Principles of Biochemistry

by Horton, Robert; Moran, Laurence A.; Scrimgeour, Gray; Perry, Marc; Rawn, David

• ISBN13: 9780130266729
• ISBN10: 0130266728
• Edition: 3rd
• Format: Hardcover
• Copyright: 2006-01-01
• Publisher: Pearson College Div

Summary

For one-semester introductory courses in Biochemistry. May be taught out of departments of chemistry, biology, or biochemistry. This concise, introductory text focuses on the basic principles of biochemistry, filling the gap between the encyclopedic volumes and the cursory overview texts. Widely praised in its previous edition for accuracy, 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

PART ONE Introduction
Introduction to Biochemistry	3	(22)
Biochemistry Is a Modern Science	4	(1)
The Chemical Elements of Life	5	(3)
Many Important Biomolecules Are Polymers	8	(6)
Proteins	8	(1)
Polysaccharides	9	(1)
Nucleic Acids	10	(2)
Lipids and Membranes	12	(2)
The Energetics of Life	14	(1)
Biochemistry and Evolution	15	(1)
The Cell Is the Basic Unit of Life	15	(1)
Prokaryotic Cells: Structural Features	16	(1)
Eukaryotic Cells: Structural Features	17	(4)
The Nucleus	17	(2)
The Endoplasmic Reticulum and Golgi Apparatus	19	(1)
Mitochondria and Chloroplasts	19	(1)
Specialized Vesicles	20	(1)
The Cytoskeleton	21	(1)
A Picture of the Living Cell	21	(2)
Biochemistry Is Multidisciplinary	23	(2)
Appendix: The Special Terminology of Biochemistry	23	(1)
Selected Readings	24	(1)
Water	25	(26)
The Water Molecule Is Polar	26	(1)
Hydrogen Bonding in Water	27	(1)
Ionic and Polar Substances Dissolve in Water	28	(1)
Nonpolar Substances Are Insoluble in Water	29	(2)
Noncovalent Interactions in Biomolecules	31	(2)
Charge-Charge Interactions	31	(1)
Hydrogen Bonds	31	(1)
Van der Waals Forces	32	(1)
Hydrophobic Interactions	33	(1)
Water Is Nucleophilic	33	(2)
Ionization of Water	35	(1)
The pH Scale	36	(1)
Acid Dissociation Constants of Weak Acids	37	(3)
Buffered Solutions Resist Changes in pH	40	(11)
Summary	43	(1)
Problems	43	(2)
Selected Readings	45	(6)
PART TWO Structure and Function of Biomolecules
Amino Acids and the Primary Structures of Proteins	51	(30)
General Structure of Amino Acids	52	(3)
An Alternative Nomenclature	54	(1)
Structures of the 20 Common Amino Acids	55	(4)
Aliphatic R Groups	55	(1)
Aromatic R Groups	56	(1)
Sulfur-Containing R Groups	57	(1)
Side Chains with Alcohol Groups	57	(1)
Basic R Groups	58	(1)
Acidic R Groups and Their Amide Derivatives	58	(1)
The Hydrophobicity of Amino Acid Side Chains	58	(1)
Other Amino Acids and Amino Acid Derivatives	59	(1)
Ionization of Amino Acids	60	(4)
Peptide Bonds Link Amino Acids in Proteins	64	(2)
Protein Purification Techniques	66	(3)
Amino Acid Composition of Proteins	69	(1)
Determining the Sequence of Amino Acid Residues	70	(3)
Protein Sequencing Strategies	73	(4)
Comparisons of the Primary Structures of Proteins Reveal Evolutionary Relationships	77	(4)
Summary	78	(1)
Problems	79	(1)
Selected Readings	80	(1)
Proteins: Three-Dimensional Structure and Function	81	(49)
There Are Four Levels of Protein Structure	83	(1)
Methods for Determining Protein Structure	84	(2)
The Conformation of the Peptide Group	86	(3)
The α Helix	89	(3)
β Strands and β Sheets	92	(2)
Loops and Turns	94	(2)
Tertiary Structure of Proteins	96	(6)
Supersecondary Structures	96	(1)
Domains	97	(5)
Domain Structure and Function	102	(1)
Quaternary Structure	102	(2)
Protein Denaturation and Renaturation	104	(3)
Protein Folding and Stability	107	(5)
The Hydrophobic Effect	107	(2)
Hydrogen Bonding	109	(1)
Van der Waals Interactions and Charge-Charge Interactions	110	(1)
Protein Folding Is Assisted by Chaperones	110	(2)
Collagen, a Fibrous Protein	112	(2)
Structures of Myoglobin and Hemoglobin	114	(2)
Oxygen Binding to Myoglobin and Hemoglobin	116	(5)
Oxygen Binds Reversibly to Heme	116	(1)
Oxygen-Binding Curves of Myoglobin and Hemoglobin	117	(2)
Hemoglobin Is an Allosteric Protein	119	(2)
Antibodies Bind Specific Antigens	121	(9)
Summary	124	(1)
Problems	125	(2)
Selected Readings	127	(3)
Properties of Enzymes	130	(32)
The Six Classes of Enzymes	131	(2)
Kinetic Experiments Reveal Enzyme Properties	133	(2)
Chemical Kinetics	133	(1)
Enzyme Kinetics	134	(1)
The Michaelis-Menten Equation	135	(4)
Derivation of the Michaelis-Menten Equation	137	(1)
The Meanings of Km	138	(1)
Kinetic Constants Indicate Enzyme Activity and Specificity	139	(1)
Measurement of Km and Vmax	140	(1)
Kinetics of Multisubstrate Reactions	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)
Site-Directed Mutagenesis Modifies Enzymes	148	(1)
Regulation of Enzyme Activity	148	(7)
Phosphofructokinase Is an Allosteric Enzyme	149	(1)
General Properties of Allosteric Enzymes	150	(2)
Two Theories of Allosteric Regulation	152	(2)
Regulation by Covalent Modification	154	(1)
Multienzyme Complexes and Multifunctional Enzymes	155	(7)
Summary	156	(1)
Problems	156	(3)
Selected Readings	159	(3)
Mechanisms of Enzymes	162	(35)
The Terminology of Mechanistic Chemistry	162	(2)
Catalysts Stabilize Transition States	164	(2)
Chemical Modes of Enzymatic Catalysis	166	(4)
Polar Amino Acid Residues in Active Sites	166	(1)
Acid-Base Catalysis	167	(1)
Covalent Catalysis	168	(1)
pH Affects Enzymatic Rates	169	(1)
Diffusion-Controlled Reactions	170	(4)
Triose Phosphate Isomerase	171	(2)
Superoxide Dismutase	173	(1)
Binding Modes of Enzymatic Catalysis	174	(6)
The Proximity Effects	175	(2)
Weak Binding of Substrates to Enzymes	177	(1)
Transition-State Stabilization	178	(2)
Induced Fit	180	(2)
Lysozyme Binds an Ionic Intermediate Tightly	182	(3)
Proposed Transition State for a Bimolecular Reaction	185	(1)
Properties of Serine Proteases	185	(12)
Zymogens Are Inactive Enzyme Precursors	186	(1)
Substrate Specificity of Serine Proteases	187	(1)
Serine Proteases Use Both the Chemical and the Binding Modes of Catalysis	188	(4)
Summary	192	(1)
Problems	193	(2)
Selected Readings	195	(2)
Coenzymes and Vitamins	197	(34)
Many Enzymes Require Inorganic Cations	198	(1)
Coenzyme Classification	199	(4)
Metabolite Coenzymes	199	(1)
Nucleosides and Nucleotides	200	(2)
Vitamin-Derived Coenzymes and Nutrition	202	(1)
Vitamin C: A Vitamin but Not a Coenzyme	202	(1)
NADÅ and NADPÅ	203	(4)
NAD Binding to Dehydrogenases	206	(1)
FAD and FMN	207	(4)
An FAD-Requiring Hydroxylase That Has a Unique Test for Its Proper Substrate	208	(1)
Coenzyme A	209	(2)
Thiamine Pyrophosphate	211	(1)
Pyridoxal Phosphate	212	(3)
Biotin	215	(1)
Tetrahydrofolate	216	(2)
Cobalamin	218	(1)
Lipoamide	219	(1)
Lipid Vitamins	220	(2)
Vitamin A	220	(1)
Vitamin D	221	(1)
Vitamin E	221	(1)
Vitamin K	222	(1)
Ubiquinone	222	(1)
Protein Coenzymes	223	(1)
Cytochromes	224	(7)
Summary	226	(1)
Problems	227	(3)
Selected Readings	230	(1)
Carbohydrates	231	(33)
Most Monosaccharides Are Chiral Compounds	232	(4)
Cyclization of Aldoses and Ketoses	236	(2)
Conformations of Monosaccharides	238	(2)
Derivatives of Monosaccharides	240	(3)
Sugar Phosphates	240	(1)
Deoxy Sugars	240	(1)
Amino Sugars	240	(2)
Sugar Alcohols	242	(1)
Sugar Acids	242	(1)
Ascorbic Acid	243	(1)
Disaccharides and Other Glycosides	243	(3)
Structures of Disaccharides	243	(2)
Reducing and Nonreducing Sugars	245	(1)
Nucleosides and Other Glycosides	245	(1)
Nodulation Factors Are Lipo-oligosaccharides	246	(1)
Polysaccharides	246	(5)
Starch and Glycogen	247	(2)
Cellulose and Chitin	249	(2)
Glycoconjugates	251	(13)
Proteoglycans	251	(2)
Decorin and Collagen	253	(1)
Peptidoglycans	253	(1)
Glycoproteins	254	(4)
Summary	258	(1)
Problems	259	(2)
Selected Readings	261	(3)
Lipids and Membranes	264	(45)
Structural and Functional Diversity of Lipids	264	(1)
Fatty Acids	265	(4)
Trans Fatty Acids and Margarine	268	(1)
Triacylglycerols	269	(1)
Glycerophospholipids	270	(2)
Sphingolipids	272	(2)
Steroids	274	(2)
Other Biologically Important Lipids	276	(3)
Special Nonaqueous Techniques Must Be Used to Study Lipids	278	(1)
Biological Membranes Are Composed of Lipid Bilayers and Proteins	279	(3)
Lipid Bilayers	280	(1)
Fluid Mosaic Model of Biological Membranes	281	(1)
Lipid Bilayers and Membranes Are Dynamic Structures	282	(3)
Three Classes of Membrane Proteins	285	(2)
Membrane Transport	287	(6)
Pores and Channels	288	(1)
Passive Transport	289	(1)
Active Transport	290	(1)
Endocytosis and Exocytosis	291	(1)
The Hot Spice of Chili Peppers	292	(1)
Transduction of Extracellular Signals	293	(16)
G Proteins Are Signal Transducers	294	(1)
The Adenylyl Cyclase Signaling Pathway	295	(2)
The Inositol-Phospholipid Signaling Pathway	297	(1)
Bacterial Toxins and G Proteins	298	(2)
Receptor Tyrosine Kinases	300	(1)
Summary	301	(1)
Problems	302	(1)
Selected Readings	303	(6)
PART THREE Metabolism and Bioenergetics
Introduction to Metabolism	309	(31)
Metabolism Is the Sum of Cellular Reactions	309	(4)
Metabolic Pathways Are Sequences of Reactions	311	(1)
Metabolism Proceeds by Discrete Steps	312	(1)
Metabolic Pathways Are Regulated	313	(2)
Major Pathways in Cells	315	(2)
Compartmentation and Interorgan Metabolism	317	(1)
Thermodynamics and Metabolism	318	(4)
Metabolic Pathways Are in a Steady State	319	(1)
Free-Energy Change	319	(1)
Equilibrium Constants and Standard Free-Energy Changes	320	(1)
Actual Free-Energy Change, Not Standard Free-Energy Change, Determines the Spontaneity of Cellular Reactions	321	(1)
The Free Energy of ATP	322	(4)
The Metabolic Roles of ATP	326	(3)
Phosphoryl-Group Transfer	327	(1)
Production of ATP by Phosphoryl-Group Transfer	327	(1)
Nucleotidyl-Group Transfer	328	(1)
Thioesters Have High Free Energies of Hydrolysis	329	(1)
Reduced Coenzymes Conserve Energy From Biological Oxidations	330	(5)
Free-Energy Change Is Related to Reduction Potential	331	(2)
Electron Transfer from NADH Provides Free Energy	333	(1)
NADÅ and NADH Differ in Their Ultraviolet Absorption Spectra	334	(1)
Experimental Methods for Studying Metabolism	335	(5)
Summary	336	(1)
Problems	336	(1)
Selected Readings	337	(3)
Glycolysis	340	(32)
Glycolysis Is a Ubiquitous Pathways	341	(4)
Elucidation of the Glycolytic Pathway	344	(1)
Glycolysis Has 10 Enzyme-Catalyzed Steps	345	(9)
Arsenate Poisoning	351	(3)
The Fate of Pyruvate	354	(2)
Metabolism of Pyruvate to Ethanol	355	(1)
Reduction of Pyruvate to Lactate	355	(1)
Free-Energy Changes in Glycolysis	356	(1)
Regulation of Glycolysis	357	(6)
Regulation of Hexose Transporters	357	(2)
Regulation of Hexokinase	359	(1)
Glucose 6-Phosphate Has a Pivotal Metabolic Role in Liver	359	(1)
Regulation of Phosphofructokinase-1	360	(1)
Regulation of Pyruvate Kinase	361	(2)
The Pasteur Effect	363	(1)
Other Sugars Can Enter Glycolysis	363	(2)
Fructose Is Converted to Glyceraldehyde 3-Phosphate	363	(1)
Galactose Is Converted to Glucose 1-Phosphate	364	(1)
Mannose Is Converted to Fructose 6-Phosphate	365	(1)
Formation of 2,3-Bisphosphoglycerate in Red Blood Cells	365	(7)
Summary	366	(1)
Problems	367	(1)
Selected Readings	368	(4)
The Citric Acid Cycle	372	(27)
Entry of Pyruvate into the Mitochondrion	373	(1)
Conversion of Pyruvate to Acetyl CoA	373	(4)
The Citric Acid Cycle Oxidizes Acetyl CoA	377	(2)
The Citric Acid Cycle Can Be a Multistep Catalyst	379	(8)
Three-Point Attachment of Prochiral Substrates to Enzymes	383	(4)
Reduced Coenzymes Fuel the Production of ATP	387	(1)
Regulation of the Citric Acid Cycle	388	(3)
Entry and Exit of Metabolites	391	(2)
The Glyoxylate Cycle	393	(6)
Summary	396	(1)
Problems	397	(1)
Selected Readings	398	(1)
Additional Pathways in Carbohydrate Metabolism	399	(30)
Glycogen Degradation	400	(2)
Glycogen Phosphorylase	400	(2)
Metabolism of Glycose 1-Phosphate	402	(1)
Glycogen Synthesis	402	(2)
Glycogen Storage Diseases	403	(1)
Regulation of Glycogen Metabolism	404	(4)
Hormones Rgulate Glycogen Metabolism	404	(1)
Reciprocal Regulation of Glycogen Phosphorylase and Glycogen Synthase	405	(1)
Intracellular Regulation of Glycogen Metabolism Involves Interconvertible Enzymes	406	(2)
Gluconeogenesis	408	(4)
Precursors for Gluconeogenesis	412	(2)
Lactate	412	(1)
Amino Acids	412	(1)
Glycerol	413	(1)
Propionate and Lactate	413	(1)
Subcellular Locations of Gluconeogenic Enzymes	414	(1)
Regulation of Gluconeogenesis	415	(2)
Glucose Is Sometimes Converted to Sorbitol	417	(1)
The Pentose Phosphate Pathway	417	(4)
Interconversions Catalyzed by Transketolase and Transaldolase	421	(3)
Maintenance of Glucose Levels in Mammals	424	(5)
Summary	426	(1)
Problems	427	(1)
Selected Readings	428	(1)
Electron Transport and Oxidative Phosphorylation	429	(33)
Superoxide Anions	430	(1)
Cytochrome P450	431	(1)
Hydrogenase and Fumarate Reductase	431	(1)
Oxidative Phosphorylation in Mitochondria	432	(2)
The Mitochondrion	434	(1)
The Chemiosmotic Theory	435	(3)
New Lipid Vesicles, or Liposomes	437	(1)
The Protonmotive Force	438	(2)
Overview of Electron Transport	440	(3)
Complexes I Through IV	440	(3)
Cofactors in Electron Transport	443	(1)
Complex I	443	(1)
Complex II	444	(1)
Complex III	445	(2)
Complex IV	447	(2)
Complex V: ATP Synthase	449	(3)
Active Transport of ATP, ADP, and P, Across the Mitochondrial Membrane	452	(1)
The P/O Ratio	452	(1)
Are Proton Leaks Functional?	453	(1)
Aerobic Oxidation of Cytosolic NADH	453	(3)
Regulation of Oxidative Phosphorylation	456	(6)
Summary	456	(1)
Problems	457	(1)
Selected Readings	458	(4)
Photosynthesis	462	(28)
Photosynthesis Consists of Two Major Processes	463	(1)
The Chloroplast	463	(1)
Chlorophy II and Other Pigments Capture Light	464	(3)
Light-Capturing Pigments	465	(2)
Photosystems	467	(1)
Electron Transport in Photosynthesis	467	(6)
Electron Transport from PSII through Cytochrome bf	470	(1)
PSI and Beyond	471	(2)
Photoposphorylation and Cyclic Electron Flow	473	(1)
The Dark Reactions	474	(1)
Ribulose 1,5-Bisphosphate Carboxylase-Oxygenase	474	(3)
The RPP Cycle	477	(2)
Oxygenation of Ribulose 1,5-Bisphosphate	479	(1)
Additional Carbon-Fixing Pathways	480	(2)
The C4 Pathway Concentrates CO2	480	(1)
Nocturnal CO2 Fixation	480	(2)
Synthesis of Sucrose and Starch from RPP Metabolites	482	(8)
Summary	485	(1)
Problems	485	(2)
Selected Readings	487	(3)
Lipid Metabolism	490	(40)
Absorption and Mobilization of Fatty Acids	490	(6)
Absorption of Dietary Lipids	491	(1)
Lipoproteins	492	(1)
Our High-Fat Diets	492	(3)
Storage and Mobilization of Fatty Acids	495	(1)
Fatty Acid Oxidation	496	(3)
Activation of Fatty Acids	496	(1)
Transport of Fatty Acyl CoA into Mitochondria	496	(1)
The Reactions of β-Oxidation	497	(2)
ATP Generation from Fatty Acid Oxidation	499	(1)
βOxidation of Odd-Chain and Unsaturated Fatty Acids	499	(3)
Ketone Bodies Are Fuel Molecules	502	(3)
Ketone Bodies Are Synthesized in the Liver	502	(1)
Ketone Bodies Are Oxidized in Mitochondria	503	(1)
Altered Carbohydrate and Lipid Metabolism in Diabetes	504	(1)
Fatty Acid Synthesis	505	(6)
Transport of Acetyl CoA to the Cytosol	506	(1)
Carboxylation of Acetyl CoA	507	(1)
The Reactions of Fatty Acid Synthesis	507	(4)
Fatty Acid Elongation and Desaturation	511	(1)
Regulation of Fatty Acid Oxidation	512	(1)
Synthesis of Eicosanoids	513	(1)
Synthesis of Triacylglycerols and Glycerophospholipids	514	(4)
Search for a Replacement for Aspirin	515	(3)
Synthesis of Ether Lipids	518	(1)
Synthesis of Sphingolipids	518	(4)
Lysosomal Storage Diseases	521	(1)
Synthesis of Cholesterol	522	(4)
Stage 1: Acetyl CoA Isopentenyl Pyrophosphate	522	(1)
Isopentenly Pyrophosphate to Squalene	523	(2)
Stage 3: Squalene to Cholesterol	525	(1)
Other Products of Cholesterol Metabolism	525	(1)
Lipids are Made at a Variety of Sites	526	(4)
Acetyl CoA Is a Major Metabolite in Liver	526	(1)
Summary	527	(1)
Problems	528	(1)
Selected Readings	529	(1)
Amino Acid Metabolism	530	(38)
The Nitrogen Cycle and Nitrogen Fixation	531	(2)
Assimilation of Ammonia	533	(4)
Ammonia Is Incorporated into Glutamate	533	(1)
Glutamine Is a Nitrogen Carrier	534	(1)
Regulation of Glutamine Synthetase in E. Coli	535	(1)
How Some Enzymes Transfer Ammonia from Glutamine	535	(2)
Transamination Reactions	537	(2)
Synthesis of Nonessential Amino Acids	539	(5)
Alanine, Asparagine, Aspartate, Glutamate, and Glutamine	539	(1)
Serine, Glycine, and Cysteine	540	(2)
Proline and Arginine	542	(1)
Tyrosine	542	(1)
Phenylketonuria, a Defect in Tyrosine Formation	543	(1)
Synthesis of Essential Amino Acids	544	(5)
Lysine, Methionine, Threonine, and the Branched-Chain Amino Acids	544	(1)
Histidine	545	(1)
Aromatic Amino Acids	546	(3)
Protein Turnover	549	(1)
Apoptosis---Programmed Cell Death	549	(1)
Amino Acid Catabolism	550	(1)
The Urea Cycle Converts Ammonia into Urea	550	(5)
The Reactions of the Urea Cycle	552	(1)
The Liver Is Organized for Removing Toxic Ammonia	553	(1)
Ancillary Reactions of the Urea Cycle	554	(1)
Catabolism of the Carbon of Amino Acids	555	(8)
Alanine, Asparagine, Aspartate, Glutamate, and Glutamine	556	(1)
Arginine, Histidine, and Proline	556	(1)
Glysine and Serine	557	(1)
Threonine	558	(1)
The Branched-Chain Amino Acids	558	(2)
Methionine	560	(1)
Cysteine	561	(1)
Phenylalanine, Tryptophan, and Tyrosine	561	(1)
Lysine	562	(1)
Diseases of Amino Acid Metabolism	562	(1)
Renal Glutamine Metabolism Produces Bicarbonate	563	(1)
Synthesis of Nitric Oxide from Arginnine	564	(4)
Summary	565	(1)
Problems	565	(2)
Selected Readings	567	(1)
Nucleotide Metabolism	568	(31)
Synthesis of Purine Nucleotides	569	(3)
Other Purine Nucleotides are Synthesized from IMP	572	(2)
Synthesis of Pyrimidine Nucleotides	574	(4)
The Pathway for De Novo Pyrimidine Synthesis	574	(2)
Regulation of DE Novo Pyrimidine Synthesis	576	(2)
CTP Is Synthesized from UMP	578	(1)
Reduction of Ribonucleotides to Deoxyribonucleotides	579	(1)
Methylation of DUMP Produces dTMP	580	(4)
Free Radicals in the Reduction of Ribonucleotides	581	(3)
Salvage of Purines and Pyrimidines	584	(2)
Purine Catabolism	586	(3)
Adenosine Has Hormone and Neurotransmitter Properties	587	(2)
The Purine Nucleotide Cycle in Muscle	589	(2)
Pyrimidine Catabolism	591	(8)
Summary	591	(1)
Problems	592	(1)
Selected Readings	593	(6)
PART FOUR Biological Information Flow
Nucleic Acids	599	(33)
Nucleotides are the Building Blocks of Nucleic Acids	600	(6)
Ribose and Deoxyribose	600	(1)
Purines and Pyrimidines	601	(1)
Nucleosides	602	(2)
Nucleotides	604	(2)
DNA Is Double-Stranded	606	(8)
Nucleotides are Joined by 3'-5' Phosphodiester Linkages	607	(2)
Two Antiparallel Strands Form a Double Helix	609	(1)
Weak Forces Stabilize the Double Helix	610	(3)
Conformations of Double-Stranded DNA	613	(1)
DNA Can Be Supercoiled	614	(1)
Cells Contain Several Kinds of RNA	615	(1)
DNA Is Packaged in Chromation in Eukaryotic Cells	616	(5)
Nucleosomes	617	(2)
Histones Can be Acetuylated and Deacetylated	619	(1)
Higher Levels of Chromatin Structure	619	(1)
Bacterial DNA Packaging	620	(1)
Nucleases and Hydrolysis of Nucleic Acids	621	(6)
Alkaline Hydrolysis of RNA	621	(2)
Ribonuclease-Catalyzed Hydrolysis of RNA	623	(1)
Restriction Endonucleases	623	(3)
EcoRI Binds Tightly to DNA	626	(1)
Uses of Restriction Endonucleases	627	(5)
Summary	629	(1)
Problems	629	(2)
Selected Readings	631	(1)
DNA Replication, Repair, and Recombination	632	(34)
Chromosomal DNA Replication Is Bidirectional	633	(2)
DNA Polymerase	635	(4)
Chain Elongation Is a Nucleotidyl-Group-Transfer Reaction	637	(1)
DNA Polymerase III Remains Bound to the Replication Fork	637	(1)
Proofreading Corrects Polymerization Errors	638	(1)
DNA Polymerase Synthesizes Two Strands Simultaneously	639	(5)
Lagging-Strand Synthesis Is Discontinuous	639	(1)
Each Okazaki Fragment Begins with an RNA Primer	640	(1)
Okazaki Fragments Are Joined by the Action of DNA Polymerase I and DNA Ligase	641	(3)
Model of the Replisome	644	(2)
Initiation and Termination of DNA Replication	646	(1)
Sequencing DNA Using Dideoxynucleotides	647	(2)
DNA Replication in Eukaryotes	649	(1)
Repair of Damaged DNA	650	(15)
Repair after Photodimerization: An Example of Direct Repair	651	(1)
Excision Repair	652	(13)
Homologous Recombination	665	(1)
The Holliday Model of General Recombination	655	(2)
Recombination in E. coli	657	(1)
Recombination Can Be a Form of Repair	658	(2)
Summary	660	(1)
Problems	661	(2)
Selected Readings	663	(3)
Transcription and RNA Processing	666	(34)
Types of RNA	667	(1)
RNA Polymerase	668	(2)
RNA Polymerase Is an Oligomeric Protein	668	(1)
The Chain Elongation Reaction	669	(1)
Transcription Initiation	670	(6)
Genes Have a 5'→ 3' Orientation	671	(1)
The Transcription Complex Assembles at a Promoter	671	(2)
The σ Subunit Recognizes the Promoter	673	(1)
RNA Polymerase Changes Conformation	674	(2)
Transcription Termination	676	(2)
Transcription in Eukaryotes	678	(3)
Eukaryotic RNA Polymerases	678	(1)
Eukaryotic RNA Factors	678	(3)
Transcription of Genes Is Regulated	681	(2)
The lac Operon. an Example of Negative and Positive Regulation	683	(6)
lac Repressor Blocks Transcription	683	(1)
The Structure of lac Repressor	684	(2)
cAMP Regulatory Protein Activates Transcription	686	(3)
Posttranscriptional Modification of RNA	689	(2)
Transfer RNA Processing	689	(1)
Ribosomal RNA Processing	689	(2)
Eukaryotic mRNA Processing	691	(9)
Eukaryotic mRNA Molecules Have Modified Ends	691	(2)
Some Eukaryotic mRNA Precursors Are Spliced	693	(5)
Summary	698	(1)
Problems	698	(1)
Selected Readings	699	(1)
Protein Synthesis	700	(35)
The Genetic Code	700	(3)
Transfer RNA	703	(3)
The Three-Dimensional Structure of tRNA	703	(2)
tRNA Anticodons Base-Pair with mRNA Codons	705	(1)
Aminoacyl-tRNA Synthetases	706	(3)
The Aminoacyl-tRNA Synthetases Reaction	706	(1)
Specificity of Aminoacyl-tRNA Synthetase Reaction	706	(3)
Proofreading Activity of Aminoacyl-tRNA Synthetases	709	(1)
Ribosomes	709	(3)
Ribosomes Are Composed of Both Ribosomal RNA and Protein	710	(1)
Ribosomes Contain Two Aminoacyl-tRNA Binding Sites	711	(1)
Initiation of Translation	712	(3)
Initiator tRNA	712	(1)
Initiation Complexes Assemble Only at Initiation Codons	712	(1)
Initiation Factors Help Form the Initiation Complex	713	(2)
Translation Initiation in Eukaryotes	715	(1)
Chain Elongation Is a Three-Step Microcycle	715	(5)
Elongation Factors Dock an Aminoacyl-tRNA in the A Site	716	(2)
Peptidyl Transferase Catalyzes Peptide Bond Formation	718	(2)
Translocation Moves the Ribosome by One Codon	720	(1)
Termination of Translation	720	(2)
Protein Synthesis Is Energetically Expensive	722	(1)
Regulation of Protein Synthesis	722	(6)
Ribosomal Protein Synthesis Is Coupled to Ribosome Assembly in E. coli	722	(1)
Some Antibiotics Inhibit Protein Synthesis	723	(1)
Globin Synthesis Depends on Heme Availability	724	(1)
The E. coli trp Operon Is Regulated by Repression and Attenuation	725	(3)
Posttranslational Processing	728	(7)
The Signal Hypothesis	728	(4)
Glycosylation of Proteins	732	(1)
Summary	733	(1)
Problems	733	(1)
Selected Readings	734	(1)
Recombinant DNA Technology	735	(32)
Making Recombinant DNA	735	(2)
Cloning Vectors	737	(5)
Plasmid Vectors	739	(1)
Bacteriophage β Vectors	739	(2)
Shuttle Vectors	741	(1)
Yeast Artificial Chromosomes as Vectors	741	(1)
Identification of Host Cells Containing Recombinant DNA	742	(2)
Selection Strategies Use Marker Genes	742	(1)
Selection in Eukaryotes	743	(1)
Visual Markers: Insertional Inactivation of the β-Galactosidase Gene	744	(1)
Genomic Libraries	744	(1)
The Human Genome Project	745	(1)
cDNA Libraries Are Made from Messenger RNA	745	(2)
Screening a Library	747	(2)
Chromosome Walking	749	(1)
Expression of Proteins Using Recombinant DNA Technology	750	(3)
Prokaryotic Expression Vectors	750	(1)
Expression of Proteins in Eukaryotes	751	(2)
Applications of Recombinant DNA Technology	753	(2)
Genetic Engineering of Plants	753	(2)
Genetic Engineering in Prokaryotes	755	(1)
Applications to Human Diseases	755	(2)
The Polymerase Chain Reaction Amplifies Selected DNA Sequences	757	(3)
Medical Uses of PCR	759	(1)
Site-Directed Mutagenesis of Cloned DNA	760	(7)
Summary	761	(1)
Problems	761	(2)
Selected Readings	763	(4)
Solutions	767	(54)
Illustration Credits	821	(2)
Glossary	823	(14)
Index	837