Table of Contents
1. Biology and the Tree of Life.
The Cell Theory. The Theory of Evolution by Natural Selection. The
Tree of Life. Biological Science.Box 1.1: Scientific Names and
Terms.Box 1.2: Medicine, Economics and the Tree of Life.Essay:
Where Do Humans Fit on the Tree of Life?
UNIT I. THE ORIGIN AND EARLY EVOLUTION OF LIFE.
2. The Atoms and Molecules of Ancient Earth.
The Ancient Earth. The Building Blocks of Chemical Evolution.
Chemical Reactions, Chemical Energy, and Chemical Evolution. The
Composition of the Early Atmosphere: Redox Reactions and the
importance of Carbon. The Early Oceans and the Properties of
Water.Box 2.1: Atomic Mass.Box 2.2: Bond Types Form a
Continuum.Essay: The Search for Extraterrestrial Life.
3.
Macromolecules and the RNA World.
The Start of Chemical Evolution: Experimental Simulations. The
Building Blocks of Macromolecules. The First Macromolecules. The
First Living Entity.Box 3.1: How Do Biologists Define Life?Box 3.2:
Gel Electrophoresis and Autoradiography.Box 3.3: How Proteins
Catalyze Reactions.Box 3.4: Models in Biology: The Double
Helix.Essay: Molecular Handedness and the Thalidomide Tragedy.
4.
Membranes and the First Cells.
Lipid Chemistry. Phospholipid Bilayers. Why Molecules Move Across
Lipid Bilayers: Diffusion and Osmosis. Membrane Proteins.Box 4.1:
The Transmission Electron Microscope.Box 4.2: The Scanning Electron
Microscope.Box 4.3: The Fluid-Mosaic Model.Essay: The Molecular
Basis of Cystic Fibrosis.
UNIT II. CELL FUNCTIONS.
5. Cell Structure and Function.
A Tour of the Cell. The Nucleus of Nuclear Transport. The
Endomembrane System: Synthesis and Distribution of Cellular
Products. The Cytoskeleton.Box 5.1: An Introduction to
Centrifugation.Essay: Organelles and Human Disease.
6.
Respiration and Fermentation.
An Overview of Cellular Respiration. Glycolysis. The Krebs Cycle.
Electron Transport and Chemiosmosis. Fermentation. How Does
Cellular Respiration Interact with Other Metabolic Pathways.Essay:
ATP Production During Exercise.
7. Photosynthesis.
What Is Photosynthesis? How Does Chlorophyll Capture Light Energy?
The Photosynthetic Reaction Centers. The Calvin Cycle.Box 7.1:
Types of Plastids.Box 7.2: Why Was the Oxygen Revolution
Important?Essay: Are Rising CO2 Levels in the Atmosphere Affecting
Plant Productivity.
8. Cell Division.
Mitosis and the Cell Cycle. How Does Mitosis Take Place? Control of
the Cell Cycle. Cancer: Out-of-Control Cell Division.Box 8.1:
Cell-Culture Methods.Box 8.2: Cell Division in Bacteria.Essay:
Cancer Chemotherapy.
UNIT III. GENE STRUCTURE AND EXPRESSION.
9. Meiosis.
How Does Meiosis Occur? The Consequences of Meiosis? Why Does
Meiosis Exist? Why Sex? Mistakes in Meiosis.Box 9.1: Karyotyping
Techniques.Box 9.2: Experimental Evidence for Physical Exchange of
Chromosome Segments During Crossing Over.Box 9.3: Recombination in
Bacteria.Essay: Seedless Fruits.
10. Mendel and the Gene.
Mendel's Experiments with a Single Trait? Mendel's Experiments with
Two Traits. The Chromosome Theory of Inheritance. Testing and
Extending the Chromosome Theory. Extending Mendel's Rules.Box 10.1:
Combining Probabilities.Box 10.2: Sample Size and Chance
Fluctuations.Essay: Does “Genetic Determinism” Exist?
11. How Do
Genes Work?
DNA as the Hereditary Material. What Do Genes Do? The Genetic Code?
The Central Dogma of Molecular Biology.Box 11.1: RNA Genomes:
Exceptions to the Central Dogma.Essay: How Do Viruses Work?
12.
DNA Synthesis, Mutation, and Repair.
Testing Early Hypotheses About DNA Replication. A Comprehensive
Model for DNA Synthesis. Analyzing DNA Sequences in the Laboratory.
The Molecular Basis of Mutation. Repairing Damaged DNA.Essay: The
Genetic Basis of Cancer.
13. Transcription and
Translation.
Transcription in Bacteria. Transcription in Eukaryotes. An
Introduction to Translation. The of Transfer RNA. The Ribosome.
Post-Transitional Events.Box 13.1: An Introduction to X-Ray
Crystallography.Box 13.2: Prions.Essay: Transcription, Translation,
and Toxins.
14. Control of Gene Expression in Bacteria.
Gene Regulation and Information Flow. Identifying the Genes
Involved in Lactose Metabolism. The Discovery of the Repressor.
Catabolite Repression and Positive Control. The Operator and the
Repressor—An Introduction to DNA-Binding Proteins.Box 14.1: Gene
Transfer in Bacteria.Box 14.2: Negative Control and Attentuation in
the trp Operon.Box 14.3: DNA Footprinting.Essay: Controlling the
Expression of Disease-Causing Genes.
15. Control of Gene
Expression in Eukaryotes.
Mechanisms of Gene Regulation—An Overview. Eukaryotic DNA and the
Regulation of Gene Expression. Regulatory Sequences in DNA.
Regulatory Proteins. Post-Transcriptional Processing. Linking
Cancer with Defects in Gene Regulation.Box 15.1: Recombinant DNA
Technology.Box 15.2: Southern Blotting.Essay: Gene Regulation and
the Green Revolution.
16. Genomes.
An Introduction to Whole-Genome Sequencing. Bacterial and Archaeal
Genomes. Eukaryotic Genomes. Future Prospects.Box 16.1:
Bioinformatics.Essay: Genomics and Issues of Privacy.
17. Genetic
Engineering and its Applications.
Using Recombinant DNA Techniques to Manufacture Proteins: The
Effort to Cure Pituitary Dwarfism. Gene Hunting Based on Pedigree
Analysis. Can Gene Therapy Cure Inherited Diseases in Humans?
Biotechnology in Agriculture.Box 17.1: Genome Sequencing and Gene
Hunting.Box 17.2: Genetic Testing.Essay: Controversies over
Genetically Modified Foods.
UNIT IV. DEVELOPMENTAL BIOLOGY.
18. An Introduction to Development.
Developmental Stages and Patterns. Does the Genetic Makeup of Cells
Changes as Development Proceeds? What Causes Differential Gene
Expression?Essay: Human Cloning.
19. Early Development.
Gametogenesis. Fertilization. Cleavage. Gastrulation.Box 19.1:
Visualizing mRNAs by Situ Hybridization.Essay: Treating Human
Infertility.
20. What Determines a Cell's Fate?
Pattern Formation in Drosophila. Pattern Formation in Arabidopsis.
Differentiation: Becoming a Specialized Cell. Box 20.1: Maternal
Effect Inheritance.Box 20.2: Programmed Cell Death.Essay: Human
Stem Cells.
UNIT V. EVOLUTIONARY PATTERNS AND PROCESSES.
21. Darwinism and the Evidence for Evolution.
The Evidence for Evolution. How Natural Selection Works. Evolution
in Action: Recent Research on Natural Selection.Box 21.1: The
Evidence for Evolution.Box 21.2: How Natural Selection Works.Box
21.3: Evolutionary Theory Before Darwin.Box 21.4: Problems in
Estimating the Heritability of Traits.Essay: The Debate over
“Scientific Creationism”.
22. Evolutionary Processes.
Why is Genetic Diversity Important? Analyzing Allele Frequency
Change: The Hardy-Weinberg Principle. Mutation. Migration.
Inbreeding. Natural Selection. Sexual Selection.Essay: Evolutionary
Theory and Human Health.
23. Speciation.
Defining and Identifying Species. Isolation and Divergence in
Sympatry. Isolation and Divergence in Allopatry. Secondary
Contact.Box 23.1: How Do Researchers Estimate Phylogenetic
Trees?Essay: Human Races.
24. The History of Life.
Tools for Studying History. The Cambrian Explosion. The Genetic
Mechanisms of Change. Adaptive Radiations. Mass Extinctions.Box
24.1: The Molecular Clock.Essay: Is a Mass Extinction Event Under
Way Now?
UNIT VI. THE DIVERSIFICATION OF LIFE.
25. Bacteria and Archaea.
What Are the Bacteria and Archaea? Metabolic Diversity in Bacteria
and Archaea? Bacteria, Archaea, and Global Change. Bacterial
Diseases.Box 25.1: Cultural Techniques as a Research Tool.Essay:
Antibiotics and the Evolution of Resistance.
26. Viruses.
What Are the Viruses? What Is HIV? How Does and HIV Infection
Begin? How Does HIV Replicate Its Genome? How Are Viral Proteins
Translated and Processed? How Are Viruses Transmitted to New
Hosts?Box 26.1: Where Did Viruses Come From?Essay: Emerging
Viruses.
27. Protists.
What Are the Protists? Themes in the Evolution of Protists? The
Origin of Mitochondria and Chloroplasts. How Do Protists Affect
Human Health and Welfare?Box 27.1: How Should We Name the Tree of
Life's Major Branches?Essay: Revolutions in Science.
28. Land
Plants.
Phylogenies and the Fossil Record: origins and Diversification. The
Transition to Land: Key Innovations and Trends. Strategies for
Photon Capture. Food, Fuel, and Fiber: Human Use of Pants.Essay:
Genetic Diversity in Crop Plants?
29. Fungi.
What Are the Fungi? Growth, Digestion, and Absorption. Mutualism.
Parasitism.Box 29.1: The Problem of Convergence.Box 29.2: Fungi at
Work.Essay: Why Are Frogs Dying?
30. Animals.
Origins and Early Diversification. Feeding. Key Innovations in the
Radiation of Arthropods. Key Innovations in the Radiation of
Vertebrates. Human Evolution.Essay: So Human An Animal.
UNIT VII. HOW PLANTS WORK.
31. Plant Form and Function.
The Diversity of Plant Form. Cells, Tissues, Organs, and Systems.
The Anatomy of Plant Growth. Studying Adaptation.Box 31.1:
Nonvascular Plants.Box 31.2: Monocots and Dicots.Box 31.3:
Tree-Ring Studies.Essay: Wood as a Structural Material.
32. Water
and Sugar Transport in Plants.
Water Potential and Cell-to-Cell Movement. Transpiration and Water
Movement from Roots to Leaves. Translocation.Essay: Irrigated
Agriculture.
33. Plant Nutrition.
Nutritional Requirements. Soil. Nutrient Uptake. Nitrogen Fixation.
Nutritional Adaptation of Plants.Essay: Tropical Soils.
34.
Sensory Systems in Plants.
Sensing Light. How Do Plants Perceive Gravity? How Do Plants
Respond to Touch?Essay: Can Plants Tell Time?
35. Communication:
Chemical Signals.
Phototropism. Apical Dominance. Growth and Dormancy.Box 35.1:
Cytokinins.Essay: Herbicides.
36. Plant Reproduction.
An Introduction to Plant Reproduction. Reproductive Structures.
Pollination and Fertilization. The Seed.Box 36.1: Pure and Applied
Science.Essay: Why Do Wasps Try to Copulate with Hammer
Orchids?
37. Plant Defense Systems.
Barriers to Entry. Plant Poisons. The Cost of Defense. Responding
to Pathogens. Responding to Herbivores.Essay: Chemical Prospecting.
UNIT VIII. HOW ANIMALS WORK.
38. Animal Form and Function.
The Nature of Natural Selection. The Nature of Adaptation. Tissues,
Organs, and Systems: How Does Structure Correlate with Function?
Body Size and Scaling. Homeostasis.Essay: Is Fever Adaptive?
39.
Water and Electrolyte Balance in Animals.
Osmotic Stress and Osmoregulation. Water and Electrolyte Balance in
Aquatic Environments. Water and Electrolyte Balance in Terrestrial
Invertebrates. Water and Electrolyte Balance in Terrestrial
Vertebrates.Essay: Life in the Desert.
40. Animal
Nutrition.
Nutritional Requirements. Obtaining Food: The Structure and
Function of Beaks, Teeth, and Mouthparts. Digestion. Nutritional
Homeostasis—Glucose as a Case Study.Essay: Cholesterol, Heart
Disease, and Diet.
41. Gas Exchange and Circulation.
Air and Water as Respiratory Media. Organs of Gas Exchange. Blood.
The Circulatory System. Homeostasis in Blood Pressure and Blood
Chemistry.Box 41.1: Measuring Blood Pressure.Essay: Smoking and
Lung Function.
42. Electrical Signals in Animals.
Principles of Electrical Signaling. Dissecting the Action
Potential. The Synapse. The Vertebrate Nervous System.Box 42.1: The
Nernst Equation and the Goldman Equation.Essay: Can Brain Tissue
Transplants Help People with Parkinson's Disease?
43. Animal
Sensory Systems and Movement.
How Do Sensory Organs Convey Information to the Brain? Hearing?
Vision? Taste and Smell. Movement.Box 43.1: Senses that Humans
Don't Have.Box 43.2: Vertebrate Versus Cephalopod Eyes.Essay:
Sprinters and Marathoners—Born or Made?
44. Chemical Signals in
Animals.
Cataloging Hormone Structure and Function. What Do Hormones Do? How
Is the Production of Hormones Regulated? How Do Hormones Act on
Target Cells?Box 44.1: A Closer Look at Thyroxine and the Thyroid
Gland.Box 44.2: Oxytocin and ADH.Essay: Do Humans Produce
Pheromones?
45. Animal Reproduction.
Asexual and Sexual Reproduction. Fertilization and Egg Development.
Reproductive Structures and Their Functions. The Role of Sex
Hormones in Mammalian Reproduction. Human Pregnancy and Birth.Box
45.1: Unusual Aspects of Fertilization.Box 45.2: Abuse of Synthetic
Steroids.Essay: Contraception.
46. The Immune System in
Animals.
Innate Immunity. The Acquired Immune Response: Recognition. The
Acquired Immune Response: Activation. The Acquired Immune Response:
Culmination.Box 46.1: Producing Monoclonal Antibodies.Box 46.2: How
Does the Immune System Distinguish Self from Non-Self?Box 46.3: The
ELISA Test.Essay: Allergies.
UNIT IX. ECOLOGY.
47. Behavior.
The Role of Genes. How Animals Act: Neural and Hormonal Control.
The Adaptive Consequences of Behavior. The Evolution of
Behavior.Box 47.1: Using Reverse Genetics to Study Behavior.Box
47.2: Conditional Strategies and the Nature/Nurture Debate.Box
47.3: The Importance of Observation in Behavioral Studies.Box 47.4:
Calculating the Coefficient of Relatedness.Essay: Children at
Risk.
48. Population Ecology.
Population Growth. How Do the Sizes of Populations Change over
Time? Population Structure. Demography and Conservation.Box 48.1:
What's the Best Way to Clean Up an Oil Spill?Box 48.2:
Mark-Recapture Studies.Essay: What Limits Human Population
Growth?
49. Species Interactions.
Parasitism. Predation. Herbivory. Competition. Mutualism.Essay:
Predator Control.
50. Community Ecology.
Climate and the Distribution of Ecological Communities. How
Predictable Are Community Assemblages? Species Diversity in
Ecological Communities.Box 50.1: Measuring Species Diversity.Essay:
Let-It-Burn Policies.
51. Ecosystems.
Energy Flow and Trophic Structure. Biogeochemical Cycles.Essay:
Global Warming.
52. Biodiversity and Conservation.
How Many Species Are Being Lost, and Why? Why Should We Care?
Setting Conservation Priorities.Box 52.1: Why Do Small Populations
Become Inbred, and Why is Inbreeding Harmful?Essay: Metaphors for
the Future: Easter Island and Guanacaste.
Appendix.
Glossary.
Index.About the Author
Scott Freeman received his Ph.D. in Zoology from the
University of Washington and was nominated for an Excellence in
Teaching Award in 1989. He was subsequently awarded an Albert Sloan
Postdoctoral Fellowship in Molecular Evolution at Princeton
University to investigate how generation time affects the rate of
molecular evolution. Dr. Freeman's research publications explore a
range of topics from the behavioral ecology of nest parasitism to
the molecular systematics of the blackbird family. As an affiliate
faculty member at the University of Washington, he has taught
courses in evolution and has played an active role in the redesign
of the general biology course. He is currently teaching the majors
general biology course using an inquiry-based approach that
emphasizes the logic of experimental design and the mastery of core
concepts required for success in upper-level courses. Dr. Freeman
is the co-author of Evolutionary Analysis, which presents
evolutionary principles in the same spirit of inquiry that drives
research.