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Biological Science, Canadian Edition., 2e (Freeman et al.) UPDATED VERSION

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Contents Chapter 1 Biology and the Tree of Life 1 1.1 The Cell Theory 2 Are All Organisms Made of Cells? 2 Where Do Cells Come From? 2 1.2 The Theory of Evolution by Natural Selection 4 What Is Evolution? 4 What Is Natural Selection? 4 1.3 The Tree of Life 5 Linnaean Taxonomy 6 BOX 1.1 Scientific Names and Terms 6 Using Molecules to Understand the Tree of Life 8 1.4 Doing Biology 10 Why Do Giraffes Have Long Necks? An Introduction to Hypothesis Testing 10 Why Are Chili Peppers Hot? An Introduction to Experimental Design 12 ESSAY Where Do Humans Fit on the Tree of Life? 15 CHAPTER REVIEW 16 UNIT 1 The Origin and Early Evolution of Life 19 Chapter 2 The Atoms and Molecules of Ancient Earth 20 2.1 The Ancient Earth 20 Studying the Formation of Planets 21 When Did Chemical Evolution Take Place? 21 2.2 The Building Blocks of Chemical Evolution 24 What Atoms Are Found in Organisms? 24 How Does Covalent Bonding Hold Molecules Together? 24 How Does Ionic Bonding Hold Molecules Together? 26 Some Simple Molecules Formed from H, C, N, and O 27 2.3 Chemical Reactions, Chemical Evolution, and Chemical Energy 29 How Do Chemical Reactions Happen? 30 What Is Energy? 30 Chemical Evolution: A Model System 32 How Did Chemical Energy Change during Chemical Evolution? 34 2.4 The Composition of the Early Atmosphere: Redox Reactions and the Importance of Carbon 35 What Is a Redox Reaction? 35 BOX 2.1 Some Other Approaches to Understanding Redox Reactions 36 What Happens When Carbon Is Reduced? 36 The Early Oceans and the Properties of Water 39 Why Is Water Such an Efficient Solvent? 39 How Does Water_s Structure Correlate with Its Properties? 40 Acid-Base Reactions and pH 41 What Was Water_s Role in Chemical Evolution? 42 ESSAY The Search for Extraterrestrial Life 43 CHAPTER REVIEW 44 Chapter 3 Protein Structure and Function 46 3.1 Early Origin-of-Life Experiments 47 BOX 3.1 Was Miller Correct about Conditions on Ancient Earth? 48 3.2 Amino Acids and Polymerization 48 The Structure of Amino Acids 49 How Do Amino Acids Link to Form Proteins? 53 3.3 What Do Proteins Look Like? 56 Primary Structure 57 Secondary Structure 57 Tertiary Structure 58 Quaternary Structure 59 Folding and Function 60 BOX 3.2 Prions 62 3.4 What Do Proteins Do? 62 Proteins Have Diverse Functions in Cells 62 An Introduction to Catalysis 63 How Do Enzymes Work? 64 Was the First Living Entity a Protein? 70 ESSAY Molecular Handedness and the Thalidomide Tragedy 70 CHAPTER REVIEW 71 Chapter 4 Nucleic Acids and the RNA World 74 4.1 What Is a Nucleic Acid? 75 Could Chemical Evolution Result in the Production of Nucleotides? 76 How Do Nucleotides Polymerize to Form Nucleic Acids? 76 BOX 4.1 Gel Electrophoresis and Autoradiography 78 4.2 DNA Structure and Function 79 BOX 4.2 An Introduction to X-Ray Crystallography 80 DNA Is an Information-Containing Molecule 82 Is DNA a Catalytic Molecule? 82 4.3 RNA Structure and Function 83 RNA as an Information-Containing Molecule 84 Is RNA a Catalytic Molecule? 85 4.4 The First Life-Form 85 ESSAY The Human Side of Research 87 CHAPTER REVIEW 88 Chapter 5 An Introduction to Carbohydrates 90 5.1 Sugars as Monomers 91 5.2 The Structure of Polysaccharides 92 BOX 5.1 Lactose Intolerance and Galactosemia 93 Starch: A Storage Polysaccharide in Plants 94 Glycogen: A Highly Branched Storage Polysaccharide in Animals 95 Cellulose: A Structural Polysaccharide in Plants 95 Chitin: A Structural Polysaccharide in Animals 96 Peptidoglycan: A Structural Polysaccharide in Bacteria 96 Polysaccharides and Chemical Evolution 96 BOX 5.2 How Do the Penicillins and Cephalosporins Kill Bacteria? 96 5.3 What Do Carbohydrates Do? 97 The Role of Carbohydrates in Cell Identity 97 The Role of Carbohydrates in Energy Production and Storage 98 Carbohydrates as Structural Molecules 99 ESSAY Why Do We Have a Sweet Tooth? 101 CHAPTER REVIEW 101 Chapter 6 Lipids, Membranes, and the First Cells 103 6.1 Lipids 104 BOX 6.1 Electron Microscopy 104 What Is a Lipid? 106 A Look at Three Types of Lipids Found in Cells 106 The Structures of Membrane Lipids 108 6.2 Phospholipid Bilayers 109 Artificial Membranes as an Experimental System 109 Selective Permeability of Lipid Bilayers 110 Does the Type of Lipid in a Membrane Affect Its Permeability? 111 Why Does Temperature Affect the Fluidity and Permeability of Membranes? 112 6.3 Why Molecules Move across Lipid Bilayers: Diffusion and Osmosis 113 6.4 Membrane Proteins 116 Systems for Studying Membrane Proteins 118 How Do Membrane Proteins Affect Ions and Molecules? 118 ESSAY The Molecular Basis of Cystic Fibrosis 123 CHAPTER REVIEW 125 UNIT 2 Cell Structure and Function 127 Chapter 7 Inside the Cell 128 7.1 What_s Inside the Cell? 129 Prokaryotic Cells 129 Eukaryotic Cells 131 How Does Cell Structure Correlate with Function? 138 The Dynamic Cell 139 BOX 7.1 How Does a Centrifuge Work? 140 BOX 7.2 Techniques for Studying the Dynamic Cell 141 7.2 The Nuclear Envelope: Transport Into and Out of the Nucleus 142 How Are Molecules Imported into the Nucleus? 143 How Are Molecules Exported from the Nucleus? 144 7.3 The Endomembrane System: Manufacturing and Shipping Proteins 145 Entering the Endomembrane System: The Signal Hypothesis 146 Getting from the ER to the Golgi 147 What Happens Inside the Golgi Apparatus? 147 How Are Products Shipped from the Golgi? 148 7.4 The Dynamic Cytoskeleton 149 Actin Filaments 150 Intermediate Filaments 151 Microtubules 152 Cilia and Flagella: Moving the Entire Cell 154 ESSAY Organelles and Human Disease 156 CHAPTER REVIEW 156 Chapter 8 Cell-Cell Interactions 159 8.1 The Cell Surface 160 The Structure and Function of an Extracellular Layer 160 The Plant Cell Wall 160 The Extracellular Matrix in Animals 162 BOX 8.1 What Happens When the Extracellular Matrix Is Defective? 163 8.2 How Do Adjacent Cells Connect and Communicate? 163 Cell-Cell Attachments 165 Cell-Cell Gaps 169 8.3 How Do Distant Cells Communicate? 170 Signal Reception 170 Signal Processing 171 Signal Response 172 Signal Deactivation 174 ESSAY How Do ViagraÀ, LevitraÀ, and CialisÀ Work? 175 CHAPTER REVIEW 174 Chapter 9 Cellular Respiration and Fermentation 177 9.1 An Overview of Cellular Respiration 178 The Nature of Chemical Energy and Redox Reactions 179 Using Redox Reactions to Produce ATP 180 Processing Glucose: Glycolysis 180 The Krebs Cycle 180 Electron Transport 182 Methods of Producing ATP 182 9.2 Glycolysis 183 A Closer Look at the Glycolytic Reactions 183 How Is Glycolysis Regulated? 184 9.3 The Krebs Cycle 186 Converting Pyruvate to Acetyl CoA 187 How Is the Krebs Cycle Regulated? 188 What Happens to the NADH and FADH2? 190 9.4 Electron Transport and Chemiosmosis 190 Components of the Electron Transport Chain 191 The Chemiosmotic Hypothesis 192 How Is the Electron Transport Chain Organized? 193 The Discovery of ATP Synthase 194 Oxidative Phosphorylation 194 9.5 Fermentation 196 9.6 How Does Cellular Respiration Interact with Other Metabolic Pathways? 197 Processing Proteins and Fats as Fuel 197 Anabolic Pathways Synthesize Key Molecules 198 ESSAY ATP Production during Exercise 199 CHAPTER REVIEW 199 Chapter 10 Photosynthesis 202 10.1 An Overview of Photosynthesis 203 Photosynthesis: Two Distinct Sets of Reactions 203 The Structure of the Chloroplast 204 BOX 10.1 Types of Plastids 205 10.2 How Does Chlorophyll Capture Light Energy? 206 Photosynthetic Pigments Absorb Light 206 BOX 10.2 How Do Researchers Measure Absorption Spectra? 207 When Light Is Absorbed, Electrons Enter an Excited State 209 10.3 The Discovery of Photosystems I and II 211 How Does Photosystem II Work? 212 How Does Photosystem I Work? 214 The Z Scheme: Photosystems I and II Work Together 215 10.4 How Is Carbon Dioxide Reduced to Produce Glucose? 217 The Calvin Cycle 217 The Discovery of Rubisco 219 How Is Carbon Dioxide Delivered to Rubisco? 220 What Happens to the Sugar That Is Produced by Photosynthesis? 222 ESSAY Are Rising CO2 Levels in the Atmosphere Affecting the Rate of Photosynthesis? 224 CHAPTER REVIEW 225 Chapter 11 The Cell Cycle 227 11.1 Mitosis and the Cell Cycle 228 The Cell Cycle 229 When Does Chromosome Replication Occur? 229 The Discovery of the Gap Phases 230 BOX 11.1 Cell- Culture Methods 231 BOX 11.2 How Do Bacteria Divide? 232 11.2 How Does Mitosis Take Place? 232 Events in Mitosis 232 Cytokinesis 235 How Do Chromosomes Move during Mitosis? 237 11.3 Control of the Cell Cycle 238 The Discovery of Cell-Cycle Regulatory Molecules 238 Cell-Cycle Checkpoints 240 11.4 Cancer: Out-of-Control Cell Division 241 Properties of Cancer Cells 242 Cancer Involves Loss of Cell-Cycle Control 242 ESSAY Cancer Chemotherapy 244 CHAPTER REVIEW 245 UNIT 3 Gene Structure and Expression 247 Chapter 12 Meiosis 248 12.1 How Does Meiosis Occur? 249 BOX 12.1 Karyotyping Techniques 250 An Overview of Meiosis 252 The Phases of Meiosis I 253 The Phases of Meiosis II 255 A Closer Look at Key Events in Prophase of Meiosis I 257 12.2 The Consequences of Meiosis 258 Chromosomes and Heredity 258 How Does the Separation and Distribution of Homologous Chromosomes Produce Genetic Variation? 258 The Role of Crossing Over 259 How Does Fertilization Affect Genetic Variation? 259 12.3 Why Does Meiosis Exist? Why Sex? 260 The Paradox of Sex 261 When Do Meiosis and Fertilization Occur during the Life of an Organism? 263 12.4 Mistakes in Meiosis 264 How Do Mistakes Occur? 264 Why Do Mistakes Occur? 265 ESSAY Seedless Fruits 266 CHAPTER REVIEW 267 Chapter 13 Mendel and the Gene 269 13.1 Mendel_s Experiments with a Single Trait 270 What Questions Was Mendel Trying to Answer? 270 Garden Peas Serve as the First Model Organism in Genetics 270 Inheritance of a Single Trait 272 The Nature and Behavior of the Hereditary Determinants 273 BOX 13.1 Why Do Punnett Squares Work? 275 Testing the Model 275 13.2 Mendel_s Experiments with Two Traits 276 BOX 13.2 Sample Size and Chance Fluctuations 278 Using a Testcross to Confirm Predictions 278 Mendel_s Contributions to the Study of Heredity 279 13.3 The Chromosome Theory of Inheritance 279 13.4 Testing and Extending the Chromosome Theory 281 The Discovery of Sex-Linked Traits 281 The Discovery of Sex Chromosomes 281 X-Linked Inheritance and the Chromosome Theory 282 What Happens When Genes Are Located on the Same Chromosome? 283 13.5 Extending Mendel_s Rules 287 Incomplete Dominance and Codominance 288 Multiple Alleles and Polymorphic Traits 289 Pleiotropy 289 Genes Are Affected by the Physical Environment and Genetic Environment 290 Organelle Genomes 291 Quantitative Traits 291 13.6 Applying Mendel_s Rules to Humans 294 Are Alleles Recessive or Dominant? 294 Is the Trait Autosomal or Sex-Linked? 295 ESSAY Does "Genetic Determinism" Exist? 297 CHAPTER REVIEW 298 Chapter 14 DNA Synthesis 303 14.1 DNA as the Hereditary Material 304 Is DNA the Genetic Material? 305 14.2 Testing Early Hypotheses about DNA Replication 307 The Meselson-Stahl Experiment 308 The Discovery of DNA Polymerase 310 14.3 A Comprehensive Model for DNA Synthesis 311 Opening the Helix 312 Synthesis of the Leading Strand 313 Synthesis of the Lagging Strand 313 14.4 Replicating the Ends of Linear Chromosomes 316 14.5 Repairing Mistakes in DNA Synthesis 318 How Is DNA Polymerase Proofread? 318 Mismatch Repair 319 14.6 Repairing Damaged DNA 320 DNA Nucleotide Excision Repair: An Overview 320 Xeroderma Pigmentosum: A Case Study 321 ESSAY DNA Mismatch Repair and Cancer 322 CHAPTER REVIEW 323 Chapter 15 How Genes Work 325 15.1 What Do Genes Do? 326 The Molecular Basis of Hereditary Diseases 326 Genes and Enzymes 326 15.2 The Genetic Code 328 RNA as the Intermediary between Genes and Proteins 329 How Long Is a Word in the Genetic Code? 330 How Did Researchers Crack the Code? 332 BOX 15.1 The Evolution of the Genetic Code 333 15.3 The Central Dogma of Molecular Biology 334 ESSAY Exceptions to the Central Dogma 335 CHAPTER REVIEW 336 Chapter 16 Transcription and Translation 338 16.1 Transcription in Bacteria 339 RNA Polymerase Structure and Function 340 Initiation: How Does Transcription Begin in Bacteria? 340 Elongation and Termination 341 16.2 Transcription in Eukaryotes 342 The Startling Discovery of Eukaryotic Genes in Pieces 342 BOX 16.1 Toxins and Transcription 343 Exons, Introns, and RNA Splicing 344 Other Aspects of Transcript Processing: Caps and Tails 345 16.3 An Introduction to Translation 345 Ribosomes Are the Site of Protein Synthesis 346 How Does an mRNA Triplet Specify an Amino Acid? 347 16.4 The Role of Transfer RNA 347 Connecting Structure with Function 348 How Many tRNAs Are There? 349 16.5 Ribosomes and the Mechanism of Translation 350 Initiation 351 Elongation 352 Termination 353 16.6 The Molecular Basis of Mutation 355 ESSAY Antibiotics That Poison the Ribosome 358 CHAPTER REVIEW 359 Chapter 17 Control of Gene Expression in Bacteria 362 17.1 Gene Regulation and Information Flow 363 Mechanisms of Regulation_an Overview 363 Metabolizing Lactose_A Model System 364 17.2 Identifying the Genes Involved in Lactose Metabolism 365 Screening Mutants_Replica Plating and Indicator Plates 365 Different Classes of Lactose Metabolism Mutants 366 Several Genes Are Involved in Metabolizing Lactose 367 17.3 The Discovery of the Repressor 368 The lac Operon 369 Testing the lac Operon Model 369 BOX 17.1 Almost Parallel Worlds: Similarities and Contrasts in Control of the trp and lac Operons 370 The Impact of the lac Operon Model 370 17.4 Catabolite Repression and Positive Control 371 How Does Glucose Influence Formation of the CAP-cAMP Complex? 372 14.5 The Operator and the Repressor_an Introduction to DNA- Binding Proteins 374 Finding the Operator 374 BOX 17.2 DNA Footprinting 374 DNA Binding via the Helix-Turn-Helix Motif 376 How Does the Inducer Change the Repressor_s Affinity for DNA? 378 Future Directions 378 ESSAY Control of Gene Expression in Bacterial Pathogens 378 CHAPTER REVIEW 380 Chapter 18 Control of Gene Expression in Eukaryotes 382 18.1 Mechanisms of Gene Regulation_an Overview 383 18.2 Eukaryotic DNA and the Regulation of Gene Expression 383 Chromatin Structure 384 Evidence that Chromatin Structure Is Altered in Active Genes 384 How Is Chromatin Altered? 385 18.3 Regulatory Sequences and Regulatory Proteins 386 Promoter-Proximal Elements 386 Enhancers 386 How Do Enhancers Work? 388 18.4 Transcription Initiation 390 18.5 Post-Transcriptional Control 392 Alternative Splicing of mRNAs 392 Translational Control 393 Post-Translational Control 393 A 50-Year Retrospective: How Does Gene Expression in Bacteria and in Eukaryotes Compare? 394 18.6 Linking Cancer with Defects in Gene Regulation 395 p53_ Guardian of the Genome 395 STAT Mutations in Cancer 397 ESSAY Fly Eyes and Other Strange Tales of Gene Regulation 398 CHAPTER REVIEW 399 Chapter 19 Analyzing and Engineering Genes 401 19.1 Using Recombinant DNA Techniques to Manufacture Proteins: The Effort to Cure Pituitary Dwarfism 402 Why Did Early Efforts to Treat the Disease Fail? 402 Using Recombinant DNA Technology to Produce a Safe Supply of Growth Hormone 402 BOX 19.1 How Do Plasmids Move between Cells Naturally? 404 Ethical Concerns over Recombinant Growth Hormone 407 19.2 Analyzing DNA: Did Our Ancestors Mate with Neanderthals? 407 The Polymerase Chain Reaction (PCR) 408 Dideoxy Sequencing 409 19.3 Gene Hunting Based on Pedigree Analysis: The Huntington_s Disease Story 411 How Was the Huntington_s Disease Gene Found? 411 BOX 19.2 Southern Blotting 412 Genetic Testing 416 Ethical Concerns over Genetic Testing 417 19.4 Can Gene Therapy Cure Inherited Diseases in Humans? Research on Severe Immune Disorders 417 How Can Novel Alleles Be Introduced into Human Cells? 417 Using Gene Therapy to Treat X-Linked Immune Deficiency 418 Ethical Concerns over Gene Therapy 420 19.5 Biotechnology in Agriculture: The Development of Golden Rice 420 Rice as a Target Crop 421 Synthesizing _-Carotene in Rice 421 The Agrobacterium Transformation System 421 Golden Rice 422 ESSAY Controversies over Genetically Modified Foods 423 CHAPTER REVIEW 424 Chapter 20 Genomics 426 20.1 Whole-Genome Sequencing 426 Recent Technological Advances 427 Which Sequences Are Genes? 428 BOX 20.1 Shotgun Sequencing and Bioinformatics 428 20.2 Bacterial and Archaeal Genomes 431 The Natural History of Prokaryotic Genomes 431 Evidence for Lateral Gene Transfer 432 20.3 Eukaryotic Genomes 433 Natural History: Types of Sequences 433 What Is a Gene Family? 436 20.4 Comparative Genomics 437 Understanding Virulence 437 Studying Adaptation 437 Gene Number and Alternative Splicing 438 Sequence Similarity and the Importance of Regulatory Sequences 439 20.5 Future Prospects 439 Functional Genomics and Proteomics 439 Medical Implications 441 ESSAY Genomics and Genetic Discrimination 442 CHAPTER REVIEW 443 UNIT 4 Developmental Biology 445 Chapter 21 Early Development 446 21.1 Gametogenesis 447 Sperm Structure and Function 447 Egg Structure and Function 448 21.2 Fertilization 449 Fertilization in Sea Urchins 449 Fertilization in Mammals 452 Fertilization in Flowering Plants 452 21.3 Cleavage and Gastrulation 453 Controlling Cleavage Patterns 454 Activating the Zygotic Genome 456 BOX 21.1 Visualizing mRNAs by in Situ Hybridization 457 Gastrulation 458 Organizing the Major Body Axes 458 The Spemann-Mangold Experiments 459 21.4 Patterns of Development 461 Embryonic Development in Arabidopsis thaliana 462 An Invertebrate Model: Drosophila melanogaster 463 A Vertebrate Model: The Frog 464 Early Development in Humans 464 Making Sense of Developmental Variation and Similarity 465 ESSAY Treating Human Infertility 466 CHAPTER REVIEW 467 Chapter 22 Pattern Formation and Cell Differentiation 469 22.1 Pattern Formation in Drosophila 470 The Discovery of bicoid 470 BOX 22.1 Maternal Effect Inheritance 471 The Discovery of Segmentation Genes 473 The Discovery of Homeotic Genes 476 Drosophila as a Model Organism 477 22.2 Pattern Formation in Arabidopsis 478 The Root-to-Shoot Axis of Embryos 478 Flower Development in Adults 479 22.3 Does the Genetic Makeup of Cells Change as Development Proceeds? 481 Are Differentiated Animal Cells Genetically Equivalent? 481 BOX 22.2 Regulatory Evolution 482 BOX 22.3 Human Cloning? 484 22.4 Differentiation: Becoming a Specialized Cell 484 Organizing Mesoderm into Somites 485 BOX 22.4 Apoptosis: Programmed Cell Death 486 Determination of Muscle Cells 488 ESSAY Human Stem Cells 489 CHAPTER REVIEW 490 UNIT 5 Evolutionary Processes and Patterns 493 Chapter 23 Evolution by Natural Selection 494 BOX 23.1 Why Darwin Gets Most of the Credit 495 23.1 The Pattern of Evolution: Have Species Changed through Time? 496 Evidence for Change through Time 496 Evidence That Species Are Related 498 How Do Biologists Distinguish Homology from Analogy? 501 Darwinism and the Pattern Component of Evolution 502 23.2 The Process of Evolution: How Does Natural Selection Work? 503 BOX 23.2 Evolutionary Theory before Darwin 503 23.3 Evolution in Action: Recent Research on Natural Selection 504 How Did Mycobacterium tuberculosis Become Resistant to Antibiotics? 504 Why Are Beak Size, Beak Shape, and Body Size Changing in Galìpagos Finches? 506 Can Natural Selection Be Studied Experimentally? 508 23.4 The Nature of Natural Selection and Adaptation 510 Selection Acts on Individuals, but Evolutionary Change Occurs in Populations 510 Evolution Is Not Progressive 510 Not All Traits Are Adaptive 511 ESSAY The Debate over "Scientific Creationism" 512 CHAPTER REVIEW 513 Chapter 24 Evolutionary Processes 516 24.1 Analyzing Change in Allele Frequencies: The Hardy-Weinberg Principle 517 The Hardy-Weinberg Model Makes Important Assumptions 518 How Does the Hardy-Weinberg Principle Serve as a Null Hypothesis? 518 24.2 Natural Selection and Sexual Selection 520 Directional Selection 521 Stabilizing Selection 522 Disruptive Selection 522 Sexual Selection 523 24.3 Genetic Drift 527 Experimental Studies of Genetic Drift 528 Genetic Drift in Natural Populations 529 24.4 Gene Flow 530 24.5 Mutation 531 Mutation as an Evolutionary Mechanism 531 What Role Does Mutation Play in Evolutionary Change? 532 24.6 Inbreeding 533 ESSAY Evolutionary Theory and Human Health 535 CHAPTER REVIEW 536 Chapter 25 Speciation 538 25.1 Defining and Identifying Species 539 The Biological Species Concept 539 The Morphospecies Concept 539 The Phylogenetic Species Concept 540 Species Definitions in Action: The Case of the Dusky Seaside Sparrow 541 25.2 Isolation and Divergence in Allopatry 543 Dispersal and Colonization Isolate Populations 543 Vicariance Isolates Populations 544 25.3 Isolation and Divergence in Sympatry 545 Can Natural Selection Cause Speciation Even When Gene Flow Is Possible? 546 How Can Polyploidy Lead to Speciation? 547 25.4 What Happens When Isolated Populations Come into Contact? 549 Reinforcement 549 Hybrid Zones 550 New Species Through Hybridization 550 ESSAY Human Races 553 CHAPTER REVIEW 554 Chapter 26 Phylogenies and the History of Life 556 26.1 Tools for Studying History: Phylogenies and the Fossil Record 556 Using Phylogenies 557 Using the Fossil Record 561 BOX 26.1 The Molecular Clock 566 26.2 The Cambrian Explosion 566 Cambrian Fossils: An Overview 567 The Doushantuo Microfossils 568 The Ediacaran Faunas 569 The Burgess Shale Faunas 569 26.3 The Genetic Mechanisms of Change 569 Gene Duplications and the Cambrian Explosion 569 Changes in Gene Expression: The Origin of the Foot 571 26.4 Adaptive Radiations 573 Colonization Events as a Trigger 574 The Role of Morphological Innovation 575 26.5 Mass Extinctions 575 How Do Background and Mass Extinctions Differ? 576 What Killed the Dinosaurs? 576 ESSAY Is a Mass Extinction Event Under Way Now? 578 CHAPTER REVIEW 579 UNIT 6 The Diversification of Life 581 Chapter 27 Bacteria and Archaea 582 27.1 Why Do Biologists Study Bacteria and Archaea? 583 Bacterial Diseases 583 Bioremediation 584 Extremophiles 585 Global Change 586 BOX 27.1 A Model Organism: Escherichia coli 588 27.2 How Do Biologists Study Bacteria and Archaea? 589 Using Enrichment Cultures 589 Using Direct Sequencing 590 Evaluating Molecular Phylogenies 590 27.3 What Themes Occur in the Diversification of Bacteria and Archaea? 592 Morphological Diversity 592 Metabolic Diversity 594 27.4 Key Lineages of Bacteria and Archaea 598 Bacteria 598 TTL3Spirochaeles (Spirochetes) 599 TTL3Chlamydiales 599 TTL3High-GC Gram Positives 600 TTL3Cyanobacteria 600 TTL3Low-GC Gram Positives 601 TTL3Proteobacteria 601 BOX 27.2 Lateral Gene Transfer and Metabolic Diversity in Bacteria 602 Archaea 602 TTL3Crenarchaeota 603 TTL3Euryarchaeota 603 ESSAY Antibiotics and the Evolution of Drug Resistance 604 CHAPTER REVIEW 605 Chapter 28 Protists 607 28.1 Why Do Biologists Study Protists? 608 Impacts on Human Health and Welfare 608 Ecological Importance of Protists 610 28.2 How Do Biologists Study Protists? 612 Microscopy: Studying Cell Structure 612 Evaluating Molecular Phylogenies 612 BOX 28.1 How Should We Name the Major Branches on the Tree of Life? 614 Combining Data from Microscopy and Phylogenies: Understanding the Origin of Mitochondria and Chloroplasts 615 Discovering New Lineages via Direct Sequencing 617 28.3 What Themes Occur in the Diversification of Protists? 617 BOX 28.2 A Model Organism: Dictyostelium discoideum 618 Morphological Diversity 619 How Do Protists Find Food? 621 How Do Protists Move? 623 How Do Protists Reproduce? 626 28.4 Key Lineages of Protists 627 TTL3Diplomonadida 627 TTL3Parabasalida 628 TTL3Euglenida 628 Alveolata 629 TTL3Ciliata 629 TTL3Dinoflagellata 629 TTL3Apicomplexa 630 Stramenopila (Heterokonta) 630 TTL3Oomycota 630 TTL3Diatoms 631 TTL3Phaeophyta (Brown Algae) 631 Cercozoa 632 TTL3Foraminifera 632 Plantae 632 TTL3Rhodophyta (Red Algae) 633 Amoebozoa 633 TTL3Myxogastrida (Plasmodial Slime Molds) 633 ESSAY Revolutions in Science 634 CHAPTER REVIEW 634 Chapter 29 Green Plants 637 29.1 Why Do Biologists Study the Green Plants? 638 Plants Provide Ecosystem Services 638 Agricultural Research: Domestication and Selective Breeding 639 Plant-Based Fuels and Fibers 640 Bioprospecting 642 29.2 How Do Biologists Study Green Plants? 643 BOX 29.1 A Model Organism: Arabidopsis thaliana 643 Using the Fossil Record 645 Evaluating Molecular Phylogenies 647 29.3 What Themes Occur in the Diversification of Green Plants? 648 The Transition to Land, I: How Did Plants Adapt to Dry Conditions? 648 The Transition to Land, II: How Do Plants Reproduce in Dry Conditions? 651 The Angiosperm Radiation 658 29.4 Key Lineages of Green Plants 661 Green Algae 661 TTL3Ulvobionta 662 TTL3Coleochaetales 662 TTL3Charales (Stoneworts) 663 TTL3Hepaticophyta (Liverworts) 663 TTL3Anthocerophyta (Hornworts) 664 TTL3Bryophyta (Mosses) 664 Seedless Vascular Plants 665 TTL3Lycophyta (Lycophytes, or Club Mosses) 665 TTL3Psilotophyta (Whisk Ferns) 666 TTL3Sphenophyta (or Equisetophyta) (Horsetails) 666 TTL3Pteridophyta (Ferns) 667 Seed Plants 667 TTL3Gnetophyta (Gnetophytes) 668 TTL3Cycadophyta (Cycads) 668 TTL3Ginkgophyta (Ginkgoes) 669 TTL3Coniferophyta (Conifers) 669 TTL3Anthophyta (Angiosperms) 670 ESSAY Genetic Diversity in Crop Plants 671 CHAPTER REVIEW 672 Chapter 30 Fungi 674 30.1 Why Do Biologists Study Fungi? 675 Fungi Feed Land Plants 675 Fungi Speed the Carbon Cycle on Land 675 Fungi Have Important Economic Impacts 676 30.2 How Do Biologists Study Fungi? 677 Analyzing Morphological Traits 678 BOX 30.1 A Model Organism: Saccharomyces cerevisiae 679 Evaluating Molecular Phylogenies 680 Experimental Studies of Mutualism 682 30.3 What Themes Occur in the Diversification of Fungi? 684 Fungi Participate in Several Types of Mutualisms 684 Adaptations That Make Fungi Effective Decomposers 686 Variation in Life Cycles 687 30.4 Key Lineages of Fungi 690 TTL3Chytridiomycota (Chytrids) 691 TTL2Zygomycota TTL3Mucorales and Other Basal Lineages 691 TTL3Glomeromycota (AMF) 692 TTL3Basidiomycota (Club Fungi) 693 Ascomycota (Sac Fungi) 693 TTL2Ascomycota TTL3Lichen-Formers 693 TTL2Ascomycota TTL3Non-Lichen-Formers 694 ESSAY Why Are Frogs Dying? 695 CHAPTER REVIEW 695 Chapter 31 An Introduction to Animals 698 31.1 Why Do Biologists Study Animals? 699 31.2 How Do Biologists Study Animals? 700 Analyzing Comparative Morphology 700 BOX 31.1 A Model Organism: Hydra 702 Using the Fossil Record 708 Evaluating Molecular Phylogenies 708 31.3 What Themes Occur in the Diversification of Animals? 710 Feeding 710 Movement 713 Reproduction and Life Cycles 715 31.4 Key Lineages of Animals 718 TTL3Choanoflagellates (Collar Flagellates) 718 TTL3Porifera (Sponges) 719 TTL3Cnidaria (Jellyfish, Corals, Anemones, Hydroids, Sea Fans) 719 TTL3Ctenophora (Comb Jellies) 720 TTL3Acoelomorpha 721 ESSAY Coral Bleaching 721 CHAPTER REVIEW 722 Chapter 32 Protostome Animals 724 32.1 Why Do Biologists Study Protostomes? 725 BOX 32.1 Model Organisms: Caenorhabditis and Drosophila 725 Crustaceans and Mollusks Are Important Animals in Marine Ecosystems 726 Insects, Spiders, and Mites Are Important Animals in Terrestrial Ecosystems 726 32.2 How Do Biologists Study Protostomes? 728 Analyzing Morphological Traits 728 Using the Fossil Record 730 Evaluating Molecular Phylogenies 730 32.3 What Themes Occur in the Diversification of Protostomes? 731 Feeding 732 Movement 733 Reproduction and Life Cycles 734 32.4 Key Lineages: Lophotrochozoans 734 TTL3Rotifera (Rotifers) 735 TTL3Platyhelminthes (Flatworms) 736 TTL3Annelida (Segmented Worms) 737 Mollusca (Mollusks) 738 TTL2Mollusca TTL3Bivalvia (Clams, Mussels, Scallops, Oysters) 738 TTL2Mollusca TTL3Gastropoda (Snails, Slugs, Nudibranchs) 739 TTL2Mollusca TTL3Polyplacophora (Chitons) 739 TTL2Mollusca TTL3Cephalopoda (Squid, Nautilus, Octopuses) 740 32.5 Key Lineages: Ecdysozoans 740 TTL3Nematoda (Roundworms) 741 Arthropoda (Arthropods) 742 TTL2Arthropoda TTL3Myriapods (Millipedes, Centipedes) 742 TTL2Arthropoda TTL3Chelicerata (Spiders, Ticks, Mites, Horseshoe Crabs, Daddy Longlegs, Scorpions) 743 TTL2Arthropoda TTL3Insecta (Insects) 744 TTL2Arthropoda TTL3Crustaceans (Shrimp, Lobster, Crabs, Barnacles, Isopods, Copepods) 744 TTL3Arthropoda Crustaceans (Shrimp, Lobster, Crabs, Barnacles, Isopods, Copepods) 745 ESSAY The Role of Natural History in Biological Science 745 CHAPTER REVIEW 746 Chapter 33 Deuterostome Animals 749 33.1 Why Do Biologists Study Deuterostome Animals? 750 33.2 How Do Biologists Study Deuterostomes? 751 Analyzing Morphological Traits 751 Using the Fossil Record 753 Evaluating Molecular Phylogenies 755 33.3 What Themes Occur in the Diversification of Deuterostomes? 756 Feeding 756 BOX 33.1 Model Organisms: Sea Urchins, Zebrafish, and Mice 757 Movement 758 BOX 33.2 The Evolution of Flight in Birds 760 Reproduction 761 33.4 Key Lineages: Echinodermata 763 TTL2Echinodermata TTL3Asteroidea (Sea Stars) 764 TTL2Echinodermata TTL3Echinoidea (Sea Urchins and Sand Dollars) 764 33.5 Key Lineages: Chordata 765 TTL2Chordata TTL3Myxinoidea (Hagfish) and Petromyzontoidea (Lampreys) 765 TTL2Chordata TTL3Chondrichthyes (Sharks, Rays, Skates) 766 TTL2Chordata TTL3Actinopterygii (Ray-Finned Fishes) 766 TTL2Chordata TTL3Actinistia (Coelacanths) and Dipnoi (Lungfish) 767 TTL2Chordata TTL3Amphibia (Frogs, Salamanders, Caecilians) 768 Chordata: Mammalia (Mammals) 768 TTL1Chordata TTL2Mammalia TTL3Monotremata (Platypuses and Echidnas) 769 TTL1Chordata TTL2Mammalia TTL3Marsupiala (Marsupials) 769 TTL1Chordata TTL2Mammalia TTL3Eutheria (Placental Mammals) 770 Chordata: Reptilia (Turtles, Snakes and Lizards, Crocodiles, Birds) 770 TTL1Chordata TTL2Reptilia TTL3Testudinia (Turtles and Tortoises) 771 TTL1Chordata TTL2Reptilia TTL3Lepidosauria (Lizards, Snakes) 771 TTL1Chordata TTL2Reptilia TTL3Crocodilia (Crocodiles, Alligators) 772 TTL1Chordata TTL2Reptilia TTL3Aves (Birds) 772 33.6 Key Lineages: The Hominin Radiation 773 The Primates 773 Fossil Humans 774 The Out-of-Africa Hypothesis 776 ESSAY So Human an Animal 777 CHAPTER REVIEW 778 CHAPTER REVIEW Chapter 34 Viruses 780 34.1 Why Do Biologists Study Viruses? 781 Recent Viral Epidemics in Humans 781 Current Viral Epidemics in Humans: HIV 782 34.2 How Do Biologists Study Viruses? 783 Analyzing Morphological Traits 784 BOX 34.1 How Are Vaccines Developed? 785 Analyzing the Phases of the Lytic Cycle 788 BOX 34.2 HIV Drug Cocktails and the Evolution of Drug Resistance 792 34.3 What Themes Occur in the Diversification of Viruses? 793 The Nature of the Viral Genetic Material 793 Where Did Viruses Come From? 794 Emerging Viruses, Emerging Diseases 794 BOX 34.3 Where Did HIV Originate? 795 34.4 Key Lineages of Viruses 796 TTL3Double-Stranded DNA (dsDNA) Viruses 797 TTL3RNA Reverse-Transcribing Viruses (Retroviruses) 797 TTL3Double-Stranded RNA (dsRNA) Viruses 798 TTL3Negative-Sense Single-Stranded RNA ([_]ssRNA) Viruses 798 TTL3Positive-Sense Single-Stranded RNA ([+]ssRNA) Viruses 799 ESSAY The SARS Outbreak 799 CHAPTER REVIEW 800 UNIT 7 How Plants Work 803 Chapter 35 Plant Form and Function 804 35.1 The Diversity of Plant Form 805 The Diversity of Roots: North American Prairie Plants 806 The Diversity of Shoots: Hawaiian Silverswords 807 35.2 Plant Cells and Tissues 811 The Diversity of Plant Cells 812 BOX 35.1 Plant Poisons and the Cost of Defense 813 The Diversity of Plant Tissues 815 35.3 The Anatomy of Plant Growth 818 Primary Growth: The Root System 819 Primary Growth: The Shoot System 820 BOX 35.2 Tree-Ring Studies 824 ESSAY Wood as a Structural Material 825 CHAPTER REVIEW 825 Chapter 36 Water and Sugar Transport in Plants 828 36.1 Water Potential and Cell-to-Cell Movement 829 What Factors Affect Water Potential? 829 Calculating Water Potential 830 Water Potentials in Soils, Plants, and the Atmosphere 830 BOX 36.1 How Do Plants Adapt to Dry Soils? 832 BOX 36.2 How Do Plants Adapt to Salty Soils? 833 36.2 Root Pressure and Short-Distance Transport 834 36.3 Transpiration and Long-Distance Water Transport 835 The Cohesion-Tension Theory 836 Water Absorption and Water Loss 841 36.4 Translocation 842 The Anatomy of Phloem 843 The Pressure-Flow Hypothesis 844 Phloem Loading 845 BOX 36.3 How Are Solutes Transported across Membranes? 845 Phloem Unloading 848 ESSAY Irrigated Agriculture 849 CHAPTER REVIEW 849 Chapter 37 Plant Nutrition 852 37.1 Nutritional Requirements 853 Essential Nutrients 853 Nutrient Deficiencies 855 37.2 Soil 856 Soil Conservation 856 Nutrient Availability 858 37.3 Nutrient Uptake 859 Mechanisms of Nutrient Uptake 859 Mechanisms of Ion Exclusion 861 BOX 37.1 Can Phytoremediation Help Clean Up Contaminated Soils? 862 37.4 Nitrogen Fixation 863 How Do Nitrogen-Fixing Bacteria Colonize Plant Roots? 863 How Do Host Plants Respond to Contact from a Symbiotic Bacterium? 863 37.5 Nutritional Adaptations of Plants 864 Epiphytic Plants 865 Parasitic Plants 865 Carnivorous Plants 867 BOX 37.2 Why Are Bogs So Nutrient Poor? 867 ESSAY Tropical Soils 868 CHAPTER REVIEW 869 Chapter 38 Sensory Systems in Plants 871 38.1 Sensing Light 872 What Do Plants See? 872 How Do Plants See? 875 From Perception to Response: Signal Transduction 877 38.2 Gravity Perception 878 The Statolith Hypothesis 878 Is the Gravity Sensor a Transmembrane Protein? 879 38.3 How Do Plants Respond to Wind and Touch? 879 An Introduction to Electrical Signaling 880 Action Potentials 881 How Does the Venus Flytrap Close? 881 38.4 How Do Plants Sense Attacks by Parasites? 882 The Gene-for-Gene Hypothesis 882 Why Do So Many Resistance Genes Exist? 883 ESSAY Can Plants Tell Time? 885 CHAPTER REVIEW 886 Chapter 39 Communication: Chemical Signals 888 39.1 Plant Hormones_An Overview 888 39.2 Auxin and Phototropism 891 The Cholodny-Went Hypothesis 891 Isolating and Characterizing Auxin 892 How Does Auxin Produce the Phototropic Response? 893 39.3 Auxin and Apical Dominance 894 Polar Transport of Auxin 895 An Overview of Auxin Action 896 39.4 Cytokinins and Cell Division 896 BOX 39.1 The Use of Hormones to Grow Plant Cells in Culture 897 39.5 Gibberellins and ABA: Growth and Dormancy 898 Gibberellins Stimulate Shoot Elongation 898 Gibberellins and ABA Interact during Seed Dormancy and Germination 899 ABA Closes Guard Cells in Stomata 901 39.6 Ethylene and Senescence 902 39.7 Salicylic Acid, Systemin, and Pheromones: Defense Signals 904 Salicylic Acid Extends the Hypersensitive Response to Pathogens 904 Systemin Leads to the Production of Insecticides 905 Pheromones Released from Wounds Recruit Help from Wasps 906 ESSAY Hormones as Herbicides 907 CHAPTER REVIEW 907 Chapter 40 Plant Reproduction 910 40.1 An Introduction to Plant Reproduction 911 Sexual Reproduction 911 Plant Life Cycles 912 Asexual Reproduction 912 40.2 Reproductive Structures 914 When Does Flowering Occur? 914 The General Structure of the Flower 915 Producing the Female Gametophyte 915 BOX 40.1 Is There a Flowering Hormone? 916 Producing the Male Gametophyte 918 40.3 Pollination and Fertilization 919 Pollination 919 BOX 40.2 Selfing, Outcrossing, and Self-Incompatibility 920 Fertilization 922 40.4 The Seed 923 Embryogenesis 923 The Role of Drying in Seed Maturation 924 BOX 40.3 Pure and Applied Science 924 Fruit Development and Seed Dispersal 925 Seed Dormancy 925 Seed Germination 927 ESSAY Why Do Wasps Try to Mate with Hammer Orchids? 929 CHAPTER REVIEW 930 UNIT 8 How Animals Work 933 Chapter 41 Animal Form and Function 934 41.1 Form, Function, and Adaptation 935 Trade-Offs 935 41.2 Tissues, Organs, and Systems: How Does Structure Correlate with Function? 937 Tissues 937 Organs and Systems 939 41.3 How Does Body Size Affect Animal Physiology? 940 Surface Area/Volume Relationships 941 Do All Aspects of an Animal_s Body Increase in Size Proportionately? 944 41.4 Homeostasis 945 Regulation and Feedback 946 41.5 How Do Animals Regulate Body Temperature? 947 Gaining and Losing Heat 947 BOX 41.1 A Closer Look at Torpor and Hibernation 949 Ectothermy Versus Endothermy 951 ESSAY Is Fever Adaptive? 952 CHAPTER REVIEW 952 Chapter 42 Water and Electrolyte Balance in Animals 955 42.1 Osmoregulation and Osmotic Stress 956 42.2 Water and Electrolyte Balance in Aquatic Environments 958 How Do Sharks Osmoregulate? 958 BOX 42.1 Passive and Active Transport: A Quick Review 959 How Do Salmon Osmoregulate? 960 42.3 Water and Electrolyte Balance in Terrestrial Insects 962 How Do Insects Minimize Water Loss from the Body Surface? 962 Types of Nitrogenous Wastes: Impact on Water Balance 963 Maintaining Homeostasis: The Excretory System 963 42.4 Water and Electrolyte Balance in Terrestrial Vertebrates 965 The Structure of the Kidney 966 Filtration: The Renal Corpuscle 966 Reabsorption: The Proximal Tubule 968 Creating an Osmotic Gradient: The Loop of Henle 969 Regulating Water and Electrolyte Balance: The Distal Tubule and the Collecting Duct 972 ESSAY Life in the Desert 973 CHAPTER REVIEW 974 Chapter 43 Animal Nutrition 977 43.1 Nutritional Requirements 978 Meeting Basic Needs 978 Nutrition and Athletic Performance 979 43.2 Obtaining Food: The Structure and Function of Mouthparts 981 43.3 How Are Nutrients Digested and Absorbed? 983 The Mouth and Esophagus 985 The Stomach 986 The Small Intestine 989 The Large Intestine 993 43.4 Nutritional Homeostasis_Glucose as a Case Study 993 Insulin_s Role in Homeostasis 994 The Type II Diabetes Mellitus Epidemic 995 ESSAY Cholesterol, Diet, and Disease 996 CHAPTER REVIEW 997 Chapter 44 Gas Exchange and Circulation 999 44.1 Air and Water as Respiratory Media 999 How Do Oxygen and Carbon Dioxide Behave in Air? 1000 How Do Oxygen and Carbon Dioxide Behave in Water? 1001 44.2 Organs of Gas Exchange 1002 Design Parameters: The Law of Diffusion 1002 How Do Gills Work? 1003 How Do Trachae Work? 1004 How Do Lungs Work? 1005 BOX 44.1 Respiratory Distress Syndrome in Premature Infants 1008 Homeostatic Control of Ventilation 1009 44.3 Blood 1009 Oxygen Delivery: The Bohr Effect 1010 CO2 Transport and the Buffering of Blood pH 1011 Homeostatic Control of Oxygen-Carrying Capacity 1012 BOX 44.2 Blood Doping and Erthryopoeitin Abuse by Athletes 1013 44.4 The Circulatory System 1013 Open Circulatory Systems 1014 Closed Circulatory Systems 1014 The Heart 1016 Regulation of Blood Pressure and Blood Flow 1020 BOX 44.3 Hypertension and the Measurement of Blood Pressure 1021 ESSAY Smoking and Lung Function 1023 CHAPTER REVIEW 1024 Chapter 45 Electrical Signals in Animals 1026 45.1 Principles of Electrical Signaling 1027 The Anatomy of a Neuron 1027 An Introduction to Membrane Potentials 1028 The Resting Potential 1029 Using the Nernst and Goldman Equations 1030 Using Microelectrodes to Measure Membrane Potentials 1031 What Is an Action Potential? 1032 45.2 Dissecting the Action Potential 1032 Distinct Ion Currents Are Responsible for Depolarization and Repolarization 1033 Voltage-Gated Channels 1033 The Role of the Sodium-Potassium Pump 1035 How Is the Action Potential Propagated? 1036 45.3 The Synapse 1038 What Do Neurotransmitters Do? 1039 Postsynaptic Potentials and Summation 1041 What Happens When Ligand-Gated Channels Are Defective? 1042 45.4 The Vertebrate Nervous System 1044 A Closer Look at the Peripheral Nervous System 1044 Functional Anatomy of the CNS 1044 How Does Memory Work? 1047 ESSAY Can Brain Tissue Transplants Help People with Parkinson_s Disease? 1049 CHAPTER REVIEW 1050 Chapter 46 Animal Sensory Systems and Movement 1052 46.1 How Do Sensory Organs Convey Information to the Brain? 1053 Sensory Transduction 1053 BOX 46.1 Senses That Humans Don_t Have 1054 Transmitting Information to the Brain 1055 46.2 Hearing 1055 How Do Sensory Cells Respond to Sound Waves and Other Forms of Pressure? 1055 The Mammalian Ear 1056 Sensory Worlds: What Do Other Animals Hear? 1058 46.3 Vision 1059 The Vertebrate Eye 1060 BOX 46.2 Vertebrate versus Cephalopod Eyes 1061 Sensory Worlds: Do Other Animals See Color? 1063 46.4 Taste and Smell 1064 Taste: Detecting Molecules in the Mouth 1064 Olfaction: Detecting Molecules in the Air 1065 46.5 Movement 1066 Skeletons 1066 How Do Muscles Contract? 1067 ESSAY Sprinters and Marathoners_Born or Made? 1073 CHAPTER REVIEW 1074 Chapter 47 Chemical Signals in Animals 1076 47.1 Cataloging Hormone Structure and Function 1077 How Do Researchers Identify a Hormone? 1078 Chemical Characteristics of Hormones 1079 The Human Endocrine System_An Overview 1080 47.2 What Do Hormones Do? 1081 How Do Hormones Coordinate Responses to Environmental Change? 1081 BOX 47.1 A Closer Look at Thyroxine and the Thyroid Gland 1082 How Do Hormones Direct Developmental Processes? 1083 How Are Hormones Involved in Homeostasis? 1084 BOX 47.2 Is Human Obesity Caused by Leptin Deficiency? 1087 47.3 How Is the Production of Hormones Regulated? 1088 The Hypothalamus and Pituitary Gland 1088 Control of Epinephrine by Sympathetic Nerves 1091 47.4 How Do Hormones Act on Target Cells? 1091 Steroid Hormones and Intracellular Receptors 1091 Hormones That Bind to Cell-Surface Receptors 1092 ESSAY Do Humans Produce Pheromones? 1096 CHAPTER REVIEW 1097 Chapter 48 Animal Reproduction 1099 48.1 Asexual and Sexual Reproduction 1100 Mechanisms of Asexual Reproduction 1100 Switching Reproductive Modes: A Case History 1100 Mechanisms of Sexual Reproduction: Gametogenesis 1101 48.2 Fertilization and Egg Development 1102 External Fertilization 1102 Internal Fertilization and Sperm Competition 1103 BOX 48.1 Unusual Aspects of Fertilization 1103 Oviparity and Viviparity 1105 48.3 Reproductive Structures and Their Functions 1105 The Male Reproductive System 1106 The Female Reproductive System 1108 48.4 The Role of Sex Hormones in Mammalian Reproduction 1109 Puberty 1109 BOX 48.2 Abuse of Synthetic Steroids 1110 Female Sex Hormones and the Menstrual Cycle 1111 48.5 Human Pregnancy and Birth 1113 Major Events during Pregnancy 1114 How Does the Mother Nourish the Fetus? 1115 Birth 1116 ESSAY Contraception 1117 CHAPTER REVIEW 1118 Chapter 49 The Immune System in Animals 1120 49.1 Innate Immunity 1121 Barriers to Entry 1121 The Innate Immune Response 1122 49.2 The Acquired Immune Response: Recognition 1124 An Introduction to Lymphocytes and the Immune System 1124 The Discovery of B Cells and T Cells 1125 Antigen Recognition and Clonal Selection 1125 BOX 49.1 How Are Monoclonal Antibodies Produced? 1128 How Does the Immune System Distinguish Self from Nonself? 1132 49.3 The Acquired Immune Response: Activation 1132 Antigen Presentation by MHC Proteins: Activating T Cells 1132 B-Cell Activation and Antibody Secretion 1134 Antigen Presentation by Infected Cells: A Signal for Action by CD8+ T Cells 1134 49.4 The Acquired Immune Response: Culmination 1135 Killing Bacteria 1135 Destroying Viruses 1135 Why Does the Immune System Reject Foreign Tissues and Organs? 1136 Responding to Future Infections: Immunological Memory 1137 BOX 49.2 The ELISA Test 1138 ESSAY Allergies 1139 CHAPTER REVIEW 1140 UNIT 9 Ecology 1143 Chapter 50 An Introduction to Ecology 1144 50.1 Areas of Ecological Study 1145 Organismal Ecology 1145 Population Ecology 1145 Community Ecology 1146 Ecosystem Ecology 1146 How Do Ecology and Conservation Efforts Interact? 1146 50.2 The Nature of the Environment 1146 Climate 1147 50.3 Types of Terrestrial and Aquatic Ecosystems 1149 Terrestrial Biomes 1150 BOX 50.1 Thermoclines and Lake Turnover 1157 BOX 50.2 Deep-Sea Life 1160 50.4 Biogeography 1160 The Role of History 1161 Biotic Factors 1161 Abiotic Factors 1162 ESSAY Battling Invasive Species 1164 CHAPTER REVIEW 1164 Chapter 51 Behavior 1166 51.1 Types of Behavior_An Overview 1167 Fixed Action Patterns 1168 BOX 51.1 A Closer Look at Behavior Genetics 1169 Conditional Strategies 1171 51.2 Learning 1172 Simple Types of Learning: Classical Conditioning and Imprinting 1172 More Complex Types of Learning: Birdsong 1173 Can Animals Think? 1174 What Is the Adaptive Significance of Learning? 1175 51.3 How Animals Act: Hormonal Control 1177 51.4 Communication 1178 Modes of Communication 1179 A Case History: The Honeybee Dance 1180 Honesty and Deceit in Communication 1181 51.5 Orientation, Navigation, and Migration 1183 Migration: Why Do Animals Move with a Change of Seasons? 1184 Navigation: How Do Animals Find Their Way? 1184 51.6 The Evolution of Self-Sacrificing Behavior 1185 Do Organisms Do Things for the Good of the Species? 1186 BOX 51.2 Calculating the Coefficient of Relatedness 1187 Reciprocal Altruism 1188 ESSAY Children at Risk 1189 CHAPTER REVIEW 1190 Chapter 52 Population Ecology 1192 52.1 Demography 1193 Life Tables 1193 The Role of Life History 1195 BOX 52.1 Using Life Tables to Calculate Population Growth Rates 1196 52.2 Population Growth 1196 Exponential Growth 1196 Logistic Growth 1197 BOX 52.2 Developing and Applying Population Growth Equations: A Closer Look 1197 What Limits Growth Rates and Population Sizes? 1200 52.3 Population Dynamics 1201 Population Cycles: The Case of the Red Grouse 1201 Age Structure 1203 Analyzing Change in the Growth Rate of Human Populations 1205 52.4 How Can Population Ecology Help Endangered Species? 1206 Preserving Metapopulations 1206 BOX 52.3 Mark-Recapture Studies 1208 Using Life-Table Data to Make Population Projections 1208 Population Viability Analysis 1210 ESSAY What Limits Human Population Growth? 1211 CHAPTER REVIEW 1211 Chapter 53 Community Ecology 1214 53.1 Species Interactions 1214 Competition 1215 Consumption 1220 Mutualism 1227 53.2 Community Structure 1229 Clements and Gleason: Two Views of Community Dynamics 1229 Disturbance and Change in Ecological Communities 1231 What Disturbances Occur, and How Frequent and Severe Are They? 1232 Succession: The Development of Communities after Disturbance 1233 53.3 Species Diversity in Ecological Communities 1236 Global Patterns in Species Diversity 1236 BOX 53.1 Measuring Species Diversity 1237 The Role of Diversity in Ecological Communities 1238 ESSAY Let-It-Burn Policies 1240 CHAPTER REVIEW 1241 Chapter 54 Ecosystems 1243 54.1 Energy Flow and Trophic Structure 1244 Global Patterns in Productivity 1244 How Does Energy Flow through an Ecosystem? 1247 Analyzing Energy Flow: A Case History 1251 54.2 Biogeochemical Cycles 1252 Biogeochemical Cycles in Ecosystems 1253 Global Biogeochemical Cycles 1255 54.3 Human Impacts on Ecosystems 1258 Global Warming 1259 ESSAY Phosphate Pollution, Acid Rain, and the Ozone Hole: Hope for Ecosystem Recovery? 1261 CHAPTER REVIEW 1262 Chapter 55 Biodiversity and Conservation 1265 55.1 What Is Biodiversity? 1266 Biodiversity Can Be Measured and Analyzed at Several Levels 1266 Why Is Biodiversity Important? 1267 55.2 How Do Biologists Study Biodiversity? 1268 Quantifying Genetic Diversity 1268 Estimating the Total Number of Species Living Today 1268 Steps in Understanding Biodiversity 1269 Biodiversity and Ecosystem Function 1270 55.3 Threats to Biodiversity 1272 Humans Have Affected Biodiversity throughout History 1272 Current Threats to Biodiversity 1275 How Can Biologists Predict Future Extinction Rates? 1277 55.4 Conserving Biodiversity: Biology, Sociology, Economics, and Politics 1277 The Role of Governmental and Private Agencies 1278 Conservation Strategies 1279 Looking to the Future 1279 ESSAY Models for the Future: The Malpai Borderlands and Guanacaste 1280 CHAPTER REVIEW 1281 Appendix A-1 Glossary G- 1 Credits C-1 Index I-1

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[Solved] Biological Science, Canadian Edition., 2e (Freeman et al.) UPDATED VERSION

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Contents Chapter 1 Biology and the Tree of Life 1 1.1 The Cell Theory 2 Are All Organisms Made of Cells? 2 Where Do Cells Come From? 2 1.2 The Theory of Evolution by Natural Selection 4 What Is Evolution? 4 What Is Natural Selection? 4 1.3 The Tree of Life 5 Linnaean Taxonomy 6 BOX 1.1 Scientific Names and Terms 6 Using Molecules to Understand the Tree of Life 8 1.4 Doing Biology 10 Why Do Giraffes Have Long Necks? An Introduction to Hypothesis Testing 10 Why Are Chili Peppers Hot? An Introduction to Experimental Design 12 ESSAY Where Do Humans Fit on the Tree of Life? 15 CHAPTER REVIEW 16 UNIT 1 The Origin and Early Evolution of Life 19 Chapter 2 The Atoms and Molecules of Ancient Earth 20 2.1 The Ancient Earth 20 Studying the Formation of Planets 21 When Did Chemical Evolution Take Place? 21 2.2 The Building Blocks of Chemical Evolution 24 What Atoms Are Found in Organisms? 24 How Does Covalent Bonding Hold Molecules Together? 24 How Does Ionic Bonding Hold Molecules Together? 26 Some Simple Molecules Formed from H, C, N, and O 27 2.3 Chemical Reactions, Chemical Evolution, and Chemical Energy 29 How Do Chemical Reactions Happen? 30 What Is Energy? 30 Chemical Evolution: A Model System 32 How Did Chemical Energy Change during Chemical Evolution? 34 2.4 The Composition of the Early Atmosphere: Redox Reactions and the Importance of Carbon 35 What Is a Redox Reaction? 35 BOX 2.1 Some Other Approaches to Understanding Redox Reactions 36 What Happens When Carbon Is Reduced? 36 The Early Oceans and the Properties of Water 39 Why Is Water Such an Efficient Solvent? 39 How Does Water_s Structure Correlate with Its Properties? 40 Acid-Base Reactions and pH 41 What Was Water_s Role in Chemical Evolution? 42 ESSAY The Search for Extraterrestrial Life 43 CHAPTER REVIEW 44 Chapter 3 Protein Structure and Function 46 3.1 Early Origin-of-Life Experiments 47 BOX 3.1 Was Miller Correct about Conditions on Ancient Earth? 48 3.2 Amino Acids and Polymerization 48 The Structure of Amino Acids 49 How Do Amino Acids Link to Form Proteins? 53 3.3 What Do Proteins Look Like? 56 Primary Structure 57 Secondary Structure 57 Tertiary Structure 58 Quaternary Structure 59 Folding and Function 60 BOX 3.2 Prions 62 3.4 What Do Proteins Do? 62 Proteins Have Diverse Functions in Cells 62 An Introduction to Catalysis 63 How Do Enzymes Work? 64 Was the First Living Entity a Protein? 70 ESSAY Molecular Handedness and the Thalidomide Tragedy 70 CHAPTER REVIEW 71 Chapter 4 Nucleic Acids and the RNA World 74 4.1 What Is a Nucleic Acid? 75 Could Chemical Evolution Result in the Production of Nucleotides? 76 How Do Nucleotides Polymerize to Form Nucleic Acids? 76 BOX 4.1 Gel Electrophoresis and Autoradiography 78 4.2 DNA Structure and Function 79 BOX 4.2 An Introduction to X-Ray Crystallography 80 DNA Is an Information-Containing Molecule 82 Is DNA a Catalytic Molecule? 82 4.3 RNA Structure and Function 83 RNA as an Information-Containing Molecule 84 Is RNA a Catalytic Molecule? 85 4.4 The First Life-Form 85 ESSAY The Human Side of Research 87 CHAPTER REVIEW 88 Chapter 5 An Introduction to Carbohydrates 90 5.1 Sugars as Monomers 91 5.2 The Structure of Polysaccharides 92 BOX 5.1 Lactose Intolerance and Galactosemia 93 Starch: A Storage Polysaccharide in Plants 94 Glycogen: A Highly Branched Storage Polysaccharide in Animals 95 Cellulose: A Structural Polysaccharide in Plants 95 Chitin: A Structural Polysaccharide in Animals 96 Peptidoglycan: A Structural Polysaccharide in Bacteria 96 Polysaccharides and Chemical Evolution 96 BOX 5.2 How Do the Penicillins and Cephalosporins Kill Bacteria? 96 5.3 What Do Carbohydrates Do? 97 The Role of Carbohydrates in Cell Identity 97 The Role of Carbohydrates in Energy Production and Storage 98 Carbohydrates as Structural Molecules 99 ESSAY Why Do We Have a Sweet Tooth? 101 CHAPTER REVIEW 101 Chapter 6 Lipids, Membranes, and the First Cells 103 6.1 Lipids 104 BOX 6.1 Electron Microscopy 104 What Is a Lipid? 106 A Look at Three Types of Lipids Found in Cells 106 The Structures of Membrane Lipids 108 6.2 Phospholipid Bilayers 109 Artificial Membranes as an Experimental System 109 Selective Permeability of Lipid Bilayers 110 Does the Type of Lipid in a Membrane Affect Its Permeability? 111 Why Does Temperature Affect the Fluidity and Permeability of Membranes? 112 6.3 Why Molecules Move across Lipid Bilayers: Diffusion and Osmosis 113 6.4 Membrane Proteins 116 Systems for Studying Membrane Proteins 118 How Do Membrane Proteins Affect Ions and Molecules? 118 ESSAY The Molecular Basis of Cystic Fibrosis 123 CHAPTER REVIEW 125 UNIT 2 Cell Structure and Function 127 Chapter 7 Inside the Cell 128 7.1 What_s Inside the Cell? 129 Prokaryotic Cells 129 Eukaryotic Cells 131 How Does Cell Structure Correlate with Function? 138 The Dynamic Cell 139 BOX 7.1 How Does a Centrifuge Work? 140 BOX 7.2 Techniques for Studying the Dynamic Cell 141 7.2 The Nuclear Envelope: Transport Into and Out of the Nucleus 142 How Are Molecules Imported into the Nucleus? 143 How Are Molecules Exported from the Nucleus? 144 7.3 The Endomembrane System: Manufacturing and Shipping Proteins 145 Entering the Endomembrane System: The Signal Hypothesis 146 Getting from the ER to the Golgi 147 What Happens Inside the Golgi Apparatus? 147 How Are Products Shipped from the Golgi? 148 7.4 The Dynamic Cytoskeleton 149 Actin Filaments 150 Intermediate Filaments 151 Microtubules 152 Cilia and Flagella: Moving the Entire Cell 154 ESSAY Organelles and Human Disease 156 CHAPTER REVIEW 156 Chapter 8 Cell-Cell Interactions 159 8.1 The Cell Surface 160 The Structure and Function of an Extracellular Layer 160 The Plant Cell Wall 160 The Extracellular Matrix in Animals 162 BOX 8.1 What Happens When the Extracellular Matrix Is Defective? 163 8.2 How Do Adjacent Cells Connect and Communicate? 163 Cell-Cell Attachments 165 Cell-Cell Gaps 169 8.3 How Do Distant Cells Communicate? 170 Signal Reception 170 Signal Processing 171 Signal Response 172 Signal Deactivation 174 ESSAY How Do ViagraÀ, LevitraÀ, and CialisÀ Work? 175 CHAPTER REVIEW 174 Chapter 9 Cellular Respiration and Fermentation 177 9.1 An Overview of Cellular Respiration 178 The Nature of Chemical Energy and Redox Reactions 179 Using Redox Reactions to Produce ATP 180 Processing Glucose: Glycolysis 180 The Krebs Cycle 180 Electron Transport 182 Methods of Producing ATP 182 9.2 Glycolysis 183 A Closer Look at the Glycolytic Reactions 183 How Is Glycolysis Regulated? 184 9.3 The Krebs Cycle 186 Converting Pyruvate to Acetyl CoA 187 How Is the Krebs Cycle Regulated? 188 What Happens to the NADH and FADH2? 190 9.4 Electron Transport and Chemiosmosis 190 Components of the Electron Transport Chain 191 The Chemiosmotic Hypothesis 192 How Is the Electron Transport Chain Organized? 193 The Discovery of ATP Synthase 194 Oxidative Phosphorylation 194 9.5 Fermentation 196 9.6 How Does Cellular Respiration Interact with Other Metabolic Pathways? 197 Processing Proteins and Fats as Fuel 197 Anabolic Pathways Synthesize Key Molecules 198 ESSAY ATP Production during Exercise 199 CHAPTER REVIEW 199 Chapter 10 Photosynthesis 202 10.1 An Overview of Photosynthesis 203 Photosynthesis: Two Distinct Sets of Reactions 203 The Structure of the Chloroplast 204 BOX 10.1 Types of Plastids 205 10.2 How Does Chlorophyll Capture Light Energy? 206 Photosynthetic Pigments Absorb Light 206 BOX 10.2 How Do Researchers Measure Absorption Spectra? 207 When Light Is Absorbed, Electrons Enter an Excited State 209 10.3 The Discovery of Photosystems I and II 211 How Does Photosystem II Work? 212 How Does Photosystem I Work? 214 The Z Scheme: Photosystems I and II Work Together 215 10.4 How Is Carbon Dioxide Reduced to Produce Glucose? 217 The Calvin Cycle 217 The Discovery of Rubisco 219 How Is Carbon Dioxide Delivered to Rubisco? 220 What Happens to the Sugar That Is Produced by Photosynthesis? 222 ESSAY Are Rising CO2 Levels in the Atmosphere Affecting the Rate of Photosynthesis? 224 CHAPTER REVIEW 225 Chapter 11 The Cell Cycle 227 11.1 Mitosis and the Cell Cycle 228 The Cell Cycle 229 When Does Chromosome Replication Occur? 229 The Discovery of the Gap Phases 230 BOX 11.1 Cell- Culture Methods 231 BOX 11.2 How Do Bacteria Divide? 232 11.2 How Does Mitosis Take Place? 232 Events in Mitosis 232 Cytokinesis 235 How Do Chromosomes Move during Mitosis? 237 11.3 Control of the Cell Cycle 238 The Discovery of Cell-Cycle Regulatory Molecules 238 Cell-Cycle Checkpoints 240 11.4 Cancer: Out-of-Control Cell Division 241 Properties of Cancer Cells 242 Cancer Involves Loss of Cell-Cycle Control 242 ESSAY Cancer Chemotherapy 244 CHAPTER REVIEW 245 UNIT 3 Gene Structure and Expression 247 Chapter 12 Meiosis 248 12.1 How Does Meiosis Occur? 249 BOX 12.1 Karyotyping Techniques 250 An Overview of Meiosis 252 The Phases of Meiosis I 253 The Phases of Meiosis II 255 A Closer Look at Key Events in Prophase of Meiosis I 257 12.2 The Consequences of Meiosis 258 Chromosomes and Heredity 258 How Does the Separation and Distribution of Homologous Chromosomes Produce Genetic Variation? 258 The Role of Crossing Over 259 How Does Fertilization Affect Genetic Variation? 259 12.3 Why Does Meiosis Exist? Why Sex? 260 The Paradox of Sex 261 When Do Meiosis and Fertilization Occur during the Life of an Organism? 263 12.4 Mistakes in Meiosis 264 How Do Mistakes Occur? 264 Why Do Mistakes Occur? 265 ESSAY Seedless Fruits 266 CHAPTER REVIEW 267 Chapter 13 Mendel and the Gene 269 13.1 Mendel_s Experiments with a Single Trait 270 What Questions Was Mendel Trying to Answer? 270 Garden Peas Serve as the First Model Organism in Genetics 270 Inheritance of a Single Trait 272 The Nature and Behavior of the Hereditary Determinants 273 BOX 13.1 Why Do Punnett Squares Work? 275 Testing the Model 275 13.2 Mendel_s Experiments with Two Traits 276 BOX 13.2 Sample Size and Chance Fluctuations 278 Using a Testcross to Confirm Predictions 278 Mendel_s Contributions to the Study of Heredity 279 13.3 The Chromosome Theory of Inheritance 279 13.4 Testing and Extending the Chromosome Theory 281 The Discovery of Sex-Linked Traits 281 The Discovery of Sex Chromosomes 281 X-Linked Inheritance and the Chromosome Theory 282 What Happens When Genes Are Located on the Same Chromosome? 283 13.5 Extending Mendel_s Rules 287 Incomplete Dominance and Codominance 288 Multiple Alleles and Polymorphic Traits 289 Pleiotropy 289 Genes Are Affected by the Physical Environment and Genetic Environment 290 Organelle Genomes 291 Quantitative Traits 291 13.6 Applying Mendel_s Rules to Humans 294 Are Alleles Recessive or Dominant? 294 Is the Trait Autosomal or Sex-Linked? 295 ESSAY Does "Genetic Determinism" Exist? 297 CHAPTER REVIEW 298 Chapter 14 DNA Synthesis 303 14.1 DNA as the Hereditary Material 304 Is DNA the Genetic Material? 305 14.2 Testing Early Hypotheses about DNA Replication 307 The Meselson-Stahl Experiment 308 The Discovery of DNA Polymerase 310 14.3 A Comprehensive Model for DNA Synthesis 311 Opening the Helix 312 Synthesis of the Leading Strand 313 Synthesis of the Lagging Strand 313 14.4 Replicating the Ends of Linear Chromosomes 316 14.5 Repairing Mistakes in DNA Synthesis 318 How Is DNA Polymerase Proofread? 318 Mismatch Repair 319 14.6 Repairing Damaged DNA 320 DNA Nucleotide Excision Repair: An Overview 320 Xeroderma Pigmentosum: A Case Study 321 ESSAY DNA Mismatch Repair and Cancer 322 CHAPTER REVIEW 323 Chapter 15 How Genes Work 325 15.1 What Do Genes Do? 326 The Molecular Basis of Hereditary Diseases 326 Genes and Enzymes 326 15.2 The Genetic Code 328 RNA as the Intermediary between Genes and Proteins 329 How Long Is a Word in the Genetic Code? 330 How Did Researchers Crack the Code? 332 BOX 15.1 The Evolution of the Genetic Code 333 15.3 The Central...
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