Lehninger Principles of Biochemistry 8th Edition David Nelson Test Bank

Author: David L. Nelson; Michael M. Cox
ISBN-10: 1319228003
ISBN-13: 9781319228002
ISBN-13:9781319322342
ISBN-13:9781319230906
Edition: 8th Edition

Lehninger Principles of Biochemistry 8th Edition Nelson Test Bank PDF

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Table of Contents

1. Chapter 1 The Foundations of Biochemistry
2. 1.1 Cellular Foundations
3. Cells Are the Structural and Functional Units of All Living Organisms
4. Cellular Dimensions Are Limited by Diffusion
5. Organisms Belong to Three Distinct Domains of Life
6. Organisms Differ Widely in Their Sources of Energy and Biosynthetic Precursors
7. Bacterial and Archaeal Cells Share Common Features but Differ in Important Ways
8. Eukaryotic Cells Have a Variety of Membranous Organelles, Which Can Be Isolated for Study
9. The Cytoplasm Is Organized by the Cytoskeleton and Is Highly Dynamic
10. Cells Build Supramolecular Structures
11. In Vitro Studies May Overlook Important Interactions among Molecules
12. 1.2 Chemical Foundations
13. Biomolecules Are Compounds of Carbon with a Variety of Functional Groups
14. Cells Contain a Universal Set of Small Molecules
15. Macromolecules Are the Major Constituents of Cells
16. Three-Dimensional Structure Is Described by Configuration and Conformation
17. Interactions between Biomolecules Are Stereospecific
18. 1.3 Physical Foundations
19. Living Organisms Exist in a Dynamic Steady State, Never at Equilibrium with Their Surroundings
20. Organisms Transform Energy and Matter from Their Surroundings
21. Creating and Maintaining Order Requires Work and Energy
22. Energy Coupling Links Reactions in Biology
23. K[eq] and ΔG° Are Measures of a Reaction’s Tendency to Proceed Spontaneously
24. Enzymes Promote Sequences of Chemical Reactions
25. Metabolism Is Regulated to Achieve Balance and Economy
26. 1.4 Genetic Foundations
27. Genetic Continuity Is Vested in Single DNA Molecules
28. The Structure of DNA Allows Its Replication and Repair with Near-Perfect Fidelity
29. The Linear Sequence in DNA Encodes Proteins with Three-Dimensional Structures
30. 1.5 Evolutionary Foundations
31. Changes in the Hereditary Instructions Allow Evolution
32. Biomolecules First Arose by Chemical Evolution
33. RNA or Related Precursors May Have Been the First Genes and Catalysts
34. Biological Evolution Began More Than Three and a Half Billion Years Ago
35. The First Cell Probably Used Inorganic Fuels
36. Eukaryotic Cells Evolved from Simpler Precursors in Several Stages
37. Molecular Anatomy Reveals Evolutionary Relationships
38. Functional Genomics Shows the Allocations of Genes to Specific Cellular Processes
39. Genomic Comparisons Have Increasing Importance in Medicine
40. Chapter Review
41. Key Terms
42. Problems
43. Part I Structure and Catalysis
44. Chapter 2 Water, The Solvent of Life
45. 2.1 Weak Interactions in Aqueous Systems
46. Hydrogen Bonding Gives Water Its Unusual Properties
47. Water Forms Hydrogen Bonds with Polar Solutes
48. Water Interacts Electrostatically with Charged Solutes
49. Nonpolar Gases Are Poorly Soluble in Water
50. Nonpolar Compounds Force Energetically Unfavorable Changes in the Structure of Water
51. van der Waals Interactions Are Weak Interatomic Attractions
52. Weak Interactions Are Crucial to Macromolecular Structure and Function
53. Concentrated Solutes Produce Osmotic Pressure
54. 2.2 Ionization of Water, Weak Acids, and Weak Bases
55. Pure Water Is Slightly Ionized
56. The Ionization of Water Is Expressed by an Equilibrium Constant
57. The pH Scale Designates the H[+] and H[−] Concentrations
58. Weak Acids and Bases Have Characteristic Acid Dissociation Constants
59. Titration Curves Reveal the p[Ka] of Weak Acids
60. 2.3 Buffering against pH Changes in Biological Systems
61. Buffers Are Mixtures of Weak Acids and Their Conjugate Bases
62. The Henderson-Hasselbalch Equation Relates pH, p[Ka], and Buffer Concentration
63. Weak Acids or Bases Buffer Cells and Tissues against pH Changes
64. Untreated Diabetes Produces Life-Threatening Acidosis
65. Chapter Review
66. Key Terms
67. Problems
68. Chapter 3 Amino Acids, Peptides, and Proteins
69. 3.1 Amino Acids
70. Amino Acids Share Common Structural Features
71. The Amino Acid Residues in Proteins Are L Stereoisomers
72. Amino Acids Can Be Classified by R Group
73. Uncommon Amino Acids Also Have Important Functions
74. Amino Acids Can Act as Acids and Bases
75. Amino Acids Differ in Their Acid-Base Properties
76. 3.2 Peptides and Proteins
77. Peptides Are Chains of Amino Acids
78. Peptides Can Be Distinguished by Their Ionization Behavior
79. Biologically Active Peptides and Polypeptides Occur in a Vast Range of Sizes and Compositions
80. Some Proteins Contain Chemical Groups Other Than Amino Acids
81. 3.3 Working with Proteins
82. Proteins Can Be Separated and Purified
83. Proteins Can Be Separated and Characterized by Electrophoresis
84. Unseparated Proteins Are Detected and Quantified Based on Their Functions
85. 3.4 The Structure of Proteins: Primary Structure
86. The Function of a Protein Depends on Its Amino Acid Sequence
87. Protein Structure Is Studied Using Methods That Exploit Protein Chemistry
88. Mass Spectrometry Provides Information on Molecular Mass, Amino Acid Sequence, and Entire Proteomes
89. Small Peptides and Proteins Can Be Chemically Synthesized
90. Amino Acid Sequences Provide Important Biochemical Information
91. Protein Sequences Help Elucidate the History of Life on Earth
92. Chapter Review
93. Key Terms
94. Problems
95. Chapter 4 The Three-Dimensional Structure of Proteins
96. 4.1 Overview of Protein Structure
97. A Protein’s Conformation Is Stabilized Largely by Weak Interactions
98. Packing of Hydrophobic Amino Acids Away from Water Favors Protein Folding
99. Polar Groups Contribute Hydrogen Bonds and Ion Pairs to Protein Folding
100. Individual van der Waals Interactions Are Weak but Combine to Promote Folding
101. The Peptide Bond Is Rigid and Planar
102. 4.2 Protein Secondary Structure
103. The α Helix Is a Common Protein Secondary Structure
104. Amino Acid Sequence Affects Stability of the α Helix
105. The β Conformation Organizes Polypeptide Chains into Sheets
106. β Turns Are Common in Proteins
107. Common Secondary Structures Have Characteristic Dihedral Angles
108. Common Secondary Structures Can Be Assessed by Circular Dichroism
109. 4.3 Protein Tertiary and Quaternary Structures
110. Fibrous Proteins Are Adapted for a Structural Function
111. Structural Diversity Reflects Functional Diversity in Globular Proteins
112. Myoglobin Provided Early Clues about the Complexity of Globular Protein Structure
113. Globular Proteins Have a Variety of Tertiary Structures
114. Some Proteins or Protein Segments Are Intrinsically Disordered
115. Protein Motifs Are the Basis for Protein Structural Classification
116. Protein Quaternary Structures Range from Simple Dimers to Large Complexes
117. 4.4 Protein Denaturation and Folding
118. Loss of Protein Structure Results in Loss of Function
119. Amino Acid Sequence Determines Tertiary Structure
120. Polypeptides Fold Rapidly by a Stepwise Process
121. Some Proteins Undergo Assisted Folding
122. Defects in Protein Folding Are the Molecular Basis for Many Human Genetic Disorders
123. 4.5 Determination of Protein and Biomolecular Structures
124. X-ray Diffraction Produces Electron Density Maps from Protein Crystals
125. Distances between Protein Atoms Can Be Measured by Nuclear Magnetic Resonance
126. Thousands of Individual Molecules Are Used to Determine Structures by Cryo-Electron Microscopy
127. Chapter Review
128. Key Terms
129. Problems
130. Chapter 5 Protein Function
131. 5.1 Reversible Binding of a Protein to a Ligand: Oxygen-Binding Proteins
132. Oxygen Can Bind to a Heme Prosthetic Group
133. Globins Are a Family of Oxygen-Binding Proteins
134. Myoglobin Has a Single Binding Site for Oxygen
135. Protein-Ligand Interactions Can Be Described Quantitatively
136. Protein Structure Affects How Ligands Bind
137. Hemoglobin Transports Oxygen in Blood
138. Hemoglobin Subunits Are Structurally Similar to Myoglobin
139. Hemoglobin Undergoes a Structural Change on Binding Oxygen
140. Hemoglobin Binds Oxygen Cooperatively
141. Cooperative Ligand Binding Can Be Described Quantitatively
142. Two Models Suggest Mechanisms for Cooperative Binding
143. Hemoglobin Also Transports H[+] and CO[2]
144. Oxygen Binding to Hemoglobin Is Regulated by 2,3-Bisphosphoglycerate
145. Sickle Cell Anemia Is a Molecular Disease of Hemoglobin
146. 5.2 Complementary Interactions between Proteins and Ligands: The Immune System and Immunoglobulins
147. The Immune Response Includes a Specialized Array of Cells and Proteins
148. Antibodies Have Two Identical Antigen-Binding Sites
149. Antibodies Bind Tightly and Specifically to Antigen
150. The Antibody-Antigen Interaction Is the Basis for a Variety of Important Analytical Procedures
151. 5.3 Protein Interactions Modulated by Chemical Energy: Actin, Myosin, and Molecular Motors
152. The Major Proteins of Muscle Are Myosin and Actin
153. Additional Proteins Organize the Thin and Thick Filaments into Ordered Structures
154. Myosin Thick Filaments Slide along Actin Thin Filaments
155. Chapter Review
156. Key Terms
157. Problems
158. Chapter 6 Enzymes
159. 6.1 An Introduction to Enzymes
160. Most Enzymes Are Proteins
161. Enzymes Are Classified by the Reactions They Catalyze
162. 6.2 How Enzymes Work
163. Enzymes Affect Reaction Rates, Not Equilibria
164. Reaction Rates and Equilibria Have Precise Thermodynamic Definitions
165. A Few Principles Explain the Catalytic Power and Specificity of Enzymes
166. Noncovalent Interactions between Enzyme and Substrate Are Optimized in the Transition State
167. Covalent Interactions and Metal Ions Contribute to Catalysis
168. 6.3 Enzyme Kinetics as an Approach to Understanding Mechanism
169. Substrate Concentration Affects the Rate of Enzyme-Catalyzed Reactions
170. The Relationship between Substrate Concentration and Reaction Rate Can Be Expressed with the Michaelis-Menten Equation
171. Michaelis-Menten Kinetics Can Be Analyzed Quantitatively
172. Kinetic Parameters Are Used to Compare Enzyme Activities
173. Many Enzymes Catalyze Reactions with Two or More Substrates
174. Enzyme Activity Depends on pH
175. Pre–Steady State Kinetics Can Provide Evidence for Specific Reaction Steps
176. Enzymes Are Subject to Reversible or Irreversible Inhibition
177. 6.4 Examples of Enzymatic Reactions
178. The Chymotrypsin Mechanism Involves Acylation and Deacylation of a Ser Residue
179. An Understanding of Protease Mechanisms Leads to New Treatments for HIV Infection
180. Hexokinase Undergoes Induced Fit on Substrate Binding
181. The Enolase Reaction Mechanism Requires Metal Ions
182. An Understanding of Enzyme Mechanism Produces Useful Antibiotics
183. 6.5 Regulatory Enzymes
184. Allosteric Enzymes Undergo Conformational Changes in Response to Modulator Binding
185. The Kinetic Properties of Allosteric Enzymes Diverge from Michaelis-Menten Behavior
186. Some Enzymes Are Regulated by Reversible Covalent Modification
187. Phosphoryl Groups Affect the Structure and Catalytic Activity of Enzymes
188. Multiple Phosphorylations Allow Exquisite Regulatory Control
189. Some Enzymes and Other Proteins Are Regulated by Proteolytic Cleavage of an Enzyme Precursor
190. A Cascade of Proteolytically Activated Zymogens Leads to Blood Coagulation
191. Some Regulatory Enzymes Use Several Regulatory Mechanisms
192. Chapter Review
193. Key Terms
194. Problems
195. Chapter 7 Carbohydrates and Glycobiology
196. 7.1 Monosaccharides and Disaccharides
197. The Two Families of Monosaccharides Are Aldoses and Ketoses
198. Monosaccharides Have Asymmetric Centers
199. The Common Monosaccharides Have Cyclic Structures
200. Organisms Contain a Variety of Hexose Derivatives
201. Sugars That Are, or Can Form, Aldehydes Are Reducing Sugars
202. 7.2 Polysaccharides
203. Some Homopolysaccharides Are Storage Forms of Fuel
204. Some Homopolysaccharides Serve Structural Roles
205. Steric Factors and Hydrogen Bonding Influence Homopolysaccharide Folding
206. Peptidoglycan Reinforces the Bacterial Cell Wall
207. Glycosaminoglycans Are Heteropolysaccharides of the Extracellular Matrix
208. 7.3 Glycoconjugates: Proteoglycans, Glycoproteins, and Glycolipids
209. Proteoglycans Are Glycosaminoglycan-Containing Macromolecules of the Cell Surface and Extracellular Matrix
210. Glycoproteins Have Covalently Attached Oligosaccharides
211. Glycolipids and Lipopolysaccharides Are Membrane Components
212. 7.4 Carbohydrates as Informational Molecules: The Sugar Code
213. Oligosaccharide Structures Are Information-Dense
214. Lectins Are Proteins That Read the Sugar Code and Mediate Many Biological Processes
215. Lectin-Carbohydrate Interactions Are Highly Specific and Often Multivalent
216. 7.5 Working with Carbohydrates
217. Chapter Review
218. Key Terms
219. Problems
220. Chapter 8 Nucleotides and Nucleic Acids
221. 8.1 Some Basic Definitions and Conventions
222. Nucleotides and Nucleic Acids Have Characteristic Bases and Pentoses
223. Phosphodiester Bonds Link Successive Nucleotides in Nucleic Acids
224. The Properties of Nucleotide Bases Affect the Three-Dimensional Structure of Nucleic Acids
225. 8.2 Nucleic Acid Structure
226. DNA Is a Double Helix That Stores Genetic Information
227. DNA Can Occur in Different Three-Dimensional Forms
228. Certain DNA Sequences Adopt Unusual Structures
229. Messenger RNAs Code for Polypeptide Chains
230. Many RNAs Have More Complex Three-Dimensional Structures
231. 8.3 Nucleic Acid Chemistry
232. Double-Helical DNA and RNA Can Be Denatured
233. Nucleotides and Nucleic Acids Undergo Nonenzymatic Transformations
234. Some Bases of DNA Are Methylated
235. The Chemical Synthesis of DNA Has Been Automated
236. Gene Sequences Can Be Amplified with the Polymerase Chain Reaction
237. The Sequences of Long DNA Strands Can Be Determined
238. DNA Sequencing Technologies Are Advancing Rapidly
239. 8.4 Other Functions of Nucleotides
240. Nucleotides Carry Chemical Energy in Cells
241. Adenine Nucleotides Are Components of Many Enzyme Cofactors
242. Some Nucleotides Are Regulatory Molecules
243. Adenine Nucleotides Also Serve as Signals
244. Chapter Review
245. Key Terms
246. Problems
247. Chapter 9 DNA-Based Information Technologies
248. 9.1 Studying Genes and Their Products
249. Genes Can Be Isolated by DNA Cloning
250. Restriction Endonucleases and DNA Ligases Yield Recombinant DNA
251. Cloning Vectors Allow Amplification of Inserted DNA Segments
252. Cloned Genes Can Be Expressed to Amplify Protein Production
253. Many Different Systems Are Used to Express Recombinant Proteins
254. Alteration of Cloned Genes Produces Altered Proteins
255. Terminal Tags Provide Handles for Affinity Purification
256. The Polymerase Chain Reaction Offers Many Options for Cloning Experiments
257. DNA Libraries Are Specialized Catalogs of Genetic Information
258. 9.2 Exploring Protein Function on the Scale of Cells or Whole Organisms
259. Sequence or Structural Relationships Can Suggest Protein Function
260. When and Where a Protein Is Present in a Cell Can Suggest Protein Function
261. Knowing What a Protein Interacts with Can Suggest Its Function
262. The Effect of Deleting or Altering a Protein Can Suggest Its Function
263. Many Proteins Are Still Undiscovered
264. 9.3 Genomics and the Human Story
265. The Human Genome Contains Many Types of Sequences
266. Genome Sequencing Informs Us about Our Humanity
267. Genome Comparisons Help Locate Genes Involved in Disease
268. Genome Sequences Inform Us about Our Past and Provide Opportunities for the Future
269. Chapter Review
270. Key Terms
271. Problems
272. Chapter 10 Lipids
273. 10.1 Storage Lipids
274. Fatty Acids Are Hydrocarbon Derivatives
275. Triacylglycerols Are Fatty Acid Esters of Glycerol
276. Triacylglycerols Provide Stored Energy and Insulation
277. Partial Hydrogenation of Cooking Oils Improves Their Stability but Creates Fatty Acids with Harmful Health Effects
278. Waxes Serve as Energy Stores and Water Repellents
279. 10.2 Structural Lipids in Membranes
280. Glycerophospholipids Are Derivatives of Phosphatidic Acid
281. Some Glycerophospholipids Have Ether-Linked Fatty Acids
282. Galactolipids of Plants and Ether-Linked Lipids of Archaea Are Environmental Adaptations
283. Sphingolipids Are Derivatives of Sphingosine
284. Sphingolipids at Cell Surfaces Are Sites of Biological Recognition
285. Phospholipids and Sphingolipids Are Degraded in Lysosomes
286. Sterols Have Four Fused Carbon Rings
287. 10.3 Lipids as Signals, Cofactors, and Pigments
288. Phosphatidylinositols and Sphingosine Derivatives Act as Intracellular Signals
289. Eicosanoids Carry Messages to Nearby Cells
290. Steroid Hormones Carry Messages between Tissues
291. Vascular Plants Produce Thousands of Volatile Signals
292. Vitamins A and D Are Hormone Precursors
293. Vitamins E and K and the Lipid Quinones Are Oxidation-Reduction Cofactors
294. Dolichols Activate Sugar Precursors for Biosynthesis
295. Many Natural Pigments Are Lipidic Conjugated Dienes
296. Polyketides Are Natural Products with Potent Biological Activities
297. 10.4 Working with Lipids
298. Lipid Extraction Requires Organic Solvents
299. Adsorption Chromatography Separates Lipids of Different Polarity
300. Gas Chromatography Resolves Mixtures of Volatile Lipid Derivatives
301. Specific Hydrolysis Aids in Determination of Lipid Structure
302. Mass Spectrometry Reveals Complete Lipid Structure
303. Lipidomics Seeks to Catalog All Lipids and Their Functions
304. Chapter Review
305. Key Terms
306. Problems
307. Chapter 11 Biological Membranes and Transport
308. 11.1 The Composition and Architecture of Membranes
309. The Lipid Bilayer Is Stable in Water
310. Bilayer Architecture Underlies the Structure and Function of Biological Membranes
311. The Endomembrane System Is Dynamic and Functionally Differentiated
312. Membrane Proteins Are Receptors, Transporters, and Enzymes
313. Membrane Proteins Differ in the Nature of Their Association with the Membrane Bilayer
314. The Topology of an Integral Membrane Protein Can Often Be Predicted from Its Sequence
315. Covalently Attached Lipids Anchor or Direct Some Membrane Proteins
316. 11.2 Membrane Dynamics
317. Acyl Groups in the Bilayer Interior Are Ordered to Varying Degrees
318. Transbilayer Movement of Lipids Requires Catalysis
319. Lipids and Proteins Diffuse Laterally in the Bilayer
320. Sphingolipids and Cholesterol Cluster Together in Membrane Rafts
321. Membrane Curvature and Fusion Are Central to Many Biological Processes
322. Integral Proteins of the Plasma Membrane Are Involved in Surface Adhesion, Signaling, and Other Cellular Processes
323. 11.3 Solute Transport across Membranes
324. Transport May Be Passive or Active
325. Transporters and Ion Channels Share Some Structural Properties but Have Different Mechanisms
326. The Glucose Transporter of Erythrocytes Mediates Passive Transport
327. The Chloride-Bicarbonate Exchanger Catalyzes Electroneutral Cotransport of Anions across the Plasma Membrane
328. Active Transport Results in Solute Movement against a Concentration or Electrochemical Gradient
329. P-Type ATPases Undergo Phosphorylation during Their Catalytic Cycles
330. V-Type and F-Type ATPases Are ATP-Driven Proton Pumps
331. ABC Transporters Use ATP to Drive the Active Transport of a Wide Variety of Substrates
332. Ion Gradients Provide the Energy for Secondary Active Transport
333. Aquaporins Form Hydrophilic Transmembrane Channels for the Passage of Water
334. Ion-Selective Channels Allow Rapid Movement of Ions across Membranes
335. The Structure of a K[+] Channel Reveals the Basis for Its Specificity
336. Chapter Review
337. Key Terms
338. Problems
339. Chapter 12 Biochemical Signaling
340. 12.1 General Features of Signal Transduction
341. Signal-Transducing Systems Share Common Features
342. The General Process of Signal Transduction in Animals Is Universal
343. 12.2 G Protein–Coupled Receptors and Second Messengers
344. The β-Adrenergic Receptor System Acts through the Second Messenger cAMP
345. Cyclic AMP Activates Protein Kinase A
346. Several Mechanisms Cause Termination of the β-Adrenergic Response
347. The β-Adrenergic Receptor Is Desensitized by Phosphorylation and by Association with Arrestin
348. Cyclic AMP Acts as a Second Messenger for Many Regulatory Molecules
349. G Proteins Act as Self-Limiting Switches in Many Processes
350. Diacylglycerol, Inositol Trisphosphate, and Ca2+ Have Related Roles as Second Messengers
351. Calcium Is a Second Messenger That Is Limited in Space and Time
352. 12.3 GPCRs in Vision, Olfaction, and Gustation
353. The Vertebrate Eye Uses Classic GPCR Mechanisms
354. Vertebrate Olfaction and Gustation Use Mechanisms Similar to the Visual System
355. All GPCR Systems Share Universal Features
356. 12.4 Receptor Tyrosine Kinases
357. Stimulation of the Insulin Receptor Initiates a Cascade of Protein Phosphorylation Reactions
358. The Membrane Phospholipid PIP3 Functions at a Branch in Insulin Signaling
359. Cross Talk among Signaling Systems Is Common and Complex
360. 12.5 Multivalent Adaptor Proteins and Membrane Rafts
361. Protein Modules Bind Phosphorylated Tyr, Ser, or Thr Residues in Partner Proteins
362. Membrane Rafts and Caveolae Segregate Signaling Proteins
363. 12.6 Gated Ion Channels
364. Ion Channels Underlie Rapid Electrical Signaling in Excitable Cells
365. Voltage-Gated Ion Channels Produce Neuronal Action Potentials
366. Neurons Have Receptor Channels That Respond to Different Neurotransmitters
367. Toxins Target Ion Channels
368. 12.7 Regulation of Transcription by Nuclear Hormone Receptors
369. 12.8 Regulation of the Cell Cycle by Protein Kinases
370. The Cell Cycle Has Four Stages
371. Levels of Cyclin-Dependent Protein Kinases Oscillate
372. CDKs Are Regulated by Phosphorylation, Cyclin Degradation, Growth Factors, and Specific Inhibitors
373. CDKs Regulate Cell Division by Phosphorylating Critical Proteins
374. 12.9 Oncogenes, Tumor Suppressor Genes, and Programmed Cell Death
375. Oncogenes Are Mutant Forms of the Genes for Proteins That Regulate the Cell Cycle
376. Defects in Certain Genes Remove Normal Restraints on Cell Division
377. Apoptosis Is Programmed Cell Suicide
378. Chapter Review
379. Key Terms
380. Problems
381. Part II Bioenergetics and Metabolism
382. Chapter 13 Introduction to Metabolism
383. 13.1 Bioenergetics and Thermodynamics
384. Biological Energy Transformations Obey the Laws of Thermodynamics
385. Standard Free-Energy Change Is Directly Related to the Equilibrium Constant
386. Actual Free-Energy Changes Depend on Reactant and Product Concentrations
387. Standard Free-Energy Changes Are Additive
388. 13.2 Chemical Logic and Common Biochemical Reactions
389. Biochemical Reactions Occur in Repeating Patterns
390. Biochemical and Chemical Equations Are Not Identical
391. 13.3 Phosphoryl Group Transfers and ATP
392. The Free-Energy Change for ATP Hydrolysis Is Large and Negative
393. Other Phosphorylated Compounds and Thioesters Also Have Large, Negative Free Energies of Hydrolysis
394. ATP Provides Energy by Group Transfers, Not by Simple Hydrolysis
395. ATP Donates Phosphoryl, Pyrophosphoryl, and Adenylyl Groups
396. Assembly of Informational Macromolecules Requires Energy
397. Transphosphorylations between Nucleotides Occur in All Cell Types
398. 13.4 Biological Oxidation-Reduction Reactions
399. The Flow of Electrons Can Do Biological Work
400. Oxidation-Reductions Can Be Described as Half-Reactions
401. Biological Oxidations Often Involve Dehydrogenation
402. Reduction Potentials Measure Affinity for Electrons
403. Standard Reduction Potentials Can Be Used to Calculate Free-Energy Change
404. A Few Types of Coenzymes and Proteins Serve as Universal Electron Carriers
405. NAD Has Important Functions in Addition to Electron Transfer
406. Flavin Nucleotides Are Tightly Bound in Flavoproteins
407. 13.5 Regulation of Metabolic Pathways
408. Cells and Organisms Maintain a Dynamic Steady State
409. Both the Amount and the Catalytic Activity of an Enzyme Can Be Regulated
410. Reactions Far from Equilibrium in Cells Are Common Points of Regulation
411. Adenine Nucleotides Play Special Roles in Metabolic Regulation
412. Chapter Review
413. Key Terms
414. Problems
415. Chapter 14 Glycolysis, Gluconeogenesis, and the Pentose Phosphate Pathway
416. 14.1 Glycolysis
417. An Overview: Glycolysis Has Two Phases
418. The Preparatory Phase of Glycolysis Requires ATP
419. The Payoff Phase of Glycolysis Yields ATP and NADH
420. The Overall Balance Sheet Shows a Net Gain of Two ATP and Two NADH Per Glucose
421. 14.2 Feeder Pathways for Glycolysis
422. Endogenous Glycogen and Starch Are Degraded by Phosphorolysis
423. Dietary Polysaccharides and Disaccharides Undergo Hydrolysis to Monosaccharides
424. 14.3 Fates of Pyruvate
425. The Pasteur and Warburg Effects Are Due to Dependence on Glycolysis Alone for ATP Production
426. Pyruvate Is the Terminal Electron Acceptor in Lactic Acid Fermentation
427. Ethanol Is the Reduced Product in Ethanol Fermentation
428. Fermentations Produce Some Common Foods and Industrial Chemicals
429. 14.4 Gluconeogenesis
430. The First Bypass: Conversion of Pyruvate to Phosphoenolpyruvate Requires Two Exergonic Reactions
431. The Second and Third Bypasses Are Simple Dephosphorylations by Phosphatases
432. Gluconeogenesis Is Energetically Expensive, But Essential
433. Mammals Cannot Convert Fatty Acids to Glucose; Plants and Microorganisms Can
434. 14.5 Coordinated Regulation of Glycolysis and Gluconeogenesis
435. Hexokinase Isozymes Are Affected Differently by Their Product, Glucose 6-Phosphate
436. Phosphofructokinase-1 and Fructose 1,6-Bisphosphatase Are Reciprocally Regulated
437. Fructose 2,6-Bisphosphate Is a Potent Allosteric Regulator of PFK-1 and FBPase-1
438. Xylulose 5-Phosphate Is a Key Regulator of Carbohydrate and Fat Metabolism
439. The Glycolytic Enzyme Pyruvate Kinase Is Allosterically Inhibited by ATP
440. Conversion of Pyruvate to Phosphoenolpyruvate Is Stimulated When Fatty Acids Are Available
441. Transcriptional Regulation Changes the Number of Enzyme Molecules
442. 14.6 Pentose Phosphate Pathway of Glucose Oxidation
443. The Oxidative Phase Produces NADPH and Pentose Phosphates
444. The Nonoxidative Phase Recycles Pentose Phosphates to Glucose 6-Phosphate
445. Glucose 6-Phosphate Is Partitioned between Glycolysis and the Pentose Phosphate Pathway
446. Thiamine Deficiency Causes Beriberi and Wernicke-Korsakoff Syndrome
447. Chapter Review
448. Key Terms
449. Problems
450. Chapter 15 The Metabolism of Glycogen in Animals
451. 15.1 The Structure and Function of Glycogen
452. Vertebrate Animals Require a Ready Fuel Source for Brain and Muscle
453. Glycogen Granules Have Many Tiers of Branched Chains of d-Glucose
454. 15.2 Breakdown and Synthesis of Glycogen
455. Glycogen Breakdown Is Catalyzed by Glycogen Phosphorylase
456. Glucose 1-Phosphate Can Enter Glycolysis or, in Liver, Replenish Blood Glucose
457. The Sugar Nucleotide UDP-Glucose Donates Glucose for Glycogen Synthesis
458. Glycogenin Primes the Initial Sugar Residues in Glycogen
459. 15.3 Coordinated Regulation of Glycogen Breakdown and Synthesis
460. Glycogen Phosphorylase Is Regulated by Hormone-Stimulated Phosphorylation and by Allosteric Effectors
461. Glycogen Synthase Also Is Subject to Multiple Levels of Regulation
462. Allosteric and Hormonal Signals Coordinate Carbohydrate Metabolism Globally
463. Carbohydrate and Lipid Metabolism Are Integrated by Hormonal and Allosteric Mechanisms
464. Chapter Review
465. Key Terms
466. Problems
467. Chapter 16 The Citric Acid Cycle
468. 16.1 Production of Acetyl-CoA (Activated Acetate)
469. Pyruvate Is Oxidized to Acetyl-CoA and CO2
470. The PDH Complex Employs Three Enzymes and Five Coenzymes to Oxidize Pyruvate
471. The PDH Complex Channels Its Intermediates through Five Reactions
472. 16.2 Reactions of the Citric Acid Cycle
473. The Sequence of Reactions in the Citric Acid Cycle Makes Chemical Sense
474. The Citric Acid Cycle Has Eight Steps
475. The Energy of Oxidations in the Cycle Is Efficiently Conserved
476. 16.3 The Hub of Intermediary Metabolism
477. The Citric Acid Cycle Serves in Both Catabolic and Anabolic Processes
478. Anaplerotic Reactions Replenish Citric Acid Cycle Intermediates
479. Biotin in Pyruvate Carboxylase Carries One-Carbon (CO2) Groups
480. 16.4 Regulation of the Citric Acid Cycle
481. Production of Acetyl-CoA by the PDH Complex Is Regulated by Allosteric and Covalent Mechanisms
482. The Citric Acid Cycle Is Also Regulated at Three Exergonic Steps
483. Citric Acid Cycle Activity Changes in Tumors
484. Certain Intermediates Are Channeled through Metabolons
485. Chapter Review
486. Key Terms
487. Problems
488. Chapter 17 Fatty Acid Catabolism
489. 17.1 Digestion, Mobilization, and Transport of Fats
490. Dietary Fats Are Absorbed in the Small Intestine
491. Hormones Trigger Mobilization of Stored Triacylglycerols
492. Fatty Acids Are Activated and Transported into Mitochondria
493. 17.2 Oxidation of Fatty Acids
494. The β Oxidation of Saturated Fatty Acids Has Four Basic Steps
495. The Four β-Oxidation Steps Are Repeated to Yield Acetyl-CoA and ATP
496. Acetyl-CoA Can Be Further Oxidized in the Citric Acid Cycle
497. Oxidation of Unsaturated Fatty Acids Requires Two Additional Reactions
498. Complete Oxidation of Odd-Number Fatty Acids Requires Three Extra Reactions
499. Fatty Acid Oxidation Is Tightly Regulated
500. Transcription Factors Turn on the Synthesis of Proteins for Lipid Catabolism
501. Genetic Defects in Fatty Acyl–CoA Dehydrogenases Cause Serious Disease
502. Peroxisomes Also Carry Out β Oxidation
503. Phytanic Acid Undergoes α Oxidation in Peroxisomes
504. 17.3 Ketone Bodies
505. Ketone Bodies, Formed in the Liver, Are Exported to Other Organs as Fuel
506. Ketone Bodies Are Overproduced in Diabetes and during Starvation
507. Chapter Review
508. Key Terms
509. Problems
510. Chapter 18 Amino Acid Oxidation and the Production of Urea
511. 18.1 Metabolic Fates of Amino Groups
512. Dietary Protein Is Enzymatically Degraded to Amino Acids
513. Pyridoxal Phosphate Participates in the Transfer of α-Amino Groups to α-Ketoglutarate
514. Glutamate Releases Its Amino Group as Ammonia in the Liver
515. Glutamine Transports Ammonia in the Bloodstream
516. Alanine Transports Ammonia from Skeletal Muscles to the Liver
517. Ammonia Is Toxic to Animals
518. 18.2 Nitrogen Excretion and the Urea Cycle
519. Urea Is Produced from Ammonia in Five Enzymatic Steps
520. The Citric Acid and Urea Cycles Can Be Linked
521. The Activity of the Urea Cycle Is Regulated at Two Levels
522. Pathway Interconnections Reduce the Energetic Cost of Urea Synthesis
523. Genetic Defects in the Urea Cycle Can Be Life-Threatening
524. 18.3 Pathways of Amino Acid Degradation
525. Some Amino Acids Can Contribute to Gluconeogenesis, Others to Ketone Body Formation
526. Several Enzyme Cofactors Play Important Roles in Amino Acid Catabolism
527. Six Amino Acids Are Degraded to Pyruvate
528. Seven Amino Acids Are Degraded to Acetyl-CoA
529. Phenylalanine Catabolism Is Genetically Defective in Some People
530. Five Amino Acids Are Converted to -Ketoglutarate
531. Four Amino Acids Are Converted to Succinyl-CoA
532. Branched-Chain Amino Acids Are Not Degraded in the Liver
533. Asparagine and Aspartate Are Degraded to Oxaloacetate
534. Chapter Review
535. Key Terms
536. Problems
537. Chapter 19 Oxidative Phosphorylation
538. 19.1 The Mitochondrial Respiratory Chain
539. Electrons Are Funneled to Universal Electron Acceptors
540. Electrons Pass through a Series of Membrane-Bound Carriers
541. Electron Carriers Function in Multienzyme Complexes
542. Mitochondrial Complexes Associate in Respirasomes
543. Other Pathways Donate Electrons to the Respiratory Chain via Ubiquinone
544. The Energy of Electron Transfer Is Efficiently Conserved in a Proton Gradient
545. Reactive Oxygen Species Are Generated during Oxidative Phosphorylation
546. 19.2 ATP Synthesis
547. In the Chemiosmotic Model, Oxidation and Phosphorylation Are Obligately Coupled
548. ATP Synthase Has Two Functional Domains, F[0] and F[1]
549. ATP Is Stabilized Relative to ADP on the Surface of F[1]
550. The Proton Gradient Drives the Release of ATP from the Enzyme Surface
551. Each β Subunit of ATP Synthase Can Assume Three Different Conformations
552. Rotational Catalysis Is Key to the Binding-Change Mechanism for ATP Synthesis
553. Chemiosmotic Coupling Allows Nonintegral Stoichiometries of O[2] Consumption and ATP Synthesis
554. The Proton-Motive Force Energizes Active Transport
555. Shuttle Systems Indirectly Convey Cytosolic NADH into Mitochondria for Oxidation
556. 19.3 Regulation of Oxidative Phosphorylation
557. Oxidative Phosphorylation Is Regulated by Cellular Energy Needs
558. An Inhibitory Protein Prevents ATP Hydrolysis during Hypoxia
559. Hypoxia Leads to ROS Production and Several Adaptive Responses
560. ATP-Producing Pathways Are Coordinately Regulated
561. 19.4 Mitochondria in Thermogenesis, Steroid Synthesis, and Apoptosis
562. Uncoupled Mitochondria in Brown Adipose Tissue Produce Heat
563. Mitochondrial P-450 Monooxygenases Catalyze Steroid Hydroxylations
564. Mitochondria Are Central to the Initiation of Apoptosis
565. 19.5 Mitochondrial Genes: Their Origin and the Effects of Mutations
566. Mitochondria Evolved from Endosymbiotic Bacteria
567. Mutations in Mitochondrial DNA Accumulate throughout the Life of the Organism
568. Some Mutations in Mitochondrial Genomes Cause Disease
569. A Rare Form of Diabetes Results from Defects in the Mitochondria of Pancreatic β Cells
570. Chapter Review
571. Key Terms
572. Problems
573. Chapter 20 Photosynthesis and Carbohydrate Synthesis in Plants
574. 20.1 Light Absorption
575. Chloroplasts Are the Site of Light-Driven Electron Flow and Photosynthesis in Plants
576. Chlorophylls Absorb Light Energy for Photosynthesis
577. Chlorophylls Funnel Absorbed Energy to Reaction Centers by Exciton Transfer
578. 20.2 Photochemical Reaction Centers
579. Photosynthetic Bacteria Have Two Types of Reaction Center
580. In Vascular Plants, Two Reaction Centers Act in Tandem
581. The Cytochrome b[6]f Complex Links Photosystems II and I, Conserving the Energy of Electron Transfer
582. Cyclic Electron Transfer Allows Variation in the Ratio of ATP/NADPH Synthesized
583. State Transitions Change the Distribution of LHCII between the Two Photosystems
584. Water Is Split at the Oxygen-Evolving Center
585. 20.3 Evolution of a Universal Mechanism for ATP Synthesis
586. A Proton Gradient Couples Electron Flow and Phosphorylation
587. The Approximate Stoichiometry of Photophosphorylation Has Been Established
588. The ATP Synthase Structure and Mechanism Are Nearly Universal
589. 20.4 CO[2]-Assimilation Reactions
590. Carbon Dioxide Assimilation Occurs in Three Stages
591. Synthesis of Each Triose Phosphate from CO[2] Requires Six NADPH and Nine ATP
592. A Transport System Exports Triose Phosphates from the Chloroplast and Imports Phosphate
593. Four Enzymes of the Calvin Cycle Are Indirectly Activated by Light
594. 20.5 Photorespiration and the C[4] and CAM Pathways
595. Photorespiration Results from Rubisco’s Oxygenase Activity
596. Phosphoglycolate Is Salvaged in a Costly Set of Reactions in C[3] Plants
597. In C[4] Plants, CO[2] Fixation and Rubisco Activity Are Spatially Separated
598. In CAM Plants, CO[2] Capture and Rubisco Action Are Temporally Separated
599. 20.6 Biosynthesis of Starch, Sucrose, and Cellulose
600. ADP-Glucose Is the Substrate for Starch Synthesis in Plant Plastids and for Glycogen Synthesis in Bacteria
601. UDP-Glucose Is the Substrate for Sucrose Synthesis in the Cytosol of Leaf Cells
602. Conversion of Triose Phosphates to Sucrose and Starch Is Tightly Regulated
603. The Glyoxylate Cycle and Gluconeogenesis Produce Glucose in Germinating Seeds
604. Cellulose Is Synthesized by Supramolecular Structures in the Plasma Membrane
605. Pools of Common Intermediates Link Pathways in Different Organelles
606. Chapter Review
607. Key Terms
608. Problems
609. Chapter 21 Lipid Biosynthesis
610. 21.1 Biosynthesis of Fatty Acids and Eicosanoids
611. Malonyl-CoA Is Formed from Acetyl-CoA and Bicarbonate
612. Fatty Acid Synthesis Proceeds in a Repeating Reaction Sequence
613. The Mammalian Fatty Acid Synthase Has Multiple Active Sites
614. Fatty Acid Synthase Receives the Acetyl and Malonyl Groups
615. The Fatty Acid Synthase Reactions Are Repeated to Form Palmitate
616. Fatty Acid Synthesis Is a Cytosolic Process in Most Eukaryotes but Takes Place in the Chloroplasts in Plants
617. Acetate Is Shuttled out of Mitochondria as Citrate
618. Fatty Acid Biosynthesis Is Tightly Regulated
619. Long-Chain Saturated Fatty Acids Are Synthesized from Palmitate
620. Desaturation of Fatty Acids Requires a Mixed-Function Oxidase
621. Eicosanoids Are Formed from 20- and 22-Carbon Polyunsaturated Fatty Acids
622. 21.2 Biosynthesis of Triacylglycerols
623. Triacylglycerols and Glycerophospholipids Are Synthesized from the Same Precursors
624. Triacylglycerol Biosynthesis in Animals Is Regulated by Hormones
625. Adipose Tissue Generates Glycerol 3-Phosphate by Glyceroneogenesis
626. Thiazolidinediones Treat Type 2 Diabetes by Increasing Glyceroneogenesis
627. 21.3 Biosynthesis of Membrane Phospholipids
628. Cells Have Two Strategies for Attaching Phospholipid Head Groups
629. Pathways for Phospholipid Biosynthesis Are Interrelated
630. Eukaryotic Membrane Phospholipids Are Subject to Remodeling
631. Plasmalogen Synthesis Requires Formation of an Ether-Linked Fatty Alcohol
632. Sphingolipid and Glycerophospholipid Synthesis Share Precursors and Some Mechanisms
633. Polar Lipids Are Targeted to Specific Cellular Membranes
634. 21.4 Cholesterol, Steroids, and Isoprenoids: Biosynthesis, Regulation, and Transport
635. Cholesterol Is Made from Acetyl-CoA in Four Stages
636. Cholesterol Has Several Fates
637. Cholesterol and Other Lipids Are Carried on Plasma Lipoproteins
638. HDL Carries Out Reverse Cholesterol Transport
639. Cholesteryl Esters Enter Cells by Receptor-Mediated Endocytosis
640. Cholesterol Synthesis and Transport Are Regulated at Several Levels
641. Dysregulation of Cholesterol Metabolism Can Lead to Cardiovascular Disease
642. Reverse Cholesterol Transport by HDL Counters Plaque Formation and Atherosclerosis
643. Steroid Hormones Are Formed by Side-Chain Cleavage and Oxidation of Cholesterol
644. Intermediates in Cholesterol Biosynthesis Have Many Alternative Fates
645. Chapter Review
646. Key Terms
647. Problems
648. Chapter 22 Biosynthesis of Amino Acids, Nucleotides, and Related Molecules
649. 22.1 Overview of Nitrogen Metabolism
650. A Global Nitrogen Cycling Network Maintains a Pool of Biologically Available Nitrogen
651. Nitrogen Is Fixed by Enzymes of the Nitrogenase Complex
652. Ammonia Is Incorporated into Biomolecules through Glutamate and Glutamine
653. Glutamine Synthetase Is a Primary Regulatory Point in Nitrogen Metabolism
654. Several Classes of Reactions Play Special Roles in the Biosynthesis of Amino Acids and Nucleotides
655. 22.2 Biosynthesis of Amino Acids
656. Organisms Vary Greatly in Their Ability to Synthesize the 20 Common Amino Acids
657. α-Ketoglutarate Gives Rise to Glutamate, Glutamine, Proline, and Arginine
658. Serine, Glycine, and Cysteine Are Derived from 3-Phosphoglycerate
659. Three Nonessential and Six Essential Amino Acids Are Synthesized from Oxaloacetate and Pyruvate
660. Chorismate Is a Key Intermediate in the Synthesis of Tryptophan, Phenylalanine, and Tyrosine
661. Histidine Biosynthesis Uses Precursors of Purine Biosynthesis
662. Amino Acid Biosynthesis Is under Allosteric Regulation
663. 22.3 Molecules Derived from Amino Acids
664. Glycine Is a Precursor of Porphyrins
665. Heme Degradation Has Multiple Functions
666. Amino Acids Are Precursors of Creatine and Glutathione
667. d-Amino Acids Are Found Primarily in Bacteria
668. Aromatic Amino Acids Are Precursors of Many Plant Substances
669. Biological Amines Are Products of Amino Acid Decarboxylation
670. Arginine Is the Precursor for Biological Synthesis of Nitric Oxide
671. 22.4 Biosynthesis and Degradation of Nucleotides
672. De Novo Purine Nucleotide Synthesis Begins with PRPP
673. Purine Nucleotide Biosynthesis Is Regulated by Feedback Inhibition
674. Pyrimidine Nucleotides Are Made from Aspartate, PRPP, and Carbamoyl Phosphate
675. Pyrimidine Nucleotide Biosynthesis Is Regulated by Feedback Inhibition
676. Nucleoside Monophosphates Are Converted to Nucleoside Triphosphates
677. Ribonucleotides Are the Precursors of Deoxyribonucleotides
678. Thymidylate Is Derived from dCDP and dUMP
679. Degradation of Purines and Pyrimidines Produces Uric Acid and Urea, Respectively
680. Purine and Pyrimidine Bases Are Recycled by Salvage Pathways
681. Excess Uric Acid Causes Gout
682. Many Chemotherapeutic Agents Target Enzymes in Nucleotide Biosynthetic Pathways
683. Chapter Review
684. Key Terms
685. Problems
686. Chapter 23 Hormonal Regulation and Integration of Mammalian Metabolism
687. 23.1 Hormone Structure and Action
688. Hormones Act through Specific High-Affinity Cellular Receptors
689. Hormones Are Chemically Diverse
690. Some Hormones Are Released by a “Top-Down” Hierarchy of Neuronal and Hormonal Signals
691. “Bottom-Up” Hormonal Systems Send Signals Back to the Brain and to Other Tissues
692. 23.2 Tissue-Specific Metabolism
693. The Liver Processes and Distributes Nutrients
694. Adipose Tissues Store and Supply Fatty Acids
695. Brown and Beige Adipose Tissues Are Thermogenic
696. Muscles Use ATP for Mechanical Work
697. The Brain Uses Energy for Transmission of Electrical Impulses
698. Blood Carries Oxygen, Metabolites, and Hormones
699. 23.3 Hormonal Regulation of Fuel Metabolism
700. Insulin Counters High Blood Glucose in the Well-Fed State
701. Pancreatic β Cells Secrete Insulin in Response to Changes in Blood Glucose
702. Glucagon Counters Low Blood Glucose
703. During Fasting and Starvation, Metabolism Shifts to Provide Fuel for the Brain
704. Epinephrine Signals Impending Activity
705. Cortisol Signals Stress, Including Low Blood Glucose
706. 23.4 Obesity and the Regulation of Body Mass
707. Adipose Tissue Has Important Endocrine Functions
708. Leptin Stimulates Production of Anorexigenic Peptide Hormones
709. Leptin Triggers a Signaling Cascade That Regulates Gene Expression
710. Adiponectin Acts through AMPK to Increase Insulin Sensitivity
711. AMPK Coordinates Catabolism and Anabolism in Response to Metabolic Stress
712. The mTORC1 Pathway Coordinates Cell Growth with the Supply of Nutrients and Energy
713. Diet Regulates the Expression of Genes Central to Maintaining Body Mass
714. Short-Term Eating Behavior Is Influenced by Ghrelin, PPY3–36, and Cannabinoids
715. Microbial Symbionts in the Gut Influence Energy Metabolism and Adipogenesis
716. 23.5 Diabetes Mellitus
717. Diabetes Mellitus Arises from Defects in Insulin Production or Action
718. Carboxylic Acids (Ketone Bodies) Accumulate in the Blood of Those with Untreated Diabetes
719. In Type 2 Diabetes the Tissues Become Insensitive to Insulin
720. Type 2 Diabetes Is Managed with Diet, Exercise, Medication, and Surgery
721. Chapter Review
722. Key Terms
723. Problems
724. Part III Information Pathways
725. Chapter 24 Genes and Chromosomes
726. 24.1 Chromosomal Elements
727. Genes Are Segments of DNA That Code for Polypeptide Chains and RNAs
728. DNA Molecules Are Much Longer than the Cellular or Viral Packages That Contain Them
729. Eukaryotic Genes and Chromosomes Are Very Complex
730. 24.2 DNA Supercoiling
731. Most Cellular DNA Is Underwound
732. DNA Underwinding Is Defined by Topological Linking Number
733. Topoisomerases Catalyze Changes in the Linking Number of DNA
734. DNA Compaction Requires a Special Form of Supercoiling
735. 24.3 The Structure of Chromosomes
736. Chromatin Consists of DNA, Proteins, and RNA
737. Histones Are Small, Basic Proteins
738. Nucleosomes Are the Fundamental Organizational Units of Chromatin
739. Nucleosomes Are Packed into Highly Condensed Chromosome Structures
740. Condensed Chromosome Structures Are Maintained by SMC Proteins
741. Bacterial DNA Is Also Highly Organized
742. Chapter Review
743. Key Terms
744. Problems
745. Chapter 25 DNA Metabolism
746. 25.1 DNA Replication
747. DNA Replication Follows a Set of Fundamental Rules
748. DNA Is Degraded by Nucleases
749. DNA Is Synthesized by DNA Polymerases
750. Replication Is Very Accurate
751. E. coli Has at Least Five DNA Polymerases
752. DNA Replication Requires Many Enzymes and Protein Factors
753. Replication of the E. coli Chromosome Proceeds in Stages
754. Replication in Eukaryotic Cells Is Similar but More Complex
755. Viral DNA Polymerases Provide Targets for Antiviral Therapy
756. 25.2 DNA Repair
757. Mutations Are Linked to Cancer
758. All Cells Have Multiple DNA Repair Systems
759. The Interaction of Replication Forks with DNA Damage Can Lead to Error-Prone Translesion DNA Synthesis
760. 25.3 DNA Recombination
761. Bacterial Homologous Recombination Is a DNA Repair Function
762. Eukaryotic Homologous Recombination Is Required for Proper Chromosome Segregation during Meiosis
763. Some Double-Strand Breaks Are Repaired by Nonhomologous End Joining
764. Site-Specific Recombination Results in Precise DNA Rearrangements
765. Transposable Genetic Elements Move from One Location to Another
766. Immunoglobulin Genes Assemble by Recombination
767. Chapter Review
768. Key Terms
769. Problems
770. Chapter 26 RNA Metabolism
771. 26.1 DNA-Dependent Synthesis of RNA
772. RNA Is Synthesized by RNA Polymerases
773. RNA Synthesis Begins at Promoters
774. Transcription Is Regulated at Several Levels
775. Specific Sequences Signal Termination of RNA Synthesis
776. Eukaryotic Cells Have Three Kinds of Nuclear RNA Polymerases
777. RNA Polymerase II Requires Many Other Protein Factors for Its Activity
778. RNA Polymerases Are Drug Targets
779. 26.2 RNA Processing
780. Eukaryotic mRNAs Are Capped at the 5′ End
781. Both Introns and Exons Are Transcribed from DNA into RNA
782. RNA Catalyzes the Splicing of Introns
783. In Eukaryotes the Spliceosome Carries out Nuclear pre-mRNA Splicing
784. Proteins Catalyze Splicing of tRNAs
785. Eukaryotic mRNAs Have a Distinctive 3′ End Structure
786. A Gene Can Give Rise to Multiple Products by Differential RNA Processing
787. Ribosomal RNAs and tRNAs Also Undergo Processing
788. Special-Function RNAs Undergo Several Types of Processing
789. Cellular mRNAs Are Degraded at Different Rates
790. 26.3 RNA-Dependent Synthesis of RNA and DNA
791. Reverse Transcriptase Produces DNA from Viral RNA
792. Some Retroviruses Cause Cancer and AIDS
793. Many Transposons, Retroviruses, and Introns May Have a Common Evolutionary Origin
794. Telomerase Is a Specialized Reverse Transcriptase
795. Some RNAs Are Replicated by RNA-Dependent RNA Polymerase
796. RNA-Dependent RNA Polymerases Share a Common Structural Fold
797. 26.4 Catalytic RNAs and the RNA World Hypothesis
798. Ribozymes Share Features with Protein Enzymes
799. Ribozymes Participate in a Variety of Biological Processes
800. Ribozymes Provide Clues to the Origin of Life in an RNA World
801. Chapter Review
802. Key Terms
803. Problems
804. Chapter 27 Protein Metabolism
805. 27.1 The Genetic Code
806. The Genetic Code Was Cracked Using Artificial mRNA Templates
807. Wobble Allows Some tRNAs to Recognize More than One Codon
808. The Genetic Code Is Mutation-Resistant
809. Translational Frameshifting Affects How the Code Is Read
810. Some mRNAs Are Edited before Translation
811. 27.2 Protein Synthesis
812. The Ribosome Is a Complex Supramolecular Machine
813. Transfer RNAs Have Characteristic Structural Features
814. Stage 1: Aminoacyl-tRNA Synthetases Attach the Correct Amino Acids to Their tRNAs
815. Stage 2: A Specific Amino Acid Initiates Protein Synthesis
816. Stage 3: Peptide Bonds Are Formed in the Elongation Stage
817. Stage 4: Termination of Polypeptide Synthesis Requires a Special Signal
818. Stage 5: Newly Synthesized Polypeptide Chains Undergo Folding and Processing
819. Protein Synthesis Is Inhibited by Many Antibiotics and Toxins
820. 27.3 Protein Targeting and Degradation
821. Posttranslational Modification of Many Eukaryotic Proteins Begins in the Endoplasmic Reticulum
822. Glycosylation Plays a Key Role in Protein Targeting
823. Signal Sequences for Nuclear Transport Are Not Cleaved
824. Bacteria Also Use Signal Sequences for Protein Targeting
825. Cells Import Proteins by Receptor-Mediated Endocytosis
826. Protein Degradation Is Mediated by Specialized Systems in All Cells
827. Chapter Review
828. Key Terms
829. Problems
830. Chapter 28 Regulation of Gene Expression
831. 28.1 The Proteins and RNAs of Gene Regulation
832. RNA Polymerase Binds to DNA at Promoters
833. Transcription Initiation Is Regulated by Proteins and RNAs
834. Many Bacterial Genes Are Clustered and Regulated in Operons
835. The lac Operon Is Subject to Negative Regulation
836. Regulatory Proteins Have Discrete DNA-Binding Domains
837. Regulatory Proteins Also Have Protein-Protein Interaction Domains
838. 28.2 Regulation of Gene Expression in Bacteria
839. The lac Operon Undergoes Positive Regulation
840. Many Genes for Amino Acid Biosynthetic Enzymes Are Regulated by Transcription Attenuation
841. Induction of the SOS Response Requires Destruction of Repressor Proteins
842. Synthesis of Ribosomal Proteins Is Coordinated with rRNA Synthesis
843. The Function of Some mRNAs Is Regulated by Small RNAs in Cis or in Trans
844. Some Genes Are Regulated by Genetic Recombination
845. 28.3 Regulation of Gene Expression in Eukaryotes
846. Transcriptionally Active Chromatin Is Structurally Distinct from Inactive Chromatin
847. Most Eukaryotic Promoters Are Positively Regulated
848. DNA-Binding Activators and Coactivators Facilitate Assembly of the Basal Transcription Factors
849. The Genes of Galactose Metabolism in Yeast Are Subject to Both Positive and Negative Regulation
850. Transcription Activators Have a Modular Structure
851. Eukaryotic Gene Expression Can Be Regulated by Intercellular and Intracellular Signals
852. Regulation Can Result from Phosphorylation of Nuclear Transcription Factors
853. Many Eukaryotic mRNAs Are Subject to Translational Repression
854. Posttranscriptional Gene Silencing Is Mediated by RNA Interference
855. RNA-Mediated Regulation of Gene Expression Takes Many Forms in Eukaryotes
856. Development Is Controlled by Cascades of Regulatory Proteins
857. Stem Cells Have Developmental Potential That Can Be Controlled
858. Chapter Review
859. Key Terms
860. Problems
861. Note
862. Abbreviated Solutions to Problems
863. Glossary
864. Index

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