9780521804745

Anatomy of Gene Regulation: A Three-dimensional Structural Analysis

by
  • ISBN13:

    9780521804745

  • ISBN10:

    0521804744

  • Edition: 1st
  • Format: Paperback
  • Copyright: 2003-01-13
  • Publisher: Cambridge University Press
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Summary

No longer simple line drawings on a page, molecular structures can now be viewed in full-figured glory, often in color and even with interactive possibilities. Anatomy of Gene Regulation is the first book to present the parts and processes of gene regulation at the three-dimensional level. Vivid structures of nucleic acids and their companion proteins are revealed in full-color, three-dimensional form. Beginning with a general introduction to three-dimensional structures, the book looks at the organization of the genome, the structure of DNA, DNA replication and transcription, splicing, protein synthesis, and ultimate protein death. Throughout, the text employs a discussion of genetics and structural mechanics. The concise and unique synthesis of information will offer insight into gene regulation, and into the development of methods to interfere with regulation at diseased states. This textbook and its accompanying web site are appropriate for both undergraduate and graduate students in genetics, molecular biology, structural biology, and biochemistry courses.

Author Biography

Panagiotis A. Tsonis: University of Dayton

Table of Contents

Preface xi
A General Introduction to 3-D Structures
1(5)
The Higher Organization of the Genome
6(8)
Packing DNA in the Chromosomes
6(2)
The Three-Dimensional Structure of the Nucleosome
8(2)
Other Proteins
10(4)
Structure of DNA and Telomeres
14(12)
The Three-Dimensional Structure of DNA
14(3)
Telomeres
17(9)
Structure of OnTEBP and Interaction with Telomeric Sequences
19(1)
Structure of Yeast RAP1
20(6)
DNA Replication
26(47)
The Prereplicative Complex
28(2)
Replication Origins in Prokaryotes
28(1)
Replication Origins in Eukaryotes
28(2)
Elongation and the Synthesis of New DNA Strands
30(20)
DNA Polymerases
30(1)
The Three-Dimensional Structure of DNA pol I
31(2)
The Incorporation of the Incoming Nucleotide
33(3)
The Three-Dimensional Structure of the DNA Polymerase from Phage RB69
36(1)
The Three-Dimensional Structure of Human DNA Polymerase Beta
36(2)
Editing
38(1)
Processivity of DNA Polymerases and the Structure of the Clamp
39(2)
The Loading of the Clamp
41(1)
Processivity Factors of Eukaryotic DNA Polymerases
42(1)
Synthesis of the Primers in the Lagging Strand
42(3)
Processing of the Okazaki Fragments into a Continuous Strand
45(3)
The Single-Stranded DNA-Binding Proteins
48(1)
Viewing the Replication Complex
48(2)
Helicases
50(8)
The E. coli Rep Helicase
51(2)
The Bacillus stearothermophilus PcrA Helicase
53(1)
The Bacteriophage T7 Helicase Domain
53(5)
Topoisomerases
58(9)
The 3-D Structure of Human Topo I
61(1)
Mechanism of Cleavage and Relaxation of DNA
61(4)
The Structure of Yeast Topoisomerase II
65(2)
Termination of Replication
67(4)
Box: How Drugs Induce Mutations
71(2)
Transcription in Prokaryotes
73(31)
Structure and Function of Prokaryotic RNA Polymerase
74(3)
The 3-D Structure of the Thermus Aquaticus RNA Pol
77(9)
Regulation in Prokaryotes
86(4)
The Helix-Turn-Helix Motif in Prokaryotic Gene Regulation
87(1)
The Lac Operon
87(2)
The Pur Repressor
89(1)
The Trp Repressor
89(1)
Catabolite Activator Protein
90(1)
Regulation in Phages
90(8)
The 434 Phage
92(3)
The Lambda Phage
95(3)
Termination of Prokaryotic Transcription
98(6)
The Attenuator
101(3)
Transcription in Eukaryotes
104(49)
Structure and Function of the Yeast RNA Pol II
105(3)
Comparison of Prokaryotic and Eukaryotic RNA Polymerases with the T7 RNA Polymerase
108(3)
Regulation in Eukaryotes
111(9)
Regulation in Class I Genes
111(1)
Regulation in Class III Genes
111(2)
Structure of TFIIIA
113(2)
Regulation in Class II Genes
115(1)
The Basal Transcriptional Apparatus in Class II Genes
115(1)
Structure and Function of TFIID
116(2)
Structure of TFIIA
118(1)
Structure of TFIIB
119(1)
Structure of TFIIH
120(1)
Transcriptional Activation in Eukaryotes
120(8)
Liver-Specific Transcription
121(1)
The GAL Regulatory System
122(1)
The Steroid Hormone Receptors
123(1)
The Homeodomain-Containing Genes
124(3)
The Mediator
127(1)
Chromatin Structure and Gene Regulation
128(2)
Regulation of Cell Fate by Homeodomains: The Yeast Mat Genes
130(2)
Structural Features of Class II DNA-Binding Domains
132(20)
The Helix-Turn-Helix Motif
133(2)
The Zinc-Binding Domains
135(1)
The Class 1 Zinc-Binding Domains
136(4)
The Class 2 Zinc-Binding Domains
140(2)
The Class 3 Zinc-Binding Domains
142(1)
Other DNA-Binding Domains
143(1)
The Leucine Zipper
144(1)
The Immunoglobulin Fold in NFAT
145(3)
The T Domain
148(1)
Signal Transducers and Activators of Transcription Proteins
148(4)
Box: Most Frequent Base-Amino Acid Interactions
152(1)
Splicing
153(19)
Splicing of the Nuclear Pre-mRNA Introns
155(5)
The First Transesterification
155(1)
The Second Transesterification
155(1)
The Spliceosome
156(1)
Structure and Assembly of snRNPs
156(1)
Other Splicing Factors
157(2)
The Events of Splicing
159(1)
Splicing of Group II Introns
160(3)
Splicing of Group I Introns
163(4)
Other Ribozymes
167(5)
Structure of the Hammerhead Ribozyme
167(3)
The Interesting Case of Group I Splicing by a Protein, Tyrosyl-tRNA Synthetase
170(2)
Modifications of mRNA
172(12)
The Capping of the 5' Ends
172(6)
Structure of the Yeast RNA 5'-Triphosphatase
173(1)
Structure of the Guanyltransferase
173(5)
Maturation at The 3' End: Addition of polyA
178(3)
3-D Structure of the polyA-Binding Protein
179(1)
Maturation of mRNA Lacking polyA Tails
180(1)
RNA Editing
181(1)
RNA Interference
182(2)
Compartmentalization of Transcription
184(7)
Splicing Factors
185(1)
Visualization of Single Transcripts
185(2)
The Moving of Transcripts Out of the Nucleus
187(3)
Shuttling mRNA-Binding Proteins
190(1)
Segregation of Replication and Transcription
190(1)
Protein Synthesis
191(50)
The Major Players in Protein Synthesis
193(9)
The 3-D Structure of tRNA
193(1)
The Charging of tRNA with Amino Acid
194(1)
The 3-D Structure of E. coli Glutaminyl-tRNA Synthetase and Its Interactions with tRNAGln
195(5)
The Ribosome
200(2)
Initiation
202(8)
Initiation in Prokaryotes
203(1)
Initiation in Eukaryotes
203(2)
The Structure of IF-1
205(1)
The Structure of IF-3
205(2)
The Structure of IF-2/eIF-5B
207(1)
The Structure of eIF-4E and eIF-4G
207(2)
The Structure of eIF-1 and eIF-1A
209(1)
Elongation
210(9)
The Structure of Elongation Factors EF-Tu and EF-G
212(2)
Movement of tRNAs During Translocation
214(3)
Movement of EF-G and Conformational Changes of the Ribosome During Translocation
217(2)
Interactions Between the 30S and 50S Subunits
219(13)
Interactions Between tRNA and rRNAs
221(1)
Interactions Between tRNA and 16S rRNA
222(1)
Interactions Between tRNA and 23S rRNA
223(7)
Interactions Between tRNA and 5S rRNA
230(2)
The Decoding Center of the Ribosome
232(4)
The Peptide Bond Center
236(1)
Termination of Protein Synthesis
237(2)
The Three-Dimensional Structure of Human eRF1
237(1)
Mechanism of Stop Codon Recognition
238(1)
The Ribosome Recycling Factor
239(1)
Box: How Do Antibiotics Work? A Lesson from the 3-D Structure of the Ribosome
239(2)
The Birth and Death of Proteins
241(18)
The Signal Peptide and Its Recognition
242(1)
Structure and Function of the Signal Recognition Particle
243(4)
The Barrel of Birth . . .
247(8)
The 3-D Structure of DnaK and Hsp70
249(2)
The 3-D Structure of DnaJ
251(1)
The 3-D Structure of GrpE
251(1)
The 3-D Structure of Prefoldin
252(1)
The 3-D Structure of GroEL and GroEs
252(3)
. . . And The Barrel of Death
255(4)
Further Reading and References 259(12)
Index 271

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