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Copyright, iv
Preface, xiii
Organization and Features of The Cell, xv
Media and Supplements to Accompany The Cell, xvii
Part I. Introduction, 1
1. An Overview of Cells and Cell Research, 3
The Origin and Evolution of Cells, 4
The First Cell, 4
The Evolution of Metabolism, 6
Present-Day Prokaryotes, 8
Eukaryotic Cells, 8
The Origin of Eukaryotes, 9
The Development of Multicellular Organisms, 12
Cells as Experimental Models, 16
E. coli, 16
Yeasts, 17
Caenorhabditis elegans, 18
Drosophila melanogaster, 18
Arabidopsis thaliana, 19
Vertebrates, 19
Tools of Cell Biology, 21
Light Microscopy, 21
Electron Microscopy, 28
Subcellular Fractionation, 30
Growth of Animal Cells in Culture, 33
Key Experiment: Animal Cell Culture, 34
Culture of Plant Cells, 36
Viruses, 37
Molecular Medicine: Viruses and Cancer, 37
Summary and Key Terms, 39
Questions, 41
References and Further Reading, 42
2. The Composition of Cells, 43
The Molecules of Cells, 43
Carbohydrates, 44
Lipids, 46
Nucleic Acids, 49
Proteins, 52
Key Experiment: The Folding of Polypeptide Chains, 54
Cell Membranes, 58
Membrane Lipids, 58
Membrane Proteins, 60
Key Experiment: The Structure of Cell Membranes, 60
Transport across Cell Membranes, 63
Proteomics: Large-Scale Analysis of Cell Proteins, 64
Identification of Cell Proteins, 65
Global Analysis of Protein Localization, 67
Protein Interactions, 68
Summary and Key Terms, 70
Questions, 71
References and Further Reading, 71
3. Cell Metabolism, 73
The Central Role of Enzymes as Biological Catalysts, 73
The Catalytic Activity of Enzymes, 73
Mechanisms of Enzymatic Catalysis, 74
Coenzymes, 76
Regulation of Enzyme Activity, 79
Metabolic Energy, 81
Free Energy and ATP, 81
The Generation of ATP from Glucose, 84
The Derivation of Energy from Other Organic Molecules, 89
Photosynthesis, 89
The Biosynthesis of Cell Constituents, 91
Carbohydrates, 92
Lipids, 93
Proteins, 94
Nucleic Acids, 96
Molecular Medicine: Phenylketonuria, 97
Key Experiment: Antimetabolites and Chemotherapy, 98
Summary and Key Terms, 99
Questions, 100
References and Further Reading, 101
4. Fundamentals of Molecular Biology, 103
Heredity, Genes, and DNA, 103
Genes and Chromosomes, 104
Genes and Enzymes, 105
Identification of DNA as the Genetic Material, 107
The Structure of DNA, 108
Replication of DNA, 109
Expression of Genetic Information, 110
Colinearity of Genes and Proteins, 111
The Role of Messenger RNA, 112
The Genetic Code, 113
RNA Viruses and Reverse Transcription, 115
Key Experiment: The DNA Provirus Hypothesis, 116
Recombinant DNA, 118
Restriction Endonucleases, 118
Generation of Recombinant DNA Molecules, 120
Vectors for Recombinant DNA, 121
DNA Sequencing, 124
Expression of Cloned Genes, 124
Detection of Nucleic Acids and Proteins, 127
Amplification of DNA by the Polymerase Chain Reaction, 128
Nucleic Acid Hybridization, 130
Antibodies as Probes for Proteins, 133
Gene Function in Eukaryotes, 136
Genetic Analysis in Yeasts, 136
Gene Transfer in Plants and Animals, 137
Mutagenesis of Cloned DNAs, 140
Introducing Mutations into Cellular Genes, 141
Interfering with Cellular Gene Expression, 143
Key Experiment: RNA Interference, 146
Summary and Key Terms, 148
Questions, 150
References and Further Reading, 150
II. The Flow of Genetic Information, 153
5. The Organization and Sequences of Cellular Genomes, 155
The Complexity of Eukaryotic Genomes, 155
Introns and Exons, 157
Key Experiment: The Discovery of Introns, 158
Repetitive DNA Sequences, 161
Gene Duplication and Pseudogenes, 164
The Composition of Higher Eukaryotic Genomes, 165
Chromosomes and Chromatin, 166
Chromatin, 166
Centromeres, 170
Telomeres, 174
The Sequences of Complete Genomes, 176
Prokaryotic Genomes, 177
The Yeast Genome, 178
The Genomes of Caenorhabditis elegans, Drosophila melanogaster and Other Invertebrates, 180
Plant Genomes, 182
The Human Genome, 184
Key Experiment: The Human Genome, 186
The Genomes of Other Vertebrates, 188
Bioinformatics and Systems Biology, 191
Systematic Screens of Gene Function, 191
Regulation of Gene Expression, 192
Variation among Individuals and Genomic Medicine, 194
Summary and Key Terms, 195
Questions, 198
References and Further Reading, 198
6. Replication, Maintenance, and Rearrangements of Genomic DNA, 201
DNA Replication, 201
DNA Polymerases, 202
The Replication Fork, 203
The Fidelity of Replication, 210
Origins and the Initiation of Replication, 211
Telomeres and Telomerase: Maintaining the Ends of Chromosomes, 214
DNA Repair, 216
Direct Reversal of DNA Damage, 216
Excision Repair, 219
Translesion DNA Synthesis, 224
Molecular Medicine: Colon Cancer and DNA Repair, 225
Repair of Double-Strand Breaks, 226
Recombination between Homologous DNA Sequences, 227
Models of Homologous Recombination, 228
Enzymes Involved in Homologous Recombination, 229
DNA Rearrangements, 233
Site-Specific Recombination, 234
Key Experiment: Rearrangement of Immunoglobulin Genes, 236
Transposition via DNA Intermediates, 240
Transposition via RNA Intermediates, 242
Gene Amplification, 245
Summary and Key Terms, 247
Questions, 249
References and Further Reading, 249
7. RNA Synthesis and Processing, 251
Transcription in Prokaryotes, 251
RNA Polymerase and Transcription, 252
Repressors and Negative Control of Transcription, 256
Positive Control of Transcription, 258
Eukaryotic RNA Polymerases and General Transcription Factors, 258
Eukaryotic RNA Polymerases, 259
General Transcription Factors and Initiation of Transcription by RNA Polymerase II, 259
Transcription by RNA Polymerases I and III, 263
Regulation of Transcription in Eukaryotes, 265
cis-Acting Regulatory Sequences: Promoters and Enhancers, 265
Transcription Factor Binding Sites, 269
Transcriptional Regulatory Proteins, 270
Key Experiment: Isolation of a Eukaryotic Transcription Factor, 272
Structure and Function of Transcriptional Activators, 273
Eukaryotic Repressors, 276
Regulation of Elongation, 278
Relationship of Chromatin Structure to Transcription, 278
Regulation of Transcription by Noncoding RNAs, 285
DNA Methylation, 286
RNA Processing and Turnover, 287
Processing of Ribosomal and Transfer RNAs, 288
Processing of mRNA in Eukaryotes, 290
Splicing Mechanisms, 293
Key Experiment: The Discovery of snRNPs, 294
Alternative Splicing, 298
RNA Editing, 300
RNA Degradation, 301
Summary and Key Terms, 303
Questions, 305
References and Further Reading, 306
8. Protein Synthesis, Processing, and Regulation, 309
Translation of mRNA, 309
Transfer RNAs, 310
The Ribosome, 311
Key Experiment: Catalytic Role of Ribosomal RNA, 316
The Organization of mRNAs and the Initiation of Translation, 317
The Process of Translation, 318
Regulation of Translation, 323
Protein Folding and Processing, 329
Chaperones and Protein Folding, 330
Enzymes that Catalyze Protein Folding, 332
Protein Cleavage, 333
Glycosylation, 335
Attachment of Lipids, 337
Regulation of Protein Function, 340
Regulation by Small Molecules, 340
Protein Phosphorylation, 341
Protein-Protein Interactions, 343
Key Experiment: The Discovery of Protein-Tyrosine Kinases, 344
Protein Degradation, 345
The Ubiquitin-Proteasome Pathway, 345
Lysosomal Proteolysis, 348
Summary and Key Terms, 349
Questions, 351
References and Further Reading, 351
Part III. Cell Structure and Function, 353
9. The Nucleus, 355
The Nuclear Envelope and Traffic between the Nucleus and the Cytoplasm, 355
Structure of the Nuclear Envelope, 356
Molecular Medicine: Nuclear Lamina Diseases, 358
The Nuclear Pore Complex, 360
Selective Transport of Proteins to and from the Nucleus, 361
Key Experiment: Identification of Nuclear Localization Signals, 362
Regulation of Nuclear Protein Import, 367
Transport of RNAs, 368
Internal Organization of the Nucleus, 369
Chromosomes and Higher-Order Chromatin Structure, 370
Sub-Compartments within the Nucleus, 372
The Nucleolus and rRNA Processing, 374
Ribosomal RNA Genes and the Organization of the Nucleolus, 375
Transcription and Processing of rRNA, 376
Ribosome Assembly, 378
Summary and Key Terms, 379
Questions, 381
References and Further Reading, 381
10. Protein Sorting and Transport: The Endoplasmic Reticulum, Golgi Apparatus, and Lysosomes, 383
The Endoplasmic Reticulum, 383
The Endoplasmic Reticulum and Protein Secretion, 384
Targeting Proteins to the Endoplasmic Reticulum, 386
Key Experiment: The Signal Hypothesis, 388
Insertion of Proteins into the ER Membrane, 391
Protein Folding and Processing in the ER, 396
Quality Control in the ER, 398
The Smooth ER and Lipid Synthesis, 402
Export of Proteins and Lipids from the ER, 405
The Golgi Apparatus, 408
Organization of the Golgi, 408
Protein Glycosylation within the Golgi, 410
Lipid and Polysaccharide Metabolism in the Golgi, 412
Protein Sorting and Export from the Golgi Apparatus, 413
The Mechanism of Vesicular Transport, 416
Experimental Approaches to Understanding Vesicular Transport, 416
Cargo Selection, Coat Proteins, and Vesicle Budding, 418
Vesicle Fusion, 420
Lysosomes, 423
Lysosomal Acid Hydrolases, 423
Molecular Medicine: Gaucher Disease, 425
Endocytosis and Lysosome Formation, 426
Phagocytosis and Autophagy, 426
Summary and Key Terms, 429
Questions, 431
References and Further Reading, 431
11. Bioenergetics and Metabolism: Mitochondria, Chloroplasts, and Peroxisomes, 433
Mitochondria, 433
Organization and Function of Mitochondria, 434
The Genetic System of Mitochondria, 435
Protein Import and Mitochondrial Assembly, 437
Molecular Medicine: Diseases of Mitochondria: Leber's Hereditary Optic Neuropathy, 438
The Mechanism of Oxidative Phosphorylation, 445
The Electron Transport Chain, 445
Chemiosmotic Coupling, 446
Key Experiment: The Chemiosmotic Theory, 448
Transport of Metabolites across the Inner Membrane, 450
Chloroplasts and Other Plastids, 452
The Structure and Function of Chloroplasts, 452
The Chloroplast Genome, 454
Import and Sorting of Chloroplast Proteins, 455
Other Plastids, 457
Photosynthesis, 459
Electron Flow through Photosystems I and II, 460
Cyclic Electron Flow, 463
ATP Synthesis, 464
Peroxisomes, 464
Functions of Peroxisomes, 465
Peroxisome Assembly, 467
Summary and Key Terms, 469
Questions, 471
References and Further Reading, 471
12. The Cytoskeleton and Cell Movement, 473
Structure and Organization of Actin Filaments, 473
Assembly and Disassembly of Actin Filaments, 474
Organization of Actin Filaments, 479
Association of Actin Filaments with the Plasma Membrane, 481
Protrusions of the Cell Surface, 485
Actin, Myosin, and Cell Movement, 487
Muscle Contraction, 487
Contractile Assemblies of Actin and Myosin in Nonmuscle Cells, 492
Nonmuscle Myosins, 493
Formation of Protrusions and Cell Movement, 494
Intermediate Filaments, 496
Intermediate Filament Proteins, 496
Assembly of Intermediate Filaments, 498
Intracellular Organization of Intermediate Filaments, 499
Functions of Keratins and Neurofilaments: Diseases of the Skin and Nervous System, 501
Key Experiment: Expression of Mutant Keratin Causes Abnormal Skin Development, 502
Microtubules, 504
Structure and Dynamic Organization of Microtubules, 504
Assembly of Microtubules, 507
Organization of Microtubules within Cells, 509
Microtubule Motors and Movement, 511
Identification of Microtubule Motor Proteins, 511
Key Experiment: The Isolation of Kinesin, 512
Cargo Transport and Intracellular Organization, 515
Cilia and Flagella, 516
Reorganization of Microtubules during Mitosis, 519
Chromosome Movement, 520
Summary and Key Terms, 522
Questions, 525
References and Further Reading, 525
13. The Plasma Membrane, 529
Structure of the Plasma Membrane, 529
The Phospholipid Bilayer, 529
Membrane Proteins, 533
Mobility of Membrane Proteins, 538
The Glycocalyx, 540
Transport of Small Molecules, 540
Passive Diffusion, 541
Facilitated Diffusion and Carrier Proteins, 542
Ion Channels, 544
Active Transport Driven by ATP Hydrolysis, 551
Molecular Medicine: Cystic Fibrosis, 554
Active Transport Driven by Ion Gradients, 555
Endocytosis, 557
Phagocytosis, 557
Receptor-Mediated Endocytosis, 558
Key Experiment: The LDL Receptor, 560
Protein Trafficking in Endocytosis, 563
Summary and Key Terms, 567
Questions, 568
References and Further Reading, 568
14. Cell Walls, the Extracellular Matrix, and Cell Interactions, 571
Cell Walls, 571
Bacterial Cell Walls, 571
Eukaryotic Cell Walls, 572
The Extracellular Matrix and Cell-Matrix Interactions, 577
Matrix Structural Proteins, 578
Matrix Polysaccharides, 581
Matrix Adhesion Proteins, 582
Cell-Matrix Interactions, 583
Key Experiment: The Characterization of Integrins, 584
Cell-Cell Interactions, 587
Adhesion Junctions, 587
Tight Junctions, 590
Gap Junctions, 591
Molecular Medicine: Gap Junction Diseases, 594
Plasmodesmata, 595
Summary and Key Terms, 596
Questions, 598
References and Further Reading, 598
Part IV. Cell Regulation, 602
15. Cell Signaling, 603
Signaling Molecules and Their Receptors, 603
Modes of Cell-Cell Signaling, 604
Steroid Hormones and the Nuclear Receptor Superfamily, 605
Nitric Oxide and Carbon Monoxide, 607
Neurotransmitters, 608
Peptide Hormones and Growth Factors, 609
Eicosanoids, 610
Plant Hormones, 612
Functions of Cell Surface Receptors, 613
G Protein-Coupled Receptors, 613
Receptor Protein-Tyrosine Kinases, 615
Key Experiment: G Protein-Coupled Receptors and Odor Detection, 616
Cytokine Receptors and Nonreceptor Protein-Tyrosine Kinases, 620
Receptors Linked to Other Enzymatic Activities, 620
Pathways of Intracellular Signal Transduction, 621
The cAMP Pathway: Second Messengers and Protein Phosphorylation, 622
Cyclic GMP, 624
Phospholipids and Ca²⁺, 625
The PI 3-Kinase/Akt and mTOR Pathways, 628
MAP Kinase Pathways, 630
Molecular Medicine: Cancer: Signal Transduction and the ras Oncogenes, 633
The JAK/STAT and TGF-β/Smad Pathways, 636
NF-κB Signaling, 637
The Hedgehog, Wnt, and Notch Pathways, 638
Signal Transduction and the Cytoskeleton, 641
Integrins and Signal Transduction, 641
Regulation of the Actin Cytoskeleton, 642
Signaling Networks, 644
Feedback and Crosstalk, 644
Networks of Cellular Signal Transduction, 646
Summary and Key Terms, 647
Questions, 650
References and Further Reading, 650
16. The Cell Cycle, 653
The Eukaryotic Cell Cycle, 653
Phases of the Cell Cycle, 654
Regulation of the Cell Cycle by Cell Growth and Extracellular Signals, 655
Cell Cycle Checkpoints, 657
Restricting DNA Replication to Once per Cell Cycle, 659
Regulators of Cell Cycle Progression, 659
Protein Kinases and Cell Cycle Regulation, 659
Key Experiment: The Discovery of MPF, 660
Key Experiment: The Identification of Cyclin, 663
Families of Cyclins and Cyclin-Dependent Kinases, 664
Growth Factors and the Regulation of G₁ Cdk's, 667
DNA Damage Checkpoints, 670
The Events of M Phase, 672
Stages of Mitosis, 672
Cdk1/Cyclin B and Progression to Metaphase, 675
The Spindle Assembly Checkpoint and Progression to Anaphase, 678
Cytokinesis, 680
Meiosis and Fertilization, 681
The Process of Meiosis, 681
Regulation of Oocyte Meiosis, 684
Fertilization, 687
Summary and Key Terms, 688
Questions, 690
References and Further Reading, 691
17. Cell Death and Cell Renewal, 693
Programmed Cell Death, 693
The Events of Apoptosis, 694
Key Experiment: Identification of Genes Required for Programmed Cell Death, 696
Caspases: The Executioners of Apoptosis, 697
Central Regulators of Apoptosis: The Bcl-2 Family, 699
Signaling Pathways that Regulate Apoptosis, 701
Alternative Pathways of Programmed Cell Death, 705
Stem Cells and the Maintenance of Adult Tissues, 705
Proliferation of Differentiated Cells, 706
Stem Cells, 708
Medical Applications of Adult Stem Cells, 713
Embryonic Stem Cells and Therapeutic Cloning, 714
Key Experiment: Culture of Embryonic Stem Cells, 715
Embryonic Stem Cells, 716
Somatic Cell Nuclear Transfer, 718
Induced Pluripotent Stem Cells, 719
Summary and Key Terms, 720
Questions, 722
References and Further Reading, 722
18. Cancer, 725
The Development and Causes of Cancer, 725
Types of Cancer, 725
The Development of Cancer, 727
Causes of Cancer, 729
Properties of Cancer Cells, 730
Transformation of Cells in Culture, 734
Tumor Viruses, 735
Hepatitis B and C Viruses, 735
SV40 and Polyomavirus, 736
Papillomaviruses, 737
Adenoviruses, 737
Herpesviruses, 738
Retroviruses, 738
Oncogenes, 739
Retroviral Oncogenes, 739
Proto-Oncogenes, 740
Key Experiment: The Discovery of Proto-Oncogenes, 742
Oncogenes in Human Cancer, 743
Functions of Oncogene Products, 747
Tumor Suppressor Genes, 752
Identification of Tumor Suppressor Genes, 752
Functions of Tumor Suppressor Gene Products, 756
Roles of Oncogenes and Tumor Suppressor Genes in Tumor Development, 759
Molecular Approaches to Cancer Treatment, 761
Prevention and Early Detection, 761
Molecular Diagnosis, 762
Treatment, 763
Molecular Medicine: Imatinib: Cancer Treatment Targeted against the bcr/abl Oncogene, 766
Summary and Key Terms, 767
Questions, 769
References and Further Reading, 770
Answers to Questions, 773
Glossary, 783
Index, 799

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