The Cell: A Molecular Approach, Fourth Edition

Part I Introduction......Page 25
1 An Overview of Cells and Cell Research......Page 27
The First Cell......Page 28
The Evolution of Metabolism......Page 31
Present-Day Prokaryotes......Page 32
Eukaryotic Cells......Page 33
The Origin of Eukaryotes......Page 34
The Development of Multicellular Organisms......Page 36
E. coli......Page 40
Caenorhabditis elegans......Page 41
Drosophila melanogaster......Page 42
Vertebrates......Page 43
Light Microscopy......Page 45
Electron Microscopy......Page 51
Subcellular Fractionation......Page 54
Growth of Animal Cells in Culture......Page 57
Viruses......Page 60
KEY EXPERIMENT Animal Cell Culture......Page 59
MOLECULAR MEDICINE Viruses and Cancer......Page 61
Summary and Key Terms......Page 63
References and Further Reading......Page 65
The Molecules of Cells......Page 67
Carbohydrates......Page 68
Lipids......Page 70
Nucleic Acids......Page 74
Proteins......Page 76
Cell Membranes......Page 82
Membrane Lipids......Page 84
Membrane Proteins......Page 85
Transport across Cell Membranes......Page 87
Identification of Cell Proteins......Page 89
Global Analysis of Protein Localization......Page 92
Protein Interactions......Page 93
KEY EXPERIMENT The Folding of Polypeptide Chains......Page 78
KEY EXPERIMENT The Structure of Cell Membranes......Page 83
References and Further Reading......Page 95
The Catalytic Activity of Enzymes......Page 97
Mechanisms of Enzymatic Catalysis......Page 98
Coenzymes......Page 102
Regulation of Enzyme Activity......Page 103
Free Energy and ATP......Page 105
The Generation of ATP from Glucose......Page 108
The Derivation of Energy from Other Organic Molecules......Page 113
Photosynthesis......Page 114
The Biosynthesis of Cell Constituents......Page 115
Carbohydrates......Page 116
Lipids......Page 117
Proteins......Page 118
Nucleic Acids......Page 121
KEY EXPERIMENT Antimetabolites and Chemotherapy......Page 122
MOLECULAR MEDICINE Phenylketonuria......Page 120
Summary and Key Terms......Page 124
References and Further Reading......Page 125
Heredity, Genes, and DNA......Page 127
Genes and Chromosomes......Page 128
Identification of DNA as the Genetic Material......Page 131
The Structure of DNA......Page 132
Replication of DNA......Page 134
Colinearity of Genes and Proteins......Page 135
The Role of Messenger RNA......Page 136
The Genetic Code......Page 137
RNA Viruses and Reverse Transcription......Page 139
Restriction Endonucleases......Page 142
Generation of Recombinant DNA Molecules......Page 145
Vectors for Recombinant DNA......Page 146
DNA Sequencing......Page 149
Expression of Cloned Genes......Page 150
Amplification of DNA by the Polymerase Chain Reaction......Page 153
Nucleic Acid Hybridization......Page 155
Antibodies as Probes for Proteins......Page 158
Genetic Analysis in Yeasts......Page 161
Gene Transfer in Plants and Animals......Page 163
Introducing Mutations into Cellular Genes......Page 166
Interfering with Cellular Gene Expression......Page 169
KEY EXPERIMENT The DNA Provirus Hypothesis......Page 140
MOLECULAR MEDICINE HIV and AIDS......Page 144
Summary and Key Terms......Page 171
Questions......Page 173
References and Further Reading......Page 174
PART II The Flow of Genetic Information......Page 177
The Complexity of Eukaryotic Genomes......Page 179
Introns and Exons......Page 181
Repetitive DNA Sequences......Page 185
Gene Duplication and Pseudogenes......Page 188
The Composition of Higher Eukaryotic Genomes......Page 189
Chromatin......Page 190
Centromeres......Page 195
Telomeres......Page 199
The Sequences of Complete Genomes......Page 200
Prokaryotic Genomes......Page 201
The Yeast Genome......Page 202
The Genomes of Caenorhabditis elegans and Drosophila melanogaster......Page 204
Plant Genomes......Page 207
The Human Genome......Page 209
The Genomes of Other Vertebrates......Page 214
Bioinformatics and Systems Biology......Page 216
Systematic Screens of Gene Function......Page 217
Regulation of Gene Expression......Page 218
Variation among Individuals and Genomic Medicine......Page 219
KEY EXPERIMENT The Discovery of Introns......Page 182
KEY EXPERIMENT The Human Genome......Page 212
Summary and Key Terms......Page 220
Questions......Page 222
References and Further Reading......Page 223
6 Replication, Maintenance, and Rearrangements of Genomic DNA......Page 225
The Replication Fork......Page 226
The Fidelity of Replication......Page 233
Origins and the Initiation of Replication......Page 235
Telomeres and Telomerase: Maintaining the Ends of Chromosomes......Page 238
Direct Reversal of DNA Damage......Page 240
Excision Repair......Page 243
Translesion DNA Synthesis......Page 247
Recombinational Repair......Page 249
Recombination between Homologous DNA Sequences......Page 251
Models of Homologous Recombination......Page 252
Enzymes Involved in Homologous Recombination......Page 253
Site-Specific Recombination......Page 257
Transposition via DNA Intermediates......Page 263
Transposition via RNA Intermediates......Page 266
Gene Amplification......Page 271
KEY EXPERIMENT Rearrangement of Immunoglobulin Genes......Page 264
MOLECULAR MEDICINE Colon Cancer and DNA Repair......Page 248
Summary and Key Terms......Page 273
Questions......Page 274
References and Further Reading......Page 275
7 RNA Synthesis and Processing......Page 277
RNA Polymerase and Transcription......Page 278
Repressors and Negative Control of Transcription......Page 282
Positive Control of Transcription......Page 285
General Transcription Factors and Initiation of Transcription by RNA Polymerase II......Page 286
Transcription by RNA Polymerases I and III......Page 290
Regulation of Transcription in Eukaryotes......Page 292
cis-Acting Regulatory Sequences: Promoters and Enhancers......Page 293
Transcription Factor Binding Sites......Page 296
Transcriptional Regulatory Proteins......Page 297
Structure and Function of Transcriptional Activators......Page 301
Eukaryotic Repressors......Page 304
Relationship of Chromatin Structure to Transcription......Page 305
Regulation of Transcription by Noncoding RNAs......Page 309
DNAMethylation......Page 310
Processing of Ribosomal and Transfer RNAs......Page 311
Processing of mRNA in Eukaryotes......Page 314
Splicing Mechanisms......Page 316
Alternative Splicing......Page 323
RNA Editing......Page 324
RNA Degradation......Page 325
KEY EXPERIMENT Isolation of a Eukaryotic Transcription Factor......Page 300
KEY EXPERIMENT The Discovery of snRNPs......Page 318
Summary and Key Terms......Page 327
References and Further Reading......Page 330
Translation of mRNA......Page 333
Transfer RNAs......Page 334
The Ribosome......Page 335
The Organization of mRNAs and the Initiation of Translation......Page 341
The Process of Translation......Page 343
Regulation of Translation......Page 349
Protein Folding and Processing......Page 353
Chaperones and Protein Folding......Page 354
Enzymes that Catalyze Protein Folding......Page 356
Protein Cleavage......Page 357
Glycosylation......Page 359
Attachment of Lipids......Page 361
Regulation of Protein Function......Page 363
Regulation by Small Molecules......Page 364
Protein Phosphorylation......Page 365
The Ubiquitin-Proteasome Pathway......Page 368
Lysosomal Proteolysis......Page 371
KEY EXPERIMENT Catalytic Role of Ribosomal RNA......Page 340
MOLECULAR MEDICINE Antibiotic Resistance and the Ribosome......Page 344
Summary and Key Terms......Page 372
References and Further Reading......Page 374
PART III Cell Structure and Function......Page 377
The Nuclear Envelope and Traffic between the Nucleus and the Cytoplasm......Page 379
Structure of the Nuclear Envelope......Page 380
The Nuclear Pore Complex......Page 385
Selective Transport of Proteins to and from the Nucleus......Page 386
Regulation of Nuclear Protein Import......Page 392
Transport of RNAs......Page 393
Chromosomes and Higher-Order Chromatin Structure......Page 395
Sub-Compartments within the Nucleus......Page 398
The Nucleolus and rRNA Processing......Page 399
Ribosomal RNA Genes and the Organization of the Nucleolus......Page 400
Transcription and Processing of rRNA......Page 401
Ribosome Assembly......Page 403
KEY EXPERIMENT Identification of Nuclear Localization Signals......Page 388
MOLECULAR MEDICINE Nuclear Lamina Diseases......Page 383
Summary and Key Terms......Page 404
References and Further Reading......Page 406
10 Protein Sorting and Transport: The Endoplasmic Reticulum, Golgi Apparatus, and Lysosomes......Page 409
The Endoplasmic Reticulum and Protein Secretion......Page 410
Targeting Proteins to the Endoplasmic Reticulum......Page 411
Insertion of Proteins into the ER Membrane......Page 417
Protein Folding and Processing in the ER......Page 422
Quality Control in the ER......Page 424
The Smooth ER and Lipid Synthesis......Page 427
Export of Proteins and Lipids from the ER......Page 430
The Golgi Apparatus......Page 432
Organization of the Golgi......Page 433
Protein Glycosylation within the Golgi......Page 434
Lipid and Polysaccharide Metabolism in the Golgi......Page 437
Protein Sorting and Export from the Golgi Apparatus......Page 438
Experimental Approaches to Understanding Vesicular Transport......Page 441
Cargo Selection, Coat Proteins, and Vesicle Budding......Page 443
Vesicle Fusion......Page 444
Endocytosis and Lysosome Formation......Page 448
Phagocytosis and Autophagy......Page 452
KEY EXPERIMENT The Signal Hypothesis......Page 414
MOLECULAR MEDICINE Gaucher Disease......Page 450
References and Further Reading......Page 455
11 Bioenergetics and Metabolism: Mitochondria, Chloroplasts, and Peroxisomes......Page 457
Organization and Function of Mitochondria......Page 458
The Genetic System of Mitochondria......Page 459
Protein Import and Mitochondrial Assembly......Page 461
The Mechanism of Oxidative Phosphorylation......Page 467
The Electron Transport Chain......Page 468
Chemiosmotic Coupling......Page 469
Transport of Metabolites across the Inner Membrane......Page 474
The Structure and Function of Chloroplasts......Page 475
The Chloroplast Genome......Page 476
Import and Sorting of Chloroplast Proteins......Page 478
Other Plastids......Page 480
Photosynthesis......Page 482
Electron Flow through Photosystems I and II......Page 483
Cyclic Electron Flow......Page 485
Peroxisomes......Page 486
Functions of Peroxisomes......Page 487
Peroxisome Assembly......Page 489
KEY EXPERIMENT The Chemiosmotic Theory......Page 472
MOLECULAR MEDICINE Diseases of Mitochondria: Leber\'s Hereditary Optic Neuropathy......Page 462
Summary and Key Terms......Page 491
Questions......Page 493
References and Further Reading......Page 494
Structure and Organization of Actin Filaments......Page 497
Assembly and Disassembly of Actin Filaments......Page 498
Organization of Actin Filaments......Page 504
Association of Actin Filaments with the Plasma Membrane......Page 506
Protrusions of the Cell Surface......Page 509
Actin, Myosin, and Cell Movement......Page 510
Muscle Contraction......Page 511
Contractile Assemblies of Actin and Myosin in Nonmuscle Cells......Page 515
Nonmuscle Myosins......Page 517
Formation of Protrusions and Cell Movement......Page 519
Intermediate Filament Proteins......Page 521
Assembly of Intermediate Filaments......Page 522
Intracellular Organization of Intermediate Filaments......Page 523
KEY EXPERIMENT Expression of Mutant Keratin Causes Abnormal Skin Development......Page 526
Structure and Dynamic Organization of Microtubules......Page 529
Assembly of Microtubules......Page 531
Organization of Microtubules within Cells......Page 534
Identification of Microtubule Motor Proteins......Page 535
KEY EXPERIMENT The Isolation of Kinesin......Page 538
Cilia and Flagella......Page 541
Reorganization of Microtubules during Mitosis......Page 544
Chromosome Movement......Page 545
Summary and Key Terms......Page 547
References and Further Reading......Page 550
Structure of the Plasma Membrane......Page 553
The Phospholipid Bilayer......Page 554
Membrane Proteins......Page 556
Mobility of Membrane Proteins......Page 561
Transport of Small Molecules......Page 564
Passive Diffusion......Page 565
Facilitated Diffusion and Carrier Proteins......Page 566
Ion Channels......Page 567
Active Transport Driven by ATP Hydrolysis......Page 574
Active Transport Driven by Ion Gradients......Page 579
Endocytosis......Page 580
Phagocytosis......Page 581
Receptor-Mediated Endocytosis......Page 582
Protein Trafficking in Endocytosis......Page 587
KEY EXPERIMENT The LDL Receptor......Page 583
MOLECULAR MEDICINE Cystic Fibrosis......Page 578
Summary and Key Terms......Page 590
References and Further Reading......Page 591
Cell Walls......Page 593
Eukaryotic Cell Walls......Page 594
Matrix Structural Proteins......Page 599
Matrix Polysaccharides......Page 602
Matrix Adhesion Proteins......Page 603
Cell-Matrix Interactions......Page 604
Adhesion Junctions......Page 608
Tight Junctions......Page 612
Gap Junctions......Page 613
Plasmodesmata......Page 616
KEY EXPERIMENT The Characterization of Integrin......Page 606
MOLECULAR MEDICINE Gap Junction Diseases......Page 615
Summary and Key Terms......Page 617
Questions......Page 618
References and Further Reading......Page 619
PART IV Cell Regulation......Page 621
15 Cell Signaling......Page 623
Modes of Cell-Cell Signaling......Page 624
Steroid Hormones and the Nuclear Receptor Superfamily......Page 625
Nitric Oxide and Carbon Monoxide......Page 627
Neurotransmitters......Page 628
Peptide Hormones and Growth Factors......Page 629
Eicosanoids......Page 631
Plant Hormones......Page 632
Functions of Cell Surface Receptors......Page 633
G Protein-Coupled Receptors......Page 634
KEY EXPERIMENT The Src Protein-Tyrosine Kinase......Page 636
Receptors Linked to Other Enzymatic Activities......Page 640
Pathways of Intracellular Signal Transduction......Page 641
The cAMP Pathway: Second Messengers and Protein Phosphorylation......Page 642
Cyclic GMP......Page 644
Phospholipids and Ca2+......Page 645
The PI 3-Kinase/Akt and mTOR Pathways......Page 648
MAP Kinase Pathways......Page 651
The JAK/STAT and TGF-beta j3/Smad Pathways......Page 657
The Hedgehog, Wnt, and Notch Pathways......Page 658
Integrins and Signal Transduction......Page 661
Regulation of the Actin Cytoskeleton......Page 662
Feedback and Crosstalk......Page 664
Networks of Cellular Signal Transduction......Page 665
MOLECULAR MEDICINE Cancer: Signal Transduction and the ras Oncogenes......Page 653
Summary and Key Terms......Page 667
References and Further Reading......Page 670
16 The Cell Cyde......Page 673
Phases of the Cell Cycle......Page 674
Regulation of the Cell Cycle by Cell Growth and Extracellular Signals......Page 676
Cell Cycle Checkpoints......Page 678
Restricting DNA Replication to Once per Cell Cycle......Page 680
Protein Kinases and Cell Cycle Regulation......Page 681
Families of Cyclins and Cyclin-Dependent Kinases......Page 685
Growth Factors and the Regulation of G1 Cdk\'s......Page 689
DNA Damage Checkpoints......Page 691
Stages of Mitosis......Page 693
Cdk1/Cyclin B and Progression to Metaphase......Page 696
The Spindle Assembly Checkpoint and Progression to Anaphase......Page 699
Cytokinesis......Page 701
The Process of Meiosis......Page 702
Regulation of Oocyte Meiosis......Page 705
Fertilization......Page 708
KEY EXPERIMENT The Discovery of MPF......Page 682
KEY EXPERIMENT The Identification of Cyclin......Page 686
Summary and Key Terms......Page 709
References and Further Reading......Page 711
17 Cell Death and Cell Renewal......Page 713
The Events of Apoptosis......Page 714
Caspases: The Executioners of Apoptosis......Page 716
Central Regulators of Apoptosis: The Bcl-2 Family......Page 719
Signaling Pathways that Regulate Apoptosis......Page 722
Proliferation of Differentiated Cells......Page 724
Stem Cells......Page 727
Medical Applications of Adult Stem Cells......Page 732
Embryonic Stem Cells and Therapeutic Cloning......Page 733
KEY EXPERIMENT Culture of Embryonic Stem Cells......Page 734
Somatic Cell Nuclear Transfer......Page 737
KEY EXPERIMENT Identification of Genes Required for Programmed Cell Death......Page 718
Summary and Key Terms......Page 740
References and Further Reading......Page 741
The Development and Causes of Cancer......Page 743
Types of Cancer......Page 744
The Development of Cancer......Page 745
Causes of Cancer......Page 747
Properties of Cancer Cells......Page 748
Transformation of Cells in Culture......Page 752
Hepatitis B and C Viruses......Page 753
SV40 and Polyomavirus......Page 754
Adenoviruses......Page 755
Retroviruses......Page 756
Oncogenes......Page 757
Retroviral Oncogenes......Page 758
Proto-Oncogenes......Page 759
Oncogenes in Human Cancer......Page 762
Functions of Oncogene Products......Page 765
Identification of Tumor Suppressor Genes......Page 770
Functions of Tumor Suppressor Gene Products......Page 774
Roles of Oncogenes and Tumor Suppressor Genes in Tumor Development......Page 777
Prevention and Early Detection......Page 779
Treatment......Page 780
KEY EXPERIMENT The Discovery of Proto-Oncogenes......Page 761
MOLECULAR MEDICINE STI-571: Cancer Treatment Targeted against the bcr/abl Oncogene......Page 783
Summary and Key Terms......Page 785
References and Further Reading......Page 787
Answers to Questions......Page 791
Glossary......Page 803
Index......Page 823