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Lewins Genes XI

Lewins Genes XI

Lewins Genes XI

  • By: Jocelyn E. Krebs, Stephen T. Kilpatrick & Elliott

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ISBN: 9789380853710

Bind: Paperback

Year: 2014

Pages: 968

Size: 216 x 279 mm

Publisher: Jones & Bartlett Learning

Published in India by: Jones & Bartlett India

Exclusive Distributors: Viva Books

Sales Territory: India, Nepal, Pakistan, Bangladesh, Sri Lanka



Molecular Biology is a rapidly advancing field with a constant flow of new information and cutting-edge developments that impact our lives. Lewin's GENES has long been the essential resource for providing the teaching community with the most modern presentation to this dynamic area of study. Lewin"s GENES XI continues this tradition by introducing the most current data from the field, covering gene structure, sequencing, organization, and expression.  A wealth of subject-matter experts, from top institutions, to provide content updates and revisions in their individual areas of study. A reorganized chapter presentation provides a clear, more student-friendly introduction to course material than ever before. .

New and Key Features of Lewin"s GENES XI:

  • Updated content throughout to keep pace with this fast-paced field.
  • Reorganized chapter presentation provides a clear, student-friendly introduction to course material.
  • Expanded coverage describing the connection between replication and the cell cycle is included, and presents eukaryotes as well as prokaryotes.

A wealth of pedagogical features throughout the text help student better understand and retain important data

Target Audience:

 Written for the upper-devision undergraduate or graduate Molecular Biology course, offered at the college and university level, within the departments of biology, molecular & cellular biology, and biochemistry.



Part 1: Genes and Chromosomes

Chapter 1: Genes Are DNA • Introduction • DNA Is the Genetic Material of Bacteria and Viruses • DNA Is the Genetic Material of Eukaryotic Cells • Polynucleotide Chains Have Nitrogenous Bases Linked to a Sugar?Phosphate Backbone • Supercoiling Affects the Structure of DNA • DNA Is a Double Helix • DNA Replication Is Semi conservative • Polymerases Act on Separated DNA Strands at the Replication Fork • Genetic Information Can Be Provided by DNA or RNA • Nucleic Acids Hybridize by Base Pairing • Mutations Change the Sequence of DNA • Mutations May Affect Single Base Pairs or Longer Sequences • The Effects of Mutations Can Be Reversed • Mutations Are Concentrated at Hotspots • Many Hotspots Result from Modified Bases • Some Hereditary Agents Are Extremely Small • Summary • References

Chapter 2: Genes Encode RNAs and Polypeptides • Introduction • Most Genes Encode Polypeptides • Mutations in the Same Gene Cannot Complement • Mutations May Cause Loss of Function or Gain of Function • A Locus May Have Many Different Mutant Alleles • A Locus May Have More Than One Wild-Type Allele • Recombination Occurs by Physical Exchange of DNA • The Genetic Code Is Triplet • Every Coding Sequence Has Three Possible Reading Frames • Bacterial Genes Are Colinear with Their Products • Several Processes Are Required to Express the Product of a Gene • Proteins Are trans-Acting but Sites on DNA Are cis-Acting • Summary • References

Chapter 3: Methods in Molecular Biology and Genetic Engineering • Introduction • Nucleases • Cloning • Cloning Vectors Can Be Specialized for Different Purposes • Nucleic Acid Detection • DNA Separation Techniques • DNA Sequencing • PCR and RT-PCR • Blotting Methods • DNA Microarrays • Chromatin Immunoprecipitation • Gene Knockouts and Transgenics • Summary

 Chapter 4: The Interrupted Gene • Edited by Donald Forsdyke • Introduction • An Interrupted Gene Consists of Exons and Introns • Exon and Intron Base Compositions Differ • Organization of Interrupted Genes May Be Conserved • Exon Sequences Under Negative Selection Are Conserved but Introns Vary • Exon Sequences Under Positive Selection Vary but Introns Are Conserved • Genes Show a Wide Distribution of Sizes Due Primarily to Intron Size and Number Variation • Some DNA Sequences Encode More Than One Polypeptide • Some Exons Can Be Equated with Protein Functional Domains • Members of a Gene Family Have a Common Organization • There Are Many Forms of Information in DNA • Summary • References

Chapter 5: The Content of the Genome • Introduction • Genomes Can Be Mapped at Several Levels of Resolution • Individual Genomes Show Extensive Variation • RFLPs and SNPs Can Be Used for Genetic Mapping • Eukaryotic Genomes Contain Nonrepetitive and Repetitive DNA Sequences • Eukaryotic Protein-Coding Genes Can Be Identified by the Conservation of Exons • The Conservation of Genome Organization Helps to Identify Genes • Some Organelles Have DNA • Organelle Genomes Are Circular DNAs That Encode Organelle Proteins • The Chloroplast Genome Encodes Many Proteins and RNAs • Mitochondria and Chloroplasts Evolved by Endosymbiosis • Summary • References

Chapter 6: Genome Sequences and Gene Numbers • Introduction • Prokaryotic Gene Numbers Range Over an Order of Magnitude • Total Gene Number Is Known for Several Eukaryotes • How Many Different Types of Genes Are There? • The Human Genome Has Fewer Genes Than Originally Expected • How Are Genes and Other Sequences Distributed in the Genome? • The Y Chromosome Has Several Male-Specific Genes • How Many Genes Are Essential? • About 10,000 Genes Are Expressed at Widely Differing Levels in a Eukaryotic Cell • Expressed Gene Number Can Be Measured En Masse • Summary • References

Chapter 7: Clusters and Repeats • Introduction • Unequal Crossing Over Rearranges Gene Clusters • Genes for rRNA Form Tandem Repeats Including an Invariant Transcription Unit • Crossover Fixation Could Maintain Identical Repeats • Satellite DNAs Often Lie in Heterochromatin • Arthropod Satellites Have Very Short Identical Repeats • Mammalian Satellites Consist of Hierarchical Repeats • Minisatellites Are Useful for Genetic Mapping • Summary • References

Chapter 8: Genome Evolution • Introduction • DNA Sequences Evolve by Mutation and a Sorting Mechanism • Selection Can Be Detected by Measuring Sequence Variation • A Constant Rate of Sequence Divergence Is a Molecular Clock • The Rate of Neutral Substitution Can Be Measured from Divergence of Repeated Sequences • How Did Interrupted Genes Evolve? • Why Are Some Genomes So Large? • Morphological Complexity Evolves by Adding New Gene Functions • Gene Duplication Contributes to Genome Evolution • Globin Clusters Arise by Duplication and Divergence • Pseudogenes Are Nonfunctional Gene Copies • Genome Duplication Has Played a Role in Plant and Vertebrate Evolution • What Is the Role of Transposable Elements in Genome Evolution? • There May Be Biases in Mutation, Gene Conversion, and Codon Usage • Summary • References

Chapter 9: Chromosomes • Edited by Hank W. Bass • Introduction • Viral Genomes Are Packaged into Their Coats • The Bacterial Genome Is a Nucleoid • The Bacterial Genome Is Supercoiled • Eukaryotic DNA Has Loops and Domains Attached to a Scaffold • Specific Sequences Attach DNA to an Interphase Matrix • Chromatin Is Divided into Euchromatin and Heterochromatin • Chromosomes Have Banding Patterns • Lampbrush Chromosomes Are Extended • Polytene Chromosomes Form Bands • Polytene Chromosomes Expand at Sites of Gene Expression • The Eukaryotic Chromosome Is a Segregation Device • Regional Centromeres Contain a Centromeric HistoneH3 Variant and Repetitive DNA • Point Centromeres in S.cerevisiae Contain Short,Essential DNA Sequences • The S.cerevisiae Centromere Binds a Protein Complex • Telomeres Have Simple Repeating Sequences • Telomeres Seal the Chromosome Ends and Function in Meiotic Chromosome Pairing • Telomeres Are Synthesized by a Ribonucleoprotein Enzyme • Telomeres Are Essential for Survival • Summary • References ?
Chapter 10: Chromatin • Introduction • DNA Is Organized in Arrays of Nucleosomes • The Nucleosome Is the Subunit of All Chromatin • Nucleosomes Are Covalently Modified • Histone Variants Produce Alternative Nucleosomes • DNA Structure Varies on the Nucleosomal Surface • The Path of Nucleosomes in the Chromatin Fiber • Replication of Chromatin Requires Assembly of Nucleosomes • Do Nucleosomes Lie at Specific Positions? • Nucleosomes Are Displaced and Reassembled During Transcription • DNase Sensitivity Detects Changes in Chromatin Structure • Insulators Define Transcriptionally Independent Domains • An LCR May Control a Domain • Summary • References

Part 2: DNA Replication and Recombination
Chapter 11: Replication Is Connected to the Cell Cycle • Edited by Barbara Funnell • Introduction • Bacterial Replication Is Connected to the Cell Cycle • The Septum Divides a Bacterium into Progeny That Each Contain a Chromosome • Mutations in Division or Segregation Affect Cell Shape • FtsZ Is Necessary for Septum Formation • min and noc/slm Genes Regulate the Location of the Septum • Chromosomal Segregation May Require Site-Specific Recombination • Partition Involves Separation of the Chromosomes • The Eukaryotic Growth Factor Signal Transduction Pathway • Checkpoint Control for Entry Into S Phase: p 53a Guardian of the Checkpoint • Checkpoint Control for Entry into S Phase: Rb, aGuardian of the Checkpoint • Summary • References

Chapter 12: The Replicon: Initiation of Replication • Edited by Stephen D. Bell ?Introduction • An Origin Usually Initiates Bidirectional Replication • The Bacterial Genome Is (Usually) a Single Circular Replicon • Methylation of the Bacterial Origin Regulates Initiation • Initiation: Creating the Replication Forks at the Origin oriC • Multiple Mechanisms Exist to Prevent Premature Reinitiation of Replication • Archaeal Chromosomes Can Contain Multiple Replicons • Each Eukaryotic Chromosome Contains Many Replicons • Replication Origins Can Be Isolated in Yeast • Licensing Factor Controls Eukaryotic Rereplication • Licensing Factor Binds to ORC • Summary • References

Chapter 13: DNA Replication • Edited by Peter Burgers • Introduction • DNA Polymerases Are the Enzymes That Make DNA • DNA Polymerases Have Various Nuclease Activities • DNA Polymerases Control the Fidelity of Replication • DNA Polymerases Have a Common Structure • The Two New DNA Strands Have Different Modes of Synthesis • Replication Requires a Helicase and a Single-Strand Binding Protein • Priming Is Required to Start DNA Synthesis • Coordinating Synthesis of the Lagging and Leading Strands • DNA Polymerase Holoenzyme Consists of Subcomplexes • The Clamp Controls Association of Core Enzyme with DNA • Okazaki Fragments Are Linked by Ligase • Separate Eukaryotic DNA Polymerases Undertake Initiation and Elongation • Lesion Bypass Requires Polymerase Replacement • Termination of Replication • Summary • References ?

Chapter 14: Extrachromosomal Replicons • Edited by S??ren Johannes S??rensen and Lars Hestbjerg Hansen • Introduction • The Ends of Linear DNA Are a Problem for Replication • Terminal Proteins Enable Initiation at the Ends of Viral DNAs • Rolling Circles Produce Multimers of a Replicon • Rolling Circles Are Used to Replicate Phage Genomes • The F Plasmid Is Transferred by Conjugation Between Bacteria • Conjugation Transfers Single-Stranded DNA • Single-Copy Plasmids Have a Partitioning System • Plasmid Incompatibility Is Determined by the Replicon • The ColE1 Compatibility System Is Controlled by an RNA Regulator • How Do Mitochondria Replicate and Segregate? • D Loops Maintain Mitochondrial Origins • The Bacterial Ti Plasmid Causes Crown Gall Disease in Plants • T-DNA Carries Genes Required for Infection • Transfer of T-DNA Resembles Bacterial Conjugation • Summary • References

Chapter 15: Homologous and Site-Specific Recombination • Edited by Hannah L. Klein and Samantha Hoot •  Introduction • Homologous Recombination Occurs Between Synapsed Chromosomes in Meiosis • Double-Strand Breaks Initiate Recombination • Gene Conversion Accounts for Interallelic Recombination • The Synthesis-Dependent Strand-Annealing Model • The Single-Strand Annealing Mechanism Function sat Some Double-Strand Breaks • Break-Induced Replication Can Repair Double-Strand Breaks •  Recombining Meiotic Chromosomes Are Connected by the Synaptonemal Complex • The Synaptonemal Complex Forms After Double-Strand Breaks • Pairing and Synaptonemal Complex Formation Are Independent • The Bacterial RecBCD System Is Stimulated by chi Sequences • Strand-Transfer Proteins Catalyze Single-Strand Assimilation • Holiday Junctions Must Be Resolved • Eukaryotic Genes Involved in Homologous Recombination • Specialized Recombination Involves Specific Sites • Site-Specific Recombination Involves Breakage and Reunion • Site-Specific Recombination Resembles Topoisomerase Activity • Lambda Recombination Occurs in an Intasome • Yeast Can Switch Silent and Active Loci for Mating Type • Unidirectional Gene Conversion Is Initiated by the Recipient MAT Locus • Antigenic Variation in Trypanosomes Uses Homologous Recombination • Recombination Pathways Adapted for Experimental Systems • Summary • References

Chapter 16: Repair Systems • Introduction • Repair Systems Correct Damage to DNA • Excision Repair Systems in E. Coli • Eukaryotic Nucleotide Excision Repair Pathways • Base Excision Repair Systems Require Glycosylases • Error-Prone Repair and Translesion Synthesis • Controlling the Direction of Mismatch Repair • Recombination-Repair Systems in E. coli • Recombination Is an Important Mechanism to Recover from Replication Errors • Recombination-Repair of Double-Strand Breaks in Eukaryotes • Nonhomologous End-Joining Also Repairs Double-Strand Breaks • DNA Repair in Eukaryotes Occurs in the Context of Chromatin • RecA Triggers the SOS System • Summary • References

Chapter 17: Transposable Elements and Retroviruses • Edited by Damon Lisch • Introduction • Insertion Sequences Are Simple Transposition Modules • Transposition Occurs by Both Replicative and Nonreplicative Mechanisms • Transposons Cause Rearrangement of DNA • Replicative Transposition Proceeds Through a Cointegrate • Nonreplicative Transposition Proceeds by Breakage and Reunion • Transposons Form Superfamilies and Families • The Role of Transposable Elements in Hybrid Dysgenesis • P Elements Are Activated in the Germline • The Retrovirus Lifecycle Involves Transposition-Like Events • Retroviral Genes Code for Polyproteins • Viral DNA Is Generated by Reverse Transcription • Viral DNA Integrates into the Chromosome • Retroviruses May Transduce Cellular Sequences • Retroelements Fall into Three Classes • Yeast Ty Elements Resemble Retroviruses • The Alu Family Has Many Widely Dispersed Members • LINEs Use an Endonuclease to Generate a Priming End • Summary • References ?

hapter 18: Somatic Recombination and Hypermutationin the Immune System • The Immune System: Innate and AdaptiveImmunity • The Innate Response Utilizes Conserved Recognition Molecules and Signaling Pathways • Adaptive Immunity • Clonal Selection Amplifies Lymphocytes That Respond to a Given Antigen • Ig Genes Are Assembled from Discrete DNA Segments in B Lymphocytes • L Chains Are Assembled by a Single Recombination Event • H Chains Are Assembled by Two Sequential Recombination Events • Recombination Generates Extensive Diversity • V(D)J DNA Recombination Uses RSS and Occurs by Deletion or Inversion • Allelic Exclusion Is Triggered by Productive Rearrangements • RAG1 /RAG2 Catalyze Breakage and Religation of V(D)J Gene Segments • B Cell Differentiation: Early IgH Chain Expression Is Modulated by RNA Processing • Class Switching Is Effected by DNA Recombination(Class Switch DNA Recombination [CSR]) • CSR Involves AID and Elements of the NHEJ Pathway • Somatic Hypermutation (SHM) Generates Additional Diversity • SHM Is Mediated by AID, Ung, Elements of the Mismatch DNA Repair (MMR) Machinery, and Translesion DNA Synthesis (TLS) Polymerases • Chromatin Modification in V(D)J Recombination, CSR, and SHM • Expressed Igs in Avians Are Assembled from Pseudogenes • B Cell Differentiation in the Bone Marrow and the Periphery: Generation of Memory B Cells Enables a Prompt and Strong Secondary Response • The T Cell Receptor for Antigen (TCR) Is Related tothe BCR • The TCR Functions in Conjunction with the MHC • The Major Histocompatibility Complex (MHC) Locus Comprises a Cohort of Genes Involved in Immune Recognition • Summary • References

Part 3: Transcription and Posttranscriptional Mechanisms
Chapter 19: Prokaryotic Transcription • Edited by Richard Gourse • ? Introduction • Transcription Occurs by Base Pairing in a ?Bubble?of Unpaired DNA • The Transcription Reaction Has Three Stages • Bacterial RNA Polymerase Consists of Multiple Subunits • RNA Polymerase Holoenzyme Consists of the Core Enzyme and Sigma Factor • How Does RNA Polymerase Find Promoter Sequences? • The Holoenzyme Goes Through Transitions in the Process of Recognizing and Escaping from Promoters • Sigma Factor Controls Binding to DNA by Recognizing Specific Sequences in Promoters • Promoter Efficiencies Can Be Increased or Decreased by Mutation • Multiple Regions in RNA Polymerase Directly Contact Promoter DNA • RNA Polymerase?Promoter and DNA?Protein Interactions Are the Same for Promoter Recognition and DNA Melting • Interactions Between Sigma Factor and Core RNA Polymerase Change During Promoter Escape • A Model for Enzyme Movement Is Suggested by the Crystal Structure • A Stalled RNA Polymerase Can Restart • Bacterial RNA Polymerase Terminates at Discrete Sites • How Does Rho Factor Work? • Supercoiling Is an Important Feature of Transcription • Phage T17RNA Polymerase Is a Useful Model System • Competition for Sigma Factors Can Regulate Initiation • Sigma Factors May Be Organized into Cascades • Sporulation Is Controlled by Sigma Factors • Antitermination Can Be a Regulatory Event • Summary • References

Chapter 20: Eukaryotic Transcription • Introduction • Eukaryotic RNA Polymerases Consist of Many Subunits • RNA Polymerase I Has a Bipartite Promoter • RNA Polymerase III Uses Downstream and Upstream Promoters • The Start Point for RNA Polymerase II • TBP Is a Universal Factor • The Basal Apparatus Assembles at the Promoter • Initiation Is Followed by Promoter Clearance and Elongation • Enhancers Contain Bidirectional Elements That Assist Initiation • Enhancers Work by Increasing the Concentration of Activators Near the Promoter • Gene Expression Is Associated with Demethylation • CpG Islands Are Regulatory Targets • Summary • References

Chapter 21: RNA Splicing and Processing • Introduction • The 5" End of Eukaryotic mRNA Is Capped • Nuclear Splice Sites Are Short Sequences • Splice Sites Are Read in Pairs • Pre-mRNA Splicing Proceeds Through a Lariat • snRNAs Are Required for Splicing • Commitment of Pre-mRNA to the Splicing Pathway • The Spliceosome Assembly Pathway • An Alternative Spliceosome Uses Different snRNPsto Process the Minor Class of Introns • Pre-mRNA Splicing Likely Shares the Mechanism with Group II Autocatalytic Introns • Splicing Is Temporally and Functionally Coupled with Multiple Steps in Gene Expression • Alternative Splicing Is a Rule, Rather Than an Exception, in Multicellular Eukaryotes • Splicing Can Be Regulated by Exonic and Intronic Splicing Enhancers and Silencers • trans-Splicing Reactions Use Small RNAs • The • 3? Ends of mRNAs Are Generated by Cleavageand Polyadenylation • The 3? mRNA End Processing Is Critical for Terminationof Transcription • The  3? End Formation of Histone mRNA RequiresU7 snRNA • tRNA Splicing Involves Cutting and Rejoining inSeparate Reactions • The Unfolded Protein Response Is Related to tRNA Splicing • Production of rRNA Requires Cleavage Events andInvolves Small RNAs • Summary • References

Chapter 22: mRNA Stability and Localization • Edited by Ellen Baker • Introduction • Messenger RNAs Are Unstable Molecules • Eukaryotic mRNAs Exist in the Form of mRNPs from Their Birth to Their Death • Prokaryotic mRNA Degradation Involves Multiple Enzymes • Most Eukaryotic mRNA Is Degraded via Two Deadenylation-Dependent Pathways • Other Degradation Pathways Target Specificm RNAs • mRNA-Specific Half-Lives Are Controlled by Sequences or Structures Within the mRNA • Newly Synthesized RNAs Are Checked for Defects viaa Nuclear Surveillance System • Quality Control of mRNA Translation Is Performed by Cytoplasmic Surveillance Systems • Translationally Silenced mRNAs Are Sequestered in a Variety of RNA Granules • Some Eukaryotic mRNAs Are Localized to Specific Regions of a Cell • Summary • References

Chapter 23: Catalytic RNA • Edited by Douglas J. Briant • Introduction • Group I Introns Undertake Self-Splicing by Transesterification • Group I Introns Form a Characteristic Secondary Structure • Ribozymes Have Various Catalytic Activities • Some Group I Introns Encode Endonucleases That Sponsor Mobility • Group II Introns May Encode Multifunction Proteins • Some Autosplicing Introns Require Maturases • The Catalytic Activity of RNase P Is Due toRNA • Viroids Have Catalytic Activity • RNA Editing Occurs at Individual Bases • RNA Editing Can Be Directed by Guide RNAs • Protein Splicing Is Autocatalytic • Summary • References

Chapter 24: Translation • Introduction • Translation Occurs by Initiation, Elongation, and Termination • Special Mechanisms Control the Accuracy of Translation • Initiation in Bacteria Needs 30S Subunits and Accessory Factors • Initiation Involves Base Pairing Between mRNA andrRNA • A Special Initiator tRNA Starts the Polypeptide Chain • Use of fMet-tRNAf Is Controlled by IF-2 and the Ribosome • Small Subunits Scan for Initiation Sites on Eukaryotic mRNA • Eukaryotes Use a Complex of Many Initiation Factors • Elongation Factor Tu Loads Aminoacyl-tRNA intothe A Site • The Polypeptide Chain Is Transferred to Aminoacyl-tRNA • Translocation Moves the Ribosome • Elongation Factors Bind Alternately to the Ribosome • Three Codons Terminate Translation • Termination Codons Are Recognized by Protein Factors • Ribosomal RNA Pervades Both Ribosomal Subunits • Ribosomes Have Several Active Centers • 16S rRNA Plays an Active Role in Translation • 32S rRNA Has Peptidyl Transferase Activity • Ribosomal Structures Change When the Subunits Come Together • Translation Can Be Regulated • The Cycle of Bacterial Messenger RNA • Summary • References

Chapter 25: Using the Genetic Code • Edited by John Perona • Introduction • Related Codons Represent Chemically Similar Amino Acids • Codon?Anticodon Recognition Involves Wobbling • tRNAs Are Processed from Longer Precursors • tRNA Contains Modified Bases • Modified Bases Affect Anticodon?Codon Pairing • There Are Sporadic Alterations of the Universal Code • Novel Amino Acids Can Be Inserted at Certain Stop Codons • tRNAs Are Charged with Amino Acids by Aminoacyl-RNASynthetases • Aminoacyl-tRNA Synthetases Fall into Two Classes • Synthetases Use Proofreading to Improve Accuracy • Suppressor tRNAs Have Mutated Anticodons That Read New Codons • There Are Nonsense Suppressors for Each Termination Codon • Suppressors May Compete with Wild-Type Reading ofthe Code • The Ribosome Influences the Accuracy of Translation • Frameshifting Occurs at Slippery Sequences • Other Recoding Events: Translational Bypassing and the tmRNA Mechanism to Free Stalled Ribosomes • Summary • References

Part 4: Gene Regulation

Chapter 26: The Operon • Edited by Liskin Swint-Kruse • Introduction • Structural Gene Clusters Are CoordinatelyControlled • The lac Operon Is Negative Inducible • lac Repressor Is Controlled by a Small-Molecule Inducer • cis-Acting Constitutive Mutations Identify the Operator • trans-Acting Mutations Identify the Regulator Gene • lac Repressor Is a Tetramer Made of Two Dimers • lac Repressor Binding to the Operator Is Regulated by an Allosteric Change in Conformation • lac Repressor Binds to Three Operators and Interacts with RNA Polymerase • The Operator Competes with Low-Affinity Sites to Bind Repressor • The lac Operon Has a Second Layer of Control:Catabolite Repression • The trp Operon Is a Repressible Operon with Three Transcription Units • The trp Operon Is Also Controlled by Attenuation • Attenuation Can Be Controlled by Translation • Stringent Control by Stable RNA Transcription • r-Protein Synthesis Is Controlled byAutoregulation • Summary • References
Chapter 27: Phage Strategies • Introduction • Lytic Development Is Divided into Two Periods • Lytic Development Is Controlled by a Cascade • Two Types of Regulatory Events Control the Lytic Cascade • The Phage T7 and T4 Genomes Show Functional Clustering • Lambda Immediate Early and Delayed Early Genes Are Needed for Both Lysogeny and the Lytic Cycle • The Lytic Cycle Depends on Antitermination bypN • Lysogeny Is Maintained by the Lambda Repressor Protein • The Lambda Repressor and Its Operators Define the Immunity Region • The DNA-Binding Form of the Lambda Repressor Is aDimer • Lambda Repressor Uses a Helix-Turn-Helix Motif toBind DNA • Lambda Repressor Dimers Bind Cooperatively to the Operator • Lambda Repressor Maintains an Autoregulatory Circuit • Cooperative Interactions Increase the Sensitivity of Regulation • The cII and cIII Genes Are Needed to Establish Lysogeny • A Poor Promoter Requires cII Protein • Lysogeny Requires Several Events • The Cro Repressor Is Needed for Lytic Infection • What Determines the Balance Between Lysogeny and the Lytic Cycle? • Summary • References ?

Chapter 28: Eukaryotic Transcription Regulation • Introduction • How Is a Gene Turned On? • Mechanism of Action of Activators and Repressors • Independent Domains Bind DNA and Activate Transcription • The Two-Hybrid Assay Detects Protein?Protein Interactions • Activators Interact with the Basal Apparatus • There Are Many Types of DNA-Binding Domains • Chromatin Remodeling Is an Active Process • Nucleosome Organization or Content May Be Changed at the Promoter • Histone Acetylation Is Associated with Transcription Activation • Methylation of Histones and DNA IsConnected • Promoter Activation Involves Multiple Changes to Chromatin • Histone Phosphorylation Affects Chromatin Structure • Yeast GAL Genes: A Model for Activation and Repression • Summary • References

Chapter 29: Epigenetic Effects AreInherited • Edited by Trygve Tollefsbol • Introduction • Heterochromatin Propagates from a Nucleation Event • Heterochromatin Depends on Interactions with Histones • Polycomb and Trithorax Are Antagonistic Repressors and Activators • X Chromosomes Undergo Global Changes • Chromosome Condensation Is Caused by Condensins • CpG Islands Are Subject to Methylation • DNA Methylation Is Responsible forImprinting • Contents • Oppositely Imprinted Genes Can Be Controlled by a Single Center • Epigenetic Effects Can Be Inherited • Yeast Prions Show Unusual Inheritance • Prions Cause Diseases in Mammals • Summary • References

Chapter 30: Regulatory RNA • Introduction • A Riboswitch Can Alter Its Structure According toIts Environment • Noncoding RNAs Can Be Used to Regulate Gene Expression • Bacteria Contain Regulator RNAs • MicroRNAs Are Widespread Regulators in Eukaryotes • How Does RNA Interference Work? • Heterochromatin Formation Requires MicroRNAs • Summary • References • Glossary • Index


About the Authors: 

Jocelyn E. Krebs, PhD-Associate Professor, University of Alaska, Anchorage

Jocelyn E. Krebs has been a member of the Department of Biological Sciences at the University of Alaska Anchorage since 2000. She received her B.A. in Biological Sciences from Bard College in 1991 and her PhD in Molecular and Cell Biology from the University of California Berkeley in 1997. Her research focuses on the mechanisms by which DNA transactions such as transcription and repair are accomplished in the context of chromatin. Her teaching interests are in Molecular Biology (taught at the undergraduate, graduate, and first-year medical school levels), as well as the Molecular Biology of Cancer.

Stephen T. Kilpatrick, PhD-Associate Professor, University of Pittsburgh at Johnstown

Stephen T. Kilpatrick is an Associate Professor of Biology at the University of Pittsburgh at Johnstown (UPJ). He received a B.S.  in Biology for Eastern College (now Eastern University) and a PhD from the Program in Ecology and Evolutionary Biology at Brown University. His research an teaching interests are in evolutionary molecular genetics. UPJ is an undergraduate degree-granting campus of the University of Pittsburgh, and
Dr. Kilpatrick regularly teaches undergraduate courses in majors introductory biology, genetics, evolution, molecular genetics, and biostatistics. Prior to coauthoring the Second Edition of Lewin's Essential Genes, Dr. Kilpatrick has co-authored the test banks for the first edition and for Lewin's GENES VIII and GENES IX. He has also authored ancillaries and pedagogical materials for several introductory non-majors and majors biology and genetics textbooks.

Elliott S. Goldstein. Goldstein, PhD-Associate Professor, Arizona State University

Elliott S. Goldstein earned his B.S. in Biology from the University of Hartford (Connecticut) and his Ph.D. in Genetics from the University of Minnesota, Department of Genetics and Cell Biology. Following this, he was awarded an N.I.H. Postdoctoral Fellowship to work with Dr. Sheldon Penman at the Massachusetts Institute of Technology. Leaving Boston, he joined the faculty at Arizona State University in Tempe, where he is an Associate Professor in the Cellular, Molecular and Biosciences program in the School of Life Sciences, and in the Honors Disciplinary Program. His research interests are in the area of molecular and developmental genetics of early embryogenesis in Drosophila melanogaster. In recent years, he has focused on the Drosophila counterparts of the human proto-oncogenes jun and fos. His primary teaching responsibilities are in the undergraduate General Genetics course as well as the graduate level Molecular Genetics course.


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