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Principles Of Biochemistry

by ; ; ; ;
Edition:
4th
ISBN13:

9780131453067

ISBN10:
0131453068
Format:
Hardcover
Pub. Date:
6/29/2005
Publisher(s):
Prentice Hall
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Summary

This concise, introductory text focuses on the basic principles of biochemistry, filling the gap between the encyclopedic volumes and the cursory overview texts.Principles of Biochemistry, 4/ehas a well-deserved reputation for being the most accurate biochemistry textbook in the market. Widely praised in its previous edition for currency, and clarity of exposition, the new edition has been thoroughly revised and updated to reflect recent changes in this dynamic discipline.

Table of Contents

Preface xxv
PART ONE Introduction
Introduction to Biochemistry
1(25)
Biochemistry Is a Modern Science
2(1)
The Chemical Elements of Life
3(2)
Many Important Macromolecules Are Polymers
5(6)
Proteins
6(1)
Polysaccharides
7(2)
Nucleic Acids
9(1)
Lipids and Membranes
10(1)
The Energetics of Life
11(4)
Reaction Rates and Equilibria
12(1)
Thermodynamics
13(2)
Equilibrium Constants and Standard Gibbs Free Energy Changes
15(1)
Biochemistry and Evolution
15(1)
The Cell Is the Basic Unit of Life
16(1)
Prokaryotic Cells: Structural Features
17(1)
Eukaryotic Cells: Structural Features
18(4)
The Nucleus
18(1)
The Endoplasmic Reticulum and Golgi Apparatus
19(1)
Mitochondria and Chloroplasts
20(1)
Specialized Vesicles
21(1)
The Cytoskeleton
22(1)
A Picture of the Living Cell
22(2)
Biochemistry Is Multidisciplinary
24(2)
Appendix: The Special Terminology of Biochemistry
24(1)
Selected Readings
25(1)
Water
26(26)
The Water Molecule Is Polar
27(1)
Hydrogen Bonding in Water
28(2)
Water Is an Excellent Solvent
30(2)
Ionic and Polar Substances Dissolve in Water
30(1)
Cellular Concentrations and Diffusion
31(1)
Osmotic Pressure
31(1)
Nonpolar Substances Are Insoluble in Water
32(1)
Noncovalent Interactions
33(3)
Charge--charge Interactions
33(1)
Hydrogen Bonds
34(1)
Van der Waals Forces
35(1)
Hydrophobic Interactions
36(1)
Water Is Nucleophilic
36(1)
Ionization of Water
37(2)
The pH Scale
39(2)
Box 2.1 The little ``p'' in pH.
40(1)
Acid Dissociation Constants of Weak Acids
41(5)
Buffered Solutions Resist Changes in pH
46(6)
Summary
49(1)
Problems
49(2)
Selected Readings
51(1)
PART TWO Structure and Function
Amino Acids and the Primary Structures of Proteins
52(32)
General Structure of Amino Acids
53(2)
Structures of the 20 Common Amino Acids
55(6)
Box 3.1 An Alternative Nomenclature
56(1)
Aliphatic R Groups
57(1)
Box 3.2 Common Names of Amino Acids
57(1)
Aromatic R Groups
58(1)
Sulfur-Containing R Groups
58(1)
Side Chains with Alcohol Groups
59(1)
Basic R Groups
59(1)
Acidic R Groups and Their Amide Derivatives
60(1)
The Hydrophobicity of Amino Acid Side Chains
60(1)
Other Amino Acids and Amino Acid Derivatives
61(1)
Ionization of Amino Acids
62(4)
Peptide Bonds Link Amino Acids in Proteins
66(1)
Protein Purification Techniques
67(2)
Analytical Techniques
69(3)
Amino Acid Composition of Proteins
72(1)
Determining the Sequence of Amino Acid Residues
73(2)
Protein Sequencing Strategies
75(3)
Comparisons of the Primary Structures of Proteins Reveal Evolutionary Relationships
78(6)
Summary
81(1)
Problems
81(2)
Selected Readings
83(1)
Proteins: Three-Dimensional Structure and Function
84(45)
There Are Four Levels of Protein Structure
86(1)
Methods for Determining Protein Structure
87(3)
The Conformation of the Peptide Group
90(2)
The α Helix
92(3)
β Strands and β Sheets
95(2)
Loops and Turns
97(1)
Teritary Structure of Proteins
98(6)
Supersecondary Structures
99(1)
Domains
100(4)
Domain Structure and Function
104(1)
Quaternary Structure
104(3)
Protein Denaturation and Renaturation
107(3)
Protein Folding and Stability
110(5)
The Hydrophobic Effect
110(1)
Hydrogen Bonding
111(1)
Van der Waals Interactions and Charge--Charge Interactions
112(1)
Protein Folding Is Assisted by Molecular Chaperones
112(3)
Collagen, a Fibrous Protein
115(1)
Structures of Myoglobin and Hemoglobin
116(2)
Oxygen Binding to Myoglobin and Hemoglobin
118(5)
Oxygen Binds Reversibly to Heme
118(1)
Oxygen-Binding Curves of Myoglobin and Hemoglobin
119(2)
Hemoglobin Is an Allosteric Protein
121(2)
Antibodies Bind Specific Antigens
123(6)
Summary
125(1)
Problems
125(2)
Selected Readings
127(2)
Properties of Enzymes
129(29)
The Six Classes of Enzymes
130(2)
Kinetic Experiments Reveal Enzyme Properties
132(3)
Chemical Kinetics
133(1)
Enzyme Kinetics
134(1)
The Michaelis--Menten Equation
135(4)
Derivation of the Michaelis--Menten Equation
137(1)
The Catalytic Constant kcat
138(1)
The Meanings of Km
138(1)
Kinetic Constants Indicate Enzyme Activity and Catalytic Proficiency
139(1)
Measurement of Km and Vmax
140(1)
Kinetics of Multisubstrate Reactions
141(1)
Box 5.1 Hyperbolas versus Straight Lines
141(1)
Reversible Enzyme Inhibition
142(5)
Competitive Inhibition
143(2)
Uncompetitive Inhibition
145(1)
Noncompetitive Inhibition
146(1)
Uses of Enzyme Inhibition
146(1)
Irreversible Enzyme Inhibition
147(1)
Allosteric Enzymes
148(1)
Regulation of Enzyme Activity
148(6)
Phosphofructokinase Is an Allosteric Enzyme
149(1)
General Properties of Allosteric Enzymes
150(2)
Two Theories of Allosteric Regulation
152(1)
Regulation by Covalent Modification
153(1)
Multienzyme Complexes and Multifunctional Enzymes
154(4)
Summary
154(1)
Problems
155(2)
Selected Readings
157(1)
Mechanisms of Enzymes
158(34)
The Terminology of Mechanistic Chemistry
158(2)
Nucleophilic Substitutions
159(1)
Cleavage Reactions
160(1)
Oxidation---Reduction Reactions
160(1)
Catalysts Stabilize Transition States
160(2)
Chemical Modes of Enzymatic Catalysis
162(5)
Box 6.1 Site-Directed Mutagenesis Modifies Enzymes
163(1)
Polar Amino Acid Residues in Active Sites
163(1)
Acid-Base Catalysis
164(1)
Covalent Catalysis
165(1)
pH Affects Enzymatic Rates
166(1)
Diffusion-Controlled Reactions
167(4)
Triose Phosphate Isomerase
167(3)
Superoxide Dismutase
170(1)
Binding Modes of Enzymatic Catalysis
171(7)
The Proximity Effect
172(1)
Weak Binding of Substrates of Enzymes
172(2)
Induced Fit
174(1)
Transition-State Stabilization
175(3)
Lysozyme
178(4)
Box 6.2 Proposed Transition State for a Bimolecular Reaction
181(1)
Properties of Serine Proteases
182(10)
Zymogens Are Inactive Enzyme Precursors
182(1)
Substrate Specificity of Serine Proteases
183(1)
Serine Proteases Use Both the Chemical and the Binding Modes of Catalysis
184(4)
Summary
188(1)
Problems
188(3)
Selected Readings
191(1)
Coenzymes and Vitamins
192(30)
Many Enzymes Require Inorganic Cations
193(1)
Coenzyme Classification
193(3)
Box 7.1 Vitamin C: A Vitamin but Not a Coenzyme
195(1)
ATP and Other Nucleotide Cosubstrates
196(1)
NADP and NAD
197(3)
Box 7.2 NAD Binding to Dehydrogenases
199(1)
FAD and FMN
200(1)
Coenzyme A
201(1)
Thiamine Pyrophosphate
202(1)
Pyridoxal Phosphate
203(4)
Biotin
207(1)
Tetrahydrofolate
208(2)
Cobalamin
210(1)
Lipoamide
211(1)
Lipid Vitamins
212(2)
Vitamin A
213(1)
Vitamin D
213(1)
Vitamin E
213(1)
Vitamin K
214(1)
Ubiquinone
214(1)
Protein Coenzymes
215(1)
Cytochromes
216(6)
Summary
218(1)
Problems
219(2)
Selected Readings
221(1)
Carbohydrates
222(31)
Most Monosaccharides Are Chiral Compounds
223(3)
Cyclization of Aldoses and Ketoses
226(3)
Conformations of Monosaccharides
229(2)
Derivatives of Monosaccharides
231(3)
Sugar Phosphates
231(1)
Deoxy Sugars
231(1)
Amino Sugars
231(1)
Sugar Alcohols
232(1)
Sugar Acids
233(1)
Ascorbic Acid
234(1)
Disaccharides and Other Glycosides
234(3)
Structures of Disaccharides
234(2)
Reducing and Nonreducing Sugars
236(1)
Nucleosides and Other Glycosides
236(1)
Polysaccharides
237(4)
Starch and Glycogen
237(2)
Cellulose and Chitin
239(2)
Glycoconjugates
241(12)
Proteoglycans
241(2)
Box 8.1 Nodulation Factors Are Lipo-oligosaccharides
243(1)
Peptidoglycans
243(1)
Glycoproteins
244(4)
Box 8.2 ABO Blood Group
248(1)
Summary
249(1)
Problems
250(2)
Selected Readings
252(1)
Lipids and Membranes
253(43)
Structural and Functional Diversity of Lipids
253(1)
Fatty Acids
254(4)
Box 9.1 Common Names of Fatty Acids
255(1)
Box 9.2 Trans Fatty Acids and Margarine
256(2)
Triacylglycerols
258(1)
Glycerophospholipids
259(3)
Sphingolipids
262(2)
Steroids
264(1)
Other Biologically Important Lipids
265(2)
Biological Membranes Are Composed of Lipid Bilayers and Proteins
267(4)
Box 9.3 Special Nonaqueous Techniques Must Be Used to Study Lipids
268(1)
Lipid Bilayers
269(1)
Fluid Mosaic Model of Biological Membranes
270(1)
Lipid Bilayers and Membranes Are Dynamic Structures
271(3)
Three Classes of Membrane Proteins
274(4)
Box 9.4 New Lipid Vesicles, or Liposomes
275(3)
Membrane Transport
278(6)
Thermodynamics of Membrane Transport
279(1)
Pores and Channels
280(1)
Passive Transport
281(1)
Active Transport
281(2)
Endocytosis and Exocytosis
283(1)
Box 9.5 The Hot Spice of Chili Peppers
284(1)
Transduction of Extracellular Signals
284(12)
G Proteins Are Signal Transducers
285(2)
The Adenylyl Cyclase Signaling Pathway
287(1)
The Inositol--Phospholipid Signaling Pathway
288(1)
Box 9.6 Bacterial Toxins and G Proteins
289(2)
Receptor Tyrosine Kinases
291(1)
Summary
292(1)
Problems
292(2)
Selected Readings
294(2)
PART THREE Metabolism and Bioenergetics
Introduction to Metabolism
296(31)
Metabolism Is the Sum of Cellular Reactions
296(2)
Metabolic Pathways
298(6)
Pathways Are Sequences of Reactions
299(1)
Metabolism Proceeds by Discrete Steps
300(1)
Metabolic Pathways Are Regulated
301(2)
Evolution of Metabolic Pathways
303(1)
Major Pathways in Cells
304(2)
Compartmentation and Interorgan Metabolism
306(2)
Actual Gibbs Free Energy Change, Not Standard Free Energy Change, Determines the Spontaneity of Metabolic Reactions
308(2)
The Free Energy of ATP
310(3)
The Metabolic Roles of ATP
313(4)
Phosphoryl-Group Transfer
314(1)
Production of ATP by Phosphoryl Group Transfer
315(1)
Nucleotidyl Group Transfer
316(1)
Thioesters Have High Free Energies of Hydrolysis
317(1)
Reduced Coenzymes Conserve Energy from Biological Oxidations
318(5)
Gibbs Free Energy Change Is Related to Reduction Potential
319(3)
Electron Transfer from NADH Provides Free Energy
322(1)
Box 10.1 NAD and NADH Differ in Their Ultraviolet Absorption Spectra
322(1)
Experimental Methods for Studying Metabolism
323(4)
Summary
324(1)
Problems
324(2)
Selected Readings
326(1)
Glycolysis
327(30)
The Enzymatic Reactions of Glycolysis
328(1)
The Ten Enzyme-Catalyzed Steps of Glycolysis
328(12)
Box 11.1 A Brief History of the Glycolytic Pathway
332(6)
Box 11.2 Formation of 2,3-Bisphosphoglycerate in Red Blood Cells
338(2)
Box 11.3 Arsenate Poisoning
340(1)
The Fate of Pyruvate
340(3)
Metabolism of Pyruvate to Ethanol
341(1)
Reduction of Pyruvate to Lactate
342(1)
Free Energy Changes in Glycolysis
343(1)
Regulation of Glycolysis
344(6)
Regulation of Hexose Transporters
344(2)
Regulation of Hexokinase
346(1)
Box 11.4 Glucose 6-Phosphate Has a Pivotal Metabolic Role in the Liver
346(1)
Regulation of Phosphofructokinase-1
347(1)
Regulation of Pyruvate Kinase
348(2)
The Pasteur Effect
350(1)
Other Sugars Can Enter Glycolysis
350(2)
Fructose Is Converted to Glyceraldehyde 3-Phosphate
350(1)
Galactose Is Converted to Glucose 1-Phosphate
351(1)
Mannose Is Converted to Fructose 6-Phosphate
352(1)
The Entner--Doudoroff Pathway in Bacteria
352(5)
Summary
354(1)
Problems
354(1)
Selected Readings
355(2)
Gluconeogenesis, The Pentose Phosphate Pathway, and Glycogen Metabolism
357(27)
Gluconeogenesis
358(4)
Pyruvate Carboxylase
359(1)
Phosphoenolpyruvate Carboxykinase
360(1)
Fructose 1,6-bisphosphatase
361(1)
Glucose 6-phosphatase
361(1)
Precursors for Gluconeogenesis
362(2)
Lactate
362(1)
Amino Acids
363(1)
Glycerol
363(1)
Propionate and Lactate
363(1)
Acetate
364(1)
Regulation of Gluconeogenesis
364(2)
Box 12.1 Glucose Is Sometimes Converted to Sorbitol
366(1)
The Pentose Phosphate Pathway
366(5)
Oxidative Stage
368(1)
Nonoxidative Stage
368(1)
Box 12.2 Glucose 6-phosphate Dehydrogenase Deficiency in Humans
369(1)
Interconversions Catalyzed by Transketolase and Transaldolase
370(1)
Glycogen Metabolism
371(3)
Glycogen Synthesis
371(1)
Glycogen Degradation
372(2)
Regulation of Glycogen Metabolism
374(5)
Hormones Regulate Glycogen Metabolism
375(1)
Reciprocal Regulation of Glycogen Phosphorylase and Glycogen Synthase
375(1)
Intracellular Regulation of Glycogen Metabolism Involves Interconvertible Enzymes
376(2)
Box 12.3 Glycogen Storage Diseases
378(1)
Maintenance of Glucose Levels in Mammals
379(5)
Summary
381(1)
Problems
382(1)
Selected Readings
383(1)
The Citric Acid Cycle
384(31)
Conversion of Pyruvate to Acetyl CoA
385(6)
The Citric Acid Cycle Oxidizes Acetyl CoA
391(2)
The Citric Acid Cycle Enzymes
393(10)
Box 13.1 Where Do the Electrons Come From?
394(3)
Box 13.2 Three-point Attachment of Prochiral Substrates to Enzymes
397(5)
Box 13.3 Converting One Enzyme into Another
402(1)
Reduced Coenzymes Can Fuel the Production of ATP
403(1)
Regulation of the Citric Acid Cycle
404(2)
The Citric Acid Cycle Isn't Always a ``Cycle''
406(1)
The Glyoxylate Pathway
407(3)
Evolution of the Citric Acid Cycle
410(5)
Summary
354(1)
Problems
354(1)
Selected Readings
355(60)
Electron Transport and ATP Synthesis
415(29)
Overview of Membrane-associated Electron Transport and ATP Synthesis
416(1)
The Mitochondrion
416(2)
The Chemiosmotic Theory and the Protonmotive Force
418(3)
Historical Background: The Chemiosmotic Theory
418(2)
The Protonmotive Force
420(1)
Electron Transport
421(3)
``Complexes I Through IV
421(3)
Cofactors in Electron Transport
424(1)
Complex I
424(1)
Complex II
425(2)
Complex III
427(2)
Complex IV
429(3)
Complex V: ATP Synthase
432(3)
Box 14.1 Proton Leaks and Heat Production
435(1)
Active Transport of ATP, ADP, and Pi Across the Mitochondrial Membrane
435(1)
The P/O Ratio
436(1)
NADH Shuttle Mechanisms in Eukaryotes
436(3)
Box 14.2 The High Cost of Living
439(1)
Other Terminal Electron Acceptors and Donors
439(1)
Superoxide Anions
440(4)
Summary
441(1)
Problems
441(1)
Selected Readings
442(2)
Photosynthesis
444(35)
Light-Gathering Pigments
445(4)
Bacterial Photosystems
449(11)
Photosystem II
449(3)
Photosystem I
452(2)
Coupled Photosystems and Cytochrome bf
454(4)
Reduction Potentials and Gibbs Free Energy in Photosynthesis
458(1)
Photosynthesis Takes Place within Internal Membranes
459(1)
Plant Photosynthesis
460(4)
Chloroplasts
460(1)
Box 15.1 Bacteriorhodopsin
461(2)
Plant Photosystems
463(1)
Organization of Chloroplast Photosystems
463(1)
Fixation of CO2: The Calvin Cycle
464(7)
The Calvin Cycle
465(1)
Rubisco: Ribulose 1,5-bisphosphate Carboxylase-oxygenase
465(4)
Oxygenation of Ribulose 1,5-Bisphosphate
469(1)
Calvin Cycle: Reduction and Regeneration Stages
470(1)
Box 15.2 Building a Better Rubisco
470(1)
Sucrose and Starch Metabolism in Plants
471(2)
Additional Carbon-Fixation Pathways
473(6)
Box 15.3 Gregor Mendel's Wrinkled Peas
473(1)
The C4 Pathway
474(1)
Crassulacean Acid Metabolism (CAM)
474(2)
Carbon Fixation in Bacteria
476(1)
Summary
477(1)
Problems
477(1)
Selected Readings
478(1)
Lipid Metabolism
479(41)
Fatty Acid Synthesis
480(5)
Synthesis of Malonyl ACP and Acetyl ACP
480(1)
The Initiation Reaction of Fatty Acid Synthesis
481(1)
The Elongation Reactions of Fatty Acid Synthesis
482(1)
Activation of Fatty Acids
483(1)
Fatty Acid Extension and Desaturation
484(1)
Synthesis of Triacylglycerols and Glycerophospholipids
485(3)
Synthesis of Eicosanoids
488(2)
Box 16.1 The Search for a Replacement for Aspirin
490(1)
Synthesis of Ether Lipids
490(1)
Synthesis of Sphingolipids
491(4)
Box 16.2 Lysosomal Storage Diseases
493(1)
Box 16.3 Regulating Cholesterol Levels
494(1)
Synthesis of Cholesterol
495(3)
Stage 1: Acetyl CoA to Isopentenyl Diphosphate
495(1)
Stage 2: Isopentenyl Diphosphate to Squalene
496(1)
Stage 3: Squalene to Cholesterol
496(1)
Other Products of Isoprenoid Metabolism
496(2)
Fatty Acid Oxidation
498(8)
The Reactions of β-Oxidation
499(1)
Fatty Acid Synthesis and β-Oxidation
500(1)
Transport of Fatty Acyl CoA into Mitochondria
501(1)
Box 16.4 A Trifunctional Enzyme for β-Oxidation
502(1)
ATP Generation from Fatty Acid Oxidation
502(2)
β-Oxidation of Odd-Chain and Unsaturated Fatty Acids
504(2)
Eukaryotic Lipids Are Made at a Variety of Sites
506(1)
Lipid Metabolism Is Regulated by Hormones in Mammals
507(2)
Absorption and Mobilization of Fuel Lipids in Mammals
509(4)
Absorption of Dietary Lipids
509(1)
Lipoproteins
510(3)
Box 16.5 Lipoprotein Lipase and Coronary Heart Disease
513(1)
Serum Albumin
513(1)
Ketone Bodies Are Fuel Molecules
513(7)
Ketone Bodies Are Synthesized in the Liver
514(1)
Ketone Bodies Are Oxidized in Mitochondria
515(1)
Box 16.6 Altered Carbohydrate and Lipid Metabolism in Diabetes
516(1)
Summary
517(1)
Problems
517(2)
Selected Readings
519(1)
Amino Acid Metabolism
520(37)
The Nitrogen Cycle and Nitrogen Fixation
521(2)
Assimilation of Ammonia
523(3)
Ammonia Is Incorporated into Glutamate and Glutamine
524(1)
Transamination Reactions
524(2)
Synthesis of Amino Acids
526(10)
Aspartate and Asparagine
526(1)
Box 17.1 Childhood Acute Lymphoblastic Leukemia Can Be Treated with Asparaginase
526(1)
Lysine, Methionine, and Threonine
527(1)
Alanine, Valine, Leucine, and Isoleucine
528(1)
Glutamate, Glutamine, Arginine, and Proline
529(1)
Serine, Glycine, and Cysteine
530(1)
Phenylalanine, Tyrosine, and Tryptophan
531(4)
Box 17.2 Genetically Modified Food
Box 17.3 Essential and Nonessential Amino Acids in Animals
Histidine
535(1)
Amino Acids as Metabolic Precursors
536(2)
Products Derived from Glutamate, Glutamine, and Aspartate
536(1)
Products Derived from Serine and Glycine
536(1)
Synthesis of Nitric Oxide from Arginine
536(2)
Protein Turnover
538(1)
Box 17.4 Apoptosis---Programmed Cell Death
538(1)
Amino Acid Catabolism
539(10)
Alanine, Asparagine, Aspartate, Glutamate, and Glutamine
541(1)
Arginine, Histidine, and Proline
541(1)
Glycine and Serine
542(1)
Threonine
543(1)
The Branched-Chain Amino Acids
543(2)
Methionine
545(1)
Cysteine
546(1)
Phenylalanine, Tryptophan, and Tyrosine
546(1)
Box 17.5 Phenylketonuria, a Defect in Tyrosine Formation
546(2)
Lysine
548(1)
Box 17.6 Diseases of Amino Acid Metabolism
548(1)
The Urea Cycle Converts Ammonia into Urea
549(4)
Synthesis of Carbamoyl Phosphate
549(1)
The Reactions of the Urea Cycle
549(1)
Ancillary Reactions of the Urea Cycle
550(1)
Box 17.7 The Liver Is Organized for Removing Toxic Ammonia
551(2)
Renal Glutamine Metabolism Produces Bicarbonate
553(4)
Summary
554(1)
Problems
555(1)
Selected Readings
556(1)
Nucleotide Metabolism
557(26)
Synthesis of Purine Nucleotides
558(3)
Other Purine Nucleotides Are Synthesized from IMP
561(2)
Box 18.1 Common Names of the Bases
561(2)
Synthesis of Pyrimidine Nucleotides
563(5)
The Pathway for Pyrimidine Synthesis
564(1)
Box 18.2 How Some Enzymes Transfer Ammonia from Glutamine
565(1)
Regulation of Pyrimidine Synthesis
566(2)
CTP Is Synthesized from UMP
568(1)
Reduction of Ribonucleotides to Deoxyribonucleotides
569(1)
Methylation of dUMP Produces dTMP
570(3)
Box 18.3 Free Radicals in the Reduction of Ribonucleotides
570(2)
Box 18.4 Cancer Drugs Inhibit dTTP Synthesis
572(1)
Salvage of Purines and Pyrimidines
573(1)
Purine Catabolism
574(4)
Box 18.5 Lesch-Nyhan Syndrome and Gout
574(4)
The Purine Nucleotide Cycle in Muscle
578(1)
Pyrimidine Catabolism
579(4)
Summary
580(1)
Problems
580(1)
Selected Readings
581(2)
PART FOUR Biological Information Flow
Nucleic Acids
583(32)
Nucleotides Are the Building Blocks of Nucleic Acids
584(6)
Ribose and Deoxyribose
584(1)
Purines and Pyrimidines
585(1)
Nucleosides
586(1)
Nucleotides
587(3)
DNA Is Double-Stranded
590(7)
Nucleotides Are Joined by 3'--5' Phosphodiester Linkages
590(2)
Two Antiparallel Strands Form a Double Helix
592(3)
Weak Forces Stabilize the Double Helix
595(2)
Conformations of Double-Stranded DNA
597(1)
DNA Can Be Supercoiled
597(2)
Cells Contain Several Kinds of RNA
599(1)
DNA Is Packaged in Chromatin in Eukaryotic Cells
599(6)
Nucleosomes
600(1)
Box 19.1 Histones Can Be Acetylated and Deacetylated
601(2)
Higher Levels of Chromatin Structure
603(1)
Bacterial DNA Packaging
604(1)
Nucleases and Hydrolysis of Nucleic Acids
605(5)
Alkaline Hydrolysis of RNA
605(1)
Ribonuclease-Catalyzed Hydrolysis of RNA
605(3)
Restriction Endonucleases
608(2)
EcoRI Binds Tightly to DNA
610(1)
Uses of Restriction Endonucleases
610(5)
Summary
612(1)
Problems
612(1)
Selected Readings
613(2)
DNA Replication, Repair, and Recombination
615(32)
Chromosomal DNA Replication Is Bidirectional
616(2)
DNA Polymerase
618(4)
Chain Elongation Is a Nucleotidyl-Group-Transfer Reaction
619(2)
DNA Polymerase III Remains Bound to the Replication Fork
621(1)
Proofreading Corrects Polymerization Errors
621(1)
DNA Polymerase Synthesizes Two Strands Simultaneously
622(4)
Lagging-Strand Synthesis Is Discontinuous
623(1)
Each Okazaki Fragment Begins with an RNA Primer
623(1)
Okazaki Fragments Are Joined by the Action of DNA Polymerase I and DNA Ligase
624(2)
Model of the Replisome
626(3)
Initiation and Termination of DNA Replication
629(1)
DNA Replication in Eukaryotes
630(4)
Box 20.1 Sequencing DNA Using Dideoxynucleotides
632(2)
Repair of Damaged DNA
634(5)
Repair after Photodimerization: An Example of Direct Repair
635(1)
Excision Repair
635(4)
Homologous Recombination
639(8)
The Holliday Model of General Recombination
639(1)
Recombination in E. coli
640(1)
Recombination Can Be a Form of Repair
641(2)
Box 20.2 Molecular Links Between DNA Repair and Breast Cancer
643(1)
Summary
644(1)
Problems
645(1)
Selected Readings
646(1)
Transcription and RNA Processing
647(36)
Types of RNA
648(1)
RNA Polymerase
649(3)
RNA Polymerase Is an Oligomeric Protein
649(1)
The Chain Elongation Reaction
650(2)
Transcription Initiation
652(4)
Genes Have a 5'→3' Orientation
652(1)
The Transcription Complex Assembles at a Promoter
652(3)
The σ Subunit Recognizes the Promoter
655(1)
RNA Polymerase Changes Conformation
655(1)
Transcription Termination
656(3)
Transcription in Eukaryotes
659(4)
Eukaryotic RNA Polymerases
659(3)
Eukaryotic Transcription Factors
662(1)
The Role of Chromatin in Eukaryotic Transcription
663(1)
Transcription of Genes Is Regulated
663(2)
The lac Operon, an Example of Negative and Positive Regulation
665(5)
lac Repressor Blocks Transcription
665(2)
The Structure of lac Repressor
667(1)
cAMP Regulatory Protein Activates Transcription
668(2)
Posttranscriptional Modification of RNA
670(4)
Transfer RNA Processing
671(1)
Ribosomal RNA Processing
672(2)
Eukaryotic mRNA Processing
674(9)
Eukaryotic mRNA Molecules Have Modified Ends
674(3)
Some Eukaryotic mRNA Precursors Are Spliced
677(3)
Summary
680(1)
Problems
680(2)
Selected Readings
682(1)
Protein Synthesis
683(36)
The Genetic Code
683(3)
Transfer RNA
686(2)
The Three-Dimensional Structure of tRNA
686(2)
tRNA Anticodons Base-Pair with mRNA Codons
688(1)
Aminoacyl-tRNA Synthetases
688(4)
The Aminoacyl-tRNA Synthetase Reaction
689(1)
Specificity of Aminoacyl-tRNA Synthetases
689(2)
Proofreading Activity of Aminoacyl-tRNA Synthetases
691(1)
Ribosomes
692(3)
Ribosomes Are Composed of Both Ribosomal RNA and Protein
693(2)
Ribosomes Contain Two Aminoacyl-tRNA Binding Sites
695(1)
Initiation of Translation
695(2)
Initiator tRNA
695(1)
Initiation Complexes Assemble Only at Initiation Codons
695(1)
Initiation Factors Help Form the Initiation Complex
696(1)
Translation Initiation in Eukaryotes
697(1)
Chain Elongation Is a Three-Step Microcycle
697(8)
Elongation Factors Dock an Aminoacyl-tRNA in the A Site
699(1)
Peptidyl Transferase Catalyzes Peptide Bond Formation
700(1)
Translocation Moves the Ribosome by One Codon
701(4)
Termination of Translation
705(1)
Protein Synthesis Is Energetically Expensive
705(1)
Regulation of Protein Synthesis
705(7)
Ribosomal Protein Synthesis Is Coupled to Ribosome Assembly in E. coli
706(1)
Box 22.1 Some Antibiotics Inhibit Protein Synthesis
707(1)
Globin Synthesis Depends on Heme Availability
707(1)
The E. coli trp Operon Is Regulated by Repression and Attenuation
708(4)
Posttranslational Processing
712(7)
The Signal Hypothesis
712(4)
Glycosylation of Proteins
716(1)
Summary
716(1)
Problems
717(1)
Selected Readings
718(1)
Recombinant DNA Technology
719(30)
Making Recombinant DNA
719(2)
Cloning Vectors
721(6)
Plasmid Vectors
723(1)
Bacteriophage λ Vectors
723(1)
Shuttle Vectors
724(1)
Yeast Artificial Chromosomes as Vectors
724(3)
Identification of Host Cells Containing Recombinant DNA
727(1)
Selection Strategies Use Marker Genes
727(1)
Selection in Eukaryotes
727(1)
Visual Markers: Insertional Inactivation of the β-Galactosidase Gene
727(1)
Genomic Libraries
728(1)
Box 23.1 The Human Genome Project
728(1)
cDNA Libraries Are Made from Messenger RNA
729(1)
Screening a Library
730(3)
Chromosome Walking
733(1)
Expression of Proteins Using Recombinant DNA Technology
734(1)
Prokaryotic Expression Vectors
734(1)
Expression of Proteins in Eukaryotes
734(1)
Applications of Recombinant DNA Technology
735(4)
Genetic Engineering of Plants
737(1)
Genetic Engineering in Prokaryotes
737(2)
Applications to Human Diseases
739(2)
The Polymerase Chain Reaction Amplifies Selected DNA Sequences
741(2)
Box 23.2 Medical Uses of PCR
741(2)
Site-Directed Mutagenesis of Cloned DNA
743(6)
Summary
744(1)
Problems
745(2)
Selected Readings
747(2)
Solutions 749(60)
Illustration Credits 809(2)
Glossary 811(16)
Index 827


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