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MOLECULARAND
CELLULARBIOLOGY
STEPHEN L. WOLFEUniversity of California at Davis
TechnischeHochschuleDarmsta^FACHBEREjCH1.0-bICt.OGiE
BibWb^iek -- Bi
Inv.-N.v
Wadsworth Publishing CompanyBelmont, California
A Division of Wadsworth, Inc.
DETAILED CONTENTS
i
INTRODUCTION TO CELLAND MOLECULAR BIOLOGY
Introduction to Cell Structure 2
Prokaryotic Cells 6
Eukaryotic Cells 8The Nucleus 10 The Cytoplasm 12Specialized Cytoplasmic Structures of PlantCells 19
Viruses 23Viral Structure 23 Viral Infective Cycles 24Origin and Significance of Viruses 28 Viroidsand Prions 28
Historical Origins of Cell and Molecular Biology 29The Discovery of Cells 29 Development of theCell Theory 30 Early Chemical Investigationsin Cell Biology 32 Integration of Chemical andMorphological Studies 32 The MolecularRevolution 35
CHEMICAL BONDS AND BIOLOGICAL MOLECULES
Chemical Bonds Important in Biological Molecules 39Ionic Bonds 40 Covalent Bonds 40 UnequalElectron Sharing, Hydrogen Bonds, and Water 42van der Waals Forces 43
Functional Groups in Biological Molecules 44The Hydroxyl Group and Alcohols 44 TheCarbonyl Group, Aldehydes, and Ketones 45
INFORMATION BOX 2-1: Condensation andHydrolysis 46
The Carboxyl Group and Organic Acids 46The Amino Group 46 The PhosphateGroup 47 The Sulfhydryl Group 47
Major Classes of Biological Molecules:Carbohydrates 47
Carbohydrate Structure 47.- INFORMATION BOX 2-2: Adds, Bases, and pH 48
INFORMATION BOX 2-3: Stereoisomers 51Linkage of Monosaccharides into Disaccharidesand Polysaccharides 51
Lipids 53Neutral Lipids 53 Phospholipids 55Steroids 57 Glycolipids 58
Proteins 59The Amino Acid Subunits of Proteins 59Primary Structure: The Linkage of Amino Acidsto Form Proteins 62 Secondary Structure:Restrictions on the Movement of PolypeptideChains 62 Tertiary Structure: The Three-Dimensional Structure of Polypeptide Chains 65Quaternary Structure: Associations of MultiplePolypeptide Chains 67 Combination ofProteins with Other Substances 68
INFORMATION BOX 2-4: The Coiled Coil 69
Nucleotides and Nucleic Acids 70The Nucleotides 71 DNA and RNA 72
SUPPLEMENT 2-1: Atomic Structure 77The Atomic Nucleus 77 The Electrons of anAtom 78
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ENERGY, ENZYMES, AND BIOLOGICAL REACTIONS
Chemical and Physical Laws Governing Reactions 80Spontaneous Reactions and the Laws ofThermodynamics 80 Using the First andSecond Laws to Predict the Rate and Directionof Chemical Reactions 81 ReversibleReactions 82 How Living Organisms PushReversible Reactions Uphill 82 The StandardFree Energy Change 83
The Role of Enzymes in Biological Reactions 85Enzymes and Enzymatic Catalysis 85 Enzymesand Activation Energy 85 Characteristics ofProtein-Based Enzymes 86 Enzyme-SubstrateComplexes and the Active Site 88 CatalyticMechanisms at the Active Site 89 MechanismsContributing to the Transition State 91
THE EXPERIMENTAL PROCESS: Catalytic Antibodies:
Tailor-Made Catalysts 92The Active Site, Transition State, and ReversibleReactions 95
Factors Affecting Enzyme Activity 95.The Effects of Substrate Concentration onEnzyme Activity 95 Enzyme Regulation byAllostery and Covalent Modification 98
RNA-Based Catalysts 101SUPPLEMENT 3-1: A Quantitative Treatment of EnzymeSaturation and Inhibition: The Michaelis-MentenEquation 105
EHAl'TI-R 4
MAJOR INVESTIGATIVE METHODS OF CELL ANDMOLECULAR BIOLOGY
Light and Electron Microscopy 108The Light Microscope and Its Applications 108Electron Microscopy 112
Preparation of Specimens for Microscopy 117Specimen Preparation for Light Microscopy 117Specimen Preparation for Electron Microscopy 119
Cell Culture 121Culturing Cells from Higher Eukaryotes 121Cell Fusion 123
Fractionation and Purification of Cell Structuresand Molecules 123
Centrifugation 124 Gel Electrophoresis 126Chromatography 130
Methods for Characterizing Individual CellMolecules 132
X-Ray Diffraction 132 Obtaining DNASequences in Quantity 134
INFORMATION BOX 4-1: DNA Melting and
Reannealing 135THE EXPERIMENTAL PROCESS: The Unlikely Origin
of the Polymerase Chain Reaction 140
DNA Sequencing 142 Deducing ProteinSequences from DNA Sequences 145
SUPPLEMENT 4-1: Lenses and Image Formation in theLight Microscope 149
: CHAPTER 5
THE STRUCTURE OF CELLULAR MEMBRANES
Lipid and Protein Molecules of BiologicalMembranes 153
Membrane Lipids 154INFORMATION BOX 5-1: Phosphoglyceride
Structure 156INFORMATION BOX 5-2: Sphingolipid Structure 158
Membrane Proteins 159INFORMATION BOX 5-3: Hopanoids 160
Phospholipid Bilayers and Biological Membranes 163Physical Characteristics of Artificial andNatural Bilayers 163 Effects of Cholesterol onthe Phase Transition 164 Regulation of thePhase Transition in Living Organisms 165
The Fluid Mosaic Model and Its SupportingEvidence 166
Features of the Fluid Mosaic Model 166Evidence Supporting the Fluid MosaicModel 169
THE EXPERIMENTAL PROCESS: How Do Ions Get
Across Membranes? 174
Membrane Biogenesis 179Lipid Biogenesis and MembraneAsymmetry 179 Origins of MembraneProteins 180
Historical Developments Leading to the Fluid MosaicModel 181
The Discovery of Membrane Lipids andBilayers 181 Membrane Proteins and theDanielli-Davson Model 182 Final StepsToward the Fluid Mosaic Model 183SUPPLEMENT 5-1: Membrane Fusion 186
FUNCTIONS OF MEMBRANES IN IONIC AND
ECULAR TRANSPORT
|ive Transport 190
fiffusion as the Basis for Passive Transport 190phe Effects of Semipermeable Membranes ondiffusion 191 Biological Membranes andpassive Transport: Facilitated Diffusion 193[Transporter Types Operating in Facilitated"Diffusion 196
j p EXPERIMENTAL PROCESS: Identification of the
pnino Acids Forming the Conduction PathwayiPotassium Channels 198
he Passive Transport of Water Through LipidSlayers 204
jive Transport 205
[Characteristics of Active Transport 205P-Type Direct Active Transport Pumps 206V-Type Direct Active Transport Pumps 210Indirect Active Transport Pumps 211^Transport, Membrane Potentials, and Nervediction 212jlembrane Potentials 212 Voltage-Gatedlembrane Channels and the Action
potential 213MFORMATION BOX 6-1: Coordination of Passive
and Active Transport in the Maintenance of•llular Ion Concentrations 214TORMATION BOX 6-2: Quantitative Estimations
f Membrane Potential: The Nernst Equation 216FORMATION BOX 6-3: The Voltage Clamp 217
Movement of Impulses Along an Axon:opagation of the Action Potential 218
altatory Conduction in Myelinatedvleurons 219 Ligand-Gated MembraneChannels and the Conduction of Nerve
Impulses Between Neurons and Other Cells 220
SUPPLEMENT 6-1: Transport in Bacteria 227
Porins and Transport Through the Outer Membraneof Gram-Negative Bacteria 227 Transport Throughthe Bacterial Plasma Membrane 228 •
j CHAPTER 7
THE CELL SURFACE ANDINTRACELLULAR COMMUNICATION
Molecules of the Cell Surface 233Membrane Glycolipids and Glycoproteins in CellRecognition 234
Major Histocompatibility Complex (MHC)Molecules 234 Blood Groups and OtherSurface Markers 235
Surface Receptors and Receptor-ResponseMechanisms 236
Receptors Binding Peptide Hormones, GrowthFactors, and Neurotransmitters 238 Receptorswith Integral Protein Kinase Activity 239Receptors with Separate Protein KinaseActivity 241 Operation of the cAMP andInsP3/DAG Receptor-Response Pathways 245
THE EXPERIMENTAL PROCESS: The Road to the
Phosphoinositide-Generated SecondMessengers 248INFORMATION BOX 7-1: Calmodulin 251
Integration, Regulation, and Termination ofReceptor-Response Activity 252
Cell Adhesion 253Characteristics of Cell Adhesion 254 Types ofCell Adhesion Molecules 254
Developmental Interactions of Cell AdhesionMolecules 255Cell Junctions 256
Adhesive Junctions 256 Tight Junctions 260~~" Gap Junctions 262
SUPPLEMENT 7-1: Recognition, Reception, and CellAdhesion in Bacteria 270
Bacterial Recognition and Adhesion 270 BacterialReceptors Inducing Internal Responses 271
; CHAPTER 8
THE EXTRACELLULAR MATRIXOF EUKARYOTIC CELLS
Animal Extracellular Structures 274The Primary Fiber: Collagens 274 The NetworkSurrounding Collagen Fibers: Proteoglycans 279Linkage of the Collagen-Proteoglycan Complex tothe Cell Surface 282
Extracellular Structures of Plants: Cell Walls 287Molecular Constituents of Plant Cell Walls 287Cell Wall Structure 292 Cell Wall Growth inHigher Plants 293 Plasmodesmata:Communicating Junctions of Plant Cells 295
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THE EXPERIMENTAL PROCESS: Cell/CellCommunication in Plants: An Open and ShutCase 296SUPPLEMENT 8-1: Cell Walls in Prokaryotes 302
Cell Wall Structure in Gram-Positive and Gram-Negative Bacteria 302 Molecular Constituents ofProkaryotic Cell Walls 303 The Capsule 308 CellWall Structure in Cyanobacteria 308
| CHAPTER 9
ENERGY FOR CELL ACTIVITIES: CELLULAROXIDATIONS AND THE MITOCHONDRION
Pathways Producing ATP: An Overview 310The Source of Electrons at Elevated EnergyLevels 311 The Electron Transport System 311 ""-ATP Synthesis 311
Oxidative Reactions Supplying Electrons for ElectronTransport 311
INFORMATION BOX 9-1: Oxidation andReduction 312
The First Major Stage: Glycolysis 312INFORMATION BOX 9-2: The Pentose PhosphatePathway 319
The Second Major Stage: Pyruvate Oxidationand the Citric Acid Cycle 320 The Products ofComplete Glucose Oxidation 327 FunnelingFats and Proteins into Oxidative Pathways 327
The Mitochondrial Electron Transport System 327Carrier Groups and Their Sequence in ElectronTransport 328
INFORMATION BOX 9-3: Placing Electron Carriersin Sequence 332
Organization of Prosthetic Groups withProteins in Electron Transport 333H+ Pumping by the Electron TransportSystem 335 Discovery of MitochondrialElectron Transport 337
The Mitochondrial FOF1 ATPase and ATPSynthesis 337
Structure of ̂ F , ATPase 337 „THE EXPERIMENTAL PROCESS: Divide and Conquer:Deciphering the Functions of a Polypeptide of theChloroplast ATP Synthase 338
The Mechanism of ATP Synthesis by F^F,ATPase 343 Evidence That an H+ GradientDrives ATP Synthesis 344 Total ATPProduction from Glucose Oxidation 344
Some Details of Mitochondrial Structure andOccurrence 345
Mitochondrial Inclusions 345 Isolation ofMitochondrial Components 345 Occurrence ofMitochondria 347
Mitochondrial Transport 347INFORMATION BOX 9-4: Mitochondria and HeatGeneration 348
Porins and Transport Through the OuterMembrane 349 Transport Carriers of the InnerMembrane 350
Oxidative Reactions in Microbodies: Peroxisomes andGlyoxisomes 351
Microbodies and Fatty Acid Oxidation 353Microbodies and the Glyoxylate Cycle:Glyoxisomes 354 The Glycolate Pathway 355Other Biochemical Pathways inMicrobodies 355 Microbodies and the CellularEconomy 356
SUPPLEMENT 9-1: FATTYACID OXIDATION 360Bacterial F ^ ATPase 361
SUPPLEMENT 9-2: Oxidative Metabolism inProkaryotes 362
Electron Transport in Bacteria 362 Oxidations andATP Synthesis in Cyanobacteria 364
•JE.
SYNTHESIS AND THE CHLOROPLAST
irivays of Photosynthesis: An Overview 367"|he First Major Step: The Light Reactions 367
"he Second Major Step: The Dark Reactions 368iLocation of the Light and Dark Reactions inEukaryotes: The Chloroplast 369
Ight Reactions 370Ight and Light Absorption 370 The Structureof Chlorophyll and Other Light-AbsorbingMolecules 371 The Organization of
|Photosynthetic Pigments in Chloroplasts 373he Electron Transport System Linking the
|Photosystems 374 Cyclic Electron Flow Withinhe Z Pathway 379 H+ Pumping by the Z"athway 380 Using the H+ Gradient to
Synthesize ATP 380 Organization of Light-|Reaction Components in Thylakoid|Membranes 381 The Light Reactionspand the Chemiosmotic Mechanism 382
INFORMATION BOX 10-1: Balancing theBhotosystems 384fbark Reactions 385Tracing the Pathways of the Dark Reactions 385
he C3 Cycle 386[INFORMATION BOX 10-2: The Oxygenase Activity
JMRuBP Carboxylase and Photorespiration: AnEvolutionary Fly in the PhotosyntheticOintment 390
he C4 Cycle 391HE EXPERIMENTAL PROCESS: The C4 Pathway: A
^Surprise Option for Photosynthetic Carbon
ssimilation 392
he Details of Chloroplast Structure andurrence 394
Soroplast Transport 396SUPPLEMENT 10-1: The C4 Cycle and CAMMetabolism 402* The C4 Cycle 402 The CAM Pathway 404SUPPLEMENT 10-2: Plastids and Plastiddevelopment 404
SUPPLEMENT 10-3: Photosynthesis in Prokaryotes 407The Photosynthetic Bacteria 407
The Motile Functions of Microtubules 429Dynein and Microtubule Sliding 429 MotileSystems Based on Microtubule Sliding: Flagellaand Cilia 432 Cytoplasmic Dynein andKinesin in Fast Axonal Transport 440
THE EXPERIMENTAL PROCESS: Identification of
Microtubule Motors Involved in AxonalTransport 442
Motile Systems Based on MicrotubuleGrowth 444 Other Microtubule-PoweredMechanisms 444
SUPPLEMENT 11-1: Bacterial Flagella 447Structure 447 The Flagellar Motor 448 FlagellarRotation and Bacterial Swimming Behavior 450
HBfaCHAPTER 12
1CROTUBULES AND MICROTUBULE-BASEDLfiMOTILITY
IKrotubule Structure and Biochemistry 418"** .Microtubule Structure 418" The Tubulins 419
gPolymerization of Tubulins into Microtubules 421Microtubule Polarity, Dynamic Instability, andTreadmilling 421 Cellular Factors RegulatingMicrotubule Polymerization 425 Cellular Centersof Microtubule Polymerization: MTOCs 426Microtubule Poisons 427
MICROFILAMENTS AND MICROFILAMENT-BASEDCELL MOTILITY
Structure and Biochemistry of Microfilaments 452Microfilament Structure 452 Actins 454Assembly of Actin Molecules intoMicrofilaments 455 Microfilament Polarityand Treadmilling 455 Factors ModifyingMicrofilament Polymerization 457 Parallels inthe Biochemistry of Microfilaments andMicrotubules 460
Myosin and Microfilament-Based Motility 460
, Myosin Structure 460 Myosin II</; Superstructures: Thick Filaments 463
The Myosin Crossbridge Cycle 463THE EXPERIMENTAL PROCESS: Do the Two Heads of
the Myosin Molecule Function Independently orCooperatively? 464
Regulation of the Crossbridging Cycle 467Microfilament-Based Motile Systems 471
Striated Muscle Cells 471
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INFORMATION BOX 12-1: A Primer of Muscle CellTerms 474INFORMATION BOX 12-2: Storage and Supply of
ATP in Striated Muscle Cells 478Smooth Muscle Cells 480 Microfilament-BasedMotility in Nonmuscle Cells 482 MovementsGenerated by Microfilament Growth 486
SUPPLEMENT 12-1: Motility Without Microtubules orMicrofilaments 491
Motile Systems Based on Ca2+-Sensitive ContractileProteins 491
MICROTUBULES, MICROFILAMENTS,AND INTERMEDIATE FILAMENTS INTHE CYTOSKELETON
Structure and Biochemistry of IntermediateFilaments 496
Intermediate Filament Structure 497THE EXPERIMENTAL PROCESS: Of Mice and Men:Genetic Skin Diseases Arising from Defects inKeratin Filaments 498
Individual Intermediate Filament Types 502Intermediate Filament Assembly 504Intermediate Filament-Associated Proteins(IFAPs) 505 Intermediate FilamentRegulation 505
Cytoskeletal Roles of Intermediate Filaments,Microtubules, and Microfilaments 506
. Functions of Microtubules, Microfilaments, andIntermediate Filaments 506 Interlinkers andIntegration of the Cytoskeleton 507 OtherCytoskeletal Elements 508
Major Domains and Subdivisions of theCytoskeleton 508
Cytoskeletal Systems Associated with thePlasma Membrane 509 The Cytoskeleton of
the Cell Cortex 514 Cytoskeletal Structures ofthe Inner Cytoplasm 514
Dynamic Changes in the Cytoskeleton 517Cytoskeletal Alterations Related toMotility 517 Cytoskeletal Alterations inDeveloping Cells 517 CytoskeletalRearrangements During Cell Division 518Cytoskeletal Abnormalities and Disease 520
THE NUCLEUS AND ITSMOLECULAR CONSTITUENTS
DNA Structure 525The Watson-Crick Model 525
INFORMATION BOX 14-1: DNA Melting and
Renaturation 528Refinements to the Model: B-DNA and OtherDNA Conformations 529
THE EXPERIMENTAL PROCESS: The Discovery ofLeft-Handed Z-DNA 532INFORMATION BOX 14-2: Inverted Sequences
(Palindromes) 534Cruciform DNA 535 Chemical Modification ofDNA 536 DNA Supercoiling 537
Proteins Associated with DNA in EukaryoticNuclei 538
Histones 539 Nonhistone Proteins 541INFORMATION BOX 14-3: HistoneModifications 542
Combination of DNA and Histones in .Nucleosomes 546
Experiments Leading to the Discovery ofNucleosomes 547
INFORMATION BOX 14-4: DNA Endonucleases andNucleosome Periodicity 548
Nucleosome Assembly 549 NucleosomePhasing 550 Nucleosome Alteration DuringTranscription and Replication 551 Higher-Order Structure in Chromatin 551
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sization of Chromatin in the Cell Nucleus 553gterochromatin and Euchromatin 553fffolds and Domains 554 The Nuclear§rix555
puhdary of the Eukaryotic Nucleus: The Nuclear%fuclear Envelope Structure 557 Transport
ough the Nuclear Envelope 561EMENT 14-1: Nuclear Structure in
karyotes 567acterial Nucleoid Structure 567 Bacterialucleoid Proteins 568 Nucleoid Structure inIfanobacteria 569 Dinoflagellates: Eukaryotesitfi Prokaryotic DNA Organization 569IXMENT 14-2: Annulate Lamellae 571
JTRANSCRIPTION AND PROCESSINGJf :
Serai Features of RNA Structure, Transcription, andessing 574RNA Structure 574 RNA Transcription 575F̂ORMATION BOX 15-1: Footprinting 578
sIA Processing 581Icription and Processing of Messenger RNA 582' hRNA Structure 582 Isolation of mRNAs 585
!-mRNAs 585 Structure of mRNAejies 587 Transcription of Pre-mRNAs 596guessing Pre-mRNAs 596
piption and Processing of Ribosomal RNA 602| | e rRNAs 602IORMATION BOX 15-2: Determining Secondaryuctures in RNAs 604
|RNA Gene Structure, Transcription andgtrpcessing 607 5S rRNA Genes, Transcription,"fa Processing 613 rRNA and thelueleolus 616if 'gription and Processing of Transfer RNA 618ifA Structure 619 tRNA Genes 621 tRNA
transcription and Processing 622II RNAs: Small Nuclear and Small CytoplasmicH26|hRNAs: Genes, Transcription, and ,
sing 626 scRNAs628 \ Jptions in Chromatin Structure DuringIription 628
^Iterations in Regions Containing mRNAnes 628 Alterations in Regions Containing
JRNA Genes 629gE EXPERIMENTAL PROCESS: What Happens When
|A Polytnerase Encounters a Nucleosome? 630i|pLEMENT 15-1: RNA Transcription and Processing
^Prokaryotes 639Jiacteriai RNA Polymerase 639 Bacterial Genes and
heir Promoters 640 Sequence Elements Indicatingfermination of Bacterial Transcription 641Bacterial Transcription 642 mRNA Genes,Jjanscfiption, and Processing in Bacteria 642
Bacterial rRNAs and Their Genes, Transcription,and Processing 643 Bacterial tRNA Genes,Transcription, and Processing 645
I CIIAPTIIR 16
THE INTERACTION OF mRNA, rRNA,AND tRNA IN PROTEIN SYNTHESIS
The Assembly of Polypeptides on Ribosomes 650Initiation 652
THE EXPERIMENTAL PROCESS: When Sperm MeetsEgg: Initiation Factors and TranslationalControl at Fertilization 656
Elongation 658 Termination 663Ribosome Structure 665
Major Structural Features of Ribosomes 665Isolating and Identifying RibosomalProteins 667 Locating Individual Proteins,rRNAs, and Functions in Ribosomes 668Assembly of Ribosomes in the Test Tube 669
INFORMATION BOX 16-1: Locating RibosomalProteins and rRNAs 670
The Genetic Code for Protein Synthesis 671Solving the Code 671 Features of the GeneticCode 672 Degeneracy and the WobbleHypothesis 673 Exceptions to the Universalityof the Genetic Code 674 Preferences in CodonUsage 675
Amino Acid Activation 676The Reactions of Amino Acid Activation 676The Aminoacyl-tRNA Synthetase Enzymes 677
Posttranslational Modification and Folding of NewlyAssembled Polypeptides 680
Chemical Modifications 680 PolypeptideFolding 682
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SUPPLEMENT 16-1: Protein Synthesis inProkaryotes 687
Polypeptide Assembly in Bacteria 687 BacterialRibosomal Proteins 690
SUPPLEMENT 16-2: Nonribosomal Mechanisms ofProtein Synthesis 691
TRANSCRIPTIONAL ANDTRANSLATIONAL REGULATION
Transcriptional Regulation in Eukaryotes 694THE EXPERIMENTAL PROCESS: Sequential Clues tothe DNA Binding Specificity ofMyc 696
Regulation by Two Interacting Proteins: TheGAL4/80 System of Saccharomyces 699Regulation by a Heterodimer: Gene Control byAP-1 in Mammals 701 Cooperative Regulationof the Serum Albumin Gene 701 GenesControlled in Groups and Networks byRegulatory Proteins 702
Mechanisms Modifying Transcriptional Control byRegulatory Proteins 708
DNA Methylation and Genetic Regulation 708Histone Modifications and GeneticRegulation 710 Other Mechanisms AffectingTranscription 713
Specialized Mechanisms Regulating rRNA Genes 714Posttranscriptional Regulation 715
Posttranscriptional Regulation During mRNAProcessing 715 Posttranscriptional Regulationof mRNA Transport and Stability 716
Translational Regulation 717Translational Controls Regulating Steps inInitiation 717 Translational Controls at LaterStages of Protein Synthesis 720
Posttranslational Regulation 720SUPPLEMENT 17-1: Regulation in Prokaryotes 727
Transcriptional Regulation in Bacteria 727Translational Regulation in Bacteria 734
SUPPLEMENT 17-2: mRNA Transcription andRegulation in Polytene Chromosomes 736
Development and Structure of PolyteneChromosomes 736 Active Sites on PolyteneChromosomes: Bands and Puffs 737
CIIAPIIK IS
ORGANIZATION OF THE GENOMEAND GENETIC REARRANGEMENTS
Organization of Eukaryotic Genomes: AnOverview 740The Organization of Coding Sequences 741
mRNA Genes 741 rRNA, tRNA, andsn/scRNA Genes 746
Repetitive Sequences in Eukaryotic Genomes 750Moderately Repeated Sequences 752 HighlyRepeated Sequences 753
INFORMATION BOX 18-1: DMA Fingerprinting 754THE EXPERIMENTAL PROCESS: Repeated DNA
Sequences and Mobile Elements 756INFORMATION BOX 18-2: Alu and LINE
Sequences 758
Genetic Rearrangements 760INFORMATION BOX 18-3: Sequencing Human andOther Genomes 762
Genetic Rearrangements by Movement ofTransposable Elements 763 Examples ofEukaryotic Transposable Elements 765Transposable Elements and ProcessedPseudogenes 768 Genetic Rearrangements byUnequal Crossing Over 768 GeneticRearrangements by Translocations 769 DNATransfers Between Species 770 Movement ofDNA Segments Between Organelle and NuclearGenomes 770
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SUPPLEMENT 18-1: Genome Structure and GeneticRearrangement in Prokaryotes 774
Prokaryotic Genomes 774 Genetic Rearrangementsin Bacteria 776
SUPPLEMENT 18-2: Genetic Engineering 782Genetic Engineering in Animals 782 GeneticEngineering in Plants 786 Engineering Bacteria forProtein Production 787 The Ethics of GeneticEngineering 788
PROGRAMMED GENETIC REARRANGEMENTS INPRODUCTION OF ANTIBODIES
ithe Production of Antibodies 790Antibody Structure 791 The Antibody GeneGroups 793 The Genetic RearrangementsAssembling Antibody Genes 798 Stimulationof B Cells Producing an Antibody Type: ClonalSelection 803
THE EXPERIMENTAL PROCESS: Instruction or
Selection: The Role of Antigen in AntibodyProduction 804
he Immune Response 806MHC and the Immune Response 807 MHCBinding by T Cells 809 B Cells and theSecretion of Antibodies to the Body Exterior 814
Malfunctions of the Immune System 815Autoimmune Diseases 815 Infective AgentsThat Defeat or Sidestep the ImmuneResponse 816
itibodies in Research 816NFORMATION BOX 19-1: The Production of
Variable Surface Groups in TrypanosomaBruceii 817SUPPLEMENT 19-1: AIDS 820
HIV Infection 820 Symptoms and Progress of[ AIDS 821 Transmission and Prevention ofI AIDS 822 Possible Origins of the Disease 822Research Toward Protection or Cure 823
CHAPTER 20
PROTEIN SORTING, DISTRIBUTION, SECRETION,AND ENDOCYTOSIS
Primary Way Stations in Protein Distribution: The ERand Golgi Complex 825
Structure and Molecular Constituents of theSystem 825 Evidence That Proteins MoveSequentially Through the System 831Coordination of the ER and Golgi Complex inProcessing Reactions 834 -
The Mechanisms Sorting and DistributingProteins 835
Signals Directing Proteins to InitialDestinations 835 Signals Directing ProteinsPast the Entry Membrane 835 Identifying andCharacterizing Signals 835
Mechanisms Targeting Proteins to the ER 836The Signal Hypothesis 836 Characteristics ofER-Directing Signals 839
THE EXPERIMENTAL PROCESS: Redirecting ProteinTraffic from Cytoplasm to the SecretoryPathway: A Test of the Signal Hypothesis 840
The Signal Peptidase 842 Stop-Transfer *Signals 842 Postinsertion Signals and FurtherDestinations for ER-Directed Proteins 844
Distribution of Proteins to Locations Outside the ER-Golgi Pathway 849
Distribution to Mitochondria andChloroplasts 849 Signals Directing Proteins tothe Nuclear Interior 854 Distribution toMicrobodies 854
Exocytosis and Endocytosis 855Exocytosis 855 Endocytosis 857 Endocytosis,Exocytosis, and Membrane Recycling 866
SUPPLEMENT 20-1: Protein Sorting, Distribution, andSecretion in Prokaryotes 871SUPPLEMENT 20-2: Reactions Adding Sugar Units toProteins in the ER and Golgi Complex 873
<II\PUU 21
CYTOPLASMIC GENETIC SYSTEMS
The Discovery of DNA and Genes in Mitochondria andChloroplasts 877
Cytoplasmic Inheritance of Mutations Affectingthe Organelles 877 The Search for DNA inOrganelles 879
The Organelle DNAs 881Isolation of the DNA 881 The DNA Circles ofMitochondria 881 Chloroplast DNA 882
Genes'and Genome Structure in the Organelles 883Mitochondrial Genes 883 Chloroplast Genesand Genomes 889
Transcription and Translation in Mitochondria andChloroplasts 892
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Transcription and Processing inMitochondria 893 Transcription andProcessing in Chloroplasts 895 PolypeptideAssembly in Mitochondria aridChloroplasts 896 Transcriptional andTranslational Regulation in the Organelles 899
Origins of the Organelle Genomes 900Genetic Information in Centrioles 901
THE EXPERIMENTAL PROCESS: Escape of DNA fromMitochondria to the Nucleus During Evolutionand in Real Time 902
THE CELL CYCLE, CELL CYCLE REGULATION,AND CANCER
An Overview of the Mitotic Cell Cycle 910Interphase 910 Mitotic Cell Division 911Alterations in the Cell Cycle 915
Cell Cycle Regulation: Factors Modifying the CellCycle 917
Regulation of Growth and Division ThroughSurface Receptors 917 Alterations in IonTransport 919 pH and the Cell Cycle 920Histone and Nonhistone Modifications 920Polyamines and Cell Cycle Modification 922Modification by Cytoplasmic Volume 923
Genes Regulating the Cell Cycle 923Cell Cycle Genes Discovered Through the Studyof Mutants 924 Equivalents of the cdc2/28and cdcl3 Genes in Higher Eukaryotes 926Cell Cycle Genes Identified Through the Studyof Oncogenes 929
THE EXPERIMENTAL PROCESS: Finding Cyclins andAfter 930
--' Alterations Changing Proto-Oncogenes intoOncogenes 935
Cancer: Characteristics and Causes 939The Characteristics of Cancer 939 Establishingthe Genetic Basis of Cancer 940 Viruses and -Cancer 941 Multistep Progression fromInitiation to Malignancy 942 The Role ofChemicals and Radiation in MultistepProgression 944
P
DNA REPLICATION AND REPAIR
Semiconservative DNA Replication 952The Reactions of DNA Replication 955
An Overview of Replication 955 TheSpecialized Mechanisms of DNAReplication 959
INFORMATION BOX 23-1: Tautomers and BaseMismatches During Replication 961
The Enzymes and Factors of DNAReplication 962 Telomere Replication:Replacing the Primer of the Leading Chain 971
THE EXPERIMENTAL PROCESS: Telomerase: TheSearch for a Hypothetical Enzyme 972 *
Initiation of Replication: Replication Origins andReplicons 975
Replication Origins 975 Replicons 978Replicons and DNA Amplification 979
DNA Repair 981Mismatch Repair 981 Repair of DNAAlterations Arising from Chemicals orRadiation 982
INFORMATION BOX 23-2: Mutations and TheirEffects 983
Duplication of Chromosomal Proteins inEukaryotes 984
Synthesis of Chromosomal Proteins 984Nucleosomes and DNA Replication 986
SUPPLEMENT 23-1: The Taylor ExperimentDemonstrating That DNA Replication IsSemiconservative in Eukaryotes 992
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ilENT 23-2: Alteration of DNA By Chemicals'diation 993ahon of DNA by Chemicals 993 Alterations
ng from Radiation 994,IENT 23-3: DMA Replication in Mitochondria
hloroplasts 997
EAR AND CYTOPLASMIC DIVISION
i of Prophase 1000Ijiromosome Condensation 1000entromeres, Telomeres, Replication Origins,
I Artificial Chromosomes 1007 Spindleformation 1007 Breakdown of the Nucleoluspd Nuclear Envelope 1017
I of Metaphase 1018
I of Anaphase 1019Rromatid Separation 1019 Components of
Re Anaphase Movement 1020^EXPERIMENTAL PROCESS: Spindle Elongation in9: The Relative Roles of Microtubule Sliding! Tubulin Polymerization 1022
Mechanisms of the Anaphase Movement 1024>ther Models for Anaphase Movement 1026egulation of the Anaphase Movement 1029
|s of Telophase 1030[^organization of the Nucleolus 1030fe-formation of the Nuclear Envelope 1031
|ion of the Cytoplasm: Cytokinesis 1032furrowing 1032 Cell Plate Formation 1034Distribution of Cytoplasmic Organelles bycytokinesis 1036 Division of Mitochondriabd'Chloroplasts 1037
Genetic Regulation of Mitosis and CytoplasmicDivision 1038
SUPPLEMENT 24-1: Q, G, C, and R Bands in MetaphaseChromosomes 1043SUPPLEMENT 24-1: Cell Division in Bacteria 1045
CHAPTER 25 'y
MEIOSIS AND GENETIC RECOMBINATION
An Overview of Meiotic Cell Division 1050Premeiotic Interphase 1050 Meiosis 1050Meiotic Prophase 11051 The MeioticDivisions 1057
INFORMATION BOX 25-1: Division of the SexChromosomes in Meiosis 1059
RNA Transcription and Protein Synthesis inMeiosis 1061 The Time and Place ofMeiosis 1061
The Mechanism of Recombination 1062Classical Recombination 1062 ExperimentsEstablishing the Mechanism and Timing ofRecombination 1063 Intragenic Recombination1065 Molecular Models for Recombination 1068Enzymes and Factors of Recombination 1072
THE EXPERIMENTAL PROCESS: m-rec: An EnzymeThat Effects Genetic Recombination in MeioticCells 1074
The Synaptonemal Complex and GeneticRecombination 1077
Structure of the Synaptonemal Complex 1077Formation and Disassembly of theSynaptonemal Complex 1079 SynaptonemalComplexes and Recombination Nodules 1080
The Regulation of Meiosis 1080SUPPLEMENT 25-1: The Rolling Circle Mechanism ofDNA Amplification 1085
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SUPPLEMENT 25-2: Lampbrush Chromosomes and RNASynthesis During Meiotic Prophase 1086
The Structure of Lampbrush Chromosomes 1087The Function of Lampbrush Chromosomes 1088Nucleolar Transcription During the LampbrushStage 1089
GAMETOGENESIS AND FERTILIZATION
Development of Motile Male Gametes 1091Spermiogenesis in Animals 1091Spermiogenesis in Plants 1096
Development of Female Gametes 1097Animal Oogenesis 1097 The Mature AnimalEgg 1103 Oogenesis in Lower Plants 1104
Fertilization in Animals 1104The Mechanisms of Fertilization 1104
THE EXPERIMENTAL PROCESS: The Electrical
Polyspermy Block 1110Gametogenesis and Fertilization in Higher Plants 1113
Gametogenesis in Flowering Plants 1113Fertilization in Flowering Plants 1115
SUPPLEMENT 26-1: Replacement of Somatic Histonesby Sperm Histones or Protamines 1119
THE ORIGINS OF CELLULAR LIFE
Stages in the Evolution of Cellular Life 1123Stage One: Formation of the Earth and ItsPrimitive Atmosphere 1123 Stage Two:Spontaneous Formation of OrganicMolecules 1125 • Stage Three: Formation ofMolecular Aggregates 1128
THE EXPERIMENTAL PROCESS: How Were PeptidesFormed in the Prebiotic Era? 1130
Stage Four: The Development of Life in thePrimitive Aggregates 1132 Stage Five: TheEvolution of Cells from Precells 1137
Later Metabolic Developments and the Origins ofEukaryotic Cells 1137
Photosynthesis, Oxygen Evolution, andRespiration 1137 The Appearance ofEukaryotic Cells 1139 Reconstruction ofAncient Lineages Leading to ContemporaryProkaryotes and Eukaryotes 1141
Index 1146
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