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  基因分子生物学（...
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本书由6位生物学界著名专家合作编著，第一作者沃森（1962年诺贝尔医学或生理学奖获得者）系DNA双螺旋结构发现者、分子生物学科奠基人、人类基因组计划的发起者。本书自1965年第一版出版以来得到生物学界的广泛关注和认可，迄今已成为分子生物学经典教科书。第六版保持前几版的一贯特色：适用于分子生物学科需求；保持与学科进展的同步性，体现最新、最权威的学科知识。
　　全书分为5大部分，合计22章，分别是：I.化学与遗传学（5章）——孟德尔世界，核酸遗传信息的传递，弱化学相互作用的重要性，高能键的重要性，弱键与强健决定的大分子结构。II.基因组的维系（6章）——DNA与RNA的结构，基因组结构、染色质与染色体，DNA复制，DNA突变与修复，分子水平的同源重组，位点特异性重组和DNA移位。III.基因组的表达（4章）——转录，RNA剪接，翻译，遗传密码。IV.调控（5章）——原核生物的转录调控，真核生物的转录调控，RNAs的调控，发育与进化中的基因调控，基因组学与系统生物学。V.研究方法（2章）——分子生物学技术，模式生物。

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• 目录
  PART 1 CHEMISTRY AND GENETICS, 1
  1 The Mendelian View of the World, 5
  2 Nucleic Acids Convey Genetic Information, 19
  3 The Importance of Weak Chemical Interactions, 43
  4 The Importance of High-Energy Bonds, 57
  5 Weak and Strong Bonds Determine Macromolecular Structure, 71
  PART 2 MAINTENANCE OF THE GENOME, 95
  6 The Structures of DNA and RNA, 101
  7 Genome Structure, Chromatin, and the Nucleosome, 135
  8 The Replication of DNA, 195
  9 The Mutability and Repair of DNA, 257
  10 Homologous Recombination at the Molecular Level, 283
  11 Site-Specific Recombination and Transposition of DNA, 319
  PART 3 EXPRESSION OF THE GENOME, 371
  12 Mechanisms of Transcription, 377
  13 RNA Splicing, 415
  14 Translation, 457
  15 The Genetic Code, 521
  PART 4 REGULATION, 541
  16 Transcriptional Regulation in Prokaryotes, 547
  17 Transcriptional Regulation in Eukaryotes, 589
  18 Regulatory RNAs, 633
  19 Gene Regulation in Development and Evolution, 661
  20 Genome Analysis and Systems Biology, 703
  PART 5 METHODS, 733
  20 Techniques of Molecular Biology, 739
  21 Model Organisms, 783
  Index, 819
  Detailed Contents
  PART 1 CHEMISTRY AND GENETICS, 1
  CHAPTER1 · The Mendelian View of the World, 5
  Mendel’s Discoveries, 6
  The Principle of Independent Segregation, 6
  ADVANCED CONCEPTS BOX 1-1 Mendelian Laws, 6
  Some Alleles Are neither Dominant nor Recessive, 8
  Principle of Independent Assortment, 8
  Chromosomal Theory of Heredity, 8
  Gene Linkage and Crossing Over, 9
  KEY EXPERIMENTS BOX 1-2 Genes Are Linked to Chromosomes, 10
  Chromosome Mapping, 12
  The Origin of Genetic Variability through Mutations, 15
  Early Speculations about What Genes Are and How They Act, 16
  Preliminary Attempts to Find a Gene–Protein Relationship, 16
  SUMMARY, 17
  BIBLIOGRAPHY, 18
  CHAPTER2 · Nucleic Acids Convey Genetic Information, 19
  Avery’s Bombshell: DNA Can Carry Genetic Specificity, 20
  Viral Genes Are Also Nucleic Acids, 21
  The Double Helix, 21
  Finding the Polymerases That Make DNA, 23
  KEY EXPERIMENTS BOX 2-1 Chargaff’s Rules, 24
  Experimental Evidence Favors Strand Separation during DNA Replication, 25
  The Genetic Information within DNA Is Conveyed by the Sequence of Its Four Nucleotide Building Blocks, 28
  KEY EXPERIMENTS BOX 2-2, Evidence That Genes Control Amino Acid Sequences in Proteins, 29
  DNA Cannot Be the Template That Directly Orders Amino Acids during Protein Synthesis, 30
  RNA Is Chemically Very Similar to DNA, 30
  The Central Dogma, 32
  The Adaptor Hypothesis of Crick, 32
  Discovery of Transfer RNA, 32
  The Paradox of the Nonspecific-Appearing Ribosomes, 33
  Discovery of Messenger RNA (mRNA), 34
  Enzymatic Synthesis of RNA upon DNA Templates, 35
  Establishing the Genetic Code, 36
  Establishing the Direction of Protein Synthesis, 38
  Start and Stop Signals Are Also Encoded within DNA, 39
  The Era of Genomics, 39
  SUMMARY, 40
  BIBLIOGRAPHY, 41
  CHAPTER3 · The Importance of Weak Chemical Interactions, 43
  Characteristics of Chemical Bonds, 43
  Chemical Bonds Are Explainable in Quantum-Mechanical Terms, 44
  Chemical-Bond Formation Involves a Change in the Form of Energy, 45
  Equilibrium between Bond Making and Breaking, 45
  The Concept of Free Energy, 46
  Keq Is Exponentially Related to ΔG, 46
  Covalent Bonds Are Very Strong, 46
  Weak Bonds in Biological Systems, 47
  Weak Bonds Have Energies between 1 and 7 kcal/mol, 47
  Weak Bonds Are Constantly Made and Broken at Physiological Temperatures, 47
  The Distinction between Polar and Nonpolar Molecules, 47
  van der Waals Forces, 48
  Hydrogen Bonds, 49
  Some Ionic Bonds Are Hydrogen Bonds, 50
  Weak Interactions Demand Complementary Molecular Surfaces, 51
  Water Molecules Form Hydrogen Bonds, 51
  Weak Bonds between Molecules in Aqueous Solutions, 51
  Organic Molecules That Tend to Form Hydrogen Bonds Are Water Soluble, 52
  ADVANCED CONCEPTS BOX 3-1 The Uniqueness of Molecular Shapes and the Concept of Selective Stickiness, 53
  Hydrophobic “Bonds” Stabilize Macromolecules, 54
  The Advantage of ΔG between 2 and 5 kcal/mole, 55
  Weak Bonds Attach Enzymes to Substrates, 55
  Weak Bonds Mediate Most Protein–DNA and Protein–Protein Interactions, 55
  SUMMARY, 56
  BIBLIOGRAPHY, 56
  CHAPTER4 · The Importance of High-Energy Bonds, 57
  Molecules That Donate Energy Are Thermodynamically Unstable, 57
  Enzymes Lower Activation Energies in Biochemical Reactions, 59
  Free Energy in Biomolecules, 60
  High-Energy Bonds Hydrolyze with Large Negative ΔG, 60
  High-Energy Bonds in Biosynthetic Reactions, 62
  Peptide Bonds Hydrolyze Spontaneously, 62
  Coupling of Negative with Positive ΔG, 63
  Activation of Precursors in Group Transfer Reactions, 63
  ATP Versatility in Group Transfer, 64
  Activation of Amino Acids by Attachment of AMP, 65
  Nucleic Acid Precursors Are Activated by the Presence of , 66
  The Value of ~ Release in Nucleic Acid Synthesis, 66
  Splits Characterize Most Biosynthetic Reactions, 67
  SUMMARY, 68
  BIBLIOGRAPHY, 69
  CHAPTER5 · Weak and Strong Bonds Determine Macromolecular Structure, 71
  Higher-Order Structures Are Determined by Intra- and Intermolecular Interactions, 71
  DNA Can Form a Regular Helix, 71
  RNA Forms a Wide Variety of Structures, 73
  Chemical Features of Protein Building Blocks, 73
  The Peptide Bond, 75
  There Are Four Levels of Protein Structure, 75
  α Helices and β Sheets Are the Common Forms of Secondary Structure, 76
  TECHNIQUES BOX 5-1 Determination of Protein Structure, 78
  The Specific Conformation of a Protein Results from Its Pattern of Hydrogen Bonds, 80
  α Helices Come Together to Form Coiled-Coils, 80
  Most Proteins Are Modular, Containing Two or Three Domains, 82
  Proteins Are Composed of a Surprisingly Small Number of Structural Motifs, 82
  ADVANCED CONCEPTS BOX 5-2 Large Proteins Are Often Constructed of Several Smaller Polypeptide Chains, 83
  Different Protein Functions Arise from Various Domain Combinations, 84
  Weak Bonds Correctly Position Proteins along DNA and RNA Molecules, 85
  Proteins Scan along DNA to Locate a Specific DNA-Binding Site, 87
  Diverse Strategies for Protein Recognition of RNA, 88
  Allostery: Regulation of a Protein’s Function by Changing Its Shape, 90
  The Structural Basis of Allosteric Regulation Is Known for Examples Involving Small Ligands, Protein–Protein Interactions, and Protein Modification, 90
  Not All Regulation of Proteins Is Mediated by Allosteric Events, 93
  SUMMARY, 93
  BIBLIOGRAPHY, 94
  PART2 MAINTENANCE OF THE GENOME, 95
  CHAPTER6 · The Structures of DNA and RNA, 101
  DNA Structure,102
  DNA Is Composed of Polynucleotide Chains, 102
  Each Base Has Its Preferred Tautomeric Form, 104
  The Two Strands of the Double Helix Are Held Together by Base Pairing in an Antiparallel Orientation, 105
  The Two Chains of the Double Helix Have Complementary Sequences, 106
  Hydrogen Bonding Is Important for the Specificity of Base Pairing, 106
  Bases Can Flip Out from the Double Helix, 107
  DNA Is Usually a Right-Handed Double Helix, 107
  The Double Helix Has Minor and Major Grooves, 108
  KEY EXPERIMENTS BOX 6-1 DNA Has 10.5 Base Pairs per Turn of the Helix in Solution: The Mica Experiment, 108
  The Major Groove Is Rich in Chemical Information, 109
  The Double Helix Exists in Multiple Conformations, 110
  KEY EXPERIMENTS BOX 6-2 How Spots on an X-ray Film Reveal the Structure of DNA, 112
  DNA Can Sometimes Form a Left-Handed Helix, 113
  DNA Strands Can Separate (Denature) and Reassociate, 113
  Some DNA Molecules Are Circles, 116
  DNA Topology, 117
  Linking Number Is an Invariant Topological Property of Covalently Closed, Circular DNA, 117
  Linking Number Is Composed of Twist and Writhe, 117
  Lk0 Is the Linking Number of Fully Relaxed cccDNA under Physiological Conditions, 119
  DNA in Cells Is Negatively Supercoiled, 120
  Nucleosomes Introduce Negative Supercoiling in Eukaryotes, 120
  Topoisomerases Can Relax Supercoiled DNA, 121
  Prokaryotes Have a Special Topoisomerase That Introduces Supercoils into DNA, 121
  Topoisomerases Also Unknot and Disentangle DNA Molecules, 121
  Topoisomerases Use a Covalent Protein–DNA Linkage to Cleave and Rejoin DNA Strands, 123
  Topoisomerases Form an Enzyme Bridge and Pass DNA Segments through Each Other, 123
  DNA Topoisomers Can Be Separated by Electrophoresis, 125
  Ethidium Ions Cause DNA to Unwind, 126
  RNA Structure, 127
  RNA Contains Ribose and Uracil and Is Usually Single-Stranded, 127
  RNA Chains Fold Back on Themselves to Form Local Regions of Double Helix Similar to A-Form DNA, 127
  KEY EXPERIMENTS BOX 6-3 Proving that DNA Has a Helical Periodicity of about 10.5 Base Pairs per Turn from the Topological Properties of DNA Rings, 128
  RNA Can Fold Up into Complex Tertiary Structures, 129
  Some RNAs Are Enzymes, 130
  The Hammerhead Ribozyme Cleaves RNA by the Formation of a 2′, 3′ Cyclic Phosphate, 131
  Did Life Evolve from an RNA World?, 132
  SUMMARY, 132
  BIBLIOGRAPHY, 133
  CHAPTER7 · Genome Structure, Chromatin, and the Nucleosome, 135
  Genome Sequence and Chromosome Diversity, 136
  Chromosomes Can Be Circular or Linear, 136
  Every Cell Maintains a Characteristic Number of Chromosomes, 137
  Genome Size Is Related to the Complexity of the Organism, 139
  The E. coli Genome Is Composed Almost Entirely of Genes, 140
  More Complex Organisms Have Decreased Gene Density, 140
  Genes Make Up Only a Small Proportion of the Eukaryotic Chromosomal DNA, 141
  The Majority of Human Intergenic Sequences Are Composed of Repetitive DNA, 143
  Chromosome Duplication and Segregation, 144
  Eukaryotic Chromosomes Require Centromeres, Telomeres, and Origins of Replication to Be Maintained during Cell Division, 144
  Eukaryotic Chromosome Duplication and Segregation Occur in Separate Phases of the Cell Cycle, 147
  Chromosome Structure Changes as Eukaryotic Cells Divide, 149
  Sister-Chromatid Cohesion and Chromosome Condensation Are Mediated by SMC Proteins, 150
  Mitosis Maintains the Parental Chromosome Number, 152
  During Gap Phases, Cells Prepare for the Next Cell Cycle Stage and Check That the Previous Stage Is Completed Correctly, 152
  Meiosis Reduces the Parental Chromosome Number, 154
  Different Levels of Chromosome Structure Can Be Observed by Microscopy, 156
  The Nucleosome, 157
  Nucleosomes Are the Building Blocks of Chromosomes, 157
  KEY EXPERIMENTS BOX 7-1 Micrococcal Nuclease and the DNA Associated with the Nucleosome, 158
  Histones Are Small, Positively Charged Proteins, 159
  The Atomic Structure of the Nucleosome, 160
  Histones Bind Characteristic Regions of DNA within the Nucleosome, 162
  Many DNA Sequence–Independent Contacts Mediate the Interaction between the Core Histones and DNA, 162
  The Histone Amino-Terminal Tails Stabilize DNA Wrapping around the Octamer, 165
  Wrapping of the DNA around the Histone Protein Core Stores Negative Superhelicity, 166
  KEY EXPERIMENTS BOX 7-2 Nucleosomes and Superhelical Density, 166
  Higher-Order Chromatin Structure, 169
  Heterochromatin and Euchromatin, 169
  Histone H1 Binds to the Linker DNA between Nucleosomes, 169
  Nucleosome Arrays Can Form More Complex Structures: The 30-nm Fiber, 170
  The Histone Amino-Terminal Tails Are Required for the Formation of the 30-nm Fiber, 172
  Further Compaction of DNA Involves Large Loops of Nucleosomal DNA, 172
  Histone Variants Alter Nucleosome Function, 174
  Regulation of Chromatin Structure, 174
  The Interaction of DNA with the Histone Octamer Is Dynamic, 174
  Nucleosome-Remodeling Complexes Facilitate Nucleosome Movement, 175
  Some Nucleosomes Are Found in Specific Positions: Nucleosome Positioning, 179
  KEY EXPERIMENTS BOX 7-3 Determining Nucleosome Position in the Cell, 180
  Modification of the Amino-Terminal Tails of the Histones Alters Chromatin Accessibility, 182
  Protein Domains in Nucleosome-Remodeling and -Modifying Complexes Recognize Modified Histones, 184
  Specific Enzymes Are Responsible for Histone Modification, 185
  Nucleosome Modification and Remodeling Work Together to Increase DNA Accessibility, 186
  Nucleosome Assembly, 187
  Nucleosomes Are Assembled Immediately after DNA Replication, 187
  Assembly of Nucleosomes Requires Histone “Chaperones,” 189
  SUMMARY, 192
  BIBLIOGRAPHY, 193
  CHAPTER8 · The Replication of DNA, 195
  The Chemistry of DNA Synthesis, 196
  DNA Synthesis Requires Deoxynucleoside Triphosphates and a Primer:Template Junction, 196
  DNA Is Synthesized by Extending the 3′ End of the Primer, 197
  Hydrolysis of Pyrophosphate Is the Driving Force for DNA Synthesis, 198
  The Mechanism of DNA Polymerase, 198
  DNA Polymerases Use a Single Active Site to Catalyze DNA Synthesis, 198
  TECHNIQUES BOX 8-1 Incorporation Assays Can Be Used to Measure Nucleic Acid and Protein Synthesis, 200
  DNA Polymerases Resemble a Hand That Grips the Primer:Template Junction, 202
  MEDICAL CONNECTIONS BOX 8-2 Anticancer and Antiviral Agents Target DNA Replication, 203
  DNA Polymerases Are Processive Enzymes, 207
  Exonucleases Proofread Newly Synthesized DNA, 208
  The Replication Fork, 209
  Both Strands of DNA Are Synthesized Together at the Replication Fork, 209
  The Initiation of a New Strand of DNA Requires an RNA Primer, 210
  RNA Primers Must Be Removed to Complete DNA Replication, 211
  DNA Helicases Unwind the Double Helix in Advance of the Replication Fork, 211
  TECHNIQUES BOX 8-3 Determining the Polarity of a DNA Helicase, 212
  DNA Helicase Pulls Single-Stranded DNA through a Central Protein Pore, 214
  Single-Stranded DNA-Binding Proteins Stabilize ssDNA prior to Replication, 215
  Topoisomerases Remove Supercoils Produced by DNA Unwinding at the Replication Fork, 216
  Replication Fork Enzymes Extend the Range of DNA Polymerase Substrates, 217
  The Specialization of DNA Polymerases, 218
  DNA Polymerases Are Specialized for Different Roles in the Cell, 218
  Sliding Clamps Dramatically Increase DNA Polymerase Processivity, 219
  Sliding Clamps Are Opened and Placed on DNA by Clamp Loaders, 222
  ADVANCED CONCEPTS BOX 8-4 ATP Control of Protein Function: Loading a Sliding Clamp, 223
  DNA Synthesis at the Replication Fork, 225
  Interactions between Replication Fork Proteins Form the E. coli Replisome, 228
  Initiation of DNA Replication, 230
  Specific Genomic DNA Sequences Direct the Initiation of DNA Replication, 230
  The Replicon Model of Replication Initiation, 230
  Replicator Sequences Include Initiator Binding Sites and Easily Unwound DNA, 231
  KEY EXPERIMENTS BOX 8-5 The Identification of Origins of Replication and Replicators, 232
  Binding and Unwinding: Origin Selection and Activation by the Initiator Protein, 235
  Protein–Protein and Protein–DNA Interactions Direct the Initiation Process, 235
  ADVANCED CONCEPTS BOX 8-6 The Replication Factory Hypothesis, 237
  Eukaryotic Chromosomes Are Replicated Exactly Once per Cell Cycle, 239
  Prereplicative Complex Formation Is the First Step in the Initiation of Replication in Eukaryotes, 240
  Pre-RC Formation and Activation Are Regulated to Allow Only a Single Round of Replication during Each Cell Cycle, 241
  Similarities between Eukaryotic and Prokaryotic DNA Replication Initiation, 244
  ADVANCED CONCEPTS BOX 8-7 E. coli DNA Replication Is Regulated by DnaA·ATP Levels and SeqA, 244
  Finishing Replication, 246
  Type II Topoisomerases Are Required to Separate Daughter DNA Molecules, 246
  Lagging-Strand Synthesis Is Unable to Copy the Extreme Ends of Linear Chromosomes, 247
  Telomerase Is a Novel DNA Polymerase That Does Not Require an Exogenous Template, 248
  Telomerase Solves the End Replication Problem by Extending the 3′ End of the Chromosome, 250
  MEDICAL CONNECTIONS BOX 8-8 Aging, Cancer, and the Telomere Hypothesis, 251
  Telomere-Binding Proteins Regulate Telomerase Activity and Telomere Length, 252
  Telomere-Binding Proteins Protect Chromosome Ends, 253
  SUMMARY, 255
  BIBLIOGRAPHY, 256
  CHAPTER9 · The Mutability and Repair of DNA, 257
  Replication Errors and Their Repair, 258
  The Nature of Mutations, 258
  Some Replication Errors Escape Proofreading, 259
  MEDICAL CONNECTIONS BOX 9-1 Expansion of Triple Repeats Causes Disease, 259
  Mismatch Repair Removes Errors That Escape Proofreading, 260
  DNA Damage, 265
  DNA Undergoes Damage Spontaneously from Hydrolysis and Deamination, 265
  DNA Is Damaged by Alkylation, Oxidation, and Radiation, 265
  MEDICAL CONNECTIONS BOX 9-2 The Ames Test, 266
  Mutations Are Also Caused by Base Analogs and Intercalating Agents, 268
  Repair of DNA Damage, 269
  Direct Reversal of DNA Damage, 270
  Base Excision Repair Enzymes Remove Damaged Bases by a Base-Flipping Mechanism, 270
  Nucleotide Excision Repair Enzymes Cleave Damaged DNA on Either Side of the Lesion, 273
  Recombination Repairs DNA Breaks by Retrieving Sequence Information from Undamaged DNA, 275
  DSBs in DNA Are Also Repaired by Direct Joining of Broken Ends, 275
  MEDICAL CONNECTIONS BOX 9-3 Nonhomologous End Joining, 276
  Translesion DNA Synthesis Enables Replication to Proceed across DNA Damage, 278
  ADVANCED CONCEPTS BOX 9-4 The Y Family of DNA Polymerases, 280
  SUMMARY, 281
  BIBLIOGRAPHY, 282
  CHAPTER10 · Homologous Recombination at the Molecular Level, 283
  DNA Breaks Are Common and Initiate Recombination, 284
  Models for Homologous Recombination, 284
  Strand Invasion Is a Key Early Step in Homologous Recombination, 286
  Resolving Holliday Junctions Is a Key Step to Finishing Genetic Exchange, 288
  The Double-Strand Break–Repair Model Describes Many Recombination Events, 288
  Homologous Recombination Protein Machines, 291
  ADVANCED CONCEPTS BOX 10-1 How to Resolve a Recombination Intermediate with Two Holliday Junctions, 292
  The RecBCD Helicase/Nuclease Processes Broken DNA Molecules for Recombination, 293
  Chi Sites Control RecBCD, 296
  RecA Protein Assembles on Single-Stranded DNA and Promotes Strand Invasion, 297
  Newly Base-Paired Partners Are Established within the RecA Filament, 299
  RecA Homologs Are Present in All Organisms, 301
  The RuvAB Complex Specifically Recognizes Holliday Junctions and Promotes Branch Migration, 301
  RuvC Cleaves Specific DNA Strands at the Holliday Junction to Finish Recombination, 302
  Homologous Recombination in Eukaryotes, 303
  Homologous Recombination Has Additional Functions in Eukaryotes, 303
  Homologous Recombination Is Required for Chromosome Segregation during Meiosis, 304
  Programmed Generation of Double-Stranded DNA Breaks Occurs during Meiosis, 305
  MRX Protein Processes the Cleaved DNA Ends for Assembly of the RecA-like Strand-Exchange Proteins, 307
  Dmc1 Is a RecA-like Protein That Specifically Functions in Meiotic Recombination, 308
  Many Proteins Function Together to Promote Meiotic Recombination, 308
  MEDICAL CONNECTIONS BOX 10-2 The Product of the Tumor Suppressor Gene BRCA2 Interacts with Rad51 Protein and Controls Genome Stability, 309
  Mating-Type Switching, 310
  Mating-Type Switching Is Initiated by a Site-Specific Double- Strand Break, 311
  Mating-Type Switching Is a Gene Conversion Event and Not Associated with Crossing Over, 312
  Genetic Consequences of the Mechanism of Homologous Recombination, 314
  One Cause of Gene Conversion Is DNA Repair during Recombination, 315
  SUMMARY, 316
  BIBLIOGRAPHY, 317
  CHAPTER11 · Site-Specific Recombination and Transposition of DNA, 319
  Conservative Site-Specific Recombination, 320
  Site-Specific Recombination Occurs at Specific DNA
  Sequences in the Target DNA, 320
  Site-Specific Recombinases Cleave and Rejoin DNA Using a Covalent Protein–DNA Intermediate, 322
  Serine Recombinases Introduce Double-Strand Breaks in DNA and Then Swap Strands to Promote Recombination, 324
  Structure of the Serine Recombinase–DNA Complex Indicates That Subunits Rotate to Achieve Strand Exchange, 325
  Tyrosine Recombinases Break and Rejoin One Pair of DNA Strands at a Time, 326
  Structures of Tyrosine Recombinases Bound to DNA Reveal the Mechanism of DNA Exchange, 327
  MEDICAL CONNECTIONS BOX 11-1 Application of Site-Specific Recombination to Genetic Engineering, 327
  Biological Roles of Site-Specific Recombination, 328
  λ Integrase Promotes the Integration and Excision of a Viral Genome into the Host-Cell Chromosome, 329
  Bacteriophage λ Excision Requires a New DNA-Bending Protein, 331
  The Hin Recombinase Inverts a Segment of DNA Allowing Expression of Alternative Genes, 331
  Hin Recombination Requires a DNA Enhancer, 332
  Recombinases Convert Multimeric Circular DNA Molecules into Monomers, 333
  There Are Other Mechanisms to Direct Recombination to Specific Segments of DNA, 334
  Transposition, 334
  Some Genetic Elements Move to New Chromosomal Locations by Transposition, 334
  ADVANCED CONCEPTS BOX 11-2 The Xer Recombinase Catalyzes the Monomerization of Bacterial Chromosomes and of Many Bacterial Plasmids, 335
  There Are Three Principal Classes of Transposable Elements, 338
  DNA Transposons Carry a Transposase Gene, Flanked by Recombination Sites, 339
  Transposons Exist as Both Autonomous and Nonautonomous Elements, 339
  Virus-like Retrotransposons and Retroviruses Carry Terminal Repeat Sequences and Two Genes
  Important for Recombination, 340
  Poly-A Retrotransposons Look Like Genes, 340
  DNA Transposition by a Cut-and-Paste Mechanism, 340
  The Intermediate in Cut-and-Paste Transposition Is Finished by Gap Repair, 342
  There Are Multiple Mechanisms for Cleaving the Nontransferred Strand during DNA Transposition, 343
  DNA Transposition by a Replicative Mechanism, 345
  Virus-like Retrotransposons and Retroviruses Move Using an RNA Intermediate, 347
  ADVANCED CONCEPTS BOX 11-3 The Pathway of Retroviral cDNA Formation, 349
  DNA Transposases and Retroviral Integrases Are Members of a Protein Superfamily, 351
  Poly-A Retrotransposons Move by a “Reverse Splicing” Mechanism, 352
  Examples of Transposable Elements and Their Regulation, 354
  IS4-Family Transposons Are Compact Elements with Multiple Mechanisms for Copy Number Control, 355
  KEY EXPERIMENTS BOX 11-4 Maize Elements and the Discovery of Transposons, 356
  Tn10 Transposition Is Coupled to Cellular DNA Replication, 358
  Phage Mu Is an Extremely Robust Transposon, 359
  Mu Uses Target Immunity to Avoid Transposing into Its Own DNA, 359
  ADVANCED CONCEPTS BOX 11-5 Mechanism of Transposition Target Immunity, 361
  Tc1/mariner Elements Are Extremely Successful DNA Elements in Eukaryotes, 362
  Yeast Ty Elements Transpose into Safe Havens in the Genome, 362
  LINEs Promote Their Own Transposition and Even Transpose Cellular RNAs, 363
  V(D)J Recombination, 365
  The Early Events in V(D)J Recombination Occur by a Mechanism Similar to Transposon Excision, 367
  SUMMARY, 369
  BIBLIOGRAPHY, 369
  EXPRESSION OF THE GENOME, 371
  CHAPTER12 · Mechanisms of Transcription, 377
  RNA Polymerases and the Transcription Cycle, 378
  RNA Polymerases Come in Different Forms but Share Many Features, 378
  Transcription by RNA Polymerase Proceeds in a Series of Steps, 380
  Transcription Initiation Involves Three Defined Steps, 382
  The Transcription Cycle in Bacteria, 383
  Bacterial Promoters Vary in Strength and Sequence but Have Certain Defining Features, 383
  The σ Factor Mediates Binding of Polymerase to the Promoter, 384
  Transition to the Open Complex Involves Structural Changes in RNA Polymerase and in the Promoter DNA, 386
  TECHNIQUES BOX 12-1 Consensus Sequences, 388
  Transcription Is Initiated by RNA Polymerase without the Need for a Primer, 388
  During Initial Transcription, RNA Polymerase Remains Stationary and Pulls Downstream DNA into Itself, 389
  Promoter Escape Involves Breaking Polymerase–Promoter Interactions and Polymerase Core–σ Interactions, 390
  The Elongating Polymerase Is a Processive Machine That Synthesizes and Proofreads RNA, 391
  ADVANCED CONCEPTS BOX 12-2 The Single-Subunit RNA Polymerases, 393
  RNA Polymerase Can Become Arrested and Need Removing, 394
  Transcription Is Terminated by Signals within the RNA Sequence, 394
  Transcription in Eukaryotes, 396
  RNA Polymerase II Core Promoters Are Made Up of Combinations of Four Different Sequence Elements, 397
  RNA Polymerase II Forms a Preinitiation Complex with General Transcription Factors at the Promoter, 398
  Promoter Escape Requires Phosphorylation of the Polymerase “Tail,” 398
  TBP Binds to and Distorts DNA Using a β Sheet Inserted into the Minor Groove, 400
  The Other General Transcription Factors Also Have Specific Roles in Initiation, 401
  In Vivo, Transcription Initiation Requires Additional Proteins, Including the Mediator Complex, 402
  Mediator Consists of Many Subunits, Some Conserved from Yeast to Human, 403
  A New Set of Factors Stimulate Pol II Elongation and RNA Proofreading, 404
  Elongating RNA Polymerase Must Deal with Histones in Its Path, 405
  Elongating Polymerase Is Associated with a New Set of Protein Factors Required for Various Types of RNA Processing, 406
  Transcription Termination Is Linked to RNA Destruction by a Highly Processive RNase, 410
  Transcription by RNA Polymerases I and III, 410
  RNA Pol I and Pol III Recognize Distinct Promoters, Using Distinct Sets of Transcription Factors, but Still Require TBP, 410
  Pol III Promoters Are Found Downstream of Transcription Start Site, 412
  SUMMARY, 413
  BIBLIOGRAPHY, 414
  CHAPTER13 · RNA Splicing, 415
  The Chemistry of RNA Splicing, 417
  Sequences within the RNA Determine Where Splicing Occurs, 417
  The Intron Is Removed in a Form Called a Lariat as the Flanking Exons Are Joined, 418
  KEY EXPERIMENTS BOX 13-1 Adenovirus and the Discovery of Splicing, 419
  Exons from Different RNA Molecules Can Be Fused by trans-Splicing, 421
  The Spliceosome Machinery, 422
  RNA Splicing Is Carried Out by a Large Complex Called the Spliceosome, 422
  Splicing Pathways, 424
  Assembly, Rearrangements, and Catalysis within the Spliceosome: The Splicing Pathway, 424
  Self-Splicing Introns Reveal That RNA Can Catalyze RNA Splicing, 426
  Group I Introns Release a Linear Intron Rather Than a Lariat, 426
  KEY EXPERIMENTS BOX 13-2 Converting Group I Introns into Ribozymes, 428
  How Does the Spliceosome Find the Splice Sites Reliably?, 430
  A Small Group of Introns Are Spliced by an Alternative Spliceosome Composed of a Different Set of snRNPs, 432
  Alternative Splicing, 432
  Single Genes Can Produce Multiple Products by Alternative Splicing, 432
  Several Mechanisms Exist to Ensure Mutually Exclusive Splicing, 435
  The Curious Case of the Drosophila Dscam Gene: Mutually Exclusive Splicing on a Grand Scale, 436
  Mutually Exclusive Splicing of Dscam Exon 6 Cannot Be Accounted for by Any Standard Mechanism and Instead Uses a Novel Strategy, 437
  Alternative Splicing Is Regulated by Activators and Repressors, 439
  Regulation of Alternative Splicing Determines the Sex of Flies, 441
  KEY EXPERIMENTS BOX 13-3 Identification of Docking Site and Selector Sequences, 442
  MEDICAL CONNECTIONS BOX 13-4 Defects in Pre-mRNA Splicing Cause Human Disease, 445
  Exon Shuffling, 446
  Exons Are Shuffled by Recombination to Produce Genes Encoding New Proteins, 446
  RNA Editing, 448
  RNA Editing Is Another Way of Altering the Sequence of an mRNA, 448
  Guide RNAs Direct the Insertion and Deletion of Uridines, 450
  MEDICAL CONNECTIONS BOX 13-5 Deaminases and HIV, 450
  mRNA Transport, 452
  Once Processed, mRNA Is Packaged and Exported from the Nucleus into the Cytoplasm for Translation, 452
  SUMMARY, 454
  BIBLIOGRAPHY, 455
  CHAPTER14 · Translation, 457
  Messenger RNA, 458
  Polypeptide Chains Are Specified by Open Reading Frames, 458
  Prokaryotic mRNAs Have a Ribosome-Binding Site That Recruits the Translational Machinery, 459
  Eukaryotic mRNAs Are Modified at Their 5′ and 3′ Ends to Facilitate Translation, 460
  Transfer RNA, 461
  tRNAs Are Adaptors between Codons and Amino Acids, 461
  ADVANCED CONCEPTS BOX 14-1 CCA-Adding Enzymes: Synthesizing RNA without a Template, 462
  tRNAs Share a Common Secondary Structure That Resembles a Cloverleaf, 462
  tRNAs Have an L-shaped Three-Dimensional Structure, 463
  Attachment of Amino Acids to tRNA, 464
  tRNAs Are Charged by the Attachment of an Amino Acid to the 3′-Terminal Adenosine Nucleotide via a High-Energy Acyl Linkage, 464
  Aminoacyl-tRNA Synthetases Charge tRNAs in Two Steps, 464
  Each Aminoacyl-tRNA Synthetase Attaches a Single Amino Acid to One or More tRNAs, 466
  tRNA Synthetases Recognize Unique Structural Features of Cognate tRNAs, 466
  Aminoacyl-tRNA Formation Is Very Accurate, 468
  Some Aminoacyl-tRNA Synthetases Use an Editing Pocket to Charge tRNAs with High Accuracy, 468
  The Ribosome Is Unable to Discriminate between Correctly and Incorrectly Charged tRNAs, 469
  The Ribosome, 469
  ADVANCED CONCEPTS BOX 14-2 Selenocysteine, 470
  The Ribosome Is Composed of a Large and a Small Subunit, 471
  The Large and Small Subunits Undergo Association and Dissociation during Each Cycle of
  Translation, 472
  New Amino Acids Are Attached to the Carboxyl Terminus of the Growing Polypeptide Chain, 474
  Peptide Bonds Are Formed by Transfer of the Growing Polypeptide Chain from One tRNA to Another, 474
  Ribosomal RNAs Are Both Structural and Catalytic Determinants of the Ribosome, 475
  The Ribosome Has Three Binding Sites for tRNA, 475
  Channels through the Ribosome Allow the mRNA and Growing Polypeptide to Enter and/or Exit the Ribosome, 476
  Initiation of Translation, 479
  Prokaryotic mRNAs Are Initially Recruited to the Small Subunit by Base Pairing to rRNA, 480
  A Specialized tRNA Charged with a Modified Methionine Binds Directly to the Prokaryotic Small Subunit, 480
  Three Initiation Factors Direct the Assembly of an Initiation Complex That Contains mRNA and the Initiator tRNA, 481
  Eukaryotic Ribosomes Are Recruited to the mRNA by the 5′ Cap, 482
  The Start Codon Is Found by Scanning Downstream from the 5′ End of the mRNA, 483
  ADVANCED CONCEPTS BOX 14-3 uORFs and IRESs: Exceptions That Prove the Rule, 485
  Translation Initiation Factors Hold Eukaryotic mRNAs in Circles, 487
  Translation Elongation, 487
  Aminoacyl-tRNAs Are Delivered to the A Site by Elongation Factor EF-Tu, 488
  The Ribosome Uses Multiple Mechanisms to Select against Incorrect Aminoacyl-tRNAs, 488
  The Ribosome Is a Ribozyme, 491
  Peptide Bond Formation and the Elongation Factor EF-G Drive Translocation of the tRNAs and the mRNA, 492
  EF-G Drives Translocation by Displacing the tRNA Bound to the A Site, 494
  EF-Tu–GDP and EF-G–GDP Must Exchange GDP for GTP prior to Participating in a New Round of Elongation, 495
  A Cycle of Peptide Bond Formation Consumes Two Molecules of GTP and One Molecule of ATP, 495
  Termination of Translation, 496
  Release Factors Terminate Translation in Response to Stop Codons, 496
  Short Regions of Class I Release Factors Recognize Stop Codons and Trigger Release of the Peptidyl Chain, 496
  ADVANCED CONCEPTS BOX 14-4 GTP-Binding Proteins, Conformational Switching, and the Fidelity and Ordering of the Events of Translation, 498
  GDP/GTP Exchange and GTP Hydrolysis Control the Function of the Class II Release Factor, 499
  The Ribosome Recycling Factor Mimics a tRNA, 500
  MEDICAL CONNECTIONS BOX 14-5 Antibiotics Arrest Cell Division by Blocking Specific Steps in Translation, 502
  Regulation of Translation, 503
  Protein or RNA Binding Near the Ribosome-Binding Site Negatively Regulates Bacterial Translation Initiation, 504
  Regulation of Prokaryotic Translation: Ribosomal Proteins Are Translational Repressors of Their Own Synthesis, 505
  Global Regulators of Eukaryotic Translation Target Key Factors Required for mRNA Recognition and Initator tRNA Ribosome Binding, 508
  Spatial Control of Translation by mRNA-Specific 4E-BPs, 510
  An Iron-Regulated, RNA-Binding Protein Controls Translation of Ferritin, 511
  Translation of thet Yeast Transcriptional Activator Gcn4 Is Controlled by Short Upstream ORFs and Ternary Complex Abundance, 512
  Translation-Dependent Regulation of mRNA and Protein Stability, 514
  The SsrA RNA Rescues Ribosomes That Translate Broken mRNAs, 514
  Eukaryotic Cells Degrade mRNAs That Are Incomplete or Have Premature Stop Codons, 516
  SUMMARY, 518
  BIBLIOGRAPHY, 519
  CHAPTER15 · The Genetic Code, 521
  The Code Is Degenerate, 521
  Perceiving Order in the Makeup of the Code, 522
  Wobble in the Anticodon, 523
  Three Codons Direct Chain Termination, 525
  How the Code Was Cracked, 525
  Stimulation of Amino Acid Incorporation by Synthetic mRNAs, 526
  Poly-U Codes for Polyphenylalanine, 527
  Mixed Copolymers Allowed Additional Codon Assignments, 527
  Transfer RNA Binding to Defined Trinucleotide Codons, 528
  Codon Assignments from Repeating Copolymers, 529
  Three Rules Govern the Genetic Code, 530
  Three Kinds of Point Mutations Alter the Genetic Code, 531
  Genetic Proof That the Code Is Read in Units of Three, 532
  Suppressor Mutations Can Reside in the Same or a Different Gene, 532
  Intergenic Suppression Involves Mutant tRNAs, 533
  Nonsense Suppressors Also Read Normal Termination Signals, 535
  Proving the Validity of the Genetic Code, 535
  The Code Is Nearly Universal, 536
  SUMMARY, 538
  BIBLIOGRAPHY, 538
  REGULATION, 541
  PART4 REGULATION, 541
  CHAPTER16 · Transcriptional Regulation in Prokaryotes, 547
  Principles of Transcriptional Regulation, 547
  Gene Expression Is Controlled by Regulatory Proteins, 547
  Most Activators and Repressors Act at the Level of Transcription Initiation, 548
  Many Promoters Are Regulated by Activators That Help RNA Polymerase Bind DNA and by Repressors That Block That Binding, 548
  Some Activators and Repressors Work by Allostery and Regulate Steps in Transcriptional Initiation after RNA Polymerase Binding, 550
  Action at a Distance and DNA Looping, 551
  Cooperative Binding and Allostery Have Many Roles in Gene Regulation, 552
  Antitermination and Beyond: Not All of Gene Regulation Targets Transcription Initiation, 552
  Regulation of Transcription Initiation: Examples from Prokaryotes, 553
  An Activator and a Repressor Together Control the lac Genes, 553
  CAP and Lac Repressor Have Opposing Effects on RNA Polymerase Binding to the lac Promoter, 554
  CAP Has Separate Activating and DNA-Binding Surfaces, 555
  CAP and Lac Repressor Bind DNA Using a Common Structural Motif, 556
  KEY EXPERIMENTS BOX 16-1 Activator Bypass Experiments, 557
  The Activities of Lac Repressor and CAP Are Controlled Allosterically by Their Signals, 559
  Combinatorial Control: CAP Controls Other Genes As Well, 560
  KEY EXPERIMENTS BOX 16-2 Jacob, Monod, and the Ideas Behind Gene Regulation, 561
  Alternative σ Factors Direct RNA Polymerase to Alternative Sets of Promoters, 563
  NtrC and MerR: Transcriptional Activators That Work by Allostery Rather than by Recruitment, 564
  NtrC Has ATPase Activity and Works from DNA Sites Far from the Gene, 564
  MerR Activates Transcription by Twisting Promoter DNA, 565
  Some Repressors Hold RNA Polymerase at the Promoter Rather than Excluding It, 566
  AraC and Control of the araBAD Operon by Antiactivation, 567
  The Case of Bacteriophage λ: Layers of Regulation, 568
  Alternative Patterns of Gene Expression Control Lytic and Lysogenic Growth, 569
  Regulatory Proteins and Their Binding Sites, 570
  λ Repressor Binds to Operator Sites Cooperatively, 571
  ADVANCED CONCEPTS BOX 16-3 Concentration, Affinity, and Cooperative Binding, 572
  Repressor and Cro Bind in Different Patterns to Control Lytic and Lysogenic Growth, 573
  Lysogenic Induction Requires Proteolytic Cleavage of λ Repressor, 574
  Negative Autoregulation of Repressor Requires Long- Distance Interactions and a Large DNA Loop, 575
  Another Activator, λ CII, Controls the Decision between Lytic and Lysogenic Growth upon Infection of a New Host, 577
  The Number of Phage Particles Infecting a Given Cell Affects Whether the Infection Proceeds Lytically or Lysogenically, 578
  Growth Conditions of E. coli Control the Stability of CII Protein and thus the Lytic/Lysogenic Choice, 578
  KEY EXPERIMENTS BOX 16-4 Evolution of the λ Switch, 579
  KEY EXPERIMENTS BOX 16-5 Genetic Approaches That Identified Genes Involved in the Lytic/Lysogenic Choice, 581
  Transcriptional Antitermination in λ Development, 582
  Retroregulation: An Interplay of Controls on RNA Synthesis and Stability Determines int Gene Expression, 584
  SUMMARY, 585
  BIBLIOGRAPHY, 586
  CHAPTER17 · Transcriptional Regulation in Eukaryotes, 589
  Conserved Mechanisms of Transcriptional Regulation from Yeast to Mammals, 591
  Activators Have Separate DNA-Binding and Activating Functions, 591
  Eukaryotic Regulators Use a Range of DNA-Binding Domains, but DNA Recognition Involves the Same Principles as Found in Bacteria, 593
  TECHNIQUES BOX 17-1 The Two-Hybrid Assay, 594
  Activating Regions Are Not Well-Defined Structures, 596
  Recruitment of Protein Complexes to Genes by Eukaryotic Activators, 597
  Activators Recruit the Transcriptional Machinery to the Gene, 597
  Activators Also Recruit Nucleosome Modifiers That Help the Transcriptional Machinery Bind at the Promoter or Initiate Transcription, 598
  Activators Recruit an Additional Factor Needed for Efficient Initiation or Elongation at Some Promoters, 600
  Action at a Distance: Loops and Insulators, 601
  Appropriate Regulation of Some Groups of Genes Requires Locus Control Regions, 603
  KEY EXPERIMENTS BOX 17-2 Long-Distance Interactions on the Same and Different Chromosomes, 604
  Signal Integration and Combinatorial Control, 605
  Activators Work Synergistically to Integrate Signals, 605
  Signal Integration: The HO Gene Is Controlled by Two Regulators—One Recruits Nucleosome Modifiers and the Other Recruits Mediator, 607
  Signal Integration: Cooperative Binding of Activators at the Human β-Interferon Gene, 608
  Combinatorial Control Lies at the Heart of the Complexity and Diversity of Eukaryotes, 610
  Combinatorial Control of the Mating-Type Genes from S. cerevisiae, 611
  KEY EXPERIMENTS BOX 17-3 Evolvability of a Regulatory Circuit, 612
  Transcriptional Repressors, 613
  Signal Transduction and the Control of Transcriptional Regulators, 615
  Signals Are Often Communicated to Transcriptional Regulators through Signal Transduction Pathways, 615
  Signals Control the Activities of Eukaryotic Transcriptional Regulators in a Variety of Ways, 617
  Activators and Repressors Sometimes Come in Pieces, 619
  Gene “Silencing” by Modification of Histones and DNA, 620
  Silencing in Yeast Is Mediated by Deacetylation and Methylation of Histones, 621
  In Drosophila, HP1 Recognizes Methylated Histones and Condenses Chromatin, 622
  ADVANCED CONCEPTS BOX 17-4 Is There a Histone Code?, 623
  DNA Methylation Is Associated with Silenced Genes in Mammalian Cells, 624
  MEDICAL CONNECTIONS BOX 17-5 Transcriptional Repression and Human Disease, 626
  Epigenetic Gene Regulation, 626
  Some States of Gene Expression Are Inherited through Cell Division Even When the Initiating Signal Is No Longer Present, 627
  MEDICAL CONNECTIONS BOX 17-6 Using Transcription Factors to Reprogram Somatic Cells into Embryonic Stem Cells, 629
  SUMMARY, 630
  BIBLIOGRAPHY, 631
  CHAPTER18 · Regulatory RNAs, 633
  Regulation by RNAs in Bacteria, 633
  Riboswitches Reside within the Transcripts of Genes Whose Expression They Control through Changes in Secondary Structure, 635
  ADVANCED CONCEPTS BOX 18-1 Amino Acid Biosynthetic Operons Are Controlled by Attenuation, 639
  RNA Interference Is a Major Regulatory Mechanism in Eukaryotes, 641
  Short RNAs That Silence Genes Are Produced from a Variety of Sources and Direct the Silencing of Genes in Three Different Ways, 641
  Synthesis and Function of miRNA Molecules, 643
  miRNAs Have a Characteristic Structure That Assists in Identifying Them and Their Target Genes, 643
  An Active miRNA Is Generated through a Two-Step Nucleolytic Processing, 645
  Dicer Is the Second RNA-Cleaving Enzyme Involved in miRNA Production, 646
  Incorporation of a Guide Strand RNA into RISC Makes the Mature Complex That Is Ready to Silence Gene Expression, 647
  siRNAs Are Regulatory RNAs Generated from Long Double-Stranded RNAs, 649
  Small RNAs Can Transcriptionally Silence Genes by Directing Chromatin Modification, 649
  KEY EXPERIMENTS BOX 18-2 History of miRNAs and RNAi, 650
  The Evolution and Exploitation of RNAi, 652
  Did RNAi Evolve As an Immune System?, 652
  RNAi Has Become a Powerful Tool for Manipulating Gene Expression, 654
  MEDICAL CONNECTIONS BOX 18-3 RNAi and Human Disease, 656
  Regulatory RNAs and X-inactivation, 657
  X-inactivation Creates Mosaic Individuals, 657
  Xist Is an RNA Regulator That Inactivates a Single X Chromosome in Female Mammals, 657
  SUMMARY, 659
  BIBLIOGRAPHY, 660
  CHAPTER19 · Gene Regulation in Development and Evolution, 661
  TECHNIQUES BOX 19-1 Microarray Assays: Theory and Practice, 662
  Three Strategies by Which Cells Are Instructed to Express Specific Sets of Genes during Development, 663
  Some mRNAs Become Localized within Eggs and Embryos because of an Intrinsic Polarity in the Cytoskeleton, 663
  Cell-to-Cell Contact and Secreted Cell-Signaling Molecules Both Elicit Changes in Gene Expression in Neighboring Cells, 664
  Gradients of Secreted Signaling Molecules Can Instruct Cells to Follow Different Pathways of Development Based on Their Location, 665
  Examples of the Three Strategies for Establishing Differential Gene Expression, 666
  The Localized Ash1 Repressor Controls Mating Type in Yeast by Silencing the HO Gene, 666
  ADVANCED CONCEPTS BOX 19-2 Review of Cytoskeleton: Asymmetry and Growth, 669
  A Localized mRNA Initiates Muscle Differentiation in the Sea Squirt Embryo, 670
  ADVANCED CONCEPTS BOX 19-3 Overview of Ciona Development, 671
  Cell-to-Cell Contact Elicits Differential Gene Expression in the Sporulating Bacterium, Bacillus subtilis, 672
  A Skin–Nerve Regulatory Switch Is Controlled by Notch Signaling in the Insect Central Nervous System, 673
  A Gradient of the Sonic Hedgehog Morphogen Controls the Formation of Different Neurons in the Vertebrate Neural Tube, 674
  The Molecular Biology of Drosophila Embryogenesis, 676
  An Overview of Drosophila Embryogenesis, 676
  ADVANCED CONCEPTS BOX 19-4 Overview of Drosophila Development, 677
  A Morphogen Gradient Controls Dorsoventral Patterning of the Drosophila Embryo, 679
  Segmentation Is Initiated by Localized RNAs at the Anterior and Posterior Poles of the Unfertilized Egg, 682
  Bicoid and Nanos Regulate hunchback, 683
  KEY EXPERIMENTS BOX 19-5 The Role of Activator Synergy in Development, 684
  MEDICAL CONNECTIONS BOX 19-6 Stem Cells, 686
  The Gradient of Hunchback Repressor Establishes Different Limits of Gap Gene Expression, 687
  Hunchback and Gap Proteins Produce Segmentation Stripes of Gene Expression, 688
  Gap Repressor Gradients Produce Many Stripes of Gene Expression, 689
  KEY EXPERIMENTS BOX 19-7 cis-Regulatory Sequences in Animal Development and Evolution, 690
  Short-Range Transcriptional Repressors Permit Different Enhancers to Work Independently of One Another within the Complex eve Regulatory Region, 692
  Homeotic Genes: An Important Class of Developmental Regulators, 693
  Changes in Homeotic Gene Expression Are Responsible for Arthropod Diversity, 695
  Arthropods Are Remarkably Diverse, 695
  Changes in Ubx Expression Explain Modification of Limbs among the Crustaceans, 695
  ADVANCED CONCEPTS BOX 19-8 Homeotic Genes of Drosophila Are Organized in Special Chromosome Clusters, 696
  Why Insects Lack Abdominal Limbs, 698
  Modification of Flight Limbs Might Arise from the Evolution of Regulatory DNA Sequences, 699
  SUMMARY, 701
  BIBLIOGRAPHY, 702
  CHAPTER20 · Genome Analysis and Systems Biology, 703
  Genomics Overview, 703
  Bioinformatics Tools Facilitate the Genome-wide Identification of Protein-Coding Genes, 703
  Whole-Genome Tiling Arrays Are Used to Visualize the Transcriptome, 704
  Regulatory DNA Sequences Can Be Identified by Using Specialized Alignment Tools, 706
  The ChIP-Chip Assay Is the Best Method for Identifying Enhancers, 708
  TECHNIQUES BOX 20-1 Bioinformatics Methods for the Identification of Complex Enhancers, 708
  Diverse Animals Contain Remarkably Similar Sets of Genes, 711
  Many Animals Contain Anomalous Genes, 712
  Synteny Is Evolutionarily Ancient, 713
  Deep Sequencing Is Being Used to Explore Human Origins, 715
  Systems Biology, 715
  Transcription Circuits Consist of Nodes and Edges, 716
  Negative Autoregulation Dampens Noise and Allows a Rapid Response Time, 717
  Gene Expression Is Noisy, 718
  Positive Autoregulation Delays Gene Expression, 720
  Some Regulatory Circuits Lock in Alternative Stable States, 720
  Feed-Forward Loops Are Three-Node Networks with Beneficial Properties, 722
  KEY EXPERIMENTS BOX 20-2 Bistability and Hysteresis, 722
  Feed-Forward Loops Are Used in Development, 725
  Some Circuits Generate Oscillating Patterns of Gene Expression, 727
  Synthetic Circuits Mimic Some of the Features of Natural Regulatory Networks, 729
  Prospects, 730
  SUMMARY, 730
  BIBLIOGRAPHY, 731
  P METHODS, 733
  PART5 METHODS, 733
  CHAPTER21 · Techniques of Molecular Biology, 739
  Nucleic Acids, 740
  Electrophoresis through a Gel Separates DNA and RNA Molecules according to Size, 740
  Restriction Endonucleases Cleave DNA Molecules at Particular Sites, 742
  DNA Hybridization Can Be Used to Identify Specific DNA Molecules, 743
  Hybridization Probes Can Identify Electrophoretically Separated DNAs and RNAs, 744
  Isolation of Specific Segments of DNA, 746
  DNA Cloning, 746
  Cloning DNA in Plasmid Vectors, 746
  Vector DNA Can Be Introduced into Host Organisms by Transformation, 748
  Libraries of DNA Molecules Can Be Created by Cloning, 748
  Hybridization Can Be Used to Identify a Specific Clone in a DNA Library, 749
  Chemically Synthesized Oligonucleotides, 750
  The Polymerase Chain Reaction Amplifies DNAs by Repeated Rounds of DNA Replication in Vitro, 751
  TECHNIQUES BOX 21-1 Forensics and the Polymerase Chain Reaction, 753
  Nested Sets of DNA Fragments Reveal Nucleotide Sequences, 753
  KEY EXPERIMENTS BOX 21-2 Sequenators Are Used for High- Throughput Sequencing, 757
  Shotgun Sequencing a Bacterial Genome, 757
  The Shotgun Strategy Permits a Partial Assembly of Large Genome Sequences, 758
  The Paired-End Strategy Permits the Assembly of Large- Genome Scaffolds, 760
  The $1000 Human Genome Is within Reach, 762
  Proteins, 764
  Specific Proteins Can Be Purified from Cell Extracts, 764
  Purification of a Protein Requires a Specific Assay, 764
  Preparation of Cell Extracts Containing Active Proteins, 765
  Proteins Can Be Separated from One Another Using Column Chromatography, 765
  Affinity Chromatography Can Facilitate More Rapid Protein Purification, 767
  Separation of Proteins on Polyacrylamide Gels, 768
  Antibodies Are Used to Visualize Electrophoretically Separated Proteins, 769
  Protein Molecules Can Be Directly Sequenced, 769
  Proteomics, 771
  Combining Liquid Chromatography with Mass Spectrometry Identifies Individual Proteins within a Complex Extract, 771
  Proteome Comparisons Identify Important Differences beween Cells, 773
  Mass Spectrometry Can Also Monitor Protein Modification States, 773
  Protein–Protein Interactions Can Yield Information about Protein Function, 774
  Nucleic Acid–Protein Interactions, 775
  The Electrophoretic Mobility of DNA Is Altered by Protein Binding, 776
  DNA-Bound Protein Protects the DNA from Nucleases and Chemical Modification, 777
  Chromatin Immunoprecipitation Can Detect Protein Association with DNA in the Cell, 778
  In Vitro Selection Can Be Used to Identify a Protein’s DNAor RNA-Binding Site, 780
  BIBLIOGRAPHY, 782
  CHAPTER22 · Model Organisms, 783
  Bacteriophage, 784
  Assays of Phage Growth, 786
  The Single-Step Growth Curve, 787
  Phage Crosses and Complementation Tests, 787
  Transduction and Recombinant DNA, 788
  Bacteria, 789
  Assays of Bacterial Growth, 789
  Bacteria Exchange DNA by Sexual Conjugation, Phage-Mediated Transduction, and DNA-Mediated Transformation, 790
  Bacterial Plasmids Can Be Used as Cloning Vectors, 791
  Transposons Can Be Used to Generate Insertional Mutations and Gene and Operon Fusions, 791
  Studies on the Molecular Biology of Bacteria Have Been Enhanced by Recombinant DNA Technology, Whole- Genome Sequencing, and Transcriptional Profiling, 793
  Biochemical Analysis Is Especially Powerful in Simple Cells with Well-Developed Tools of Traditional and Molecular Genetics, 793
  Bacteria Are Accessible to Cytological Analysis, 793
  Phage and Bacteria Told Us Most of the Fundamental Things about the Gene, 794
  Baker’s Yeast, Saccharomyces cerevisiae, 795
  The Existence of Haploid and Diploid Cells Facilitate Genetic Analysis of S. cerevisiae, 795
  Generating Precise Mutations in Yeast Is Easy, 796
  S. cerevisiae Has a Small, Well-Characterized Genome, 796
  S. cerevisiae Cells Change Shape as They Grow, 797
  Arabidopsis, 798
  Arabidopsis Has a Fast Life Cycle with Haploid and Diploid Phases, 798
  Arabidopsis Is Easily Transformed for Reverse Genetics, 799
  Arabidopsis Has a Small Genome That Is Readily Manipulated, 800
  Epigenetics, 801
  Plants Respond to the Environment, 801
  Development and Pattern Formation, 802
  The Nematode Worm, Caenorhabditis elegans, 802
  C.elegans Has a Very Rapid Life Cycle, 803
  C.elegans Is Composed of Relatively Few, Well-Studied Cell Lineages, 804
  The Cell Death Pathway Was Discovered in C. elegans, 805
  RNAi Was Discovered in C. elegans, 805
  The Fruit Fly, Drosophila melanogaster, 806
  Drosophila Has a Rapid Life Cycle, 806
  The First Genome Maps Were Produced in Drosophila, 807
  Genetic Mosaics Permit the Analysis of Lethal Genes in Adult Flies, 809
  The Yeast FLP Recombinase Permits the Efficient Production of Genetic Mosaics, 809
  It Is Easy to Create Transgenic Fruit Flies that Carry Foreign DNA, 810
  The House Mouse, Mus musculus, 812
  Mouse Embryonic Development Depends on Stem Cells, 813
  It Is Easy to Introduce Foreign DNA into the Mouse Embryo, 813
  Homologous Recombination Permits the Selective Ablation of Individual Genes, 814
  Mice Exhibit Epigenetic Inheritance, 816
  BIBLIOGRAPHY, 818
  Index, 819
  Box Contents
  Advanced Concepts
  BOX 1-1 Mendelian Laws, 6
  BOX 3-1 The Uniqueness of Molecular Shapes and the Concept of Selective Stickiness, 53
  BOX 5-2 Large Proteins Are Often Constructed of Several Smaller Polypeptide Chains, 83
  BOX 8-4 ATP Control of Protein Function: Loading a Sliding Clamp, 223
  BOX 8-6 The Replication Factory Hypothesis, 237
  BOX 8-7 E. coli DNA Replication Is Regulated by DnaA·ATP Levels and SeqA, 244
  BOX 9-4 The Y Family of DNA Polymerases, 280
  BOX 10-1 How to Resolve a Recombination Intermediate with Two Holliday Junctions, 292
  BOX 11-2 The Xer Recombinase Catalyzes the Monomerization of Bacterial Chromosomes and of Many Bacterial Plasmids, 335
  BOX 11-3 The Pathway of Retroviral cDNA Formation, 349
  BOX 11-5 Mechanism of Transposition Target Immunity, 361
  BOX 12-2 The Single-Subunit RNA Polymerases, 393
  BOX 14-1 CCA-Adding Enzymes: Synthesizing RNA without a Template, 462
  BOX 14-2 Selenocysteine, 470
  BOX 14-3 uORFs and IRESs: Exceptions That Prove the Rule, 485
  BOX 14-4 GTP-Binding Proteins, Conformational Switching, and the Fidelity and Ordering of the Events of Translation, 498
  BOX 16-3 Concentration, Affinity, and Cooperative Binding, 572
  BOX 17-4 Is There a Histone Code?, 623
  BOX 18-1 Amino Acid Biosynthetic Operons Are Controlled by Attenuation, 639
  BOX 19-2 Review of Cytoskeleton: Asymmetry and Growth, 669
  BOX 19-3 Overview of Ciona Development, 671
  BOX 19-4 Overview of Drosophila Development, 677
  BOX 19-8 Homeotic Genes of Drosophila Are Organized in Special Chromosome Clusters, 696
  Key Experiments
  BOX 1-2 Genes Are Linked to Chromosomes, 10
  BOX 2-1 Chargaff’s Rules, 24
  BOX 2-2 Evidence That Genes Control Amino Acid Sequences in Proteins, 29
  BOX 6-1 DNA Has 10.5 Base Pairs per Turn of the Helix in Solution: The Mica Experiment, 108
  BOX 6-2 How Spots on an X-ray Film Reveal the Structure of DNA, 112
  BOX 6-3 Proving that DNA Has a Helical Periodicity of about 10.5 Base Pairs per Turn from the Topological Properties of DNA Rings, 128
  BOX 7-1 Micrococcal Nuclease and the DNA Associated with the Nucleosome, 158
  BOX 7-2 Nucleosomes and Superhelical Density, 166
  BOX 7-3 Determining Nucleosome Position in the Cell, 180
  BOX 8-5 The Identification of Origins of Replication and Replicators, 232
  BOX 11-4 Maize Elements and the Discovery of Transposons, 356
  BOX 13-1 Adenovirus and the Discovery of Splicing, 419
  BOX 13-2 Converting Group I Introns into Ribozymes, 428
  BOX 13-3 Identification of Docking Site and Selector Sequences, 442
  BOX 16-1 Activator Bypass Experiments, 557
  BOX 16-2 Jacob, Monod, and the Ideas Behind Gene Regulation, 561
  BOX 16-4 Evolution of the λ Switch, 579
  BOX 16-5 Genetic Approaches That Identified Genes Involved in the Lytic/Lysogenic Choice, 581
  BOX 17-2 Long-Distance Interactions on the Same and Different Chromosomes, 604
  BOX 17-3 Evolvability of a Regulatory Circuit, 612
  BOX 18-2 History of miRNAs and RNAi, 650
  BOX 19-5 The Role of Activator Synergy in Development, 684
  BOX 19-7 cis-Regulatory Sequences in Animal Development and Evolution, 690
  BOX 20-2 Bistability and Hysteresis, 722
  BOX 21-2 Sequenators Are Used for High-Throughput Sequencing, 757
  Medical Connections
  BOX 8-2 Anticancer and Antiviral Agents Target DNA Replication, 203
  BOX 8-8 Aging, Cancer, and the Telomere Hypothesis, 251
  BOX 9-1 Expansion of Triple Repeats Causes Disease, 259
  BOX 9-2 The Ames Test, 266
  BOX 9-3 Nonhomologous End Joining, 276
  BOX 10-2 The Product of the Tumor Suppressor Gene BRCA2 Interacts with Rad51 Protein and Controls Genome Stability, 309
  BOX 11-1 Application of Site-Specific Recombination to Genetic Engineering, 327
  BOX 13-4 Defects in Pre-mRNA Splicing Cause Human Disease, 445
  BOX 13-5 Deaminases and HIV, 450
  BOX 14-5 Antibiotics Arrest Cell Division by Blocking Specific Steps in Translation, 502
  BOX 17-5 Transcriptional Repression and Human Disease, 626
  BOX 17-6 Using Transcription Factors to Reprogram Somatic Cells into Embryonic Stem Cells, 629
  BOX 18-3 RNAi and Human Disease, 656
  BOX 19-6 Stem Cells, 686
  Techniques
  BOX 5-1 Determination of Protein Structure, 78
  BOX 8-1 Incorporation Assays Can Be Used to Measure Nucleic Acid and Protein Synthesis, 200
  BOX 8-3 Determining the Polarity of a DNA Helicase, 212
  BOX 12-1 Consensus Sequences, 388
  BOX 17-1 The Two-Hybrid Assay, 594
  BOX 19-1 Microarray Assays: Theory and Practice, 662
  BOX 20-1 Bioinformatics Methods for the Identification of Complex Enhancers, 708
  BOX 21-1 Forensics and the Polymerase Chain Reaction, 753