Biology

Cover......Page 1
Title Page......Page 2
Copyright......Page 3
Contents......Page 22
1.1 The Science of Life......Page 30
1.2 The Nature of Science......Page 33
1.3 An Example of Scientific Inquiry: Darwin and Evolution......Page 37
1.4 Unifying Themes in Biology......Page 41
2 The Nature of Molecules and the Properties of Water......Page 46
2.1 The Nature of Atoms......Page 47
2.2 Elements Found in Living Systems......Page 51
2.3 The Nature of Chemical Bonds......Page 52
2.4 Water: A Vital Compound......Page 54
2.5 Properties of Water......Page 57
2.6 Acids and Bases......Page 58
3 The Chemical Building Blocks of Life......Page 62
3.1 Carbon: The Framework of Biological Molecules......Page 63
3.2 Carbohydrates: Energy Storage and Structural Molecules......Page 67
3.3 Nucleic Acids: Information Molecules......Page 70
3.4 Proteins: Molecules with Diverse Structures and Functions......Page 73
3.5 Lipids: Hydrophobic Molecules......Page 82
4.1 Cell Theory......Page 88
4.2 Prokaryotic Cells......Page 92
4.3 Eukaryotic Cells......Page 94
4.4 The Endomembrane System......Page 98
4.5 Mitochondria and Chloroplasts: Cellular Generators......Page 102
4.6 The Cytoskeleton......Page 104
4.7 Extracellular Structures and Cell Movement......Page 108
4.8 Cell-to-Cell Interactions......Page 111
5.1 The Structure of Membranes......Page 117
5.2 Phospholipids: The Membrane’s Foundation......Page 121
5.3 Proteins: Multifunctional Components......Page 122
5.4 Passive Transport Across Membranes......Page 125
5.5 Active Transport Across Membranes......Page 128
5.6 Bulk Transport by Endocytosis and Exocytosis......Page 131
6 Energy and Metabolism......Page 136
6.1 The Flow of Energy in Living Systems......Page 137
6.2 The Laws of Thermodynamics and Free Energy......Page 138
6.3 ATP: The Energy Currency of Cells......Page 141
6.4 Enzymes: Biological Catalysts......Page 142
6.5 Metabolism: The Chemical Description of Cell Function......Page 146
7 How Cells Harvest Energy......Page 151
7.1 Overview of Respiration......Page 152
7.2 Glycolysis: Splitting Glucose......Page 156
7.3 The Oxidation of Pyruvate to Produce Acetyl-CoA......Page 159
7.4 The Krebs Cycle......Page 160
7.5 The Electron Transport Chain and Chemiosmosis......Page 163
7.6 Energy Yield of Aerobic Respiration......Page 166
7.7 Regulation of Aerobic Respiration......Page 167
7.8 Oxidation Without O[sub(2)]......Page 168
7.9 Catabolism of Proteins and Fats......Page 169
7.10 Evolution of Metabolism......Page 171
8.1 Overview of Photosynthesis......Page 176
8.2 The Discovery of Photosynthetic Processes......Page 178
8.3 Pigments......Page 180
8.4 Photosystem Organization......Page 183
8.5 The Light-Dependent Reactions......Page 185
8.6 Carbon Fixation: The Calvin Cycle......Page 189
8.7 Photorespiration......Page 192
9.1 Overview of Cell Communication......Page 197
9.2 Receptor Types......Page 200
9.3 Intracellular Receptors......Page 202
9.4 Signal Transduction Through Receptor Kinases......Page 203
9.5 Signal Transduction Through G Protein-Coupled Receptors......Page 208
10 How Cells Divide......Page 215
10.1 Bacterial Cell Division......Page 216
10.2 Eukaryotic Chromosomes......Page 218
10.3 Overview of the Eukaryotic Cell Cycle......Page 221
10.4 Interphase: Preparation for Mitosis......Page 222
10.5 M Phase: Chromosome Segregation and the Division of Cytoplasmic Contents......Page 223
10.6 Control of the Cell Cycle......Page 227
11.1 Sexual Reproduction Requires Meiosis......Page 236
11.2 Features of Meiosis......Page 238
11.3 The Process of Meiosis......Page 239
11.4 Summing Up: Meiosis Versus Mitosis......Page 244
12.1 The Mystery of Heredity......Page 250
12.2 Monohybrid Crosses: The Principle of Segregation......Page 253
12.3 Dihybrid Crosses: The Principle of Independent Assortment......Page 257
12.4 Probability: Predicting the Results of Crosses......Page 259
12.5 The Testcross: Revealing Unknown Genotypes......Page 260
12.6 Extensions to Mendel......Page 261
13 Chromosomes, Mapping, and the Meiosis–Inheritance Connection......Page 268
13.1 Sex Linkage and the Chromosomal Theory of Inheritance......Page 269
13.2 Sex Chromosomes and Sex Determination......Page 270
13.4 Genetic Mapping......Page 273
13.5 Selected Human Genetic Disorders......Page 278
14.1 The Nature of the Genetic Material......Page 285
14.2 DNA Structure......Page 288
14.3 Basic Characteristics of DNA Replication......Page 292
14.4 Prokaryotic Replication......Page 295
14.5 Eukaryotic Replication......Page 300
14.6 DNA Repair......Page 302
15.1 The Nature of Genes......Page 307
15.2 The Genetic Code......Page 311
15.3 Prokaryotic Transcription......Page 313
15.4 Eukaryotic Transcription......Page 316
15.5 Eukaryotic pre-mRNA Splicing......Page 318
15.6 The Structure of tRNA and Ribosomes......Page 320
15.7 The Process of Translation......Page 322
15.8 Summarizing Gene Expression......Page 326
15.9 Mutation: Altered Genes......Page 328
16.1 Control of Gene Expression......Page 333
16.2 Regulatory Proteins......Page 334
16.3 Prokaryotic Regulation......Page 337
16.4 Eukaryotic Regulation......Page 341
16.5 Eukaryotic Chromatin Structure......Page 345
16.6 Eukaryotic Posttranscriptional Regulation......Page 346
16.7 Protein Degradation......Page 351
17.1 DNA Manipulation......Page 356
17.2 Molecular Cloning......Page 359
17.3 DNA Analysis......Page 364
17.4 Genetic Engineering......Page 370
17.5 Medical Applications......Page 372
17.6 Agricultural Applications......Page 375
18.1 Mapping Genomes......Page 381
18.2 Whole-Genome Sequencing......Page 385
18.3 Characterizing Genomes......Page 387
18.4 Genomics and Proteomics......Page 391
18.5 Applications of Genomics......Page 396
19.1 The Process of Development......Page 401
19.2 Cell Division......Page 402
19.3 Cell Differentiation......Page 404
19.4 Nuclear Reprogramming......Page 409
19.5 Pattern Formation......Page 412
19.6 Morphogenesis......Page 419
20.1 Genetic Variation and Evolution......Page 425
20.2 Changes in Allele Frequency......Page 427
20.3 Five Agents of Evolutionary Change......Page 430
20.4 Fitness and Its Measurement......Page 434
20.5 Interactions Among Evolutionary Forces......Page 435
20.6 Maintenance of Variation......Page 436
20.7 Selection Acting on Traits Affected by Multiple Genes......Page 438
20.8 Experimental Studies of Natural Selection......Page 440
20.9 The Limits of Selection......Page 442
21 The Evidence for Evolution......Page 446
21.1 The Beaks of Darwin’s Finches: Evidence of Natural Selection......Page 447
21.2 Peppered Moths and Industrial Melanism: More Evidence of Selection......Page 449
21.3 Artificial Selection: Human-Initiated Change......Page 451
21.4 Fossil Evidence of Evolution......Page 453
21.5 Anatomical Evidence for Evolution......Page 457
21.6 Convergent Evolution and the Biogeographical Record......Page 459
21.7 Darwin’s Critics......Page 461
22 The Origin of Species......Page 465
22.1 The Nature of Species and the Biological Species Concept......Page 466
22.2 Natural Selection and Reproductive Isolation......Page 470
22.3 The Role of Genetic Drift and Natural Selection in Speciation......Page 472
22.4 The Geography of Speciation......Page 473
22.5 Adaptive Radiation and Biological Diversity......Page 475
22.6 The Pace of Evolution......Page 480
22.7 Speciation and Extinction Through Time......Page 481
23.1 Systematics......Page 485
23.2 Cladistics......Page 487
23.3 Systematics and Classification......Page 490
23.4 Phylogenetics and Comparative Biology......Page 493
23.5 Phylogenetics and Disease Evolution......Page 499
24.1 Comparative Genomics......Page 503
24.2 Whole-Genome Duplications......Page 506
24.3 Evolution Within Genomes......Page 510
24.4 Gene Function and Expression Patterns......Page 513
24.5 Nonprotein-Coding DNA and Regulatory Function......Page 514
24.6 Genome Size and Gene Number......Page 515
24.7 Genome Analysis and Disease Prevention and Treatment......Page 516
24.8 Crop Improvement Through Genome Analysis......Page 518
25.1 Overview of Evolutionary Developmental Biology......Page 521
25.2 One or Two Gene Mutations, New Form......Page 524
25.3 Same Gene, New Function......Page 525
25.4 Different Genes, Convergent Function......Page 527
25.5 Gene Duplication and Divergence......Page 528
25.6 Functional Analysis of Genes Across Species......Page 529
25.7 Diversity of Eyes in the Natural World: A Case Study......Page 530
26 The Tree of Life......Page 536
26.1 Origins of Life......Page 537
26.2 Classification of Organisms......Page 541
26.3 Grouping Organisms......Page 543
26.5 Origin of Plants......Page 549
26.6 Sorting out the Animals......Page 551
27 Viruses......Page 557
27.1 The Nature of Viruses......Page 558
27.2 Bacteriophages: Bacterial Viruses......Page 562
27.3 Human Immunodeficiency Virus (HIV)......Page 564
27.4 Other Viral Diseases......Page 568
27.5 Prions and Viroids: Subviral Particles......Page 570
28 Prokaryotes......Page 574
28.1 The First Cells......Page 575
28.2 Prokaryotic Diversity......Page 576
28.3 Prokaryotic Cell Structure......Page 580
28.4 Prokaryotic Genetics......Page 583
28.5 Prokaryotic Metabolism......Page 588
28.6 Human Bacterial Disease......Page 589
28.7 Beneficial Prokaryotes......Page 592
29 Protists......Page 596
29.1 Eukaryotic Origins and Endosymbiosis......Page 597
29.2 Defining Protists......Page 600
29.3 Diplomonads and Parabasalids: Flagellated Protists Lacking Mitochondria......Page 601
29.4 Euglenozoa: A Diverse Group in Which Some Members Have Chloroplasts......Page 602
29.5 Alveolata: Protists with Submembrane Vesicles......Page 605
29.6 Stramenopila: Protists with Fine Hairs......Page 609
29.7 Rhodophyta: Red Algae......Page 611
29.9 Protists Without a Clade......Page 612
30.1 Defining Plants......Page 617
30.2 Chlorophytes and Charophytes: Green Algae......Page 620
30.3 Bryophytes: Dominant Gametophyte Generation......Page 622
30.4 Tracheophyte Plants: Roots, Stems, and Leaves......Page 625
30.6 Pterophytes: Ferns and Their Relatives......Page 627
30.7 The Evolution of Seed Plants......Page 631
30.8 Gymnosperms: Plants with “Naked Seeds”......Page 632
30.9 Angiosperms: The Flowering Plants......Page 635
31.1 Defining Fungi......Page 643
31.2 Microsporidia: Unicellular Parasites......Page 647
31.3 Chytridiomycota and Relatives: Fungi with Flagellated Zoospores......Page 648
31.4 Zygomycota: Fungi that Produce Zygotes......Page 649
31.6 Basidiomycota: The Club (Basidium) Fungi......Page 651
31.7 Ascomycota: The Sac (Ascus) Fungi......Page 652
31.8 Ecology of Fungi......Page 654
31.9 Fungal Parasites and Pathogens......Page 658
32 Overview of Animal Diversity......Page 662
32.1 Some General Features of Animals......Page 663
32.2 Evolution of the Animal Body Plan......Page 665
32.3 The Classification of Animals......Page 669
32.4 The Roots of the Animal Tree of Life......Page 674
33 Noncoelomate Invertebrates......Page 678
33.1 Parazoa: Animals That Lack Specialized Tissues......Page 679
33.2 Eumetazoa: Animals with True Tissues......Page 681
33.3 The Bilaterian Acoelomates......Page 685
33.4 The Pseudocoelomates......Page 690
34.1 Phylum Mollusca: The Mollusks......Page 695
34.2 Phylum Nemertea: The Ribbon Worms......Page 701
34.3 Phylum Annelida: The Annelids......Page 702
34.4 The Lophophorates: Bryozoa and Brachiopoda......Page 705
34.5 Phylum Arthropoda: The Arthropods......Page 707
34.6 Phylum Echinodermata: The Echinoderms......Page 716
35 Vertebrates......Page 722
35.1 The Chordates......Page 723
35.2 The Nonvertebrate Chordates......Page 724
35.3 The Vertebrate Chordates......Page 725
35.4 Fishes......Page 727
35.5 Amphibians......Page 732
35.6 Reptiles......Page 735
35.7 Birds......Page 741
35.8 Mammals......Page 745
35.9 Evolution of the Primates......Page 750
36 Plant Form......Page 758
36.1 Organization of the Plant Body: An Overview......Page 759
36.2 Plant Tissues......Page 762
36.3 Roots: Anchoring and Absorption Structures......Page 768
36.4 Stems: Support for Above-Ground Organs......Page 772
36.5 Leaves: Photosynthetic Organs......Page 776
37 Vegetative Plant Development......Page 782
37.1 Embryo Development......Page 783
37.2 Seeds......Page 789
37.3 Fruits......Page 790
37.4 Germination......Page 793
38 Transport in Plants......Page 798
38.1 Transport Mechanisms......Page 799
38.2 Water and Mineral Absorption......Page 802
38.3 Xylem Transport......Page 805
38.4 The Rate of Transpiration......Page 807
38.5 Water-Stress Responses......Page 809
38.6 Phloem Transport......Page 810
39 Plant Nutrition and Soils......Page 815
39.1 Soils: The Substrates on Which Plants Depend......Page 816
39.2 Plant Nutrients......Page 819
39.3 Special Nutritional Strategies......Page 821
39.4 Carbon–Nitrogen Balance and Global Change......Page 824
39.5 Phytoremediation......Page 826
40.1 Physical Defenses......Page 831
40.2 Chemical Defenses......Page 834
40.3 Animals that Protect Plants......Page 838
40.4 Systemic Responses to Invaders......Page 839
41 Sensory Systems in Plants......Page 843
41.1 Responses to Light......Page 844
41.2 Responses to Gravity......Page 848
41.3 Responses to Mechanical Stimuli......Page 850
41.4 Responses to Water and Temperature......Page 852
41.5 Hormones and Sensory Systems......Page 854
42 Plant Reproduction......Page 868
42.1 Reproductive Development......Page 869
42.2 Flower Production......Page 871
42.3 Structure and Evolution of Flowers......Page 877
42.4 Pollination and Fertilization......Page 880
42.5 Asexual Reproduction......Page 886
42.6 Plant Life Spans......Page 888
43 The Animal Body and Principles of Regulation......Page 892
43.1 Organization of the Vertebrate Body......Page 893
43.2 Epithelial Tissue......Page 894
43.3 Connective Tissue......Page 897
43.4 Muscle Tissue......Page 899
43.6 Overview of Vertebrate Organ Systems......Page 901
43.7 Homeostasis......Page 905
43.8 Regulating Body Temperature......Page 907
44 The Nervous System......Page 916
44.1 Nervous System Organization......Page 917
44.2 The Mechanism of Nerve Impulse Transmission......Page 919
44.3 Synapses: Where Neurons Communicate with Other Cells......Page 925
44.4 The Central Nervous System: Brain and Spinal Cord......Page 930
44.5 The Peripheral Nervous System: Sensory and Motor Neurons......Page 938
45 Sensory Systems......Page 944
45.1 Overview of Sensory Receptors......Page 945
45.2 Mechanoreceptors: Touch and Pressure......Page 946
45.3 Hearing, Vibration, and Detection of Body Position......Page 949
45.4 Chemoreceptors: Taste, Smell, and pH......Page 954
45.5 Vision......Page 957
45.6 The Diversity of Sensory Experiences......Page 962
46 The Endocrine System......Page 966
46.1 Regulation of Body Processes by Chemical Messengers......Page 967
46.2 Actions of Lipophilic Versus Hydrophilic Hormones......Page 972
46.3 The Pituitary and Hypothalamus: The Body’s Control Centers......Page 975
46.4 The Major Peripheral Endocrine Glands......Page 980
46.5 Other Hormones and Their Effects......Page 984
47 The Musculoskeletal System......Page 990
47.1 Types of Skeletal Systems......Page 991
47.2 A Closer Look at Bone......Page 992
47.3 Joints and Skeletal Movement......Page 996
47.4 Muscle Contraction......Page 998
47.5 Modes of Animal Locomotion......Page 1004
48 The Digestive System......Page 1010
48.1 Types of Digestive Systems......Page 1011
48.2 The Mouth and Teeth: Food Capture and Bulk Processing......Page 1013
48.3 The Esophagus and the Stomach: The Early Stages of Digestion......Page 1014
48.4 The Intestines: Breakdown, Absorption, and Elimination......Page 1016
48.5 Variations in Vertebrate Digestive Systems......Page 1019
48.6 Neural and Hormonal Regulation of the Digestive Tract......Page 1022
48.7 Accessory Organ Function......Page 1023
48.8 Food Energy, Energy Expenditure, and Essential Nutrients......Page 1024
49 The Respiratory System......Page 1030
49.1 Gas Exchange Across Respiratory Surfaces......Page 1031
49.2 Gills, Cutaneous Respiration, and Tracheal Systems......Page 1033
49.3 Lungs......Page 1035
49.4 Structures and Mechanisms of Ventilation in Mammals......Page 1038
49.5 Transport of Gases in Body Fluids......Page 1041
50.1 The Components of Blood......Page 1047
50.2 Invertebrate Circulatory Systems......Page 1051
50.3 Vertebrate Circulatory Systems......Page 1052
50.4 The Four-Chambered Heart and the Blood Vessels......Page 1055
50.5 Characteristics of Blood Vessels......Page 1059
50.6 Regulation of Blood Flow and Blood Pressure......Page 1063
51.1 Osmolarity and Osmotic Balance......Page 1067
51.2 Osmoregulatory Organs......Page 1069
51.3 Evolution of the Vertebrate Kidney......Page 1071
51.4 Nitrogenous Wastes: Ammonia, Urea, and Uric Acid......Page 1073
51.5 The Mammalian Kidney......Page 1074
51.6 Hormonal Control of Osmoregulatory Functions......Page 1079
52.1 Innate Immunity......Page 1084
52.2 Adaptive Immunity......Page 1090
52.3 Cell-Mediated Immunity......Page 1095
52.4 Humoral Immunity and Antibody Production......Page 1097
52.5 Autoimmunity and Hypersensitivity......Page 1104
52.6 Antibodies in Medical Treatment and Diagnosis......Page 1106
52.7 Pathogens That Evade the Immune System......Page 1108
53.1 Animal Reproductive Strategies......Page 1113
53.2 Vertebrate Fertilization and Development......Page 1116
53.3 Structure and Function of the Human Male Reproductive System......Page 1120
53.4 Structure and Function of the Human Female Reproductive System......Page 1123
53.5 Contraception and Infertility Treatments......Page 1127
54 Animal Development......Page 1134
54.1 Fertilization......Page 1135
54.2 Cleavage and the Blastula Stage......Page 1139
54.3 Gastrulation......Page 1141
54.4 Organogenesis......Page 1145
54.5 Vertebrate Axis Formation......Page 1151
54.6 Human Development......Page 1154
55 Behavioral Biology......Page 1161
55.1 The Natural History of Behavior......Page 1162
55.2 Nerve Cells, Neurotransmitters, Hormones, and Behavior......Page 1163
55.3 Behavioral Genetics......Page 1164
55.4 Learning......Page 1166
55.5 The Development of Behavior......Page 1168
55.6 Animal Cognition......Page 1170
55.7 Orientation and Migratory Behavior......Page 1171
55.8 Animal Communication......Page 1173
55.9 Behavioral Ecology......Page 1176
55.10 Reproductive Strategies and Sexual Selection......Page 1179
55.11 Altruism......Page 1183
55.12 The Evolution of Group Living and Animal Societies......Page 1186
56.1 The Environmental Challenges......Page 1191
56.2 Populations: Groups of a Single Species in One Place......Page 1194
56.3 Population Demography and Dynamics......Page 1197
56.4 Life History and the Cost of Reproduction......Page 1200
56.5 Environmental Limits to Population Growth......Page 1202
56.6 Factors That Regulate Populations......Page 1204
56.7 Human Population Growth......Page 1207
57 Community Ecology......Page 1214
57.1 Biological Communities: Species Living Together......Page 1215
57.2 The Ecological Niche Concept......Page 1217
57.3 Predator–Prey Relationships......Page 1221
57.4 The Many Types of Species Interactions......Page 1225
57.5 Ecological Succession, Disturbance, and Species Richness......Page 1231
58 Dynamics of Ecosystems......Page 1236
58.1 Biogeochemical Cycles......Page 1237
58.2 The Flow of Energy in Ecosystems......Page 1243
58.3 Trophic-Level Interactions......Page 1248
58.4 Biodiversity and Ecosystem Stability......Page 1252
58.5 Island Biogeography......Page 1255
59.1 Ecosystem Effects of Sun, Wind, and Water......Page 1259
59.2 Earth’s Biomes......Page 1264
59.3 Freshwater Habitats......Page 1267
59.4 Marine Habitats......Page 1270
59.5 Human Impacts on the Biosphere: Pollution and Resource Depletion......Page 1274
59.6 Human Impacts on the Biosphere: Climate Change......Page 1279
60 Conservation Biology......Page 1285
60.1 Overview of the Biodiversity Crisis......Page 1286
60.2 The Value of Biodiversity......Page 1290
60.3 Factors Responsible for Extinction......Page 1293
60.4 Approaches for Preserving Endangered Species and Ecosystems......Page 1304
Appendix A......Page 1310
Glossary......Page 1344
Credits......Page 1368
Index......Page 1374