Anatomy of Gene Regulation: A Three-dimensional Structural Analysis

by Panagiotis A. Tsonis

• ISBN13: 9780521804745
• ISBN10: 0521804744
• Edition: 1st
• Format: Paperback
• Copyright: 2003-01-13
• Publisher: Cambridge University Press

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