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Test Bank for Molecular Biology, 5th Edition: Robert Weaver

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Test Bank for Molecular Biology, 5th Edition: Robert Weaver

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  • ISBN-10 ‏ : ‎ 0073525324
  • ISBN-13 ‏ : ‎ 978-0073525327
  • Author: Robert Weaver

Molecular Biology, 5/e by Robert Weaver, is designed for an introductory course in molecular biology. Molecular Biology 5/e focuses on the fundamental concepts of molecular biology emphasizing experimentation. In particular author, Rob Weaver, focuses on the study of genes and their activities at the molecular level. Through the combination of excellent illustrations and clear, succinct writing students are presented fundamental molecular biology concepts.

 

Table of Content:

  1. PART I Introduction
  2. CHAPTER 1 A Brief History
  3. 1.1 Transmission Genetics
  4. Mendel’s Laws of Inheritance
  5. The Chromosome Theory of Inheritance
  6. Genetic Recombination and Mapping
  7. Physical Evidence for Recombination
  8. 1.2 Molecular Genetics
  9. The Discovery of DNA
  10. The Relationship Between Genes and Proteins
  11. Activities of Genes
  12. 1.3 The Three Domains of Life
  13. CHAPTER 2 The Molecular Nature of Genes
  14. 2.1 The Nature of Genetic Material
  15. Transformation in Bacteria
  16. The Chemical Nature of Polynucleotides
  17. 2.2 DNA Structure
  18. Experimental Background
  19. The Double Helix
  20. 2.3 Genes Made of RNA
  21. 2.4 Physical Chemistry of Nucleic Acids
  22. A Variety of DNA Structures
  23. DNAs of Various Sizes and Shapes
  24. CHAPTER 3 An Introduction to Gene Function
  25. 3.1 Storing Information
  26. Overview of Gene Expression
  27. Protein Structure
  28. Protein Function
  29. Discovery of Messenger RNA
  30. Transcription
  31. Translation
  32. 3.2 Replication
  33. 3.3 Mutations
  34. Sickle Cell Disease
  35. PART II Methods of Molecular Biology
  36. CHAPTER 4 Molecular Cloning Methods
  37. 4.1 Gene Cloning
  38. The Role of Restriction Endonucleases
  39. Vectors
  40. Identifying a Specific Clone with a Specific Probe
  41. cDNA Cloning
  42. Rapid Amplification of cDNA Ends
  43. 4.2 The Polymerase Chain Reaction
  44. Standard PCR
  45. Box 4.1 Jurassic Park: More than a Fantasy?
  46. Using Reverse Transcriptase PCR (RT-PCR) in cDNA Cloning
  47. Real-Time PCR
  48. 4.3 Methods of Expressing Cloned Genes
  49. Expression Vectors
  50. Other Eukaryotic Vectors
  51. Using the Ti Plasmid to Transfer Genes to Plants
  52. CHAPTER 5 Molecular Tools for Studying Genes and Gene Activity
  53. 5.1 Molecular Separations
  54. Gel Electrophoresis
  55. Two-Dimensional Gel Electrophoresis
  56. Ion-Exchange Chromatography
  57. Gel Filtration Chromatography
  58. Affinity Chromatography
  59. 5.2 Labeled Tracers
  60. Autoradiography
  61. Phosphorimaging
  62. Liquid Scintillation Counting
  63. Nonradioactive Tracers
  64. 5.3 Using Nucleic Acid Hybridization
  65. Southern Blots: Identifying Specific DNA Fragments
  66. DNA Fingerprinting and DNA Typing
  67. Forensic Uses of DNA Fingerprinting and DNA Typing
  68. In Situ Hybridization: Locating Genes in Chromosomes
  69. Immunoblots (Western Blots)
  70. 5.4 DNA Sequencing and Physical Mapping
  71. The Sanger Chain-Termination Sequencing Method
  72. Automated DNA Sequencing
  73. High-Throughput Sequencing
  74. Restriction Mapping
  75. 5.5 Protein Engineering with Cloned Genes: Site-Directed Mutagenesis
  76. 5.6 Mapping and Quantifying Transcripts
  77. Northern Blots
  78. S1 Mapping
  79. Primer Extension
  80. Run-Off Transcription and G-Less Cassette Transcription
  81. 5.7 Measuring Transcription Rates in Vivo
  82. Nuclear Run-On Transcription
  83. Reporter Gene Transcription
  84. Measuring Protein Accumulation in Vivo
  85. 5.8 Assaying DNA–Protein Interactions
  86. Filter Binding
  87. Gel Mobility Shift
  88. DNase Footprinting
  89. DMS Footprinting and Other Footprinting Methods
  90. Chromatin Immunoprecipitation (ChIP)
  91. 5.9 Assaying Protein–Protein Interactions
  92. 5.10 Finding RNA Sequences That Interact with Other Molecules
  93. SELEX
  94. Functional SELEX
  95. 5.11 Knockouts and Transgenics
  96. Knockout Mice
  97. Transgenic Mice
  98. PART III Transcription in Bacteria
  99. CHAPTER 6 The Mechanism of Transcription in Bacteria
  100. 6.1 RNA Polymerase Structure
  101. Sigma (σ) as a Specificity Factor
  102. 6.2 Promoters
  103. Binding of RNA Polymerase to Promoters
  104. Promoter Structure
  105. 6.3 Transcription Initiation
  106. Sigma Stimulates Transcription Initiation
  107. Reuse of σ
  108. The Stochastic σ-Cycle Model
  109. Local DNA Melting at the Promoter
  110. Promoter Clearance
  111. Structure and Function of σ
  112. The Role of the α-Subunit in UP Element Recognition
  113. 6.4 Elongation
  114. Core Polymerase Functions in Elongation
  115. Structure of the Elongation Complex
  116. 6.5 Termination of Transcription
  117. Rho-Independent Termination
  118. Rho-Dependent Termination
  119. CHAPTER 7 Operons: Fine Control of Bacterial Transcription
  120. 7.1 The lac Operon
  121. Negative Control of the lac Operon
  122. Discovery of the Operon
  123. Repressor–Operator Interactions
  124. The Mechanism of Repression
  125. Positive Control of the lac Operon
  126. The Mechanism of CAP Action
  127. 7.2 The ara Operon
  128. The ara Operon Repression Loop
  129. Evidence for the ara Operon Repression Loop
  130. Autoregulation of araC
  131. 7.3 The trp Operon
  132. Tryptophan’s Role in Negative Control of the trp Operon
  133. Control of the trp Operon by Attenuation
  134. Defeating Attenuation
  135. 7.4 Riboswitches
  136. CHAPTER 8 Major Shifts in Bacterial Transcription
  137. 8.1 Sigma Factor Switching
  138. Phage Infection
  139. Sporulation
  140. Genes with Multiple Promoters
  141. Other σ Switches
  142. Anti-σ-Factors
  143. 8.2 The RNA Polymerase Encoded in Phage T7
  144. 8.3 Infection of E. coli by Phage λ
  145. Lytic Reproduction of Phage λ
  146. Establishing Lysogeny
  147. Autoregulation of the cI Gene During Lysogeny
  148. Determining the Fate of a λ Infection: Lysis or Lysogeny
  149. Lysogen Induction
  150. CHAPTER 9 DNA–Protein Interactions in Bacteria
  151. 9.1 The λ Family of Repressors
  152. Probing Binding Specificity by Site-Directed Mutagenesis
  153. Box 9.1 X-Ray Crystallography
  154. High-Resolution Analysis of λ Repressor–Operator Interactions
  155. High-Resolution Analysis of Phage 434 Repressor–Operator Interactions
  156. 9.2 The trp Repressor
  157. The Role of Tryptophan
  158. 9.3 General Considerations on Protein–DNA Interactions
  159. Hydrogen Bonding Capabilities of the Four Different Base Pairs
  160. The Importance of Multimeric DNA-Binding Proteins
  161. 9.4 DNA-Binding Proteins: Action at a Distance
  162. The gal Operon
  163. Duplicated λ Operators
  164. Enhancers
  165. PART IV Transcription in Eukaryotes
  166. CHAPTER 10 Eukaryotic RNA Polymerases and Their Promoters
  167. 10.1 Multiple Forms of Eukaryotic RNA Polymerase
  168. Separation of the Three Nuclear Polymerases
  169. The Roles of the Three RNA Polymerases
  170. RNA Polymerase Subunit Structures
  171. 10.2 Promoters
  172. Class II Promoters
  173. Class I Promoters
  174. Class III Promoters
  175. 10.3 Enhancers and Silencers
  176. Enhancers
  177. Silencers
  178. CHAPTER 11 General Transcription Factors in Eukaryotes
  179. 11.1 Class II Factors
  180. The Class II Preinitiation Complex
  181. Structure and Function of TFIID
  182. Structure and Function of TFIIB
  183. Structure and Function of TFIIH
  184. The Mediator Complex and the RNA Polymerase II Holoenzyme
  185. Elongation Factors
  186. 11.2 Class I Factors
  187. The Core-Binding Factor
  188. The UPE-Binding Factor
  189. Structure and Function of SL1
  190. 11.3 Class III Factors
  191. TFIIIA
  192. TFIIIB and C
  193. The Role of TBP
  194. CHAPTER 12 Transcription Activators in Eukaryotes
  195. 12.1 Categories of Activators
  196. DNA-Binding Domains
  197. Transcription-Activating Domains
  198. 12.2 Structures of the DNA-Binding Motifs of Activators
  199. Zinc Fingers
  200. The GAL4 Protein
  201. The Nuclear Receptors
  202. Homeodomains
  203. The bZIP and bHLH Domains
  204. 12.3 Independence of the Domains of Activators
  205. 12.4 Functions of Activators
  206. Recruitment of TFIID
  207. Recruitment of the Holoenzyme
  208. 12.5 Interaction Among Activators
  209. Dimerization
  210. Action at a Distance
  211. Box 12.1 Genomic Imprinting
  212. Transcription Factories
  213. Complex Enhancers
  214. Architectural Transcription Factors
  215. Enhanceosomes
  216. Insulators
  217. 12.6 Regulation of Transcription Factors
  218. Coactivators
  219. Activator Ubiquitylation
  220. Activator Sumoylation
  221. Activator Acetylation
  222. Signal Transduction Pathways
  223. CHAPTER 13 Chromatin Structure and Its Effects on Transcription
  224. 13.1 Chromatin Structure
  225. Histones
  226. Nucleosomes
  227. The 30-nm Fiber
  228. Higher-Order Chromatin Folding
  229. 13.3 Chromatin Structure and Gene Activity
  230. The Effects of Histones on Transcription of Class II Genes
  231. Nucleosome Positioning
  232. Histone Acetylation
  233. Histone Deacetylation
  234. Chromatin Remodeling
  235. Heterochromatin and Silencing
  236. Nucleosomes and Transcription Elongation
  237. PART V Post-Transcriptional Events
  238. CHAPTER 14 RNA Processing I: Splicing
  239. 14.1 Genes in Pieces
  240. Evidence for Split Genes
  241. RNA Splicing
  242. Splicing Signals
  243. Effect of Splicing on Gene Expression
  244. 14.2 The Mechanism of Splicing of Nuclear mRNA Precursors
  245. A Branched Intermediate
  246. A Signal at the Branch
  247. Spliceosomes
  248. Spliceosome Assembly and Function
  249. Commitment, Splice Site Selection, and Alternative Splicing
  250. Control of Splicing
  251. 14.3 Self-Splicing RNAs
  252. Group I Introns
  253. Group II Introns
  254. CHAPTER 15 RNA Processing II: Capping and Polyadenylation
  255. 15.1 Capping
  256. Cap Structure
  257. Cap Synthesis
  258. Functions of Caps
  259. 15.2 Polyadenylation
  260. Poly(A)
  261. Functions of Poly(A)
  262. Basic Mechanism of Polyadenylation
  263. Polyadenylation Signals
  264. Cleavage and Polyadenylation of a Pre-mRNA
  265. Poly(A) Polymerase
  266. Turnover of Poly(A)
  267. 15.3 Coordination of mRNA Processing Events
  268. Binding of the CTD of Rpb1 to mRNA-Processing Proteins
  269. Changes in Association of RNA-Processing Proteins with the CTD Correlate with Changes in CTD Phospho
  270. A CTD Code?
  271. Coupling Transcription Termination with mRNA 3′-End Processing
  272. Mechanism of Termination
  273. Role of Polyadenylation in mRNA Transport
  274. CHAPTER 16 Other RNA Processing Events and Post-Transcriptional Control of Gene Expression
  275. 16.1 Ribosomal RNA Processing
  276. Eukaryotic rRNA Processing
  277. Bacterial rRNA Processing
  278. 16.2 Transfer RNA Processing
  279. Cutting Apart Polycistronic Precursors
  280. Forming Mature 5′-Ends
  281. Forming Mature 3′-Ends
  282. 16.3 Trans-Splicing
  283. The Mechanism of Trans-Splicing
  284. 16.4 RNA Editing
  285. Mechanism of Editing
  286. Editing by Nucleotide Deamination
  287. 16.5 Post-Transcriptional Control of Gene Expression: mRNA Stability
  288. Casein mRNA Stability
  289. Transferrin Receptor mRNA Stability
  290. 16.6 Post-Transcriptional Control of Gene Expression: RNA Interference
  291. Mechanism of RNAi
  292. Amplification of siRNA
  293. Role of the RNAi Machinery in Heterochromatin Formation and Gene Silencing
  294. 16.7 Piwi-Interacting RNAs and Transposon Control
  295. 16.8 Post-Transcriptional Control of Gene Expression: MicroRNAs
  296. Silencing of Translation by miRNAs
  297. Stimulation of Translation by miRNAs
  298. 16.9 Translation Repression, mRNA Degradation, and P-Bodies
  299. Processing Bodies
  300. Degradation of mRNAs in P-Bodies
  301. Relief of Repression in P-Bodies
  302. Other Small RNAs
  303. PART VI Translation
  304. CHAPTER 17 The Mechanism of Translation I: Initiation
  305. 17.1 Initiation of Translation in Bacteria
  306. tRNA Charging
  307. Dissociation of Ribosomes
  308. Formation of the 30S Initiation Complex
  309. Formation of the 70S Initiation Complex
  310. Summary of Initiation in Bacteria
  311. 17.2 Initiation in Eukaryotes
  312. The Scanning Model of Initiation
  313. Eukaryotic Initiation Factors
  314. 17.3 Control of Initiation
  315. Bacterial Translational Control
  316. Eukaryotic Translational Control
  317. CHAPTER 18 The Mechanism of Translation II: Elongation and Termination
  318. 18.1 The Direction of Polypeptide Synthesis and of mRNA Translation
  319. 18.2 The Genetic Code
  320. Nonoverlapping Codons
  321. No Gaps in the Code
  322. The Triplet Code
  323. Breaking the Code
  324. Unusual Base Pairs Between Codon and Anticodon
  325. The (Almost) Universal Code
  326. 18.3 The Elongation Cycle
  327. Overview of Elongation
  328. A Three-Site Model of the Ribosome
  329. Elongation Step 1: Binding an Aminoacyl-tRNA to the A Site of the Ribosome
  330. Elongation Step 2: Peptide Bond Formation
  331. Elongation Step 3: Translocation
  332. G Proteins and Translation
  333. The Structures of EF-Tu and EF-G
  334. 18.4 Termination
  335. Termination Codons
  336. Stop Codon Suppression
  337. Release Factors
  338. Dealing with Aberrant Termination
  339. Use of Stop Codons to Insert Unusual Amino Acids
  340. 18.5 Posttranslation
  341. Folding Nascent Proteins
  342. Release of Ribosomes from mRNA
  343. CHAPTER 19 Ribosomes and Transfer RNA
  344. 19.1 Ribosomes
  345. Fine Structure of the 70S Ribosome
  346. Ribosome Composition
  347. Fine Structure of the 30S Subunit
  348. Fine Structure of the 50S Subunit
  349. Ribosome Structure and the Mechanism of Translation
  350. Polysomes
  351. 19.2 Transfer RNA
  352. The Discovery of tRNA
  353. tRNA Structure
  354. Recognition of tRNAs by Aminoacyl-tRNA Synthetase: The Second Genetic Code
  355. Proofreading and Editing by Aminoacyl-tRNA Synthetases
  356. PART VII DNA Replication, Recombination, and Transposition
  357. CHAPTER 20 DNA Replication, Damage, and Repair
  358. 20.1 General Features of DNA Replication
  359. Semiconservative Replication
  360. At Least Semidiscontinuous Replication
  361. Priming of DNA Synthesis
  362. Bidirectional Replication
  363. Rolling Circle Replication
  364. 20.2 Enzymology of DNA Replication
  365. Three DNA Polymerases in E. coli
  366. Fidelity of Replication
  367. Multiple Eukaryotic DNA Polymerases
  368. Strand Separation
  369. Single-Strand DNA-Binding Proteins
  370. Topoisomerases
  371. 20.3 DNA Damage and Repair
  372. Damage Caused by Alkylation of Bases
  373. Damage Caused by Ultraviolet Radiation
  374. Damage Caused by Gamma and X-Rays
  375. Directly Undoing DNA Damage
  376. Excision Repair
  377. Double-Strand Break Repair in Eukaryotes
  378. Mismatch Repair
  379. Failure of Mismatch Repair in Humans
  380. Coping with DNA Damage Without Repairing It
  381. CHAPTER 21 DNA Replication II: Detailed Mechanism
  382. 21.1 Initiation
  383. Priming in E. coli
  384. Priming in Eukaryotes
  385. 21.2 Elongation
  386. Speed of Replication
  387. The Pol III Holoenzyme and Processivity of Replication
  388. 21.3 Termination
  389. Decatenation: Disentangling Daughter DNAs
  390. Termination in Eukaryotes
  391. Box 21.1 Telomeres, the Hayflick Limit, and Cancer
  392. Telomere Structure and Telomere-Binding Proteins in Lower Eukaryotes
  393. CHAPTER 22 Homologous Recombination
  394. 22.1 The RecBCD Pathway for Homologous Recombination
  395. 22.2 Experimental Support for the RecBCD Pathway
  396. RecA
  397. RecBCD
  398. RuvA and RuvB
  399. RuvC
  400. 22.3 Meiotic Recombination
  401. The Mechanism of Meiotic Recombination: Overview
  402. The Double-Stranded DNA Break
  403. Creation of Single-Stranded Ends at DSBs
  404. 22.4 Gene Conversion
  405. CHAPTER 23 Transposition
  406. 23.1 Bacterial Transposons
  407. Discovery of Bacterial Transposons
  408. Insertion Sequences: The Simplest Bacterial Transposons
  409. More Complex Transposons
  410. Mechanisms of Transposition
  411. 23.2 Eukaryotic Transposons
  412. The First Examples of Transposable Elements: Ds and Ac of Maize
  413. P Elements
  414. 23.3 Rearrangement of Immunoglobulin Genes
  415. Recombination Signals
  416. The Recombinase
  417. Mechanism of V(D)J Recombination
  418. 23.4 Retrotransposons
  419. Retroviruses
  420. Retrotransposons
  421. PART VIII Genomes
  422. CHAPTER 24 Introduction to Genomics: DNA Sequencing on a Genomic Scale
  423. 24.1 Positional Cloning: An Introduction to Genomics
  424. Classical Tools of Positional Cloning
  425. Identifying the Gene Mutated in a Human Disease
  426. 24.2 Techniques in Genomic Sequencing
  427. The Human Genome Project
  428. Vectors for Large-Scale Genome Projects
  429. The Clone-by-Clone Strategy
  430. Shotgun Sequencing
  431. Sequencing Standards
  432. 24.3 Studying and Comparing Genomic Sequences
  433. The Human Genome
  434. Personal Genomics
  435. Other Vertebrate Genomes
  436. The Minimal Genome
  437. The Barcode of Life
  438. CHAPTER 25 Genomics II: Functional Genomics, Proteomics, and Bioinformatics
  439. 25.1 Functional Genomics: Gene Expression on a Genomic Scale
  440. Transcriptomics
  441. Genomic Functional Profiling
  442. Single-Nucleotide Polymorphisms: Pharmacogenomics
  443. 25.2 Proteomics
  444. Protein Separations
  445. Protein Analysis
  446. Quantitative Proteomics
  447. Protein Interactions
  448. 25.3 Bioinformatics
  449. Finding Regulatory Motifs in Mammalian Genomes
  450. Using the Databases Yourself
  451. Glossary
  452. Index

 

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