Anatomy of gene regulation : a three dimensional structural analysis

Select an Action

Place Hold(s)
Add to My Lists
Email
Print

Title:

Personal Author:

Tsonis, Panagiotis A.

Publication Information:

Cambridge, UK : Cambridge University Press, 2003

ISBN:

9780521804745

Subject Term:

Genetic regulation

Nucleic acids -- Structure

Proteins -- Structure

Three-dimensional imaging in biology

Available:*

Library	Item Barcode	Call Number	Material Type	Item Category 1	Status
Searching... PSZ JB	30000010113694	QH450 T76 2003	Open Access Book	Book	Searching... Unknown

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. This concise and unique synthesis and its accompanying web site offer insight into gene regulation, and into the development of methods to interfere with regulation at diseased states.

Author Notes

Panagiotis A. Tsonis: University of Dayton

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

Available:*

On Order

Summary

Summary

Author Notes

Table of Contents