THE CELL A Molecular Approach Sixth Edition Geoffrey M. Cooper Robert E. Hausman Boston University Sinauer Associates, Inc. Publishers Sunderland, Massachusetts U.S.A.
Brief Contents PART I 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 151 Chapter 5 Chapter 6 The Organization and Sequences of Cellular Genomes 153 Replication, Maintenance, and Rearrangements of Genomic DNA 191 Chapter 7 RNA Synthesis and Processing 239 Chapter 8 Protein Synthesis, Processing, and Regulation 297 PART III Cell Structure and Function 343 Chapter 9 The Nucleus 345 Chapter 10 Protein Sorting and Transport 373 Chapter 11 Bioenergetics and Metabolism 421 Chapter 12 The Cytoskeleton and Cell Movement 459 Chapter 13 The Plasma Membrane 515 Chapter 14 Cell Walls, the Extracellular Matrix, and Cell Interactions 557 PART IV Cell Regulation 587 Chapter 15 Cell Signaling 589 Chapter 16 The Cell Cycle 641 Chapter 17 Cell Death and Cell Renewal 681 Chapter 18 Cancer 713
Contents Preface xix Organization and Features of The Cell xxi Media and Supplements to Accompany The Cell xxiii Part I Introduction 1 CHAPTER 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 9 The origin of eukaryotes 10 The development of multicellular organisms 13 Cells as Experimental Models 17 E. coli 17 Yeasts 18 Caenorhabditis elegans 18 Drosophila melanogaster 19 Arabidopsis thaliana 19 Vertebrates 20 Tools of Cell Biology 22 Light microscopy 22 Electron microscopy 28 Subcellular fractionation 31 Growth of animal cells in culture 32 Culture of plant cells 36 Viruses 36 Animal Cell Culture 34 Viruses and Cancer 37 Summary and Key Terms 39 Questions 40 References and Further Reading 41 CHAPTER 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 59 Transport across cell membranes 62 Proteomics: Large-Scale Analysis of Cell Proteins 65 Identification of cell proteins 65 Global analysis of protein localization 67 Protein interactions 68
Contents ix The Folding of Polypeptide Chains 54 The Structure of Cell Membranes 62 Summary and Key Terms 70 Questions 71 References and Further Reading 71 CHAPTER 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 90 The Biosynthesis of Cell Constituents 91 Carbohydrates 92 Lipids 93 Proteins 94 Nucleic acids 98 Antimetabolites and Chemotherapy 97 Phenylketonuria 98 Summary and Key Terms 99 Questions 100 References and Further Reading 101 CHAPTER 4 Fundamentals of Molecular Biology 103 Heredity, Genes, and DNA 103 Genes and chromosomes 103 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 120 Vectors for recombinant DNA 122 DNA sequencing 124 Expression of cloned genes 126 Detection of Nucleic Acids and Proteins 127 Amplification of DNA by the polymerase chain reaction 127 Nucleic acid hybridization 129 Antibodies as probes for proteins 132 Gene Function in Eukaryotes 135 Genetic analysis in yeasts 135 Gene transfer in plants and animals 136 Mutagenesis of cloned DNAs 139 Introducing mutations into cellular genes 140 Interfering with cellular gene expression 142 The DNA Provirus Hypothesis 117 RNA Interference 144 Summary and Key Terms 146 Questions 148 References and Further Reading 148
x Contents Part II The Flow of Genetic Information 151 CHAPTER 5 The Organization and Sequences of Cellular Genomes 153 The Complexity of Eukaryotic Genomes 153 Introns and exons 155 Repetitive DNA sequences 159 Gene duplication and pseudogenes 161 The Sequences of Complete Genomes 162 The genomes of bacteria and yeast 163 The genomes of Caenorhabditis elegans, Drosophila melanogaster, and other invertebrates 165 Plant genomes 166 The human genome 166 The genomes of other vertebrates 169 Chromosomes and Chromatin 171 Chromatin 172 Centromeres 176 Telomeres 180 Bioinformatics and Systems Biology 181 Systematic screens of gene function 181 Regulation of gene expression 182 Variation among individuals and genomic medicine 184 The Discovery of Introns 156 The Human Genome 167 Summary and Key Terms 186 Questions 187 References and Further Reading 188 CHAPTER 6 Replication, Maintenance, and Rearrangements of Genomic DNA 191 DNA Replication 191 DNA polymerases 192 The replication fork 193 The fidelity of replication 200 Origins and the initiation of replication 201 Telomeres and telomerase: maintaining the ends of chromosomes 205 DNA Repair 207 Direct reversal of DNA damage 208 Excision repair 210 Base-excision repair 210 Nucleotide-excision repair 210 Transcription-coupled repair 213 Mismatch repair 213 Translesion DNA synthesis 216 Repair of double-strand breaks 216 DNA Rearrangements 219 Site-specific recombination 219 Transposition via DNA intermediates 227 Transposition via RNA intermediates 228 Gene amplification 232 Colon Cancer and DNA Repair 215 Rearrangement of Immunoglobulin Genes 220
Contents xi Summary and Key Terms 233 Questions 235 References and Further Reading 236 CHAPTER 7 RNA Synthesis and Processing 239 Transcription in Prokaryotes 239 RNA polymerase and transcription 240 Repressors and negative control of transcription 243 Positive control of transcription 245 Eukaryotic RNA Polymerases and General Transcription Factors 245 Eukaryotic RNA polymerases 246 General transcription factors and initiation of transcription by RNA polymerase II 246 Transcription by RNA polymerases I and III 250 Regulation of Transcription in Eukaryotes 251 cis-acting regulatory sequences: promoters and enhancers 251 Transcription factor binding sites 255 Transcriptional regulatory proteins 258 Structure and function of transcriptional activators 260 Eukaryotic repressors 263 Regulation of elongation 264 Relationship of chromatin structure to transcription 266 Regulation of transcription by noncoding RNAs 271 DNA methylation 273 RNA Processing and Turnover 275 Processing of ribosomal and transfer RNAs 275 Processing of mrna in eukaryotes 277 Splicing mechanisms 279 Alternative splicing 286 RNA editing 288 RNA degradation 289 Isolation of a Eukaryotic Transcription Factor 259 The Discovery of snrnps 284 Summary and Key Terms 291 Questions 293 References and Further Reading 294 CHAPTER 8 Protein Synthesis, Processing, and Regulation 297 Translation of mrna 297 Transfer RNAs 298 The ribosome 299 The organization of mrnas and the initiation of translation 305 The process of translation 307 Regulation of translation 313 Protein Folding and Processing 319 Chaperones and protein folding 319 Enzymes that catalyze protein folding 322 Protein cleavage 323 Glycosylation 325 Attachment of lipids 327 Regulation of Protein Function 329 Regulation by small molecules 329 Protein phosphorylation and other modifications 330 Protein-protein interactions 335 Protein Degradation 335 The ubiquitin-proteasome pathway 335 Lysosomal proteolysis 338 Catalytic Role of Ribosomal RNA 304 The Discovery of Protein-Tyrosine Kinases 333 Summary and Key Terms 339 Questions 340 References and Further Reading 341
xii Contents Part III Cell Structure and Function 343 CHAPTER 9 The Nucleus 345 The Nuclear Envelope and Traffic between the Nucleus and the Cytoplasm 345 Structure of the nuclear envelope 346 The nuclear pore complex 350 Selective transport of proteins to and from the nucleus 353 Regulation of nuclear protein import 356 Transport of RNAs 357 Internal Organization of the Nucleus 359 Chromosome organization and gene expression 359 Sub-compartments within the nucleus 362 The Nucleolus and rrna Processing 365 Ribosomal RNA genes and the organization of the nucleolus 365 Transcription and processing of rrna 367 Ribosome assembly 368 Additional functions of the nucleolus 369 Nuclear Lamina Diseases 348 Identification of Nuclear Localization Signals 352 Summary and Key Terms 370 Questions 371 References and Further Reading 372 CHAPTER 10 Protein Sorting and Transport 373 The Endoplasmic Reticulum 373 The endoplasmic reticulum and protein secretion 374 Targeting proteins to the endoplasmic reticulum 376 Insertion of proteins into the ER membrane 381 Protein folding and processing in the ER 386 Quality control in the ER 389 The smooth ER and lipid synthesis 392 Export of proteins and lipids from the ER 395 The Golgi Apparatus 398 Organization of the Golgi 398 Protein glycosylation within the Golgi 400 Lipid and polysaccharide metabolism in the Golgi 402 Protein sorting and export from the Golgi apparatus 403 The Mechanism of Vesicular Transport 406 Experimental approaches to understanding vesicular transport 406 Cargo selection, coat proteins, and vesicle budding 407 Vesicle fusion 410 Lysosomes 412 Lysosomal acid hydrolases 412 Endocytosis and lysosome formation 414 Phagocytosis and autophagy 416
Contents xiii The Signal Hypothesis 378 Gaucher Disease 413 Summary and Key Terms 417 Questions 419 References and Further Reading 419 CHAPTER 11 Bioenergetics and Metabolism 421 Mitochondria 421 Organization and function of mitochondria 422 The genetic system of mitochondria 424 Protein import and mitochondrial assembly 425 The Mechanism of Oxidative Phosphorylation 431 The electron transport chain 431 Chemiosmotic coupling 432 Transport of metabolites across the inner membrane 436 Chloroplasts and Other Plastids 438 The structure and function of chloroplasts 438 The chloroplast genome 440 Import and sorting of chloroplast proteins 441 Other plastids 444 Photosynthesis 446 Electron transport 446 ATP synthesis 449 Peroxisomes 450 Functions of peroxisomes 451 Peroxisome assembly 453 Diseases of Mitochondria: Leber s Hereditary Optic Neuropathy 426 The Chemiosmotic Theory 434 Summary and Key Terms 455 Questions 457 References and Further Reading 458 CHAPTER 12 The Cytoskeleton and Cell Movement 459 Structure and Organization of Actin Filaments 459 Assembly and disassembly of actin filaments 460 Organization of actin filaments 465 Association of actin filaments with the plasma membrane 467 Protrusions of the cell surface 471 Actin, Myosin, and Cell Movement 472 Muscle contraction 473 Contractile assemblies of actin and myosin in nonmuscle cells 477 Unconventional myosins 479 Formation of protrusions and cell movement 480 Microtubules 482 Structure and dynamic organization of microtubules 482 Assembly of microtubules 485 Organization of microtubules within cells 488 Microtubule Motors and Movement 490 Identification of microtubule motor proteins 490 Cargo transport and intracellular organization 493 Cilia and flagella 496 Reorganization of microtubules during mitosis 499 Chromosome movement 500 Intermediate Filaments 502 Intermediate filament proteins 502 Assembly of intermediate filaments 504 Intracellular organization of intermediate filaments 505 Functions of intermediate filaments: keratins and diseases of the skin 507 The Isolation of Kinesin 491
xiv Contents Expression of Mutant Keratin Causes Abnormal Skin Development 508 Summary and Key Terms 510 Questions 512 References and Further Reading 512 CHAPTER 13 The Plasma Membrane 515 Structure of the Plasma Membrane 515 The phospholipid bilayer 515 Membrane proteins 519 Mobility of membrane proteins 524 The glycocalyx 525 Transport of Small Molecules 526 Passive diffusion 526 Facilitated diffusion and carrier proteins 527 Ion channels 529 Active transport driven by ATP hydrolysis 537 Active transport driven by ion gradients 540 Endocytosis 544 Phagocytosis 544 Receptor-mediated endocytosis 545 Protein trafficking in endocytosis 550 Cystic Fibrosis 541 The LDL Receptor 548 Summary and Key Terms 553 Questions 554 References and Further Reading 555 CHAPTER 14 Cell Walls, the Extracellular Matrix, and Cell Interactions 557 Cell Walls 557 Bacterial cell walls 557 Eukaryotic cell walls 557 The Extracellular Matrix and Cell-Matrix Interactions 564 Matrix structural proteins 564 Matrix polysaccharides 568 Matrix adhesion proteins 569 Cell-matrix interactions 571 Cell-Cell Interactions 574 Adhesion junctions 574 Tight junctions 577 Gap junctions 578 Plasmodesmata 581 The Characterization of Integrin 572 Gap Junction Diseases 580 Summary and Key Terms 582 Questions 583 References and Further Reading 584
Contents xv Part IV Cell Regulation 587 CHAPTER 15 Cell Signaling 589 Signaling Molecules and Their Receptors 589 Modes of cell-cell signaling 590 Steroid hormones and the nuclear receptor superfamily 591 Nitric oxide and carbon monoxide 593 Neurotransmitters 594 Peptide hormones and growth factors 594 Eicosanoids 596 Plant hormones 598 Functions of Cell Surface Receptors 599 G protein-coupled receptors 600 Receptor protein-tyrosine kinases 603 Cytokine receptors and nonreceptor protein-tyrosine kinases 606 Receptors linked to other enzymatic activities 607 Pathways of Intracellular Signal Transduction 608 The camp pathway: second messengers and protein phosphorylation 608 Cyclic GMP 611 Phospholipids and Ca 2+ 612 The PI 3-kinase/Akt and mtor pathways 615 MAP kinase pathways 617 The JAK/STAT and TGF-b/Smad pathways 623 NF-kB signaling 625 The Hedgehog, Wnt, and Notch pathways 625 Signal Transduction and the Cytoskeleton 628 Integrins and signal transduction 628 Signaling from cell adhesion molecules 630 Regulation of the actin cytoskeleton 630 Signaling Networks 632 Feedback and crosstalk 632 Networks of cellular signal transduction 634 G Protein-Coupled Receptors and Odor Detection 601 Cancer: Signal Transduction and the ras Oncogenes 620 Summary and Key Terms 635 Questions 637 References and Further Reading 638 CHAPTER 16 The Cell Cycle 641 The Eukaryotic Cell Cycle 641 Phases of the cell cycle 642 Regulation of the cell cycle by cell growth and extracellular signals 644 Cell cycle checkpoints 646 Restricting DNA replication to once per cell cycle 647 Regulators of Cell Cycle Progression 647 Protein kinases and cell cycle regulation 647 Families of cyclins and cyclin-dependent kinases 653 Growth factors and the regulation of G 1 Cdk s 655 DNA damage checkpoints 658 The Events of M Phase 659 Stages of mitosis 659 Entry into mitosis 662 The spindle assembly checkpoint and progression to anaphase 666
xvi Contents Cytokinesis 667 Meiosis and Fertilization 668 The process of meiosis 668 Regulation of oocyte meiosis 671 Fertilization 673 The Discovery of MPF 649 The Identification of Cyclin 652 Summary and Key Terms 675 Questions 677 References and Further Reading 677 CHAPTER 17 Cell Death and Cell Renewal 681 Programmed Cell Death 681 The events of apoptosis 682 Caspases: the executioners of apoptosis 685 Central regulators of apoptosis: the Bcl-2 family 686 Signaling pathways that regulate apoptosis 689 Alternative pathways of programmed cell death 692 Stem Cells and the Maintenance of Adult Tissues 692 Proliferation of differentiated cells 693 Stem cells 695 Medical applications of adult stem cells 701 Pluripotent Stem Cells, Cellular Reprogramming, and Regenerative Medicine 703 Embryonic stem cells 704 Somatic cell nuclear transfer 705 Induced pluripotent stem cells 707 Transdifferentiation of somatic cells 708 Identification of Genes Required for Programmed Cell Death 684 Culture of Embryonic Stem Cells 702 Summary and Key Terms 708 Questions 710 References and Further Reading 710 CHAPTER 18 Cancer 713 The Development and Causes of Cancer 713 Types of cancer 713 The development of cancer 715 Causes of cancer 717 Properties of cancer cells 718 Transformation of cells in culture 722 Tumor Viruses 723 Hepatitis B and C viruses 723 Small DNA tumor viruses 724 Herpesviruses 726 Retroviruses 726 Oncogenes 727 Retroviral oncogenes 727 Proto-oncogenes 728 Oncogenes in human cancer 731 Functions of oncogene products 735 Tumor Suppressor Genes 741 Identification of tumor suppressor genes 741 Functions of tumor suppressor gene products 745 Roles of oncogenes and tumor suppressor genes in tumor development 748 Molecular Approaches to Cancer Treatment 749 Prevention and early detection 749 Treatment 750 The Discovery of Proto-Oncogenes 730 Imatinib: Cancer Treatment Targeted against the bcr/abl Oncogene 752
Contents xvii Summary and Key Terms 755 Questions 757 References and Further Reading 757 Answers to Questions 761 Glossary 773 Illustration Credits 797 Index 799