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Anatomy of Gene Regulation : A Three-Dimensional Structural Analysis - Panagiotis Antonios Tsonis

Anatomy of Gene Regulation

A Three-Dimensional Structural Analysis

Hardcover Published: 13th January 2003
ISBN: 9780521800303
Number Of Pages: 298

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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.

' ... beautiful and informative three-dimensional images of the nucleosome, RNA and DNA polymerases and the ribosome. Years of genetic and biochemical data spring to life when mapped onto these structures, and future experiments can be designed with much greater precision. Many of us who teach molecular biology at the undergraduate or graduate level have tried to convey this excitement by incorporating structures into our teaching. What might otherwise be dry descriptions of protein interactions or catalytic steps take on greater clarity and tangibility when students can see the molecules. Pangiotis Tsonis has compiled and summarized a great deal of structural information in his new book entitled Anatomy of Gene Regulations. It's a terrific idea and a laudable effort.' Nature Structural Biology 'So this book presents a very wide-ranging coverage of three-dimensional structural aspects only in a concise and attractive format with very readable text ... I enjoyed this book as a handy source to dip into for structural insights and for the author's obvious pleasure in communicating these to his audience.' Heredity

Prefacep. xi
A General Introduction to 3-D Structuresp. 1
The Higher Organization of the Genomep. 6
Packing DNA in the Chromosomesp. 6
The Three-Dimensional Structure of the Nucleosomep. 8
Other Proteinsp. 10
Structure of DNA and Telomeresp. 14
The Three-Dimensional Structure of DNAp. 14
Telomeresp. 14
Structure of OnTEBP and Interaction with Telomeric Sequencesp. 19
Structure of Yeast RAP1p. 20
DNA Replicationp. 26
The Prereplicative Complexp. 28
Replication Origins in Prokaryotesp. 28
Replication Origins in Eukaryotesp. 28
Elongation and the Synthesis of New DNA Strandsp. 30
DNA Polymerasesp. 30
The Three-Dimensional Structure of DNA pol Ip. 31
The Incorporation of the Incoming Nucleotidep. 33
The Three-Dimensional Structure of the DNA Polymerase from Phage RB69p. 36
The Three-Dimensional Structure of Human DNA Polymerase Betap. 36
Editingp. 38
Processivity of DNA Polymerases and the Structure of the Clampp. 39
The Loading of the Clampp. 41
Processivity Factors of Eukaryotic DNA Polymerasesp. 42
Synthesis of the Primers in the Lagging Strandp. 42
Processing of the Okazaki Fragments into a Continuous Strandp. 45
The Single-Stranded DNA-Binding Proteinsp. 48
Viewing the Replication Complexp. 48
Helicasesp. 50
The E. coli Rep Helicasep. 51
The Bacillus stearothermophilus PcrA Helicasep. 53
The Bacteriophage T7 Helicase Domainp. 53
Topoisomerasesp. 58
The 3-D Structure of Human Topo Ip. 61
Mechanism of Cleavage and Relaxation of DNAp. 61
The Structure of Yeast Topoisomerase IIp. 65
Termination of Replicationp. 67
Box: How Drugs Induce Mutationsp. 71
Transcription in Prokaryotesp. 73
Structure and Function of Prokaryotic RNA Polymerasep. 74
The 3-D Structure of the Thermus Aquaticus RNA Polp. 77
Regulation in Prokaryotesp. 86
The Helix-Turn-Helix Motif in Prokaryotic Gene Regulationp. 87
The Lac Operonp. 87
The Pur Repressorp. 89
The Trp Repressorp. 89
Catabolite Activator Proteinp. 90
Regulation in Phagesp. 90
The 434 Phagep. 92
The Lambda Phagep. 95
Termination of Prokaryotic Transcriptionp. 98
The Attenuatorp. 101
Transcription in Eukaryotesp. 104
Structure and Function of the Yeast RNA Pol IIp. 105
Comparison of Prokaryotic and Eukaryotic RNA Polymerases with the T7 RNA Polymerasep. 108
Regulation in Eukaryotesp. 111
Regulation in Class I Genesp. 111
Regulation in Class III Genesp. 111
Structure of TFIIIAp. 113
Regulation in Class II Genesp. 115
The Basal Transcriptional Apparatus in Class II Genesp. 115
Structure and Function of TFIIDp. 116
Structure of TFIIAp. 118
Structure of TFIIBp. 119
Structure of TFIIHp. 120
Transcriptional Activation in Eukaryotesp. 120
Liver-Specific Transcriptionp. 121
The GAL Regulatory Systemp. 122
The Steroid Hormone Receptorsp. 123
The Homeodomain-Containing Genesp. 124
The Mediatorp. 127
Chromatin Structure and Gene Regulationp. 128
Regulation of Cell Fate by Homeodomains: The Yeast Mat Genesp. 130
Structural Features of Class II DNA-Binding Domainsp. 132
The Helix-Turn-Helix Motifp. 133
The Zinc-Binding Domainsp. 135
The Class 1 Zinc-Binding Domainsp. 136
The Class 2 Zinc-Binding Domainsp. 140
The Class 3 Zinc-Binding Domainsp. 142
Other DNA-Binding Domainsp. 143
The Leucine Zipperp. 144
The Immunoglobulin Fold in NFATp. 145
The T Domainp. 148
Signal Transducers and Activators of Transcription Proteinsp. 148
Box: Most Frequent Base-Amino Acid Interactionsp. 152
Splicingp. 153
Splicing of the Nuclear Pre-mRNA Intronsp. 155
The First Transesterificationp. 155
The Second Transesterificationp. 155
The Spliceosomep. 156
Structure and Assembly of snRNPsp. 156
Other Splicing Factorsp. 157
The Events of Splicingp. 159
Splicing of Group II Intronsp. 160
Splicing of Group I Intronsp. 163
Other Ribozymesp. 167
Structure of the Hammerhead Ribozymep. 167
The Interesting Case of Group I Splicing by a Protein, Tyrosyl-tRNA Synthetasep. 170
Modifications of mRNAp. 172
The Capping of the 5' Endsp. 172
Structure of the Yeast RNA 5'-Triphosphatasep. 173
Structure of the Guanyltransferasep. 173
Maturation at The 3' End: Addition of polyAp. 178
3-D Structure of the polyA-Binding Proteinp. 179
Maturation of mRNA Lacking polyA Tailsp. 180
RNA Editingp. 181
RNA Interferencep. 182
Compartmentalization of Transcriptionp. 184
Splicing Factorsp. 185
Visualization of Single Transcriptsp. 185
The Moving of Transcripts Out of the Nucleusp. 187
Shuttling mRNA-Binding Proteinsp. 190
Segregation of Replication and Transcriptionp. 190
Protein Synthesisp. 191
The Major Players in Protein Synthesisp. 193
The 3-D Structure of tRNAp. 193
The Charging of tRNA with Amino Acidp. 194
The 3-D Structure of E. coli Glutaminyl-tRNA Synthetase and Its Interactions with tRNA[superscript Gln]p. 195
The Ribosomep. 200
Initiationp. 202
Initiation in Prokaryotesp. 203
Initiation in Eukaryotesp. 203
The Structure of IF-1p. 205
The Structure of IF-3p. 205
The Structure of IF-2/eIF-5Bp. 207
The Structure of eIF-4E and eIF-4Gp. 207
The Structure of eIF-1 and eIF-1Ap. 209
Elongationp. 210
The Structure of Elongation Factors EF-Tu and EF-Gp. 212
Movement of tRNAs During Translocationp. 214
Movement of EF-G and Conformational Changes of the Ribosome During Translocationp. 217
Interactions Between the 30S and 50S Subunitsp. 219
Interactions Between tRNA and rRNAsp. 221
Interactions Between tRNA and 16S rRNAp. 222
Interactions Between tRNA and 23S rRNAp. 223
Interactions Between tRNA and 5S rRNAp. 230
The Decoding Center of the Ribosomep. 232
The Peptide Bond Centerp. 236
Termination of Protein Synthesisp. 237
The Three-Dimensional Structure of Human eRF1p. 237
Mechanism of Stop Codon Recognitionp. 238
The Ribosome Recycling Factorp. 239
Box: How Do Antibiotics Work? A Lesson from the 3-D Structure of the Ribosomep. 239
The Birth and Death of Proteinsp. 241
The Signal Peptide and Its Recognitionp. 242
Structure and Function of the Signal Recognition Particlep. 243
The Barrel of Birth...p. 247
The 3-D Structure of DnaK and Hsp70p. 249
The 3-D Structure of DnaJp. 251
The 3-D Structure of GrpEp. 251
The 3-D Structure of Prefoldinp. 252
The 3-D Structure of GroEL and GroEsp. 252
...And The Barrel of Deathp. 255
Further Reading and Referencesp. 259
Indexp. 271
Table of Contents provided by Syndetics. All Rights Reserved.

ISBN: 9780521800303
ISBN-10: 0521800307
Audience: Professional
Format: Hardcover
Language: English
Number Of Pages: 298
Published: 13th January 2003
Publisher: Cambridge University Press
Country of Publication: GB
Dimensions (cm): 25.0 x 17.1  x 1.9
Weight (kg): 0.74