THE CELL. GEOFFREY M. COOPER ROBERT E. HAUSMAN Boston University. Fifth Edition. ASM PRESS Washington, D.C. Sunderland, Massachusetts

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1 THE CELL Fifth Edition GEOFFREY M. COOPER ROBERT E. HAUSMAN Boston University ASM PRESS Washington, D.C. 1 SINAUER ASSOCIATES, INC. Sunderland, Massachusetts

2 Brief Contents PARTI Introduction 1 Chapter 1 An Overview of Cells and Cell Research 3 Chapter 2 The Composition of Cells 43 Chapter 3 Cell Metabolism 73 Chapter 4 Fundamentals of Molecular Biology 103 PART II The Flow of Genetic Information 153 Chapter 5 The Organization and Sequences of Cellular Genomes 155 Chapter 6 Replication, Maintenance, and Rearrangements of Genomic DNA 201 Chapter 7 RNA Synthesis and Processing 251 Chapter 8 Protein Synthesis, Processing, and Regulation 309 PART III Cell Structure and Function 353 Chapter 9 The Nucleus 355 Chapter 10 Protein Sorting and Transport: The Endoplasmic Reticulum, Golgi Apparatus, and Lysosomes 383 Chapter 11 Bioenergetics and Metabolism: Mitochondria, Chloroplasts, and Peroxisomes 433 Chapter 12 The Cytoskeleton and Cell Movement 473 Chapter 13 The Plasma Membrane 529 Chapter 14 Cell Walls, the Extracellular Matrix, and Cell Interactions 571 PART IV Cell Regulation 601 Chapter 15 Cell Signaling 603 Chapter 16 The Cell Cycle 653 Chapter 17 Cell Death and Cell Renewal 693 Chapter 18 Cancer 725

3 Contents Preface xiii Organization and Features of The Cell xv Media and Supplements to Accompany The Cell xvii 1An 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 f. co// 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 Culture of Plant Cells 36 Viruses 37 Animal Cell Culture 34 Viruses and Cancer 37 PART I INTRODUCTION 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 Cell Membranes 58 Membrane Lipids 58 Membrane Proteins 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 The Folding of Polypeptide Chains 54 The Structure of Cell Membranes 60 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 Phenylketonuria 97 Antimetabolites and Chemotherapy 98 Summary and Key Terms 99 Questions 100 References and Further Reading 101

4 CONTENTS VII 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 Recombinant DNA 118 Restriction Endonucleases 118 Generation of Recombinant DNA "Molecules V20 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 The DNA Provirus Hypothesis 116 RNA Interference 146 Summary and Key Terms 148 Questions ISO References and Further Reading ISO PART II The Organization 5 and Sequences of Cellular Genomes 155 The Complexity of Eukaryotic Genomes 155 Intronsand Exons 157 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 FLOW OF GENETIC INFORMATION 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 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 The Discovery of Introns 158 The Human Genome 186 Summary and Key Terms 195 Questions 198 References and Further Reading 198 Replication, 6 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

5 VIM CONTENTS DNA Repair 216 Direct Reversal of DNA Damage 216 Excision Repair 219 Translesion DNA Synthesis 224 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 Transposition via DNA Intermediates 240 Transposition via RNA- Intermediates 242 Gene Amplification 245 Colon Cancer and DNA Repair 225 Rearrangement of Immunoglobulin Genes 236 Summary and Key Terms 247 Questions 249 References and Further Reading 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 c/5-acting Regulatory Sequences: Promoters and Enhancers 265 Transcription Factor Binding Sites 269 Transcriptional Regulatory Proteins 270 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 Alternative Splicing 298 RNA Editing 300 RNA Degradation 301 Isolation of a Eukaryotic Transcription Factor 272 The Discovery of snrnps 294 Summary and Key Terms 303 Questions 305 References and Further Reading Protein Synthesis, Processing, and Regulation 309 Translation of mrna 309 Transfer RNAs 310 TheRibosome 311 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 Protein Degradation 345 The Ubiquitin-Proteasome Pathway 345 Lysosomal Proteolysis 348 Catalytic Role of Ribosomal RNA 316 The Discovery of Protein-Tyrosine Kinases 344 Summary and Key Terms 349 Questions 351 References and Further Reading 351

6 CONTENTS IX PART III 9 The Nucleus 355 The Nuclear Envelope and Traffic between the Nucleus and the Cytoplasm 355 Structure of the Nuclear Envelope 356 The Nuclear Pore Complex 360 Selective Transport of Proteins to and from the Nucleus 361 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 Nuclear Lamina Diseases 358 Identification of Nuclear Localization Signals 362 Summary and Key Terms 379 Questions 381 References and Further Reading 381 CELL STRUCTURE AND FUNCTION 111 Protein Sorting V 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 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 Endocytosis and Lysosome Formation 426 Phagocytosis and Autophagy 426 The Signal Hypothesis 388 Caucher Disease 425 Summary and Key Terms 429 Questions 431 References and Further Reading Bioenergetics and I 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 The Mechanism of Oxidative Phosphorylation 445 The Electron Transport Chain 445 Chemiosmotic Coupling 446 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

7 CONTENTS 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 Diseases of Mitochondria: Leber's Hereditary Optic Neuropathy 438 The Chemiosmotic Theory 448 Summary and Key Terms 469 Questions 471 References and Further Reading 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 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 Cargo Transport and Intracellular Organization 515 Cilia and Flagella 516 Reorganization of Microtubules during Mitosis 519 Chromosome Movement 520 Expression of Mutant Keratin Causes Abnormal Skin Development 502 The Isolation of Kinesin 512 Summary and Key Terms 522 Questions 525 References and Further Reading 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 Active Transport Driven by Ion Gradients 555 Endocytosis 557 Phagocytosis 557 Receptor-Mediated Endocytosis 558 Protein Trafficking in Endocytosis 563 Cystic Fibrosis 554 The LDL Receptor 560 Summary and Key Terms 567 Questions 568 References and Further Reading 568 Cell Walls, the 14 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 Cell-Cell Interactions 587 Adhesion junctions 587 Tight Junctions 590 Gap Junctions 591 Plasmodesmata 595 The Characterization of Integrins 584 Gap Junction Diseases 594 Summary and Key Terms 596 Questions 598 References and Further Reading 598

8 CONTENTS XI Ik Cell Signaling J 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 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 Ca The PI 3-Kinase/Akt and mtor Pathways 628 MAP Kinase Pathways 630 The JAK/STAT and TGF-/3/Smad Pathways 636 NF-JCB Signaling 637 The Hedgehog, Wnt, and Notch Pathways 638 PART IV CELL REGULATION 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 C Protein-Coupled Receptors and Odor Detection 616 Cancer: Signal Transduction and the rasoncogenes 633 Summary and Key Terms 647 Questions 650 References and Further Reading The Eukaryotic Cell Cycle 653 The 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 Families of Cyclins and Cyclin- Dependent Kinases 664 Growth Factors and the Regulation of G, 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 The Discovery of MPF 660 The Identification of Cyclin 663 Summary and Key Terms 688 Questions 690 References and Further Reading Programmed Cell Death 693 Cell Death and Cell Renewal 693 The Events of Apoptosis 694 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

9 XII CONTENTS 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 Embryonic Stem Cells 716 Somatic Cell Nuclear Transfer 718 Induced Pluripotent Stem Cells 719 Identification of Genes Required for Programmed Cell Death 696 Culture of Embryonic Stem Cells 715 Summary and Key Terms 720 Questions 722 References and Further Reading 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 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 The Discovery of Proto-Oncogenes 742 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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