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Molecular biology 5th ed r weaver (mcgraw hill, 2012) Molecular biology 5th ed r weaver (mcgraw hill, 2012) Molecular biology 5th ed r weaver (mcgraw hill, 2012) Molecular biology 5th ed r weaver (mcgraw hill, 2012) Molecular biology 5th ed r weaver (mcgraw hill, 2012) Molecular biology 5th ed r weaver (mcgraw hill, 2012) Molecular biology 5th ed r weaver (mcgraw hill, 2012)
This page intentionally left blank This page intentionally left blank wea25324_fm_i-xx.indd Page i 12/22/10 10:16 PM user-f468 /Volume/208/MHCE016/san74946_disk1of1/0073374946/san74946_pagefiles Molecular Biology Fifth Edition R o b e r t F We a v e r University of Kansas TM wea25324_fm_i-xx.indd Page ii 30/12/10 5:25 PM user-f467 /Volume/208/MHCE016/san74946_disk1of1/0073374946/san75292_pagefile TM MOLECULAR BIOLOGY, FIFTH EDITION Published by McGraw-Hill, a business unit of The McGraw-Hill Companies, Inc., 1221 Avenue of the Americas, New York, NY 10020 Copyright © 2012 by The McGraw-Hill Companies, Inc All rights reserved Previous editions © 2008, 2005, and 2002 No part of this publication may be reproduced or distributed in any form or by any means, or stored in a database or retrieval system, without the prior written consent of The McGraw-Hill Companies, Inc., including, but not limited to, in any network or other electronic storage or transmission, or broadcast for distance learning Some ancillaries, including electronic and print components, may not be available to customers outside the United States This book is printed on acid-free paper QDB /QDB ISBN 978-0-07-352532-7 MHID 0-07-352532-4 Vice President & Editor-in-Chief: Marty Lange Vice President EDP/Central Publishing Services: Kimberly Meriwether David Publisher: Janice Roerig-Blong Executive Marketing Manager: Patrick E Reidy Project Manager: Robin A Reed Design Coordinator: Brenda A Rolwes Cover Designer: Studio Montage, St Louis, Missouri Lead Photo Research Coordinator: Carrie K Burger Cover Image: © Getty Images RF Buyer: Sandy Ludovissy Media Project Manager: Balaji Sundararaman Compositor: Aptara®, Inc Typeface: 10/12 Sabon Printer: Quad/Graphics All credits appearing on page or at the end of the book are considered to be an extension of the copyright page Library of Congress Cataloging-in-Publication Data Weaver, Robert Franklin, 1942Molecular biology / Robert F Weaver.—5th ed p cm ISBN 978–0–07–352532–7 (hardcover : alk paper) Molecular biology I Title QH506.W43 2011 572.8—dc22 2010051759 www.mhhe.com wea25324_fm_i-xx.indd Page iii 12/22/10 10:16 PM user-f468 /Volume/208/MHCE016/san74946_disk1of1/0073374946/san74946_pagefiles To Camilla and Nora wea25324_fm_i-xx.indd Page iv 12/22/10 10:16 PM user-f468 A B O U T T H E /Volume/208/MHCE016/san74946_disk1of1/0073374946/san74946_pagefiles A U T H O R Rob Weaver was born in Topeka, Kansas, and grew up in Arlington, Virginia He received his bachelor’s degree in chemistry from the College of Wooster in Wooster, Ohio, in 1964 He earned his Ph.D in biochemistry at Duke University in 1969, then spent two years doing postdoctoral research at the University of California, San Francisco, where he studied the structure of eukaryotic RNA polymerases with William J Rutter He joined the faculty of the University of Kansas as an assistant professor of biochemistry in 1971, was promoted to associate professor, and then to full professor in 1981 In 1984, he became chair of the Department of Biochemistry, (Source: Ashvini C Ganesh) and served in that capacity until he was named Associate Dean of the College of Liberal Arts and Sciences in 1995 Prof Weaver is the divisional dean for the science and mathematics departments within the College, which includes supervising 10 different departments and programs As a professor of molecular biosciences, he teaches courses in introductory molecular biology and the molecular biology of cancer In his research laboratory, undergraduates and graduate students have participated in research on the molecular biology of a baculovirus that infects caterpillars Prof Weaver is the author of many scientific papers resulting from research funded by the National Institutes of Health, the National Science Foundation, and the American Cancer Society He has also coauthored two genetics textbooks and has written two articles on molecular biology in the National Geographic Magazine He has spent two years performing research in European laboratories as an American Cancer Society Research Scholar, one year in Zurich, Switzerland, and one year in Oxford, England iv wea25324_fm_i-xx.indd Page v 12/22/10 10:16 PM user-f468 /Volume/208/MHCE016/san74946_disk1of1/0073374946/san74946_pagefiles B R I E F C O N T E N T S About the Author iv Preface xiii Acknowledgments xvii Guide to Experimental Techniques in Molecular Biology xix PA R T V PA R T I Post-Transcriptional Events Introduction 14 RNA Processing I: Splicing 394 15 RNA Processing II: Capping and Polyadenylation 436 16 Other RNA Processing Events and Post-Transcriptional Control of Gene Expression 471 A Brief History The Molecular Nature of Genes 12 An Introduction to Gene Function 30 PA R T I I Methods in Molecular Biology Molecular Cloning Methods 49 Molecular Tools for Studying Genes and Gene Activity 75 PA R T I I I Transcription in Bacteria Translation 17 The Mechanism of Translation I: Initiation 522 18 The Mechanism of Translation II: Elongation and Termination 560 19 Ribosomes and Transfer RNA 601 PA R T V I I The Mechanism of Transcription in Bacteria 121 Operons: Fine Control of Bacterial Transcription 167 Major Shifts in Bacterial Transcription 196 DNA–Protein Interactions in Bacteria 222 PA R T I V Transcription in Eukaryotes 10 Eukaryotic RNA Polymerases and Their Promoters 244 11 General Transcription Factors in Eukaryotes 273 12 Transcription Activators in Eukaryotes 13 Chromatin Structure and Its Effects on Transcription 355 PA R T V I DNA Replication, Recombination, and Transposition 20 21 22 23 DNA Replication, Damage, and Repair 636 DNA Replication II: Detailed Mechanism 677 Homologous Recombination 709 Transposition 732 PA R T V I I I Genomes 314 24 Introduction to Genomics: DNA Sequencing on a Genomic Scale 759 25 Genomics II: Functional Genomics, Proteomics, and Bioinformatics 789 Glossary 827 Index 856 v wea25324_fm_i-xx.indd Page vi 12/22/10 10:16 PM user-f468 C O N T /Volume/208/MHCE016/san74946_disk1of1/0073374946/san74946_pagefiles E N T S About the Author iv Preface xiii Acknowledgments xvii Guide to Experimental Techniques in Molecular Biology xix CHAPTER An Introduction to Gene Function 30 3.1 3.2 3.3 35 39 Replication 45 Mutations 45 45 Genetic Recombination and Mapping Physical Evidence for Recombination The Discovery of DNA 37 The Chromosome Theory of Inheritance Molecular Genetics 31 40 Sickle Cell Disease Mendel’s Laws of Inheritance PA R T I I Methods of Molecular Biology 5 CHAPTER The Relationship Between Genes and Proteins 1.3 Protein Function Translation Transmission Genetics Activities of Genes 31 Transcription CHAPTER 1.2 Protein Structure Discovery of Messenger RNA Introduction 1.1 31 Overview of Gene Expression PA R T I A Brief History Storing Information The Three Domains of Life Molecular Cloning Methods 4.1 Gene Cloning 50 The Role of Restriction Endonucleases Vectors 49 50 53 Identifying a Specific Clone with a Specific Probe 58 CHAPTER cDNA Cloning The Molecular Nature of Genes 2.1 The Nature of Genetic Material Transformation in Bacteria DNA Structure 2.3 2.4 13 The Polymerase Chain Reaction 62 62 Using Reverse Transcriptase PCR (RT-PCR) in cDNA Cloning 64 19 Real-Time PCR Genes Made of RNA 22 Physical Chemistry of Nucleic Acids 23 DNAs of Various Sizes and Shapes vi 61 Box 4.1 Jurassic Park: More than a Fantasy? 15 19 A Variety of DNA Structures Rapid Amplification of cDNA Ends Standard PCR 18 Experimental Background The Double Helix 4.2 13 The Chemical Nature of Polynucleotides 2.2 12 60 27 4.3 23 64 Methods of Expressing Cloned Genes Expression Vectors 65 Other Eukaryotic Vectors 71 Using the Ti Plasmid to Transfer Genes to Plants 71 65 63 wea25324_fm_i-xx.indd Page vii 12/22/10 10:16 PM user-f468 /Volume/208/MHCE016/san74946_disk1of1/0073374946/san74946_pagefiles Contents CHAPTER Molecular Tools for Studying Genes and Gene Activity 75 5.1 Molecular Separations Gel Electrophoresis 76 80 Gel Filtration Chromatography 80 82 Autoradiography 82 Phosphorimaging 83 79 PA R T I I I CHAPTER 84 The Mechanism of Transcription in Bacteria 121 84 Using Nucleic Acid Hybridization 85 Southern Blots: Identifying Specific DNA Fragments 85 DNA Fingerprinting and DNA Typing 6.2 122 123 89 126 Sigma Stimulates Transcription Initiation 89 Reuse of s 129 Automated DNA Sequencing 91 High-Throughput Sequencing 93 Promoter Clearance S1 Mapping 6.4 6.5 102 Nuclear Run-On Transcription Reporter Gene Transcription Rho-Dependent Termination 104 Assaying DNA–Protein Interactions 106 156 159 108 Operons: Fine Control of Bacterial Transcription 167 7.1 The lac Operon 168 Negative Control of the lac Operon 109 Discovery of the Operon 109 The Mechanism of Repression 112 112 169 169 Repressor–Operator Interactions DMS Footprinting and Other Footprinting Methods 109 Assaying Protein–Protein Interactions 146 156 CHAPTER 108 Chromatin Immunoprecipitation (ChIP) 144 104 105 Measuring Protein Accumulation in Vivo Termination of Transcription Rho-Independent Termination Measuring Transcription Rates in Vivo DNase Footprinting 144 Structure of the Elongation Complex 100 Gel Mobility Shift Elongation Core Polymerase Functions in Elongation Run-Off Transcription and G-Less Cassette Transcription 103 Filter Binding 139 The Role of the a-Subunit in UP Element Recognition 142 99 Primer Extension 132 134 Structure and Function of s Protein Engineering with Cloned Genes: Site-Directed Mutagenesis 97 Mapping and Quantifying Transcripts 99 127 128 The Stochastic s-Cycle Model 95 123 125 Transcription Initiation Local DNA Melting at the Promoter Northern Blots 5.9 Promoters Promoter Structure 6.3 DNA Sequencing and Physical Mapping Restriction Mapping 5.8 122 Binding of RNA Polymerase to Promoters The Sanger Chain-Termination Sequencing Method 90 5.7 RNA Polymerase Structure Sigma (s) as a Specificity Factor In Situ Hybridization: Locating Genes in Chromosomes 88 Immunoblots (Western Blots) 6.1 86 Forensic Uses of DNA Fingerprinting and DNA Typing 87 5.6 115 Transcription in Bacteria Nonradioactive Tracers 5.5 115 115 Transgenic Mice 81 Liquid Scintillation Counting 5.4 114 5.11 Knockouts and Transgenics Ion-Exchange Chromatography Labeled Tracers 114 Functional SELEX Knockout Mice Affinity Chromatography 5.3 SELEX 76 Two-Dimensional Gel Electrophoresis 5.2 5.10 Finding RNA Sequences That Interact with Other Molecules 114 173 174 Positive Control of the lac Operon The Mechanism of CAP Action 177 178 vii wea25324_ndx_856-892.indd Page 878 878 12/28/10 5:46 PM user-f494 /Volume/204/MHDQ268/wea25324_disk1of1/0073525324/wea25324_pagefile Index Polyacrylamide gel electrophoresis (PAGE), 78, 605 See also SDS-PAGE Polyadenylation, 442 See also specific element or factor cleavage and, 448–450 cytoplasmic, 455–456 factors required for, 455t initiation of, 450–451 maturation-specific, 456f mechanism of, 445–446 model of, 454f mRNA recruitment affected by, 444f mRNA translatability affected by, 444f in mRNA transport, 466 phases of, demonstration of, 451f process of, 445f signals, 446–448 AAUAAA motif, 446–448, 447f consensus sequence data on, 447f site of minimum efficient, 447f transcription beyond, 445, 446f transcription termination linked to, 462f Poly(ADP-ribose) (PAR), 389, 390f, 667 Poly(ADP-ribose) glycohydrolase (PARG), 389 Poly(ADP-ribose) polymerase (PARP), 389, 667 Polycistronic mRNA, 533 Polycistronic precursors, 475 Polymerase chain reaction (PCR), 62 DNA amplification with, 62 editing direction analysis with, 480f real-time, 64–65, 65f reverse transcriptase, cDNA cloning with, 64, 64f site-directed mutagenesis based on, 98f standard, 62 Polynucleotide(s) chemical nature of, 15–17 hybridization of, 26–27 Polynucleotide probe, 59 Polypeptide, 5, 31 C-terminus of, 32 exit tunnel, 616f globular form of, 34 homo-, 564 Ku, 665 N-terminus of, 32 polarity of, 32 production of, 8, 37 synthesis of, 561–562 Polysomes, 621–622 CAT-1’s relocation to, 516f of Chironomus, 622f in cytoplasm, 622 mRNA flow to, 514 Pore 1, 254 Positional cloning, 760 classical tools of, 760 CpG islands and, 761–762 exon trapping and, 761, 762f RFLP detection and, 760, 761f Positive strand phage, 527 Positive transcription elongation factor-b (P-TEFb), 296 Postsynapsis, 715 Post-TC See Posttermination complex Posttermination complex (Post-TC), 595 Posttranscriptional gene silencing (PTGS), 489 POT1, 700 Pot1 telomere binding to, 703f telomere protection by, 702–704 telomeric DNA binding of, 703f ppGpp See Guanosine 59-diphosphate 39-diphosphate Precleavage complex, model of, 449f Preinitiation complex, 274 building of, 274f class II, 274–275 model of, 295f phosphorylation of, 290f yeast, recruitment of, 324f Premature termination codon, 591 Presynapsis, 712, 713f Pribnow box, 125 Primary miRNA (pri-miRNA), 509 Primase, 678 Primer, 641 extension of, 102–103, 102f removal of, 647f gaps from, 695f RNA DNA synthesis with, 641 measurement of, 642f reverse transcript with, 748f tRNA, 746–747 Primer-binding site (PBS), 747 Priming of DNA synthesis, 641–642, 641f in E coli, 678 in eukaryotes, 679 at oriC site, 679f pri-miRNA See Primary miRNA Primosome, 678 Processed pseudogenes, 754 Processing See also Messenger RNA; Ribosomal RNA; RNA; Transfer RNA of 45S rRNA precursor, 473f excess region trimming as, 473 Processing bodies (P-bodies), 510 CAT-1’s relocation from, 516f mRNA degradation in, 511–513 repression relief in, 514–515, 517 Prokaryote, 5, Prolactin, casein mRNA half-life affected by, 484, 484t Proliferating cell nuclear antigen (PCNA), 650 Proline chemical structure of, 32f isomerization, of histones, 356t wea25324_ndx_856-892.indd Page 879 12/28/10 5:46 PM user-f494 /Volume/204/MHDQ268/wea25324_disk1of1/0073525324/wea25324_pagefile Index Proline-rich domains, 315 Promoter(s), 123, 259 See also specific promoters bacterial, 125f, 126 class I, 263–264 class II, 259–263 class III, 264–267 clearance, 127, 134–139 general transcription factors in, 294f scrunching and, 136–139 closed complex, 125 DNA melting at, 132–134 elements core, 125, 259, 260f, 263 downstream, 260–262 upstream, 259, 263 enhancer interaction with, 239, 331f genomic functional profiling and, 808, 809f internal, 264–265 multiple, genes with, 201 open complex, 125, 175f, 179f phage T7’s, 133f polymerase II-like, 265–267 proximal, 259 elements, 262–263 pausing of, 296 RNA polymerase binding to, 123–125, 124f sigma (s) subunit and, 123f of RNA polymerase III, 265f of rRNA, 263f structure of, 125–126 TBP and, 280f, 282f TFIID factor and, 280f in transcription, 39 weakness of, 179 Promyelocytic leukemia activator (PML activator), 347 Proofreading by aminoacyl-tRNA synthetases, 630–632 DNA polymerase I and, 646 in DNA synthesis, 646f in elongation, 155 of transcript, 298–299, 298f in translation, 576–577 Prophage, 203, 218f Proteasome, 346–347 Protein See also Proteomics DNA interactions with, 235 assays of, 108 base pairs’ hydrogen bonding capability and, 235–236 multimeric DNA-binding proteins in, 236–237 Protein(s), See also Enzyme; specific proteins accumulation of, measurement of, 106 analysis of, 813–814 MALDI-TOF for, 813, 813f mass spectrometry for, 813, 813f chaperone, 347 domain, 315 engineering, 97–99 folding of, importance of, 594 footprinting, 691–692, 692f function of, 35 fusion, 65, 66f expression vectors producing, 67–69 genes’ relationship with, 6–7, 35–37 growth direction of, amino to carboxyl, 562 interactions among, 816–819 mass spectrometry detection of, 817f protein microchip detection of, 818f microchip, 818f mRNA secondary structure affected by, 546–548 nascent, folding of, 594–595 scaffold, 541 separation of, 812 sequencing, 46 structure of, 31–35 amino acids in, 31 domains in, 34 motifs in, 35 peptide bonds in, 31 primary, 32 quaternary, 35 secondary, 33, 33f tertiary, 34, 34f synthesis of DAI and, 549 translation and, 43 ubiquitylated, 346 unknown, enhancers binding to, 805, 807–808 Protein kinase A (PKA), 344 Protein-protein interaction assays of, 112–114 immunoprecipitation as, 112 yeast two-hybrid assay as, 113 mass spectrometry detection of, 817f Proteome, 812 Proteomics, 790, 812 comparative, 815–816 protein analysis in, 813–814 MALDI-TOF for, 813, 813f mass spectrometry for, 813, 813f protein interactions in, 816–819 mass spectrometry detection of, 817f protein microchip detection of, 818f protein separation in, 812 quantitative, 814–815 Proto-oncogenes, 350 Protozoa, genetic code variations in, 567, 568t Provirus, 746 DNA of structure of, 748f synthesis of, 749f replication hypothesis, 746, 746f Proximal promoter, 259 elements, 262–263 pausing, 296 879 wea25324_ndx_856-892.indd Page 880 880 12/28/10 5:46 PM user-f494 /Volume/204/MHDQ268/wea25324_disk1of1/0073525324/wea25324_pagefile Index Proximal sequence element (PSE), 266 Prp28 protein, 413 PSE See Proximal sequence element Pseudogene, 479, 754, 775 Pseudouridine, 624, 625f P-TEFb See Positive transcription elongation factor-b PTGS See Posttranscriptional gene silencing pUC series plasmids, 53 Pulse-chase procedure, 473, 484 Pulsed-field gel electrophoresis (PFGE), 78, 78f Purine, 16, 17f Puromycin, 570 activity of, 571f assay for peptide bond formation, 579f for peptidyl transferase, 578f reaction, 579 ribosome reactivity to, 570 structure of, 571f Pyrimidine, 16 chemical structure of, 17f dimers, 658, 658f Pyrosequencing, 93–94, 94f Pyrrolysine, 593, 593f Q gene, 205 Q protein, 205, 210 Q utilization site (qut site), 210 Quelling, in fungi, 489 qut site See Q utilization site R2Bm element, 751 cleavage activity of, 751f DNA nicking activity of, 751f reverse transcription of, 752, 752f R2D2 protein, 493 RACE See Rapid amplification of cDNA ends Rad6 enzyme, 386 RAD25 protein, 292, 293f Radiation hybrid mapping, 772–773 Radioactive tracers, 82 Raf protein, 349f, 350 RAG1, 744–745 Rag-1, 743 RAG2, 744–745 Rag-2, 743 ram state, 608–610 RAP1 protein, 383, 700 Rapid amplification of cDNA ends (RACE), 61–62, 61f Rapid turnover determinant, 486–487 Rare cutters, 51 Ras exchanger, 349 Ras protein, 349–350, 349f RdRP See RNA-directed RNA polymerase RE1 silencing transcription factor (REST), 802 Reading frame, 43, 563 See also Open reading frame Real-time PCR, 64–65, 65f recA gene, 218, 710 RecA protein, 218, 710, 712 postsynapsis and, 715 presynapsis and, 712–713 single-stranded DNA binding to, 712, 713f strand exchange and, 715 synapsis and, 713–714, 713f RecBCD pathway, 710–711, 711f Chi site dependence of, 715–716 evidence for, 712 RecBCD protein, 710, 715–717, 716f Recombinant, crossover, 711 DNA, 53 noncrossover, 711 patch, 711 Recombinase, 743 Recombination, 4–5 homologous, 709–710 intermolecular, 710f intramolecular, 710f RecBCD pathway for, 710–712, 711f meiotic, 721–722, 722f physical evidence for, repair, 668–669, 669f signals of, 742–743 V(D)J, 743–745 Recombination signal sequence (RSS), 742 cleavage of, mechanism of, 744f Regulatory motifs, in mammalian genomes, 820–821 Regulon, 802 Rel, 587, 587f Release factor, 43, 586f assay for, 587, 587f eukaryotic, 588 stop codons and, 587t Remodeling chromatin, 376 complexes of, 376–377 DSB repair with, 666–667 mechanism of, 377–378 models of, 377f restriction sites and, 378f in HO gene, 378–379 in IFN-b, 379–383 Renaturation, 26 Renilla reniformis, 553 Reovirus cap charge of, 437 RNA stability and, 440f structure of, 437, 438f synthesis of, 439f Repair See DNA repair Repeat element, 424 Replicating forks, 642 Replication, 22f, 637 See also Origin of replication bidirectional, 642–645 wea25324_ndx_856-892.indd Page 881 12/28/10 5:46 PM user-f494 /Volume/204/MHDQ268/wea25324_disk1of1/0073525324/wea25324_pagefile Index eukaryotic, 644f evidence for, 643f origin of replication in, 643 conservative, 45, 637, 637f–638f continuous, 639f discontinuous, 639, 639f dispersive, 45, 637, 637f–638f enzymology of, 646 fidelity of, 649–650 general features of, 637 hypotheses for, 45f, 637f–638f outcomes of, 637 provirus, 746, 746f initiation of, 678 lagging strand, 693f processivity of, 683–684 b clamp and, 684–686, 685f–686f clamp loader and, 687–688 retrovirus cycle of, 746f mechanism of, 747–749 rolling circle, 645–646 phage lambda (l), 646f schematic of, 645f strands produced by, number of, 645 semiconservative, 7, 45, 637–638, 637f–638f semidiscontinuous, 639–641, 639f–640f speed of, 683 strand separation in, 651 helicase for, 651, 652f termination of, 694 decatenation in, 694–695 eukaryotic, 695 theta mode of, 642f unidirectional, 642 Replication intermediate (RI), 681, 681f Replication protein A (RPA), 704 Replicative form, 645 Replicative transposition, 734, 735–736, 736f Replicon, 645 Replisome, 679 Reporter gene, 105, 107f Reporter gene transcription, 105–106 REST See RE1 silencing transcription factor Restriction endonuclease, 50–53 cutting sites of, 51t recognition sequences of, 51t resistance maintenance, 52f Restriction fragment length polymorphism (RFLP), 333, 760 detection of, 760, 760f Huntington disease-associated, 763f polymorphism degree in, 770 positional cloning and, 760, 761f Restriction mapping, 95 experiment in, 96f Southern blot in, 97f Restriction site, 52 Restriction-modification system (R-M system), 51 Retained intron, 425 Retinoic acid receptor X (RXR), 320 Retrohoming, 754–755, 755f Retrotransposition, target-primed, 753 Retrotransposon, 340, 745, 749 gypsy, 340 LTR-containing, 749–750 nonautonomous, 754 non-LTR, 749, 751–754 Retrovirus, 745–746 DNA of, synthesis of, 749f replication of cycle of, 746f mechanism of, 747–749 RNA of, structure of, 748f Reverse transcriptase, 745 evidence for, 746 RNase’s effect on, 748f TERT, 698 Reverse transcriptase PCR (RT-PCR), 64, 64f Reverse transcription, 60, 745 of R2Bm, 752, 752f RNA primer in, 748f Reversion, in maize, 737, 738f RF1, 587–588, 587t 70S initiation complex with, 619–620, 620f structure of, 620f RF2, 587–588, 587t, 619–620 RF3, 587–588 RFLP See Restriction fragment length polymorphism RFN elements, in riboswitches, 190, 191f Rho, 156 chain elongation affected by, 159–160 mechanism of, 161–162 RNA synthesis rate decreased by, 160f transcript length reduced by, 160, 160f transcript release cased by, 160, 161f Rho-dependent terminators, 156, 159 chain elongation and, 159–160 termination model of, 161–162, 161f transcript length and, 160, 160f transcript release and, 160, 161f Rho-independent terminators See Intrinsic terminators RI See Replication intermediate ribD operon, 190, 191f Ribonuclease See RNase Ribonucleic acid See RNA Ribonucleoside triphosphates, 40 Ribose See also Deoxyribose; Poly(ADP-ribose) chemical structure of, 17f in RNA, 15 Ribosomal recycling factor (RRF), 595, 596f Ribosomal RNA (rRNA), 8, 41 See also specific rRNA precursor processing of, 474f transcription of, 472, 472f processing of, 472 881 wea25324_ndx_856-892.indd Page 882 882 12/28/10 5:46 PM user-f494 /Volume/204/MHDQ268/wea25324_disk1of1/0073525324/wea25324_pagefile Index Ribosomal RNA (rRNA)—Cont bacterial, 474–475, 474f eukaryotic, 472–474 promoter elements, 263f Ribosome(s), 602 See also specific ribosomes addition site of, 43 aminoacyl-tRNA binding to, 572t, 573–576, 574f binding of GDPCP and, 574t GTP and, 573f, 574t composition of, 605–606 dissociation of, 523–525 of E coli, 41f E site of, 43 eukaryotic cytoplasmic, 604 lysyl-tRNA binding to, 565f P site of, 43 fMet-tRNA in, 572f Phe-tRNA binding to, 573, 573f, 574t puromycin-reactive/unreactive, 570 release from mRNA of, posttranslation, 595–597 structure of, 617f, 618 subunits exchange of, 524f–525f three-site model of, 570–572 fMet-tRNA in, 570–572 in translation, 40–41, 616 tRNA binding to, 572t Riboswitch, 190–192, 546 aptamer in, 190, 192 expression platform of, 192 model of action of, 192f RFN element in, 190 Ribosylation, ADP, 356t Ribothymidine, 625f Rifampicin, 128 RING finger LIM domain-binding protein (RLIM), 346 RISC See RNA-induced silencing complex RISC loading complex (RLC), 493 RITS See RNA-induced transcriptional silencing complex RLC See RISC loading complex RLIM See RING finger LIM domain-binding protein R-looping, 395, 396f R-M system See Restriction-modification system RNA See also specific RNA action; specific RNA type chemical composition of chemical structures in, 17f nitrogenous bases in, 15 nucleosides in, 16 phosphoric acid in, 15 ribose in, 15 creation of, 39f discovery of, DNA hybrid with, 146, 147f, 148 genes made of, 22–23 internal guide sequences of, 409 mRNA secondary structure affected by, 546–548 phosphorimager scan of, 83f processing of, CTD in, 460f pull-down, 499 self-splicing, 427 sequence discovery, 114 splicing, 396–397 stability of, reovirus cap and, 440, 440f transport of, cap function in, 441 in virus, 23 RNA editing, 479 direction of, PCR analysis of, 480f gRNA’s role in, 480–481, 481f of hypothetical sequence, 481f mechanism of, 479–482, 482f by nucleotide deamination, 482–483 panediting in, 479 RNA helicase, 540, 540f RNA interference (RNAi) allele-specific, 592 cleavage boundary and, 490f dsRNA-induced, 489f gene expression posttranscriptional control and, 488–489, 502 in genomic functional profiling, 800–801 heterochromatin formation and, 495–497, 496f mechanism of, 489–494 simplified model of, 491f transgene silencing ability of, 494 RNA ligase, 482 RNA polymerase, 39 See also Alpha (a) subunit; Beta (b) subunit; Sigma (s) subunit(s); specific RNA polymerase affinity labeling of, 146f a-amanitin sensitivity of, 247f core, 122, 122t eukaryotic, 245 in flowering plants, 247–248 holoenzyme, 122, 122t lac promoter dissociated from, 176f lambda (l) repressor’s interaction with, 215–217, 215f melting by, 135f phage T7 encoded, 202–203 promoter binding to, 123–125, 124f sigma (s) subunit and, 123f roles of, 246–248, 246t scrunching of abortive transcription and, 135–139, 137f promoter clearance and, 136–139 universality of, 138–139 separation of, 245f structure of, 122 active site similarity in, 153 subunit, 248 subunits of common, 250 composition of, with phage SP01, 198f core, 250 purification of, 145f wea25324_ndx_856-892.indd Page 883 12/28/10 5:46 PM user-f494 /Volume/204/MHDQ268/wea25324_disk1of1/0073525324/wea25324_pagefile Index Rpb1, 250–252 structure of, 248 RNA polymerase I, 245–246, 246t RNA polymerase II, 245 active site of, 257f addition site of, 256, 256f–257f CTD of ChIP analysis of, 459f phosphorylation of, 290–292, 291f splicing and, 420–421, 420f, 422f–423f E site of, 256, 256f in elongation complex, 253–255 nucleotide selection in, 255–256, 258 Rpb4/7 in, 258–259 structure of, 248–250, 252–255, 253f subunits of, 248t, 251t, 252f TFIIB contacts with, 289f TGS and, 500 transcription assignments of, 246, 246t yeast, 248t, 250, 251t RNA polymerase II holoenzyme, 295–296 RNA polymerase IIA, 252 RNA polymerase IIB, 252 RNA polymerase III, 245 promoters of, 265f transcription assignments of, 246–247, 246t RNA polymerase IIO, 252 RNA polymerase IV, 248, 500 RNA polymerase V, 248, 500 RNA primer in DNA synthesis, 641 measurement of, 642f in reverse transcript, 748f RNA synthesis a-amanitin’s effect on, 247f nucleotide insertion in, two-step model for, 153f rate of, rho’s effect on, 160f RNA triphosphatase, 438 RNA X, 410–411, 411f RNA-dependent DNA polymerase, 745 RNA-directed RNA polymerase (RdRP), 495 RNAi See RNA interference RNA-induced silencing complex (RISC), 491, 493f RNA-induced transcriptional silencing complex (RITS), 496 RNase mapping, 102 reverse transcriptase activity affected by, 748f RNase E, 475 RNase H, 60, 748 RNase III, 474–475 RNase P, 429 action of, 475f cleavage catalyzed by, 475 RNase protection assay, 102 RNase R, 589 RNase T1, 400f RNase T2, 400f 883 Rolling circle replication, 645–646 in phage lambda (l), 646f schematic of, 645f strands produced by, number of, 645 RPA See Replication protein A Rpb1, 457, 458f rpoH gene heat shock and, 545 secondary structure of, 546f rpoH mRNA, 545 rpoS mRNA, 546f RRF See Ribosomal recycling factor rrn genes, 125 rRNA See Ribosomal RNA rrnB P1 promoter, 126 RsD, 202 rsd gene, 202 RSS See Recombination signal sequence Rudder, 255 Run-off transcription, 103–104, 103f Run-on transcription See Nuclear run-on transcription RuvA, 717–719 complexes with, models of, 721f crystal structure of, 709f function of, 711 Holliday junction interaction with, 717f, 718, 719f structure of, 718f RuvB, 717–719 branch migration driven by, 718 complexes with, models of, 721f function of, 711 Holliday junction interaction with, 717f RuvC, 719–721 complexes with, models of, 721f function of, 711 Holliday junction interaction with, 720f RXR See Retinoic acid receptor X S pneumoniae See Streptococcus pneumoniae S1 mapping, 100–102 of 39-end, 101f of 59-end, 100f BamHI in, 100–101 end-filling and, 101, 102f S1 nuclease, 100 S6 kinase (S6K1), 550 S6K1 See S6 kinase S6K1 Aly/REF-like substrate (SKAR), 551 SAGA complex, 285 SAGE See Serial analysis of gene expression Sanger, Frederick, 89 Sanger chain-termination sequencing method, 90–91, 90f SANT domain, 376 SANT-like ISWI domain (SLIDE), 376 Scaffold proteins, 541 Scintillation fluid, 84 Scintillations, 84 wea25324_ndx_856-892.indd Page 884 884 12/28/10 5:46 PM user-f494 /Volume/204/MHDQ268/wea25324_disk1of1/0073525324/wea25324_pagefile Index Scrunching during abortive transcription, 135–139, 137f abortive transcription and, 135–139, 137f promoter clearance and, 136–139 universality of, 138–139 SD sequence See Shine-Dalgarno sequence SDS See Sodium dodecyl sulfate SDS-PAGE, 78f, 79, 605 Sea urchin, 336, 337f Sec insertion sequence (SECIS), 593 SECIS See Sec insertion sequence Sedimentation coefficient, 41 Seed BAC, 773 Selective 29-hydroxyl acylation analyzed by primer extension (SHAPE), 594 Selenocysteine, 593 SELEX See Systematic evolution of ligands by exponential enrichment Semiconservative replication, 7, 45, 637–638, 637f–638f Semidiscontinuous replication, 639–641, 639f–640f Sequenator, 93 Sequence-tagged connector (STC), 773 Sequence-tagged site (STS), 771, 771f–772f Sequencing, 89 automated, 91, 92f, 93 clone-by-clone strategy of, 770 comparisons in, 774 film of, typical, 91f first organism sequenced by, 765 high-throughput, 93–95 lessons learned from, 767 milestones in, 768t physical mapping before, 95 protein, 46 pyrosequencing, 93–94, 94f read length in, 93 resolution of, 769 Sanger method of, 90–91, 90f shotgun, 768, 773–774 standards of, 774 tag, 804 techniques of, 765–767 vectors for, 769 bacterial artificial chromosomes as, 769–770, 770f cloning of, 769 yeast artificial chromosomes as, 769, 769f Serial analysis of gene expression (SAGE), 794, 795f, 796 Serine, 32f 7SL RNA gene, 265–266 70S initiation complex, 531 formation of, 531–532 GTP in, 531–532 RF1 interaction with, 619–620, 620f RF2 interaction with, 619–620 schematic representation of, 605f structure of, 602, 604–605 codon-anticodon base-pairing in, 602, 604f crystal, 602, 603f intersubunit bridges in, 602, 604f of T thermophilus, 602, 603f, 604 Sex chromosome, Sex lethal gene (Sxl gene), 422–423 SF1 protein, 419 SF2/ASF proteins, 417f SH2 domain, 349 SH3 domain, 349 SHAPE See Selective 29-hydroxyl acylation analyzed by primer extension Shelterin proteins, 700–702 cell cycle arrest suppressed by, 704–705 inappropriate repair suppressed by, 704–705 telomeres affected by, 700 Shelterin-telomere complex, 702f Shine-Dalgarno sequence (SD sequence), 43, 529, 533 Short hairpin RNA (shRNA), 494 Short interfering RNA (siRNA), 489 amplification of, 494–495, 495f endo-, 517 RISC and, 493f silencing by, 505 TGS induced by, 498–500, 498f Short interspersed elements (SINE), 754 Shotgun sequencing, 768, 773–774 shRNA See Short hairpin RNA Shuttle vector, 69 Sickle cell disease, 45–47 Sigma factor switching, 197 anti-sigma factors and, 202 heat shock response and, 201–202 multiple promoters and, 201 phage infection and, 197–198 Sigma (s) subunit(s), 122 cycle, 129f obligate release, 129 stochastic model of, 129–132 E coli’s binding of, 141f–142f interactions of, 140f region in, 139 region in, 139–140 region in, 140 region 4, 140–142 FRET analysis of, 131f function of, 139–142 reuse of, 128–129, 128f RNA polymerase-promoter binding and, 123f as specificity factor, 122–123 structure of, 139–142, 140f transcription elongation with association of, 131f stimulation of, 128f transcription initiation stimulation by, 127–128, 128f Signal transduction pathway, 344, 348–350 Raf and, 349f, 350 Ras and, 349–350, 349f wea25324_ndx_856-892.indd Page 885 12/28/10 5:46 PM user-f494 /Volume/204/MHDQ268/wea25324_disk1of1/0073525324/wea25324_pagefile Index SILAC See Stable isotope labeling by amino acids in cell culture Silencer, 267, 269 See also specific silencer Silencing, 374, 383–384 See also specific silencing complex/factor by miRNA, 505–506, 506f near telomeres, 383 PTGS, 489 by siRNA, 505 TGS plants with, 500 RNA polymerase II and, 500 RNA polymerase IV/V and, 500 siRNA-induced, 498–500, 498f transgene, RNAi-induced, 494 Silencing mediator for retinoid and thyroid hormone receptors (SMRT), 374 Silent mutation, 45 Simian virus 40 (SV40) early control region of, 267f minichromosome of DNase hypersensitivity in, 369f nucleosome-free zone in, 368f–369f ori location in, 680f origin of replication in, 679–680 SIN3 corepressor, 374 SIN3A corepressor, 374 SINE See Short interspersed elements Single-nucleotide polymorphism (SNP), 790 pharmacogenomics and, 810–812 tag, 811 Single-particle cryo-electron microscopy See Cryo-electron microscopy Single-strand DNA-binding proteins (SSB), 651–653 temperature-sensitive mutation in, 653f t-loop binding of, 701f SIR2 protein, 383 SIR3 protein, 383 SIR4 protein, 383 siRISC, 505 siRNA See Short interfering RNA Site-directed mutagenesis, 97–99 binding specificity probing by, 223, 226–229 PCR-based, 98f 16S rRNA, 606–607, 607f 60S ribosomal particle, 538f SKAR See S6K1 Aly/REF-like substrate Ski complex, 590 Ski7p, 590 SL See Spliced leader SL1 factor, 299 structure and function of, 301–303 transcription activation by, 301f SLIDE See SANT-like ISWI domain 7SL RNA, 247 Slu7 splicing factor, 419–420 Sm protein, 413 Small nuclear RNA (snRNA), 246, 402 See also specific snRNA mRNA splicing involvement of, 409–411 specificity of, 415 structure of, 413, 414f, 415 Small nucleolar RNA (snoRNA), 474 Small nucleolar RNP (snoRNP), 474 Small RNA (sRNA), 546 Small ubiquitin-related modifier (SUMO), 347 SMCC See SRB and MED-containing cofactor SMCC/TRAP complex, 344 SmpB protein, 589 SMRT See Silencing mediator for retinoid and thyroid hormone receptors snoRNA See Small nucleolar RNA snoRNP See Small nucleolar RNP SNP See Single-nucleotide polymorphism snRNA See Small nuclear RNA Sodium dodecyl sulfate (SDS), 78 Sos protein, 349 SOS response, 218, 669 See also Error-prone bypass Southern, Edward, 85 Southern blot, 85–86, 85f See also DNA fingerprinting for DNase hypersensitivity detection, 369, 370f of HindIII fragments, 764f in restriction mapping, 97f Spearman’s rank correlation, 816 Specialized genes, 260 Spectinomycin, 608 Spectrometry See Mass spectrometry Spliced leader (SL) encoding of, 477 joining of, 477f Spliceosomes, 402–403, 402f active center of, 409f assembly of, 411 cycle of, 411–413 function of, 411 minor, 415 in mRNA precursor, 402–403, 402f, 410f Splicing, 395 alternative, 421–424 Drosophila and, 422, 423f mouse and, 423f patterns of, 425f as cap function, 441 cis-, 477 debranching enzyme with, 478f control of, 425–426 ESE and, 425–426 ESS and, 425–426, 427f evidence for, 395–396 factors, 415, 419–420 gene expression affected by, 398–399 GTP and, 428, 429f lariat model of, 399 885 wea25324_ndx_856-892.indd Page 886 886 12/28/10 5:46 PM user-f494 /Volume/204/MHDQ268/wea25324_disk1of1/0073525324/wea25324_pagefile Index Splicing—Cont mRNA precursor branch signals in, 401–402 branched intermediate in, 399–401, 401f mechanism of, 399, 399f snRNP involvement in, 409–411 spliceosomes in, 402–403, 402f, 410f NAS, 591–592, 591f outline of, 396f RNA, 396–397, 427 RNA polymerase II CTD in, 420–421, 420f, 422f–423f self-, 427 signals of, 397–398 site selection, 419–420 trans-, 477 debranching enzyme with, 478f mechanism of, 477–479 organisms with, 471 scheme of, 478f in trypanosomes, 471, 477, 478f Spo11 DSB fragments associated with, 724, 724f–725f oligonucleotides linked to, 726, 726f–727f spo11D gene, 200, 200f Sporulation of B subtilis, 199–200 of N crassa, 37f spoVG gene, 201, 201f Squelching, 344 SR proteins, 417 SRB and MED-containing cofactor (SMCC), 344 SRC See Steroid receptor coactivator SRC-1, 345 SRC-2, 345 SRC-3, 345 sRNA See Small RNA SSB See Single-strand DNA-binding proteins Stable isotope labeling by amino acids in cell culture (SILAC), 815 Standard-type, Start codon, 45 STC See Sequence-tagged connector Stem cell, 115, 116f Steroid receptor coactivator (SRC), 345 Sticky ends, 51 Stochastic release model, 129–132 Stop codon, 43, 565f decoding center interactions with, 621f release factors response to, 587t suppression of, 586, 587f UAA, 621f unusual amino acid insertion with, 593 Strand exchange RecA protein and, 715 RecBCD-dependence of, 716f Streptococcus pneumoniae (S pneumoniae), 13 melting curve of, 25f virulent to avirulent transformation in, 13, 14f Streptolydigin, 145 Streptomycin, 577, 608, 609f Strong stop DNA, 747 Structural genomics, 790 STS See Sequence-tagged site Subterminal repetitive region, 738 SUMO See Small ubiquitin-related modifier Sumoylation activator, 347–348 of histones, 356t of transcription factors, 343 Supercoil, 155, 653–654 Superhelix, 155, 653 Superinfection, 217 Supernatant, 81 Supershift, 109 Superwobble hypothesis, 567 Suppressor mutation, 584 SV40 See Simian virus 40 SV40 early promoter, 261f SWI/SNF protein complex family, 376–378, 377f, 381f Swiss-Prot database, 820 SWR1, 666–667 Sxl gene See Sex lethal gene Synapsis post-, 715 pres-, 712, 713f RecA and, 713–714, 713f Syntenic block, 777 Synteny, conserved, 780f Synthesis of cap, 438–440, 439f DNA lagging strand synthesis in, 689–694, 689f priming of, 641–642, 641f proofreading in, 646f in provirus/retrovirus, 749f RNA primer in, 641 temperature-sensitivity of, 653f of b-galactosidase, 178f of lagging strand, 689–694, 689f of oligonucleotides, 127f of pantothenate, 36f of polypeptides, 561–562 protein DAI and, 549 in translation, 43 RNA a-amanitin’s effect on, 247f nucleotide insertion in, two-step model for, 153f rate of, rho’s effect on, 160f translesion, 670 Synthetase-tRNA complexes See also specific tRNA synthetase class I, 630, 630f wea25324_ndx_856-892.indd Page 887 12/28/10 5:46 PM user-f494 /Volume/204/MHDQ268/wea25324_disk1of1/0073525324/wea25324_pagefile Index class II, 630, 630f structures of, 629–630, 629f Synthetic lethal screen, 418 Synthetic messenger experiment, 564 Synthetic mRNA, 564f Systematic evolution of ligands by exponential enrichment (SELEX), 114–115, 114f T aquaticus See Thermus aquaticus T thermophilus See Thermus thermophilus T4 DNA, 122 T4 RNA, 123 TAF See TBP-associated factor Tag, 794 expressed sequence, 773 isotope coded affinity, 814–815, 814f–815f sequencing, 804 SNP, 811 Tagging enzyme (TE), 794 Taq polymerase, 62, 647, 647f Target of rapamycin (mTOR), 550 Target-primed retrotransposition, 753 TATA box, 259–261 TATA box binding protein (TBP), 276–278 mutations in, 279f promoter interaction model of, 282f promoter-related activities of, 280f role of, 307–308 universality of, exceptions to, 284–286 versatility of, 278–279 Taxonomy, 784 TBP See TATA box binding protein TBP-associated factor (TAF), 276, 279–284 functions of, 280 hsp70 promoter binding by, 281f universality of, exceptions to, 284–286 TBP-free TAF-containing complex (TFTC), 285, 286f TBP-like factor (TLF), 285 TBP-related factor (TRF1), 285, 700, 701f TBP-TATA box complex, 278f T-cell receptor, 740, 743 T-cell receptor a-chain gene (TCRa gene), 337, 337f TCRa gene See T-cell receptor a-chain gene T-DNA, 71, 73f TdT See Terminal deoxynucleotidyl transferase TE See Tagging enzyme Telomerase, 695 activity of, identification of, 696, 696f mutant, 698 sequence addition by, 696–697 Telomerase reverse transcriptase (TERT), 698 Telomere formation of, 697f Hayflick limit and, 699b maintenance of, 695–696, 698 Pot1 binding to, 703f Pot1 protection of, 702–704 887 shelterin’s effect on, 700 silencing near, 383 structure of, 698–700 eukaryotic, 702 model of, 383f Telomere position effect (TPE), 383 Telomere-binding proteins in eukaryotes, 702 mammalian, 700–702 Telomere-loop (T-loop), 700 formation of, 700–701, 700f mammalian, model of, 701f SSB binding to, 701f TRF1 binding to, 701f Temperate phage, 203 Temperature-sensitive mutation, 653f -10 box sequence, 125 Terminal deoxynucleotidyl transferase (TdT), 61 Terminal transferase See Terminal deoxynucleotidyl transferase Terminal uridylyl transferase (TUTase), 482 Termination See also Antitermination codon, 584–586, 591 E coli region of, 694f models of intrinsic terminator, 157–158, 158f rho-dependent terminator, 161–162, 161f torpedo, 465f premature, codon, 591 replication, 694 decatenation in, 694–695 eukaryotic, 695 transcription, 40, 156 CoTC element in, 463–466 b-globin torpedo model of, 465f mechanism of, 462–466 mRNA 39-end processing and, 461–462 polyadenylation linked to, 462f translation, 43, 45, 522, 584 aberrant, 588 premature, 591–592 termination codons in, 584–586 Terminator(s), 40, 156 intrinsic, 156 attenuation assay and, 157f hairpins in, 156 inverted repeats in, 156 N protein in, 208f NusA protein in, 208, 208f structure of, 156–157 termination model with, 157–158, 158f trp attenuator in, 156–157 mutant, 159f rho-dependent, 156, 159 chain elongation and, 159–160 termination model of, 161–162, 161f transcript length and, 160, 160f transcript release and, 160, 161f wea25324_ndx_856-892.indd Page 888 888 12/28/10 5:46 PM user-f494 /Volume/204/MHDQ268/wea25324_disk1of1/0073525324/wea25324_pagefile Index TERT See Telomerase reverse transcriptase Tetrahymena, 695–696, 697f, 698 Tetrahymena 26S rRNA gene, 427–428, 428f, 430f Tetranucleosome, 361f Tetranucleotides, 564 Tetrapeptides, 564 TFB See Transcription factor B TFIIA factor, 274–275 TFIIB factor, 274–275 B finger of, 287f function of, 286–288 RNA polymerase II contacts with, 289f structure of, 286–288 TFIIB recognition element (BRE), 259–262 TFIID factor, 274–275 acidic activation domain binding to, 325f function of, 276 promoter-related activities of, 280f recruitment of, 324–325, 381f structure of, 276 three-dimensional model of, 286f TFIIE factor, 274–275 TFIIF factor, 274–275 TFIIH factor, 274–275 function of, 288, 289–294 helicase activity of, 292f RNA polymerase II phosphorylation by, 291f structure of, 288, 289–294 transcription bubble creation and, 292–294 TFIIIA, 303 TFIIIB, 304–306 polymerase III transcription with, 306f transcription start model with, 305f TFIIIC, 304–306 binding abilities of, 306 transcription start model with, 305f TFIIS, 296 elongation affected by, 296f transcript proofreading stimulated by, 298–299, 298f transcription arrest reversed by, 296–298, 297f TfR See Transferrin receptor TfR mRNA destabilization of, iron-caused, 488f stability of, 484 degradation pathway in, 487–488 iron response elements and, 485–486 rapid turnover determinant in, 486–487 TFTC See TBP-free TAF-containing complex TGS See Transcriptional gene silencing Thermal cycler, 62 Thermophile, Thermus aquaticus (T aquaticus), 62, 579–580 core polymerase from, 148–149 crystal structure of, 149f holoenzyme-DNA complex of RF complex of, 150f–151f structure of, 150–151 Thermus thermophilus (T thermophilus), 152 70S initiation complex of, 602, 603f, 604 strand separation in, 152f tmRNA structure of, 589f thi box, 547–548 Thiamine pyrophosphate (TPP), 547–548, 547f thiC gene, 547 thiM gene, 547 thiM mRNA, 547 binding properties of, 548 TPP binding by, 547f, 548 4-Thiouridine, 625f -35 box sequence, 125 30S ribosomal subunit, 525, 602 antibiotics’ interaction with, 607–611 paromomycin, 610 spectinomycin, 608 streptomycin, 609f decoding activity of, 608 decoding center of, 611, 611f domain closure of, 617 fMet-tRNA binding to, 531 formation of, 525–526 GDPCP in, 531f GTP in, 531f initiation factors’ roles in, 530t initiation factors’ interaction with, 611–612 mRNA binding to, 527–530 structure of, 606–607 codon-anticodon base pairs in, 610f crystal, 607f, 612f sites in, 608f translocation activity of, 608 two-dimensional gel electrophoresis of, 606f 3C See Chromosome conformation capture 39-box, 461 Threonine, 32f Thymidine, 16 Thymine, 15 chemical structure of, 17f nucleoside/deoxynucleoside of, 16 Thyroid hormone, 375 Thyroid hormone receptor (TR), 320, 375 Thyroid hormone receptor associated protein (TRAP), 344 Thyroid hormone response element (TRE), 375 Ti plasmid See Tumor-inducing plasmid TIGR See The Institute for Genomic Research Tiling arrays, 804 TIN2 See TRF1-interacting factor-2 tk promoter, 262f TLD See tRNA-like domain TLF See TBP-like factor T-loop See Telomere-loop TLS See Translesion synthesis tmRNA See Transfer-messenger RNA tmRNA-mediated ribosome rescue, 588 wea25324_ndx_856-892.indd Page 889 12/28/10 5:46 PM user-f494 /Volume/204/MHDQ268/wea25324_disk1of1/0073525324/wea25324_pagefile Index Tn3 replicative transposition of, 735–736, 736f structure of, 735f TNF a See Tumor necrosis factor-a Toeprint assay 40S ribosomal subunit leading edge location with, 542 principle of, 543f results of, 543f Topoisomerases, 154–155, 154f, 653–655 assay for, 654f function of, 653 type I, 654 type II, 654 G-segment of, 655 mechanism of, 654–655 segment-passing by, 655, 656f structure of, 655f T-segment of, 655 Torpedo model, 465f TPE See Telomere position effect TPP See Thiamine pyrophosphate TPP1, 700 TR See Thyroid hormone receptor tra gene See transformer gene Tracer labeled, 82 nonradioactive, 84, 84f radioactive, 82 Trans-acting gene, 171 Transcribed fragments, 797 Transcribed spacer, 472 Transcript 39-end of, 101f 59-end of, 100f abortive, 126 length of, rho’s effect on, 160, 160f mapping and quantifying, 99 proofreading of, TFIIS stimulation of, 298–299, 298f release of, rho’s initiation of, 160, 161f reverse, RNA primer in, 748f Transcript walking technique, 146 Transcription, 8, 31, 39–40 See also Elongation abortive inchworming hypothesis of, 135 scrunching during, 135–139, 137f transient excursion hypothesis of, 135 activation of lac P1 in, 182f, 182t model of, 367f SL1 factor in, 301f UBF in, 301f activators’ enhancement of, model of, 283f arrest, 296 reversal of, TFIIS-caused, 296–298, 297f asymmetrical, 40 in bacteria, 121 beginning of, 45 889 bubble, 254f, 292–294 of CAT, 552 class II gene, 365 DNA as material of, 13–14 dynamic process of, 154 elongation in, 40, 128f, 131f gene expression and, 8, 31 posttranscriptional control of, 483, 488–489, 502 G-less cassette, 103 H1 histone’s effect on, 365–367 initiation of, 39, 126–127 general transcription factors in, 294f sigma (s) stimulation of, 127–128, 128f stages of, 127f of introns, 397f leftward, N protein’s effect on, 206f NER-coupled, 664 nuclear run-on, 104–105, 105f pause, 296 phage lambda (l)’s phases of, 204 beyond polyadenylation site, 445, 446f promoter region in, 39 rates of, measurement of, 104 reporter gene, 105–106 reverse, 60, 745 of R2Bm, 752, 752f RNA primer in, 748f RNA polymerase II/III’s assignments in, 246–247, 246t of rRNA precursor, 472, 472f run-off, 103–104, 103f stages of, 40f start model, with TFIIIB/TFIIIC, 305f temporal control of phage lambda (l) and, 206f phage SP01 and, 197f phage T7 and, 203f termination of, 40, 156 CoTC element in, 463–466 b-globin torpedo model of, 465f mechanism of, 462–466 mRNA 39-end processing and, 461–462 polyadenylation linked to, 462f translation simultaneous with, 622f translation’s relationship to, 394–395 Transcription factor(s), 267 See also specific factors acetylation of, 343 general, 267, 273–274 in elongation, 294f initiation with, 294f in promoter clearance, 294f gene-specific, 273, 315 methylation of, 343 regulation of, 343 sumoylation of, 343 target site location, 802–805 ubiquitylation of, 343 Transcription factor B (TFB), 288 wea25324_ndx_856-892.indd Page 890 890 12/28/10 5:46 PM user-f494 /Volume/204/MHDQ268/wea25324_disk1of1/0073525324/wea25324_pagefile Index Transcription factories, 334–336 detection of, 335f number of, 335–336 Transcription unit, 445 Transcription-activating domain, 315–316 Transcriptional gene silencing (TGS) in plants, 500 RNA polymerase II and, 500 RNA polymerase IV/V and, 500 siRNA-induced, 498–500, 498f Transcriptional mapping, 797 of human chromosomes, 798f whole chromosome, 797–799 Transcriptome, 790 Transcriptomics, 790 Transcripts of unknown function (TUF), 797 Transesterification, 725 TRANSFAC database, 821 Transfection, 71 Transfer RNA (tRNA), 623 See also Aminoacyl-tRNA; Synthetase-tRNA complexes; specific tRNA amino acid linked to, 523f aminoacylation of derivatives of, 628t charging, 523 codon-anticodon recognition and, 42f discovery of, 623, 623f initiator, scanning role of, 537f isoaccepting species of, 566–567 modified, polypeptidyl transferase activity and, 615f nucleosides in, modified, 624, 625f primer, 746–747 processing of, 475 mature 39-end formation in, 476 mature 59-end formation in, 475–476 polycistronic precursor cutting in, 475 recognition of, aminoacyl-tRNA synthetase, 626–627, 626f ribosome binding to, 572t structure of, 42f, 623–626 acceptor stem in, 623, 624f, 627–628 anticodon in, 628–629 anticodon loop in, 624, 646f cloverleaf secondary, 623, 624f dihydrouracil loop in, 624, 646f stereo view of, 626f tertiary, 626 three-dimensional, 625f variable loop in, 624, 624f in translation, 41–42 initiation, eukaryotic, 533 Transfer-messenger RNA (tmRNA) in bacteria, 588 mechanism of, 590f structure of, 589 of T thermophilus, 589f Transferrin receptor (TfR), 484, 485f–486f Transformation in bacteria, 13 of S pneumoniae, 13, 14f transformer gene (tra gene), 422–423 Transfrags, 797 Transgene, RNAi silencing of, 494 Transgenics, 115 Transgenic mice, 115, 118, 807f Transgenic plant, 71 Transition mutations, 568 Translation, 8, 31, 40 accuracy vs speed in, 577 beginning of, 45 direction of, 561–562, 561f–562f efficiency of, 536f elongation in, 43, 44f, 522 error tolerance in, 577 eukaryotic, 548 G proteins and, 582–583 initiation of, 522 AUG codon in, 534–535 bacterial, 523, 533, 533f, 545 blockage of, miRNA-induced, 553–555 control of, 545 eukaryotic, 533, 538–539, 538f Maskin-controlled, 551–552, 551f scanning model of, 533–537, 534f of luciferase, 441t mRNA structure and, 43, 44f nascent protein folding after, 594–595 nick, 60, 61f pioneer round of, 542, 621 of poly(A), 443f posttranslation events and, 593–594 proofreading in, 576–577 protein synthesis initiation in, 43 repression of eIF2a phosphorylation in, 549f mRNA-binding protein in, 552–553 ribosomes in, 40–41, 616 release of, 595–597 sRNA and, 546 stages of, 522 start codon, 45 stimulation of cap-binding protein’s, 539f miRNA, 507, 509 PHAS-I phosphorylation in, 550f termination of, 43, 45, 522, 584 aberrant, 588 premature, 591–592 termination codons in, 584–586 trans, 589 transcription simultaneous with, 622f transcription’s relationship to, 394–395 tRNA in, 41–42, 533 Translesion synthesis (TLS), 670 wea25324_ndx_856-892.indd Page 891 12/28/10 5:46 PM user-f494 /Volume/204/MHDQ268/wea25324_disk1of1/0073525324/wea25324_pagefile Index Translocation, 43, 617 elongation, 580 EF2’s role in, 580 EF-G’s role in, 580–582, 581f, 581t GTP’s role in, 580–582, 581f, 581t kinetics of, 582f mRNA three-nucleotide movement in, 580 structural basis of, 619f by 30S ribosomal subunit, 608 Transmission genetics, Transpeptidation, 614 Transposable element, 733 Transposase, 733 Transposition, 732 catalyzation of, 733 of L1 element, 752, 753f mechanisms of, 734 nonreplicative, 734, 736–737, 737f replicative, 734 Tn3, 735–736, 736f tracking of, 735f of Ty transposon, 750f Transposon bacterial, 733 simple, 733 complex, 734 eukaryotic, 737 inverted terminal repeats in, 734f maize affected by, 738f Trans-splicing, 477 debranching enzyme with, 478f mechanism of, 477–479 organisms with, 471 scheme of, 478f in trypanosomes, 471, 477, 478f trans-translation, 589 Transversion mutations, 568 TRAP See Thyroid hormone receptor associated protein trc promoter, 66 TRE See Thyroid hormone response element TRF1 See TBP-related factor TRF1-interacting factor-2 (TIN2), 700 TRF2, 700 Trigger factor, 594–595, 595f Trinucleotide, 17, 18f tRNA See Transfer RNA tRNA 39 processing endoribonuclease (39 tRNase), 476 tRNA-like domain (TLD), 588 39tRNase See tRNA 39 processing endoribonuclease Trombone model, 689 trp attenuator, 156–157, 187, 188f trp leader, 187, 188f trp operon, 186 anabolic enzymes coded by, 186 attenuation of, 187–188, 187f defeating, 188–190, 189f leader-attenuator transcript structures in, 188f trp attenuator in, 187 trp leader in, 187 negative control of, 186f aporepressor in, 186 tryptophan’s role in, 186–187 trp repressor, 234 aporepressor compared to, 235f helix-turn-helix motif of, 234 tryptophan binding site on, 235f tryptophan’s effect on shape of, 234–235 Trypanosomes RNA editing in, 479 trans-splicing in, 471, 477, 478f Trypsin, 561 Tryptophan binding site of, on trp repressor, 235f chemical structure of, 32f in trp operon negative control, 186–187 trp repressor’s shape altered by, 234–235 tudor control region, 285, 285f TUF See Transcripts of unknown function Tumor necrosis factor-a (TNF a), 507 Tumor suppressor gene, 823 Tumor-inducing plasmid (Ti plasmid), 71, 72f, 73 TUTase See Terminal uridylyl transferase 12 signal, 742 12/23 rule, 742 23 signal, 742 28S rRNA, 473 Ty transposon, 750, 750f Tyrosine, 32f U1 snRNA, 402–403, 404f, 414f U2 snRNA, 402, 405–406, 406f U2AF See U2-associated factor U2-associated factor (U2AF), 419–420 U4 snRNA, 402, 408–409 U4atac snRNA, 415 U5 snRNA, 402, 406–408, 407f, 409f U6 snRNA, 247, 402–404, 405f, 409f U6atac snRNA, 415 U11 snRNA, 415 U12 snRNA, 415 UAF See Upstream activity factor UBF See Upstream binding factor Ubiquitin, 346 Ubiquitylated protein, 346 Ubiquitylation activator, 346–347 of histones, 356t of transcription factors, 343 UBS See Upstream binding site Ultracentrifugation, 13–14 Ultraviolet absorption spectrophotometry, 14 Ultraviolet radiation, 658 umuC gene, 669 null allele of, 670 unmutability of, 670f 891 wea25324_ndx_856-892.indd Page 892 892 12/28/10 5:46 PM user-f494 /Volume/204/MHDQ268/wea25324_disk1of1/0073525324/wea25324_pagefile Index umuD gene, 669 umuDC promoter, 669, 671f Unidirectional replication, 642 UP element, 125 alpha (a) subunit’s role in, 142–144, 143f footprinting of, 143f Up mutation, 125 UPE-binding factor, 300–301 Upf1, 591 Upf2, 591 Upstream activity factor (UAF), 299 Upstream binding factor (UBF), 299, 301f Upstream binding site (UBS), 158, 208 Upstream promoter elements, 259, 263 Uracil, 15 chemical structure of, 17f nucleoside/deoxynucleoside of, 16 Uracil N-glycosylase, 640 Urea, as denaturing agent, 144 Uridine, 16 Uridylates, 482 Vaccinia virus cap, 437 Valine chemical structure of, 32f stereo view of, 631f Variable number tandem repeats (VNTR), 770–771 Variable region, 740 Vector(s), 53 See also Expression vector; specific vectors cosmid as, 57 eukaryotic, 58, 69–71 insert joined to, 54f phage as, 54–58 phage lambda (l), 55, 57 phage M13, 57–58 phagemid as, 58 plasmid as, 53–54 sequencing, 769 bacterial artificial chromosomes as, 769–770, 770f cloning of, 769 yeast artificial chromosomes as, 769, 769f shuttle, 69 very high capacity, 58 Vegetative growth, of B subtilis, 199 Virion, 746 Virulent phage, 203 Virus See also specific virus as genetic package, 22 life status of, 22–23 RNA genes in, 23 V(D)J joining, 741 V(D)J recombination, 743–745 VNTR See Variable number tandem repeats VP16 transcription factor, 324–325 Watson, James, 7, 7f, 20 See also Watson-Crick base pair Watson-Crick base pair, 566f Western blot, 89, 89f far, 457, 458f, 550 protein accumulation measurement with, 106 white gene, 341 Wild-type, Wobble base pair, 566, 566f Wobble hypothesis, 566–567 Wobble position, 566, 566f Wyosine, 625f Xenopus borealis, 264–265 Xeroderma pigmentosum (XP), 662–663 XP See Xeroderma pigmentosum XPA gene, 663–664 XPB gene, 664 XPC protein, 663–664 XPD gene, 664 XPF gene, 664 XPG gene, 663 XP-V, 663 X-ray crystallography, 149, 224b–227b diffraction angles in, 227b electron-density map in, 224b light microscopy compared to, 224f MIR in, 224b phase angles in, 224b resolution of, 226b wavelengths of, 227b x-ray reflection in, 224f X-ray diffraction analysis See X-ray crystallography X-ray radiation, 658–659 Xrn2 exonuclease, 465 YAC See Yeast artificial chromosomes Yarus analog, 613 Yeast genome of analysis of, 284t variations in, 567, 568t HO gene of, 378–379 origin of replication in, 680–683 preinitiation complex recruitment of, 324f RNA polymerase II subunits of, 248t, 250, 251t transcription requirements of, 284t Yeast artificial chromosomes (YAC), 769, 769f Yeast two-hybrid assay, 113, 113f yellow gene, 341 Z-DNA, 24 Zinc finger, 303, 315–316 DNA interactions with, 317 DNA-binding proteins compared to, 317–318 finger structure in, 316–317, 316f schematic diagram of, 317f Zinc-containing modules, 315 Zipper, 255 ... courses in introductory molecular biology and the molecular biology of cancer In his research laboratory, undergraduates and graduate students have participated in research on the molecular biology. .. Services: Kimberly Meriwether David Publisher: Janice Roerig-Blong Executive Marketing Manager: Patrick E Reidy Project Manager: Robin A Reed Design Coordinator: Brenda A Rolwes Cover Designer: Studio... Analysis of l Repressor–Operator Interactions 229 High-Resolution Analysis of Phage 434 Repressor–Operator Interactions 232 The trp Repressor Elongation Factors 11.2 234 The Role of Tryptophan 9.3