Mary K. Campbell

838 Pages·2012·31.67 MB·English

90410_00a_fep_pEP2-3.qxd 10/18/07 3:00 PM Page 2
LIST OF ABBREVIATIONS
A Adenine
ACAT Acyl-CoA cholesterol acyl transferase
ACP Acyl carrier protein
ADP Adenosine diphosphate
AIDS Acquired immunodeficiency syndrome
AMP Adenosine monophosphate
ATCase Aspartate transcarbamoylase
ATP Adenosine triphosphate
bp Base pairs
C Cytosine
cAMP Cyclic adenosine monophosphate
CAP Catabolite activator protein
CDP Cytidine diphosphate
Chl Chlorophyll
CMP Cytidine monophosphate
CoA (CoA-SH) Coenzyme A
CoQ Coenzyme Q
CTP Cytidine triphosphate
d Deoxy
DNA Deoxyribonucleic acid
DNase Deoxyribonuclease
DV Daily value
EF Elongation factor
ER Endoplasmic reticulum
FAD Flavin adenine dinucleotide (oxidized form)
FADH Flavin adenine dinucleotide (reduced form)
2
fMet N-Formylmethionine
FMN Flavin mononucleotide
G Guanine
GDP Guanosine diphosphate
GMP Guanosine monophosphate
GSH Glutathione (reduced form)
GSSG Glutathione (oxidized form)
GTP Guanosine triphosphate
Hb Hemoglobin
HDL High-density lipoprotein
HIV Human immunodeficiency virus
HMG-CoA (cid:2)-Hydroxy-(cid:2)-methylglutaryl-CoA
HPLC High-performance liquid chromatography
90410_00a_fep_pEP2-3.qxd 10/18/07 3:00 PM Page 3
IF Initiation factor
K Michaelis constant
M
LDL Low-density lipoprotein
Mb Myoglobin
NAD(cid:3) Nicotinamide adenine dinucleotide (oxidized form)
NADH Nicotinamide adenine dinucleotide (reduced form)
NADP(cid:3) Nicotinamide adenine dinucleotide phosphate
(oxidized form)
NADPH Nicotinamide adenine dinucleotide phosphate
(reduced form)
P Phosphate ion
i
PAGE Polyacrylamide gel electrophoresis
PCR Polymerase chain reaction
PEP Phosphoenolpyruvate
PIP Phosphatidylinositol bisphosphate
2
PKU Phenylketonuria
Pol DNA polymerase
PP Pyrophosphate ion
i
PRPP Phosphoribosylpyrophosphate
PS Photosystem
RF Release factor
RFLPs Restriction-fragment-length polymorphisms
RNA Ribonucleic acid
RNase Ribonuclease
mRNA Messenger RNA
rRNA Ribosomal RNA
tRNA Transfer RNA
snRNP Small nuclear ribounuclear protein
S Svedberg unit
SCID Severe combined immune deficiency
SSB Single-strand binding protein
SV40 Simian virus 40
T Thymine
TDP Thymidine diphosphate
TMP Thymidine monophosphate
TTP Thymidine triphosphate
U Uracil
UDP Uridine diphosphate
UMP Uridine monophosphate
UTP Uridine triphosphate
V Maximal velocity
max
90410_00b_se_pEP4.qxd 10/18/07 2:59 PM Page 1
Assess your understanding with the best
online study tool you’ll ever use!
Take charge of your learning with Integrated—chapter by chapter—
BiochemistryNow™ with this text
www.thomsonedu.com/login Look for these
Designed to maximize your time investment,BiochemistryNow references in the Sign in at www.thomsonedu.com/login
helps you succeed by focusing your study time on the textbook.They to test yourself on these concepts.
concepts that you’re having the most difficulty mastering. direct you to the
BiochemistryNowgauges your unique study needs and corresponding media-enhanced activities on
provides you with a Personalized Learning Planthat enhances BiochemistryNow.This precise page-by-page integration
your problem-solving skills and conceptual understanding. enables you to go beyond reading about biochemistry—
you’ll actually experience it in action!
How does it work?
The BiochemistryNowsystem includes three
powerful assessment components:
(cid:2) What Do I Know?This diagnostic Pre-
Testbased on the chapter-opening Critical
Questionsgives you an initial assessment of
your knowledge.
(cid:2) What Do I Need to Learn?Based on
the automatically graded Pre-Test,you
receive a Personalized Learning Planthat
outlines key elements for review. .....
(cid:2) What Have I Learned?After working ......
through your Personalized Learning Plan,
you can complete a Post-Testto assess your knowledge.
.......
With a click of the mouse, the unique
...
interactive activities contained at
BiochemistryNow allow you to: ......
(cid:2) Create a Personalized Learning Planor review for an ......
exam using the Pre-Test Web quizzes ...
(cid:2) Explore biochemical concepts ......
through simulations and
tutorials with Biochemistry (cid:2) ACTIVE FIGURE 4.11 A triple helix.
Interactive Poly (Gly—Pro—Pro) is a collagen-like right-handed
triple helix composed of three left-handed helical
(cid:2) View Active Figuresto interact chains. (Adapted from M. H. Miller and H. A. Scheraga, (cid:2) ACTIVE FIGURE 4.11A triple helix.
with text illustrations and quiz 1976, Calculation of the structures of collagen models. Role Poly (Gly—Pro—Pro) is a collagen-like right-handed
triple helix composed of three left-handed helical
yourselfon the concepts of interchain interactions in determining the triple- chains. (Adapted from M. H. Miller and H. A. Scheraga,
helical coiled-coil conformations. I. Poly(glycyl-prolyl-prolyl). 1976, Calculation of the structures of collagen models. Role
of interchain interactions in determining the triple-
(cid:2) Assess your mastery ofcore Journal of Polymer Science Symposium 54:171–200. helical coiled-coil conformations. I. Poly(glycyl-prolyl-prolyl).
© 1976 John Wiley & Sons, Inc. Reprinted by permission.) Journal of Polymer Science Symposium 54:171–200.
concepts and skills by Sign in at www.thomsonedu.com/login to explore an © 1976 John Wiley & Sons, Inc. Reprinted by permission.)
Sign in at www.thomsonedu.com/login to explore an
completing the Post-Test interactive version of this figure. interactive version of this figure.
Log on today using the access code that may have been packaged with your new copy of this text
(or purchase a code by entering ISBN 0-495-39480-7 at www.ichapters.com).By giving you a better
understanding ofexactly what you need to focus on,BiochemistryNowsaves you time and brings you a step closer to success.
BIOCHEMISTRY
6
th
EDITION
Mary K. Campbell
Mount Holyoke College
Shawn O. Farrell
Colorado State University
Australia (cid:129) Canada (cid:129) Mexico (cid:129) Singapore (cid:129) Spain
United Kingdom (cid:129) United States
9900441100__0000__ffmm__ppii--xxvviiiiii..iinndddd ii 1100//1188//0077 55::2233::3333 PPMM
Biochemistry, Sixth Edition
Mary K. Campbell, Shawn O. Farrell
Acquisitions Editor: Lisa Lockwood Permissions Editor: Roberta Broyers
Development Editor: Alyssa White Production Service: Lachina Publishing Services
Assistant Editor: Ashley Summers Text Designer: Roy Neuhaus
Editorial Assistant: Elizabeth Woods Photo Researcher: Dena Digilio Betz
Technology Project Manager: Lisa Weber Copy Editor: Amy Schneider
Marketing Manager: Amee Mosley Illustrator: 2064design
Marketing Assistant: Elizabeth Wong Cover Designer: Dare Porter
Marketing Communications Manager: Talia Wise Cover Photos: small image: Alfred Pasieka/Photo Researchers, Inc.
Content Project Manager, Editorial Production: Teresa L. Trego large image: © Photomorgana/CORBIS
Creative Director: Rob Hugel Compositor: Lachina Publishing Services
Art Director: John Walker Printer: Transcontinental/Beauceville
Print Buyer: Judy Inouye
© 2009 Thomson Brooks/Cole, a part of The Thomson Corporation. Thomson Higher Education
Thomson, the Star logo, and Brooks/Cole are trademarks used herein 10 Davis Drive
under license. Belmont, CA 94002-3098
USA
ALL RIGHTS RESERVED. No part of this work covered by the copyright
hereon may be reproduced or used in any form or by any means—graphic,
electronic, or mechanical, including photocopying, recording, taping, web
distribution, information storage and retrieval systems, or in any other
manner—without the written permission of the publisher.
Printed in Canada
1 2 3 4 5 6 7 11 10 09 08
For more information about our products, contact us at:
Thomson Learning Academic Resource Center
1-800-423-0563
For permission to use material from this text or product, submit a
request online at http://www.thomsonrights.com.
Any additional questions about permissions can be submitted by
e-mail to [email protected].
Library of Congress Control Number: 2007935160
Student Edition:
ISBN-13: 978-0-495-39041-1
ISBN-10: 0-495-39041-0
Instructor’s Edition
ISBN-13: 978-0-495-39045-9
ISBN-10: 0-495-39045-3
9900441100__0000__ffmm__ppii--xxvviiiiii..iinndddd iiii 1100//1188//0077 55::2233::3344 PPMM
To all of those who made this text possible and especially to all of
the students who will use it.
—Mary K. Campbell
To the returning adult students in my class, especially those with
children and a full-time job… my applause.
—Shawn O. Farrell
9900441100__0000__ffmm__ppii--xxvviiiiii..iinndddd iiiiii 1100//1188//0077 55::2233::3344 PPMM
About the Authors
Mary K. Campbell
Mary K. Campbell is professor emeritus of chemistry at Mount Holyoke
College, where she taught a one-semester biochemistry course and advised
undergraduates working on biochemical research projects. She frequently
taught general chemistry and physical chemistry as well. At some point in her
36 years at Mount Holyoke, she taught every subfield of chemistry, except the
lecture portion of organic chemistry. Her avid interest in writing led to the pub-
lication of the first five highly successful editions of this textbook. Originally
from Philadelphia, Mary received her Ph.D. from Indiana University and did
postdoctoral work in biophysical chemistry at Johns Hopkins University. Her
area of interest includes researching the physical chemistry of biomolecules,
specifically, spectroscopic studies of protein–nucleic acid interactions.
Mary enjoys traveling and has recently visited Australia and New Zealand.
She can frequently be seen hiking the Appalachian Trail.
Shawn O. Farrell
Shawn O. Farrell grew up in northern California and received a B.S. degree
in biochemistry from the University of California, Davis, where he studied car-
bohydrate metabolism. He completed his Ph.D. in biochemistry at Michigan
State University, where he studied fatty acid metabolism. For the last 18 years,
Shawn has worked at Colorado State University teaching undergraduate bio-
chemistry lecture and laboratory courses. Because of his interest in biochemi-
cal education, Shawn has written a number of scientific journal articles about
teaching biochemistry. He is the coauthor (with Lynn E. Taylor) of Experiments
in Biochemistry: A Hands-On Approach. Shawn became interested in biochemistry
while in college because it coincided with his passion for bicycle racing. An
active outdoorsman, Shawn raced competitively for 17 years and now offici-
ates at bicycle races around the world. He is currently the Technical Director
of USA Cycling, the national governing body of bicycle racing in the United
States. He is also a distance runner and an avid fly fisherman, and recently
achieved his third-degree black belt in Tae Kwon Do and first-degree black
belt in combat hapkido. Shawn has also written articles on fly fishing for Salmon
Trout Steelheader magazine. His other passions are soccer, chess, and foreign lan-
guages. He is fluent in Spanish and French and is currently learning German
and Italian.
9900441100__0000__ffmm__ppii--xxvviiiiii..iinndddd iivv 1100//1188//0077 55::2233::3344 PPMM
Brief Contents
1
Biochemistry and the Organization of Cells 1
2
Water: The Solvent for Biochemical Reactions 37
3
Amino Acids and Peptides 65
4
The Three-Dimensional Structure of Proteins 87
5
Protein Purification and Characterization Techniques 123
6
The Behavior of Proteins: Enzymes 143
7
The Behavior of Proteins: Enzymes, Mechanisms, and Control 171
8
Lipids and Proteins Are Associated in Biological Membranes 201
9
Nucleic Acids: How Structure Conveys Information 235
10
Biosynthesis of Nucleic Acids: Replication 261
11
Transcription of the Genetic Code: The Biosynthesis of RNA 287
12
Protein Synthesis: Translation of the Genetic Message 331
13
Nucleic Acid Biotechnology Techniques 363
14
Viruses, Cancer, and Immunology 405
15
The Importance of Energy Changes and Electron Transfer in Metabolism 439
16
Carbohydrates 461
17
Glycolysis 493
18
Storage Mechanisms and Control in Carbohydrate Metabolism 519
19
The Citric Acid Cycle 545
20
Electron Transport and Oxidative Phosphorylation 577
21
Lipid Metabolism 607
22
Photosynthesis 645
23
The Metabolism of Nitrogen 671
24
Integration of Metabolism: Cellular Signaling 707
Magazine: Hot Topics in Biochemistry
Doping in Sports: Good Science Gone Bad 737
Bird Flu: The Next Pandemic? 740
Single Nucleotide Polymorphisms: Changing One Base Can Make a Big Difference 742
HPV Vaccines: Waging the War on Cervical Cancer 745
Stem Cells: Hope or Hype? 747
Hide and Seek: Finding a Cure for HIV 749
9900441100__0000__ffmm__ppii--xxvviiiiii..iinndddd vv 1100//1188//0077 55::2233::3377 PPMM
Contents
1
Biochemistry and the Biochemical Connections: Lactic Acid—Not Always the Bad Guy 61
Organization of Cells
1 Summary 61
1.1 Basic Themes 1 Review Exercises 62
1.2 Chemical Foundations of Biochemistry 3 Annotated Bibliography 64
1.3 The Beginnings of Biology: Origin of Life 5
3
The Earth and Its Age 5 Amino Acids and Peptides 65
Biochemical Connections: Why Structural Formulas Are
3.1 Amino Acids Exist in a Three-Dimensional
So Important 6
World 65
B iomolecules 7
3.2 Individual Amino Acids: Their Structures
M olecules to Cells 11
and Properties 66
1.4 The Biggest Biological Distinction—Prokaryotes Uncommon Amino Acids 70
and Eukaryotes 14
Biochemical Connections: Amino Acids to Calm Down and Pep Up 72
1.5 Prokaryotic Cells 16
3.3 Amino Acids Can Act as Both Acids
1.6 Eukaryotic Cells 16 and Bases 73
1.7 Five Kingdoms, Three Domains 22 3.4 The Peptide Bond 77
Biochemical Connections: Extremophiles: The Toast of the Industry 25 3.5 Small Peptides with Physiological Activity 79
1.8 Common Ground for All Cells 25 Biochemical Connections: Amino Acids Go Many Different Places 79
Biochemical Connections: Aspartame, the Sweet Peptide 80
1.9 Biochemical Energetics 27
Biochemical Connections: Phenylketonuria—Little Molecules Have
1.10 Energy and Change 29
Big Effects 82
1.11 Spontaneity in Biochemical Reactions 30 Biochemical Connections: Peptide Hormones—More Small Molecules
with Big Effects 83
1.12 Life and Thermodynamics 31
Biochemical Connections: Predicting Reactions 32 Summary 84
Summary 33 Review Exercises 84
Review Exercises 34 Annotated Bibliography 86
Annotated Bibliography 36
4
The Three-Dimensional
2 Structure of Proteins
Water: The Solvent for 87
Biochemical Reactions 37 4.1 Protein Structure and Function 87
2.1 Water and Polarity 37 4.2 Primary Structure of Proteins 88
Solvent Properties of Water 38 4.3 Secondary Structure of Proteins 89
2.2 Hydrogen Bonds 42 Periodic Structures in Protein Backbones 89
Other Biologically Important Hydrogen Bonds 45 Biochemical Connections: Complete Proteins and Nutrition 90
Biochemical Connections: How Basic Chemistry Affects Life: Irregularities in Regular Structures 93
The Importance of the Hydrogen Bond 46 Supersecondary Structures and Domains 93
2.3 Acids, Bases, and pH 47 The Collagen Triple Helix 93
Two Types of Protein Conformations:
2.4 Titration Curves 51
Fibrous and Globular 97
2.5 Buffers 53
4.4 Tertiary Structure of Proteins 98
Biochemical Connections: Buffer Selection 59
Forces Involved in Tertiary Structures 99
Biochemical Connections: Some Physiological Consequences
Myoglobin: An Example of Protein Structure 102
of Blood Buffering 60
9900441100__0000__ffmm__ppii--xxvviiiiii..iinndddd vvii 1100//1188//0077 55::2233::3388 PPMM