Chapter 1. BIOLOGY: HOW LIFE WORKS

BIOLOGY: HOW LIFE WORKS

TABLE OF CONTENTS

About the Authors iv

Brief Contents vi

Preface viii

Acknowledgments xxi

PART 1     FROM CELLS TO ORGANISMS

CHAPTER 1     LIFE

Chemical, Cellular, and Evolutionary Foundations     1-1

       1.1 The Scientific Method     1-2

         Observation allows us to draw tentative explanations called hypotheses.     1-2

         A hypothesis makes predictions that can be tested by observation and experiments.     1-3

         HOW DO WE KNOW?
          What caused the extinction of the dinosaurs?     1-4

         General explanations of natural phenomena supported by many experiments and observations are called theories.     1-5

       1.2 Chemical and Physical Principles     1-5

         The living and nonliving worlds share the same chemical foundations and obey the same physical laws.     1-6

         The scientific method shows that living organisms come from other living organisms.     1-7

         HOW DO WE KNOW?
          Can living organisms arise from nonliving matter?     1-8

         HOW DO WE KNOW?
          Can microscopic life arise from nonliving matter?     1-8

       1.3 The Cell     1-8

         Nucleic acids store and transmit information needed for growth, function, and reproduction.     1-10

         Membranes define cells and spaces within cells.     1-11

         Metabolism converts energy from the environment into a form that can be used by cells.     1-12

         A virus is genetic material in need of a cell.     1-12

       1.4 Evolution     1-12

         Variation in populations provides the raw material for evolution, or change over time.     1-12

         Evolution predicts a nested pattern of relatedness among species, depicted as a tree.     1-13

         Evolution can be studied by means of experiments.     1-15

         HOW DO WE KNOW?
          Can evolution be demonstrated in the laboratory?     1-15

       1.5 Ecological Systems     1-16

         Basic features of anatomy, physiology, and behavior shape ecological systems.     1-16

         Ecological interactions play an important role in evolution.     1-17

       1.6 The Human Footprint     1-18

?    CASE 1 The First Cell: Life’s Origins C1-1

CHAPTER 2     THE MOLECULES OF LIFE     2-1

       2.1 Properties of Atoms     2-1

         Atoms consist of protons, neutrons, and electrons.     2-1

         Electrons occupy regions of space called orbitals.     2-3

         Elements have recurring, or periodic, chemical properties.     2-3

       2.2 Molecules and Chemical Bonds     2-4

         A covalent bond results when two atoms share electrons.     2-4

         A polar covalent bond is characterized by unequal sharing of electrons.     2-5

         A hydrogen bond is an interaction of a hydrogen atom and an electronegative atom.     2-5

         An ionic bond forms between oppositely charged ions.     2-6

         A chemical reaction involves breaking and forming chemical bonds.     2-6

       2.3 Water: The Medium of Life     2-7

         Water is a polar molecule.     2-7

         pH is a measure of the concentration of protons in solution.     2-7

         Hydrogen bonds give water many unusual properties.     2-8

       2.4 Carbon: Life’s Chemical Backbone     2-9

         Carbon atoms form four covalent bonds.     2-9

         Carbon-based molecules are structurally and functionally diverse.     2-9

       2.5 Organic Molecules     2-11

         Proteins are composed of amino acids.     2-11

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         Nucleic acids encode genetic information in their nucleotide sequence.     2-12

         Complex carbohydrates are made up of simple sugars.     2-13

         Lipids are hydrophobic molecules.     2-15

?    2.6 How Did the Molecules of Life Form?     2-17

         HOW DO WE KNOW?
          Could the building blocks of organic molecules have been generated on the early Earth?     2-18

         The building blocks of life can be generated in the laboratory.     2-18

         Experiments show how life’s building blocks can form macromolecules.     2-18

CHAPTER 3     NUCLEIC ACIDS AND THE ENCODING OF BIOLOGICAL INFORMATION     3-1

       3.1 Major Biological Functions of DNA     3-2

         DNA can transfer biological characteristics from one organism to another.     3-2

         HOW DO WE KNOW?
          What is the nature of the genetic material?     3-2

         DNA molecules are copied in the process of replication.     3-3

         Genetic information flows from DNA to RNA to protein.     3-3

         HOW DO WE KNOW?
          What is the nature of the genetic material?     3-3

       3.2 Chemical Composition and Structure of DNA     3-4

         A DNA strand consists of subunits called nucleotides.     3-4

         DNA is a linear polymer of nucleotides linked by phosphodiester bonds.     3-6

         Cellular DNA molecules take the form of a double helix.     3-6

         The three-dimensional structure of DNA gave important clues about its functions.     3-8

         Cellular DNA is coiled and packaged with proteins.     3-9

       3.3 Retrieval of Genetic Information Stored in DNA: Transcription     3-10

       ? What was the first nucleic acid molecule, and how did it arise?     3-10

         In transcription, DNA is used as a template to make complementary RNA.     3-11

         Transcription starts at a promoter and ends at a terminator.     3-12

         RNA polymerase adds successive nucleotides to the 3′ end of the transcript.     3-13

         The RNA polymerase complex is a molecular machine that opens, transcribes, and closes duplex DNA.     3-15

       3.4 Fate of the RNA Primary Transcript     3-15

         Messenger RNA carries information for the synthesis of a specific protein.     3-15

         Primary transcripts in eukaryotes undergo several types of chemical modification.     3-16

         Some RNA transcripts are processed differently from protein-coding transcripts and have functions of their own.     3-18

CHAPTER 4     TRANSLATION AND PROTEIN STRUCTURE     4-1

       4.1 Molecular Structure of Proteins     4-1

         Amino acids differ in their side chains.     4-2

         Successive amino acids in proteins are connected by peptide bonds.     4-3

         The sequence of amino acids dictates protein folding, which determines function.     4-4

         Secondary structures result from hydrogen bonding in the polypeptide backbone.     4-5

         HOW DO WE KNOW?
          What are the shapes of proteins?     4-5

         Tertiary structures result from interactions between amino acid side chains.     4-6

         Polypeptide subunits can come together to form quaternary structures.     4-7

         Chaperones help some proteins fold properly.     4-8

       4.2 Translation: How Proteins Are Synthesized     4-8

         Translation uses many molecules found in all cells.     4-8

         The genetic code shows the correspondence between codons and amino acids.     4-10

         HOW DO WE KNOW?
          How was the genetic code deciphered?     4-11

         Translation consists of initiation, elongation, and termination.     4-12

      ? How did the genetic code originate?     4-14

       4.3 Protein Evolution and the Origin of New Proteins     4-15

         Most proteins are composed of modular folding domains.     4-15

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       VISUAL SYNTHESIS Gene Expression     4-16

         Amino acid sequences evolve through mutation and selection.     4-18

CHAPTER 5     ORGANIZING PRINCIPLES

Lipids, Membranes, and Cell Compartments     5-1

       5.1 Structure of Cell Membranes     5-1

         Cell membranes are composed of two layers of lipids.     5-2

      ? How did the first cell membranes form?     5-3

         Cell membranes are dynamic.     5-3

         Proteins associate with cell membranes in different ways.     5-5

       5.2 The Plasma Membrane and Cell Wall     5-6

         HOW DO WE KNOW?
          Do proteins move in the plane of the membrane?     5-7

         The plasma membrane maintains homeostasis.     5-8

         Passive transport involves diffusion.     5-8

         Primary active transport uses the energy of ATP.     5-9

         Secondary active transport is driven by an electrochemical gradient.     5-10

         Many cells maintain size and composition using active transport.     5-11

         The cell wall provides another means of maintaining cell shape.     5-12

       5.3 The Internal Organization of Cells     5-12

         Eukaryotes and prokaryotes differ in internal organization.     5-13

         Prokaryotic cells lack a nucleus and extensive internal compartmentalization.     5-13

         Eukaryotic cells have a nucleus and specialized internal structures.     5-13

       5.4 The Endomembrane System     5-15

         The endomembrane system compartmentalizes the cell.     5-16

         The nucleus houses the genome and is the site of RNA synthesis.     5-17

         The endoplasmic reticulum is involved in protein and lipid synthesis.     5-17

         The Golgi apparatus modifies and sorts proteins and lipids.     5-18

         Lysosomes degrade macromolecules.     5-19

         Protein sorting directs proteins to their proper location in or out of the cell.     5-20

       5.5 Mitochondria and Chloroplasts     5-22

         Mitochondria provide the eukaryotic cell with most of its usable energy.     5-22

         Chloroplasts capture energy from sunlight.     5-23

CHAPTER 6     MAKING LIFE WORK

Capturing and Using Energy     6-1

       6.1 An Overview of Metabolism     6-1

         Organisms can be classified according to their energy and carbon sources.     6-2

         Metabolism is the set of chemical reactions that sustain life.     6-3

       6.2 Energy     6-3

         Kinetic and potential energy are two forms of energy.     6-3

         Chemical energy is a form of potential energy.     6-4

         ATP is the cell’s energy currency.     6-4

       6.3 The Laws of Thermodynamics     6-5

         The first law of thermodynamics: Energy is conserved.     6-5

         The second law of thermodynamics: Disorder tends to increase.     6-5

       6.4 Chemical Reactions     6-6

         A chemical reaction occurs when molecules interact.     6-6

         Chemical reactions are subject to the laws of thermodynamics.     6-7

         The hydrolysis of ATP releases energy.     6-8

         Non-spontaneous reactions are often coupled to spontaneous reactions.     6-9

       6.5 Enzymes and the Rate of Chemical Reactions     6-10

         Enzymes reduce the activation energy of a chemical reaction.     6-10

         Enzymes form a complex with reactants and products.     6-11

         Enzymes are highly specific.     6-12

         HOW DO WE KNOW?
          Do enzymes form complexes with substrates?     6-12

         HOW DO WE KNOW?
          Do enzymes form complexes with substrates?     6-13

         Enzyme activity can be influenced by inhibitors and activators.     6-13

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         Allosteric enzymes in the cell are regulated by activators and inhibitors.     6-14

      ? What naturally occurring elements might have spurred the first reactions that led to life?     6-15

CHAPTER 7     CELLULAR RESPIRATION

Harvesting Energy from Carbohydrates and Other Fuel Molecules     7-1

       7.1 An Overview of Cellular Respiration     7-1

         Cellular respiration occurs in four stages.     7-2

         Cellular respiration involves a series of redox reactions.     7-2

         Chemical energy is stored in reduced molecules such as carbohydrates and lipids.     7-4

         Electron carriers transport high-energy electrons.     7-4

         ATP is generated by substrate-level phosphorylation and oxidative phosphorylation.     7-4

       7.2 Glycolysis: The Splitting of Sugar     7-5

         Glycolysis is the partial breakdown of glucose.     7-7

       7.3 Acetyl-CoA Synthesis     7-7

         The oxidation of pyruvate connects glycolysis to the citric acid cycle.     7-7

       7.4 The Citric Acid Cycle     7-8

         The citric acid cycle produces ATP and electron carriers.     7-8

      ? What were the earliest energy-harnessing reactions?     7-10

       7.5 The Electron Transport Chain and

         Oxidative Phosphorylation     7-10

         The electron transport chain transfers electrons and pumps protons.     7-10

         The proton gradient is a source of potential energy.     7-12

         ATP synthase converts the energy of the proton gradient into the energy of ATP.     7-12

         HOW DO WE KNOW?
          Can a proton gradient drive the synthesis of ATP?     7-13

       7.6 Anaerobic Metabolism and the Evolution of Cellular Respiration     7-14

         Fermentation extracts energy from glucose in the absence of oxygen.     7-15

      ? How did early cells meet their energy requirements?     7-16

       7.7 Metabolic Integration     7-17

         Excess glucose is stored as glycogen in animals and starch in plants.     7-17

         Sugars other than glucose contribute to glycolysis.     7-17

         Fatty acids and proteins are useful sources of energy.     7-18

         The intracellular level of ATP is a key regulator of cellular respiration.     7-19

         Exercise requires several types of fuel molecules and the coordination of metabolic pathways.     7-20

CHAPTER 8     PHOTOSYNTHESIS

Using Sunlight to Build Carbohydrates     8-1

       8.1 The Natural History of Photosynthesis     8-1

         Photosynthesis is a redox reaction.     8-1

         HOW DO WE KNOW?
          Does the oxygen released by photosynthesis come from H2O or CO2?     8-2

         Photosynthesis is widely distributed.     8-3

         The evolutionary history of photosynthesis includes both horizontal gene transfer and endosymbiosis.     8-4

         The photosynthetic electron transport chain takes place on specialized membranes.     8-5

       8.2 The Calvin Cycle     8-6

         The incorporation of CO2 is catalyzed by the enzyme rubisco.     8-6

         NADPH is the reducing agent of the Calvin cycle.     8-6

         The regeneration of RuBP requires ATP.     8-7

         The steps of the Calvin cycle were determined using radioactive CO2.     8-7

         Carbohydrates are stored in the form of starch.     8-7

         HOW DO WE KNOW?
          How is CO2 used to synthesize carbohydrates?     8-8

       8.3 Capturing Sunlight into Chemical Forms     8-9

         Photosystems use light energy to set the photosynthetic electron transport chain in motion.     8-9

         HOW DO WE KNOW?
          Do chlorophyll molecules operate on their own or in groups?     8-11

         The photosynthetic electron transport chain connects two photosystems.     8-12

         The accumulation of protons in the thylakoid lumen drives the synthesis of ATP.     8-14

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         Cyclic electron transport increases the production of ATP.     8-14

         The spatial organization of the thylakoid membrane contributes to its functioning.     8-15

      ? How did early cells meet their energy requirements?     8-15

       8.4 Challenges to Photosynthetic Efficiency     8-16

         Excess light energy can cause damage.     8-16

         Photorespiration leads to a net loss of energy and carbon.     8-17

         Photosynthesis captures just a small percentage of incoming solar energy.     8-19

       VISUAL SYNTHESIS Harnessing Energy: Photosynthesis and Cellular Respiration     8-20

      ? CASE 2 Cancer: When Good Cells Go Bad C2-2

CHAPTER 9     CELL COMMUNICATION     9-1

       9.1 Principles of Cell Communication     9-1

         Cells communicate using chemical signals that bind to specific receptors.     9-2

         Signaling involves receptor activation, signal transduction, response, and termination.     9-2

       9.2 Types of Cell Signaling     9-3

         Endocrine signaling acts over long distances.     9-3

         Paracrine and autocrine signaling act over short distances.     9-4

         HOW DO WE KNOW?
          Where do growth factors come from?     9-4

         Juxtacrine signaling depends on direct cell-cell contact.     9-5

       9.3 Receptors and Receptor Activation     9-6

         Receptors can be on the cell surface or in the interior of the cell.     9-6

         There are three major types of cell-surface receptor, which act like molecular switches.     9-7

       9.4 Signal Transduction, Response, and Termination     9-8

         Signals transmitted by G protein-coupled receptors are amplified and regulated at several steps.     9-8

         Receptor kinases phosphorylate each other and activate intracellular signaling pathways.     9-11

         Ligand-gated ion channels alter the movement of ions across the plasma membrane.     9-13

      ? How do cell signaling errors lead to cancer?     9-15

         Signaling pathways can intersect with one another in a cell.     9-15

CHAPTER 10     CELL FORM AND FUNCTION

Cytoskeleton, Cellular Junctions, and Extracellular Matrix     10-1

       10.1 Tissues and Organs     10-1

         Tissues and organs are communities of cells.     10-2

         The structure of skin relates to its function.     10-2

       10.2 The Cytoskeleton     10-3

         Microtubules are hollow, tubelike polymers of tubulin dimers.     10-4

         Microfilaments are helical polymers of actin.     10-4

         Intermediate filaments are polymers of proteins that vary according to cell type.     10-4

      ? How can doctors test for the spread of cancer?     10-5

         Microtubules and microfilaments are dynamic structures.     10-6

         The cytoskeleton is an ancient feature of cells.     10-7

       10.3 Cellular Movement     10-8

         Motor proteins associate with microtubules and microfilaments to cause movement.     10-8

         Organelles with special arrangements of microtubules propel cells through the environment.     10-10

         Actin polymerization moves cells forward.     10-10

       10.4 Cell Adhesion     10-11

         Cell adhesion molecules allow cells to attach to other cells and to the extracellular matrix.     10-11

         Adherens junctions and desmosomes connect adjacent animal cells and are anchored to the cytoskeleton.     10-12

         Tight junctions prevent the movement of substances through the space between animal cells.     10-13

         Gap junctions and plasmodesmata allow the passage of substances from one cell to another.     10-15

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       10.5 The Extracellular Matrix     10-15

         The extracellular matrix of plants is the cell wall.     10-15

         The extracellular matrix is abundant in connective tissues of animals.     10-17

         The basal lamina is a special form of extracellular matrix.     10-18

      ? How do cancer cells spread throughout the body?     10-18

         Extracellular matrix proteins influence cell shape and gene expression.     10-18

         HOW DO WE KNOW?
          Can extracellular matrix proteins influence gene expression?     10-20

CHAPTER 11     CELL DIVISION

Variations, Regulation, and Cancer     11-1

       11.1 Cell Division     11-2

         Prokaryotic cells reproduce by binary fission.     11-2

         Eukaryotic cells reproduce by mitotic cell division.     11-3

         The cell cycle describes the life cycle of a eukaryotic cell.     11-3

       11.2 Mitotic Cell Division     11-4

         The DNA of eukaryotic cells is organized as chromosomes.     11-4

         Prophase: Chromosomes condense and become visible.     11-5

         Prometaphase: Chromosomes attach to the mitotic spindle.     11-6

         Metaphase: Chromosomes align as a result of dynamic changes in the mitotic spindle.     11-6

         Anaphase: Sister chromatids fully separate.     11-6

         Telophase: Nuclear envelopes re-form around newly segregated chromosomes.     11-6

         The parent cell divides into two daughter cells by cytokinesis.     11-7

       11.3 Meiotic Cell Division     11-7

         Pairing of homologous chromosomes is unique to meiosis.     11-8

         Crossing over between DNA molecules results in exchange of genetic material.     11-8

         The first meiotic division brings about the reduction in chromosome number.     11-9

         The second meiotic division resembles mitosis.     11-10

         Division of the cytoplasm often differs between the sexes.     11-11

         Meiosis is the basis of sexual reproduction.     11-13

       11.4 Regulation of the Cell Cycle     11-14

         Protein phosphorylation controls passage through the cell cycle.     11-14

         HOW DO WE KNOW?
          How is progression through the cell cycle controlled?     11-15

         Different cyclin-CDK complexes regulate each stage of the cell cycle.     11-16

         Cell cycle progression requires successful passage through multiple checkpoints.     11-16

      ? 11.5 What Genes Are Involved In Cancer?     11-18

         Oncogenes promote cancer.     11-18

         HOW DO WE KNOW?
          Can a virus cause cancer?     11-18

         Proto-oncogenes are genes that when mutated may cause cancer.     11-19

         Tumor suppressors block specific steps in the development of cancer.     11-21

         Most cancers require the accumulation of multiple mutations.     11-21

       VISUAL SYNTHESIS: Cellular Communities     11-22

      ? CASE 3 You, From A to T: Your Personal Genome C3-2

CHAPTER 12     DNA REPLICATION AND MANIPULATION     12-1

       12.1 DNA Replication     12-1

         During DNA replication, the parental strands separate and new partners are made.     12-2

         HOW DO WE KNOW?
          How is DNA replicated?     12-2

         New DNA strands grow by the addition of nucleotides to the 3′ end.     12-4

         In replicating DNA, one daughter strand is synthesized continuously and the other in a series of short pieces.     12-4

         A small stretch of RNA is needed to begin synthesis of a new DNA strand.     12-5

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         DNA polymerase is self-correcting because of its proofreading function.     12-6

         Many proteins participate in DNA replication.     12-7

       12.2 Replication of Chromosomes     12-8

         Replication of DNA in chromosomes starts at many places almost simultaneously.     12-8

         Telomerase restores tips of linear chromosomes shortened during DNA replication.     12-8

       12.3 Isolation, Identification, and Sequencing of DNA Fragments     12-10

         The polymerase chain reaction selectively amplifies regions of DNA.     12-10

         Electrophoresis separates DNA fragments by size.     12-11

         Restriction enzymes cleave DNA at particular short sequences.     12-13

         DNA strands can be separated and brought back together again.     12-14

         DNA sequencing makes use of the principles of DNA replication.     12-15

      ? What new technologies will be required to sequence your personal genome?     12-16

       12.4 Recombinant DNA and Genetically Modified Organisms     12-17

         Recombinant DNA combines DNA molecules from two sources.     12-18

         Recombinant DNA is the basis of genetically modified organisms.     12-19

CHAPTER 13     GENOMES     13-1

       13.1 Genome Sequencing     13-1

         Complete genome sequences are assembled from smaller pieces.     13-2

         HOW DO WE KNOW?
          How are whole genomes sequenced?     13-2

         Sequences that are repeated complicate sequence assembly.     13-2

      ? Why sequence your personal genome?     13-4

       13.2 Genome Annotation     13-4

         Genome annotation identifies various types of sequence.     13-4

         Genome annotation includes searching for sequence motifs.     13-5

         Comparison of genomic DNA with messenger

         RNA reveals the intron-exon structure of genes.     13-6

         An annotated genome summarizes knowledge, guides research, and reveals evolutionary relationships among organisms.     13-6

         The HIV genome illustrates the utility of genome annotation and comparison.     13-6

       13.3 Gene Number, Genome Size, and Organismal Complexity     13-7

         Gene number is not a good predictor of biological complexity.     13-7

         Viruses, bacteria, and archaeons have small, compact genomes.     13-8

         Among eukaryotes, there is no relationship between genome size and organismal complexity.     13-9

         About half of the human genome consists of repetitive DNA and transposable elements.     13-10

       13.4 Organization of Genomes     13-11

         Bacterial cells package their DNA as a nucleoid composed of many loops.     13-11

         Eukaryotic cells package their DNA as one molecule per chromosome.     13-13

         The human genome consists of 22 pairs of chromosomes and two sex chromosomes.     13-13

         Organelle DNA forms nucleoids that differ from those in bacteria.     13-14

       13.5 Viruses and Viral Genomes 13-15

         The host range of a virus is determined by viral and host surface proteins.     13-15

         Viruses can be classified by their genomes.     13-16

         Viruses have diverse sizes and shapes.     13-17

         Viruses are capable of self-assembly.     13-18

CHAPTER 14     MUTATION AND DNA REPAIR     14-1

       14.1 The Rate and Nature of Mutations     14-1

         For individual nucleotides, mutation is a rare event.     14-1

         Across the genome as a whole, mutation is common.     14-2

         Only germ-line mutations are transmitted to progeny.     14-3

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      ? What can your personal genome tell you about your genetic risk factors?     14-4

         Mutations are random with regard to an organism’s needs.     14-5

       14.2 Small-Scale Mutations     14-5

         Point mutations are changes in a single nucleotide.     14-5

         HOW DO WE KNOW?
          Do mutations occur randomly, or are they directed by the environment?     14-6

         Small insertions and deletions involve several nucleotides.     14-8

         HOW DO WE KNOW?
          What causes sectoring in corn kernels?     14-10

         Some mutations are due to the insertion of a transposable element.     14-10

       14.3 Chromosomal Mutations     14-11

         Duplications and deletions result in gain or loss of DNA.     14-11

         Gene families arise from gene duplication and evolutionary divergence.     14-12

         An inversion has a chromosomal region reversed in orientation.     14-12

         A reciprocal translocation joins segments from nonhomologous chromosomes.     14-13

       14.4 DNA Damage and Repair     14-13

         DNA damage can affect both DNA backbone and bases.     14-13

         Most DNA damage is corrected by specialized repair enzymes.     14-14

CHAPTER 15     GENETIC VARIATION     15-1

       15.1 Genotype and Phenotype     15-1

         Genotype is the genetic makeup of a cell or organism; phenotype is its observed characteristics.     15-1

         The effect of a genotype often depends on several factors.     15-2

         Some genetic differences are major risk factors for disease.     15-3

         Not all genetic differences are harmful.     15-3

         A few genetic differences are beneficial.     15-5

       15.2 Genetic Variation and Individual Uniqueness     15-6

         Areas of the genome with variable numbers of tandem repeats are useful in DNA typing.     15-6

         Some polymorphisms add or remove restriction sites in the DNA.     15-7

       15.3 Genomewide Studies of Genetic Variation     15-8

         Single-nucleotide polymorphisms (SNPs) are single base changes in the genome.     15-8

      ? How can genetic risk factors be detected?     15-9

         SNPs can be detected by DNA microarrays.     15-9

         Copy-number variation constitutes a significant proportion of genetic variation.     15-10

       15.4 Genetic Variation in Chromosomes     15-11

         Nondisjunction in meiosis results in extra or missing chromosomes.     15-11

         Some human disorders result from nondisjunction.     15-12

         HOW DO WE KNOW?
          What is the genetic basis of Down syndrome?     15-13

         Extra sex chromosomes have fewer effects than extra autosomes.     15-14

         Nondisjunction is a major cause of spontaneous abortion.     15-15

CHAPTER 16     MENDELIAN INHERITANCE     16-1

       16.1 Early Theories of Inheritance     16-1

         Early theories of heredity predicted the transmission of acquired characteristics.     16-1

         Belief in blending inheritance discouraged studies of hereditary transmission.     16-2

       16.2 The Foundations of Modern

         Transmission Genetics     16-3

         Mendel’s experimental organism was the garden pea.     16-3

         In crosses, one of the traits was dominant in the offspring.     16-4

       16.3 Segregation: Mendel’s Key Discovery     16-5

         Genes come in pairs that segregate in the formation of reproductive cells.     16-6

         The principle of segregation was tested by predicting the outcome of crosses.     16-7

35

         A testcross is a mating to an individual with the homozygous recessive genotype.     16-7

         Segregation of alleles reflects the separation of chromosomes in meiosis.     16-8

         Dominance is not universally observed.     16-8

         The principles of transmission genetics are statistical and stated in terms of probabilities.     16-9

         Mendelian segregation preserves genetic variation.     16-10

       16.4 Independent Assortment     16-10

         Independent assortment is observed when genes segregate independently of one another.     16-11

         Independent assortment reflects the random alignment of chromosomes in meiosis.     16-12

         HOW DO WE KNOW?
          How are simple traits inherited?     16-12

         Phenotypic ratios can be modified by interactions between genes.     16-14

       16.5 Patterns of Inheritance Observed in Family Histories     16-14

         Dominant traits appear in every generation.     16-15

         Recessive traits skip generations.     16-16

         Many genes have multiple alleles.     16-16

         Incomplete penetrance and variable expression can obscure inheritance patterns.     16-17

      ? How do genetic tests identify disease risk factors?     16-17

CHAPTER 17     BEYOND MENDEL

Sex Chromosomes, Linkage, and Organelles     17-1

       17.1 The X and Y Sex Chromosomes     17-1

         In many animals, sex is genetically determined and associated with chromosomal differences.     17-2

         Segregation of the sex chromosomes predicts a 1:1 ratio of females to males.     17-2

       17.2 Inheritance of Genes in the X Chromosome     17-3

         X-linked inheritance was discovered through studies of male fruit flies with white eyes.     17-3

         Genes in the X chromosome exhibit a “crisscross” inheritance pattern.     17-4

         X-linkage provided the first experimental evidence that genes are in chromosomes.     17-6

         Genes in the X chromosome show characteristic patterns in human pedigrees.     17-7

       17.3 Genetic Linkage and Recombination     17-8

         Nearby genes in the same chromosome show linkage.     17-8

         Recombination frequency is a measure of the distance between linked genes.     17-10

         Genetic mapping assigns a location to each gene along a chromosome.     17-11

         Genetic risk factors for disease can be localized by genetic mapping.     17-11

         HOW DO WE KNOW?
          Can recombination be used to construct a genetic map of a chromosome?     17-12

       17.4 Inheritance of Genes in the Y Chromosome     17-13

         Y-linked genes are transmitted from father to son to grandson.     17-13

      ? How can the Y chromosome be used to trace ancestry?     17-14

       17.5 Inheritance of Mitochondrial and Chloroplast DNA     17-15

         Mitochondrial and chloroplast genomes often show uniparental inheritance.     17-15

         Maternal inheritance is characteristic of mitochondrial diseases.     17-15

      ? How can mitochondrial DNA be used to trace ancestry?     17-16

CHAPTER 18     THE GENETIC AND ENVIRONMENTAL BASIS OF COMPLEX TRAITS     18-1

       18.1 Heredity and Environment     18-2

         Complex traits are affected by the environment.     18-2

         Complex traits are affected by multiple genes.     18-3

         The relative importance of genes and environment can be determined by differences among individuals.     18-4

         Genetic and environmental effects can interact in unpredictable ways.     18-5

       18.2 Resemblance Among Relatives     18-6

         For complex traits, offspring resemble parents but show regression toward the mean.     18-6

36

         Heritability is the proportion of the total variation due to genetic differences among individuals.     18-7

       18.3 Twin Studies     18-8

         Identical twins share the same genotype.     18-8

         Twin studies help separate the effects of genes and environment in differences among individuals.     18-9

         HOW DO WE KNOW?
          What is the relative importance of genes and the environment for complex traits?     18-10

       18.4 Complex Traits in Health and Disease     18-10

         Most common diseases and birth defects are affected by many genes that each have relatively small effects.     18-11

         Human height is affected by hundreds of genes.     18-12

      ? Can personalized medicine lead to effective treatments of common diseases?     18-12

CHAPTER 19     GENETIC AND EPIGENETIC REGULATION     19-1

       19.1 Chromatin to Messenger RNA in Eukaryotes     19-2

         Gene expression can be influenced by chemical modification of DNA or histones.     19-2

         Gene expression can be regulated at the level of an entire chromosome.     19-3

         Transcription is a key control point in gene expression.     19-5

         RNA processing is also important in gene regulation.     19-6

       19.2 Messenger RNA to Phenotype in Eukaryotes     19-8

         Small regulatory RNAs inhibit translation or promote RNA degradation.     19-8

         Translational regulation controls the rate, timing, and location of protein synthesis.     19-9

         Protein structure and chemical modification modulate protein effects on phenotype.     19-10

      ? How do lifestyle choices affect expression of your personal genome?     19-10

       19.3 Transcriptional Regulation in Prokaryotes     19-10

         Transcriptional regulation can be positive or negative.     19-11

         Lactose utilization in E. coli is the pioneering example of transcriptional regulation.     19-12

         HOW DO WE KNOW?
          How does lactose lead to the production of active ß-galactosidase enzyme?     19-12

         The repressor protein binds with the operator and prevents transcription, but not in the presence of lactose.     19-13

         The function of the lactose operon was revealed by genetic studies.     19-14

         The lactose operon is also positively regulated by CRP-cAMP.     19-14

         Transcriptional regulation determines the outcome of infection by a bacterial virus.     19-15

       VISUAL SYNTHESIS: Virus: A Genome in Need of a Cell     19-18

CHAPTER 20     GENES AND DEVELOPMENT     20-1

       20.1 Genetic Programs of Development     20-1

         The fertilized egg is a totipotent cell.     20-2

         Cellular differentiation increasingly restricts alternative fates.     20-2

         HOW DO WE KNOW?
          HOW do stem cells lose their ability to differentiate into any cell type?     20-3

      ? Can cells with your personal genome be reprogrammed for new therapies?     20-5

       20.2 Hierarchical Control of Development     20-5

         Drosophila development proceeds through egg, larval, and adult stages.     20-5

         The egg is a highly polarized cell.     20-6

         Development proceeds by progressive regionalization and specification.     20-8

         Homeotic genes determine where different body parts develop in the organism.     20-9

       20.3 Evolutionary Conservation of Key Transcription Factors in Development     20-11

         Animals have evolved a wide variety of eyes.     20-11

         Pax6 is a master regulator of eye development.     20-12

       20.4 Combinatorial Control in Development     20-13

         Floral differentiation is a model for plant development.     20-13

37

         The identity of the floral organs is determined by combinatorial control.     20-14

       20.5 Cell Signaling in Development     20-15

         A signaling molecule can cause multiple responses in the cell.     20-16

         Developmental signals are amplified and expanded.     20-16

       VISUAL SYNTHESIS Genetic Variation and Inheritance     20-18

      ? CASE 4 Malaria: Co-evolution of Humans and a Parasite C4-2

CHAPTER 21     EVOLUTION

How Genotypes and Phenotypes Change over Time     21-1

       21.1 Genetic Variation     21-1

         Population genetics is the study of patterns of genetic variation.     21-1

         Mutation and recombination are the two sources of genetic variation.     21-2

         Mutations can be harmful, neutral, or beneficial.     21-2

       21.2 Measuring Genetic Variation     21-3

         To understand patterns of genetic variation, we require information about allele frequencies.     21-3

         Early population geneticists relied on observable traits to measure variation.     21-4

         Gel electrophoresis facilitates the detection of genetic variation.     21-4

         DNA sequencing is the gold standard for measuring genetic variation.     21-4

         HOW DO WE KNOW?
          How is genetic variation measured?     21-5

       21.3 Evolution and the Hardy-Weinberg Equilibrium     21-6

         Evolution is a change in allele or genotype frequency over time.     21-6

         The Hardy-Weinberg equilibrium describes situations in which allele and genotype frequencies do not change.     21-6

         The Hardy-Weinberg equilibrium translates allele frequencies into genotype frequencies.     21-7

         The Hardy-Weinberg equilibrium is the starting point for population genetic analysis.     21-8

       21.4 Natural Selection     21-8

         Natural selection brings about adaptations.     21-8

         The Modern Synthesis is a marriage between Mendelian genetics and Darwinian evolution.     21-9

         Natural selection increases the frequency of advantageous mutations and decreases the frequency of deleterious mutations.     21-10

      ? What genetic differences have made some individuals more and some less susceptible to malaria? 21-10

         Natural selection can be stabilizing, directional, or disruptive.     21-10

         HOW DO WE KNOW?
          How far can artificial selection be taken?     21-12

         Sexual selection increases an individual’s reproductive success.     21-13

       21.5 Migration, Mutation, and Genetic Drift     21-13

         Migration reduces genetic variation between populations.     21-13

         Mutation increases genetic variation.     21-13

         Genetic drift is particularly important in small populations.     21-13

       21.6 Molecular Evolution     21-14

         The extent of sequence difference between species is a function of the time since the species diverged.     21-15

         The rate of the molecular clock varies.     21-15

CHAPTER 22     SPECIES AND SPECIATION     22-1

       22.1 The Biological Species Concept     22-1

         The species is the fundamental evolutionary unit.     22-1

         Reproductive isolation is the key to the biological species concept (BSC).     22-2

         The BSC is more useful in theory than in practice.     22-2

         The BSC does not apply to asexual or extinct organisms.     22-3

         Ring species and hybridization complicate the BSC.     22-4

         Ecology and evolution can extend the BSC.     22-4

       22.2 Reproductive Isolation     22-5

         Pre-zygotic isolating factors occur before egg fertilization.     22-5

         Post-zygotic isolating factors occur after egg fertilization.     22-6

       22.3 Speciation     22-6

         Speciation is a by-product of the genetic divergence of separated populations.     22-6

38

         Allopatric speciation is speciation that results from the geographical separation of populations.     22-6

         HOW DO WE KNOW?
          Can a vicariance event cause speciation?     22-8

         Co-speciation is speciation that occurs in response to speciation in another species.     22-11

      ? How did malaria come to infect humans?     22-11

         Can sympatric populations—those not geographically separated—undergo speciation?     22-12

         Speciation can occur instantaneously.     22-13

       22.4 Speciation and Selection     22-15

         Speciation can occur with or without natural selection.     22-15

         Natural selection can enhance reproductive isolation.     22-15

       VISUAL SYNTHESIS Speciation     22-16

CHAPTER 23     EVOLUTIONARY PATTERNS

Phylogeny and Fossils     23-1

       23.1 Reading a Phylogenetic Tree     23-1

         Phylogenetic trees provide hypotheses of evolutionary relationships.     23-2

         The search for sister groups lies at the heart of phylogenetics.     23-3

         A monophyletic group consists of a common ancestor and all its descendants.     23-4

         Taxonomic classifications are information storage and retrieval systems.     23-4

       23.2 Building a Phylogenetic Tree     23-5

         Homology is similarity by common descent.     23-5

         Shared derived characters enable biologists to reconstruct evolutionary history.     23-6

         The simplest tree is often favored among multiple possible trees.     23-6

         Molecular data complement comparative morphology in reconstructing phylogenetic history.     23-8

         HOW DO WE KNOW?
          Did an HIV-positive dentist spread the AIDS virus to his patients?     23-10

         Phylogenetic trees can help solve practical problems.     23-10

       23.3 The Fossil Record     23-11

         Fossils provide unique information.     23-11

         Fossils provide a selective record of past life.     23-12

         Geological data indicate the age and environmental setting of fossils.     23-14

         Fossils can contain unique combinations of characters.     23-16

         HOW DO WE KNOW?
          Can fossils bridge the evolutionary gap between fish and tetrapod vertebrates?     23-18

         Rare mass extinctions have altered the course of evolution.     23-18

       23.4 Comparing Evolution’s Two Great Patterns     23-19

         Phylogeny and fossils complement each other.     23-19

         Agreement between phylogenies and the fossil record provides strong evidence of evolution.     23-19

CHAPTER 24     HUMAN ORIGINS AND EVOLUTION     24-1

       24.1 The Great Apes     24-1

         Comparative anatomy shows that the human lineage branches off the great apes tree.     24-1

         Molecular analysis reveals that our lineage split from the chimpanzee lineage about 5-7 million years ago.     24-3

         HOW DO WE KNOW?
          How closely related are humans and chimpanzees?     24-3

         The fossil record gives us direct information about our evolutionary history.     24-4

       24.2 African Origins     24-6

         Studies of mitochondrial DNA reveal that modern humans evolved in Africa.     24-6

         HOW DO WE KNOW?
          When and where did the most recent common ancestor of all living humans live?     24-6

         Neanderthals disappear from the fossil record as modern humans appear but have contributed to the modern human gene pool.     24-8

       24.3 Distinct Features of Our Species     24-9

         Bipedalism was a key innovation.     24-9

         Adult humans share many features with juvenile chimpanzees.     24-10

         Humans have large brains relative to body size.     24-11

39

         The human and chimpanzee genomes help us identify genes that make us human.     24-12

       24.4 Human Genetic Variation     24-12

         The prehistory of our species has had an impact on the distribution of genetic variation.     24-13

         The recent spread of modern humans means that there are few genetic differences between groups.     24-14

         Some human differences have likely arisen by natural selection.     24-14

      ? What human genes are under selection for resistance to malaria?     24-15

       24.5 Culture, Language, and Consciousness     24-15

         Culture changes rapidly.     24-15

         Is culture uniquely human?     24-16

         Is language uniquely human?     24-17

         Is consciousness uniquely human?     24-18

PART 2     FROM ORGANISMS TO THE

         ENVIRONMENT

CHAPTER 25     CYCLING CARBON     25-1

       25.1 The Short-Term Carbon Cycle     25-1

         Photosynthesis and respiration are key processes in short-term carbon cycling.     25-2

         The regular oscillation of CO2 reflects the seasonality of photosynthesis in the Northern Hemisphere.     25-2

         Human activities play an important role in the modern carbon cycle.     25-3

         HOW DO WE KNOW?
          How much CO2 was in the atmosphere 1000 years ago?     25-3

         Carbon isotopes show that much of the CO2 added to air over the past half century comes from burning fossil fuels.     25-4

         HOW DO WE KNOW?
          What is the major source of the carbon dioxide that has accumulated in Earth’s atmosphere over the last two centuries?     25-4

       25.2 The Long-Term Carbon Cycle     25-6

         Reservoirs and fluxes are key in long-term carbon cycling.     25-6

         Physical processes add and remove CO2 from the atmosphere.     25-7

         Records of atmospheric composition over 400,000 years show periodic shifts in CO2 content.     25-9

         Variations in atmospheric CO2 over hundreds of millions of years reflect plate tectonics and evolution.     25-11

       25.3 The Carbon Cycle, Ecology, and Evolution     25-12

         Food webs trace the movement of carbon through communities.     25-12

         Trophic pyramids trace the flow of energy through communities.     25-13

         The diversity of photosynthetic organisms reflects adaptation to a wide range of environments.     25-13

         The diversity of respiring organisms reflects many sources of food.     25-14

         The carbon cycle provides a framework for understanding life’s evolutionary history.     25-14

      ? CASE 5 The Human Microbiome: Diversity Within C5-1

CHAPTER 26     BACTERIA AND ARCHAEA     26-1

       26.1 Two Prokaryotic Domains     26-1

         The bacterial cell is small but powerful.     26-1

         Diffusion limits cell size in bacteria.     26-2

         Horizontal gene transfer promotes genetic diversity in bacteria.     26-4

         The Archaea form a second prokaryotic domain.     26-5

       26.2 An Expanded Carbon Cycle     26-6

         Many photosynthetic bacteria do not produce oxygen.     26-7

         Many bacteria respire without oxygen.     26-8

         Photoheterotrophs obtain energy from light but obtain carbon from preformed organic molecules.     26-8

         Chemoautotrophy is a uniquely prokaryotic metabolism.     26-9

       26.3 Other Biogeochemical Cycles     26-10

         Bacteria and archaeons dominate Earth’s sulfur cycle.     26-10

         The nitrogen cycle is also driven by bacteria and archaeons.     26-10

       26.4 The Diversity of Bacteria     26-12

         Bacterial phylogeny is a work in progress.     26-12

40

         HOW DO WE KNOW?
          How many kinds of bacterium live in the oceans?     26-13

         What, if anything, is a bacterial species?     26-14

         Proteobacteria are the most diverse bacteria.     26-15

         The gram-positive bacteria include organisms that cause and cure disease.     26-15

         Photosynthesis is widely distributed on the bacterial tree.     26-15

       26.5 The Diversity of Archaea     26-16

         The archaeal tree has anaerobic, hyperthermophilic organisms near its base.     26-17

         The Crenarchaeota and Euryarchaeota both include acid-loving microorganisms.     26-18

         Euryarchaeote archaeons include heat-loving, methane-producing, and salt-loving microorganisms.     26-18

         Thaumarchaeota may be the most abundant cells in the oceans.     26-18

         HOW DO WE KNOW?
          How abundant are archaeons in the oceans? 26-1 9

       26.6 The Evolutionary History of Prokaryotes     26-20

         Life originated early in our planet’s history.     26-20

         Prokaryotes have coevolved with eukaryotes.     26-21

      ? How do intestinal bacteria influence human health?     26-22

CHAPTER 27     EUKARYOTIC CELLS

Origins and Diversity     27-1

       27.1 The Eukaryotic Cell: A Review     27-1

         Internal protein scaffolding and dynamic membranes organize the eukaryotic cell.     27-1

         In eukaryotic cells, energy metabolism is localized in mitochondria and chloroplasts.     27-2

         The organization of the eukaryotic genome also helps explain eukaryotic diversity.     27-2

         Sex promotes genetic diversity in eukaryotes and gives rise to distinctive life cycles.     27-3

       27.2 Eukaryotic Origins     27-4

      ? What role did symbiosis play in the origin of chloroplasts?     27-4

         HOW DO WE KNOW?
          What is the evolutionary origin of chloroplasts?     27-5

      ? What role did symbiosis play in the origin of mitochondria?     27-6

      ? How did the eukaryotic cell originate?     27-7

         In the oceans, many single-celled eukaryotes harbor symbiotic bacteria.     27-9

       27.3 Eukaryotic Diversity     27-9

         Our own group, the opisthokonts, is the most diverse eukaryotic superkingdom.     27-10

         Amoebozoans include slime molds that produce multicellular structures.     27-12

         Archaeplastids are photosynthetic organisms, including land plants.     27-13

         Other photosynthetic organisms occur in the stramenopiles and alveolates.     27-15

         Photosynthesis spread through eukaryotes by repeated endosymbioses involving eukaryotic algae.     27-16

         HOW DO WE KNOW?
          How did photosynthesis spread through the Eukarya?     27-18

         The first branch of the eukaryotic tree may separate animals and slime molds from plants and diatoms.     27-19

       27.4 The Fossil Record of Protists     27-20

         Fossils show that eukaryotes existed at least 1800 million years ago.     27-20

         Protists have continued to diversify during the age of animals.     27-21

CHAPTER 28     BEING MULTICELLULAR     28-1

       28.1 The Phylogenetic Distribution of Multicellular Organisms     28-1

         Simple multicellularity is widespread among eukaryotes.     28-1

         Complex multicellularity evolved several times.     28-3

       28.2 Diffusion vs. Bulk Transport     28-4

         Diffusion is effective only over short distances.     28-4

         Animals achieve large size by circumventing limits imposed by diffusion.     28-4

         Complex multicellular organisms have structures specialized for bulk transport.     28-5

       28.3 How to Build a Multicellular Organism     28-6

         Complex multicellularity requires adhesion between cells.     28-6

41

         HOW DO WE KNOW?
          How do bacteria influence the life cycles of choanoflagellates?     28-6

         How did animal cell adhesion originate?     28-7

         Complex multicellularity requires communication between cells.     28-7

         Complex multicellularity requires a genetic program for coordinated growth and cell differentiation.     28-8

       28.4 Variations on a Theme: Plants vs. Animals     28-10

         Cell walls shape patterns of growth and development in plants.     28-10

         Animal cells can move relative to one another.     28-11

       28.5 The Evolution of Complex Multicellularity     28-12

         Complex multicellularity appeared in the oceans 575 to 555 million years ago.     28-12

         Oxygen is necessary for complex multicellular life.     28-13

         Land plants evolved from green algae that could carry out photosynthesis on land.     28-14

         Regulatory genes have played an important role in the evolution of complex multicellular organisms.     28-15

         HOW DO WE KNOW?
          What controls color pattern in butterfly wings?     28-15

      ? CASE 6 Agriculture: Feeding a Growing Population C6-2

CHAPTER 29     PLANT STRUCTURE AND FUNCTION

Moving Photosynthesis onto Land     29-1

       29.1 Plant Structure and Function: An Evolutionary Perspective     29-1

       29.2 The Leaf: Acquiring CO2 While Avoiding Dessication     29-2

         CO2 uptake results in water loss.     29-3

         The cuticle restricts water loss from leaves but inhibits the uptake of CO2.     29-4

         Stomata allow leaves to regulate water loss and carbon gain.     29-5

         CAM plants use nocturnal CO2 storage to avoid water loss during the day.     29-6

         C4 plants suppress photorespiration.     29-7

         HOW DO WE KNOW?
          How do we know that C4 photosynthesis suppresses photorespiration?     29-8

       29.3 The Stem: Transport of Water Through Xylem     29-8

         Xylem provides a low-resistance pathway for the movement of water.     29-9

         Water is pulled through xylem by an evaporative pump.     29-10

         HOW DO WE KNOW?
          How large are the forces that allow leaves to pull water from the soil?     29-10

         The structure of xylem conduits reduces the risks of collapse and cavitation.     29-11

       29.4 The Stem: Transport of Carbohydrates Through Phloem     29-12

         Carbohydrates are pushed through phloem by an osmotic pump.     29-13

         Phloem feeds both the plant and the rhizosphere.     29-14

       29.5 The Root: Uptake of Water and Nutrients from the Soil     29-15

         Nutrient uptake by roots is highly selective.     29-15

         Nutrient uptake requires energy.     29-16

         Mycorrhizae enhance the uptake of phosphorus.     29-17

         Symbiotic nitrogen-fixing bacteria supply nitrogen to both plants and ecosystems.     29-17

      ? How has nitrogen availability influenced agricultural productivity?     29-18

CHAPTER 30     PLANT REPRODUCTION

Finding Mates and Dispersing Young     30-1

       30.1 The Plant Life Cycle and Evolution of Pollen and Seeds     30-1

         The algal sister groups of land plants have one multicellular generation in their life cycle.     30-2

         Bryophytes illustrate how the alternation of generations allows the dispersal of spores in the air.     30-2

         Vascular plants evolved a large photosynthetic sporophyte generation.     30-4

         In seed plants, the transport of pollen in air allows fertilization to occur in the absence of external sources of water.     30-6

         Seeds enhance dispersal and establishment of the next sporophyte generation.     30-8

       30.2 Flowering Plants     30-9

         Flowers are reproductive shoots specialized for the production, transfer, and receipt of pollen.     30-9

42

         The diversity of floral morphology is related to modes of pollination.     30-10

         Angiosperms have mechanisms to increase outcrossing.     30-12

         HOW DO WE KNOW?
          Can pollinator shifts enhance rates of species formation?     30-13

         Angiosperms delay provisioning their ovules until after fertilization.     30-15

         Fruits enhance the dispersal of seeds.     30-15

       30.3 Timing of Reproductive Events     30-17

         Flowering time is affected by day length.     30-17

         Photoreceptors enable plants to measure day length.     30-17

         Vernalization prevents plants from flowering until winter has passed.     30-18

         Dormant seeds can delay germination if they detect the presence of plants overhead.     30-18

         HOW DO WE KNOW?
          How do plants measure day length?     30-19

         HOW DO WE KNOW?
          How do seeds detect the presence of plants growing overhead?     30-20

      ? What is the basis for the spectacular increases in the yield of cereal grains during the Green Revolution?     30-21

       30.4 Vegetative Reproduction     30-22

CHAPTER 31     PLANT GROWTH AND DEVELOPMENT

Building the Plant Body     31-1

       31.1 Shoot Growth and Development     31-2

         Shoots grow by adding new cells at their tips.     31-2

         Stem elongation occurs primarily in a zone just below the apical meristem where new cells elongate.     31-3

         The shoot apical meristem controls the production and arrangement of leaves.     31-4

         The development of new apical meristems allows stems to branch.     31-5

         Flowers grow from and consume shoot meristems.     31-6

       31.2 Plant Hormones     31-6

         Hormones affect the growth and differentiation of plant cells.     31-7

         Auxin transport guides the development of vascular connections between leaves and stems.     31-8

      ? What is the developmental basis for the shorter stems of high-yielding rice and wheat?     31-9

         Branching is affected by multiple hormones.     31-10

       31.3 Secondary Growth     31-10

         Shoots produce two types of lateral meristem.     31-10

         The vascular cambium produces secondary xylem and phloem.     31-11

         The cork cambium produces an outer protective layer.     31-12

         Wood has both mechanical and transport functions.     31-12

       31.4 Root Growth and Development     31-13

         Roots grow by producing new cells at their tips.     31-14

         The formation of new root apical meristems allows roots to branch.     31-15

         The structures and functions of root systems are diverse. 31-15

       31.5 The Environmental Context of Growth and Development     31-16

         Plants orient the growth of their stems and roots by light and gravity.     31-17

         HOW DO WE KNOW?
          How do plants grow toward light?     31-17

         Plants grow taller and branch less when light levels are low.     31-19

         Roots elongate more and branch less when water is scarce.     31-19

         Exposure to wind results in shorter and stronger stems.     31-20

         Plants use day length as a cue to prepare for winter.     31-20

CHAPTER 32     PLANT DEFENSE

Keeping the World Green     32-1

       32.1 Protection Against Pathogens     32-1

         Plant pathogens infect and exploit host plants by a variety of mechanisms.     32-2

         An innate immune system allows plants to detect and respond to pathogens.     32-3

         Plants respond to infections by isolating infected regions.     32-4

         Mobile signals trigger defenses in uninfected tissues.     32-5

         HOW DO WE KNOW?
          Can plants develop immunity to specific pathogens?     32-6

43

         Plants defend against viral infections by producing siRNA.     32-6

         A pathogenic bacterium provides a way to modify plant genomes.     32-7

       32.2 Defense Against Herbivores     32-8

         Plants use mechanical and chemical defenses to avoid being eaten.     32-8

         Diverse chemical compounds deter herbivores.     32-9

         Some plants provide food and shelter for ants, which actively defend them.     32-11

         Grasses can regrow quickly following grazing by mammals.     32-12

       32.3 Allocating Resources to Defense     32-13

         Plants can sense and respond to herbivores.     32-13

         Plants produce volatile signals that attract insects that prey upon herbivores.     32-14

         Nutrient-rich environments select for plants that allocate more resources to growth than to defense.     32-14

         HOW DO WE KNOW?
          Can plants communicate?     32-14

         Exposure to multiple threats can lead to trade-offs.     32-16

       32.4 Defense and Plant Diversity     32-16

         Pathogens, herbivores, and seed predators can increase plant biodiversity.     32-16

         The evolution of new defenses may allow plants to diversify.     32-17

      ? Can modifying plants genetically protect crops from herbivores and pathogens?     32-17

CHAPTER 33     PLANT DIVERSITY     33-1

       33.1 Plant Diversity: An Evolutionary Overview     33-1

       33.2 Bryophytes     33-2

         Bryophytes are small, simple, and tough.     33-3

         Bryophytes exhibit several cases of convergent evolution with the vascular plants.     33-4

         Sphagnum moss plays an important role in the global carbon cycle.     33-5

       33.3 Spore-Dispersing Vascular Plants     33-5

         Rhynie cherts provide a window into the early evolution of vascular plants.     33-5

         Lycophytes are the sister group of all other vascular plants.     33-6

         Ancient lycophytes included giant trees that dominated coal swamps about 320 million years ago.     33-7

         HOW DO WE KNOW?
          Did woody plants evolve more than once?     33-8

         Ferns and horsetails are morphologically and ecologically diverse.     33-9

         An aquatic fern contributes to rice production.     33-10

       33.4 Gymnosperms     33-11

         Cycads and ginkgos are the earliest diverging groups of living gymnosperms.     33-11

         Conifers are forest giants that thrive in dry and cold climates.     33-13

         Gnetophytes are gymnosperms that have independently evolved xylem vessels and double fertilization.     33-14

       33.5 Angiosperms     33-14

         Angiosperm diversity remains a puzzle.     33-15

         Early diverging angiosperms have low diversity.     33-15

         Monocots develop according to a novel body plan.     33-16

         HOW DO WE KNOW?
          When did grasslands expand over the land surface?     33-18

         Eudicots are the most diverse group of angiosperms.     33-19

      ? What can be done to protect the genetic diversity of crop species?     33-20

       VISUAL SYNTHESIS Angiosperms: Structure and Function     33-22

CHAPTER 34     FUNGI

Structure, Function, and Diversity     34-1

       34.1 Growth and Nutrition     34-1

         Hyphae permit fungi to explore their environment for food resources.     34-2

         Fungi transport materials within their hyphae.     34-2

         Not all fungi produce hyphae.     34-2

         Fungi are principal decomposers of plant tissues.     34-3

         Fungi are important plant and animal pathogens.     34-4

         Many fungi form symbiotic associations with plants and animals.     34-5

44

         Lichens are symbioses between a fungus and a green alga or a cyanobacterium.     34-6

       34.2 Reproduction     34-7

         Fungi proliferate and disperse using spores.     34-7

         Multicellular fruiting bodies facilitate the dispersal of sexually produced spores.     34-8

         HOW DO WE KNOW?
          What determines the shape of fungal spores that are ejected into the air?     34-9

         The fungal life cycle often includes a stage in which haploid cells fuse, but nuclei do not.     34-10

         Genetically distinct mating types promote outcrossing.     34-11

         Fungi that lack sexual reproduction have other means of generating genetic diversity.     34-11

       34.3 Diversity     34-12

         Fungi are highly diverse.     34-12

         Fungi evolved from aquatic, unicellular, and flagellated ancestors.     34-12

         Zygomycetes produce hyphae undivided by septa.     34-13

         Glomeromycetes form endomycorrhizae.     34-14

         The Dikarya produce regular septa during mitosis.     34-14

         Ascomycetes are the most diverse group of fungi.     34-14

         HOW DO WE KNOW?
          Can a fungus influence the behavior of an ant?     34-16

         Basidiomycetes include smuts, rusts, and mushrooms.     34-17

      ? How do fungi threaten global wheat production?     34-19

      ? CASE 7 Predator-Prey: A Game of Life and Death C7-1

CHAPTER 35     ANIMAL NERVOUS SYSTEMS     35-1

       35.1 Nervous System Function and Evolution     35-1

         Animal nervous systems have three types of nerve cell.     35-2

         Nervous systems range from simple to complex.     35-2

      ? What body features arose as adaptations for successful predation?     35-4

       35.2 Neuron Structure     35-4

         Neurons share a common organization.     35-5

         Neurons differ in size and shape.     35-5

         Neurons are supported by other types of cell.     35-6

       35.3 Neuron Function     35-6

         The resting membrane potential is negative and results in part from the movement of potassium ions.     35-6

         Neurons are excitable cells that transmit information by action potentials.     35-8

         Neurons propagate action potentials along their axons by sequentially opening and closing adjacent Na+ and K+ ion channels.     35-8

         HOW DO WE KNOW?
          What is the resting membrane potential and what changes in electrical activity occur during an action potential?     35-11

         Nerve cells communicate at synapses.     35-12

         Signals between neurons can be excitatory or inhibitory.     35-13

       35.4 Nervous System Organization     35-15

         Nervous systems are organized into peripheral and central components.     35-15

         Nervous systems have voluntary and involuntary components.     35-16

         The nervous system helps to maintain homeostasis.     35-17

         Simple reflex circuits provide rapid responses to stimuli.     35-18

CHAPTER 36     ANIMAL SENSORY SYSTEMS AND BRAIN FUNCTION     36-1

       36.1 Animal Sensory Systems     36-1

         Specialized sensory receptors detect diverse stimuli.     36-2

         Stimuli are transmitted by changes in the firing rate of action potentials.     36-4

       36.2 Smell and Taste     36-5

         Smell and taste depend on chemoreception of molecules carried in the environment and in food.     36-5

       36.3 Sensing Gravity, Movement, and Sound     36-6

         Hair cells sense gravity and motion.     36-7

         Hair cells detect the physical vibrations of sound.     36-8

      ? How have sensory systems evolved in predators and prey?     36-10

45

       36.4 Vision     36-10

         All animals use a similar photosensitive protein called opsin to detect light.     36-11

         Animals see the world through different types of eyes.     36-11

         The structure and function of the vertebrate eye underlie image processing.     36-13

         Color vision detects different wavelengths of light.     36-14

         Local sensory processing of light determines basic features of shape and movement.     36-15

         HOW DO WE KNOW?
          How does the retina process visual information?     36-16

       36.5 Brain Organization and Function     36-17

         The brain processes and integrates information received from different sensory systems.     36-17

         The brain is divided into lobes with specialized functions.     36-18

         Information is topographically mapped into the vertebrate cerebral cortex.     36-19

       36.6 Memory and Cognition     36-20

         The brain serves an important role in memory and learning.     36-20

         Cognition involves brain information processing and decision making.     36-21

CHAPTER 37     ANIMAL MOVEMENT

Muscles and Skeletons     37-1

       37.1 Muscles: Biological Motors That Generate

         Force and Produce Movement     37-1

         Muscles can be striated or smooth.     37-1

         Skeletal muscle fibers are organized into repeating contractile units called sarcomeres.     37-2

         Muscles contract by the sliding of myosin and actin filaments.     37-4

         Calcium regulates actin-myosin interaction through excitation-contraction coupling.     37-6

         Calmodulin regulates Ca2+ activation and relaxation of smooth muscle.     37-7

       37.2 Muscle Contractile Properties     37-8

         Muscle length affects actin-myosin overlap and generation of force.     37-8

         HOW DO WE KNOW?
          How does filament overlap affect force generation in muscles?     37-8

         Muscle force and shortening velocity are inversely related.     37-9

         Antagonist pairs of muscles produce reciprocal motions at a joint.     37-10

         Muscle force is summed by an increase in stimulation frequency and the recruitment of motor units.     37-10

         Skeletal muscles have slow-twitch and fasttwitch fibers.     37-11

      ? How do different types of muscle fiber affect the speed of predators and prey?     37-12

       37.3 Animal Skeletons     37-13

         Hydrostatic skeletons support animals by muscles that act on a fluid-filled cavity.     37-13

         Exoskeletons provide hard external support and protection.     37-14

         The rigid bones of vertebrate endoskeletons are jointed for motion and can be repaired if damaged.     37-15

       37.4 Vertebrate Skeletons     37-16

         Vertebrate bones form by intramembranous and endochondral ossification.     37-16

         Joint shape determines range of motion and skeletal muscle organization.     37-17

         Muscles exert forces by skeletal levers to produce joint motion.     37-18

CHAPTER 38     ANIMAL ENDOCRINE SYSTEMS     38-1

       38.1 An Overview of Endocrine Function     38-1

         The endocrine system helps to regulate an organism’s response to its environment.     38-1

         The endocrine system is involved in growth and development.     38-2

         HOW DO WE KNOW?
          How are growth and development controlled in insects?     38-3

         The endocrine system underlies homeostasis.     38-5

       38.2 Properties of Hormones     38-7

         Three main classes of hormone are peptide, amine, and steroid hormones.     38-7

         Hormonal signals are typically amplified.     38-8

         Hormones act specifically on cells with receptors that bind the hormone.     38-11

         Hormones are evolutionarily conserved molecules with diverse functions.     38-11

46

       38.3 The Vertebrate Endocrine System     38-12

         The pituitary gland integrates diverse bodily functions by secreting hormones in response to signals from the hypothalamus.     38-13

         Many targets of pituitary hormones are endocrine tissues that also release hormones.     38-14

         Other endocrine organs have diverse functions.     38-15

      ? How does the endocrine system influence predators and prey?     38-15

       38.4 Other Forms of Chemical Communication     38-16

         Local chemical signals regulate neighboring target cells.     38-16

         Pheromones are chemical compounds released into the environment to signal behavioral cues to other species members.     38-17

CHAPTER 39     ANIMAL CARDIOVASCULAR AND RESPIRATORY SYSTEMS     39-1

       39.1 Delivery of Oxygen and Elimination of Carbon Dioxide     39-1

         Diffusion governs gas exchange over short distances.     39-2

         Bulk flow moves fluid over long distances.     39-2

       39.2 Respiratory Gas Exchange     39-3

         Many aquatic animals breathe through gills.     39-4

         Insects breathe air through tracheae.     39-5

         Terrestrial vertebrates breathe by tidal ventilation of internal lungs.     39-6

         Mammalian lungs are well adapted for gas exchange.     39-7

         The structure of bird lungs allows unidirectional airflow for increased oxygen uptake.     39-8

         Voluntary and involuntary mechanisms control breathing.     39-9

       39.3 Oxygen Transport by Hemoglobin     39-10

         Hemoglobin is an ancient molecule with diverse roles related to oxygen binding and transport.     39-10

         HOW DO WE KNOW?
          What is the molecular structure of hemoglobin and myoglobin?     39-10

         Hemoglobin reversibly binds oxygen.     39-11

         Myoglobin stores oxygen, enhancing delivery to muscle mitochondria.     39-12

         Many factors affect hemoglobin-oxygen binding.     39-12

       39.4 Circulatory Systems     39-13

         Circulatory systems have vessels of different sizes to facilitate bulk flow and diffusion.     39-15

         Arteries are muscular, elastic vessels that carry blood away from the heart under high pressure.     39-15

         Veins are thin-walled vessels that return blood to the heart under low pressure.     39-16

         Compounds and fluid move across capillary walls by diffusion, filtration, and osmosis.     39-16

      ? How do hormones and nerves provide homeostatic regulation of blood flow as well as allow an animal to respond to stress?     39-17

       39.5 The Evolution, Structure, and Function of the Heart     39-17

         Fish have two-chambered hearts and a single circulatory system.     39-18

         Amphibians and reptiles have more three-chambered hearts and partially divided circulations.     39-18

         Mammals and birds have four-chambered hearts and fully divided pulmonary and systemic circulations.     39-19

         Cardiac muscle cells are electrically connected to contract in synchrony.     39-20

         Cardiac output is regulated by the autonomic nervous system.     39-21

CHAPTER 40     ANIMAL METABOLISM, NUTRITION, AND DIGESTION     40-1

       40.1 Patterns of Animal Metabolism     40-1

         Animals rely on anaerobic and aerobic metabolism.     40-2

         Metabolic rate varies with activity level.     40-3

      ? Does body temperature limit activity level in predators and prey?     40-5

         Metabolic rate is affected by body size.     40-5

         HOW DO WE KNOW?
          How is metabolic rate affected by running speed and body size? 40-6

         Metabolic rate is linked to body temperature.     40-7

       40.2 Animal Nutrition and Diet     40-7

         Energy balance is a form of homeostasis.     40-7

       VISUAL SYNTHESIS Homeostasis and Thermoregulation     40-8

         An animal’s diet must supply nutrients that it cannot synthesize.     40-10

47

       40.3 Adaptations for Feeding     40-12

         Suspension filter feeding is common in many aquatic animals.     40-12

         Large aquatic animals apprehend prey by suction feeding and active swimming.     40-12

         Jaws and teeth provide specialized food capture and mechanical breakdown of food.     40-13

       40.4 Digestion and Absorption of Food     40-14

         The digestive tract has regional specializations.     40-14

         Digestion begins in the mouth.     40-15

         The stomach is an initial storage and digestive chamber.     40-16

         The small intestine is specialized for nutrient absorption.     40-17

         The large intestine reabsorbs water and stores waste.     40-20

         The lining of the digestive tract is composed of distinct layers.     40-21

         Plant-eating animals have specialized digestive tracts that reflect their diets.     40-21

CHAPTER 41     ANIMAL RENAL SYSTEMS

Water and Waste     41-1

       41.1 Water and Electrolyte Balance     41-1

         Osmosis governs the movement of water across cell membranes.     41-2

         Osmoregulation is the control of osmotic pressure inside cells and organisms.     41-3

         Osmoconformers match their internal solute concentration to that of the environment.     41-4

         Osmoregulators have internal solute concentrations that differ from that of their environment.     41-5

      ? Can the loss of water and electrolytes in exercise be exploited as a strategy to hunt prey?     41-6

       41.2 Excretion of Wastes in Relation to Electrolyte Balance     41-7

         The excretion of nitrogenous wastes is linked to an animal’s habitat and evolutionary history.     41-7

         Excretory organs work by filtration, reabsorption, and secretion.     41-8

         Animals have diverse excretory organs.     41-9

         Vertebrates filter blood under pressure through paired kidneys.     41-10

       41.3 Structure and Function of the Mammalian Kidney     41-12

         The mammalian kidney has an outer cortex and inner medulla.     41-12

         Glomerular filtration isolates wastes carried by the blood along with water and small solutes.     41-12

         The proximal convoluted tubule reabsorbs solutes by active transport.     41-14

         The loop of Henle acts as a countercurrent multiplier to create a concentration gradient from the cortex to the medulla.     41-14

         HOW DO WE KNOW?
          How does the mammalian kidney produce concentrated urine?     41-16

         The distal convoluted tubule secretes additional wastes.     41-17

         The final concentration of urine is determined in the collecting ducts and is under hormonal control.     41-17

         The kidneys help regulate blood pressure and blood volume.     41-19

CHAPTER 42     ANIMAL REPRODUCTION AND DEVELOPMENT     42-1

       42.1 The Evolutionary History of Reproduction     42-1

         Asexual reproduction produces clones.     42-2

         Sexual reproduction involves the formation and fusion of gametes.     42-3

         Many species reproduce both sexually and asexually.     42-4

         Exclusive asexuality is often an evolutionary dead end.     42-4

         HOW DO WE KNOW?
          Do bdelloid rotifers only reproduce asexually?     42-6

       42.2 Movement onto Land and Reproductive Adaptations     42-7

         Fertilization can take place externally or internally.     42-7

         r-strategists and K-strategists differ in number of offspring and parental care.     42-8

         Oviparous animals lay eggs, and viviparous animals give birth to live young.     42-8

       42.3 Human Reproductive Anatomy and Physiology     42-9

         The male reproductive system is specialized for the production and delivery of sperm.     42-9

48

         The female reproductive system produces eggs and supports the developing embryo.     42-11

         Hormones regulate the human reproductive system.     42-13

       42.4 Gamete Formation to Birth in Humans     42-15

         Male and female gametogenesis have shared and distinct features.     42-15

         Fertilization occurs when a sperm fuses with an oocyte.     42-16

         The first trimester includes cleavage, gastrulation, and organogenesis.     42-17

         The second and third trimesters are characterized by fetal growth.     42-19

       VISUAL SYNTHESIS Reproduction and Development     42-20

         Childbirth is initiated by hormonal changes.     42-22

CHAPTER 43     ANIMAL IMMUNE SYSTEMS     43-1

       43.1 Innate Immunity     43-1

         The skin and mucous membranes provide the first line of defense against infection.     43-2

         Some cells act broadly against diverse pathogens.     43-3

         Phagocytes recognize foreign molecules and send signals to other cells.     43-4

         Inflammation is a coordinated response to tissue injury.     43-5

         The complement system participates in the innate and adaptive immune systems.     43-6

       43.2 Adaptive Immunity: B cells, Antibodies, and Humoral Immunity     43-7

         B cells produce antibodies.     43-7

         Mammals produce five classes of antibody with different biological functions.     43-8

         Clonal selection is the basis for antibody specificity.     43-9

         Clonal selection also explains immunological memory.     43-10

         Genomic rearrangement creates antibody diversity.     43-10

         HOW DO WE KNOW?
          How is antibody diversity generated?     43-11

       43.3 Adaptive Immunity: T cells and Cell-Mediated Immunity     43-13

         T cells include helper and cytotoxic cells.     43-13

         T cells have T cell receptors on their surface.     43-14

         T cell activation requires the presence of antigen in association with MHC proteins.     43-14

         The ability to distinguish between self and non-self is acquired during T cell maturation.     43-16

       43.4 Three Infections: A Virus, Bacterium, and Eukaryote     43-16

         The flu virus evades the immune system through antigenic drift and shift.     43-17

         Tuberculosis is caused by a slow-growing, intracellular bacterium.     43-18

         The malaria parasite uses antigenic variation to change surface molecules.     43-18

      ? CASE 8 Biodiversity Hotspots: Rain Forests and Coral Reefs C8-1

CHAPTER 44     ANIMAL DIVERSITY     44-1

       44.1 A Tree of Life for More than a Million Animal Species     44-1

         Phylogenetic trees propose an evolutionary history of animals.     44-1

         Nineteenth-century biologists grouped animals by anatomical and embryological features.     44-2

         Molecular sequence comparisons have confirmed some relationships and raised new questions.     44-4

       44.2 The Simplest Animals: Sponges, Cnidarians, Ctenophores, and Placozoans     44-5

         Sponges are simple and widespread in the oceans.     44-5

         Cnidarians are the architects of life’s largest constructions: coral reefs.     44-7

         Ctenophores and placozoans represent the extremes of body organization among early branching animals.     44-8

       44.3 Bilaterian Animals     44-11

         Lophotrochozoans make up nearly half of all animal phyla, including the diverse and ecologically important annelids and mollusks.     44-11

         Ecdysozoans include arthropods, the most diverse animals.     44-14

         HOW DO WE KNOW?
          How did the diverse feeding appendages of arthropods arise?     44-16

49

         Deuterostomes include humans and other chordates, but also acorn worms and sea stars.     44-18

         Chordates include vertebrates, cephalochordates, and tunicates.     44-19

       44.4 Vertebrate Diversity     44-21

         Fish are the earliest-branching and most diverse vertebrate animals.     44-22

         The common ancestor of tetrapods had four limbs.     44-24

         Amniotes evolved terrestrial eggs.     44-25

       44.5 The Evolutionary History of Animals     44-27

         Fossils and phylogeny show that animal forms were initially simple but rapidly evolved complexity.     44-27

         The animal body plans we see today emerged during the Cambrian Period.     44-27

         Animals began to colonize the land 420 million years ago.     44-28

      ? How have coral reefs changed through time?     44-29

       VISUAL SYNTHESIS Diversity through Time     44-30

CHAPTER 45     ANIMAL BEHAVIOR     45-1

       45.1 Tinbergen’s Questions     45-1

       45.2 Genes and Behavior     45-2

         The fixed action pattern is a stereotyped behavior.     45-2

         The nervous system processes stimuli and evokes behaviors.     45-3

         Hormones can trigger certain behaviors.     45-4

         Breeding experiments can help determine the degree to which a behavior is genetic.     45-5

         Molecular techniques provide new ways of testing the role of genes in behavior.     45-6

         HOW DO WE KNOW?
          Can genes influence behavior?     45-7

       45.3 Learning     45-8

         Non-associative learning occurs without linking two events.     45-8

         Associative learning occurs when two events are linked.     45-9

         Learning takes many forms.     45-9

         HOW DO WE KNOW?
          To what extent are insects capable of learning?     45-10

       45.4 Orientation, Navigation, and Biological Clocks     45-11

         Orientation involves a directed response to a stimulus.     45-11

         Navigation is illustrated by the remarkable ability of homing in birds.     45-11

         Biological clocks provide important time cues for many behaviors.     45-12

         HOW DO WE KNOW?
          Does a biological clock play a role in birds’ ability to orient?     45-12

       45.5 Communication     45-13

         Communication is the transfer of information between a sender and receiver.     45-14

         Some forms of communication are complex and learned during a sensitive period.     45-15

         Other forms of communication convey specific information.     45-15

       45.6 Social Behavior     45-16

         Group selection is a weak explanation of altruistic behavior.     45-16

         Reciprocal altruism is one way that altruism can evolve.     45-17

         Kin selection is based on the idea that it is possible to contribute genetically to future generations by helping close relatives.     45-18

       45.7 Behavior and Sexual Selection     45-19

         Patterns of sexual selection are governed by differences between the sexes in their investment in offspring.     45-20

         Sexual selection can be intrasexual or intersexual.     45-20

CHAPTER 46     POPULATION ECOLOGY     46-1

       46.1 Populations and Their Properties     46-1

         Three key features of a population are its size, range, and density.     46-2

         Population size can increase or decrease over time.     46-3

         Carrying capacity is the maximum number of individuals a habitat can support.     46-5

         Factors that influence population growth can be dependent on or independent of its density.     46-6

         Ecologists estimate population size and density by sampling.     46-6

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         HOW DO WE KNOW?
          How many butterflies are there in a given population?     46-7

       46.2 Age-Structured Population Growth     46-8

         Birth and death rates vary with age and environment.     46-8

         Survivorship curves record changes in survival probability over an organism’s life-span.     46-9

         Patterns of survivorship vary among organisms.     46-10

         Reproductive patterns reflect the predictability of a species’ environment.     46-10

         The life history of an organism shows trade-offs among physiological functions.     46-11

       46.3 Metapopulation Dynamics     46-12

         A metapopulation is a group of populations linked by immigrants.     46-12

         Island biogeography explains species diversity on habitat islands.     46-14

      ? How do islands promote species diversification?     46-15

         Species coexistence depends on habitat diversity.     46-16

         HOW DO WE KNOW?
          Can predators and prey coexist stably in certain environments?     46-17

CHAPTER 47     SPECIES INTERACTIONS, COMMUNITIES, AND ECOSYSTEMS     47-1

       47.1. The Niche     47-1

         The niche is the ecological role played by a species in its community.     47-2

         The realized niche of a species is more restricted than its fundamental niche.     47-3

       47.2 Antagonistic Interactions Between Species     47-3

         Limited resources foster competition.     47-4

         Competition promotes niche divergence.     47-4

         Species compete for resources other than food.     47-5

         Predators and parasites can limit prey population size, minimizing competition.     47-5

       47.3 Mutualistic Interactions Between Species     47-5

         Mutualisms are interactions between species that benefit both participants.     47-6

         Mutualisms may evolve increasing interdependence.     47-6

         Mutualisms may be obligate or facultative.     47-6

         HOW DO WE KNOW?
          Have aphids and their symbiotic bacteria coevolved?     47-7

         The costs and benefits of species interactions can change over time.     47-8

       47.4 Ecological Communities     47-9

         Species that live in the same place make up communities.     47-9

         A single herbivore species can affect other herbivores and their predators.     47-9

         Keystone species have disproportionate effects on communities.     47-10

         Disturbance can modify community composition.     47-11

         Succession describes the community response to new habitats or disturbance.     47-12

       47.5 Ecosystems     47-13

         Species interactions result in food webs that cycle carbon and other elements through ecosystems.     47-13

         Species interactions form trophic pyramids that transfer energy through ecosystems.     47-15

         Light, water, nutrients, and diversity all influence rates of primary production.     47-15

         HOW DO WE KNOW?
          Does species diversity promote primary productivity?     47-16

       47.6 Biomes and Diversity Gradients     47-16

         Biomes reflect the interaction of Earth and life.     47-19

         Tropical biomes usually have more species than temperate biomes.     47-20

      ? Why are tropical species so diverse?     47-21

         Evolutionary and ecological history underpins diversity.     47-22

CHAPTER 48     THE ANTHROPOCENE

Humans as a Planetary Force     48-1

       48.1 The Anthropocene Period     48-1

         Humans are a major force on the planet.     48-1

       48.2 Human Influence on the Carbon Cycle     48-3

         As atmospheric carbon dioxide levels have increased, so has mean surface temperature.     48-3

         Changing environments affect species distribution and community composition.     48-5

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      ? How has climate change affected coral reefs around the world?     48-7

         HOW DO WE KNOW?
          What is the effect of increased atmospheric CO2 and reduced ocean pH on skeleton formation in marine algae?     48-9

         What can be done?     48-10

       48.3 Human Influence on the Nitrogen and Phosphorus Cycles     48-11

         Nitrogen fertilizer transported to lakes and the sea causes eutrophication.     48-11

       VISUAL SYNTHESIS Succession: Ecology in Microcosm     48-12

         Phosphate fertilizer is also used in agriculture, but has finite sources.     48-14

         What can be done?     48-14

       48.4 Human Influence on Evolution     48-15

      ? How has human activity affected biological diversity?     48-15

         Humans play an important role in the dispersal of species.     48-17

         Humans have altered the selective landscape for many pathogens.     48-18

         Are amphibians ecology’s “canary in the coal mine”?     48-19

       48.5 Scientists and Citizens in the 21st Century     48-19

QUICK CHECK ANSWERS     Q-1

GLOSSARY     G-1

CREDITS/SOURCES     CS-1

INDEX     I-1