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Molecular Biology of the Gene, Fifth Edition

by: Watson, James D

Molecular Biology of the Gene, Fifth Edition

by: Watson, James D

ISBN 13:
9780805346350
ISBN 10:
080534635X
Edition: 6th
Format: Hardcover
Copyright: 12/23/2003
Publisher: Cold Spring Harbor Laboratory Press
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Summary

The long-awaited new edition of James D. Watson's classic text,Molecular Biology of the Gene, has been thoroughly revised and is published to coincide with the 50th anniversary of Watson and Crick's paper on the structure of the DNA double-helix. Twenty-one concise chapters, co-authored by five highly respected molecular biologists, provide current, authoritative coverage of a fast-changing discipline, giving both historical and basic chemical context.Divided into four parts: Genetics and Chemistry, Central Dogma, Regulation, and Methods.For college instructors, students, and anyone interested in molecular biology and genetics.

PART 1 CHEMISTRY AND GENETICS

(93)

The Mendelian View of the World

(14)

Mendel's Discoveries

(2)

The Principle of Independent Segregation

(1)

Mendelian Laws

(2)

Some Alleles Are Neither Dominant Nor Recessive

(1)

Principle of Independent Assortment

(1)

Chromosomal Theory of Heredity

(1)

Gene Linkage and Crossing Over

(3)

Genes Are Linked to Chromosomes

(2)

Chromosome Mapping

(3)

The Origin of Genetic Variability Through Mutations

(1)

Early Speculations about What Genes are and How they Act

(1)

Preliminary Attempts to Find a Gene-Protein Relationship

(3)

Summary

(1)

Bibliography

(1)

Nucleic Acids Convey Genetic Information

(22)

Avery's Bombshell: DNA can carry Genetic Specificity

(1)

Viral Genes are also Nucleic Acids

(1)

The Double Helix

(7)

Chargaff's Rules

(1)

Finding the Polymerases that Make DNA

(2)

Experimental Evidence Favors Strand Separation during DNA Replication

(2)

The Genetic Information within DNA is Conveyed by the Sequence of its Four Nucleotide Building Blocks

(3)

DNA Cannot Be the Template that Directly Orders Amino Acids during Protein Synthesis

(1)

Evidence that Genes Control Amino Acid Sequence in Proteins

(1)

RNA Is Chemically Very Similar to DNA

(1)

The Central Dogma

(6)

The Adaptor Hypothesis of Crick

(1)

The Test-Tube Synthesis of Proteins

(1)

The Paradox of the Nonspecific-Appearing Ribosomes

(1)

Discovery of Messenger RNA (mRNA)

(1)

Enzymatic Synthesis of RNA upon DNA Templates

(2)

Establishing the Genetic Code

(2)

Establishing the Direction of Protein Synthesis

(1)

Start and Stop Signals Are Also Encoded within DNA

(1)

The Era of Genomics

(3)

Summary

(1)

Bibliography

(1)

The Importance of Weak Chemical Interactions

(14)

Characteristics of Chemical Bonds

(3)

Chemical Bonds Are Explainable in Quantum-Mechanical Terms

(1)

Chemical-Bond Formation Involves a Change in the Form of Energy

(1)

Equilibrium between Bond Making and Breaking

(1)

The Concept of Free Energy

(1)

Keq Is Exponentially Related to ΔG

(1)

Covalent Bonds Are Very Strong

(1)

Weak Bonds in Biological Systems

(10)

Weak Bonds Have Energies between 1 and 7 kcal/mol

(1)

Weak Bonds Are Constantly Made and Broken at Physiological Temperatures

(1)

The Distinction between Polar and Nonpolar Molecules

(1)

Van der Waals Forces

(1)

Hydrogen Bonds

(1)

Some Ionic Bonds are Hydrogen Bonds

(1)

Weak Interactions Demand Complementary Molecular Surfaces

(1)

Water Molecules Form Hydrogen Bonds

(1)

Weak Bonds between Molecules in Aqueous Solutions

(1)

The Uniqueness of Molecular Shapes and the Concept of Selective Stickiness

(1)

Organic Molecules that Tend to Form Hydrogen Bonds are Water Soluble

(1)

Hydrophobic ``Bonds'' Stabilize Macromolecules

(1)

The Advantages of ΔG between 2 and 5 kcal/mol

(1)

Weak Bonds Attach Enzymes to Substrates

(1)

Weak Bonds Mediate Most Protein: DNA and Protein: Protein Interactions

(1)

Summary

(1)

Bibliography

(1)

The Importance of High-Energy Bonds

(14)

Molecules that Donate Energy are Thermodynamically Unstable

(2)

Enzymes lower Activation Energies in Biochemical Reactions

(1)

Free Energy in Biomolecules

(2)

High-Energy Bonds Hydrolyze with Large Negative ΔG

(2)

High-Energy Bonds in Biosynthetic Reactions

(1)

Peptide Bonds Hydrolyze Spontaneously

(1)

Coupling of Negative with Positive ΔG

(1)

Activation of Precursors in Group Transfer Reactions

(8)

ATP Versality in Group Transfer

(1)

Activation of Amino Acids by Attachment of AMP

(1)

Nucleic Acid Precursors are Activated by the Presence of P ~ P

(1)

The Value of P ~ P Release in Nucleic Acid Synthesis

(1)

P ~ P Splits Characterize Most Biosynthetic Reactions

(2)

Summary

(1)

Bibliography

(2)

Weak and Strong Bonds Determine Macromolecular Structure

(24)

Higher-Order Structures are Determined by Intra and Intermolecular Interactions

(9)

DNA Can Form a Regular Helix

(2)

RNA Forms a Wide Variety of Structures

(1)

Chemical Features of Protein Building Blocks

(1)

The Peptide Bond

(1)

Three Are Four Levels of Protein Structure

(2)

α Helices and β Sheets Are the Common Forms of Secondary Structure

(1)

Determination of Protein Structure

(3)

The Specific Conformation of a Protein Results from its Pattern of Hydrogen Bonds

(3)

α Helices Come Together to Form Coiled-Coils

(1)

Most Proteins are Modular, Containing Two or Three Domains

(3)

Proteins Are Composed of a Surprisingly Small Number of Structural Motifs

(1)

Large Proteins Are Often Constructed of Several Smaller Polypeptide Chains

(1)

Different Protein Functions Arise from Various Domain Combinations

(2)

Weak Bonds Correctly Position Proteins along DNA and RNA Molecules

(3)

Proteins Scan along DNA to Locate a Specific DNA-Binding Site

(1)

Diverse Strategies for Protein Recognition of RNA

(1)

Allostery: Regulation of a Protein's Function by Changing its Shape

(6)

The Structural Basis of Allosteric Regulation Is Known for Examples Involving Small Ligands, Protein-Protein Interactions, and Protein Modification

(3)

Not All Regulation of Proteins Is Mediated by Allosteric Events

(1)

Summary

(1)

Bibliography

(1)

PART 2 MAINTENANCE OF THE GENOME

(250)

The Structures of DNA and RNA

(32)

DNA Structure

(13)

DNA Is Composed of Polynucleotide Chains

(2)

Each Base Has Its Preferred Tautomeric Form

100

(1)

The Two Strands of the Double Helix Are Held Together by Base Pairing in an Antiparallel Orientation

100

(1)

The Two Chains of the Double Helix Have Complementary Sequences

101

(1)

Hydrogen Bonding Is Important for the Specificity of Base pairing

102

(1)

Bases Can Flip Out from the Double Helix

102

(1)

DNA Is Usually a Right-Handed Double Helix

103

(1)

The Double Helix Has Minor and Major Grooves

103

(1)

The Major Groove Is Rich in Chemical Information

103

(1)

DNA Has 10.5 Base Pairs per Turn of the Helix in Solution: The Mica Experiment

104

(2)

The Double Helix Exists in Multiple Conformations

106

(1)

DNA Can Sometimes Form a Left-Handed Helix

107

(1)

DNA Strands Can Separate (Denature) and Reassociate

108

(3)

Some DNA Molecules Are Circles

111

(1)

DNA Topology

111

(11)

Linking Number Is an Invariant Topological Property of Covalently Closed, Circular DNA

112

(1)

Linking Number Is Composed ot Twist and Writhe

112

(2)

Lk0 Is the Linking Number of Fully Relaxed cccDNA under Physiological Conditions

114

(1)

DNA in Cells Is Negatively Supercoiled

114

(1)

Nucleosomes Introduce Negative Supercoiling in Eukaryotes

115

(1)

Topoisomerases Can Relax Supercoiled DNA

115

(1)

Prokaryotes Have a Special Topoisomerase that Introduces Supercoils into DNA

116

(1)

Topoisomerases also Unknot and Disentangle DNA Molecules

117

(1)

Topoisomerases Use a Covalent Protein-DNA Linkage to Cleave and Rejoin DNA Strands

118

(1)

Topoisomerases Form an Enzyme Bridge and Pass DNA Segments through Each Other

118

(2)

DNA Topoisomers Can Be Separated by Electrophoresis

120

(1)

Ethidium Ions Cause DNA to Unwind

120

(1)

Proving that DNA Has a Helical Periodicity of about 10.5 Base Pairs per Turn from the Topological Properties of DNA Rings

121

(1)

RNA Structure

122

(7)

RNA Contains Ribose and Uracil and Is Usually Single-Stranded

122

(1)

RNA Chains Fold Back on Themselves to Form Local Regions of Double Helix Similar to A-Form DNA

123

(1)

RNA Can Fold Up into Complex Tertiary Structures

124

(1)

Some RNAs Are Enzymes

125

(1)

The Hammerhead Ribozyme Cleaves RNA by the Formation of a 2',3' Cyclic Phosphate

125

(1)

Did Life Evolve from an RNA World?

126

(1)

Summary

126

(1)

Bibliography

127

(2)

Chromosomes, Chromatin, and the Nucleosome

129

(52)

Chromosome Sequence and Diversity

130

(8)

Chromosomes Can Be Circular or Linear

130

(1)

Every Cell Maintains a Characteristic Number of Chromosomes

131

(2)

Genome Size Is Related to the Complexity of the Organism

133

(1)

The E. coli Genome Is Composed almost Entirely of Genes

134

(1)

More Complex Organisms Have Decreased Gene Density

134

(1)

Genes Make Up Only a Small Proportion of the Eukaryotic Chromosomal DNA

135

(2)

The Majority of Human Intergenic Sequences Are Composed of Repetitive DNA

137

(1)

Chromosome Duplication and Segregation

138

(13)

Eukaryotic Chromosomes Require Centromeres, Telomeres, and Origins of Replication to Be Maintained during Cell Division

138

(3)

Eukaryotic Chromosome Duplication and Segregation Occur in Separate Phases of the Cell Cycle

141

(2)

Chromosome Structure Changes as Eukaryotic Cells Divide

143

(1)

Sister Chromatid Cohesion and Chromosome Condensation Are Mediated by SMC Proteins

144

(2)

Mitosis Maintains the Parental Chromosome Number

146

(1)

The Gap Phases of the Cell Cycle Allow Time to Prepare for the Next Cell Cycle Stage while also Checking that the Previous Stage Is Finished Correctly

146

(2)

Meiosis Reduces the Parental Chromosome Number

148

(2)

Different Levels of Chromosome Structure Can Be Observed by Microscopy

150

(1)

The Nucleosome

151

(9)

Nucleosomes Are the Building Blocks of Chromosomes

151

(1)

Micrococcal Nuclease and the DNA Associated with the Nucleosome

152

(1)

Histones Are Small, Positively-Charged Proteins

153

(1)

The Atomic Structure of the Nucleosome

154

(2)

Many DNA Sequence-Independent Contacts Mediate the Interaction between the Core Histones and DNA

156

(3)

The Histone N-Terminal Tails Stabilize DNA Wrapping around the Octamer

159

(1)

Higher-Order Chromatin Structure

160

(5)

Histone H1 Binds to the Linker DNA between Nucleosomes

160

(1)

Nucleosome Arrays Can Form More Complex Structures: the 30-nm Fiber

161

(1)

The Histone N-Terminal Tails Are Required for the Formation of the 30-nm Fiber

162

(1)

Further Compaction of DNA Involves Large Loops of Nucleosomal DNA

162

(1)

Histone Variants Alter Nucleosome Function

163

(2)

Regulation of Chromatin Structure

165

(10)

The Interaction of DNA with the Histone Octamer Is Dynamic

165

(1)

Nucleosome Remodeling Complexes Facilitate Nucleosome Movement

166

(2)

Some Nucleosomes Are Found in Specific Positions in vivo: Nucleosome Positioning

168

(1)

Modification of the N-Terminal Tails of the Histones Alters Chromatin Accessibility

169

(1)

Determining Nucleosome Position in the Cell

170

(3)

Specific Enzymes Are Responsible for Histone Modification

173

(1)

Nucleosome Modification and Remodeling Work Together to Increase DNA Accessibility

174

(1)

Nucleosome Assembly

175

(6)

Nucleosomes Are Assembled Immediately after DNA Replication

175

(1)

Assembly of Nucleosomes Requires Histone ``Chapterones''

176

(3)

Summary

179

(1)

Bibliography

180

(1)

The Replication of DNA

181

(54)

The Chemistry of DNA Synthesis

182

(2)

DNA Synthesis Requires Deoxynucleoside Triphosphates and a Primer: Template Junction

182

(1)

DNA Is Synthesized by Extending the 3' End of the Primer

183

(1)

Hydrolysis of Pyrophosphates Is the Driving Force for DNA Synthesis

183

(1)

The Mechanism of DNA Polymerase

184

(8)

DNA Polymerases Use a Single Active Site to Catalyze DNA Synthesis

184

(2)

DNA Polymerases Resemble a Hand that Grips the Primer: Template Junction

186

(2)

DNA Polymeras Are Processive Enzymes

188

(3)

Exonucleases Proofread Newly Synthesized DNA

191

(1)

The Replication Fork

192

(8)

Both Strands of DNA Are Synthesized Together at the Replication Fork

192

(1)

The Initiation of a New Strand of DNA Requires an RNA Primer

193

(1)

RNA Primers Must Be Removed to Complete DNA Replication

194

(1)

DNA Helicases Unwind the Double Helix in Advance of the Replication Fork

194

(1)

Single-Stranded Binding Proteins Stabilize Single-Stranded DNA Prior to Replication

195

(1)

Determining the Polarity of a DNA Helicase

196

(2)

Topoisomerases Remove Supercoils Produced by DNA Unwinding at the Replication Fork

198

(1)

Replication Fork Enzymes Extend the Range of DNA Polymerase Substrates

199

(1)

The Specialization of DNA Polymerases

200

(5)

DNA Polymerases Are Specialized for Different Roles in the Cell

200

(1)

Sliding Clamps Dramatically Increase DNA Polymerase Processivity

201

(3)

Sliding Clamps Are Opened and Placed on DNA by Clamps Loaders

204

(1)

DNA Synthesis at the Replication Fork

205

(7)

ATP Control of Protein Function: Loading a Sliding Clamp

206

(4)

Interactions between Replication Fork Proteins Form the E. coli Replisome

210

(2)

Initiation of DNA Replication

212

(2)

Specific Genomic DNA Sequences Direct the Initiation of DNA Replication

212

(1)

The Replicon Model of Replication Initiation

212

(1)

Replicator Sequences Include Initiator Binding Sites and Easily Unwound DNA

213

(1)

Binding and Unwinding: Origin Selection and Activation By the Initiator Protein

214

(14)

The Identification of Origins of Replication and Replicators

214

(3)

Protein-Protein and Protein-DNA Interactions Direct the Initiation Process

217

(1)

E. coli DNA Replication Is Regulated by DNA-ATP Levels and SeqA

217

(4)

The Replication Factory Hypothesis

221

(2)

Eukaryotic Chromosomes Are Replicated Exactly Once per Cell Cycle

223

(1)

Pre-Replicative Complex Formation Directs the Initiation of Replication in Eukaryotes

223

(2)

Pre-RC Formation and Activation Is Regulated to Allow only a Single Round of Replication during Each Cell Cycle

225

(3)

Similarities between Eukaryotic and Prokaryotic DNA Replication Initiation

228

(1)

Finishing Replication

228

(7)

Type II Topoisomerases Are Required to Separate Daughter DNA Molecules

228

(1)

Lagging Strand Synthesis Is Unable to Copy the Extreme Ends of Linear Chromosomes

229

(1)

Telomerase Is a Novel DNA Polymerase that Does Not Require an Exogenous Template

230

(2)

Telomerase Solves the End Replication Problem by Extending the 3' End of the Chromosome

232

(1)

Summary

232

(1)

Bibliography

233

(2)

The Mutability and Repair of DNA

235

(24)

Replication Errors and Their Repair

236

(6)

The Nature of Mutations

236

(1)

Some Replication Errors Escape Proofreading

237

(1)

Expansion of Triple Repeats Causes Disease

237

(1)

Mismatch Repair Removes Errors that Escape Proofreading

238

(4)

DNA Damage

242

(4)

DNA Undergoes Damage Spontaneously from Hydrolysis and Deamination

242

(1)

The Ames Test

243

(1)

DNA Is Damaged by Alkylation, Oxidation, and Radiation

244

(1)

Mutations Are also Caused by Base Analogs and Intercalating Agents

245

(1)

Repairs of DNA Damage

246

(13)

Direct Reversal of DNA Damage

247

(1)

Base Excision Repair Enzymes Remove Damaged Bases by a Base-Flipping Mechanism

248

(2)

Nucleotide Excision Repair Enzymes Cleave Damaged DNA on Either Side of the Lesion

250

(3)

Recombination Repairs DNA Breaks by Retrieving Sequence Information from Undamaged DNA

253

(1)

Translesion DNA Synthesis Enables Replication to Proceed across DNA Damage

254

(2)

The Y-Family of DNA Polymerases

256

(1)

Summary

257

(1)

Bibliography

258

(1)

Homologous Recombination at the Molecular Level

259

(34)

Models for Homologous Recombination

259

(9)

The Holiday Model Illustrates Key Steps in Homologous Recombination

260

(4)

The Double-Strand Break Repair Model More Accurately Describes Many Recombination Events

264

(2)

How to Resolve a Recombination Intermediate with Two Holliday Junctions

266

(1)

Double-Stranded DNA Breaks Arise by Numerous Means and Initiate Homologous Recombination

267

(1)

Homologous Recombination Protein Machines

268

(10)

The RecBCD Helicase/Nuclease Processes Broken DNA Molecules for Recombination

269

(3)

RecA Protein Assembles on Single-Stranded DNA and Promotes Strand Invasion

272

(2)

Newly Base-Paired Partners Are Established within the RecA Filament

274

(1)

RecA Homologs Are Present in All Organisms

275

(1)

RuvAB Complex Specifically Recognizes Holliday Junctions and Promotes Branch Migration

276

(1)

RuvC Cleaves Specific DNA Strands at the Holliday Junction to Finish Recombination

276

(2)

Homologous Recombination in Eukaryotes

278

(7)

Homologous Recombination Has Additional Functions in Eukaryotes

278

(1)

Homologous Recombination Is Required for Chromosome Segregation during Meiosis

279

(1)

Programmed Generation of Double-Stranded DNA Breaks Occurs during Meiosis

279

(3)

MRX Protein Processes the Cleaved DNA Endsfor Assembly of the RecA-like Strand-Exchange Proteins

282

(1)

Dmcl Is a RecA-like Protein that Specifically Functions in Meiotic Recombination

282

(2)

Many Proteins Function Together to Promote Meiotic Recombination

284

(1)

Mating-Type Switching

285

(3)

Mating-Type Switching Is Initiated by a Site-Specific Double-Strand Break

286

(1)

Mating-Type Switching Is a Gene Conversion Event, Not Associated with Crossing Over

286

(2)

Genetic Consequences of the Mechanism of Homologous Recombination

288

(5)

Gene Conversion Occurs because DNA Is Repaired during Recombination

289

(1)

Summary

290

(1)

Bibliography

291

(2)

Site-Specific Recombination and Transposition of DNA

293

(50)

Conservative Site-Specific Recombination

294

(8)

Site-Specific Recombination Occurs at Specific DNA Sequences in the Target DNA

294

(2)

Site-Specific Recombinases Cleave and Rejoin DNA Using a Covalent Protein-DNA Intermediate

296

(2)

Serine Recombinases Introduce Double-Stranded Breaks in DNA and then Swap Strands to Promote Recombination

298

(1)

Tyrosine Recombinases Break and Rejoin One Pair of DNA Strands at a Time

299

(1)

Structures of Tyrosine Recombinases Bound to DNA Reveal the Mechanism of DNA Exchange

300

(2)

Application of Site-Specific Recombination to Genetic Engineering

302

(1)

Biological Roles of Site-Specific Recombination

302

(8)

λ Integrase Promotes the Integration and Excision of a Viral Genome into the Host Cell Chromosome

303

(1)

Phage λ Excision Requires a New DNA-Bending Protein

304

(1)

The Hin Recombinase Inverts a Segment of DNA Allowing Expression of Alternative Genes

305

(1)

Hin Recombination Requires a DNA Enhancer

306

(1)

Recombinases Convert Multimeric Circular DNA Molecules into Monomers

307

(3)

There Are Other Mechanisms to Direct Recombination to Specific Segments of DNA

310

(1)

Transposition

310

(17)

Some Genetic Elements Move to New Chromosomal Locations by Transposition

310

(1)

There Are Three Principal Classes of Transposable Elements

311

(1)

DNA Transposons Carry a Transposase Gene, Flanked by Recombination Sites

312

(1)

Transposons Exist as Both Autonomous and Nonautonomous Elements

313

(1)

Viral-like Retrotransposons and Retroviruses Carry Terminal Repeat Sequences and Two Genes Important for Recombination

313

(1)

Poly-A Retrotransposons Look Like Genes

314

(1)

DNA Transposition by a Cut-and-Paste Mechanism

314

(2)

The Intermediate in Cut-and-Paste Transposition Is Finished by Gap Repair

316

(1)

There Are Multiple Mechanisms for Cleaving the Nontransferred Strand during DNA Transposition

316

(2)

DNA Transposition by a Replicative Mechanism

318

(2)

Viral-like Retrotransposons and Retroviruses Move Using an RNA Intermediate

320

(1)

DNA Transposases and Retroviral Integrases Are Members of a Protein Superfamily

321

(1)

The Pathway of Retroviral cDNA Formation

322

(2)

Poly-A Retrotransposons Move by a ``Reverse Splicing'' Mechanism

324

(3)

Examples of Transposable Elements and Their Regulation

327

(10)

IS4-Family Transposons Are Compact Elements with Multiple Mechanisms for Copy Number Control

327

(1)

Maize Elements and the Discovery of Transposons

328

(1)

Tn10 Transposition Is Coupled to Cellular DNA Replication

329

(2)

Phage Mu Is an Extremely Robust Transposon

331

(1)

Mu Uses Target Immunity to Avoid Transposing into Its Own DNA

331

(3)

Tc1/Mariner Elements Are Extremely Successful DNA Elements in Eukaryotes

334

(1)

Yeast Ty Elements Transpose into Safe Havens in the Genome

335

(1)

LINEs Promote Their Own Transposition and Even Transpose Cellular RNAs

336

(1)

V(D)J Recombination

337

(6)

The Early Events in V(D)J Recombination Occur by a Mechanism Similar to Transposon Excision

339

(3)

Summary

342

(1)

Bibliography

342

(1)

PART 3 EXPRESSION OF THE GENOME

343

(136)

Mechanisms of Transcription

347

(32)

RNA Polymerases And the Transcription Cycle

348

(5)

RNA Polymerases Come in Different Forms, but Share Many Features

348

(2)

Transcription by RNA Polymerase Proceeds in a Series of Steps

350

(2)

Transcription Initiation Involves Three Defined Steps

352

(1)

The Transcription Cycle in Bacteria

353

(10)

Bacterial Promoters Vary in Strength and Sequence, but Have Certain Defining Features

353

(1)

The σ Factor Mediates Binding of Polymerase to the Promoter

354

(1)

Consensus Sequences

355

(1)

Transition to the Open Complex Involves Structural Changes in RNA Polymerase and in the Promoter DNA

356

(2)

Transcription Is Initiated by RNA Polymerase without the Need for a Primer

358

(1)

RNA Polymerase Synthesizes Several Short RNAs before Entering the Elongation Phase

358

(1)

The Elongating Polymerase Is a Processive Machine that Synthesizes and Proofreads RNA

359

(1)

The Single-Subunit RNA Polymerases

360

(1)

Transcription Is Terminated by Singals within the RNA Sequence

361

(2)

Transcription in Eukaryotes

363

(16)

RNA Polymerase II Core Promoters Are Made up of Combinations of Four Different Sequence Elements

363

(1)

RNA Polymerase II Forms a Pre-Initiation Complex with General Transcription Factors at the Promoter

364

(2)

TBP Binds to and Distorts DNA Using a β Sheet Inserted into the Minor Groove

366

(1)

The Other General Transcription Factors also Have Specific Roles in Initiation

367

(1)

In Vivo, Transcription Initiation Requires Additional Proteins, Including the Mediator Complex

368

(1)

Mediator Consists of Many Subunits, Some Conserved from yeast to Human

369

(1)

A New Set of Factors Stimulate Pol II Elongation and RNA Proofreading

370

(1)

Elongating Polymerase Is Associated with a New Set of Protein Factors Required for Various Types of RNA Processing

371

(3)

RNA Polymerases I and III Recognize Distinct Promoters, Using Distinct Sets of Transcription Factors, but still Require TBP

374

(2)

Summary

376

(1)

Bibliography

377

(2)

RNA Splicing

379

(32)

The Chemistry of RNA Splicing

380

(3)

Sequences within the RNA Determine Where Splicing Occurs

380

(1)

The Intron Is Removed in a Form Called a Lariat as the Flanking Exons Are Joined

381

(2)

Exons from Different RNA Molecules Can Be Fused by Trans-Splicing

383

(1)

The Spliceosome Machinery

383

(2)

RNA Splicing Is Carried Out by a Large Complex Called the Spliceosome

383

(2)

Splicing Pathways

385

(9)

Assembly, Rearrangements, and Catalysis Within the Spliceosome: the Splicing Pathway

385

(2)

Self-Splicing Introns Reveal that RNA Can Catalyze RNA Splicing

387

(1)

Group I Introns Release a Linear Intron Rather than a Lariat

388

(1)

Converting Group I Introns into Ribozymes

389

(2)

How Does the Spliceosome Find the Splice Sites Reliably?

391

(3)

Alternative Splicing

394

(7)

Single Genes Can Produce Multiple Products by Alternative Splicing

394

(2)

Alternative Splicing Is Regulated by Activators and Repressors

396

(2)

Adenovirus and the Discovery of Splicing

398

(2)

A Small Group of Introns Are Spliced by an Alternative Spliceosome Composed of a Different Set of snRNPs

400

(1)

Exon Shuffling

401

(3)

Exons Are Shuffled by Recombination to Produce Genes Encoding New Proteins

400

(4)

RNA Editing

404

(2)

RNA Editing Is Another Way of Altering the Sequence of an mRNA

404

(2)

mRNA Transport

406

(5)

Once Processed, mRNA Is Packaged and Exported from the Nucleus into the Cytoplasm for Translation

406

(2)

Summary

408

(1)

Bibliography

409

(2)

Translation

411

(50)

Messenger RNA

412

(3)

Polypeptide Chains Are Specified by Open-Reading Frames

412

(1)

Prokaryotic mRNAs Have a Ribosome Binding Site that Recruits the Translational Machinery

413

(1)

Eukaryotic mRNAs Are Modified at Their 5' and 3' Ends to Facilitate Translation

414

(1)

Transfer RNA

415

(2)

tRNAs Are Adaptors between Codons and Amino Acids

415

(1)

tRNAs Share a Common Secondary Structure that Resembles a Cloverleaf

416

(1)

tRNAs Have an L-Shaped Three-Dimensional Structure

417

(1)

Attachment of Amino Acids to tRNA

417

(6)

tRNAs Are Charged by the Attachment of an Amino Acid to the 3' Terminal Adenosine Nucleotide via a High-Energy Acyl Linkage

417

(1)

Aminoacyl tRNA Synthetases Charge tRNAs in Two Steps

418

(1)

Each Aminoacyl tRNA Synthetase Attaches a Single Amino Acid to One or More tRNAs

419

(1)

tRNA Synthetases Recognize Unique Structural Features of Cognate tRNAs

420

(1)

Aminoacyl-tRNA Formation Is Very Accurate

421

(1)

Some Aminoacyl tRNA Synthetases Use an Editing Pocket to Charge tRNAs with High Accuracy

422

(1)

The Ribosome Is Unable to Discriminate between Correctly and Incorrectly Charged tRNAs

422

(1)

Selenocysteine

423

(1)

The Ribosome

423

(9)

The Ribosome Is Composed of a Large and a Small Subunit

425

(1)

The Large and Small Subunits Undergo Association and Dissociation during each Cycle of Translation

425

(2)

New Amino Acids Are Attached to the C-Terminus of the Growing Polypeptide Chain

427

(1)

Peptide Bonds Are Formed by Transfer of the Growing Polypeptide Chain from One tRNA to Another

428

(1)

Ribosomal RNAs Are Both Structural and Catalytic Determinats of the Ribosome

428

(1)

The Ribosome Has Three Binding Sites for tRNA

429

(1)

Channels through the Ribosome Allow the mRNA and Growing Polypeptide to Enter and/or Exit the Ribosome

430

(2)

Initiation of Translation

432

(8)

Prokaryotic mRNAs Are Initially Recruited to the Small Subunit by Base-Pairing to rRNA

433

(1)

A Specialized tRNA Charged with a Modified Methionine Binds Directly to the Prokaryotic Small Subunit

433

(1)

Three Initiation Factors Direct the Assembly of an Initiation Complex that Contains mRNA and the Initiator tRNA

433

(2)

Eukaryotic Ribosomes Are Recruited to the mRNA by the 5' Cap

435

(2)

The Start Codon Is Found by Scanning Downstream from the 5' End of the mRNA

437

(1)

Translation Initiation Factors Hold Eukaryotic mRNAs in Circles

438

(1)

uORFs and IRESs: Exceptions that Prove the Rule

439

(1)

Translation Elongation

440

(8)

Aminoacyl-tRNAs Are Delivered to the A Site by Elongation Factor EF-Tu

441

(1)

The Ribosome Uses Multiple Mechanisms to Select Against Incorrect Aminoacyl-tRNAs

441

(1)

The Ribosome Is a Ribozyme

442

(2)

Peptide Bond Formation and the Elongation Factor EF-G Drive Translocation of the tRNAs and the mRNA

444

(1)

EF-G Drives Translocation by Displacing the tRNA Bound to the A Site

445

(1)

EF-Tu-GDP and EF-G-GDP Must Exchange GDP for GTP Prior to Participating in a New Round of Elongation

446

(1)

A Cycle of Peptide Bond Formation Consumes Two Molecules of GTP and One Molecule of ATP

446

(1)

GTP-Binding Proteins, Conformational Switching, and the Fidelity and Ordering of the Events of Translation

447

(1)

Termination of Translation

448

(4)

Release Factors Terminate Translation in Response to Stop Codons

448

(1)

Short Regions of Class I Release Factors Recognize Stop Codons and Trigger Release of the Peptidyl Chain

449

(1)

GDP/GTP Exchange and GTP Hydrolysis Control the Function of the Class II Release Factor

450

(1)

The Ribosome Recycling Factor Mimics a tRNA

450

(2)

Translation-Dependent Regulation of mRNA and Protein Stability

452

(9)

The SsrA RNA Rescues Ribosomes that Translate Broken mRNAs

452

(1)

Antibiotics Arrest Cell Division by Blocking Specific Steps in Translation

453

(3)

Eukaryotic Cells Degrade mRNAs that Are Incomplete or that Have Premature Stop Codons

456

(2)

Summary

458

(1)

Bibliography

459

(2)

The Genetic Code

461

(18)

The Code is Degenerate

461

(8)

Perceiving Order in the Makeup of the Code

462

(1)

Wobble in the Anticodon

463

(1)

Three Codons Direct Chain Termination

463

(1)

How the Code Was Cracked

464

(1)

Stimulation of Amino Acid Incorporation by Synthetic mRNAs

465

(1)

Poly-U Codes for Polyphenylalanine

466

(1)

Mixed Copolymers Allowed Additional Codon Assignments

467

(1)

Transfer RNA Binding to Defined Trinucleotide Codons

468

(1)

Codon Assignments from Repeating Copolymers

468

(1)

Three Rules Govern the Genetic Code

469

(2)

Three Kinds of Point Mutations Alter the Genetic Code

470

(1)

Genetic Proof that the Code Is Read in Units of Three

471

(1)

Suppressor Mutations Can Reside in the Same or a Different Gene

471

(4)

Intergenic Suppression Involves Mutant tRNAs

472

(2)

Nonsense Suppressors also Read Normal Termination Signals

474

(1)

Proving the Validity of the Genetic Code

474

(1)

The Code is Nearly Universal

475

(4)

Summary

477

(1)

Bibliography

477

(2)

PART 4 REGULATION

479

(164)

Gene Regulation in Prokaryotes

483

(46)

Principles of Transcriptional Regulation

483

(5)

Gene Expression Is Controlled by Regulatory Proteins

483

(1)

Many Promoters Are Regulated by Activators that Help RNA Polymerase Bind DNA and by Repressors that Block that Binding

484

(1)

Some Activators Work by Allostery and Regulate Steps after RNA Polymerase Binding

485

(1)

Action at a Distance and DNA Looping

486

(1)

Cooperative Binding and Allostery Have Many Roles in Gene Regulation

487

(1)

Antitermination and Beyond: Not All of Gene Regulation Targets Transcription Initiation

487

(1)

Regulation of Transcription Initiation: Examples from Bacteria

488

(16)

An Activator and a Repressor Together Control the lac Genes

488

(1)

CAP and Lac Repressor Have Opposing Effects on RNA Polymerase Binding to the lac Promoter

489

(1)

Detecting DNA-Binding Sites

490

(2)

CAP Has Separate Activating and DNA-Binding Surfaces

492

(1)

CAP and Lac Repressor Bind DNA Using a Common Structural Motif

493

(1)

Activator Bypass Experiments

493

(3)

The Activities of Lac Repressor and CAP Are Controlled Allosterically by Their Signals

496

(1)

Jacob, Monod, and the Ideas Behind Gene Regulation

497

(2)

Combinatorial Control: CAP Controls Other Genes As Well

499

(1)

Alternative σ Factors Direct RNA Polymerase to Alternative Sets of Promoters

499

(1)

NtrC and MerR: Transcriptional Activators that Work by Allostery Rather than by Recruitment

500

(1)

NtrC Has ATPase Activity and Works from DNA Sites Far from the Gene

500

(1)

MerR Activates Transcription by Twisting Promoter DNA

501

(1)

Some Repressors Hold RNA Polymerase at the Promoter Rather than Excluding It

502

(1)

AraC and Control of the araBAD Operon by Antiactivation

503

(1)

Examples of Gene Regulation at Steps After Transcription Initiation

504

(8)

Amino Acid Biosynthetic Operons Are Controlled by Premature Transcription Termination

504

(2)

Ribosomal Proteins Are Translational Repressors of Their Own Synthesis

506

(3)

Riboswitches

509

(3)

The Case of Phage λ: Layers of Regulation

512

(17)

Alternative Patterns of Gene Expression Control Lytic and Lysogenic Growth

513

(1)

Regulatory Proteins and Their Binding Sites

514

(1)

λ Repressor Binds to Operator Sites Cooperatively

515

(1)

Concentration, Affinity, and Cooperative Binding

516

(1)

Repressor and Cro Bind in Different Patterns to Control Lytic and Lysogenic Growth

517

(1)

Lysogenic Induction Requires Proteolytic Cleavage of λ Repressor

518

(1)

Negative Autoregulation of Repressor Requires Long-Distance Interactions and a Large DNA Loop

519

(1)

Another Activator, λcII, Controls the Decision between Lytic and Lysogenic Growth upon Infection of a New Host

520

(1)

Genetic Approaches that Identified Genes Involved in the Lytic/Lysogenic Choice

521

(1)

Growth Conditions of E. coli Control the Stability of CII Protein and thus the Lytic/Lysogenic Choice

522

(1)

Transcriptional Antitermination in λ Development

523

(1)

Retroregulation: An Interplay of Controls on RNA Synthesis and Stability Determines in Gene Expression

524

(1)

Summary

525

(1)

Bibliography

526

(3)

Gene Regulation in Eukaryotes

529

(46)

Conserved Mechanisms of Transcriptional Regulation from Yeast to Mammals

531

(6)

Activators Have Separate DNA Binding and Activating Functions

531

(2)

The Two Hybrid Assay

533

(1)

Eukaryotic Regulators Use a Range of DNA-Binding Domains, but DNA Recognition Involves the Same Principles as Found in Bacteria

534

(2)

Activating Regions Are Not Well-Defined Structures

536

(1)

Recruitment of Protein Complexes to Genes By Eukaryotic Activators

537

(7)

Activators Recruit the Transcriptional Machinery to the Gene

537

(2)

Chromatin Immunoprecipitation

539

(1)

Activators also Recruit Nucleosome Modifiers that Help the Transcription Machinery Bind at the Promoter

540

(1)

Action at a Distance: Loops and Insulators

540

(3)

Appropriate Regulation of Some Groups of Genes Requires Locus Control Regions

543

(1)

Signal Integration and Combinatorial Control

544

(5)

Activators Work Together Synergistically to Integrate Signals

544

(2)

Signal Integration: the HO Gene Is Controlled by Two Regulators; One Recruits Nucleosome Modifiers and the Other Recruits Mediator

546

(1)

Signal Integration: Cooperative Binding of Activators at the Human β-Interferon Gene

546

(1)

Combinatorial Control Lies at the Heart of the Complexity and Diversity of Eukaryotes

547

(1)

Combinatorial Control of the Mating-Type Genes from Saccharomyces cerevisiae

548

(1)

Transcriptional Repressors

549

(2)

Signal Transduction and the Control of Transcriptional Regulators

551

(5)

Signals Are Often Communicated to Transcriptional Regulators through Signal Transduction Pathways

551

(1)

Signals Control the Activities of Eukaryotic Transcriptional Regulators in a Variety of Ways

552

(3)

Activators and Repressors Sometimes Come in Pieces

555

(1)

Gene ``Silencing'' by Modification of Histones and DNA

556

(6)

Silencing in Yeast is Mediated by Deacetylation and Methylation of Histones

556

(2)

Histone Modifications and the Histone Code Hypothesis

558

(1)

DNA Methylation Is Associated with Silenced Genes in Mammalian Cells

558

(2)

Some States of Gene Expression Are Inherited through Cell Division even when the Initiating Signal Is No Longer Present

560

(2)

λ Lysogens and the Epigenetic Switch

562

(1)

Eukaryotic Gene Regulation at Steps After Transcription Initiation

562

(5)

Some Activators Control Transcriptional Elongation rather than Initiation

562

(1)

The Regulation of Alternative mRNA Splicing Can Produce Different Protein Products in Different Cell Types

563

(2)

Expression of the Yeast Transcriptional Activator Gcn4 Is Controlled at the Level of Translation

565

(2)

RNAS in Gene Regulation

567

(8)

Double-Stranded RNA Inhibits Expression of Genes Homologous to that RNA

568

(1)

Short Interfering RNAs (siRNAs) Are Produced from dsRNA and Direct Machinery that Switches Off Genes in Various Ways

568

(2)

MicroRNAs Control the Expression of some Genes during Development

570

(1)

Summary

571

(1)

Bibliography

572

(3)

Gene Regulation during Development

575

(38)

Three Strategies by which Cells are Instructed to Express Specific Sets of Genes During Development

576

(4)

Some mRNAs Become Localized within Eggs and Embroys due to an Intrinsic Polarity in the Cytoskeleton

576

(1)

Cell-to-Cell Contact and Secreted Cell Signaling Molecules both elicit Changes in Gene Expression in Neighboring Cells

576

(1)

Microarray Assays: Theory and Practice

577

(1)

Gradients of Secreted Signaling Molecules Can Instruct Cells to Follow Different Pathways of Development based on Their Location

578

(2)

Examples of the Three Strategies for Establishing Differential Gene Expression

580

(10)

The Localized Ash 1 Repressor Controls Mating Type in Yeast by Silencing the HO Gene

580

(2)

Review of Cytoskeleton: Asymmetry and Growth

582

(2)

A Localized mRNA Initiates Muscle Differentiation in the Sea Squirt Embryo

584

(1)

Cell-to-Cell Contact Elicits Differential Gene Expression in the Sporulating Bacterium, B. subtilis

584

(1)

Overview of Ciona Development

585

(2)

A Skin-Nerve Regulatory Switch Is Controlled by Notch Signaling in the Insect CNS

587

(1)

A Gradient of the Sonic Hedgehog Morphogen Controls the Formation of Different Neurons in the Vertebrate Neural Tube

588

(2)

The Molecular Biology of Drosophila Embryogenesis

590

(23)

An Overview of Drosophila Embryogenesis

590

(1)

A Morphogen Gradient Controls Dorsal-Ventral patterning of the Drosophila Embryo

590

(2)

Overview of Drosophila Development

592

(5)

The Role of Activator Synergy in Development

597

(2)

Segmentation Is Initiated by Localized RNAs at the Anterior and Posterior Poles of the Unfertilized Egg

599

(2)

The Bicoid Gradient Regulates the Expression of Segmentation Genes in a Concentration-Dependent Fashion

601

(1)

Hunchback Expression Is also Regulated at the Level of Translation

602

(1)

The Gradient of Hunchback Repressor Establishes Different Limits of Gap Gene Expression

603

(1)

Hunchback and Gap Proteins Produce Segmentation Stripes of Gene Expression

604

(1)

Bioinformatics Methods for Identification of Complex Enhancers

605

(2)

Gap Repressor Gradients Produce many Stripes of Gene Expression

607

(1)

Short-Range Transcriptional Repressors Permit Different Enhancers to Work Independently of one Another within the Complex eve Regulatory Region

608

(1)

Summary

609

(1)

Bibliography

610

(3)

Comparative Genomics and the Evolution of Animal Diversity

613

(30)

Most Animals Have Essentially The Same Genes

614

(5)

How Does Gene Duplication Give Rise to Biological Diversity?

616

(1)

Gene Duplication and the Importance of Regulatory Evolution

616

(2)

Duplication of Globin Genes Produces New Expression Patterns and Diverse Protein Functions

618

(1)

Creation of New Genes Drives Bacterial Evolution

618

(1)

Three Ways Gene Expression is Changed During Evolution

619

(1)

Experimental Manipulations that Alter Animal Morphology

620

(10)

Changes in Pax6 Expression Create Ectopic Eyes

621

(1)

Changes in Antp Expression Transform Antennae into Legs

622

(1)

Importance of Protein Function: Interconversion of ftz and Antp

622

(1)

Subtle Changes in an Enhancer Sequence Can Produce New Patterns of Gene Expression

623

(1)

The Misexpression of Ubx Changes the Morphology of the Fruit Fly

624

(2)

Changes in Ubx Function Modify the Morphology of Fruit Fly Embryos

626

(1)

Changes in Ubx Target Enchancers Can Alter Patterns of Gene Expression

627

(1)

The Homeotic Genes of Drosophila Are Organized in Special Chromosome Clusters

627

(3)

Morphological Changes in Crustaceans and Insects

630

(5)

Arthropods Are Remarkably Diverse

630

(1)

Changes in Ubx Expression Explain Modifications in Limbs among the Crustaceans

630

(1)

Why Insects Lack Abdominal Limbs

631

(1)

Modification of Flight Limbs Might Arise from the Evolution of Regulatory DNA Sequences

632

(1)

Co-option of Gene Networks for Evolutionary Innovation

633

(2)

Genome Evolution and Human Origins

635

(8)

Humans Contain Surprisingly Few Genes

635

(1)

The Human Genome Is very Similar to that of the Mouse and Virtually Identical to the Chimp

636

(1)

The Evolutionary Origins of Human Speech

637

(1)

How FOXP2 Fosters Speech in Humans

637

(1)

The Future of Comparative Genome Analysis

638

(1)

Summary

639

(1)

Bibliography

640

(3)

PART 5 METHODS

643

(70)

Techniques of Molecular Biology

647

(34)

Introduction

647

(1)

Nucleic Acids

648

(24)

Electrophoresis through a Gel Separates DNA and RNA Molecules According to Size

648

(1)

Restriction Endonucleases Cleave DNA Molecules at Particular Sites

649

(2)

DNA Hybridization Can Be Used to Identify Specific DNA Molecules

651

(1)

Hybridization Probes Can Identify Electrophoretically-Separated DNAs and RNAs

652

(1)

Isolation of Specific Segments of DNA

653

(1)

DNA Cloning

654

(1)

Cloning DNA in Plasmid Vectors

654

(1)

Vector DNA Can Be Introduced into Host Organisms by Transformation

655

(1)

Libraries of DNA Molecules Can Be Created by Cloning

656

(1)

Hybridization Can Be Used to Identify a Specific Clone in a DNA Library

657

(1)

Chemically Synthesized Oligonucleotides

657

(1)

The Polymerase Chain Reaction (PCR) Amplifies DNAs by Repeated Rounds of DNA Replication in vitro

658

(2)

Nested Sets of DNA Fragments Reveal Nucleotide Sequences

660

(1)

Forensics and the Polymerase Chain Reaction

661

(2)

Shotgun Sequencing a Bacterial Genome

663

(1)

The Shotgun Strategy Permits a Partial Assembly of Large Genome Sequences

664

(1)

Sequenators Are Used for High Throughput Sequencing

665

(1)

The Paired-End Strategy Permits the Assembly of Large Genome Scaffolds

666

(1)

Genome-Wide Analyses

667

(2)

Comparative Genome Analysis

669

(3)

Proteins

672

(9)

Specific Proteins Can Be Purified from Cell Extracts

672

(1)

Purification of a Protein Requires a Specific Assay

673

(1)

Preparation of Cell Extracts Containing Active Proteins

673

(1)

Proteins Can Be Separated from One Another Using Column Chromatography

673

(1)

Affinity Chromatography Can Facilitate More Rapid Protein Purification

674

(1)

Separation of Proteins on Polyacrylamide Gels

675

(1)

Antibodies Visualize Electrophoretically-Separated Proteins

676

(1)

Protein Molecules Can Be Directly Sequenced

676

(1)

Proteomics

677

(2)

Bibliography

679

(2)

Model Organisms

681

(32)

Bacteriophage

682

(5)

Assays of Phage Growth

684

(1)

The Single-Step Growth Curve

685

(1)

Phage Crosses and Complementation Tests

685

(1)

Transduction and Recombinant DNA

686

(1)

Bacteria

687

(6)

Assays of Bacterial Growth

687

(1)

Bacteria Exchange DNA by Sexual Conjugation, Phage-Mediated Transduction, and DNA-Mediated Transformation

688

(1)

Bacterial Plasmids Can Be Used as Cloning Vectors

689

(1)

Transposons Can Be Used to Generate Insertional Mutations and Gene and Operon Fusions

689

(1)

Studies on the Molecular Biology of Bacteria Have Been Enhanced by Recombinant DNA Technology, Whole-Genome Sequencing, and Transcriptional Profiling

690

(1)

Biochemical Analysis Is Especially Powerful in Simple Cells with Well-Developed Tools of Traditional and Molecular Genetics

691

(1)

Bacteria Are Accessible to Cytological Analysis

691

(1)

Phage and Bacteria Told Us Most of the Fundamental Things about the Gene

692

(1)

Baker's Yeast, Saccharomyces cerevisiae

693

(3)

The Existence of Haploid and Diploid Cells Facilitate Genetic Analysis of S. Cerevisiae

693

(1)

Generating Precise Mutations in Yeast Is Easy

694

(1)

S. cerevisiae Has a Small, Well-Characterized Genome

694

(1)

S. cerevisiae Cells Change Shape as They Grow

695

(1)

The Nematode Worm, Caenorhabditis elegans

696

(3)

C. elegans Has a Very Rapid Life Cycle

696

(1)

C. elegans Is Composed of Relatively Few, Well Studied Cell Lineages

697

(1)

The Cell Death Pathway Was Discovered in C. elegans

698

(1)

RNAi Was Discovered in C. elegans

698

(1)

The Fruit Fly, Drosophila melanogaster

699

(6)

Drosophila Has a Rapid Life Cycle

699

(1)

The First Genome Maps Were Produced in Drosophila

700

(2)

Genetic Mosaics Permit the Analysis of Lethal Genes in Adult Flies

702

(1)

The Yeast FLP Recombinase Permits the Efficient Production of Genetic Mosaics

703

(1)

It is Easy to Create Transgenic Fruit Flies that Carry Foreign DNA

703

(2)

The House Mouse, Mus musculus

705

(8)

Mouse Embryonic Development Depends on Stem Cells

706

(1)

It is Easy to Introduce Foreign DNA into the Mouse Embryo

707

(1)

Homologous Recombination Permits the Selective Ablation of Individual Genes

707

(2)

Mice Exhibit Epigenetic Inheritance

709

(2)

Bibliography

711

(2)

Index

713

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Molecular Biology of the Gene, Fifth Edition

Molecular Biology of the Gene, Fifth Edition

9780805346350

080534635X

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Table of Contents

Supplemental Materials

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Amazon no longer offers textbook rentals. We do!

Molecular Biology of the Gene, Fifth Edition

Molecular Biology of the Gene, Fifth Edition

9780805346350

080534635X

Summary

Table of Contents

Supplemental Materials

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