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Molecular Biology of the Gene, Fifth Edition,9780805346350
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Molecular Biology of the Gene, Fifth Edition

by
Edition:
6th
ISBN13:

9780805346350

ISBN10:
080534635X
Format:
Hardcover
Pub. Date:
12/23/2003
Publisher(s):
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.

Table of Contents

PART 1 CHEMISTRY AND GENETICS
1(93)
The Mendelian View of the World
5(14)
Mendel's Discoveries
6(2)
The Principle of Independent Segregation
6(1)
Mendelian Laws
6(2)
Some Alleles Are Neither Dominant Nor Recessive
8(1)
Principle of Independent Assortment
8(1)
Chromosomal Theory of Heredity
8(1)
Gene Linkage and Crossing Over
9(3)
Genes Are Linked to Chromosomes
10(2)
Chromosome Mapping
12(3)
The Origin of Genetic Variability Through Mutations
15(1)
Early Speculations about What Genes are and How they Act
16(1)
Preliminary Attempts to Find a Gene-Protein Relationship
16(3)
Summary
17(1)
Bibliography
18(1)
Nucleic Acids Convey Genetic Information
19(22)
Avery's Bombshell: DNA can carry Genetic Specificity
20(1)
Viral Genes are also Nucleic Acids
21(1)
The Double Helix
21(7)
Chargaff's Rules
23(1)
Finding the Polymerases that Make DNA
24(2)
Experimental Evidence Favors Strand Separation during DNA Replication
26(2)
The Genetic Information within DNA is Conveyed by the Sequence of its Four Nucleotide Building Blocks
28(3)
DNA Cannot Be the Template that Directly Orders Amino Acids during Protein Synthesis
28(1)
Evidence that Genes Control Amino Acid Sequence in Proteins
29(1)
RNA Is Chemically Very Similar to DNA
30(1)
The Central Dogma
31(6)
The Adaptor Hypothesis of Crick
31(1)
The Test-Tube Synthesis of Proteins
32(1)
The Paradox of the Nonspecific-Appearing Ribosomes
32(1)
Discovery of Messenger RNA (mRNA)
33(1)
Enzymatic Synthesis of RNA upon DNA Templates
33(2)
Establishing the Genetic Code
35(2)
Establishing the Direction of Protein Synthesis
37(1)
Start and Stop Signals Are Also Encoded within DNA
38(1)
The Era of Genomics
38(3)
Summary
39(1)
Bibliography
40(1)
The Importance of Weak Chemical Interactions
41(14)
Characteristics of Chemical Bonds
41(3)
Chemical Bonds Are Explainable in Quantum-Mechanical Terms
42(1)
Chemical-Bond Formation Involves a Change in the Form of Energy
43(1)
Equilibrium between Bond Making and Breaking
43(1)
The Concept of Free Energy
44(1)
Keq Is Exponentially Related to ΔG
44(1)
Covalent Bonds Are Very Strong
44(1)
Weak Bonds in Biological Systems
45(10)
Weak Bonds Have Energies between 1 and 7 kcal/mol
45(1)
Weak Bonds Are Constantly Made and Broken at Physiological Temperatures
45(1)
The Distinction between Polar and Nonpolar Molecules
45(1)
Van der Waals Forces
46(1)
Hydrogen Bonds
47(1)
Some Ionic Bonds are Hydrogen Bonds
47(1)
Weak Interactions Demand Complementary Molecular Surfaces
48(1)
Water Molecules Form Hydrogen Bonds
49(1)
Weak Bonds between Molecules in Aqueous Solutions
49(1)
The Uniqueness of Molecular Shapes and the Concept of Selective Stickiness
50(1)
Organic Molecules that Tend to Form Hydrogen Bonds are Water Soluble
51(1)
Hydrophobic ``Bonds'' Stabilize Macromolecules
51(1)
The Advantages of ΔG between 2 and 5 kcal/mol
52(1)
Weak Bonds Attach Enzymes to Substrates
53(1)
Weak Bonds Mediate Most Protein: DNA and Protein: Protein Interactions
53(1)
Summary
53(1)
Bibliography
54(1)
The Importance of High-Energy Bonds
55(14)
Molecules that Donate Energy are Thermodynamically Unstable
55(2)
Enzymes lower Activation Energies in Biochemical Reactions
57(1)
Free Energy in Biomolecules
58(2)
High-Energy Bonds Hydrolyze with Large Negative ΔG
58(2)
High-Energy Bonds in Biosynthetic Reactions
60(1)
Peptide Bonds Hydrolyze Spontaneously
60(1)
Coupling of Negative with Positive ΔG
61(1)
Activation of Precursors in Group Transfer Reactions
61(8)
ATP Versality in Group Transfer
62(1)
Activation of Amino Acids by Attachment of AMP
63(1)
Nucleic Acid Precursors are Activated by the Presence of P ~ P
64(1)
The Value of P ~ P Release in Nucleic Acid Synthesis
64(1)
P ~ P Splits Characterize Most Biosynthetic Reactions
65(2)
Summary
67(1)
Bibliography
67(2)
Weak and Strong Bonds Determine Macromolecular Structure
69(24)
Higher-Order Structures are Determined by Intra and Intermolecular Interactions
69(9)
DNA Can Form a Regular Helix
69(2)
RNA Forms a Wide Variety of Structures
71(1)
Chemical Features of Protein Building Blocks
71(1)
The Peptide Bond
72(1)
Three Are Four Levels of Protein Structure
72(2)
α Helices and β Sheets Are the Common Forms of Secondary Structure
74(1)
Determination of Protein Structure
75(3)
The Specific Conformation of a Protein Results from its Pattern of Hydrogen Bonds
78(3)
α Helices Come Together to Form Coiled-Coils
80(1)
Most Proteins are Modular, Containing Two or Three Domains
81(3)
Proteins Are Composed of a Surprisingly Small Number of Structural Motifs
81(1)
Large Proteins Are Often Constructed of Several Smaller Polypeptide Chains
82(1)
Different Protein Functions Arise from Various Domain Combinations
82(2)
Weak Bonds Correctly Position Proteins along DNA and RNA Molecules
84(3)
Proteins Scan along DNA to Locate a Specific DNA-Binding Site
85(1)
Diverse Strategies for Protein Recognition of RNA
86(1)
Allostery: Regulation of a Protein's Function by Changing its Shape
87(6)
The Structural Basis of Allosteric Regulation Is Known for Examples Involving Small Ligands, Protein-Protein Interactions, and Protein Modification
88(3)
Not All Regulation of Proteins Is Mediated by Allosteric Events
91(1)
Summary
91(1)
Bibliography
92(1)
PART 2 MAINTENANCE OF THE GENOME
93(250)
The Structures of DNA and RNA
97(32)
DNA Structure
98(13)
DNA Is Composed of Polynucleotide Chains
98(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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