essential genes - gbvessential genes benjamin lewin. part 1 genes 19 homologous and site-specific...
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Essential GENES
Benjamin Lewin
Part 1 Genes
19 Homologous andSite-Specific Recombination 33 4
1 DNA Is the Hereditary
20 Repair Systems Handl eMaterial
1
Damage to DNA
3562 Genes Code for Proteins
23
21 Transposons
3723 Genes May Be Interrupted 38
22 Retroviruses and4 The Content of the Genome 54
Retroposons
3925 Genome Sequences
23 Recombination inand Gene Numbers
72
the Immune System
4096 Clusters and Repeats
90
Part 5 Eukaryotic Gen ePart 2 Proteins Expression7 Messenger RNA
1138 Protein Synthesis
134
24 Promoters and Enhancers 42 99 Using the Genetic Code
162
25 Regulating Eukaryotic10 Protein Localization
Transcription
449Requires Special Signals
181
26 RNA Splicing andProcessing
468
Part 3 Gene Expression
27 Catalytic RNA
490
11 Transcription
194
Part 6 The Nucleu s12 The Operon
22213 Regulatory RNA
243
28 Chromosomes
50714 Phage Strategies
258
29 Nucleosomes
52630 Chromatin Structure Is
a Focus for Regulation
550Part 4 DNA Replication and
31 Epigenetic Effects AreRecombination
Inherited
56532 Genetic Engineering
58115 The Replicon
28016 Extrachromosomal
Glossary
G-1Replicons
29017 Bacterial Replication I s
Connected to the Cell Cycle 30 318 DNA Replication
317
Index
1-1
Part 1 GenesDNA Is the Hereditary Materia l
1 .1
Introduction
11 .2
DNA Is the Genetic Material of Bacteria
21 .3
DNA Is the Genetic Material of Viruses
31 .4
DNA Is the Genetic Material of Animal Cells
41 .5
Polynucleotide Chains Have Nitrogenous Bases Linked t oa Sugar-Phosphate Backbone
41 .6
DNA Is a Double Helix
51 .7
Supercoiling Affects the Structure of DNA
81 .8 The Structure of DNA Allows Replication and Transcription
91 .9
DNA Replication Is Semiconservative
1 11 .10 DNA Strands Separate at the Replication Fork
1 21 .11 Genetic Information Can Be Provided by DNA or RNA
1 21 .12 Nucleic Acids Hybridize by Base Pairing
1 41 .13 Mutations Change the Sequence of DNA
1 51 .14 Mutations May Affect Single Base Pairs or Longer Sequences
1 61 .15 The Effects of Mutations Can Be Reversed
1 81 .16 Mutations Are Concentrated at Hotspots
1 91 .17 Many Hotspots Result from Modified Bases
201 .18 Genomes Vary Greatly in Size
201 .19 Summary
22
Genes Code for Proteins
2
2.1 Introduction
232.2 A Gene Codes for a Single Polypeptide
242.3 Mutations in the Same Gene Cannot Complement
252.4 Mutations May Cause Loss-of-Function or Gain-of-Function
262.5 A Locus May Have Many Different Mutant Alleles
272.6 A Locus May Have More Than One Wild-Type Allele
282.7 Recombination Occurs by Physical Exchange of DNA
292.8 The Probability of Recombination Depends on Distance Apart
302.9 The Genetic Code is Triplet
3 12.10 Every Sequence Has Three Possible Reading Frames
332.11 Several Processes Are Required to Express the Protein Product of a Gene
342.12 Proteins Are trans-Acting but Sites on DNA Are cis-Acting
352.13 Summary
37
Genes May Be Interrupted3.1
Introduction
383.2 Interrupted Genes Were First Detected by Comparing mRNA and DNA
393.3 Interrupted Genes Are Much Longer than the Corresponding mRNAs
413.4 Organization of Interrupted Genes Is Often Conserved
433.5 Exon Sequences Are Conserved but Introns Vary
443.6 Genes Show a Wide Distribution of Lengths
45
3.7 Some DNA Sequences Code for More than One Protein
463 .8
How Did Interrupted Genes Evolve?
483.9 Some Exons Can Be Equated with Protein Functions
503.10 The Members of a Gene Family Have a Common Organization
5 13.11 Pseudogenes Are Dead Ends of Evolution
523.12 Summary
53
The Content of the Genome
4
4.1 Introduction
544.2 Genomes Can Be Mapped by Linkage, Restriction Cleavage, or DNA Sequence 5 54.3
Individual Genomes Show Extensive Variation
564.4 RFLPs and SNPs Can Be Used for Genetic Mapping
584.5 Why Are Genomes So Large?
604.6
Eukaryotic Genomes Contain Both Nonrepetitive and Repetitive DNA Sequences 6 14.7 Genes Can Be Isolated by the Conservation of Exons
624.8
Genes Involved in Diseases Can Be Identified by Comparing Patien tDNA with Normal DNA
644.9 The Conservation of Genome Organization Helps to Identify Genes
654.10 Organelles Have DNA
674.11 Mitochondrial Genomes Are Circular DNAs that Code for Organelle Proteins
684.12 The Chloroplast Genome Codes for Many Proteins and RNAs
704.13 Organelles Evolved by Endosymbiosis
704.14 Summary
7 1
Genome Sequences and Gene Numbers
5
5.1 Introduction
725.2 Bacterial Gene Numbers Range Over an Order of Magnitude
735.3 Total Gene Number Is Known for Several Eukaryotes
755.4 The Human Genome Has Fewer Genes than Expected
765.5 How Are Genes and Other Sequences Distributed in the Genome?
785.6 The Y Chromosome Has Several Male-Specific Genes
795.7 How Many Different Types of Genes Are There?
8 15.8 More Complex Species Evolve by Adding New Gene Functions
835.9 How Many Genes Are Essential?
845.10 About 10,000 Genes Are Expressed at Widely Different Level s
in a Eukaryotic Tissue
865.11 Expressed Gene Number Can Be Measured en masse
885 .12 Summary
89
Clusters and Repeats
6
6.1 Introduction
906.2
Gene Duplication Is a Major Force in Evolution
926.3
Globin Clusters Are Formed by Duplication and Divergence
92
6.4
Sequence Divergence Is the Basis for the Evolutionary Clock
946.5 The Rate of Neutral Substitution Can Be Measured from Divergenc e
of Repeated Sequences
976.6 Unequal Crossing-Over Rearranges Gene Clusters
98
6.7
Genes for rRNA Form Tandem Repeats Including an Invariant Transcription Unit 10 06.8
Crossover Fixation Could Maintain Identical Repeats
1026.9
Satellite DNAs Often Lie in Heterochromatin
104
6.10 Arthropod Satellites Have Very Short Identical Repeats
106
6.11 Mammalian Satellites Consist of Hierarchical Repeats
1076.12 Minisatellites Are Useful for Genetic Mapping
1096.13 Summary
112
Part 2 ProteinsMessenger RNA
4,;a
7 .1
Introduction
11 37 .2
mRNA Is Produced by Transcription and Is Translated
11 47.3 Transfer RNA Forms a Cloverleaf
11 57.4 The Acceptor Stem and Anticodon Are at Ends of the Tertiary Structure
11 77.5
Messenger RNA Is Translated by Ribosomes
11 87.6 Many Ribosomes Bind to One mRNA
11 97.7 The Life Cycle of Bacterial Messenger RNA
12 17.8
Eukaryotic mRNA Is Modified During or After Its Transcription
1237.9 The 5' End of Eukaryotic mRNA Is Capped
1247.10 The Eukaryotic mRNA 3' Terminus Is Polyadenylated
1257 .11 Bacterial mRNA Degradation Involves Multiple Enzymes
1267 .12 Two Pathways Degrade Eukaryotic mRNA
1277 .13 Nonsense Mutations Trigger a Eukaryotic Surveillance System
1297.14 Eukaryotic RNAs Are Transported
1307.15 mRNAs Can Be Localized Within a Cell
13 17.16 Summary
133
Protein Synthesis
8
8.1 Introduction
1348.2
Protein Synthesis Occurs by Initiation, Elongation, and Termination
1368.3 Special Mechanisms Control the Accuracy of Protein Synthesis
1388.4
Initiation in Bacteria Needs 30S Subunits and Accessory Factors
1398.5
A Special Initiator tRNA Starts the Polypeptide Chain
14 18 .6
mRNA Binds a 30S Subunit to Create the Binding Sit efor a Complex of IF-2 and fMet-tRNAf
1428.7
Small Eukaryotic Subunits Scan for Initiation Sites on mRNA
1448.8 Elongation Factor Tu Loads Aminoacyl-tRNA into the A Site
1468.9 The Polypeptide Chain Is Transferred to Aminoacyl-tRNA
1478.10 Translocation Moves the Ribosome
1488.11 Elongation Factors Bind Alternately to the Ribosome
1508.12 Uncharged tRNA Causes the Ribosome to Trigger the Stringent Response
1508.13 Three Codons Terminate Protein Synthesis and Are Recognize d
by Protein Factors
1538.14 Ribosomal RNA Pervades Both Ribosomal Subunits
1558.15 Ribosomes Have Several Active Centers
1568.16 Both rRNAs Play Active Roles in Protein Synthesis
1588.17 Summary
160
Using the Genetic Code9.1
Introduction
1629.2 Related Codons Represent Related Amino Acids
1639.3
Codon-Anticodon Recognition Involves Wobbling
1649.4 tRNA Contains Modified Bases
1659.5 Modified Bases Affect Anticodon-Codon Pairing
1679 .6 There Are Sporadic Alterations of the Universal Code
1689 .7 Novel Amino Acids Can Be Inserted at Certain Stop Codons
1699.8 tRNAs Are Charged with Amino Acids by Synthetases
1709.9 Aminoacyl-tRNA Synthetases Fall into Two Groups
1719.10 Synthetases Use Proofreading to Improve Accuracy
1729.11 Suppressor tRNAs Have Mutated Anticodons that Read New Codons
174
9.12 Recoding Changes Codon Meanings
1769.13 Frameshifting Occurs at Slippery Sequences
1779.14 Bypassing Involves Ribosome Movement
1799.15 Summary
180
Protein Localization Requires Special Signals
10 10.1 Introduction
18 110.2
Protein Translocation May Be Post-Translational or Co-Translational
18210.3 The Signal Sequence Interacts with the SRP
18410.4 The SRP Interacts with the SRP Receptor
18610.5 The Translocon Forms a Pore
18810.6
Post-Translational Membrane Insertion Depends on Leader Sequences
18910.7
Bacteria Use Both Co-Translational and Post-Translational Translocation
19 110.8 Summary
193
Part 3 Gene ExpressionTranscription
11 .1
Introduction
19411 .2 Transcription Occurs by Base Pairing in a "Bubble" of Unpaired DNA
19611 .3
The Transcription Reaction Has Three Stages
19611 .4 A Model for Enzyme Movement Is Suggested by the Crystal Structure
19811 .5 RNA Polymerase Consists of the Core Enzyme and Sigma Factor
20011 .6 How Does RNA Polymerase Find Promoter Sequences?
20211 .7 Sigma Factor Controls Binding to DNA
20311 .8 Promoter Recognition Depends on Consensus Sequences
20511 .9
Promoter Efficiencies Can Be Increased or Decreased by Mutation
20711 .10 Supercoiling Is an Important Feature of Transcription
20811 .11 Substitution of Sigma Factors May Control Initiation
20911 .12 Sigma Factors Directly Contact DNA
21 211 .13 There Are Two Types of Terminators in E. coli
21 311 .14 Intrinsic Termination Requires a Hairpin and U-Rich Region
21 411 .15 How Does Rho Factor Work?
21 5
11 .16 Antitermination Is a Regulatory Event
21 6
11 .17 Summary
220
The Operon
1 2
12 .1 Introduction
22 2
12.2
Structural Gene Clusters Are Coordinately Controlled
224
12.3 The lac Genes Are Controlled by a Repressor
225
12.4 The lac Operon Can Be Induced
22612.5
Repressor Is Controlled by a Small Molecule Inducer
227
12.6
cis-Acting Constitutive Mutations Identify the Operator
228
12.7
trans-Acting Mutations Identify the Regulator Gene
229
12.8 Repressor Is a Tetramer Made of Two Dimers
23 112.9
Repressor Binding to the Operator Is Regulatedby an Allosteric Change in Conformation
232
12.10 Repressor Binds to Three Operators and Interacts with RNA Polymerase
234
12.11 The Operator Competes with Low-Affinity Sites to Bind Repressor
235
12.12 Repression Can Occur at Multiple Loci
237
12.13 Operons May Be Repressed or Induced
238
12.14 Cyclic AMP Is an Inducer That Activates CRP to Act at Many Operons
239
12.15 Translation Can Be Regulated
240
12.16 Summary
241
Regulatory RNAe, !
13.1
Introduction
24313.2
Alternative Secondary Structures Can Affect Translation or Transcription
244_
13.3
Termination of 8. subtilis Tip Genes Is Controlled by Tryptophan and by tRNA T̀ '
245'1"
13.4
The E. coil tryptophan Operon Is Controlled by Attenuation
24613.5
Attenuation Can Be Controlled by Translation
24713.6 Antisense RNA Can Be Used to Inactivate Gene Expression
25013.7
Small RNA Molecules Can Regulate Translation
25 113.8
Bacteria Contain Regulator RNAs
25213.9 MicroRNAs Are Regulators in Many Eukaryotes
25413.10 RNA Interference Is Related to Gene Silencing
25513.11 Summary
257
Phage Strategies
14 14.1 Introduction
25814.2
Lytic Development Is Divided into Two Periods
25914.3 Lytic Development Is Controlled by a Cascade
26 114.4 Two Types of Regulatory Event Control the Lytic Cascade
26214.5 Lambda Uses Immediate Early and Delayed Early Gene s
for Both Lysogeny and the Lytic Cycle
26414.6
The Lytic Cycle Depends on Antitermination
26414.7
Lysogeny Is Maintained by Repressor Protein
26614.8 The Repressor and Its Operators Define the Immunity Region
26714.9 The DNA-Binding Form of Repressor Is a Dimer
26814.10 Repressor Uses a Helix-Turn-Helix Motif to Bind DNA
26914.11 Repressor Dimers Bind Cooperatively to the Operator
27014.12 Repressor Maintains an Autogenous Circuit
27214.13 Cooperative Interactions Increase the Sensitivity of Regulation
27214.14 The cl/ and c/Il Genes Are Needed to Establish Lysogeny
27314.15 Lysogeny Requires Several Events
27414.16 The Cro Repressor Is Needed for Lytic Infection
27614.17 What Determines the Balance Between Lysogeny and the Lytic Cycle?
27714.18 Summary
278
Part 4 DNA Replication and RecombinationThe Replicon
1 5
15 .1 Introduction
28015.2
An Origin Usually Initiates Bidirectional Replication
28 115.3 The Bacterial Genome Is a Single Circular Replicon
28215.4
Methylation of the Bacterial Origin Regulates Initiation
28415.5 Each Eukaryotic Chromosome Contains Many Replicons
28515.6
Replication Origins Bind the ORC
28615.7 Licensing Factor Controls Rereplication and Consists of MCM Proteins
28715.8 Summary
289
Extrachromosomal Replicons
16 16.1 Introduction
29016.2 The Ends of Linear DNA Are a Problem for Replication
29 116.3 Terminal Proteins Enable Initiation at the Ends of Viral DNAs
29216.4
Rolling Circles Produce Multimers of a Replicon
29316.5 Rolling Circles Are Used to Replicate Phage Genomes
29516.6 The F Plasmid Is Transferred by Conjugation Between Bacteria
296
16.7
Conjugation Transfers Single-Stranded DNA
29716.8
The Ti Bacterial Plasmid Transfers Genes into Plant Cells
29816.9 Transfer of T -DNA Resembles Bacterial Conjugation
29916.10 Summary
302
Bacterial Replication Is Connected to the Cell Cycle
1 7
17.1 Introduction
30317.2 Bacteria Can Have Multiforked Chromosomes
30417.3 The Septum Divides a Bacterium into Progen y
Each Containing a Chromosome
30517.4
Mutations in Division or Segregation Affect Cell Shape
30617.5 FtsZ Is Necessary for Septum Formation
30717.6 min Genes Regulate the Location of the Septum
30817.7
Chromosomal Segregation May Require Site-Specific Recombination
30917.8
Partitioning Separates the Chromosomes
31017.9
Single-Copy Plasmids Have a Partitioning System
31217.10 Plasmid Incompatibility Is Determined by the Replicon
31417.11 How Do Mitochondria Replicate and Segregate?
31517.12 Summary
316
DNA Replication
8
18.1 Introduction
31 718.2 DNA Polymerases Are the Enzymes that Make DNA
31818.3
DNA Polymerases Control the Fidelity of Replication
31 918.4 DNA Polymerases Have a Common Structure
32018.5 The Two New DNA Strands Have Different Modes of Synthesis
32 118.6
Replication Requires a Helicase and Single-Strand Binding Protein
32218.7
Priming Is Required to Start DNA Synthesis
32318.8 DNA Polymerase Holoenzyme Consists of Subcomplexes
32418.9 The Clamp Controls Association of Core Enzyme with DNA
32518.10 Coordinating the Synthesis of the Lagging and Leading Strands
32618.11 Okazaki Fragments Are Linked by Ligase
32818.12 Separate Eukaryotic DNA Polymerases Undertake Initiation and Elongation
32918.13 Creating the Replication Forks at an Origin
33018.14 The Primosome Is Needed to Restart Replication
33 118.15 Summary
333
Homologous and Site-Specific Recombination
1 9
19.1 Introduction
33419.2 Breakage and Reunion Involves Heteroduplex DNA
33519.3
Double-Strand Breaks Initiate Recombination
33819.4 Recombining Chromosomes Are Connected by the Synaptonemal Complex 33 9
19.5 The Synaptonemal Complex Forms After Double-Strand Breaks
34019.6 RecBCD Generates Free Ends for Recombination
342
19.7
Strand-Transfer Proteins Catalyze Single-Strand Assimilation
343
19.8 The Ruv System Resolves Holliday Junctions
344
19.9 Topoisomerases Relax or Introduce Supercoils in DNA
34519.10 Topoisomerases Break and Reseal Strands
346
19.11 Site-Specific Recombination Resembles Topoisomerase Activity
347
19.12 Specialized Recombination in Phage Lambda Involves Specific Sites
34919.13 Yeast Mating Type Is Changed by Recombination
351
19.14 Unidirectional Transposition Is Initiated by the Recipient MATLocus
353
19.15 Summary
354
Repair Systems Handle Damage to DNA20.1
Introduction
35620.2
Mutational Damage Falls into Two General Types
35820.3
Excision Repair Systems in E cols
360`
20 .4
Base Flipping Is Used by Methylases and Glycosylases
36120.5
Error-Prone Repair and Mutator Phenotypes
36220.6
Controlling the Direction of Mismatch Repair
36320.7
Recombination-Repair Systems in E. coil
36520.8
Recombination Is Important for Correcting Replication Errors
36620.9 Eukaryotic Cells Have Conserved Repair Systems
36720.10 A Common System Repairs Double-Strand Breaks
36820.11 Defects in Repair Systems Cause Mutations to Accumulate in Tumors
37020.12 Summary
37 1
Transposons2
21 .1 Introduction
37221 .2
Insertion Sequences Are Simple Transposition Modules
37321 .3 Composite Transposons Have IS Modules
37421 .4 Transposition Occurs by Both Replicative and Nonreplicative Mechanisms
37521 .5 Transposons Cause Rearrangement of DNA
37721 .6 Common Intermediates for Transposition
37821 .7
Replicative Transposition Proceeds Through a Cointegrate
38021 .8
Nonreplicative Transposition Proceeds by Breakage and Reunion
38 121 .9 TnA Transposition Requires Transposase and Resolvase
38221 .10 Controlling Elements in Maize Cause Breakage and Rearrangements
38421 .11 Controlling Elements Form Families of Transposons
38621 .12 Transposition of P Elements Causes Hybrid Dysgenesis
38821 .13 Summary
39 1
Retroviruses and Retroposons
2 2
22.1 Introduction
39222.2
The Retrovirus Life Cycle Involves Transposition-like Events
39322.3
Retroviral Genes Code for Polyproteins
39422.4 Viral DNA Is Generated by Reverse Transcription
39522.5 Viral DNA Integrates Into the Chromosome
39822.6 Retroviruses May Transduce Cellular Sequences
39922.7 Yeast Ty Elements Resemble Retroviruses
40022.8 Many Transposable Elements Reside in D. melanogaster
40122.9 Retroposons Fall into Three Classes
40222.10 The Alu Family Has Many Widely Dispersed Members
40422.11 Processed Pseudogenes Originated as Substrates for Transposition
40522.12 LINES Use an Endonuclease to Generate a Priming End
40622.13 Summary
408
Recombination in the Immune System
2323.1 Introduction
40923.2 Immunoglobulin Genes Are Assembled from Their Parts in Lymphocytes
41 123 .3 Light Chains Are Assembled by a Single Recombination
41 323.4 Heavy Chains Are Assembled by Two Recombinations
41 523.5 Recombination Generates Extensive Diversity
41623.6 Immune Recombination Uses Two Types of Consensus Sequence
41723.7
Recombination Generates Deletions or Inversions
41823.8 The RAG Proteins Catalyze Breakage and Reunion
419
23.9 Class Switching Is Caused by a Novel Type of DNA Recombination
42223.10 Somatic Mutation Is Induced by Cytidine Deaminase and Uracil Glycosylase 42423.11 Avian Immunoglobulins Are Assembled from Pseudogenes
42523.12 T-Cell Receptors Are Related to Immunoglobulins
42723.13 Summary
428
Part 5 Eukaryotic Gene Expressio nPromoters and Enhancers
2424.1 Introduction
42924.2 Eukaryotic RNA Polymerases Consist of Many Subunits
43 124.3 RNA Polymerase I Has a Bipartite Promoter
43224.4 RNA Polymerase III Uses Both Downstream and Upstream Promoters
43324.5 The Startpoint for RNA Polymerase II
43524.6 TBP Is a Component of TF 11 D and Binds the TATA Box
43624.7 The Basal Apparatus Assembles at the Promoter
43824.8
Initiation Is Followed by Promoter Clearance
43924.9 Short Sequence Elements Bind Activators
44024.10 Enhancers Contain Bidirectional Elements that Assist Initiation
44224.11 Enhancers Contain the Same Elements that Are Found at Promoters
44324.12 Enhancers Work by Increasing the Concentratio n
of Activators Near the Promoter
44524.13 CpG Islands Are Regulatory Targets
44624.14 Summary
448
Regulating Eukaryotic Transcription
2525.1 Introduction
44925.2 There Are Several Types of Transcription Factors
45025.3 Independent Domains Bind DNA and Activate Transcription
45125.4 Activators Interact with the Basal Apparatus
45225.5 Response Elements Are Recognized by Activators
45425.6 There Are Many Types of DNA-Binding Domains
45625.7 A Zinc Finger Motif Is a DNA-Binding Domain
45825.8 Some Steroid Hormone Receptors Are Transcription Factors
45925.9 Zinc Fingers of Steroid Receptors Use a Combinatorial Code
46025.10 Binding to the Response Element Is Activated by Ligand Binding
46225.11 Homeodomains Bind Related Targets in DNA
46225.12 Helix-Loop-Helix Proteins Interact by Combinatorial Association
46425.13 Leucine Zippers Are Involved in Dimer Formation
46525.14 Summary
466
RNA Splicing and Processing
26
26.1 Introduction
46826.2 Nuclear Splice Junctions Are Short Sequences
46926.3 Splice Junctions Are Read in Pairs
47026.4 pre-mRNA Splicing Proceeds Through a Lariat
47 126.5 snRNAs Are Required for Splicing
473
26.6 U1 snRNP Initiates Splicing
47426.7 The E Complex Commits an RNA to Splicing
47526.8 5 snRNPs Form the Spliceosome
47626.9 Splicing Is Connected to Export of mRNA
47826.10 Group II Introns Autosplice via Lariat Formation
47926.11 Alternative Splicing Involves Differential Use of Splice Junctions
481
26.12 trans-Splicing Reactions Use Small RNAs
48226.13 Yeast tRNA Splicing Involves Cutting and Rejoining
48326.14 The 3' Ends of mRNAs Are Generated by Cleavage and Polyadenylation
48626.15 Small RNAs Are Required for rRNA Processing
48726.16 Summary
489
Catalytic RNA2
27.1 Introduction
49027.2
Group I Introns Undertake Self-Splicing by Transesterification
49127.3
Group I Introns Form a Characteristic Secondary Structure
49327.4
Ribozymes Have Various Catalytic Activities
49427.5
Some Group I Introns Code for Endonucleases that Sponsor Mobility
49627.6 Some Group II Introns Code for Reverse Transcriptases
49827.7
Some Autosplicing Introns Require Maturases
49927.8
Viroids Have Catalytic Activity
49927.9
RNA Editing Occurs at Individual Bases
50 127.10 RNA Editing Can Be Directed by Guide RNAs
50227.11 Protein Splicing Is Autocatalytic
50527.12 Summary
506
Part 6 The NucleusChromosomes
2828.1 Introduction
50728.2 Viral Genomes Are Packaged into Their Coats
50828.3 The Bacterial Genome Is a Supercoiled Nucleoid
51028.4 Eukaryotic DNA Has Loops and Domains Attached to a Scaffold
51228.5
Chromatin Is Divided into Euchromatin and Heterochromatin
51328.6 Chromosomes Have Banding Patterns
51 528.7 Lampbrush Chromosomes Are Extended
51 628.8 Polytene Chromosomes Form Bands That Puff at Sites of Gene Expression
51 728.9 Centromeres Often Have Extensive Repetitive DNA
51 928.10 S. cerevisiae Centromeres Have Short Protein-Binding DNA Sequences
52028.11 Telomeres Have Simple Repeating Sequences
52228.12 Telomeres Are Synthesized by a Ribonucleoprotein Enzyme
52328.13 Summary
525
Nucleosomes
2929.1 Introduction
52629.2 The Nucleosome Is the Subunit of all Chromatin
52729.3 DNA Is Coiled in Arrays of Nucleosomes
52829.4 Nucleosomes Have a Common Structure
52929.5 DNA Structure Varies on the Nucleosomal Surface
53029.6 The Nucleosome Absorbs Some Supercoiling
53229.7
Organization of the Core Particle
53329.8 The Path of Nucleosomes in the Chromatin Fiber
53429.9 Reproduction of Chromatin Requires Assembly of Nucleosomes
53529.10 Do Nucleosomes Lie at Specific Positions?
53829.11 Histone Octamers Are Displaced by Transcription
54029.12 DNAase Hypersensitive Sites Change Chromatin Structure
54229.13 Domains Define Regions that Contain Active Genes
54329.14 Insulators Block the Actions of Enhancers and Heterochromatin
54529.15 An LCR May Control a Domain
54729.16 What Constitutes a Regulatory Domain?
54829.17 Summary
549
Chromatin Structure Is a Focus for Regulation
30
30.1 Introduction
55030.2
Chromatin Remodeling Is an Active Process
55 130.3 There Are Several Chromatin Remodeling Complexes
55230.4 Nucleosome Organization May Be Changed at the Promoter
55430.5
Histone Modification Is a Key Event
55530.6
Histone Acetylation Occurs in Two Circumstances
55530.7 Acetylases Are Associated with Activators
55630.8 Deacetylases Are Associated with Repressors
55830.9 Methylation of Histones and DNA Is Connected
55830.10 Promoter Activation Is an Ordered Series of Events
55930.11 Histone Phosphorylation Affects Chromatin Structure
56030.12 Some Common Motifs Are Found in Proteins that Modify Chromatin
56 130.13 Heterochromatin Depends on Interactions with Histones
56230.14 Summary
564
Epigenetic Effects Are Inherited
31
31 .1 Introduction
56531 .2 Heterochromatin Propagates from a Nucleation Event
56631 .3
Polycomb and Trithorax Are Antagonistic Repressors and Activators
56831 .4 X Chromosomes Undergo Global Changes
57031 .5 DNA Methylation Is Perpetuated by a Maintenance Methylase
57231.6
DNA Methylation Is Responsible for Imprinting
57431.7 Yeast Prions Show Unusual Inheritance
57631.8 Prions Cause Diseases in Mammals
57831 .9 Summary
580
Genetic Engineering
3 2
32.1 Introduction
58132.2 Cloning Vectors Are Used to Amplify Donor DNA
58232.3 Cloning Vectors Can Be Specialized for Different Purposes
58532.4 Transfection Introduces Exogenous DNA into Cells
58732.5 Genes Can Be Injected into Animal Eggs
58932.6 ES Cells Can Be Incorporated into Embryonic Mice
59132.7 Gene Targeting Allows Genes to Be Replaced or Knocked Out
59232.8 Summary
594
Glossary G-1
Index I-1
Photo Credits
P-1