| Preface |
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xv | |
| About the Authors |
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xxiii | |
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PART I Genes and Chromosomes |
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1 | (226) |
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Chapter 1 Genes Are DNA and Encode RNAs and Polypeptides |
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2 | (33) |
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3 | (1) |
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1.2 DNA Is the Genetic Material of Bacteria and Viruses |
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4 | (2) |
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1.3 DNA Is the Genetic Material of Eukaryotic Cells |
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6 | (1) |
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1.4 Polynucleotide Chains Have Nitrogenous Bases Linked to a Sugar-Phosphate Backbone |
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6 | (1) |
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1.5 Supercoiling Affects the Structure of DNA |
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7 | (2) |
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1.6 DNA Is a Double Helix |
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9 | (2) |
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1.7 DNA Replication Is Semiconservative |
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11 | (1) |
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1.8 Polymerases Act on Separated DNA Strands at the Replication Fork |
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12 | (1) |
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1.9 Genetic Information Can Be Provided by DNA or RNA |
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13 | (2) |
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1.10 Nucleic Acids Hybridize by Base Pairing |
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15 | (1) |
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1.11 Mutations Change the Sequence of DNA |
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16 | (1) |
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1.12 Mutations Can Affect Single Base Pairs or Longer Sequences |
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17 | (1) |
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1.13 The Effects of Mutations Can Be Reversed |
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18 | (1) |
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1.14 Mutations Are Concentrated at Hotspots |
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19 | (1) |
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1.15 Many Hotspots Result from Modified Bases |
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19 | (1) |
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1.16 Some Hereditary Agents Are Extremely Small |
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20 | (1) |
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1.17 Most Genes Encode Polypeptides |
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21 | (1) |
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1.18 Mutations in the Same Gene Cannot Complement |
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22 | (1) |
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1.19 Mutations May Cause Loss of Function or Gain of Function |
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23 | (1) |
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1.20 A Locus Can Have Many Different Mutant Alleles |
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24 | (1) |
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1.21 A Locus Can Have More Than One Wild-Type Allele |
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25 | (1) |
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1.22 Recombination Occurs by Physical Exchange of DNA |
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25 | (2) |
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1.23 The Genetic Code Is Triplet |
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27 | (2) |
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1.24 Every Coding Sequence Has Three Possible Reading Frames |
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29 | (1) |
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1.25 Bacterial Genes Are Colinear with Their Products |
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29 | (1) |
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1.26 Several Processes Are Required to Express the Product of a Gene |
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30 | (1) |
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1.27 Proteins Are trans-Acting but Sites on DNA Are c/'s-Acting |
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31 | (4) |
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Chapter 2 Methods in Molecular Biology and Genetic Engineering |
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35 | (36) |
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35 | (1) |
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36 | (2) |
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38 | (2) |
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2.4 Cloning Vectors Can Be Specialized for Different Purposes |
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40 | (3) |
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2.5 Nucleic Acid Detection |
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43 | (2) |
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2.6 DNA Separation Techniques |
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45 | (3) |
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48 | (2) |
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50 | (5) |
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55 | (3) |
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58 | (3) |
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2.11 Chromatin Immunoprecipitation |
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61 | (1) |
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2.12 Gene Knockouts, Transgenics, and Genome Editing |
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62 | (9) |
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Chapter 3 The Interrupted Gene |
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71 | (30) |
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71 | (1) |
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3.2 An Interrupted Gene Has Exons and Introns |
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72 | (1) |
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3.3 Exon and Intron Base Compositions Differ |
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73 | (1) |
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3.4 Organization of Interrupted Genes Can Be Conserved |
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73 | (1) |
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3.5 Exon Sequences Under Negative Selection Are Conserved but Introns Vary |
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74 | (1) |
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3.6 Exon Sequences Under Positive Selection Vary but Introns Are Conserved |
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75 | (1) |
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3.7 Genes Show a Wide Distribution of Sizes Due Primarily to Intron Size and Number Variation |
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76 | (2) |
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3.8 Some DNA Sequences Encode More Than One Polypeptide |
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78 | (1) |
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3.9 Some Exons Correspond to Protein Functional Domains |
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79 | (2) |
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3.10 Members of a Gene Family Have a Common Organization |
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81 | (1) |
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3.11 There Are Many Forms of Information in DNA |
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82 | (5) |
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3.12 The Content of the Genome |
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87 | (1) |
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87 | (1) |
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4.2 Genome Mapping Reveals That Individual Genomes Show Extensive Variation |
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88 | (1) |
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4.3 SNPs Can Be Associated with Genetic Disorders |
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89 | (1) |
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4.4 Eukaryotic Genomes Contain Nonrepetitive and Repetitive DNA Sequences |
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90 | (2) |
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4.5 Eukaryotic Protein-Coding Genes Can Be Identified by the Conservation of Exons and of Genome Organization |
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92 | (2) |
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4.6 Some Eukaryotic Organelles Have DNA |
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94 | (1) |
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4.7 Organelle Genomes Are Circular DNAs That Encode Organelle Proteins |
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95 | (2) |
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4.8 The Chloroplast Genome Encodes Many Proteins and RNAs |
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97 | (1) |
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4.9 Mitochondria and Chloroplasts Evolved by Endosymbiosis |
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98 | (3) |
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Chapter 5 Genome Sequences and Evolution |
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101 | (42) |
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102 | (1) |
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5.2 Prokaryotic Gene Numbers Range Over an Order of Magnitude |
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103 | (1) |
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5.3 Total Gene Number Is Known for Several Eukaryotes |
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104 | (2) |
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5.4 How Many Different Types of Genes Are There? |
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106 | (2) |
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5.5 The Human Genome Has Fewer Genes Than Originally Expected |
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108 | (2) |
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5.6 How Are Genes and Other Sequences Distributed in the Genome? |
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110 | (1) |
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5.7 The Y Chromosome Has Several Male-Specific Genes |
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111 | (1) |
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5.8 How Many Genes Are Essential? |
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112 | (3) |
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5.9 About 10,000 Genes Are Expressed at Widely Differing Levels in a Eukaryotic Cell |
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115 | (1) |
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5.10 Expressed Gene Number Can Be Measured En Masse |
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116 | (1) |
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5.11 DNA Sequences Evolve by Mutation and a Sorting Mechanism |
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117 | (2) |
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5.12 Selection Can Be Detected by Measuring Sequence Variation |
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119 | (3) |
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5.13 A Constant Rate of Sequence Divergence Is a Molecular Clock |
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122 | (3) |
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5.14 The Rate of Neutral Substitution Can Be Measured from Divergence of Repeated Sequences |
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125 | (1) |
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5.15 How Did Interrupted Genes Evolve? |
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126 | (2) |
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5.16 Why Are Some Genomes So Large? |
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128 | (2) |
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5.17 Morphological Complexity Evolves by Adding New Gene Functions |
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130 | (1) |
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5.18 Gene Duplication Contributes to Genome Evolution |
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131 | (1) |
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5.19 Globin Clusters Arise by Duplication and Divergence |
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132 | (2) |
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8.20 Pseudogenes Have Lost Their Original Functions |
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134 | (1) |
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5.21 Genome Duplication Has Played a Role in Plant and Vertebrate Evolution |
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135 | (2) |
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5.22 What is the Role of Transposable Elements in Genome Evolution |
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137 | (1) |
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5.23 There Can Be Biases in Mutation, Gene Conversion, and Codon Usage |
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137 | (6) |
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Chapter 6 Clusters and Repeats |
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143 | (46) |
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143 | (2) |
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6.2 Unequal Crossing-Over Rearranges Gene Clusters |
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145 | (2) |
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6.3 Genes for rRNA Form Tandem Repeats Including an Invariant Transcription Unit |
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147 | (3) |
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6.4 Crossover Fixation Could Maintain Identical Repeats |
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150 | (2) |
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6.5 Satellite DNAs Often Lie in Heterochromatin |
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152 | (1) |
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6.6 Arthropod Satellites Have Very Short Identical Repeats |
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153 | (1) |
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6.7 Mammalian Satellites Consist of Hierarchical Repeats |
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154 | (3) |
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6.8 Minisatellites Are Useful for DNA Profiling |
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157 | (4) |
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161 | (1) |
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162 | (1) |
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7.2 Viral Genomes Are Packaged into Their Coats |
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163 | (2) |
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7.3 The Bacterial Genome Is a Nucleoid with Dynamic Structural Properties |
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165 | (2) |
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7.4 The Bacterial Genome Is Supercoiled and Has Four Macrodomains |
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167 | (1) |
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7.5 Eukaryotic DNA Has Loops and Domains Attached to a Scaffold |
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168 | (1) |
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7.6 Specific Sequences Attach DNA to an Interphase Matrix |
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169 | (1) |
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7.7 Chromatin Is Divided into Euchromatin and Heterochromatin |
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170 | (2) |
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7.8 Chromosomes Have Banding Patterns |
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172 | (1) |
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7.9 Lampbrush Chromosomes Are Extended |
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173 | (1) |
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7.10 Polytene Chromosomes Form Bands |
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174 | (1) |
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7.11 Polytene Chromosomes Expand at Sites of Gene Expression |
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175 | (1) |
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7.12 The Eukaryotic Chromosome Is a Segregation Device |
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176 | (1) |
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7.13 Regional Centromeres Contain a Centromeric Histone H3 Variant and Repetitive DNA |
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177 | (2) |
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7.14 Point Centromeres in S, cerevisiae Contain Short, Essential DNA Sequences |
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179 | (1) |
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7.15 The S. cerevisiae Centromere Binds a Protein Complex |
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179 | (1) |
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7.16 Telomeres Have Simple Repeating Sequences |
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180 | (1) |
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7.17 Telomeres Seal the Chromosome Ends and Function in Meiotic Chromosome Pairing |
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181 | (1) |
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7.18 Telomeres Are Synthesized by a Ribonucleoprotein Enzyme |
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182 | (2) |
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7.19 Telomeres Are Essential for Survival |
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184 | (5) |
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189 | (38) |
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189 | (1) |
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8.2 DNA Is Organized in Arrays of Nucleosomes |
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190 | (2) |
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8.3 The Nucleosome Is the Subunit of All Chromatin |
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192 | (4) |
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8.4 Nucleosomes Are Covalently Modified |
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196 | (3) |
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8.5 Histone Variants Produce Alternative Nucleosomes |
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199 | (3) |
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8.6 DNA Structure Varies on the Nucleosomal Surface |
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202 | (3) |
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8.7 The Path of Nucleosomes in the Chromatin Fiber |
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205 | (2) |
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8.8 Replication of Chromatin Requires Assembly of Nucleosomes |
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207 | (2) |
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8.9 Do Nucleosomes Lie at Specific Positions? |
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209 | (3) |
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8.10 Nucleosomes Are Displaced and Reassembled During Transcription |
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212 | (3) |
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8.11 DNase Sensitivity Detects Changes in Chromatin Structure |
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215 | (2) |
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8.12 An LCR Can Control a Domain |
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217 | (1) |
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8.13 Insulators Define Transcriptionally Independent Domains |
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218 | (9) |
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PART II DNA Replication and Recombination |
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227 | (214) |
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Chapter 9 Replication Is Connected to the Cell Cycle |
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228 | (17) |
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228 | (2) |
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9.2 Bacterial Replication Is Connected to the Cell Cycle |
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230 | (1) |
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9.3 The Shape and Spatial Organization of a Bacterium Are Important During Chromosome Segregation and Cell Division |
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231 | (1) |
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9.4 Mutations in Division or Segregation Affect Cell Shape |
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232 | (1) |
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9.5 FtsZ Is Necessary for Septum Formation |
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233 | (1) |
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9.6 Min and noc/slm Genes Regulate the Location of the Septum |
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233 | (1) |
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9.7 Partition Involves Separation of the Chromosomes |
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234 | (1) |
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9.8 Chromosomal Segregation Might Require Site-Specific Recombination |
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235 | (2) |
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9.9 The Eukaryotic Growth Factor Signal Transduction Pathway Promotes Entry to S Phase |
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237 | (2) |
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9.10 Checkpoint Control for Entry into S Phase: p53, a Guardian of the Checkpoint |
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239 | (1) |
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9.11 Checkpoint Control for Entry into S Phase: Rb, a Guardian of the Checkpoint |
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240 | (5) |
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Chapter 10 The Replicon: Initiation of Replication |
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245 | (16) |
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245 | (1) |
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10.2 An Origin Usually Initiates Bidirectional Replication |
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246 | (1) |
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10.3 The Bacterial Genome Is (Usually) a Single Circular Replicon |
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247 | (1) |
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10.4 Methylation of the Bacterial Origin Regulates Initiation |
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248 | (1) |
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10.5 Initiation: Creating the Replication Forks at the Origin oriC |
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249 | (2) |
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10.6 Multiple Mechanisms Exist to Prevent Premature Reinitiation of Replication |
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251 | (1) |
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10.7 Archaeal Chromosomes Can Contain Multiple Replicons |
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252 | (1) |
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10.8 Each Eukaryotic Chromosome Contains Many Replicons |
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252 | (1) |
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10.9 Replication Origins Can Be Isolated in Yeast |
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253 | (2) |
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10.10 Licensing Factor Controls Eukaryotic Rereplication |
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255 | (1) |
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10.11 Licensing Factor Binds to ORC |
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256 | (5) |
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Chapter 11 DNA Replication |
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261 | (22) |
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261 | (1) |
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11.2 DNA Polymerases Are the Enzymes That Make DNA |
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262 | (2) |
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11.3 DNA Polymerases Have Various Nuclease Activities |
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264 | (1) |
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11.4 DNA Polymerases Control the Fidelity of Replication |
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264 | (1) |
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11.5 DNA Polymerases Have a Common Structure |
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265 | (1) |
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11.6 The Two New DNA Strands Have Different Modes of Synthesis |
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266 | (1) |
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11.7 Replication Requires a Helicase and a Single-Stranded Binding Protein |
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267 | (1) |
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11.8 Priming Is Required to Start DNA Synthesis |
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268 | (2) |
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11.9 Coordinating Synthesis of the Lagging and Leading Strands |
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270 | (1) |
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11.10 DNA Polymerase Holoenzyme Consists of Subcomplexes |
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270 | (1) |
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11.11 The Clamp Controls Association of Core Enzyme with DNA |
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271 | (3) |
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11.12 Okazaki Fragments Are Linked by Ligase |
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274 | (2) |
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11.13 Separate Eukaryotic DNA Polymerases Undertake Initiation and Elongation |
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276 | (2) |
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11.14 Lesion Bypass Requires Polymerase Replacement |
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278 | (1) |
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11.15 Termination of Replication |
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279 | (4) |
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Chapter 12 Extrachromosomal Replicons |
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283 | (22) |
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283 | (1) |
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12.2 The Ends of Linear DNA Are a Problem for Replication |
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284 | (1) |
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12.3 Terminal Proteins Enable Initiation at the Ends of Viral DNAs |
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285 | (1) |
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12.4 Rolling Circles Produce Multimers of a Replicon |
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286 | (1) |
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12.5 Rolling Circles Are Used to Replicate Phage Genomes |
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287 | (1) |
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12.6 The F Plasmid Is Transferred by Conjugation Between Bacteria |
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288 | (2) |
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12.7 Conjugation Transfers Single-Stranded DNA |
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290 | (1) |
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12.8 Single-Copy Plasmids Have a Partitioning System |
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291 | (2) |
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12.9 Plasmid Incompatibility Is Determined by the Replicon |
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293 | (1) |
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12.10 The ColE1 Compatibility System Is Controlled by an RNA Regulator |
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293 | (3) |
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12.11 How Do Mitochondria Replicate and Segregate? |
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296 | (1) |
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12.12 D Loops Maintain Mitochondrial Origins |
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297 | (1) |
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12.13 The Bacterial Ti Plasmid Causes Crown Gall Disease in Plants |
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298 | (1) |
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12.14 T-DNA Carries Genes Required for Infection |
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299 | (2) |
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12.15 Transfer of T-DNA Resembles Bacterial Conjugation |
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301 | (4) |
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Chapter 13 Homologous and Site-Specific Recombination |
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305 | (34) |
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306 | (1) |
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13.2 Homologous Recombination Occurs Between Synapsed Chromosomes in Meiosis |
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306 | (2) |
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13.3 Double-Strand Breaks Initiate Recombination |
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308 | (2) |
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13.4 Gene Conversion Accounts for Interallelic Recombination |
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310 | (1) |
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13.5 The Synthesis-Dependent Strand-Annealing Model |
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311 | (1) |
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13.6 The Single-Strand Annealing Mechanism Functions at Some Double-Strand Breaks |
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312 | (1) |
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13.7 Break-Induced Replication Can Repair Double-Strand Breaks |
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313 | (1) |
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13.8 Recombining Meiotic Chromosomes Are Connected by the Synaptonemal Complex |
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314 | (1) |
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13.9 The Synaptonemal Complex Forms After Double-Strand Breaks |
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315 | (1) |
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13.10 Pairing and Synaptonemal Complex Formation Are Independent |
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316 | (1) |
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13.11 The Bacterial RecBCD System Is Stimulated by chi Sequences |
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317 | (1) |
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13.12 Strand-Transfer Proteins Catalyze Single-Strand Assimilation |
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318 | (3) |
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13.13 Holliday Junctions Must Be Resolved |
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321 | (1) |
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13.14 Eukaryotic Genes Involved in Homologous Recombination |
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322 | (3) |
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1 End Processing/Presynapsis |
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322 | (2) |
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324 | (1) |
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3 DNA Heteroduplex Extension and Branch Migration |
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324 | (1) |
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324 | (1) |
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13.15 Specialized Recombination Involves Specific Sites |
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325 | (1) |
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13.16 Site-Specific Recombination Involves Breakage and Reunion |
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326 | (1) |
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13.17 Site-Specific Recombination Resembles Topoisomerase Activity |
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327 | (1) |
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13.18 Lambda Recombination Occurs in an Intasome |
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328 | (1) |
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13.19 Yeast Can Switch Silent and Active Mating-Type Loci |
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329 | (2) |
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13.20 Unidirectional Gene Conversion Is Initiated by the Recipient MAT Locus |
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331 | (1) |
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13.21 Antigenic Variation in Trypanosomes Uses Homologous Recombination |
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332 | (1) |
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13.22 Recombination Pathways Adapted for Experimental Systems |
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332 | (7) |
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Chapter 14 Repair Systems |
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339 | (28) |
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339 | (2) |
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14.2 Repair Systems Correct Damage to DNA |
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341 | (2) |
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14.3 Excision Repair Systems in E. coli |
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343 | (1) |
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14.4 Eukaryotic Nucleotide Excision Repair Pathways |
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344 | (1) |
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14.5 Base Excision Repair Systems Require Glycosylases |
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345 | (4) |
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14.6 Error-Prone Repair and Translesion Synthesis |
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349 | (1) |
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14.7 Controlling the Direction of Mismatch Repair |
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349 | (3) |
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14.8 Recombination-Repair Systems in E. coli |
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352 | (1) |
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14.9 Recombination Is an Important Mechanism to Recover from Replication Errors |
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353 | (1) |
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14.10 Recombination-Repair of Double-Strand Breaks in Eukaryotes |
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354 | (2) |
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14.11 Nonhomologous End Joining Also Repairs Double-Strand Breaks |
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356 | (1) |
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14.12 DNA Repair in Eukaryotes Occurs in the Context of Chromatin |
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357 | (4) |
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14.13 RecA Triggers the SOS System |
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361 | (6) |
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Chapter 15 Transposable Elements and Retroviruses |
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367 | (30) |
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368 | (1) |
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15.2 Insertion Sequences Are Simple Transposition Modules |
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369 | (1) |
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15.3 Transposition Occurs by Both Replicative and Nonreplicative Mechanisms |
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370 | (2) |
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15.4 Transposons Cause Rearrangement of DNA |
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372 | (1) |
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15.5 Replicative Transposition Proceeds Through a Cointegrate |
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373 | (1) |
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15.6 Nonreplicative Transposition Proceeds by Breakage and Reunion |
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374 | (1) |
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15.7 Transposons Form Superfamilies and Families |
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375 | (3) |
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15.8 The Role of Transposable Elements in Hybrid Dysgenesis |
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378 | (1) |
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15.9 P Elements Are Activated in the Germ line |
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379 | (2) |
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15.10 The Retrovirus Life Cycle Involves Transposition-Like Events |
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381 | (1) |
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15.11 Retroviral Genes Code for Polyproteins |
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381 | (2) |
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15.12 Viral DNA Is Generated by Reverse Transcription |
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383 | (2) |
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15.13 Viral DNA Integrates into the Chromosome |
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385 | (1) |
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15.14 Retroviruses May Transduce Cellular Sequences |
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386 | (2) |
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15.15 Retroelements Fall into Three Classes |
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388 | (1) |
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15.16 Yeast Ty Elements Resemble Retroviruses |
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389 | (2) |
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15.17 The Alu Family Has Many Widely Dispersed Members |
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391 | (1) |
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15.18 LINEs Use an Endonuclease to Generate a Priming End |
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392 | (5) |
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Chapter 16 Somatic DNA Recombination and Hypermutation in the Immune System |
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397 | (44) |
|
|
|
16.1 The Immune System: Innate and Adaptive Immunity |
|
|
398 | (1) |
|
16.2 The Innate Response Utilizes Conserved Recognition Molecules and Signaling Pathways |
|
|
399 | (2) |
|
|
|
401 | (1) |
|
16.4 Clonal Selection Amplifies Lymphocytes That Respond to a Given Antigen |
|
|
402 | (2) |
|
16.5 Ig Genes Are Assembled from Discrete DNA Segments in B Lymphocytes |
|
|
404 | (1) |
|
16.6 L Chains Are Assembled by a Single Recombination Event |
|
|
405 | (1) |
|
16.7 H Chains Are Assembled by Two Sequential Recombination Events |
|
|
406 | (1) |
|
16.8 Recombination Generates Extensive Diversity |
|
|
407 | (1) |
|
16.9 V(D)J DNA Recombination Relies on RSS and Occurs by Deletion or Inversion |
|
|
408 | (2) |
|
16.10 Allelic Exclusion Is Triggered by Productive Rearrangements |
|
|
410 | (1) |
|
16.11 RAG1/RAG2 Catalyze Breakage and Religation of V(D)J Gene Segments |
|
|
411 | (2) |
|
16.12 B Cell Development in the Bone Marrow: From Common Lymphoid Progenitor to Mature B Cell |
|
|
413 | (2) |
|
16.13 Class Switch DNA Recombination |
|
|
415 | (1) |
|
16.14 CSR Involves AID and Elements of the NHEJ Pathway |
|
|
416 | (2) |
|
16.15 Somatic Hypermutation Generates Additional Diversity and Provides the Substrate for Higher-Affinity Submutants |
|
|
418 | (1) |
|
16.16 SHM Is Mediated by AID, Ung, Elements of the Mismatch DNA Repair Machinery, and Translesion DNA Synthesis Polymerases |
|
|
419 | (1) |
|
16.17 Igs Expressed in Avians Are Assembled from Pseudogenes |
|
|
420 | (1) |
|
16.18 Chromatin Architecture Dynamics of the IgH Locus in V(D) Recombination, CSR, and SHM |
|
|
421 | (2) |
|
16.19 Epigenetics of V(D)J Recombination, CSR, and SHM |
|
|
423 | (2) |
|
16.20 B Cell Differentiation Results in Maturation of the Antibody Response and Generation of Long-lived Plasma Cells and Memory B Cells |
|
|
425 | (1) |
|
16.21 The T Cell Receptor Antigen Is Related to the BCR |
|
|
426 | (1) |
|
16.22 The TCR Functions in Conjunction with the MHC |
|
|
427 | (1) |
|
16.23 The MHC Locus Comprises a Cohort of Genes Involved in Immune Recognition |
|
|
428 | (13) |
|
PART III Transcription and Posttranscriptional Mechanisms |
|
|
441 | (206) |
|
Chapter 17 Prokaryotic Transcription |
|
|
442 | (37) |
|
|
|
443 | (1) |
|
17.2 Transcription Occurs by Base Pairing in a "Bubble" of Unpaired DNA |
|
|
444 | (1) |
|
17.3 The Transcription Reaction Has Three Stages |
|
|
445 | (1) |
|
17.4 Bacterial RNA Polymerase Consists of Multiple Subunits |
|
|
446 | (1) |
|
17.5 RNA Polymerase Holoenzyme Consists of the Core Enzyme and Sigma Factor |
|
|
446 | (2) |
|
17.6 How Does RNA Polymerase Find Promoter Sequences? |
|
|
448 | (1) |
|
17.7 The Holoenzyme Goes Through Transitions in the Process of Recognizing and Escaping from Promoters |
|
|
448 | (3) |
|
17.8 Sigma Factor Controls Binding to DNA by Recognizing Specific Sequences in Promoters |
|
|
451 | (1) |
|
17.9 Promoter Efficiencies Can Be Increased or Decreased by Mutation |
|
|
452 | (1) |
|
17.10 Multiple Regions in RNA Polymerase Directly Contact Promoter DNA |
|
|
453 | (3) |
|
17.11 RNA Polymerase--Promoter and DNA--Protein Interactions Are the Same for Promoter Recognition and DNA Melting |
|
|
456 | (2) |
|
17.12 Interactions Between Sigma Factor and Core RNA Polymerase Change During Promoter Escape |
|
|
458 | (1) |
|
17.13 A Model for Enzyme Movement Is Suggested by the Crystal Structure |
|
|
459 | (2) |
|
17.14 A Stalled RNA Polymerase Can Restart |
|
|
461 | (1) |
|
17.15 Bacterial RNA Polymerase Terminates at Discrete Sites |
|
|
461 | (2) |
|
17.16 How Does Rho Factor Work? |
|
|
463 | (2) |
|
17.17 Supercoiling Is an Important Feature of Transcription |
|
|
465 | (1) |
|
17.18 Phage T7 RNA Polymerase Is a Useful Model System |
|
|
466 | (1) |
|
17.19 Competition for Sigma Factors Can Regulate Initiation |
|
|
466 | (2) |
|
17.20 Sigma Factors Can Be Organized into Cascades |
|
|
468 | (1) |
|
17.21 Sporulation Is Controlled by Sigma Factors |
|
|
469 | (2) |
|
17.22 Antitermination Can Be a Regulatory Event |
|
|
471 | (8) |
|
Chapter 18 Eukaryotic Transcription |
|
|
479 | (24) |
|
|
|
479 | (2) |
|
18.2 Eukaryotic RNA Polymerases Consist of Many Subunits |
|
|
481 | (1) |
|
18.3 RNA Polymerase I Has a Bipartite Promoter |
|
|
482 | (1) |
|
18.4 RNA Polymerase III Uses Downstream and Upstream Promoters |
|
|
483 | (2) |
|
18.5 The Start Point for RNA Polymerase II |
|
|
485 | (1) |
|
18.6 TBP Is a Universal Factor |
|
|
486 | (2) |
|
18.7 The Basal Apparatus Assembles at the Promoter |
|
|
488 | (2) |
|
18.8 Initiation Is Followed by Promoter Clearance and Elongation |
|
|
490 | (3) |
|
18.9 Enhancers Contain Bidirectional Elements That Assist Initiation |
|
|
493 | (1) |
|
18.10 Enhancers Work by Increasing the Concentration of Activators Near the Promoter |
|
|
494 | (1) |
|
18.11 Gene Expression Is Associated with Demethylation |
|
|
495 | (1) |
|
18.12 CpG Islands Are Regulatory Targets |
|
|
496 | (7) |
|
Chapter 19 RNA Splicing and Processing |
|
|
503 | (40) |
|
|
|
503 | (2) |
|
19.2 The 5' End of Eukaryotic mRNA Is Capped |
|
|
505 | (1) |
|
19.3 Nuclear Splice Sites Are Short Sequences |
|
|
506 | (1) |
|
19.4 Splice Sites Are Read in Pairs |
|
|
507 | (1) |
|
19.5 Pre-mRNA Splicing Proceeds Through a Lariat |
|
|
508 | (1) |
|
19.6 snRNAs Are Required for Splicing |
|
|
509 | (1) |
|
19.7 Commitment of Pre-mRNA to the Splicing Pathway |
|
|
510 | (3) |
|
19.8 The Spliceosome Assembly Pathway |
|
|
513 | (2) |
|
19.9 An Alternative Spliceosome Uses Different snRNPs to Process the Minor Class of Introns |
|
|
515 | (1) |
|
19.10 Pre-mRNA Splicing Likely Shares the Mechanism with Group II Autocatalytic Introns |
|
|
516 | (2) |
|
19.11 Splicing Is Temporally and Functionally Coupled with Multiple Steps in Gene Expression |
|
|
518 | (1) |
|
19.12 Alternative Splicing Is a Rule, Rather Than an Exception, in Multicellular Eukaryotes |
|
|
519 | (3) |
|
19.13 Splicing Can Be Regulated by Exonic and Intronic Splicing Enhancers and Silencers |
|
|
522 | (2) |
|
19.14 Trans-Splicing Reactions Use Small RNAs |
|
|
524 | (2) |
|
19.15 The 3' Ends of mRNAs Are Generated by Cleavage and Polyadenylation |
|
|
526 | (2) |
|
19.16 3' mRNA End Processing Is Critical for Termination of Transcription |
|
|
528 | (1) |
|
19.17 The 3' End Formation of Histone mRNA Requires U7 snRNA |
|
|
529 | (1) |
|
19.18 tRNA Splicing Involves Cutting and Rejoining in Separate Reactions |
|
|
530 | (3) |
|
19.19 The Unfolded Protein Response Is Related to tRNA Splicing |
|
|
533 | (1) |
|
19.20 Production of rRNA Requires Cleavage Events and Involves Small RNAs |
|
|
534 | (9) |
|
Chapter 20 mRNA Stability and Localization |
|
|
543 | (20) |
|
|
|
|
|
543 | (1) |
|
20.2 Messenger RNAs Are Unstable Molecules |
|
|
544 | (2) |
|
20.3 Eukaryotic mRNAs Exist in the Form of mRNPs from Their Birth to Their Death |
|
|
546 | (1) |
|
20.4 Prokaryotic mRNA Degradation Involves Multiple Enzymes |
|
|
546 | (2) |
|
20.5 Most Eukaryotic mRNA Is Degraded via Two Deadenylation-Dependent Pathways |
|
|
548 | (2) |
|
20.6 Other Degradation Pathways Target Specific mRNAs |
|
|
550 | (2) |
|
20.7 mRNA-Specific Half-Lives Are Controlled by Sequences or Structures Within the mRNA |
|
|
552 | (1) |
|
20.8 Newly Synthesized RNAs Are Checked for Defects via a Nuclear Surveillance System |
|
|
553 | (2) |
|
20.9 Quality Control of mRNA Translation Is Performed by Cytoplasmic Surveillance Systems |
|
|
555 | (2) |
|
20.10 Translationally Silenced mRNAs Are Sequestered in a Variety of RNA Granules |
|
|
557 | (1) |
|
20.11 Some Eukaryotic mRNAs Are Localized to Specific Regions of a Cell |
|
|
558 | (5) |
|
|
|
563 | (20) |
|
|
|
|
|
563 | (1) |
|
21.2 Group I Introns Undertake Self-Splicing by Transesterification |
|
|
564 | (3) |
|
21.3 Group I Introns Form a Characteristic Secondary Structure |
|
|
567 | (1) |
|
21.4 Ribozymes Have Various Catalytic Activities |
|
|
568 | (2) |
|
21.5 Some Group I Introns Encode Endonucleases That Sponsor Mobility |
|
|
570 | (1) |
|
21.6 Group II Introns May Encode Multifunction Proteins |
|
|
571 | (1) |
|
21.7 Some Autosplicing Introns Require Maturases |
|
|
572 | (1) |
|
21.8 The Catalytic Activity of RNase P Is Due to RNA |
|
|
573 | (1) |
|
21.9 Viroids Have Catalytic Activity |
|
|
573 | (2) |
|
21.10 RNA Editing Occurs at Individual Bases |
|
|
575 | (1) |
|
21.11 RNA Editing Can Be Directed by Guide RNAs |
|
|
576 | (2) |
|
21.12 Protein Splicing Is Autocatalytic |
|
|
578 | (5) |
|
|
|
583 | (38) |
|
|
|
583 | (1) |
|
22.2 Translation Occurs by Initiation, Elongation, and Termination |
|
|
584 | (2) |
|
22.3 Special Mechanisms Control the Accuracy of Translation |
|
|
586 | (1) |
|
22.4 Initiation in Bacteria Needs 30S Subunits and Accessory Factors |
|
|
587 | (2) |
|
22.5 Initiation Involves Base Pairing Between mRNA and rRNA |
|
|
589 | (1) |
|
22.6 A Special Initiator tRNA Starts the Polypeptide Chain |
|
|
590 | (1) |
|
22.7 Use of fMet-tRNAf Is Controlled by IF-2 and the Ribosome |
|
|
591 | (1) |
|
22.8 Small Subunits Scan for Initiation Sites on Eukaryotic mRNA |
|
|
592 | (1) |
|
22.9 Eukaryotes Use a Complex of Many Initiation Factors |
|
|
593 | (4) |
|
22.10 Elongation Factor Tu Loads Aminoacyl-tRNA into the A Site |
|
|
597 | (1) |
|
22.11 The Polypeptide Chain Is Transferred to Aminoacyl-tRNA |
|
|
598 | (1) |
|
22.12 Translocation Moves the Ribosome |
|
|
599 | (1) |
|
22.13 Elongation Factors Bind Alternately to the Ribosome |
|
|
600 | (1) |
|
22.14 Three Codons Terminate Translation |
|
|
601 | (1) |
|
22.15 Termination Codons Are Recognized by Protein Factors |
|
|
602 | (2) |
|
22.16 Ribosomal RNA Is Found Throughout Both Ribosomal Subunits |
|
|
604 | (2) |
|
22.17 Ribosomes Have Several Active Centers |
|
|
606 | (2) |
|
22.18 16S rRNA Plays an Active Role in Translation |
|
|
608 | (2) |
|
22.19 23S rRNA Has Peptidyl Transferase Activity |
|
|
610 | (1) |
|
22.20 Ribosomal Structures Change When the Subunits Come Together |
|
|
611 | (1) |
|
22.21 Translation Can Be Regulated |
|
|
612 | (1) |
|
22.22 The Cycle of Bacterial Messenger RNA |
|
|
613 | (8) |
|
Chapter 23 Using the Genetic Code |
|
|
621 | (26) |
|
|
|
621 | (1) |
|
23.2 Related Codons Represent Chemically Similar Amino Acids |
|
|
622 | (1) |
|
23.3 Codon-Anticodon Recognition Involves Wobbling |
|
|
623 | (1) |
|
23.4 tRNAs Are Processed from Longer Precursors |
|
|
624 | (1) |
|
23.5 tRNA Contains Modified Bases |
|
|
625 | (2) |
|
23.6 Modified Bases Affect Anticodon-Codon Pairing |
|
|
627 | (1) |
|
23.7 The Universal Code Has Experienced Sporadic Alterations |
|
|
628 | (2) |
|
23.8 Novel Amino Acids Can Be Inserted at Certain Stop Codons |
|
|
630 | (1) |
|
23.9 tRNAs Are Charged with Amino Acids by Aminoacyl-tRNA Synthetases |
|
|
631 | (1) |
|
23.10 Aminoacyl-tRNA Synthetases Fall into Two Classes |
|
|
632 | (2) |
|
23.11 Synthetases Use Proofreading to Improve Accuracy |
|
|
634 | (2) |
|
23.12 Suppressor tRNAs Have Mutated Anticodons That Read New Codons |
|
|
636 | (1) |
|
23.13 Each Termination Codon Has Nonsense Suppressors |
|
|
637 | (1) |
|
23.14 Suppressors May Compete with Wild-Type Reading of the Code |
|
|
638 | (1) |
|
23.15 The Ribosome Influences the Accuracy of Translation |
|
|
639 | (2) |
|
23.16 Frameshifting Occurs at Slippery Sequences |
|
|
641 | (1) |
|
23.17 Other Recoding Events: Translational Bypassing and the tmRNA Mechanism to Free Stalled Ribosomes |
|
|
642 | (5) |
|
|
|
647 | (136) |
|
|
|
648 | (29) |
|
|
|
|
|
649 | (2) |
|
24.2 Structural Gene Clusters Are Coordinately Controlled |
|
|
651 | (1) |
|
24.3 The lac Operon Is Negative Inducible |
|
|
652 | (1) |
|
24.4 The lac Repressor Is Controlled by a Small-Molecule Inducer |
|
|
653 | (2) |
|
24.5 c/s-Acting Constitutive Mutations Identify the Operator |
|
|
655 | (1) |
|
24.6 trans-Acting Mutations Identify the Regulator Gene |
|
|
655 | (1) |
|
24.7 The lac Repressor Is a Tetramer Made of Two Dimers |
|
|
656 | (2) |
|
24.8 Lac Repressor Binding to the Operator Is Regulated by an Allosteric Change in Conformation |
|
|
658 | (2) |
|
24.9 The lac Repressor Binds to Three Operators and Interacts with RNA Polymerase |
|
|
660 | (1) |
|
24.10 The Operator Competes with Low-Affinity Sites to Bind Repressor |
|
|
661 | (1) |
|
24.11 The lac Operon Has a Second Layer of Control: Catabolite Repression |
|
|
662 | (3) |
|
24.12 The trp Operon Is a Repressible Operon with Three Transcription Units |
|
|
665 | (1) |
|
24.13 The trp Operon Is Also Controlled by Attenuation |
|
|
666 | (2) |
|
24.14 Attenuation Can Be Controlled by Translation |
|
|
668 | (2) |
|
24.15 Stringent Control by Stable RNA Transcription |
|
|
670 | (1) |
|
24.16 r-Protein Synthesis Is Controlled by Autoregulation |
|
|
671 | (6) |
|
Chapter 25 Phage Strategies |
|
|
677 | (24) |
|
|
|
677 | (2) |
|
25.2 Lytic Development Is Divided into Two Periods |
|
|
679 | (1) |
|
25.3 Lytic Development Is Controlled by a Cascade |
|
|
679 | (2) |
|
25.4 Two Types of Regulatory Events Control the Lytic Cascade |
|
|
681 | (1) |
|
25.5 The Phage T7 and T4 Genomes Show Functional Clustering |
|
|
681 | (2) |
|
25.6 Lambda Immediate Early and Delayed Early Genes Are Needed for Both Lysogeny and the Lytic Cycle |
|
|
683 | (1) |
|
25.7 The Lytic Cycle Depends on Antitermination by pN |
|
|
684 | (1) |
|
25.8 Lysogeny Is Maintained by the Lambda Repressor Protein |
|
|
685 | (1) |
|
25.9 The Lambda Repressor and Its Operators Define the Immunity Region |
|
|
686 | (1) |
|
25.10 The DNA-Binding Form of the Lambda Repressor Is a Dimer |
|
|
687 | (1) |
|
25.11 The Lambda Repressor Uses a Helix-Turn-Helix Motif to Bind DNA |
|
|
688 | (1) |
|
25.12 Lambda Repressor Dimers Bind Cooperatively to the Operator |
|
|
689 | (1) |
|
25.13 The Lambda Repressor Maintains an Autoregulatory Circuit |
|
|
690 | (2) |
|
25.14 Cooperative Interactions Increase the Sensitivity of Regulation |
|
|
692 | (1) |
|
25.15 The cII and cIII Genes Are Needed to Establish Lysogeny |
|
|
692 | (1) |
|
25.16 A Poor Promoter Requires cII Protein |
|
|
693 | (1) |
|
25.17 Lysogeny Requires Several Events |
|
|
694 | (1) |
|
25.18 The Cro Repressor Is Needed for Lytic Infection |
|
|
694 | (3) |
|
25.19 What Determines the Balance Between Lysogeny and the Lytic Cycle? |
|
|
697 | (4) |
|
Chapter 26 Eukaryotic Transcription Regulation |
|
|
701 | (30) |
|
|
|
702 | (1) |
|
26.2 How Is a Gene Turned On? |
|
|
703 | (1) |
|
26.3 Mechanism of Action of Activators and Repressors |
|
|
704 | (3) |
|
26.4 Independent Domains Bind DNA and Activate Transcription |
|
|
707 | (1) |
|
26.5 The Two-Hybrid Assay Detects Protein-Protein Interactions |
|
|
707 | (1) |
|
26.6 Activators Interact with the Basal Apparatus |
|
|
708 | (3) |
|
26.7 Many Types of DNA-Binding Domains Have Been Identified |
|
|
711 | (1) |
|
26.8 Chromatin Remodeling Is an Active Process |
|
|
712 | (3) |
|
26.9 Nucleosome Organization or Content Can Be Changed at the Promoter |
|
|
715 | (1) |
|
26.10 Histone Acetylation Is Associated with Transcription Activation |
|
|
716 | (3) |
|
26.11 Methylation of Histones and DNA Is Connected |
|
|
719 | (1) |
|
26.12 Promoter Activation Involves Multiple Changes to Chromatin |
|
|
720 | (2) |
|
26.13 Histone Phosphorylation Affects Chromatin Structure |
|
|
722 | (1) |
|
26.14 Yeast GAL Genes: A Model for Activation and Repression |
|
|
722 | (9) |
|
|
|
731 | (18) |
|
|
|
|
|
731 | (1) |
|
27.2 Heterochromatin Propagates from a Nucleation Event |
|
|
732 | (2) |
|
27.3 Heterochromatin Depends on Interactions with Histones |
|
|
734 | (3) |
|
27.4 Polycomb and Trithorax Are Antagonistic Repressors and Activators |
|
|
737 | (1) |
|
27.5 CpG Islands Are Subject to Methylation |
|
|
738 | (3) |
|
27.6 Epigenetic Effects Can Be Inherited |
|
|
741 | (2) |
|
27.7 Yeast Prions Show Unusual Inheritance |
|
|
743 | (6) |
|
Chapter 28 Epigenetics II |
|
|
749 | (12) |
|
|
|
|
|
749 | (1) |
|
28.2 X Chromosomes Undergo Global Changes |
|
|
750 | (2) |
|
28.3 Chromosome Condensation Is Caused by Condensins |
|
|
752 | (3) |
|
28.4 DNA Methylation Is Responsible for Imprinting |
|
|
755 | (1) |
|
28.5 Oppositely Imprinted Genes Can Be Controlled by a Single Center |
|
|
756 | (1) |
|
28.6 Prions Cause Diseases in Mammals |
|
|
757 | (4) |
|
|
|
761 | (8) |
|
|
|
761 | (1) |
|
29.2 A Riboswitch Can Alter Its Structure According to Its Environment |
|
|
762 | (1) |
|
29.3 Noncoding RNAs Can Be Used to Regulate Gene Expression |
|
|
763 | (6) |
|
Chapter 30 Regulatory RNA |
|
|
769 | (14) |
|
|
|
769 | (1) |
|
30.2 Bacteria Contain Regulator RNAs |
|
|
770 | (2) |
|
30.3 MicroRNAs Are Widespread Regulators in Eukaryotes |
|
|
772 | (3) |
|
30.4 How Does RNA Interference Work? |
|
|
775 | (3) |
|
30.5 Heterochromatin Formation Requires MicroRNAs |
|
|
778 | (5) |
| Glossary |
|
783 | (26) |
| Index |
|
809 | |
Lisainfo e-raamatute kohta