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Genes IX / Edition 9
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Genes IX / Edition 9

2.0 1
by Benjamin Lewin

ISBN-10: 0763740632

ISBN-13: 9780763740634

Pub. Date: 03/28/2007

Publisher: Jones & Bartlett Learning

From Renowned Author Benjamin Lewin Comes The Newest Edition Of His Classic Text, Genes IX. For Decades Lewin Has Provided The Teaching Community With The Most Cutting Edge Presentation Of Molecular Biology And Molecular Genetics, Covering Gene Structure, Sequencing, Organization, And Expression. The New Ninth Edition Boasts A Fresh Modern Design And Contemporary Art


From Renowned Author Benjamin Lewin Comes The Newest Edition Of His Classic Text, Genes IX. For Decades Lewin Has Provided The Teaching Community With The Most Cutting Edge Presentation Of Molecular Biology And Molecular Genetics, Covering Gene Structure, Sequencing, Organization, And Expression. The New Ninth Edition Boasts A Fresh Modern Design And Contemporary Art Program, As Well As A New Organization Which Allows Students To Focus More Sharply On Individual Topics. Thoroughly Updated, Including A New Chapter On Epigenetic Effects, Genes IX Proves To Be The Most Current, Comprehensive And Student-Friendly Molecular Biology Text Available!

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Jones & Bartlett Learning
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Table of Contents

Preface     xvi
Genes Are DNA     1
Introduction     2
DNA Is the Genetic Material of Bacteria     3
DNA Is the Genetic Material of Viruses     4
DNA Is the Genetic Material of Animal Cells     5
Polynucleotide Chains Have Nitrogenous Bases Linked to a Sugar-Phosphate Backbone     6
DNA Is a Double Helix     6
DNA Replication Is Semiconservative     8
DNA Strands Separate at the Replication Fork     9
Genetic Information Can Be Provided by DNA or RNA     10
Nucleic Acids Hybridize by Base Pairing     12
Mutations Change the Sequence of DNA     14
Mutations May Affect Single Base Pairs or Longer Sequences     15
The Effects of Mutations Can Be Reversed     16
Mutations Are Concentrated at Hotspots     17
Many Hotspots Result from Modified Bases     18
Some Hereditary Agents Are Extremely Small     19
Summary     20
Genes Code for Proteins     23
Introduction     24
A Gene Codes for a Single Polypeptide     24
Mutations in the Same Gene Cannot Complement     25
Mutations May Cause Loss-of-Function or Gain-of-Function     26
ALocus May Have Many Different Mutant Alleles     27
A Locus May Have More than One Wild-type Allele     28
Recombination Occurs by Physical Exchange of DNA     28
The Genetic Code Is Triplet     30
Every Sequence Has Three Possible Reading Frames     31
Prokaryotic Genes Are Colinear with Their Proteins     32
Several Processes Are Required to Express the Protein Product of a Gene     33
Proteins Are Trans-acting, but Sites on DNA Are Cis-acting     35
Summary     36
The Interrupted Gene     37
Introduction     38
An Interrupted Gene Consists of Exons and Introns     38
Restriction Endonucleases Are a Key Tool in Mapping DNA     39
Organization of Interrupted Genes May Be Conserved     40
Exon Sequences Are Conserved but Introns Vary     42
Genes Show a Wide Distribution of Sizes     43
Some DNA Sequences Code for More Than One Protein     45
How Did Interrupted Genes Evolve?     47
Some Exons Can Be Equated with Protein Functions     49
The Members of a Gene Family Have a Common Organization     51
Is All Genetic Information Contained in DNA?     53
Summary     53
The Content of the Genome     55
Introduction     56
Genomes Can Be Mapped by Linkage, Restriction Cleavage, or DNA Sequence     56
Individual Genomes Show Extensive Variation     57
RFLPs and SNPs Can Be Used for Genetic Mapping     58
Why Are Genomes So Large?     60
Eukaryotic Genomes Contain Both Nonrepetitive and Repetitive DNA Sequences     61
Genes Can Be Isolated by the Conservation of Exons     63
The Conservation of Genome Organization Helps to Identify Genes     65
Organelles Have DNA     67
Organelle Genomes Are Circular DNAs That Code for Organelle Proteins     69
Mitochondrial DNA Organization Is Variable     70
The Chloroplast Genome Codes for Many Proteins and RNAs     71
Mitochondria Evolved by Endosymbiosis     72
Summary     73
Genome Sequences and Gene Numbers     76
Introduction     77
Bacterial Gene Numbers Range Over an Order of Magnitude     77
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 Sequences Distributed in the Genome?     85
The Y 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 Differing Levels     92
How Many Genes Are Expressed?     93
Expressed Gene Number Can Be Measured En Masse     93
Summary     94
Clusters and Repeats     98
Introduction     99
Gene Duplication Is a Major Force in Evolution     100
Globin Clusters Are Formed by Duplication and Divergence     101
Sequence Divergence Is the Basis for the Evolutionary Clock     104
The Rate of Neutral Substitution Can Be Measured from Divergence of Repeated Sequences     107
Pseudogenes Are Dead Ends of Evolution     108
Unequal Crossing-over Rearranges Gene Clusters     109
Genes for rRNA Form Tandem Repeats     112
The Repeated Genes for rRNA Maintain Constant Sequence     114
Crossover Fixation Could Maintain Identical Repeats     115
Satellite DNAs Often Lie in Heterochromatin     117
Arthropod Satellites Have Very Short Identical Repeats     119
Mammalian Satellites Consist of Hierarchical Repeats     120
Minisatellites Are Useful for Genetic Mapping      123
Summary     125
Messenger RNA     127
Introduction     128
mRNA Is Produced by Transcription and Is Translated     129
Transfer RNA Forms a Cloverleaf     130
The Acceptor Stem and Anticodon Are at Ends of the Tertiary Structure     131
Messenger RNA Is Translated by Ribosomes     132
Many Ribosomes Bind to One mRNA     133
The Life Cycle of Bacterial Messenger RNA     135
Eukaryotic mRNA Is Modified During or after Its Transcription     137
The 5' End of Eukaryotic mRNA Is Capped     138
The 3' Terminus Is Polyadenylated     139
Bacterial mRNA Degradation Involves Multiple Enzymes     140
mRNA Stability Depends on Its Structure and Sequence     141
mRNA Degradation Involves Multiple Activities     143
Nonsense Mutations Trigger a Surveillance System     144
Eukaryotic RNAs Are Transported     145
mRNA Can Be Specifically Localized     146
Summary     147
Protein Synthesis     151
Introduction     152
Protein Synthesis Occurs by Initiation, Elongation, and Termination     153
Special Mechanisms Control the Accuracy of Protein Synthesis      155
Initiation in Bacteria Needs 30S Subunits and Accessory Factors     157
A Special Initiator tRNA Starts the Polypeptide Chain     158
Use of fMet-tRNA[subscript f] Is Controlled by IF-2 and the Ribosome     150
Initiation Involves Base Pairing Between mRNA and rRNA     161
Small Subunits Scan for Initiation Sites on Eukaryotic mRNA     162
Eukaryotes Use a Complex of Many Initiation Factors     164
Elongation Factor Tu Loads Aminoacyl-tRNA into the A Site     167
The Polypeptide Chain Is Transferred to Aminoacyl-tRNA     168
Translocation Moves the Ribosome     169
Elongation Factors Bind Alternately to the Ribosome     170
Three Codons Terminate Protein Synthesis     172
Termination Codons Are Recognized by Protein Factors     173
Ribosomal RNA Pervades Both Ribosomat Subunits     175
Ribosomes Have Several Active Centers     177
16S rRNA Plays an Active Role in Protein Synthesis     179
23S rRNA Has Peptidyl Transferase Activity     182
Ribosomal Structures Change When the Subunits Come Together     183
Summary     183
Using the Genetic Code     189
Introduction     190
Related Codons Represent Related Amino Acids      190
Codon-Anticodon Recognition Involves Wobbling     192
tRNAs Are Processed from Longer Precursors     194
tRNA Contains Modified Bases     194
Modified Bases Affect Anticodon-Codon Pairing     196
There Are Sporadic Alterations of the Universal Code     197
Novel Amino Acids Can Be Inserted at Certain Stop Codons     199
tRNAs Are Charged with Amino Acids by Synthetases     200
Aminoacyl-tRNA Synthetases Fall into Two Groups     201
Synthetases Use Proofreading to Improve Accuracy     203
Suppressor tRNAs Have Mutated Anticodons That Read New Codons     206
There Are Nonsense Suppressors for Each Termination Codon     207
Suppressors May Compete with Wild-Type Reading of the Code     208
The Ribosome Influences the Accuracy of Translation     209
Recoding Changes Codon Meanings     211
Frameshifting Occurs at Slippery Sequences     213
Bypassing Involves Ribosome Movement     214
Summary     215
Protein Localization     218
Introduction     220
Passage Across a Membrane Requires a Special Apparatus     220
Protein Translocation May Be Posttranslational or Cotranslational     221
Chaperones May Be Required for Protein Folding     223
Chaperones Are Needed by Newly Synthesized and by Denatured Proteins     224
The Hsp70 Family Is Ubiquitous     226
Signal Sequences Initiate Translocation     227
The Signal Sequence Interacts with the SRP     228
The SRP Interacts with the SRP Receptor     229
The Translocon Forms a Pore     231
Translocation Requires Insertion into the Translocon and (Sometimes) a Ratchet in the ER     233
Reverse Translocation Sends Proteins to the Cytosol for Degradation     234
Proteins Reside in Membranes by Means of Hydrophobic Regions     235
Anchor Sequences Determine Protein Orientation     236
How Do Proteins Insert into Membranes?     238
Posttranslational Membrane Insertion Depends on Leader Sequences     240
A Hierarchy of Sequences Determines Location within Organelles     241
Inner and Outer Mitochondrial Membranes Have Different Translocons     243
Peroxisomes Employ Another Type of Translocation System     245
Bacteria Use Both Cotranslational and Posttranslational Translocation     246
The Sec System Transports Proteins into and Through the Inner Membrane     247
Sec-Independent Translocation Systems in E. coli     249
Summary      250
Transcription     256
Introduction     258
Transcription Occurs by Base Pairing in a "Bubble" of Unpaired DNA     259
The Transcription Reaction Has Three Stages     260
Phage T7 RNA Polymerase Is a Useful Model System     251
A Model for Enzyme Movement Is Suggested by the Crystal Structure     262
Bacterial RNA Polymerase Consists of Multiple Subunits     265
RNA Polymerase Consists of the Core Enzyme and Sigma Factor     267
The Association with Sigma Factor Changes at Initiation     267
A Stalled RNA Polymerase Can Restart     269
How Does RNA Polymerase Find Promoter Sequences?     270
Sigma Factor Controls Binding to DNA     271
Promoter Recognition Depends on Consensus Sequences     272
Promoter Efficiencies Can Be Increased or Decreased by Mutation     274
RNA Polymerase Binds to One Face of DNA     275
Supercoiling Is an Important Feature of Transcription     277
Substitution of Sigma Factors May Control Initiation     278
Sigma Factors Directly Contact DNA     280
Sigma Factors May Be Organized into Cascades     282
Sporulation Is Controlled by Sigma Factors     283
Bacterial RNA Polymerase Terminates at Discrete Sites      286
There Are Two Types of Terminators in E. coli     287
How Does Rho Factor Work?     288
Antitermination Is a Regulatory Event     291
Antitermination Requires Sites That Are Independent of the Terminators     292
Termination and Antitermination Factors Interact with RNA Polymerase     293
Summary     295
The Operon     300
Introduction     302
Regulation Can Be Negative or Positive     303
Structural Gene Clusters Are Coordinately Controlled     304
The lac Genes Are Controlled by a Repressor     304
The lac Operon Can Be Induced     305
Repressor Is Controlled by a Small-Molecule Inducer     306
cis-Acting Constitutive Mutations Identify the Operator     308
trans-Acting Mutations Identify the Regulator Gene     309
Multimeric Proteins Have Special Genetic Properties     309
The Repressor Monomer Has Several Domains     310
Repressor Is a Tetramer Made of Two Dimers     311
DNA-Binding Is Regulated by an Allosteric Change in Conformation     312
Mutant Phenotypes Correlate with the Domain Structure     312
Repressor Protein Binds to the Operator     313
Binding of Inducer Releases Repressor from the Operator     314
Repressor Binds to Three Operators and Interacts with RNA Polymerase     315
Repressor Is Always Bound to DNA     316
The Operator Competes with Low-Affinity Sites to Bind Repressor     317
Repression Can Occur at Multiple Loci     319
Cyclic AMP Is an Effector That Activates CRP to Act at Many Operons     320
CRP Functions in Different Ways in Different Target Operons     321
Translation Can Be Regulated     323
r-Protein Synthesis Is Controlled by Autogenous Regulation     325
Phage T4 p32 Is Controlled by an Autogenous Circuit     326
Autogenous Regulation Is Often Used to Control Synthesis of Macromolecular Assemblies     327
Summary     328
Regulatory RNA     331
Introduction     332
Alternative Secondary Structures Control Attenuation     333
Termination of Bacillus subtilis trp Genes Is Controlled by Tryptophan and by tRNA[superscript Trp]     333
The Escherichia coli tryptophan Operon Is Controlled by Attenuation     335
Attenuation Can Be Controlled by Translation     336
Antisense RNA Can Be Used to Inactivate Gene Expression     338
Small RNA Molecules Can Regulate Translation     339
Bacteria Contain Regulator RNAs     341
MicroRNAs Are Regulators in Many Eukaryotes     342
RNA Interference Is Related to Gene Silencing     343
Summary     345
Phage Strategies     349
Introduction     350
Lytic Development Is Divided into Two Periods     352
Lytic Development Is Controlled by a Cascade     353
Two Types of Regulatory Event Control the Lytic Cascade     354
The T7 and T4 Genomes Show Functional Clustering     355
Lambda Immediate Early and Delayed Early Genes Are Needed for Both Lysogeny and the Lytic Cycle     356
The Lytic Cycle Depends on Antitermination     357
Lysogeny Is Maintained by Repressor Protein     359
The Repressor and Its Operators Define the Immunity Region     360
The DNA-Binding Form of Repressor Is a Dimer     361
Repressor Uses a Helix-Turn-Helix Motif to Bind DNA     362
The Recognition Helix Determines Specificity for DNA     363
Repressor Dimers Bind Cooperatively to the Operator     364
Repressor at 0[subscript R]2 Interacts with RNA Polymerase at P[subscript RM]     365
Repressor Maintains an Autogenous Circuit     366
Cooperative Interactions Increase the Sensitivity of Regulation     367
The cII and cIII Genes Are Needed to Establish Lysogeny     368
A Poor Promoter Requires cII Protein     369
Lysogeny Requires Several Events     369
The cro Repressor Is Needed for Lytic Infection     371
What Determines the Balance Between Lysogeny and the Lytic Cycle?     373
Summary     374
The Replicon     376
Introduction     377
Replicons Can Be Linear or Circular     378
Origins Can Be Mapped by Autoradiography and Electrophoresis     379
Does Methylation at the Origin Regulate Initiation?     380
Origins May Be Sequestered after Replication     381
Each Eukaryotic Chromosome Contains Many Replicons     383
Replication Origins Can Be Isolated in Yeast     384
Licensing Factor Controls Eukaryotic Rereplication     385
Licensing Factor Consists of MCM Proteins     386
D Loops Maintain Mitochondrial Origins     388
Summary     389
Extrachromosomal Replicons     392
Introduction     393
The Ends of Linear DNA Are a Problem for Replication     393
Terminal Proteins Enable Initiation at the Ends of Viral DNAs     394
Rolling Circles Produce Multimers of a Replicon      396
Rolling Circles Are Used to Replicate Phage Genomes     397
The F Plasmid Is Transferred by Conjugation between Bacteria     398
Conjugation Transfers Single-Stranded DNA     400
The Bacterial Ti Plasmid Causes Crown Gall Disease in Plants     401
T-DNA Carries Genes Required for Infection     402
Transfer of T-DNA Resembles Bacterial Conjugation     405
Summary     407
Bacterial Replication Is Connected to the Cell Cycle     408
Introduction     409
Replication Is Connected to the Cell Cycle     410
The Septum Divides a Bacterium into Progeny That Each Contain a Chromosome     411
Mutations in Division or Segregation Affect Cell Shape     412
FtsZ Is Necessary for Septum Formation     413
min Genes Regulate the Location of the Septum     415
Chromosomal Segregation May Require Site-Specific Recombination     415
Partitioning Involves Separation of the Chromosomes     417
Single-Copy Plasmids Have a Partitioning System     419
Plasmid Incompatibility Is Determined by the Replicon     421
The ColE1 Compatibility System Is Controlled by an RNA Regulator     422
How Do Mitochondria Replicate and Segregate?     424
Summary      425
DNA Replication     428
Introduction     429
DNA Polymerases Are the Enzymes That Make DNA     430
DNA Polymerases Have Various Nuclease Activities     431
DNA Polymerases Control the Fidelity of Replication     432
DNA Polymerases Have a Common Structure     433
DNA Synthesis Is Semidiscontinuous     434
The [phi]X Model System Shows How Single-Stranded DNA Is Generated for Replication     435
Priming Is Required to Start DNA Synthesis     437
DNA Polymerase Holoenzyme Has Three Subcomplexes     439
The Clamp Controls Association of Core Enzyme with DNA     440
Coordinating Synthesis of the Lagging and Leading Strands     442
Okazaki Fragments Are Linked by Ligase     443
Separate Eukaryotic DNA Polymerases Undertake Initiation and Elongation     444
Phage T4 Provides Its Own Replication Apparatus     445
Creating the Replication Forks at an Origin     448
Common Events in Priming Replication at the Origin     450
The Primosome Is Needed to Restart Replication     451
Summary     453
Homologous and Site-Specific Recombination     457
Introduction     459
Homologous Recombination Occurs between Synapsed Chromosomes     460
Breakage and Reunion Involves Heteroduplex DNA     462
Double-Strand Breaks Initiate Recombination     464
Recombining Chromosomes Are Connected by the Synaptonemal Complex     465
The Synaptonemal Complex Forms after Double-Strand Breaks     467
Pairing and Synaptonemal Complex Formation Are Independent     469
The Bacterial RecBCD System Is stimulated by chi Sequences     470
Strand-Transfer Proteins Catalyze Single-Strand Assimilation     471
The Ruv System Resolves Holliday Junctions     473
Gene Conversion Accounts for Interallelic Recombination     475
Supercoiling Affects the Structure of DNA     476
Topoisomerases Relax or Introduce Supercoils in DNA     478
Topoisomerases Break and Reseal Strands     480
Gyrase Functions by Coil Inversion     481
Specialized Recombination Involves Specific Sites     482
Site-Specific Recombination Involves Breakage and Reunion     484
Site-Specific Recombination Resembles Topoisomerase Activity     484
Lambda Recombination Occurs in an Intasome     486
Yeast Can Switch Silent and Active Loci for Mating Type     488
The MAT Locus Codes for Regulator Proteins     490
Silent Cassettes at HML and HMR Are Repressed     492
Unidirectional Transposition Is Initiated by the Recipient MAT Locus     493
Regulation of HO Expression Controls Switching     494
Summary     496
Repair Systems     499
Introduction     500
Repair Systems Correct Damage to DNA     502
Excision Repair Systems in E. coli     503
Excision-Repair Pathways in Mammalian Cells     504
Base Flipping Is Used by Methylases and Glycosylases     506
Error-Prone Repair and Mutator Phenotypes     507
Controlling the Direction of Mismatch Repair     507
Recombination-Repair Systems in E. coli     510
Recombination Is an Important Mechanism to Recover from Replication Errors     511
RecA Triggers the SOS System     513
Eukaryotic Cells Have Conserved Repair Systems     515
A Common System Repairs Double-Strand Breaks     516
Summary     518
Transposons     521
Introduction     522
Insertion Sequences Are Simple Transposition Modules     524
Composite Transposons Have IS Modules     525
Transposition Occurs by Both Replicative and Nonreplicative Mechanisms     527
Transposons Cause Rearrangement of DNA     528
Common Intermediates for Transposition     530
Replicative Transposition Proceeds through a Cointegrate     531
Nonreplicative Transposition Proceeds by Breakage and Reunion     533
TnA Transposition Requires Transposase and Resolvase     534
Transposition of Tn10 Has Multiple Controls     536
Controlling Elements in Maize Cause Breakage and Rearrangements     538
Controlling Elements Form Families of Transposons     540
Spm Elements Influence Gene Expression     542
The Role of Transposable Elements in Hybrid Dysgenesis     544
P Elements Are Activated in the Germline     545
Summary     546
Retroviruses and Retroposons     550
Introduction     551
The Retrovirus Life Cycle Involves Transposition-Like Events     551
Retroviral Genes Code for Polyproteins     552
Viral DNA Is Generated by Reverse Transcription     554
Viral DNA Integrates into the Chromosome     556
Retroviruses May Transduce Cellular Sequences     558
Yeast Ty Elements Resemble Retroviruses     559
Many Transposable Elements Reside in Drosophila melanogaster     561
Retroposons Fall into Three Classes     562
The Alu Family Has Many Widely Dispersed Members     564
Processed Pseudogenes Originated as Substrates for Transposition     565
LINES Use an Endonuclease to Generate a Priming End     566
Summary     567
Immune Diversity     570
Introduction     572
Clonal Selection Amplifies Lymphocytes That Respond to Individual Antigens     574
Immunoglobulin Genes Are Assembled from Their Parts in Lymphocytes     575
Light Chains Are Assembled by a Single Recombination     577
Heavy Chains Are Assembled by Two Recombinations     579
Recombination Generates Extensive Diversity     580
Immune Recombination Uses Two Types of Consensus Sequence     581
Recombination Generates Deletions or Inversions     582
Allelic Exclusion Is Triggered by Productive Rearrangement     582
The RAG Proteins Catalyze Breakage and Reunion     584
Early Heavy Chain Expression Can Be Changed by RNA Processing     586
Class Switching Is Caused by DNA Recombination     587
Switching Occurs by a Novel Recombination Reaction     589
Somatic Mutation Generates Additional Diversity in Mouse and Human Being     590
Somatic Mutation Is Induced by Cytidine Deaminase and Uracil Glycosylase      591
Avian Immunoglobulins Are Assembled from Pseudogenes     593
B Cell Memory Allows a Rapid Secondary Response     594
T Cell Receptors Are Related to Immunoglobulins     595
The T Cell Receptor Functions in Conjunction with the MHC     597
The Major Histocompatibility Locus Codes for Many Genes of the Immune System     599
Innate Immunity Utilizes Conserved Signaling Pathways     602
Summary     604
Promoters and Enhancers     609
Introduction     610
Eukaryotic RNA Polymerases Consist of Many Subunits     612
Promoter Elements Are Defined by Mutations and Footprinting     613
RNA Polymerase I Has a Bipartite Promoter     614
RNA Polymerase III Uses Both Downstream and Upstream Promoters     615
TF[subscript III]B Is the Commitment Factor for Pol III Promoters     616
The Startpoint for RNA Polymerase II     618
TBP Is a Universal Factor     619
TBP Binds DNA in an Unusual Way     620
The Basal Apparatus Assembles at the Promoter     621
Initiation Is Followed by Promoter Clearance     623
A Connection between Transcription and Repair     625
Short Sequence Elements Bind Activators     627
Promoter Construction Is Flexible but Context Can Be Important     628
Enhancers Contain Bidirectional Elements That Assist Initiation     629
Enhancers Contain the Same Elements That Are Found at Promoters     630
Enhancers Work by Increasing the Concentration of Activators Near the Promoter     631
Gene Expression Is Associated with Demethylation     632
CpG Islands Are Regulatory Targets     634
Summary     635
Activating Transcription     640
Introduction     641
There Are Several Types of Transcription Factors     642
Independent Domains Bind DNA and Activate Transcription     643
The Two Hybrid Assay Detects Protein-Protein Interactions     645
Activators Interact with the Basal Apparatus     646
Some Promoter-Binding Proteins Are Repressors     648
Response Elements Are Recognized by Activators     649
There Are Many Types of DNA-Binding Domains     651
A Zinc Finger Motif Is a DNA-Binding Domain     652
Steroid Receptors Are Activators     653
Steroid Receptors Have Zinc Fingers     655
Binding to the Response Element Is Activated by Ligand-Binding     656
Steroid Receptors Recognize Response Elements by a Combinatorial Code      657
Homeodomains Bind Related Targets in DNA     658
Helix-Loop-Helix Proteins Interact by Combinatorial Association     660
Leucine Zippers Are Involved in Dimer Formation     662
Summary     663
RNA Splicing and Processing     667
Introduction     669
Nuclear Splice Junctions Are Short Sequences     670
Splice Junctions Are Read in Pairs     671
Pre-mRNA Splicing Proceeds through a Lariat     673
snRNAs Are Required for Splicing     674
U1 snRNP Initiates Splicing     676
The E Complex Can Be Formed by Intron Definition or Exon Definition     678
5 snRNPs Form the Spliceosome     679
An Alternative Splicing Apparatus Uses Different snRNPs     681
Splicing Is Connected to Export of mRNA     682
Group II Introns Autosplice via Lariat Formation     683
Alternative Splicing Involves Differential Use of Splice Junctions     685
trans-Splicing Reactions Use Small RNAs     688
Yeast tRNA Splicing Involves Cutting and Rejoining     690
The Splicing Endonuclease Recognizes tRNA     691
tRNA Cleavage and Ligation Are Separate Reactions     692
The Unfolded Protein Response Is Related to tRNA Splicing      693
The 3' Ends of polI and polIII Transcripts Are Generated by Termination     694
The 3' Ends of mRNAs Are Generated by Cleavage and Polyadenylation     695
Cleavage of the 3' End of Histone mRNA May Require a Small RNA     697
Production of rRNA Requires Cleavage Events     697
Small RNAs Are Required for rRNA Processing     699
Summary     700
Catalytic RNA     706
Introduction     707
Group I Introns Undertake Self-Splicing by Transesterification     707
Group I Introns Form a Characteristic Secondary Structure     709
Ribozymes Have Various Catalytic Activities     711
Some Group I Introns Code for Endonucleases That Sponsor Mobility     715
Group II Introns May Code for Multifunction Proteins     716
Some Autosplicing Introns Require Maturases     717
The Catalytic Activity of RNAase P Is Due to RNA     718
Viroids Have Catalytic Activity     718
RNA Editing Occurs at Individual Bases     720
RNA Editing Can Be Directed by Guide RNAs     721
Protein Splicing Is Autocatalytic     724
Summary     725
Chromosomes     729
Introduction     730
Viral Genomes Are Packaged into Their Coats     731
The Bacterial Genome Is a Nucleoid     734
The Bacterial Genome Is Supercoiled     735
Eukaryotic DNA Has Loops and Domains Attached to a Scaffold     736
Specific Sequences Attach DNA to an Interphase Matrix     737
Chromatin Is Divided into Euchromatin and Heterochromatin     738
Chromosomes Have Banding Patterns     740
Lampbrush Chromosomes Are Extended     741
Polytene Chromosomes Form Bands     742
Polytene Chromosomes Expand at Sites of Gene Expression     743
The Eukaryotic Chromosome Is a Segregation Device     744
Centromeres May Contain Repetitive DNA     746
Centromeres Have Short DNA Sequences in S. cerevisiae     747
The Centromere Binds a Protein Complex     748
Telomeres Have Simple Repeating Sequences     748
Telomeres Seat the Chromosome Ends     749
Telomeres Are Synthesized by a Ribonucleoprotein Enzyme     750
Telomeres Are Essential for Survival     752
Summary     753
Nucleosomes     757
Introduction     758
The Nucleosome Is the Subunit of All Chromatin     759
DNA Is Coiled in Arrays of Nucleosomes     761
Nucleosomes Have a Common Structure     762
DNA Structure Varies on the Nucleosomal Surface     763
The Periodicity of DNA Changes on the Nucleosome     766
Organization of the Histone Octamer     767
The Path of Nucleosomes in the Chromatin Fiber     769
Reproduction of Chromatin Requires Assembly of Nucleosomes     771
Do Nucleosomes Lie at Specific Positions?     774
Are Transcribed Genes Organized in Nucleosomes?     777
Histone Octamers Are Displaced by Transcription     779
Nucleosome Displacement and Reassembly Require Special Factors     781
Insulators Block the Actions of Enhancers and Heterochromatin     781
Insulators Can Define a Domain     783
Insulators May Act in One Direction     784
Insulators Can Vary in Strength     785
DNAase Hypersensitive Sites Reflect Changes in Chromatin Structure     786
Domains Define Regions That Contain Active Genes     788
An LCR May Control a Domain     789
What Constitutes a Regulatory Domain?     790
Summary     791
Controlling Chromatin Structure     796
Introduction     797
Chromatin Can Have Alternative States     797
Chromatin Remodeling Is an Active Process     798
Nucleosome Organization May Be Changed at the Promoter     801
Histone Modification Is a Key Event     802
Histone Acetylation Occurs in Two Circumstances     805
Acetylases Are Associated with Activators     806
Deacetylases Are Associated with Repressors     808
Methylation of Histones and DNA Is Connected     808
Chromatin States Are Interconverted by Modification     809
Promoter Activation Involves an Ordered Series of Events     809
Histone Phosphorylation Affects Chromatin Structure     810
Some Common Motifs Are Found in Proteins That Modify Chromatin     811
Summary     812
Epigenetic Effects Are Inherited     818
Introduction     819
Heterochromatin Propagates from a Nucleation Event     820
Heterochromatin Depends on Interactions with Histones     822
Polycomb and Trithorax Are Antagonistic Repressors and Activators     824
X Chromosomes Undergo Global Changes     826
Chromosome Condensation Is Caused by Condensins     828
DNA Methylation Is Perpetuated by a Maintenance Methylase     830
DNA Methylation Is Responsible for Imprinting     832
Oppositely Imprinted Genes Can Be Controlled by a Single Center     834
Epigenetic Effects Can Be Inherited     835
Yeast Prions Show Unusual Inheritance     836
Prions Cause Diseases in Mammals     839
Summary     840
Glossary     845
Index     867

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Genes IX 2 out of 5 based on 0 ratings. 1 reviews.
BC2WS More than 1 year ago
I used this textbook in a Molecular Biology course. I found it disjunct and difficult to follow. It is hard to adequately discuss protein synthesis (chapter 8) without prefacing it with an understanding of the genetic code (chapter 9). Similarly, DNA replication finds itself discussed in chapter 18, while detailed exposure to promoters & enhancers is not provided until chapter 24. The book's organization seemed random; it was not very well put together in a logical flow of information. If there is another text available, I would recommend you utilize it instead.