medusa 360
labia majora 483 megasporocyte 334
hypertonic 79
labia minora 483 meiosis 152
hypha 308
lagging strand 204 meiosis I 155
hypothalamus 432
Lampreys 381 Meiosis II 155
hypothesis 18
Lancelets 380 memory cell 461
hypothesis-based science 19
large intestine 405 meninges 430
hypotonic 79
larynx 409 menstrual cycle 487
I lateral 382 mesoglea 360
immune tolerance 465 law of dominance 177 mesohyl 358
Immunodeficiency 466 law of independent assortment mesophyll 118
incomplete dominance 184 181 metabolism 90
Inductive reasoning 19 law of segregation 179 Metagenomics 238
inferior vena cava 411 leading strand 204 metamerism 374
inflammation 454 Lichens 313 metaphase 138
inheritance of acquired life cycles 153 metaphase plate 138
characteristics 248 life sciences 18 MHC class II molecule 457
inhibin 487 life tables 496 microbial mat 289
Innate immunity 453 light-dependent reactions 119 microevolution 252
inner cell mass 479 limbic system 432 microscope 56

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 Index 599

microsporocytes 334 nitrogenous base 199 P

migration 253 non-renewable resource 537 pancreas 405, 417
mimicry 512 noncompetitive inhibition 97 pandemics 293
Minerals 407 nondisjunction 161 paper 37
mismatch repair 207 Nonpolar covalent bonds 33 parasite 515
Mitochondria 68 nontemplate strand 210 parasites 301
mitosis 136 nonvascular plants 326 parasympathetic nervous system
mitotic 135, 136 notochord 378 435
model organisms 236 nuclear envelope 65 parathyroid glands 417
model system 172 nucleic acids 49 parietal lobe 432
modern synthesis 252 nucleolus 65 Parthenogenesis 476
molds 309 nucleotide excision repair 207 passive immune 458
molecular systematics 281 nucleotides 49 Passive transport 77
molecule 9 nucleus 28, 65 pathogen 292
Mollusca 370 pectoral girdle 423
monocots 343
O
Peer-reviewed articles 23
occipital lobe 432
monocyte 454 pelagic realm 551
oceanic zone 552
monoecious 359 pellicles 301
octet rule 32
monohybrid 178 pelvic girdle 423
oils 44
monophyletic group 282 penis 481
Okazaki fragments 204
Monosaccharides 40 pepsin 404
oncogenes 141
monosomy 162 peptidoglycan 291
one-child policy 509
monotremes 388 periodic table of elements 29
oogenesis 484
mortality rate 498 peripheral nervous system (PNS)
Open circulatory systems 411
mosses 328 433
Opisthokonta 302
mRNA 209 peristalsis 402
oral cavity 403
mutation 208 permafrost 549
order 275
mutualism 514 Peroxisomes 69
organ system 10
mycelium 308 Petals 339
organelles 10, 60
Mycorrhiza 313 Petromyzontidae 381
Organisms 10
mycoses 311 pH scale 37
organogenesis 480
myelin sheath 428 Phagocytosis 82
Organs 10
myofibrils 425 Pharmacogenomics 238
origin 143
myofilaments 426 Pharyngeal slits 378
osculum 358
Myxini 381 pharynx 409
osmolarity 79
phase 135
N Osmoregulation 400
phenotype 176
nacre 372 Osmosis 78
phloem 329
nasal cavity 409 osmotic balance 400
phosphate group 199
natural killer (NK) cell 455 Osteichthyes 383
Phospholipids 45
natural sciences 18 ostracoderms 381
photic zone 551
Natural selection 249 ovarian cycle 487
photoautotrophs 116, 531
nematocysts 359 ovary 339
photon 122
Nematoda 366 oviducts 483
photosystem 122
nephrons 401 oviparity 478
phototrophs 289
neritic zone 551 ovoviparity 478
phylogenetic tree 13, 276
Net primary productivity 531 ovulation 488
phylogeny 274
neurons 427 oxidative phosphorylation 102
phylum 275
Neutrons 28
Physical maps 234
neutrophil 454
600 Index

physical sciences 18 Protostomes 356 Saturated fatty acids 44

pigment 118 pseudocoelomates 356 Savannas 545
pinocytosis 83 pseudopeptidoglycan 292 Science 17, 19
pioneer species 518 pulmonary circulation 411 scientific laws 18
pistil 339 Punnett square 178 scientific method 18
pituitary gland 416 scientific theory 18
placenta 489
Q scrotum 481
quadrat 497
planktivores 553 Sebaceous glands 387
plasma membrane 63 R Secondary consumers 527
plasmid 226 r-selected species 506 secondary immune response
Plasmodesmata 71 radial symmetry 354 462
plastid 299 radioactive isotopes 29 secondary plant compounds 568
pneumatic 387 radula 370 secondary succession 518
polar covalent bond 33 receptor-mediated endocytosis selectively permeable 76
Polymerase chain reaction (PCR) 83 Semen 481
225 Recessive 175 semiconservative replication
polyp 360 reciprocal cross 175 204
polypeptide 47 recombinant 156 seminal vesicles 482
polyploid 164 recombinant DNA 228 seminiferous tubules 481
polysaccharide 41 recombinant proteins 228 sensory-somatic nervous system
population 12 recombination 189 433
population density 496 rectum 405 sepals 339
population genetics 252 reduction division 159 septum 143, 309
population size 496 Relative species abundance 516 Sertoli cells 481
Porifera 357 renal artery 401 set point 398
post-anal tail 378 renal vein 401 sex determination 477
post-transcriptional 216 replication forks 204 sexual reproduction 474
post-translational 216 Reproductive cloning 228 shared ancestral character 283
potential energy 93 resilience 527 shared derived character 283
primary bronchi 409 resistance 527 sister taxa 277
primary consumers 527 restriction enzymes 227 Skeletal muscle tissue 425
primary immune response 461 reverse genetics 230 skull 422
primary succession 518 Rhizaria 302 small intestine 404
Primates 389 ribonucleic acid (RNA) 49 smooth endoplasmic reticulum
primer 204 Ribosomes 68 (SER) 66
producers 527 RNA polymerase 210 Smooth muscle tissue 425
progesterone 487 rooted 276 solute 78
Prokaryotes 10 rough endoplasmic reticulum solvent 36
prokaryotic cell 59 (RER) 66 somatic cell 155
prometaphase 137 rRNA 212 source water 556
promoter 209 speciation 260
prophase 137 S species 275
S phase 136
Prosimians 389 species distribution pattern 497
S-shaped curve 501
prostate gland 482 Species richness 516
salamanders 383
protein signature 241 species-area relationship 580
salivary glands 403
Proteins 45 spermatogenesis 484
saprobes 306
proteomics 241 Sphenodontia 386
sarcolemma 425
proto-oncogenes 141 spicules 358
sarcomere 426
proton 28 spindle 136
Sarcopterygii 383

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 Index 601

spiracles 367 Temperate grasslands 547 urethra 401

splicing 211 Temperature 35 urinary bladder 401
spongocoel 358 template strand 210 Urochordata 379
sporangia 322 temporal lobe 432 Urodela 383
sporophylls 329 Tertiary consumers 527 uterus 483
sporophyte 155, 321 test cross 179
Squamata 386 testes 481
V
vaccine 451
stamens 339 Testosterone 486
vacuoles 67
Starch 41 Testudines 386
vagina 484
start codon 213 tetrads 156
van der Waals interactions 34
stereoscopic vision 389 Tetrapod 378
variable 20
steroids 45 thalamus 432
variation 250
stigma 339 thallus 308
Vascular plants 326
stomach 404 Thermodynamics 91
Veins 413
stomata 118 thoracic cage 423
ventricle 411
stop codons 213 threshold of excitation 428
vertebral column 378, 423
Strobili 329 thylakoids 118
Vesicles 67
stroma 119 thymus 418
vestigial structures 257
stromatolite 290 thyroid gland 417
vicariance 261
style 339 tight junction 72
viral envelope 448
subduction 537 tissues 10
virion 447
substrates 96 Tonicity 79
Vitamins 407
Subtropical deserts 545 trachea 409
viviparity 478
Sudoriferous glands 387 tracheae 367
superior vena cava 411 tragedy of the commons 574 W
surface tension 37 trait 174 water vascular system 376
survivorship curve 499 trans-fat 44 wavelength 120
swim bladder 383 transcription bubble 209 Wetlands 557
sympathetic nervous system 434 transduction 292 whisk ferns 331
Sympatric speciation 260 transformation 292 white blood cell 454
synapses 427 transgenic 230, 233 white-nose syndrome 576
synapsis 156 translocations 161 Whole genome sequencing 236
synaptic cleft 430 tricuspid valve 411 wild type 185
syngamy 322 triglycerides 43
Synovial joints 424 triploblasts 355 X
X inactivation 163
systematics 274 trisomy 162
X-linked 187
systemic circulation 411 tRNAs 212
Xylem 329
systole 412 trophic level 527

T
trophoblast 479 Y
Tropical rainforests 544 yeasts 308
T cells 456
Tumor suppressor genes 141
tadpole 384
tunicates 379 Z
taxon 275 zero population growth 501
Taxonomy 274 U zona pellucida 479
telomerase 205 unified cell theory 59 Zygomycota 310
telomeres 205 unsaturated fatty acid 44
telophase 138 up-regulation 416
Temperate forests 548 ureter 401