Student Companion to Accompany Fundamentals of Biochemistry

428 Pages·2012·18.93 MB·English

by  Akif Uzman

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Akif Uzman Jerry Johnson Joseph Eichberg William Widger
Donald Voet Judith G. Voet Charlotte W. Pratt
K Y M C
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STUDENT COMPANION TO ACCOMPANY

FUNDAMENTALS OF
BIOCHEMISTRY
LIFE AT THE MOLECULAR LEVEL
Fourth Edition

Akif Uzman
University of Houston

Jerry Johnson
University of Houston

Joseph Eichberg
University of Houston

William Widger
University of Houston

Donald Voet
University of Pennsylvania

Judith G. Voet
Swarthmore College

Charlotte W. Pratt
Seattle, Washington

JOHN WILEY & SONS, INC
Cover Designer Madelyn Lesure
Cover Illustration Norm Christiansen
Cover Photos
(Vitruvian Man): © Odysseus/Alamy and © Dennis Hallinan/Alamy
Molecular structures clockwise from top: based on X-ray structures that were respectively determined
by Richard Dickerson and Horace Drew, Caltech; Gerard Bunick, University of Tennessee; Thomas
Steitz, Yale University; Alfonso Mondragón, Northwestern University; Venki Ramakrishnan, MRC
Laboratory of Molecular Biology, Cambridge, U.K.; Andrew Leslie and John Walker, MRC Laboratory
of Molecular Biology, Cambridge, U.K.

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Student Companion (paperback) ISBN-13 978-1-1182-1827-3

Printed in the United States of America
10 9 8 7 6 5 4 3 2 1
Contents

1 Introduction to the Chemistry of Life 1

2 Water 9

3 Nucleotides, Nucleic Acids, and Genetic Information 21

4 Amino Acids 29

5 Proteins: Primary Structure 40

6 Proteins: Three-Dimensional Structure 49

7 Protein Function: Myoglobin and Hemoglobin, Muscle
Contraction, and Antibodies 60

8 Carbohydrates 72

9 Lipids and Biological Membranes 80

10 Membrane Transport 90

11 Enzymatic Catalysis 96

12 Enzyme Kinetics, Inhibition, and Control 108

13 Biochemical Signaling 121

14 Introduction to Metabolism 128

15 Glucose Catabolism 137

16 Glycogen Metabolism and Gluconeogenesis 146

17 Citric Acid Cycle 154

18 Electron Transport and Oxidative Phosphorylation 160
19 Photosynthesis 169

20 Lipid Metabolism 176

21 Amino Acid Metabolism 188

22 Mammalian Fuel Metabolism: Integration and Regulation 197

23 Nucleotide Metabolism 203

24 Nucleic Acid Structure 210

25 DNA Replication, Repair, and Recombination 219

26 Transcription and RNA Processing 230

27 Protein Synthesis 238

28 Regulation of Gene Expression 247

Answers to Questions AQ-1

Solutions to Problems SP-1
Welcome to biochemistry! You are about to become acquainted with one of the
most exciting scientific disciplines. The biotechnology industry, with its roots in
molecular genetics, is one of the most visible manifestations of the explosion of
biochemical knowledge that has occurred during our lifetime. Drug design and
novel approaches such as gene therapy rely on the fundamental knowledge of the
chemistry of biological molecules, particularly proteins. Our most common
diseases (e.g., diabetes and heart disease) have pleiotropic multifaceted
physiological effects that are best understood in terms of biochemistry. You will
soon discover that biochemistry’s impact on our lives cannot be over-emphasized.
We are excited to bring you an ever-expanding understanding of this magnificent
subject!

Learning biochemistry is not easy but it can be fun! Most students discover
that biochemistry is a synthetic science, merging knowledge of general chemistry,
organic chemistry, and biology. Hence, a more mature and creative kind of
thinking is required to gain a deep understanding of biochemistry. In addition to a
solid foundation in chemistry and biology, you will need to recognize and
assimilate some general principles from other disciplines within biology, including
physiology, genetics, and cell biology. In this respect, biochemistry is not all that
different from nonscientific pursuits that require some degree of “lateral thinking”
across disciplines.

This Student Companion accompanies Fundamentals of Biochemistry Fourth
Edition by Donald Voet, Judith G. Voet, and Charlotte W. Pratt. It is designed to
help you master the basic concepts and exercise your analytical skills as you work
your way through the textbook. Each chapter of the Student Companion is divided
into four parts, beginning with a general summary reminding you of the topics
covered in that chapter. This is followed by a section called Essential Concepts,
which provides an overview of the main facts and ideas that are essential for your
understanding of biochemistry. This can be regarded as a set of brief notes for each
chapter, alerting you to the key facts you need to commit to memory and to the
concepts you need to master. You will soon notice that biochemical knowledge is
cumulative: new concepts often rely on a solid understanding of previously
presented concepts. Hence, one of the key goals of this Companion is to help you
gain this understanding. The third and last section is the Questions. These are
organized in a manner to help you gain a firm understanding of each section of a
chapter. Some questions ask you to recall essential facts while others exercise your
problem-solving skills. Answers to all of the questions are provided at the end of
the Student Companion. However, you do yourself a great disservice by turning to
them too soon. Don’t know the answer right away? Keep trying! Go back to the
text to find clues for yourself. Use the answers to check yours, not to fill in a
temporary void in your understanding. The Solutions to all end of chapter
problems in the text can be found after the Answers to Questions.

As a new addition to this edition of the Student Companion, we have added
three new features to select chapters: Behind the Equations, Calculation Analogies
and Play It Forward. Behind the Equations is a section that tackles key equations in
Biochemistry. This section will provide insights and learning strategies for using
and understanding what these equations are really telling us, and how to use them
intuitively. The Calculation Analogies section will tackle key equations
conceptually using simple analogies that will help students understand how to
solve problems. The Play It Forward Section will take critical concepts from early
chapters and integrate them into material in later chapters to help students see how
the content continues to build upon itself, hopefully allowing students to synthesize
Biochemistry as a discipline.

“How should I study biochemistry beyond reading the textbook and working
in this Companion?” is a likely question from students. The phrase, “if you don’t
use it, you lose it” applies here. It is pointless to simply read your biochemistry
textbook over and over. Unless you are actively engaged in working with the
material, you become a passive reader. Active engagement includes using your
hands to work problems, drawing pictures, or writing an outline or flow chart. As
you read, ask yourself questions and seek answers from your text and your
instructor. By doing these things, you use the material, and it becomes more
efficiently transferred to your long-term memory.

“How often should I study biochemistry?” is also a common question. Most
instructors agree that frequent short study sessions—even daily—will pay greater
dividends than a single long session once a week. Because short-term memory lasts
just a few minutes, take a few minutes after every class to review your notes.
Similarly, stop reading your text, and review on paper with diagrams, word charts,
flow diagrams, what you just read. Talk biochemistry with anyone who will listen.
Form a study group to enrich your knowledge and test your memory. All these
activities will result in the transfer of knowledge from short-term memory to long-
term memory. In other words, the more you use biochemistry, the better you know
it and the more fun you will have with it.

One of the truly most satisfying ways to learn biochemistry is to apply its
principles and findings to problems that integrate your knowledge. To this end, Dr.
Kathleen Cornely has developed numerous case studies that test your analytical
skills. You will find these case studies on the Fundamentals of Biochemistry 4e
Student Companion Site at www.wiley.com/college/voet. They can also be found
in the Fundamentals of Biochemistry 4e WileyPLUS course
(www.wileyplus.com). Topics for the case studies were chosen to cover a range of
interesting areas relevant to biochemistry. The cases themselves are based on data
from research reports as well as clinical studies. The prerequisites include material
that you are likely to be studying in biochemistry class, but occasionally include
concepts from genetics and immunology on a level likely to be encountered in a
first-year general biology course. The answers to the questions posed in these case
studies can be obtained from your instructor.

We have many people to thank for helping us get this Companion to you. First
and foremost, we would like to acknowledge Associate Editor, Ms. Aly Rentrop,
and Production Editor, Ms. Sandra Dumas. In addition, we would like to
acknowledge Ms. Petra Recter, Associate Publisher for Physics and Chemistry at
John Wiley and Sons for her support of this project. We are also indebted to
Caroline Breitenberger of The Ohio State University and Laura Mitchell of St.
Joseph’s University for their much-appreciated reviews of our original draft. We
would also like to thank our students at Swarthmore College, the University of
Houston, and the University of Houston-Downtown for pointing out errors and
ambiguities in earlier drafts of this work. It is still possible that errors persist, and
so we would greatly appreciate being alerted to them. Please forward you
comments to Akif Uzman ([email protected]).

Akif Uzman
Jerry Johnson
Joseph Eichberg
William Widger
Charlotte W. Pratt
Donald Voet
Judith G. Voet
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