World Headquarters Sudbury,and MA 01776 978-443-5000 Tall info@jbpub.com www.jbpub.com Mississauga, 6339 Ormindale Way W6 7PA Ontario Drive Publishers Jones and BartlettPine Publishers Bartlett Canada Bartlett Publishers Jones and CANADA 40 UK L5V 112 London Jones andwebsite, contact Bartlett's Bartlett specific available Jones bookstores organizations contact online available quantities visit details information 978-443-8000, discount books products publications through booksellers Jones email toandcorporations, information, tospecialsales@jbpub.com arecontact professional the special associations, sales most department and at Jones Publishers direCtly, call fax or our www.jbpub.com on bulk of and are qualified For and above or send an art of cer: Clayton To Marketing Manager: mechanicaL Professional including Publishing: photocopying, Book Designer: recording, or by Manager: Jones, Jr.Priest Interactive Technology Copyright © 2008 by material Jones copyright Bartlett retrieval and be form, or protected Spencer utilized DeFronzo Publishers, owner storage system, by this Inc copyright All the may reproduced or any information without written the International Barb H and and and via in any and Production Credits Andrea Jones Don W Dawn Mahon and Anne Inc Kendallville VanAarsen Jr.Spencer Cover Image: W Holland, Bruno, Jr Marketing: Ohlin Kane Production: William Kimberly Printing Cover Designer: Kristin E Research Manager: Binding: Courier ArtPotvin Director: Y.P., Science: and Anne Imagineering Media Services, Inc Jan Editor, Cathleen Sether y Acquisitions SteinbachIllustrations: Cover Printing: Courier Kendallville Composition: Y.P., Manufacturing and Inventory Photo Development and Y.P., and J Shepherd Dean W DeChambeau and synthesis Magnification: approxim Inc C © Professor feather, from aOscar messenger long of protein DNA mRNA Miller/Photo mRNA ofM first coated begins clusters molecules the Colored completion image, fromResearchers, transmission growing theTranscriptio DNA longer strand ele Production Assistant:transcriptionally Jennifer Ryan backbone )gene, A molecules of forming a feather-like, active structure This DNA pmolecules DNA transcription About the cover: by and RNA is the nucleus an the running down is strand with Numerous extend in information at one end with the as they approach is the in protein Library of Congress Cataloging-in-Publication Data / Benjamin Lewin, Benjamin index.Lewin 978-0-7637-4063-4 (alk IXpaper) Genes 0-7637-4063-2 bibliographical references p.;cm and Genetics III 2.Title Title: Genes II Genes Title: I Genetic Genes nine Processes Genome 6048 Genes-physiology RNA-genetics QU 470 DNA-genetics 576.5-dc22 Printed in the United States of America 11 08 07 10 2006010787 Proteins-genetics Brief Contents Contents Preface o o o o o o o o e e e e e Vl to the e xvi Genes Are DNA Genes Code for Proteins The Interrupted Gene 23 Messenger RNA 98 Protein Localization Transcription Homologous and Site-Specific Recombination 457 Transposons 499 521 Retroviruses and Retroposons Immune Diversity 189 Promoters and Enhancers G Catalytic RNA G Chromosomes 218 e 300 Nucleosomes 550 570 609 640 G RNA Splicing and Processing 256 Regulatory RNA 428 fa Activating Transcription 151 Usi ng the Genetic Code fa The Replicon e G) e 76 127 Protein Synthesis The Operon e 55 Genome Sequences and Gene Numbers Clusters and Repeats DNA Replication fa Repair Systems 37 The Content of the Genome Phage Strategies _ e Bacterial Replication Connected Is Cell Cycle 408 667 706 729 757 G) Controlling Chromatin Structure 796 Inherited ED Epigenetic Effects Are 331 349 376 Extrachromosomal Replicons Index 392 Glossary 845 867 v Contents a Preface xvi Several Processes Are Required to Express Product of Gene 33 Are on DNA Are Cis-acting 35 Summary 36 Genes Are DNA Introduction the to a Sugar-Phosphate DNA Is Genetic at Material of Bacteria _ the _ Semiconservative DNA Is the Genetic Material of Viruses Sequence DNA Is Genetic Material of Animal Cells lID no Oil lID IJIB Hotspots l1li 1m IIJJ Protein Organization The Interrupted Gene 37 a Introduction Distribution 38Interrupted a but Introns Introns Chains Have Nitrogenous Bases Linked Backbone Sequences An Interrupted Gene Consists of Exons and 38 Restriction Sequences a Organization Interrupted Information DNA Is Double Helix a Endonucleases Are Key Tool in Mapping DNA 39 DNA Replication Is of Genes May Be Conserved 40 DNA Replication Fork Exon Are Conserved Vary 42 Genetic Can Be Provided by DNA or RNA 10 of Sizes 43 lIB Genes Show Wide Nucleic Acids Hybridize by Base Pairing 12 Some DNA Code for More Than One Mutations Change of DNA 14 Protein 45 Mutations May Affect Single Base Pairs or Longer How Did Genes Evolve? 47 15 Some Exons Can Be Equated with Protein Functions 49 The Effects of Mutations Can Be Reversed 16 The Members of Gene Family Have Common lID Mutations Are Concentrated at Hotspots 17 51 Many Result from Modified Bases 18 Contained in DNA? 53 011 Is All Genetic Some Hereditary Agents Are Extremely Small 19 IIfJ Summary 53 Summary 20 Genes Code for Protei ns 23 .- The Content of the Genome 55 Introductionthe56 Sequences Introduction Polypeptide 24 a than Repetitive to Identify Sequence Isolated Genomes Can Be Mapped by Linkage, Restriction Individual Organization the A AGene A Codes for Single 24 Cleavage, or DNA 56 Gain-of-Function Mutations in Same Gene Cannot Complement 25 Genomes Show ExtensiveNonrepetitive Variation 57 equence Mutations May Cause Loss-of-Function RFLPs and SNPs Can Be Used for Genetic Mapping 58 or 26 Why Are Genomes So Large? 60 lIfB Locus May Have Many Different Mutant Alleles 27 Eukaryotic Genomes Contain Both Locus May Have More One Wild-type Allele 28 and DNA 61 Recombination Occurs by Physical Exchange of DNA 28 Genes Can Be by Conservation of Exons 63 The Genetic Code Is Triplet 30 B'I The Conservation of Genome Helps Every Has Three Possible Reading Frames 31 Genes 65 III!I Prokaryotic Genes Are Colinear with Their Proteins 32 theTrans-acting, but Sites Organelles Have DNA 67 a Proteins vi II:D Organelle Genomes Are Circular DNAs That Code for Organelle 69 Proteins lID Mitochondrial DNA Is Variable 70 The Chloroplast Genome Codes for Many and RNAs 71 lID Mitochondria Evolved by Endosymbiosis 72 lIB Summary 73 Proteins mg Arthropod Satellites Have Very Short Hierarchical Identical Repeats 119 Organization Minisatellites mD Mammalian Consist of Repeats 120 011 Are Useful for Genetic Mapping 123 Summary 125 Transcription -.- . Genome Sequences and Gene the Numbers 76 - Introduction 77 Bacterial Gene Numbers Range Over an Order of Bacterial YMagnitude 77 after Its Transcription Total Gene Number Is Known for Several Eukaryotes 79 How Many Different Types of Genes Are There? 81 The Human Genome Has Fewer Genes Than Expected 83 How Are Genes and Other in Genome? 85 The Chromosome Has Several Male-Specific Genes 86 More Complex Species Evolve by Adding New Gene Functions 87 How Many Genes Are Essential? 89 Genes Are Expressed at Widely DifferingActivities Levels Its Structure 92Involves Sequence a Surveillance Specifically Transported How Many Genes Are Expressed? 93Involves Stability Expressed Gene Number Can Be Measured En Masse 93 Summary 94 Messenger RNA 127 IntroductionStructure 128 Translated mRNA Is Produced at bya and Is Translated 129 Transfer RNA Forms Cloverleaf 130 The Acceptor Stem and Anticodon Are Ends of Tertiary 131 Messenger RNA Is by Ribosomes 132 Bacterial Many Ribosomes Bind to One mRNA 133 The Life Cycle of Messenger RNA 135 Eukaryotic mRNA Is Modified During or 137 The 5' End of Eukaryotic Polyadenylated mRNA Is Capped 138 The 3' Terminus Is 139 mRNA Degradation Multiple Enzymes 140 mRNA Depends on and 141 mRNA Degradation Multiple 143 Nonsense Mutations Trigger System 144 Eukaryotic RNAs Are 145 mRNA Can Be Localized 146 Summary 147 Clusters and Repeats 98 Introduction 99 Introduction Gene Duplication Is a Major Force in Evolution 100 Globin Clusters Are Formed by Duplication and Protein Synthesis 151 Divergence 101 152 Divergence Is Basis for Evolutionary Occurs by Clock 104 and Termination 153 The Rate of Neutral Substitution Can the Be Initiation, Measured the the Elongation, Subunits Control Accuracy of Protein Protein Synthesis Special MechanismsInitiation from Divergence of Repeated 107 156 Are Dead Ends of Evolution 108 in Bacteria Needs 30S and Accessory Unequal Crossing-over Rearranges Gene Clusters 109 Factors 157 Genes for rRNA Form Tandem Repeats 112 ASpecial Initiator Starts tRNA the Polypeptide The Constant Repeated Genes for rRNA Maintain Sequence Chain 158 114 Use of fMet-tRNA f Is Controlled by IF-2 and the Crossover Fixation Could Maintain Identical Repeats 115 Ribosome Satellite 160 DNAs Often Lie in 117 Base Pairing Between mRNA and rRNA 161 - . vii - Small Subunits Scan for Initiation Initiation the the Sites Subunits on Eukaryotic lID Recoding Changes Codon Meanings 211 ~ mRNA Translocation 162 Occurs Slippery 213 Codon-Anticodon Alternately Represent the Protein to a to Synthesis Subunits Eukaryotes Use Complex of Many Synthesis lID Bypassing Ribosome Movement 214 Factors 164 lID Summary 215 Elongation Factor Tu Loads Aminoacyl-tRNA 167 10 Protein LocaLization 218 The Polypeptide Chain Is Transferred Aminoacyl-tRNA 168 IDII Introduction 220 Moves Ribosome 169 lInD Passage Across a Membrane Receptor theRequires the Proteins aPosttranslational Insertion Special to the into the (Sometimes) a Ratchet Proteins Apparatus 220 Cotranslational Interacts Ubiquitous Protein Translocation Translocation a Interacts Synthesized Elongation Factors Bind SignalSequence Sequences Initiate Translocation 1m Protein May Be Ribosome 170 or 221 Three Codons Terminate Protein 172 II!II Chaperones May Be Required for Folding 223 Termination Codons Are Recognized by Factors 173 1m Chaperones Are Needed by Newly and by Denatured 224 Ribosomal RNA Pervades Both Ribosomal 175 IDD The Hsp70 Family Is 226 Ribosomes Have Several Active Centers 177 II!D 227 16S rRNA Plays an Active Role in Protein 179 IDa The Signal with SRP 228 23S rRNA Has Peptidyl Transferase Activity 182 IDB The SRP with SRP 229 Ribosomal Change When Come Together 183 In'IlD The Translocon Forms Pore 231 Summary 183 Requires Translocon and in ER 233 IIiI6 Reverse Sends Cytosol Using the Genetic Code 189 for Degradation 234 190 IDIIJ Proteins Reside inSequences Membranes Protein Orientation by Means of Hydrophobic Related Codons Related Amino Acids 190 Regions 235 Recognition Involves Wobbling 192 OIl Anchor Determine 236 _ tRNAs Are Processed from Longer Precursors 194 IDIm How Do Proteins Insert into Membranes? Insertion 238 Sequences l IB tRNA Contains Modified Bases 194 Posttranslational Membrane Depends on Leader Modified Bases Affect Anticodon-Codon Stop Sequences theinto Pairing at 196to 240 Translation the Synthetases Synthetases the Suppressor There Are Sporadic Alterations of Influences Universal IDIIJ A Hierarchy of Sequences Mitochondrial Determines withinLocation Involves Inserted at Suppressors Suppressors Code 197 Organelles 241 etases Novel Amino Acids Can BeInner Certain InJm and Outer Membranes Have Different Codons 199 Translocons 243 tRNAs Are Charged with Amino Acids InIm Peroxisomes Employ Another Type of Translocation Posttranslational Translocation by 200 System 245 the Inner Sec-Independent Translocation Proteins into Aminoacyl-tRNA Fall Two Groups 201 Cotranslational IDEO Bacteria Use Both and 246 Use Proofreading Improve Accuracy 203 ImJ The Sec System Transports and Through tRNAs Have Mutated Anticodons That Read Membrane 247 New Codons 206 ID& Systems in E coli 249 There Are Nonsense for Each Termination Codon 207 IDBJ Summary 250 Contents May Compete with Wild-Type Reading of Code 208 The Ribosome Accuracy of 209 viii am 11 Transcription 256 lID Introduction 258 a Stages lIB Transcription Occurs by Base Pairing in "Bubble" of Unpaired DNA 259 IfB The lac Genes Are Controlled by a Repressor 304 the Inducer StructureThe Alac Operon Can Be a Bacterial Subunits t IfJiI 305 AStalled Sequences? IfJJ Repressor Is Controlled by Small-Molecule 306 at Initiation Constitutive IIIJ cis-Acting Mutations IIID The Transcription Reaction Has Three 260 lID Phage 17 RNA Polymerase Is Useful Model System 261 lIB Model for Enzyme Movement Is by 308 IImI trans-Acting Mutations Gene 309 1m Multimeric Have Genetic 309 Crystal 262 161m The Repressor Monomer Has Domains 310 II.R RNA Polymerase Consists of Multiple IBID Repressor Is a Tetramer Made ofTwo Dimers 311 265 1116 DNA-Binding Is Regulated by an Allosteric Change lID RNA Polymerase Consists of Core Enzyme and Sigma in Conformation 312 Factor 267 IIIIJ Mutant Phenotypes Operators Correlate to Interacts the Operator with the Domain lID The Association with Sigma Factor Changes Structure the Operator 314 312 Inducer Protein to 267 OlD Repressor Binds 313 lIB RNA Polymerase Can 269 RIB Binding of Releases Repressor 111m How Does RNA Polymerase Find Promoter from 270 161m Repressor Binds Three and DID Sigma Factor Controls Binding to DNA 271 with RNA Polymerase 315 RIJ Promoter RecognitionSequences Depends on Consensus IIIfJ Repressor Is Always Bound to DNA 316 to Activates toAutoge Autog 272 Synthesis Regulation at P 111m The Operator Competes withr-Protein Low-Affinity Bind T4 Synthesis IIIDJ Promoter Efficiencies Can Be Increased or Decreased Autogenous at Regulation Repressor 317 by Mutation 274 Initiation Important Feature Translation 161m Repression Can Occur Multiple Loci 319 RNA Polymerase Binds to One Face of DNA 275 Substitution 11&0 Cyclic AM Is an Effector That CRP Act IIIBJ Supercoiling Is an Many Operons 320 of Transcription 277 lflii CRP Functions in Different Ways in Different Target 111m of Sigma Factors May Control Operons 321 278 ~ Can Be Regulated 323 DID Sigma Factors Directly Contact DNA 280 at IfBJ Is Controlled by SitesSporulation ofTerminators Bacterial into Cascades lID Sigma Factors May Be Organized 282 325 lID Is Controlled by Sigma Factors 283 IfB Phage p32 Is Controlled by an Circuit 326 11& RNA Polymerase Terminates Discrete 286 IfD Is Often Used Control of Macromolecular Assemblies 327 lIB) There Are Two Types in E coli 287 IBfJj Summary 328 IIIfl) How Does Rho Factor Work? 288 I:IBJ AntiterminationIndependent Is a Regulatory Sites Event 291 Antitermination OR Requires That Are 13 Regulatory RNA 331 of Terminators 292 Introduction 332 Structures l1l6I Termination and AntiterminationSpecial Properties FactorsIdentify Interact Attenuation lID Alternative Secondary Control the Polymerase Operator RNA 293 Proteins withSeveral Identify the Regulator 333 Summary 295 IIJD Termination of Bacillus subtilis trp Genes Is Controlled om om 12 The Operon 300 l1li IlfI I6D Positive Introduction 302 Regulation Can Be Negative or 303Structural Gene Clusters Are Coordinately Controlled 304 lID IDI by Tryptophan and by tRNATrp 333 The Escherichia coli tryptophan Operon Is Controlled by Attenuation 335 Translation Can Be Controlled by 336 Contents ix 15 The Replicon 376 l1li AntisenseSilencing RNA Can Regulator Be Used to to Inactivate Gene Expression 338 Regulators Interference Introduction Regulate 377 Mitochondrial Initiation? Isolated Regulate Translation 1m Small RNA Molecules Can 339 Electrophoresis Sequestered after1m Replication Methylation Rereplication Replicons CanatBethe Linear or Circular 378 D Contains Proteins Contain RNAs 341 Replication 1m Origins Can Be Mapped by Autoradiography lIB MicroRNAs Are in Many Eukaryotes 342 and 379 111m OlD RNA Summary 345 Is Related Gene 343 14 Phage Strategies 349 II!II Introduction 350 the Immunity Protein the the I.IfJAntitermination Lytic Development Is Divided into Two Periods 352 tory Operators Maintained a Functional Clustering l1li Lytic Development Is Controlled by Cascade 353 l1li Two Types of Event Control Lytic IIlII IBI IaI Does Origin 1m Origins May Be IBI Each Eukaryotic Chromosome Cascade 354 The 17 and T4 Genomes Show 355 Lambda Early and Delayed Replication Early Genes Are Needed for Both Lysogeny and Lytic Cycle 356 IIIfJ The Lytic Cycle Depends on 357 359 1m 380 381 Many Replicons 383 Origins Can Be in Yeast 384 Licensing Factor Controls Eukaryotic 385 1m 1m Licensing Factor Consists of MCM 386 IBm Loops Maintain Origins 388 IIID Summary 389 16 Extrachromosomal Replicons 392 DI Introduction 393 Initiation at the lIB The Ends of Linear DNA Are a Problem Lysogeny Is by Repressor for 393 Proteins The Repressor and Define 1m Terminal Enable Ends a Region 360 of Viral DNAs 394 DIm The DNA-Binding Form of Repressor Is a DimerInteracts 361 Determines to IraSpecificity Rolling Circles Produce Multimers of Replicon 396 IIID Repressor Uses a Helix-Tum-Helix Motif Bind ImII Rolling Circles Are Used to Replicate Phage Single-Stranded Conjugation be DNA 362 Recognition Genomes 397 Bacteria Plants Conjugation Bacterial DIf) The HelixCooperative Interactions Increase the Sensitivity F Plasmid Is Transferred by lID The for DNA 363 at 398 OI.IJ Repressor Dimers Bind Cooperatively lIB Transfers DNA 400 364 1m The Ti Plasmid Causes Crown Gall Disease DIll Repressor DI'II 0R2 365 RM Repressor Maintains an with RNA Polymerase 1mB Circuit 366 111m of 367 II!ID The cII and cIII Genes Are to Needed Establish cII Protein Lysogeny 368 the he Infection Autogenous Several 369 egulation at P Poor Promoter Requires am 111m IE) IItfa A Lysogeny Requires Events 369 Shape a The cro Repressor Is Needed for Lytic 371 What Determines Balance Between Lysogeny and Lytic Cycle? 373 Summary 374 ImI:m RII in 401 T-DNA Carries Genes Required for Infection 402 Transfer of T-DNA Resembles Bacterial Conjugation 405 Summary 407 17 Bacterial Replication Is Connected to the Cell Cycle 408 Introduction into That Connected 409 the Septum Segregation to the Mutations a Replication Is IfB Cell Cycle 410 IfJD The SeptumRegulate Divides the Bacterium Progeny Contain Chromosome 411 lID in Division or Affect Cell 412 FtsZ Is Necessary for Septum Formation 413 Genes Location of Each 415 Connected Independent IJB Chromosomal Segregation May Require Site-Specific Recombination 415 IfB Partitioning Involves Separation of Chromosomes 417 Single-Copy Plasmids Have System 419 IDIm Plasmid Incompatibility Is Determined by Replicon 421 IBID The ColE1 Compatibility System Is Controlled by an RNA the Regulator 422 a Partitioning IDI6 How Do Mitochondria Replicate and Segregate? 424 Summary 425 _ 1m Recombining Chromosomes Are by Complex 465 lID The Complex Forms Double-Strand Breaks 467 lID Pairing and Complex Formation Are 469 1m The RecBCD System Is by chi 470 IPD Catalyze Assimilation 471 the Bm The Ruv System Resolves Holliday 473 ImI Gene Conversion Accounts for 475 18 DNA Replication 428 BB Affects of DNA 476 1m Introduction 429 RIJ Topoisomerases Relax or lIB DNA Polymerases Are the Enzymes That Make DNA 430 in DNA 478 1mB DNA Polymerases Have Various Nuclease Activities Synthesis Structure 431 Semidiscontinuous the laB Topoisomerases Break and Reseal 480 Initiation 432 Single-Stranded Strands Synthesis IIiD DNA Polymerases Control the Fidelity ofa Replication DIll Gyrase Functions by Coil 481 to Start Separate IIII DNA Polymerases Have Common 433 lam 482 lIB DNA Is 434 BfJ Breakage IEIJ The