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9. Consideration of membrane transport (Chapter 20) pre-

cedes that of mitochondrially based metabolic pathways

such as the citric acid cycle, electron transport, and oxida-

tive phosphorylation. In this manner, the idea of the com-

partmentalization of biological processes can be easily as-

similated. Chapter 20 also contains a discussion of

neurotransmission because it is intimately involved with

membrane transport.

10. Discussions of both the synthesis and the degradation

of lipids have been placed in a single chapter (Chapter 25),

as have the analogous discussions of amino acids (Chapter

26) and nucleotides (Chapter 28).

11. Energy metabolism is summarized and integrated in

terms of organ specialization in Chapter 27, following the de-

scriptions of carbohydrate, lipid, and amino acid metabolism.

12. The principles of both prokaryotic and eukaryotic mo-

lecular biology are expanded from their introduction in

Chapter 5 in sequential chapters on DNA replication, re-

pair and recombination (Chapter 30), transcription (Chap-

ter 31), and translation (Chapter 32). Viruses (Chapter 33)

are then considered as paradigms of more complex cellular

functions, followed by discussions of eukaryotic gene ex-

pression (Chapter 34).

13. Chapter 35, the final chapter, is a series of minichapters

that describe the biochemistry of a variety of well-charac-

terized human physiological processes: blood clotting, the

immune response, and muscle contraction.

14. Chapters 33, 34, and 35 are available on the Book Com-

panion Site (www.wiley.com/college/voet) with the same

appearance and level of detail as the chapters in the

printed textbook.

The old adage that you learn a subject best by teaching

it simply indicates that learning is an active rather than a

passive process. The problems we provide at the end of

each chapter are therefore designed to make students

think rather than to merely regurgitate poorly assimilated

and rapidly forgotten information. Few of the problems are

trivial and some of them (particularly those marked with

an asterisk) are quite difficult. Yet, successfully working

out such problems can be one of the most rewarding as-

pects of the learning process. Only by thinking long and

hard for themselves can students make a body of knowl-

edge truly their own. The answers to the problems are

worked out in detail in the Solutions Manual for this text.

The manual can be an effective learning tool, however,

only if the student makes a serious effort to solve a prob-

lem before looking up its answer.

We have included lists of references at the end of every

chapter to provide students with starting points for inde-

pendent biochemical explorations. The enormity of the

biochemical research literature prevents us from giving all

but a few of the most seminal research reports. Rather, we

list what we have found to be the most useful reviews and

monographs on the various subjects covered in each

chapter.

Finally, although we have made every effort to make

this text error free, we are under no illusions that we have

done so. Thus, we are particularly grateful to the many

readers of previous editions, students and faculty alike,

who have taken the trouble to write us with suggestions on

how to improve the textbook and to point out errors they

have found. We earnestly hope that the readers of the

fourth edition will continue this practice.

Donald Voet

Judith G.Voet

The Book Companion Site for Biochemistry

(www.wiley.com/college/voet) provides online resources

for both students and instructors. These online resources

are designed to enhance student understanding of bio-

chemistry. They are all keyed to figures or sections in the

text and called out in the text with a red mouse icon .

Bioinformatics Exercises: A set of exercises cover the

contents and uses of databases related to nucleic acids, pro-

tein sequences, protein structures, enzyme inhibition, and

other topics. These exercises, written by Paul Craig,

Rochester Institute of Technology, Rochester, New York,

use real data sets, pose specific questions, and prompt stu-

dents to obtain information from online databases and to

access the software tools for analyzing such data.

Guided Explorations: 30 self-contained presentations,

many with narration, employ extensive animated com-

puter graphics to enhance student understanding of key

topics.

Interactive Exercises: 58 molecular structures from the

text have been rendered in Jmol by Stephen Rouse. Jmol is

a browser-independent interface for manipulating struc-

tures in three dimensions, and structures are paired with

questions designed to facilitate comprehension of con-

cepts.A Tutorial for using Jmol is also provided.

Kinemages: A set of 22 exercises comprising 55 three-

dimensional images of selected protein and nucleic acids

that can be manipulated by users as suggested by accompa-

nying text.

Animated Figures: 67 figures from the text, illustrating

various concepts, techniques, and processes, are presented

as brief animations to facilitate learning.

Student and Instructor Resources ix

STUDENT AND INSTRUCTOR RESOURCES

JWCL281_fm_i-xxviii.qxd 10/28/10 11:03 AM Page ix

Case Studies: A set of 33 case studies by Kathleen Cor-

nely, Providence College, Providence, Rhode Island, use

problem-based learning to promote understanding of bio-

chemical concepts. Each case presents data from the litera-

ture and asks questions that require students to apply prin-

ciples to novel situations often involving topics from

multiple chapters in the textbook.

In addition, a printed Solutions Manual containing detailed

solutions for all of the textbook’s end-of-chapter problems

is available for purchase.

FOR INSTRUCTORS

• PowerPoint Slides of all the figures and tables in the

text are optimized with bold leader lines and large labels

for classroom projection. The figures and tables are also

ACKNOWLEDGMENTS

available for importing individually as jpeg files from the

Wiley Image Gallery.

• Test Bank by Marilee Benore, University of Michigan–

Dearborn, Dearborn, Michigan, and Robert Kane, Baylor

University,Waco,Texas,has over 1000 questions containing

a variety of question types (multiple choice, matching, fill

in the blank, and short answer). Each question is rated by

difficulty.

• Classroom Response Questions (“clicker ques-

tions”) by Rachel Milner and Adrienne Wright, University

of Alberta, Edmonton, Alberta, Canada, are interactive

questions for classroom response systems, to facilitate

classroom participation and discussion. These questions

can also be used by instructors as prelecture questions that

help gauge students knowledge of overall concepts while

addressing common misconceptions.

This textbook is the result of the dedicated effort of numer-

ous individuals, many of whom deserve special mention:

Laura Ierardi cleverly combined text, figures, and tables in

designing each of this textbook’s pages. Suzanne Ingrao,

our Production Coordinator, skillfully managed the pro-

duction of the textbook. Madelyn Lesure designed the

book’s typography and cover. Joan Kalkut, our Editor,

skillfully organized and managed the entire project. Hilary

Newman and Elyse Rieder acquired many of the photo-

graphs in the textbook and kept track of all of them. Con-

nie Parks, our copy editor, put the final polish on the man-

uscript and eliminated large numbers of grammatical and

typographical errors. Special thanks to Alyson Rentrop,

our Associate Editor, who coordinated and managed an

exceptional supplements package, and to Tom Kulesa, Se-

nior Media Editor, and Marc Wezdecki, Media Editor, who

substantially improved and developed the media re-

sources. Much of the art in this fourth edition of Biochem-

istry is the creative legacy of the drawings made for its first

and second editions by John and Bette Woolsey and

Patrick Lane of J/B Woolsey Associates. The late Irving

Geis provided us with his extraordinary molecular art and

gave freely of his wise counsel.

The atomic coordinates of most of the proteins and nu-

cleic acids that we have drawn for use in this textbook were

obtained from the Protein Data Bank (PDB), which is ad-

ministered by the Research Collaboratory for Structural

Bioinformatics (RCSB). We created these drawings using

the molecular graphics programs PyMOL by Warren

DeLano; RIBBONS by Mike Carson; and GRASP by

Anthony Nicholls, Kim Sharp, and Barry Honig.

The interactive computer graphics diagrams that are

presented on the website that accompanies this textbook

are either Jmol images or Kinemages. Jmol is a free, open

source, interactive, Web browser applet for manipulating

molecules in three dimensions. It is based on the program

RasMol by Roger Sayle, which was generously made pub-

licly available. Kinemages are displayed by the program

KiNG, which was written and generously provided by

David C. Richardson, who also wrote and provided the

program PREKIN, which we used to help generate the

Kinemages. KiNG (Kinemage, Next Generation) is an in-

teractive system for three-dimensional vector graphics that

runs on Windows, Mac OS X, and Linux/Unix systems.

We wish especially to thank those colleagues who re-

viewed this textbook, in both its current and earlier edi-

tions, and provided us with their prudent advice:

Joseph Babitch, Texas Christian University

E.J. Berhman, Ohio State University

Karl D. Bishop, Bucknell University

Robert Blankenshop, Arizona State University

Charles L. Borders, Jr., The College of Wooster

Kenneth Brown, University of Texas at Arlington

Larry G. Butler, Purdue University

Carol Caparelli, Fox Chase Cancer Center

W. Scott Champney, East Tennessee State University

Paul F. Cook, The University of Oklahoma

Glenn Cunningham, University of Central Florida

Eugene Davidson, Georgetown University

Don Dennis, University of Delaware

Walter A. Deutsch, Louisiana State University

Kelsey R. Downum, Florida International University

William A. Eaton, National Institutes of Health

David Eisenberg, University of California at Los Angeles

Jeffrey Evans, University of Southern Mississippi

David Fahrney, Colorado State University

x Preface

JWCL281_fm_i-xxviii.qxd 10/28/10 11:03 AM Page x

Paul Fitzpatrick, Texas A&M University

Robert Fletterick, University of California at San

Francisco

Norbert C. Furumo, Eastern Illinois University

Scott Gilbert, Swarthmore College

Guido Guidotti, Harvard University

James H. Hageman, New Mexico State University

Lowell Hager, University of Illinois at Urbana–Champaign

James H. Hammons, Swarthmore College

Edward Harris, Texas A&M University

Angela Hoffman, University of Portland

Ralph A. Jacobson, California Polytechnic State

University

Eileen Jaffe, Fox Chase Cancer Center

Jan G. Jaworski, Miami University

William P. Jencks, Brandeis University

Mary Ellen Jones, University of North Carolina

Jason D. Kahn, University of Maryland

Tokuji Kimura, Wayne State University

Barrie Kitto, University of Texas at Austin

Daniel J. Kosman, State University of New York at

Buffalo

Robert D. Kuchta, University of Colorado, Boulder

Thomas Laue, University of New Hampshire

Albert Light, Purdue University

Dennis Lohr, Arizona State University

Larry Louters, Calvin College

Robert D. Lynch, University of Lowell

Harold G. Martinson, University of California at

Los Angeles

Michael Mendenhall, University of Kentucky

Sabeeha Merchant, University of California at

Los Angeles

Christopher R. Meyer, California State University at

Fullerton

Ronald Montelaro, Louisiana State University

Scott Moore, Boston University

Harry F. Noller, University of California at Santa Cruz

John Ohlsson, University of Colorado

Gary L. Powell, Clemson University

Alan R. Price, University of Michigan

Paul Price, University of California at San Diego

Thomas I. Pynadath, Kent State University

Frank M. Raushel, Texas A&M University

Ivan Rayment, University of Wisconsin

Frederick Rudolph, Rice University

Raghupathy Sarma, State University of New York at

Stony Brook

Paul R. Schimmel, The Scripps Research Institute

Thomas Schleich, University of California at Santa Cruz

Allen Scism, Central Missouri State University

Charles Shopsis, Adelphi University

Marvin A. Smith, Brigham Young University

Thomas Sneider, Colorado State University

Jochanan Stenish, Western Michigan University

Phyllis Strauss, Northeastern University

JoAnne Stubbe, Massachusetts Institute of Technology

William Sweeney, Hunter College

John Tooze, European Molecular Biology Organization

Mary Lynn Trawick, Baylor University

Francis Vella, University of Saskatchewan

Harold White, University of Delaware

William Widger, University of Houston

Ken Willeford, Mississippi State University

Lauren Williams, Georgia Institute of Technology

Jeffery T. Wong, University of Toronto

Beulah M.Woodfin, The University of New Mexico

James Zimmerman, Clemson University

D.V.

J.G.V.

Acknowledgments xi

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Guide to Media Resources xvi

PART I INTRODUCTION AND BACKGROUND 1

1 Life 3

2 Aqueous Solutions 40

3 Thermodynamic Principles: A Review 52

PART II BIOMOLECULES 65

4 Amino Acids 67

5 Nucleic Acids, Gene Expression, and Recombinant DNA Technology 82

6 Techniques of Protein and Nucleic Acid Purifications 129

7 Covalent Structures of Proteins and Nucleic Acids 163

8 Three-Dimensional Structures of Proteins 221

9 Protein Folding, Dynamics, and Structural Evolution 278

10 Hemoglobin: Protein Function in Microcosm 323

11 Sugars and Polysaccharides 359

12 Lipids and Membranes 386

PART III MECHANISMS OF ENZYME ACTION 467

13 Introduction to Enzymes 469

14 Rates of Enzymatic Reactions 482

15 Enzymatic Catalysis 506

PART IV METABOLISM 557

16 Introduction to Metabolism 559

17 Glycolysis 593

18 Glycogen Metabolism 638

19 Signal Transduction 671

20 Transport through Membranes 744

21 Citric Acid Cycle 789

22 Electron Transport and Oxidative Phosphorylation 823

23 Other Pathways of Carbohydrate Metabolism 871

24 Photosynthesis 901

25 Lipid Metabolism 940

26 Amino Acid Metabolism 1019

27 Energy Metabolism: Integration and Organ Specialization 1088

28 Nucleotide Metabolism 1107

PART V EXPRESSION AND TRANSMISSION OF GENETIC INFORMATION 1143

29 Nucleic Acid Structures 1145

30 DNA Replication, Repair, and Recombination 1173

31 Transcription 1260

32 Translation 1338

33 Viruses: Paradigms for Cellular Function W-1

34 Eukaryotic Gene Expression W-53

35 Molecular Physiology

(Chapters 33–35 are available on our website, www.wiley.com/college/voet)

xii

BRIEF CONTENTS

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Guide to Media Resources xvi

PART I

INTRODUCTION AND BACKGROUND 1

CHAPTER 1 Life 3

1. Prokaryotes 3

2. Eukaryotes 6

3. Biochemistry: A Prologue 14

4. Genetics: A Review 19

5. The Origin of Life 28

6. The Biochemical Literature 34

CHAPTER 2 Aqueous Solutions 40

1. Properties of Water 40

2. Acids, Bases, and Buffers 45

CHAPTER 3 Thermodynamic Principles:

A Review 52

1. First Law of Thermodynamics: Energy Is

Conserved 52

2. Second Law of Thermodynamics: The Universe

Tends Toward Maximum Disorder 54

3. Free Energy: The Indicator of Spontaneity 57

4. Chemical Equilibria 58

APPENDIX: Concentration Dependence of

Free Energy 61

PART II

BIOMOLECULES 65

CHAPTER 4 Amino Acids 67

1. The Amino Acids of Proteins 67

2. Optical Activity 73

3. “Nonstandard” Amino Acids 78

CHAPTER 5 Nucleic Acids, Gene

Expression, and Recombinant DNA

Technology 82

1. Nucleotides and Nucleic Acids 82

2. DNA Is the Carrier of Genetic Information 85

3. Double Helical DNA 88

4. Gene Expression and Replication:

An Overview 95

5. Molecular Cloning 104

CHAPTER 6 Techniques of Protein and

Nucleic Acid Purifications 129

1. Protein Isolation 129

2. Solubilities of Proteins 133

3. Chromatographic Separations 135

4. Electrophoresis 146

5. Ultracentrifugation 152

6. Nucleic Acid Fractionation 156

CHAPTER 7 Covalent Structures of

Proteins and Nucleic Acids 163

1. Primary Structure Determination of Proteins 164

2. Nucleic Acid Sequencing 176

3. Chemical Evolution 185

4. Bioinformatics: An Introduction 194

5. Chemical Synthesis of Polypeptides 205

6. Chemical Synthesis of Oligonucleotides 209

CHAPTER 8 Three-Dimensional

Structures of Proteins 221

1. Secondary Structure 221

2. Fibrous Proteins 232

3. Globular Proteins 241

4. Protein Stability 259

5. Quaternary Structure 266

APPENDIX: Viewing Stereo Pictures 271

CHAPTER 9 Protein Folding, Dynamics,

and Structural Evolution 278

1. Protein Folding: Theory and Experiment 278

2. Folding Accessory Proteins 290

3. Protein Structure Prediction and Design 302

4. Protein Dynamics 306

5. Conformational Diseases: Amyloids

and Prions 309

6. Structural Evolution 316

CHAPTER 10 Hemoglobin: Protein

Function in Microcosm 323

1. Hemoglobin and Myoglobin Function 323

2. Structure and Mechanism 331

3. Abnormal Hemoglobins 341

4. Allosteric Regulation 347

APPENDIX: Derivation of Symmetry Model

Equations 354

CHAPTER 11 Sugars and

Polysaccharides 359

1. Monosaccharides 359

2. Polysaccharides 365

3. Glycoproteins 373

CHAPTER 12 Lipids and Membranes 386

1. Lipid Classification 386

2. Properties of Lipid Aggregates 393

xiii

CONTENTS

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3. Biological Membranes 399

4. Membrane Assembly and Protein Targeting 418

5. Lipoproteins 449

PART III

MECHANISMS OF ENZYME ACTION 467

CHAPTER 13 Introduction to Enzymes 469

1. Historical Perspective 469

2. Substrate Specificity 470

3. Coenzymes 473

4. Regulation of Enzymatic Activity 474

5. A Primer of Enzyme Nomenclature 479

CHAPTER 14 Rates of Enzymatic

Reactions 482

1. Chemical Kinetics 482

2. Enzyme Kinetics 487

3. Inhibition 492

4. Effects of pH 496

5. Bisubstrate Reactions 497

APPENDIX: Derivations of Michaelis–Menten

Equation Variants 501

CHAPTER 15 Enzymatic Catalysis 506

1. Catalytic Mechanisms 506

2. Lysozyme 517

3. Serine Proteases 525

4. Drug Design 539

PART IV

METABOLISM 557

CHAPTER 16 Introduction to

Metabolism 559

1. Metabolic Pathways 559

2. Organic Reaction Mechanisms 562

3. Experimental Approaches to the Study

of Metabolism 569

4. Thermodynamics of Phosphate

Compounds 578

5. Oxidation–Reduction Reactions 583

6. Thermodynamics of Life 586

CHAPTER 17 Glycolysis 593

1. The Glycolytic Pathway 593

2. The Reactions of Glycolysis 595

3. Fermentation: The Anaerobic Fate

of Pyruvate 614

4. Metabolic Regulation and Control 619

5. Metabolism of Hexoses Other than Glucose 630

CHAPTER 18 Glycogen Metabolism 638

1. Glycogen Breakdown 638

2. Glycogen Synthesis 644

3. Control of Glycogen Metabolism 647

4. Glycogen Storage Diseases 666

CHAPTER 19 Signal Transduction 671

1. Hormones 671

2. Heterotrimeric G Proteins 688

3. Tyrosine Kinase–Based Signaling 699

4. The Phosphoinositide Cascade 725

CHAPTER 20 Transport through

Membranes 744

1. Thermodynamics of Transport 744

2. Kinetics and Mechanisms of Transport 745

3. ATP-Driven Active Transport 758

4. Ion Gradient–Driven Active Transport 768

5. Neurotransmission 771

CHAPTER 21 Citric Acid Cycle 789

1. Cycle Overview 789

2. Metabolic Sources of Acetyl-Coenzyme A 792

3. Enzymes of the Citric Acid Cycle 806

4. Regulation of the Citric Acid Cycle 815

5. The Amphibolic Nature of the Citric

Acid Cycle 817

CHAPTER 22 Electron Transport and

Oxidative Phosphorylation 823

1. The Mitochondrion 823

2. Electron Transport 828

3. Oxidative Phosphorylation 845

4. Control of ATP Production 862

CHAPTER 23 Other Pathways of

Carbohydrate Metabolism 871

1. Gluconeogenesis 871

2. The Glyoxylate Cycle 880

3. Biosynthesis of Oligosaccharides and

Glycoproteins 880

4. The Pentose Phosphate Pathway 892

CHAPTER 24 Photosynthesis 901

1. Chloroplasts 901

2. Light Reactions 903

3. Dark Reactions 926

CHAPTER 25 Lipid Metabolism 940

1. Lipid Digestion, Absorption, and Transport 940

2. Fatty Acid Oxidation 945

3. Ketone Bodies 959

4. Fatty Acid Biosynthesis 961

xiv

Contents

JWCL281_fm_i-xxviii.qxd 10/28/10 11:04 AM Page xiv

5. Regulation of Fatty Acid Metabolism 973

6. Cholesterol Metabolism 975

7. Eicosanoid Metabolism: Prostaglandins,

Prostacyclins, Thromboxanes, Leukotrienes,

and Lipoxins 993

8. Phospholipid and Glycolipid Metabolism 1004

CHAPTER 26 Amino Acid

Metabolism 1019

1. Amino Acid Deamination 1019

2. The Urea Cycle 1025

3. Metabolic Breakdown of Individual

Amino Acids 1029

4. Amino Acids as Biosynthetic Precursors 1047

5. Amino Acid Biosynthesis 1064

6. Nitrogen Fixation 1078

CHAPTER 27 Energy Metabolism:

Integration and Organ

Specialization 1088

1. Major Pathways and Strategies of Energy

Metabolism: A Summary 1088

2. Organ Specialization 1090

3. Metabolic Homeostasis: Regulation of Appetite,

Energy Expenditure, and Body Weight 1095

4. Metabolic Adaptation 1101

CHAPTER 28 Nucleotide

Metabolism 1107

1. Synthesis of Purine Ribonucleotides 1107

2. Synthesis of Pyrimidine Ribonucleotides 1114

3. Formation of Deoxyribonucleotides 1119

4. Nucleotide Degradation 1130

5. Biosynthesis of Nucleotide Coenzymes 1136

PART V

EXPRESSION AND TRANSMISSION

OF GENETIC INFORMATION 1143

CHAPTER 29 Nucleic Acid

Structures 1145

1. Double Helical Structures 1145

2. Forces Stabilizing Nucleic Acid Structures 1151

3. Supercoiled DNA 1158

CHAPTER 30 DNA Replication, Repair,

and Recombination 1173

1. DNA Replication: An Overview 1173

2. Enzymes of Replication 1176

3. Prokaryotic Replication 1190

4. Eukaryotic Replication 1201

5. Repair of DNA 1213

6. Recombination and Mobile Genetic

Elements 1225

7. DNA Methylation and Trinucleotide

Repeat Expansions 1246

CHAPTER 31 Transcription 1260

1. The Role of RNA in Protein Synthesis 1260

2. RNA Polymerase 1265

3. Control of Transcription in Prokaryotes 1283

4. Post-Transcriptional Processing 1301

CHAPTER 32 Translation 1338

1. The Genetic Code 1338

2. Transfer RNA and Its Aminoacylation 1345

3. Ribosomes 1362

4. Control of Eukaryotic Translation 1398

5. Post-Translational Modification 1403

6. Protein Degradation 1408

*CHAPTER 33 Viruses: Paradigms for

Cellular Function W-1

1. Tobacco Mosaic Virus W-3

2. Icosahedral Viruses W-8

3. Bacteriophage W-20

4. Influenza Virus W-40

*CHAPTER 34 Eukaryotic Gene

Expression

1. Chromosome Structure

2. Genomic Organization

3. Control of Expression

4. Cell Differentiation

*CHAPTER 35 Molecular Physiology

1. Blood Clotting

2. Immunity

3. Motility: Muscles, Vesicle Transport,

Cilia, and Flagella

INDEX

I-1

*Chapters 33, 34, and 35 are available on our book

companion website, www.wiley.com/college/voet.

␭

Contents xv

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GUIDE TO MEDIA RESOURCES

The book website (www.wiley.com/college/voet) offers the following resources to enhance student understanding of bio-

chemistry. These are all keyed to figures or sections in the text.They are called out in the text with a red mouse icon or

margin note.

Chapter

Media Type

Title

Text Reference

Page

2 Acids, Bases,

and Buffers

5 Nucleic Acids,

Gene

Expression, and

Recombinant

DNA Technology

4 Amino Acids

Animated Figure

Kinemage Exercise

Acid-base titration curves of 1-L solutions of 1M

acetic acid, H

⫺

, and NH

⫹

by a strong base

Titration curve of glycine

Titration curve of a 1-L solution of 1M H

Figure 2-11

Figure 2-13

Figure 4-6

2.1. B-DNA

Figure 5-11

Interactive Exercise

1. B-DNA

Figure 5-11

Kinemage Exercise

2-2, 17-2. The Watson–Crick base pairs

Figure 5-12

Animated Figure

Demonstration of the semiconservative nature of

DNA replication in E. coli by density gradient

ultracentrifugation

Figure 5-13

Animated Figure

UV absorbance spectra of the nucleic acid bases

and DNA

Figure 5-15

Animated Figure

Example of a DNA melting curve

Figure 5-16

Guided Exploration

1: Overview of transcription and translation

Section 5-4

Guided Exploration

2: Regulation of gene expression by the lac

repressor system

Animated Figure

Construction of a recombinant DNA molecule

Figure 5-44

109

Animated Figure

Ion exchange chromatography using stepwise elution

Figure 6-6

136

Animated Figure

Gel filtration chromatography

Figure 6-9

139

Animated Figure

Cloning of foreign DNA in ␭ phages

Figure 5-47

111

Animated Figure

Site-directed mutagenesis

Figure 5-55

119

Guided Exploration

3: PCR and site-directed mutagenesis

Section 5-5F

114

6 Techniques

of Protein and

Nucleic Acid

Purification

Animated Figure

An enzyme-linked immunosorbent assay (ELISA)

Figure 6-1

132

Animated Figure

The Edman degradation

Figure 7-4

167

Animated Figure

The amino acid sequence of a polypeptide chain is

determined by comparing the sequence of two

sets of mutually overlapping peptide fragments

Figure 7-6

171

7 Covalent

Structures of

Proteins and

Nucleic Acids

Guided Exploration

4: Protein sequence determination

Section 7-1

164

Guided Exploration

6: Bioinformatics

Section 7-4

194

Guided Exploration

5: DNA sequence determination by the chain-

terminator method

Section 7-2A

176

8 Three-

Dimensional

Structures of

Proteins

Kinemage Exercise

3-1.The peptide group

Figure 8-1, 8-2,

8-4

221,

222,

223

Kinemage Exercise

3–2.The ␣ helix

Figure 8-11,

8-12

226,

227

Guided Exploration Section 8-1B

225

7: Stable helices in proteins: the ␣ helix

Figure 5-25

xvi

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Guide to Media Resources xvii

Chapter

Media Type

Title

Text Reference

Page

Animated Figure

Guided Exploration

The right-handed ␣ helix

Figure 8-11

226

8: Hydrogen bonding in ␤ sheets

Section 8-1C

229

Guided Exploration

9: Secondary structures in proteins

Section 8-1C

229

Kinemage Exercise

3-3. ␤ Pleated sheets

229,

230,

231

Animated Figure

␤ Pleated sheets

Figure 8-16

229

Interactive Exercise

2.Triose phosphate isomerase

Figure 8-19

231

Kinemage Exercise

3-4. Beta bends (reverse turns)

Figure 8-22

233

Kinemage Exercise

4-1, 4-2. Coiled coils

Figure 8-26

235

Kinemage Exercise

4-3, 4-4. Collagen

Figure 8-29,

8-30

237

Interactive Exercise

4. Horse heart cytochrome c

Figure 8-42

247

Kinemage Exercise

6-1. Deoxy myoglobin

Figure 8-39

245

Interactive Exercise

3. Human carbonic anhydrase

Figure 8-41

(also Figure

15-5)

246

(also

512)

Kinemage Exercise

5-1. Cytochromes c

Figure 8-42

247

Kinemage Exercise

3-2.The ␣ helix

Figure 8-43

248

Kinemage Exercise

3-3. pleated sheets␤

Figure 8-44

249

Animated Figure

Some possible symmetries of proteins with

identical protomers

Figure 8-65

268

Interactive Exercise

5. Glyceraldehyde-3-phosphate dehydrogenase

Figure 8-45

249

Guided Exploration

10: Protein Evolution

Section 8-6A

316

Kinemage Exercise

5-1. Cytochromes c

Figure 9-41

317

9 Protein Fold-

ing, Dynamics,

and Structural

Evolution

Animated Figure

Reactions catalyzed by protein disulfide

isomerase (PDI)

Figure 9-15

290

Figure 8-16,

8-17, 8-18

JWCL281_fm_i-xxviii.qxd 10/28/10 11:04 AM Page xvii

xviii Guide to Media Resources

Chapter

Media Type

Title

Text Reference

Page

10 Hemoglobin:

Protein Function

in Microcosm

Animated Figure

Oxygen-dissociation curves of Mb and of Hb in

whole blood

The effects of BPG and CO

, both separately and

combined, on hemoglobin’s O

-dissociation curve

compared with that of whole blood (red curve)

Figure 10-3

326

Figure 10-8

330

Kinemage Exercise

6-1. Deoxy myoglobin

Figure 10-11,

10-12

332,

333

Kinemage Exercise

6-2, 6-3. Hemoglobin and myoglobin

Figure 10-13

334

Kinemage Exercise

6-4. Hemoglobin structure

Figure 10-15,

10-16

336

Animated Figure

Triggering mechanism for the T R transition

of Hb

Figure 10-16

336

Kinemage Exercise

6-5. Conformational changes at hemoglobin’s ␣

–␤

interface

Figure 10-17

337

Kinemage Exercise

6-3. Binding of BPG to deoxyHb

Figure 10-21

341

Kinemage Exercise

7-3. Hyaluronic acid

Figure 11-21

371

Kinemage Exercise

8-2. Photosynthetic reaction center

Figure 12-26

404

Kinemage Exercise

8-3. Porin

Figure 12-27

405

Animated Figure

The ribosomal synthesis, membrane insertion, and

initial glycosylation of an integral protein via the

secretory pathway

Figure 12-46

421

Kinemage Exercise

7-2. Sucrose

Figure 11-13

367

11 Sugars and

Polysaccharides

Kinemage Exercise

7-1. D-Glucopyranose

Figure 11-5,

11-7

362,

363

Kinemage Exercise

7-4. Structure of a complex carbohydrate

Figure 11-32

379

Kinemage Exercise

8-1.Bacteriorhodopsin

Figure 12-25

403

Animated Figure

Model for plasma triacyglycerol and cholesterol

transport in humans

Figure 12-86

452

12 Lipids and

Membranes

Guided Exploration

11: Membrane structure and the fluid mosaic model

Figures 12-15,

12-16, 12-20

396,

397,

400

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