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Principles Of Biochemistry

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

Principles Of Biochemistry

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

ISBN 13:
9780131453067
ISBN 10:
0131453068
Edition: 4th
Format: Hardcover
Copyright: 06/29/2005
Publisher: 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.

Preface

xxv

PART ONE Introduction

Introduction to Biochemistry

(25)

Biochemistry Is a Modern Science

(1)

The Chemical Elements of Life

(2)

Many Important Macromolecules Are Polymers

(6)

Proteins

(1)

Polysaccharides

(2)

Nucleic Acids

(1)

Lipids and Membranes

(1)

The Energetics of Life

(4)

Reaction Rates and Equilibria

(1)

Thermodynamics

(2)

Equilibrium Constants and Standard Gibbs Free Energy Changes

(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

(1)

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

(2)

Water Is an Excellent Solvent

(2)

Ionic and Polar Substances Dissolve in Water

(1)

Cellular Concentrations and Diffusion

(1)

Osmotic Pressure

(1)

Nonpolar Substances Are Insoluble in Water

(1)

Noncovalent Interactions

(3)

Charge--charge Interactions

(1)

Hydrogen Bonds

(1)

Van der Waals Forces

(1)

Hydrophobic Interactions

(1)

Water Is Nucleophilic

(1)

Ionization of Water

(2)

The pH Scale

(2)

Box 2.1 The little ``p'' in pH.

(1)

Acid Dissociation Constants of Weak Acids

(5)

Buffered Solutions Resist Changes in pH

(6)

Summary

(1)

Problems

(2)

Selected Readings

(1)

PART TWO Structure and Function

Amino Acids and the Primary Structures of Proteins

(32)

General Structure of Amino Acids

(2)

Structures of the 20 Common Amino Acids

(6)

Box 3.1 An Alternative Nomenclature

(1)

Aliphatic R Groups

(1)

Box 3.2 Common Names of Amino Acids

(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

(1)

Protein Purification Techniques

(2)

Analytical Techniques

(3)

Amino Acid Composition of Proteins

(1)

Determining the Sequence of Amino Acid Residues

(2)

Protein Sequencing Strategies

(3)

Comparisons of the Primary Structures of Proteins Reveal Evolutionary Relationships

(6)

Summary

(1)

Problems

(2)

Selected Readings

(1)

Proteins: Three-Dimensional Structure and Function

(45)

There Are Four Levels of Protein Structure

(1)

Methods for Determining Protein Structure

(3)

The Conformation of the Peptide Group

(2)

The α Helix

(3)

β Strands and β Sheets

(2)

Loops and Turns

(1)

Teritary Structure of Proteins

(6)

Supersecondary Structures

(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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Principles Of Biochemistry

Principles Of Biochemistry

9780131453067

0131453068

Summary

Table of Contents

Supplemental Materials

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Amazon no longer offers textbook rentals. We do!

Principles Of Biochemistry

Principles Of Biochemistry

9780131453067

0131453068

Summary

Table of Contents

Supplemental Materials

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