Rent 9780130266729 | Principles of Biochemistry | Horton, Robert; Moran, Laurence A.; Scrimgeour, Gray; Perry, Marc; Rawn, David @knetbooks.com

Summary Table of Contents

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.

PART ONE Introduction

Introduction to Biochemistry

(22)

Biochemistry Is a Modern Science

(1)

... MORE

The Chemical Elements of Life

(3)

Many Important Biomolecules Are Polymers

(6)

Proteins

(1)

Polysaccharides

(1)

Nucleic Acids

(2)

Lipids and Membranes

(2)

The Energetics of Life

(1)

Biochemistry and Evolution

(1)

The Cell Is the Basic Unit of Life

(1)

Prokaryotic Cells: Structural Features

(1)

Eukaryotic Cells: Structural Features

(4)

The Nucleus

(2)

The Endoplasmic Reticulum and Golgi Apparatus

(1)

Mitochondria and Chloroplasts

(1)

Specialized Vesicles

(1)

The Cytoskeleton

(1)

A Picture of the Living Cell

(2)

Biochemistry Is Multidisciplinary

(2)

Appendix: The Special Terminology of Biochemistry

(1)

Selected Readings

(1)

Water

(26)

The Water Molecule Is Polar

(1)

Hydrogen Bonding in Water

(1)

Ionic and Polar Substances Dissolve in Water

(1)

Nonpolar Substances Are Insoluble in Water

(2)

Noncovalent Interactions in Biomolecules

(2)

Charge-Charge Interactions

(1)

Hydrogen Bonds

(1)

Van der Waals Forces

(1)

Hydrophobic Interactions

(1)

Water Is Nucleophilic

(2)

Ionization of Water

(1)

The pH Scale

(1)

Acid Dissociation Constants of Weak Acids

(3)

Buffered Solutions Resist Changes in pH

(11)

Summary

(1)

Problems

(2)

Selected Readings

(6)

PART TWO Structure and Function of Biomolecules

Amino Acids and the Primary Structures of Proteins

(30)

General Structure of Amino Acids

(3)

An Alternative Nomenclature

(1)

Structures of the 20 Common Amino Acids

(4)

Aliphatic R Groups

(1)

Aromatic R Groups

(1)

Sulfur-Containing R Groups

(1)

Side Chains with Alcohol Groups

(1)

Basic R Groups

(1)

Acidic R Groups and Their Amide Derivatives

(1)

The Hydrophobicity of Amino Acid Side Chains

(1)

Other Amino Acids and Amino Acid Derivatives

(1)

Ionization of Amino Acids

(4)

Peptide Bonds Link Amino Acids in Proteins

(2)

Protein Purification Techniques

(3)

Amino Acid Composition of Proteins

(1)

Determining the Sequence of Amino Acid Residues

(3)

Protein Sequencing Strategies

(4)

Comparisons of the Primary Structures of Proteins Reveal Evolutionary Relationships

(4)

Summary

(1)

Problems

(1)

Selected Readings

(1)

Proteins: Three-Dimensional Structure and Function

(49)

There Are Four Levels of Protein Structure

(1)

Methods for Determining Protein Structure

(2)

The Conformation of the Peptide Group

(3)

The α Helix

(3)

β Strands and β Sheets

(2)

Loops and Turns

(2)

Tertiary Structure of Proteins

(6)

Supersecondary Structures

(1)

Domains

(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

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Principles of Biochemistry

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