Biochemistry: Student Companion

620 Pages·2002·8.169 MB·English

by  Richard I. GumportFrank H. Deis, Nancy Counts Gerber, Roger E. Koeppe, II

STUDENT COMPANION
to accompany
Biochemistry, Fifth Edition
Richard I. Gumport
College of Medicine at Urbana-Champaign,
University of Illinois
Frank H. Deis
Rutgers University
Nancy Counts Gerber
San Francisco State University
Expanded Solutions to Text Problems
contributed by
Roger E. Koeppe, II
University of Arkansas at Fayetteville
W. H. Freeman and Company
New York
eISBN: 0-7167-9758-5
© 2002 by W. H. Freeman and Company
No part of this book may be reproduced by any mechanical, photo-
graphic, or electronic process, or in the form of a phonographic record-
ing, nor may it be stored in a retrieval system, transmitted, or otherwise
copied for public or private use, without written permission from the
publisher.
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Preface, v N
Acknowledgments, vii T
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PART I: THE MOLECULAR DESIGN OF LIFE
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Chapter 1:Prelude 1
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Chapter 2:Biochemical Evolution 9
Chapter 3:Protein Structure and Function 17
Chapter 4:Exploring Proteins 33
Chapter 5:DNA, RNA, and the Flow of Genetic Information 51
Chapter 6:Exploring Genes 83
Chapter 7: Exploring Evolution 105
Chapter 8: Enzymes: Basic Concepts and Kinetics 115
Chapter 9: Catalytic Strategies 145
Chapter 10:Regulatory Strategies: Enzymes and Hemoglobin 159
Chapter 11:Carbohydrates 177
Chapter 12:Lipids and Cell Membranes 195
Chapter 13:Membrane Channels and Pumps 211
PART II: TRANSDUCING AND STORING ENERGY
Chapter 14:Metabolism: Basic Concepts and Design 229
Chapter 15:Signal-Transduction Pathways: An Introduction to Information Metabolism 247
Chapter 16: Glycolysis and Gluconeogenesis 267
Chapter 17:The Citric Acid Cycle 287
Chapter 18:Oxidative Phosphorylation 305
Chapter 19:The Light Reactions of Photosynthesis 331
Chapter 20:The Calvin Cycle and the Pentose Phosphate Pathway 345
Chapter 21:Glycogen Metabolism 361
Chapter 22:Fatty Acid Metabolism 383
Chapter 23:Protein Turnover and Amino Acid Catabolism 407
PART III: SYNTHESIZING THE MOLECULES OF LIFE
Chapter 24:The Biosynthesis of Amino Acids 425
Chapter 25:Nucleotide Biosynthesis 443
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IV CONTENTS
Chapter 26:The Biosynthesis of Membrane Lipids and Steroids 461
Chapter 27:DNA Replication, Recombination, and Repair 481
Chapter 28:RNA Synthesis and Splicing 501
Chapter 29:Protein Synthesis 517
Chapter 30:The Integration of Metabolism 533
Chapter 31:The Control of Gene Expression 551
PART IV: RESPONDING TO ENVIRONMENTAL CHANGES
Chapter 32:Sensory Systems 573
Chapter 33:The Immune System 585
Chapter 34:Molecular Motors 599
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Opening a comprehensive biochemistry text for the first time can be a daunt-
ing experience for a neophyte. So much detailed material is presented that it
is natural to wonder if you can possibly master it in one or two semesters of
study. Of course, you can’t learn everything, but experience indicates that you
can, indeed, learn the fundamental concepts in an introductory biochemistry
course. We have written this Student Companion for Biochemistryto ease your
entry into the exciting world of biochemistry.
Your goal is to “know” and “understand” biochemistry. Unfortunately,
awareness of these grand goals offers no practical help in reaching them, be-
cause they are such high-level and complex intellectual processes. In addition,
it is difficult for you to know to what extent you have attained them. We have
found that, by subdividing these goals into simpler ones and expressing them
in terms of demonstrable behaviors, you can begin to approach them and, in
addition, can readily assay your progress toward reaching them. Thus, a part
of each chapter consists of Learning Objectives that ask you to do things that
will help you to begin to understand biochemistry. When you can master the
objectives, you are well on your way to learning the material in the chapter.
It is important to add a cautionary note here. Being able to respond to all the
objectives adequately does not mean that you know biochemistry, for they are
a limited sampling of all the possible objectives; more to the point, they do
not explicitly require such higher-level activities as creation, analysis, integra-
tion, synthesis, problem-solving, evaluation, application, and appreciation.
These more advanced skills will develop to varying levels as you continue your
studies of biochemistry beyond the introductory stage.
Each chapter in the Companion consists of an introduction, Learning
Objectives, a Self-Test, Answers to Self-Test, Problems, Answers to Problems,
and Expanded Solutions to Text Problems. The introduction sets the scene,
places the chapter material in the context of what you have already learned,
and reminds you of material you may need to review in order to understand
what follows. The Learning Objectives are presented in the order that the in-
formation they encompass appears in Biochemistry. Key Words—important
concepts or vocabulary—are italicized in the objectives. Self-Test questions,
requiring primarily information recall, are followed by the answers to the
questions. A Problems section, in which more complex skills are tested, is
followed by answers to the problems. Finally, Expanded Solutions to end-of-
chapter problems in the text are presented.
The Companion may be used in many ways, and as you begin your
studies you will develop the “system” that is best for you. Over 30 years of
experience teaching introductory biochemistry to first-year medical students
has suggested one pathway that you should consider. Start by reviewing the
prerequisite chapters mentioned in the introduction and skim the Learning
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VI PREFACE
Objectives to obtain an overview of what you are to learn. Some students like also to skim
the Self-Test questions at this time to form an impression of the levels of difficulty and the
kinds of questions that will be asked. Next, read the chapter in Biochemistry, using the
Learning Objectives to help direct you to the essential concepts. Note the Key Words and look
up those you don’t know. Then attempt to meet the objectives. When you cannot satisfy an
objective, reread the relevant section of the text. You should now take the Self-Test to check
your ability to recall and apply what you have learned. Finally, solve the Problems, which
have been designed to further test your ability to apply the knowledge you have gained. It is
not sufficient simply to read the problems and look at the answers to see if you would have
done them the same way. You must struggle through the solutions yourself to benefit from
the problems. As you are using the Companion, you will, of course, be integrating what you
have learned from your studies and your lectures or laboratory exercises.
Besides helping you to learn biochemistry, you will find the Companion useful in study-
ing for examinations. Go over each of the Learning Objectives in the chapters covered by an
exam to ensure that you can respond to it knowledgeably. Similarly, review the Key Words.
Decide which chapter topics you feel uncertain about and reread them. This protocol, cou-
pled with a review of your lecture and reading notes, will prepare you well for examinations.
It is important to talk about biochemistry with others in order to learn the pronuncia-
tion of scientific terms and names and to help crystallize your thinking. Also, realize that al-
though biochemistry has a sound foundation and we understand much about the chemistry
of life, many of our concepts are hypotheses that will require modification or refinement as
more experimental evidence accrues. Alternative and sometimes contradictory explanations
exist for many biochemical observations. You should not regard the material in Biochemistry
or the Companion as dogma, and you should, wherever possible, attempt to read about any
given topic in at least two sources. Try to follow up topics that particularly interest you by
reading about them in the scientific literature. References are given in Biochemistry, and your
instructor can help you locate research and review articles. In this way, you can begin to ap-
preciate the diversity of opinion and emphasis that exists in the field of biochemistry.
The authors welcome readers’ comments, especially those drawing our attention to er-
rors in the text. Comments should be sent to:
Professor Richard I. Gumport
Department of Biochemistry
University of Illinois
600 S. Mathews Avenue
Urbana, Illinois 61801-3792
e-mail [email protected]
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The Student Companion has its origins in a curriculum guide that was initi-
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ated over 30 years ago for first-year medical students studying biochemistry
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at the College of Medicine of the University of Illinois at Urbana-Champaign.
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A number of colleagues have contributed to the Companion over the years.
We especially wish to thank Ana Jonas, Richard Mintel, and Carl Rhodes, who
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were authors on previous editions, for their contributions of concept and con-
tent, which we continue to use. We also thank our colleagues Fumio M
Matsumura, Gaetano Montelione, and Robert Niederman in the Department
of Molecular Biology and Biochemistry at Rutgers University. We also thank E
John Clark, Lowell Hager, Walter Mangel, William McClure, and Robert N
Switzer for their efforts in helping to develop the initial curriculum guide.
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Special thanks go to George Ordal and James Kaput, our fellow teachers of
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biochemistry at the College of Medicine. We thank Gordon Lindberg and
Chad Thomas for their careful reading and insightful contributions to the
book. We also thank William Sorlie for educating us to the value of learning
objectives. Thanks are also due to the many students who took the time to
criticize the Companion. Finally, RIG appreciates the sustained support pro-
vided our teaching efforts by the Department of Biochemistry and the College
of Medicine at the University of Illinois.
Richard I. Gumport
Frank H. Deis
Nancy C. Gerber
VII
The woods are lovely, dark, and deep,
But I have promises to keep,
And miles to go before I sleep,
And miles to go before I sleep.
ROBERT FROST
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Prelude: Biochemistry A
P
and the Genomic Revolution
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1
he introductory chapter of Biochemistrybegins by describing recent advances in
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this exciting branch of science. We now know the complete genome sequences
for several species, and have a nearly complete sequence for human DNA. The
implications for biology and medicine are enormous, and they are touched on in this
chapter. The authors begin with a brief explanation of the structures of DNA, RNA,
and proteins. The unity of biochemistry is an important concept. It means that we
can learn about human biochemistry by studying mice, yeast, bacteria, or any liv-
ing organism. Many biochemical interactions depend on weak noncovalent interac-
tions. Because the great majority of biochemical processes occur in water, the
properties of water and their effects on biomolecules are also described. Then fol-
lows a discussion of entropy, energy, and the laws of thermodynamics. This provides
a basis for understanding hydrophobic interactions and protein folding. Then the
authors highlight the impact of biochemistry on modern biology and medicine.
Finally, an appendix presents the most popular molecular models and other repre-
sentations used by biochemists.
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