Principles of biochemistry 4th ed h r horton, l moran, k g scrimgeour (pearson, 2006) 1

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Principles of
Biochemistry

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Principles of
Biochemistry
FOURTH EDITION
PHOTO TO
COME

H. Robert Horton
North Carolina State University

Laurence A. Moran
University of Toronto

K. Gray Scrimgeour
University of Toronto

Marc D. Perry
University of Toronto

J. David Rawn
Towson State University

Upper Saddle River, NJ 07458

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Library of Congress Cataloging-in-Publication Data
Principles of biochemistry / H. Robert Horton . . . [et al.].—4th ed.
p. cm.
Includes bibliographical references and index.
ISBN 0-13-145306-8
I. Biochemistry. I. Horton, H. Robert.
QP514.2.P745 2006
612'.015—dc22
550-dc22
2005007745

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Science should be as simple
as possible, but not simpler.
—Albert Einstein

v

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PHOTO TO
COME

The Authors
H. Robert Horton
Dr. Horton, who received his Ph.D from the
University of Missouri in 1962, is William
Neal Reynolds Professor Emeritus and
Alumni Distinguished Professor Emeritus
in the Department of Biochemistry at North
Carolina State University, where he served
on the faculty for over 30 years. Most of
Professor Horton’s research was in protein
and enzyme mechanisms.
Laurence A. Moran
After earning his Ph.D from Princeton University in 1974, Professor Moran spent four
years at the Université dè Geneve in
Switzerland. He has been a member of the
Department of Biochemistry at the University of Toronto since 1978, specializing in
molecular biology and molecular evolution.
His research findings on heat-shock genes
have been published in many scholarly

journals.
K. Gray Scrimgeour
Professor Scrimgeour received his doctorate from the University of Washington in
1961 and has been a faculty member at the
University of Toronto since 1967. He is the
author of The Chemistry and Control of Enzymatic Reactions (1977, Academic Press),
and his work on enzymatic systems has
been published in more than 50 professional journal articles during the past 40 years.
From 1984–1992, he was editor of the journal Biochemistry and Cell Biology.

Marc D. Perry
After earning his Ph.D. from the University of Toronto in 1988, Dr. Perry trained at
the University of Colorado, where he studied sex determination in the nematode
C. elegans. In 1994 he returned to the
University of Toronto as a faculty member
in the department of Molecular and Medical Genetics. His research has focused on
developmental genetics, meiosis and bioinformatics. In 2004 he joined the Heart
& Stroke / Richard Lewar Centre of
Excellence in Cardiovascular Research in
the University of Toronto’s Faculty of
Medicine.
J. David Rawn
Professor Rawn, who received his Ph.D
from Ohio State University in 1971, has
taught and done research in the Department
of Chemistry at Towson State University
for the past 25 years. He did not write chapters for Principles of Biochemistry, but his
textbook Biochemistry (1989, Neil Patterson) served as a source of information and
ideas concerning content and organization.

New problems and solutions for the fourth edition were created by Drs. Laurence A. Moran,
University of Toronto and Elizabeth S. Roberts-Kirchhoff, University of Detroit Mercy. The
remaining problems were created by Drs. Robert N. Lindquist, San Francisco State University, Marc Perry and Diane M. De Abreu of the University of Toronto.

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Student Supplements

THE BIOCHEMISTRY STUDENT COMPANION
by Allen J. Scism
Central Missouri State University

No student should be without this helpful resource. Contents include the following:
• carefully constructed drill problems for each chapter, including short-answer, multiplechoice, and challenge problems
• comprehensive, step-by-step solutions and explanations for all problems
• a remedial chapter that reviews the general and organic chemistry that students require for
biochemistry—topics are ingeniously presented in the context of a metabolic pathway
• tables of essential data

Please order through your college bookstore or call Prentice Hall at 1-800-947-7700.
The Biochemistry Student Companion
ISBN 0-13-147605-X

COMPANION WEBSITE

An online student tool that includes 3-D modules to help visualize biochemistry and MediaLabs to investigate important issues related to its particular chapter. Please visit the site at
http://www. prenhall.com/horton.

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Brief Contents
PART ONE
Introduction
1 Introduction to Biochemistry
2 Water
PART TWO
Structure and Function
3 Amino Acids and the Primary Structures of Proteins
4 Proteins: Three-Dimensional Structure and Function
5 Properties of Enzymes
6 Mechanisms of Enzymes
7 Coenzymes and Vitamins
8 Carbohydrates
9 Lipids and Membranes
PART THREE
Metabolism
and Bioenergetics
10 Introduction to Metabolism
11 Glycolysis

12 Gluconeogenesis, The Pentose Phosphate Pathway,
and Glycogen Metabolism
13 The Citric Acid Cycle
14 Electron Transport and ATP Synthesis
15 Photosynthesis
16 Lipid Metabolism
17 Amino Acid Metabolism
18 Nucleotide Metabolism
PART FOUR
Biological Information Flow
19 Nucleic Acids
20 DNA Replication, Repair, and Recombination
21 Transcription and RNA Processing
22 Protein Synthesis
23 Recombinant DNA Technology

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Contents
Preface

xxv

PART ONE

Introduction

1

Introduction to Biochemistry

1.1

Biochemistry Is a Modern Science

1.2

The Chemical Elements of Life

1.3

Many Important Macromolecules Are Polymers
A. Proteins

2
3
5

6

B. Polysaccharides
C. Nucleic Acids

7
9

D. Lipids and Membranes
1.4

1

The Energetics of Life

10

11

A. Reaction Rates and Equilibria
B. Thermodynamics

12

13

C. Equilibrium Constants and Standard Gibbs Free Energy Changes
1.5

Biochemistry and Evolution

1.6

The Cell Is the Basic Unit of Life

1.7

Prokaryotic Cells: Structural Features

17

1.8

Eukaryotic Cells: Structural Features

18

A. The Nucleus

15
16

18

B. The Endoplasmic Reticulum and Golgi Apparatus
C. Mitochondria and Chloroplasts
D. Specialized Vesicles
E. The Cytoskeleton

20

21
22

1.9

A Picture of the Living Cell

1.10

Biochemistry Is Multidisciplinary

22
24

Appendix: The Special Terminology of Biochemistry
Selected Readings

19

25

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Contents

2

Water

2.1

The Water Molecule Is Polar

27

2.2

Hydrogen Bonding in Water

28

2.3

Water Is an Excellent Solvent

26

30

A. Ionic and Polar Substances Dissolve in Water
B. Cellular Concentrations and Diffusion
C. Osmotic Pressure

31

31

2.4

Nonpolar Substances Are Insoluble in Water

2.5

Noncovalent Interactions
B. Hydrogen Bonds

33

34

C. Van der Waals Forces

35

D. Hydrophobic Interactions
2.6

Water Is Nucleophilic

2.7

Ionization of Water

2.8

The pH Scale

36

36
37

39

Box 2.1 The little “p” in pH.

40

2.9

Acid Dissociation Constants of Weak Acids

2.10

Buffered Solutions Resist Changes in pH
49

Problems

49

32

33

A. Charge–charge Interactions

Summary

30

Selected Readings

41
46

51

PART TWO
Structure and Function

3

Amino Acids and the Primary Structures of Proteins

3.1

General Structure of Amino Acids

3.2

Structures of the 20 Common Amino Acids

53

Box 3.1 An Alternative Nomenclature

A. Aliphatic R Groups

56
57

58

C. Sulfur-Containing R Groups

58

D. Side Chains with Alcohol Groups
E. Basic R Groups

55

57

Box 3.2 Common Names of Amino Acids
B. Aromatic R Groups

59

59

F. Acidic R Groups and Their Amide Derivatives

60

G. The Hydrophobicity of Amino Acid Side Chains

3.3

52

Other Amino Acids and Amino Acid Derivatives

60

61

3.4

Ionization of Amino Acids

3.5

Peptide Bonds Link Amino Acids in Proteins

62

3.6

Protein Purification Techniques

3.7

Analytical Techniques

3.8

Amino Acid Composition of Proteins

3.9

Determining the Sequence of Amino Acid Residues

3.10

Protein Sequencing Strategies

3.11

Comparisons of the Primary Structures of Proteins Reveal Evolutionary
Relationships 78

66

67

69
72
73

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Contents

Summary

81

Problems

81

Selected Readings

83

4

Proteins: Three-Dimensional Structure
and Function 84

4.1

There Are Four Levels of Protein Structure

86

4.2

Methods for Determining Protein Structure

87

4.3

The Conformation of the Peptide Group

4.4

The a Helix

4.5

b Strands and b Sheets

95

4.6

Loops and Turns

4.7

Tertiary Structure of Proteins

97
98

A. Supersecondary Structures
B. Domains

99

100

C. Domain Structure and Function
4.8

90

92

Quaternary Structure

104

104

4.9

Protein Denaturation and Renaturation

4.10

Protein Folding and Stability

110

A. The Hydrophobic Effect

110

B. Hydrogen Bonding

107

111

C. Van der Waals Interactions and Charge–Charge Interactions
D. Protein Folding Is Assisted by Molecular Chaperones
4.11

Collagen, a Fibrous Protein

4.12

Structures of Myoglobin and Hemoglobin

4.13

Oxygen Binding to Myoglobin and Hemoglobin

115

A. Oxygen Binds Reversibly to Heme

116

118

118

B. Oxygen-Binding Curves of Myoglobin and Hemoglobin
C. Hemoglobin Is an Allosteric Protein
4.14

Antibodies Bind Specific Antigens
Summary

125

Problems

125

Selected Readings

123

127

Properties of Enzymes

5.1

The Six Classes of Enzymes

5.2

Kinetic Experiments Reveal Enzyme Properties
A. Chemical Kinetics

5.3

119

121

5

B. Enzyme Kinetics

112

112

129

130
132

133
134

The Michaelis–Menten Equation

135

A. Derivation of the Michaelis–Menten Equation
B. The Catalytic Constant kcat
C. The Meanings of Km

137

138

138

5.4

Kinetic Constants Indicate Enzyme Activity and Catalytic Proficiency

5.5

Measurement of Km and Vmax

5.6

Kinetics of Multisubstrate Reactions

140
141

Box 5.1 Hyperbolas versus Straight Lines

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5.7

Reversible Enzyme Inhibition
A. Competitive Inhibition

142

143

B. Uncompetitive Inhibition

145

C. Noncompetitive Inhibition

146

D. Uses of Enzyme Inhibition

146

5.8

Irreversible Enzyme Inhibition

147

5.9

Allosteric Enzymes

5.10

Regulation of Enzyme Activity

148
148

A. Phosphofructokinase Is an Allosteric Enzyme
B. General Properties of Allosteric Enzymes
C. Two Theories of Allosteric Regulation

152

D. Regulation by Covalent Modification
5.11

149

150

153

Multienzyme Complexes and Multifunctional Enzymes
Summary

154

Problems

155

Selected Readings

157

6

Mechanisms of Enzymes

6.1

The Terminology of Mechanistic Chemistry
A. Nucleophilic Substitutions
B. Cleavage Reactions

158
158

159

160

C. Oxidation—Reduction Reactions

160

6.2

Catalysts Stabilize Transition States

6.3

Chemical Modes of Enzymatic Catalysis

160
162

Box 6.1 Site-Directed Mutagenesis Modifies Enzymes
A. Polar Amino Acid Residues in Active Sites
B. Acid–Base Catalysis
C. Covalent Catalysis

164
166

Diffusion-Controlled Reactions

167

A. Triose Phosphate Isomerase

167

B. Superoxide Dismutase
6.5

170

Binding Modes of Enzymatic Catalysis
A. The Proximity Effect

171

172

B. Weak Binding of Substrates to Enzymes
C. Induced Fit

163

163

165

D. pH Affects Enzymatic Rates
6.4

154

172

174

D. Transition-State Stabilization
6.6

Lysozyme

6.7

Properties of Serine Proteases

175

178

Box 6.2 Proposed Transition State for a Bimolecular Reaction

181

182

A. Zymogens Are Inactive Enzyme Precursors
B. Substrate Specificity of Serine Proteases

182
183

C. Serine Proteases Use Both the Chemical and the Binding
Modes of Catalysis 184

Summary

188

Problems

188

Selected Readings

191

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Contents

7

Coenzymes and Vitamins

7.1

Many Enzymes Require Inorganic Cations

7.2

Coenzyme Classification

7.3

ATP and Other Nucleotide Cosubstrates

7.4

NADP ᮍ and NAD ᮍ

192
193

193

Box 7.1 Vitamin C: A Vitamin but Not a Coenzyme
197

Box 7.2 NAD Binding to Dehydrogenases
7.5

FAD and FMN

7.6

Coenzyme A

7.7

Thiamine Pyrophosphate

7.8

Pyridoxal Phosphate

199

200
201
202

203

7.9

Biotin

7.10

Tetrahydrofolate

7.11

Cobalamin

210

7.12

Lipoamide

211

7.13

Lipid Vitamins

212

A. Vitamin A

213

207
208

B. Vitamin D

213

C. Vitamin E

213

D. Vitamin K

214

7.14

Ubiquinone

7.15

Protein Coenzymes

7.16

Cytochromes

214
215

216

Summary

218

Problems

219

Selected Readings

221

8

Carbohydrates

8.1

Most Monosaccharides Are Chiral Compounds

8.2

Cyclization of Aldoses and Ketoses

226

8.3

Conformations of Monosaccharides

229

8.4

Derivatives of Monosaccharides

222

A. Sugar Phosphates

231

C. Amino Sugars

231

E. Sugar Acids
F. Ascorbic Acid

8.7

231

232

233
234

Disaccharides and Other Glycosides
A. Structures of Disaccharides

8.6

234

234

B. Reducing and Nonreducing Sugars

236

C. Nucleosides and Other Glycosides

236

Polysaccharides

237

A. Starch and Glycogen

237

B. Cellulose and Chitin

239

Glycoconjugates
A. Proteoglycans

223

231

B. Deoxy Sugars
D. Sugar Alcohols

8.5

195

196

241
241

Box 8.1 Nodulation Factors Are Lipo-oligosaccharides

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Contents

B. Peptidoglycans

243

C. Glycoproteins

244

Box 8.2 ABO Blood Group
Summary

249

Problems

250

Selected Readings

248

252

9

Lipids and Membranes

9.1

Structural and Functional Diversity of Lipids

9.2

Fatty Acids

Inner
leaflet

253
253

254

Box 9.1 Common Names of Fatty Acids.

255

Box 9.2 Trans Fatty Acids and Margarine

256

9.3

Triacylglycerols

258

9.4

Glycerophospholipids

9.5

Sphingolipids

9.6

Steroids

9.7

Other Biologically Important Lipids

9.8

Biological Membranes Are Composed of Lipid Bilayers and Proteins

259

262

Outer
leaflet

264
265

Box 9.3 Special Nonaqueous Techniques Must Be Used to Study Lipids
A. Lipid Bilayers

270

9.9

Lipid Bilayers and Membranes Are Dynamic Structures

9.10

Three Classes of Membrane Proteins

9.11

Membrane Transport

275

278

A. Thermodynamics of Membrane Transport
B. Pores and Channels
C. Passive Transport

279

280
281
281

E. Endocytosis and Exocytosis

283

Box 9.5 The Hot Spice of Chili Peppers
Transduction of Extracellular Signals

284
284

A. G Proteins Are Signal Transducers

285

B. The Adenylyl Cyclase Signaling Pathway

287

C. The Inositol–Phospholipid Signaling Pathway
Box 9.6 Bacterial Toxins and G Proteins
D. Receptor Tyrosine Kinases
Summary

292

Problems

292

Selected Readings

271

274

Box 9.4 New Lipid Vesicles, or Liposomes

9.12

268

269

B. Fluid Mosaic Model of Biological Membranes

D. Active Transport

267

288

289

291

294

PART THREE
Metabolism and Bioenergetics

10 Introduction to Metabolism

296

10.1

Metabolism Is the Sum of Cellular Reactions

10.2

Metabolic Pathways

296

298

A. Pathways Are Sequences of Reactions

299

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Contents

B. Metabolism Proceeds by Discrete Steps
C. Metabolic Pathways Are Regulated
D. Evolution of Metabolic Pathways

300

301
303

10.3

Major Pathways in Cells

304

10.4

Compartmentation and Interorgan Metabolism

10.5

Actual Gibbs Free Energy Change, Not Standard Free Energy Change, Determines
the Spontaneity of Metabolic Reactions 308

10.6

The Free Energy of ATP

10.7

The Metabolic Roles of ATP

306

310
313

A. Phosphoryl-Group Transfer

314

B. Production of ATP by Phosphoryl Group Transfer
C. Nucleotidyl Group Transfer

315

316

10.8

Thioesters Have High Free Energies of Hydrolysis

317

10.9

Reduced Coenzymes Conserve Energy from Biological Oxidations
A. Gibbs Free Energy Change Is Related to Reduction Potential
B. Electron Transfer from NADH Provides Free Energy

318
319

322

Box 10.1 NAD ᮍ and NADH Differ in Their Ultraviolet Absorption Spectra
10.10 Experimental Methods for Studying Metabolism
Summary

324

Problems

324

Selected Readings

Insulin
α S S α
S S
S
S
β

11 Glycolysis

327

The Enzymatic Reactions of Glycolysis

11.2

The Ten Enzyme-Catalyzed Steps of Glycolysis

328
328

Box 11.1 A Brief History of the Glycolytic Pathway

332

Box 11.2 Formation of 2,3-Bisphosphoglycerate in Red Blood Cells
Box 11.3 Arsenate Poisoning

11.3

Tyrosinekinase
domains

323

326

11.1

β

The Fate of Pyruvate

338

340

340

A. Metabolism of Pyruvate to Ethanol
B. Reduction of Pyruvate to Lactate
11.4

Free Energy Changes in Glycolysis

11.5

Regulation of Glycolysis

341
342

343

344

A. Regulation of Hexose Transporters
B. Regulation of Hexokinase

344

346

Box 11.4 Glucose 6-Phosphate Has a Pivotal Metabolic Role in the Liver
C. Regulation of Phosphofructokinase-1
D. Regulation of Pyruvate Kinase
E. The Pasteur Effect
11.6

347

348

350

Other Sugars Can Enter Glycolysis

350

A. Fructose Is Converted to Glyceraldehyde 3-Phosphate

11.7

B. Galactose Is Converted to Glucose 1-Phosphate

351

C. Mannose Is Converted to Fructose 6-Phosphate

352

The Entner–Doudoroff Pathway in Bacteria
Summary

354

Problems

354

Selected Readings

322

355

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350

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Contents

12 Gluconeogenesis, The Pentose Phosphate Pathway,
and Glycogen Metabolism
12.1

Gluconeogenesis

359

B. Phosphoenolpyruvate Carboxykinase
C. Fructose 1,6-bisphosphatase
D. Glucose 6-phosphatase

C. Glycerol

Allosteric
binding
site

362

363

363

D. Propionate and Lactate
12.3

Phosphorylation
site

361

362

B. Amino Acids

E. Acetate

360

361

Precursors for Gluconeogenesis
A. Lactate

363

364

Regulation of Gluconeogenesis

364

Box 12.1 Glucose Is Sometimes Converted to Sorbitol
12.4

The Pentose Phosphate Pathway
A. Oxidative Stage

366

366

368

B. Nonoxidative Stage

368

Box 12.2 Glucose 6-phosphate Dehydrogenase Deficiency in Humans
C. Interconversions Catalyzed by Transketolase and Transaldolase
12.5

Glycogen Metabolism

369
370

371

A. Glycogen Synthesis
B. Glycogen Degradation
12.6

371
372

Regulation of Glycogen Metabolism

374

A. Hormones Regulate Glycogen Metabolism

375

B. Reciprocal Regulation of Glycogen Phosphorylase
and Glycogen Synthase 375
C. Intracellular Regulation of Glycogen Metabolism Involves Interconvertible
Enzymes 376
Box 12.3 Glycogen Storage Diseases
12.7

378

Maintenance of Glucose Levels in Mammals
Summary

381

Problems

382

Selected Readings

Catalytic site

357

358

A. Pyruvate Carboxylase

12.2

xvii

379

383

13 The Citric Acid Cycle

384

13.1

Conversion of Pyruvate to Acetyl CoA

385

13.2

The Citric Acid Cycle Oxidizes Acetyl CoA

13.3

The Citric Acid Cycle Enzymes

391

393

Box 13.1 Where Do the Electrons Come From?

394

Box 13.2 Three-point Attachment of Prochiral Substrates to Enzymes
Box 13.3 Converting One Enzyme into Another

397

402

13.4

Reduced Coenzymes Can Fuel the Production of ATP

13.5

Regulation of the Citric Acid Cycle

13.6

The Citric Acid Cycle Isn’t Always a “Cycle”

13.7

The Glyoxylate Pathway

13.8

Evolution of the Citric Acid Cycle

403

404
406

407
410

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Contents

Summary

354

Problems

354

Selected Readings
OUTSIDE

Heme b

Membrane

355

14 Electron Transport and ATP Synthesis
14.1

Overview of Membrane-associated Electron Transport and ATP Synthesis

14.2

The Mitochondrion

14.3

The Chemiosmotic Theory and the Protonmotive Force

418

A. Historical Background: The Chemiosmotic Theory

418

INSIDE

14.4

Electron Transport

420

421

A. Complexes I Through IV

Fe·S clusters

421

B. Cofactors in Electron Transport

FAD

14.5

Complex I

14.6

Complex II

14.7

Complex III

427

14.8

Complex IV

429

14.9

Complex V: ATP Synthase

424

424
425

432

Box 14.1 Proton Leaks and Heat Production

435

14.10 Active Transport of ATP, ADP, and Pi Across the Mitochondrial Membrane
14.11 The P/O Ratio

436

14.12 NADH Shuttle Mechanisms in Eukaryotes
Box 14.2 The High Cost of Living

436

439

14.13 Other Terminal Electron Acceptors and Donors
14.14 Superoxide Anions
Summary

441

Problems

441
442

15 Photosynthesis

444

15.1

Light-Gathering Pigments

15.2

Bacterial Photosystems
A. Photosystem II

445
449

449

B. Photosystem I

452

C. Coupled Photosystems and Cytochrome bf

454

D. Reduction Potentials and Gibbs Free Energy in Photosynthesis
E. Photosynthesis Takes Place within Internal Membranes
15.3

Plant Photosynthesis
A. Chloroplasts

CF0

B. Plant Photosystems

460
461

463

C. Organization of Chloroplast Photosystems
15.4

Fixation of CO2: The Calvin Cycle
A. The Calvin Cycle

463

464

465

B. Rubisco: Ribulose 1,5-bisphosphate Carboxylase–oxygenase
ADP
ϩ
Pi

ATP

ϩ
H2O

458

459

460

Box 15.1 Bacteriorhodopsin

CF1

439

440

Selected Readings

Hϩ

416

416

B. The Protonmotive Force

QH2

415

C. Oxygenation of Ribulose 1,5-Bisphosphate

469

D. Calvin Cycle: Reduction and Regeneration Stages
Box 15.2 Building a Better Rubisco

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470

465

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Contents

15.5

Sucrose and Starch Metabolism in Plants

15.6

Additional Carbon-Fixation Pathways

471
473

Box 15.3 Gregor Mendel’s Wrinkled Peas
A. The C4 Pathway

473

474

B. Crassulacean Acid Metabolism (CAM)
C. Carbon Fixation in Bacteria
Summary

477

Problems

477

Selected Readings

478

16 Lipid Metabolism
16.1

474

476

Fatty Acid Synthesis

479

480

A. Synthesis of Malonyl ACP and Acetyl ACP

480

B. The Initiation Reaction of Fatty Acid Synthesis

481

C. The Elongation Reactions of Fatty Acid Synthesis
D. Activation of Fatty Acids

482

483

E. Fatty Acid Extension and Desaturation

484

16.2

Synthesis of Triacylglycerols and Glycerophospholipids

16.3

Synthesis of Eicosanoids

16.4

Synthesis of Ether Lipids

16.5

Synthesis of Sphingolipids

Box 16.1 The Search for a Replacement for Aspirin
491
493

Box 16.3 Regulating Cholesterol Levels
Synthesis of Cholesterol

490

490

Box 16.2 Lysosomal Storage Diseases
16.6

494

495

A. Stage 1: Acetyl CoA to Isopentenyl Diphosphate
B. Stage 2: Isopentenyl Diphosphate to Squalene
C. Stage 3: Squalene to Cholesterol
Fatty Acid Oxidation

495
496

496

D. Other Products of Isoprenoid Metabolism
16.7

485

488

496

498

A. The Reactions of b-Oxidation

499

B. Fatty Acid Synthesis and b-Oxidation

500

C. Transport of Fatty Acyl CoA into Mitochondria

501

Box 16.4 A Trifunctional Enzyme for b-Oxidation

502

D. ATP Generation from Fatty Acid Oxidation

502

E. b-Oxidation of Odd-Chain and Unsaturated Fatty Acids
16.8

Eukaryotic Lipids Are Made at a Variety of Sites

16.9

Lipid Metabolism Is Regulated by Hormones in Mammals

16.10 Absorption and Mobilization of Fuel Lipids in Mammals
A. Absorption of Dietary Lipids
B. Lipoproteins

504

506
507

509

509

510

Box 16.5 Lipoprotein Lipase and Coronary Heart Disease
C. Serum Albumin

513

513

16.11 Ketone Bodies Are Fuel Molecules

513

A. Ketone Bodies Are Synthesized in the Liver
B. Ketone Bodies Are Oxidized in Mitochondria

514
515

Box 16.6 Altered Carbohydrate and Lipid Metabolism in Diabetes
Summary

516

517

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Contents

Problems

517

Selected Readings

519

17 Amino Acid Metabolism

520

17.1

The Nitrogen Cycle and Nitrogen Fixation

17.2

Assimilation of Ammonia

521

523

A. Ammonia Is Incorporated into Glutamate and Glutamine
B. Transamination Reactions
17.3

Synthesis of Amino Acids

524

524

526

A. Aspartate and Asparagine

526

Box 17.1 Childhood Acute Lymphoblastic Leukemia Can Be Treated with
Asparaginase 526
B. Lysine, Methionine, and Threonine

527

C. Alanine, Valine, Leucine, and Isoleucine

528

D. Glutamate, Glutamine, Arginine, and Proline
E. Serine, Glycine, and Cysteine

529

530

F. Phenylalanine, Tyrosine, and Tryptophan

531

Box 17.2 Genetically Modified Food
Box 17.3 Essential and Nonessential Amino Acids in Animals
G. Histidine
17.4

535

Amino Acids as Metabolic Precursors

536

A. Products Derived from Glutamate, Glutamine, and Aspartate
B. Products Derived from Serine and Glycine
C. Synthesis of Nitric Oxide from Arginine
17.5

Protein Turnover

536

538

Box 17.4 Apoptosis—Programmed Cell Death
17.6

Amino Acid Catabolism

538

539

A. Alanine, Asparagine, Aspartate, Glutamate, and Glutamine
B. Arginine, Histidine, and Proline
C. Glycine and Serine
D. Threonine
F. Methionine

542
543

545
546

H. Phenylalanine, Tryptophan, and Tyrosine

546

Box 17.5 Phenylketonuria, a Defect in Tyrosine Formation
I. Lysine

546

548

Box 17.6 Diseases of Amino Acid Metabolism
17.7

The Urea Cycle Converts Ammonia into Urea
A. Synthesis of Carbamoyl Phosphate
B. The Reactions of the Urea Cycle

548
549

549
549

C. Ancillary Reactions of the Urea Cycle

550

Box 17.7 The Liver Is Organized for Removing Toxic Ammonia
17.8

541

541

543

E. The Branched-Chain Amino Acids
G. Cysteine

536

536

Renal Glutamine Metabolism Produces Bicarbonate
Summary

554

Problems

555

Selected Readings

556

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Contents

18 Nucleotide Metabolism

557

18.1

Synthesis of Purine Nucleotides

18.2

Other Purine Nucleotides Are Synthesized from IMP

558

18.3

Synthesis of Pyrimidine Nucleotides

Box 18.1 Common Names of the Bases

561

561
563

A. The Pathway for Pyrimidine Synthesis

564

Box 18.2 How Some Enzymes Transfer Ammonia from Glutamine
B. Regulation of Pyrimidine Synthesis

566

18.4

CTP Is Synthesized from UMP

18.5

Reduction of Ribonucleotides to Deoxyribonucleotides

18.6

Methylation of dUMP Produces dTMP

568
569

570

Box 18.3 Free Radicals in the Reduction of Ribonucleotides
Box 18.4 Cancer Drugs Inhibit dTTP Synthesis
18.7

Salvage of Purines and Pyrimidines

18.8

Purine Catabolism

18.9

The Purine Nucleotide Cycle in Muscle

18.10 Pyrimidine Catabolism
580

Problems

580

570

572

573

574

Box 18.5 Lesch–Nyhan Syndrome and Gout

Summary

565

Selected Readings

574

578

579

581

PART FOUR
Biological Information Flow

19 Nucleic Acids
19.1

19.2

583

Nucleotides Are the Building Blocks of Nucleic Acids
A. Ribose and Deoxyribose

584

B. Purines and Pyrimidines

584

C. Nucleosides

586

D. Nucleotides

587

DNA Is Double-Stranded

584

590

A. Nucleotides Are Joined by 3¿ – 5¿ Phosphodiester Linkages
B. Two Antiparallel Strands Form a Double Helix
C. Weak Forces Stabilize the Double Helix
DNA Can Be Supercoiled

592

595

D. Conformations of Double-Stranded DNA
19.3

597

597

19.4

Cells Contain Several Kinds of RNA

19.5

DNA Is Packaged in Chromatin in Eukaryotic Cells
A. Nucleosomes

599
599

600

Box 19.1 Histones Can Be Acetylated and Deacetylated
B. Higher Levels of Chromatin Structure
C. Bacterial DNA Packaging
19.6

590

601

603

604

Nucleases and Hydrolysis of Nucleic Acids
A. Alkaline Hydrolysis of RNA

605

605

B. Ribonuclease-Catalyzed Hydrolysis of RNA
C. Restriction Endonucleases
D. EcoRI Binds Tightly to DNA

605

608
610

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Contents

19.7

Uses of Restriction Endonucleases
Summary

612

Problems

612

Selected Readings

610

613

20 DNA Replication, Repair, and Recombination
20.1

Chromosomal DNA Replication Is Bidirectional

20.2

DNA Polymerase

615

616

618

A. Chain Elongation Is a Nucleotidyl-Group-Transfer Reaction

619

B. DNA Polymerase III Remains Bound to the Replication Fork
C. Proofreading Corrects Polymerization Errors
20.3

621

DNA Polymerase Synthesizes Two Strands Simultaneously
A. Lagging-Strand Synthesis Is Discontinuous

621

622

623

B. Each Okazaki Fragment Begins with an RNA Primer

623

C. Okazaki Fragments Are Joined by the Action of DNA Polymerase I
and DNA Ligase 624
20.4

Model of the Replisome

626

20.5

Initiation and Termination of DNA Replication

20.6

DNA Replication in Eukaryotes

20.7

Repair of Damaged DNA

629

630

Box 20.1 Sequencing DNA Using Dideoxynucleotides

632

634

A. Repair after Photodimerization: An Example of Direct Repair
B. Excision Repair
20.8

Homologous Recombination

639

A. The Holliday Model of General Recombination
B. Recombination in E. coli

639

640

C. Recombination Can Be a Form of Repair

641

Box 20.2 Molecular Links Between DNA Repair and Breast Cancer
Summary

644

Problems

645

Selected Readings

646

21 Transcription and RNA Processing
21.1

Types of RNA

21.2

RNA Polymerase

647

648
649

A. RNA Polymerase Is an Oligomeric Protein
B. The Chain Elongation Reaction
21.3

Transcription Initiation

649

650

652

A. Genes Have a 5¿ : 3¿ Orientation

652

B. The Transcription Complex Assembles at a Promoter
C. The s Subunit Recognizes the Promoter
D. RNA Polymerase Changes Conformation
21.4

Transcription Termination

21.5

Transcription in Eukaryotes

652

655
655

656
659

A. Eukaryotic RNA Polymerases
B. Eukaryotic Transcription Factors

659
662

C. The Role of Chromatin in Eukaryotic Transcription
21.6

635

635

Transcription of Genes Is Regulated

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Contents

21.7

The lac Operon, an Example of Negative and Positive Regulation
A. lac Repressor Blocks Transcription
B. The Structure of lac Repressor

667

C. cAMP Regulatory Protein Activates Transcription
21.8

Posttranscriptional Modification of RNA
A. Transfer RNA Processing

668

670

671

B. Ribosomal RNA Processing
21.9

Eukaryotic mRNA Processing

672
674

A. Eukaryotic mRNA Molecules Have Modified Ends

674

B. Some Eukaryotic mRNA Precursors Are Spliced
Summary

680

Problems

680

Selected Readings

The Genetic Code

22.2

Transfer RNA

677

682

22 Protein Synthesis
22.1

683

683

686

A. The Three-Dimensional Structure of tRNA

686

B. tRNA Anticodons Base-Pair with mRNA Codons
22.3

Aminoacyl-tRNA Synthetases

688
M16

688

A. The Aminoacyl-tRNA Synthetase Reaction

689

B. Specificity of Aminoacyl-tRNA Synthetases

RNase III

689

C. Proofreading Activity of Aminoacyl-tRNA Synthetases
22.4

Ribosomes

665

665

691

P

692

A. Ribosomes Are Composed of Both Ribosomal RNA and Protein
B. Ribosomes Contain Two Aminoacyl-tRNA Binding Sites
22.5

Initiation of Translation
A. Initiator tRNA

695

3′

P
P

695

695

B. Initiation Complexes Assemble Only at Initiation Codons
C. Initiation Factors Help Form the Initiation Complex
D. Translation Initiation in Eukaryotes
22.6

693

5′

695

696

697

Chain Elongation Is a Three-Step Microcycle

697

A. Elongation Factors Dock an Aminoacyl-tRNA in the A Site
B. Peptidyl Transferase Catalyzes Peptide Bond Formation

C. Translocation Moves the Ribosome by One Codon
22.7

Termination of Translation

22.8

Protein Synthesis Is Energetically Expensive

22.9

Regulation of Protein Synthesis

699

700

701

705

21S particle
705

705

A. Ribosomal Protein Synthesis Is Coupled to Ribosome Assembly
in E. coli 706
Box 22.1 Some Antibiotics Inhibit Protein Synthesis 707
B. Globin Synthesis Depends on Heme Availability

707

C. The E. coli trp Operon Is Regulated by Repression and Attenuation
22.10 Posttranslational Processing 712
A. The Signal Hypothesis
B. Glycosylation of Proteins
Summary

716

Problems

717

Selected Readings

708

712
716

Complete 30S subunit

718

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Contents

23 Recombinant DNA Technology
23.1

Making Recombinant DNA

23.2

Cloning Vectors

719

719

721

A. Plasmid Vectors

723

B. Bacteriophage l Vectors
C. Shuttle Vectors

723

724

D. Yeast Artificial Chromosomes as Vectors
23.3

724

Identification of Host Cells Containing Recombinant DNA
A. Selection Strategies Use Marker Genes
B. Selection in Eukaryotes

727

727

727

C. Visual Markers: Insertional Inactivation of the b – Galactosidase Gene
23.4

Genomic Libraries

728

Box 23.1 The Human Genome Project

728

23.5

cDNA Libraries Are Made from Messenger RNA

23.6

Screening a Library

23.7

Chromosome Walking

23.8

Expression of Proteins Using Recombinant DNA Technology

733

A. Prokaryotic Expression Vectors

734

Applications of Recombinant DNA Technology
A. Genetic Engineering of Plants

735

737

B. Genetic Engineering in Prokaryotes

23.10 Applications to Human Diseases

734

734

B. Expression of Proteins in Eukaryotes
23.9

729

730

737

739

23.11 The Polymerase Chain Reaction Amplifies Selected DNA Sequences
Box 23.2 Medical Uses of PCR

741

23.12 Site-Directed Mutagenesis of Cloned DNA
Summary

744

Problems

745

Selected Readings

Solutions

749

Illustration Credits
Glossary
Index

747

809

811
827

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PHOTO TO
COME

Preface
To the Student
Welcome to biochemistry—the study of the of life at the molecular level. As you
venture into this exciting and dynamic discipline, you’ll discover many new and
wonderful things. You’ll learn how some enzymes can catalyze chemical reactions
at speeds close to theoretical limits—reactions that would otherwise occur only at
imperceptibly low rates. You’ll learn about the forces that maintain biomolecular
structure and how even some of the weakest of those forces make life possible.
You’ll also learn how biochemistry has thousands of applications in day-to-day
life—in medicine, drug design, nutrition, forensic science, agriculture, and manufacturing. In short, you’ll begin a journey of discovery about how biochemistry
makes life both possible and better.
Before we begin, we would like to offer a few words of advice:
Don’t just memorize facts; instead, understand principles
In this book, we have tried to identify the most important principles of biochemistry. Every year, a million or so research papers are published. Half of them describe the results of research in some area of biochemistry. Because the knowledge
base of biochemistry is continuously expanding, we must grasp the underlying
themes of this science in order to understand it. This textbook is designed to expand on the foundation you have acquired in your chemistry and biology courses
and to provide you with a biochemical framework that will allow you to understand
new phenomena as you meet them. As you progress in your studies, you will encounter many examples that flesh out the framework we describe in this book.
These individual facts are useful in illuminating the basic principles.
Be prepared to learn a new vocabulary
An understanding of biochemical facts requires that you learn a biochemical vocabulary. This vocabulary includes the chemical structures of a number of key molecules. These molecules are grouped into families based on their structures and
functions. You will also learn how to distinguish among members of each family
and how small molecules combine to form macromolecules such as proteins and
nucleic acids. As with any newly studied discipline, the more familiar you are with
the vocabulary the more easily you can learn and appreciate the scientific literature.
Test your understanding
True mastery of biochemistry lies with learning how to apply your knowledge and

how to solve problems. Each chapter concludes with a set of carefully crafted problems that test your understanding of core principles. Many of these problems are
mini case studies that present the problem within the context of a real biochemical
puzzle.

xxv

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