Fundamentals of biochemistry: life at the molecular level

1204 Pages·398.679 MB·English

by  Voet, Donald;Pratt, Charlotte W;Voet, Judith G

F U N D M E N T A L S O F
Biochemistry
LIFE AT
THE MOLECULAR
LEVEL
Voet Voet Pratt
F O U R T H E D I T I O N
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One- and Three-Letter Symbols for the Amino Acidsa Thermodynamic Constants and Conversion Factors
A Ala Alanine Joule (J)
B Asx Asparagine or aspartic acid 1 J!1 kg"m2"s#2 1 J!1 C"V (coulomb volt)
1 J!1 N"m (newton meter)
C Cys Cysteine
D Asp Aspartic acid Calorie (cal)
E Glu Glutamic acid 1 cal heats 1 g of H2O from 14.5 to 15.5°C
1 cal!4.184 J
F Phe Phenylalanine
G Gly Glycine Large calorie (Cal)
H His Histidine 1 Cal!1 kcal 1 Cal!4184 J
I Ile Isoleucine
Avogadro’s number (N)
K Lys Lysine N!6.0221$1023 molecules"mol#1
L Leu Leucine
Coulomb (C)
M Met Methionine
1 C!6.241$1018 electron charges
N Asn Asparagine
Faraday (!)
P Pro Proline
1 !!N electron charges
Q Gln Glutamine
1 !!96,485 C"mol#1!96,485 J"V#1"mol#1
R Arg Arginine
Kelvin temperature scale (K)
S Ser Serine
0 K!absolute zero 273.15 K!0°C
T Thr Threonine
V Val Valine Boltzmann constant (k )
B
W Trp Tryptophan kB!1.3807$10#23 J"K#1
Y Tyr Tyrosine
Gas constant (R)
Z Glx Glutamine or glutamic acid R!Nk R!1.9872 cal"K#1"mol#1
B
R!8.3145 J"K#1"mol#1 R!0.08206 L"atm"K#1"mol#1
aThe one-letter symbol for an undetermined or nonstandard amino acid is X.
The Standard Genetic Code
First Third
Position Second Position
(5! end) Position (3! end)
U C A G
UUU Phe UCU Ser UAU Tyr UGU Cys U
UUC Phe UCC Ser UAC Tyr UGC Cys C
U
UUA Leu UCA Ser UAA Stop UGA Stop A
UUG Leu UCG Ser UAG Stop UGG Trp G
CUU Leu CCU Pro CAU His CGU Arg U
CUC Leu CCC Pro CAC His CGC Arg C
C
CUA Leu CCA Pro CAA Gln CGA Arg A
CUG Leu CCG Pro CAG Gln CGG Arg G
AUU Ile ACU Thr AAU Asn AGU Ser U
AUC Ile ACC Thr AAC Asn AGC Ser C
A
AUA Ile ACA Thr AAA Lys AGA Arg A
AUG Meta ACG Thr AAG Lys AGG Arg G
GUU Val GCU Ala GAU Asp GGU Gly U
GUC Val GCC Ala GAC Asp GGC Gly C
G
GUA Val GCA Ala GAA Glu GGA Gly A
GUG Val GCG Ala GAG Glu GGG Gly G
aAUG forms part of the initiation signal as well as coding for internal Met residues.
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F O U R T H E D I T I O N
Fundamentals of
Biochemistry
L I F E A T T H E M O L E C U L A R L E V E L
Donald Voet
University of Pennsylvania
Judith G. Voet
Swarthmore College
Charlotte W. Pratt
Seattle Pacific University
John Wiley & Sons, Inc.
JWCL460_fm_i-xxxii.qxd 1/14/12 5:59 PM Page iv
To our colleagues in the laboratory and classroom who share our love of biochemistry
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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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A B O U T T H E A U T H O R S
Donald Voet received his B.S. in Chemistry from the California Institute of Technology in 1960, a Ph.D. in Chemistry
from Harvard University in 1966 under the direction of William Lipscomb, and then did his postdoctoral research in
the Biology Department at MIT with Alexander Rich. Upon completion of his postdoc in 1969, Don became a faculty
member in the Chemistry Department at the University of Pennsylvania, where he taught a variety of biochemistry
courses as well as general chemistry and X-ray crystallography. Don’s research has focused on the X-ray crystallography
of molecules of biological interest. He has been a visiting scholar at Oxford University, the University of California at
San Diego, and the Weizmann Institute of Science in Israel. Don is the coauthor of three previous editions of
Fundamentals of Biochemistry (first published in 1999) as well as four editions of Biochemistry, a more advanced textbook
(first published in 1990). Together with Judith G. Voet, Don is Co-Editor-in-Chief of the journal Biochemistry and
Molecular Biology Education. He is a member of the Education Committee of the International Union of Biochemistry
and Molecular Biology (IUBMB) and continues to be an invited speaker at numerous national and international ven-
ues. He, together with Judith G. Voet, received the 2012 award for Exemplary Contributions to Education from the
American Society for Biochemistry and Molecular Biology (ASBMB). His hobbies include backpacking, scuba diving,
skiing, travel, photography, and writing biochemistry textbooks.
Judith (“Judy”) Voet was educated in the New York City public schools and received her B.S. in Chemistry from
Antioch College and her Ph.D. in Biochemistry from Brandeis University under the direction of Robert H. Abeles. She
has done postdoctoral research at the University of Pennsylvania, Haverford College, and the Fox Chase Cancer Center.
Judy’s main area of research involves enzyme reaction mechanisms and inhibition. She taught biochemistry at the
University of Delaware before moving to Swarthmore College, where she taught biochemistry, introductory chemistry,
and instrumental methods for 26 years, reaching the position of James H. Hammons Professor of Chemistry and
Biochemistry and twice serving as department chair before going on “permanent sabbatical leave.” Judy has been a
visiting scholar at Oxford University, U.K., University of California, San Diego, University of Pennsylvania, and the
Weizmann Institute of Science, Israel. She is a coauthor of three previous editions of Fundamentals of Biochemistry and
four editions of the more advanced text, Biochemistry. Judy is Co-Editor-in-Chief of the journal Biochemistry and
Molecular Biology Education. She has been a National Councilor for the American Chemical Society (ACS) Biochemistry
Division, a member of the Education and Professional Development Committee of the American Society for
Biochemistry and Molecular Biology (ASBMB), and a member of the Education Committee of the International Union
of Biochemistry and Molecular Biology (IUBMB). She, together with Donald Voet, received the 2012 award for
Exemplary Contributions to Education from the ASBMB. Her hobbies include hiking, backpacking, scuba diving, and
tap dancing.
Charlotte Pratt received her B.S. in Biology from the University of Notre Dame and her Ph.D. in Biochemistry from
Duke University under the direction of Salvatore Pizzo. Although she originally intended to be a marine biologist, she
discovered that biochemistry offered the most compelling answers to many questions about biological structure–function
relationships and the molecular basis for human health and disease. She conducted postdoctoral research in the Center
for Thrombosis and Hemostasis at the University of North Carolina at Chapel Hill. She has taught at the University of
Washington and currently teaches and supervises undergraduate researchers at Seattle Pacific University. Developing new
teaching materials for the classroom and student laboratory is a long-term interest. In addition to working as an editor
of several biochemistry textbooks, she has co-authored Essential Biochemistry and previous editions of Fundamentals of
Biochemistry. When not teaching or writing, she enjoys hiking and gardening.
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B R I E F C O N T E N T S
PART I INTRODUCTION
1 Introduction to the Chemistry of Life 1
2 Water 22
PART II BIOMOLECULES
3 Nucleotides, Nucleic Acids, and Genetic Information 40
4 Amino Acids 76
5 Proteins: Primary Structure 93
6 Proteins: Three-Dimensional Structure 127
7 Protein Function: Myoglobin and Hemoglobin, Muscle Contraction, and Antibodies 176
8 Carbohydrates 217
9 Lipids and Biological Membranes 241
10 Membrane Transport 288
PART III ENZYMES
11 Enzymatic Catalysis 315
12 Enzyme Kinetics, Inhibition, and Control 355
13 Biochemical Signaling 396
PART IV METABOLISM
14 Introduction to Metabolism 436
15 Glucose Catabolism 472
16 Glycogen Metabolism and Gluconeogenesis 517
17 Citric Acid Cycle 551
18 Electron Transport and Oxidative Phosphorylation 581
19 Photosynthesis 623
20 Lipid Metabolism 657
21 Amino Acid Metabolism 712
22 Mammalian Fuel Metabolism: Integration and Regulation 767
PART V GENE EXPRESSION AND REPLICATION
23 Nucleotide Metabolism 793
24 Nucleic Acid Structure 821
25 DNA Replication, Repair, and Recombination 867
26 Transcription and RNA Processing 919
27 Protein Synthesis 962
28 Regulation of Gene Expression 1013
Solutions to Odd-Numbered Problems SP-1
Glossary G-1
Index I-1
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C O N T E N T S
Preface xvii 2 Chemical Properties of Water 30
Acknowledgments xxii A. Water Ionizes to Form H+ and OH! 30
B. Acids and Bases Alter the pH 32
Guide to Media Resources xxv
C. Buffers Resist Changes in pH 34
Clinical Applications xxxi
Box 2-1 Perspectives in Biochemistry: The Consequences
of Ocean Acidification 32
PART I INTRODUCTION
Box 2-2 Biochemistry in Health and Disease: The Blood
Buffering System 37
1 Introduction to the Chemistry
of Life 1 PART II BIOMOLECULES
1 The Origin of Life 2
3 Nucleotides, Nucleic Acids,
A. Biological Molecules Arose From Inorganic Materials 2
B. Complex Self-replicating Systems Evolved from Simple and Genetic Information 40
Molecules 3
1 Nucleotides 41
2 Cellular Architecture 5
2 Introduction to Nucleic Acid Structure 44
A. Cells Carry Out Metabolic Reactions 6
A. Nucleic Acids Are Polymers of Nucleotides 44
B. There are Two Types of Cells: Prokaryotes
B. DNA Forms a Double Helix 45
and Eukaryotes 7
C. RNA Is a Single-Stranded Nucleic Acid 48
C. Molecular Data Reveal Three Evolutionary Domains of
Organisms 9
3 Overview of Nucleic Acid Function 48
D. Organisms Continue to Evolove 10
A. DNA Carries Genetic Information 49
3 Thermodynamics 11 B. Genes Direct Protein Synthesis 49
A. The First law of Thermodynamics States That Energy is
4 Nucleic Acid Sequencing 51
Conserved 11
A. Restriction Endonucleases Cleave DNA at Specific
B. The Second Law of Thermodynamics States That Entropy
Sequences 52
Tends to Increase 13
B. Electrophoresis Separates Nucleic Acids According
C. The Free Energy Change Determines the Spontaneity of a
to Size 54
Process 13
C. Traditional DNA Sequencing Uses the Chain-Terminator
D. Free Energy Changes Can Be Calculated from Equilibrium
Method 55
Concentrations 15
D. Entire Genomes Have Been Sequenced 58
E. Life Obeys the Laws of Thermodynamics 18
E. Evolution Results from Sequence Mutations 60
Box 1-1 Pathways of Discovery: Lynn Margulis and the 5 Manipulating DNA 62
Theory of Endosymbiosis 10
A. Cloned DNA Is an Amplified Copy 62
Box 1-2 Perspectives in Biochemistry: Biochemical
Conventions 12 B. DNA Libraries Are Collections of Cloned DNA 66
C. DNA Is Amplified by the Polymerase Chain Reaction 67
2 Water 22 D. Recombinant DNA Technology Has Numerous Practical
Applications 68
1 Physical Properties of Water 23
A. Water is a Polar Molecule 23 Box 3-1 Pathways of Discovery: Francis Collins and the
Gene for Cystic Fibrosis 58
B. Hydrophilic Substances Dissolve in Water 25
Box 3-2 Perspectives in Biochemistry:
C. The Hydrophobic Effect Causes Nonpolar Substances to
DNA Fingerprinting 69
Aggregate in Water 26
Box 3-3 Perspectives in Biochemistry: Ethical Aspects of
D. Water Moves by Osmosis and Solutes Move by Recombinant DNA Technology 71
Diffusion 28
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4 Amino Acids 76 B. The Most Common Regular Secondary Structures are the !
Helix and the " Sheet 131
1 Amino Acid Structure 77 C. Fibrous Proteins Have Repeating Secondary
A. Amino Acids Are Dipolar Ions 80 Structures 136
B. Peptide Bonds Link Amino Acids 80 D. Most Proteins Include Nonrepetitive Structure 140
C. Amino Acid Side Chains are Nonpolar, Polar, or Charged 80
2 Tertiary Structure 142
D. The pK Values of Ionizable Groups Depend on
A. Most Protein Structures Are Determined
Nearby Groups 82
by X-Ray Crystallography or Nuclear
E. Amino Acid Names Are Abbreviated 83
Magnetic Resonance 142
2 Stereochemistry 84 B. Side Chain Location Varies with
Polarity 146
3 Amino Acid Derivatives 87 C. Tertiary Structures Contain Combinations
of Secondary Structure 148
A. Protein Side Chains May Be Modified 88
D. Structure Is Conserved More than
B. Some Amino Acids Are Biologically Active 88
Sequence 151
E. Structural Bioinformatics Provides
Box 4-1 Pathways of Discovery: William C. Rose and the
Discovery of Threonine 77 Tools for Storing, Visualizing, and
Comparing Protein Structural Information 152
Box 4-2 Perspectives in Biochemistry: The RS System 86
Box 4-3 Perspectives in Biochemistry: Green Fluorescent
3 Quaternary Structure and Symmetry 155
Protein 89
4 Protein Stability 156
5 Proteins: Primary Structure 93 A. Proteins Are Stabilized by Several Forces 157
B. Proteins Can Undergo Denaturation and Renaturation 159
1 Polypeptide Diversity 94
C. Proteins Are Dynamic Structures 161
2 Protein Purification and Analysis 95
5 Protein Folding 162
A. Purifying a Protein Requires a Strategy 96
A. Proteins Follow Folding Pathways 162
B. Salting Out Separates Proteins by Their Solubility 98
B. Molecular Chaperones Assist Protein Folding 166
C. Chromatography Involves Interaction with Mobile and
C. Some Diseases Are Caused by Protein Misfolding 169
Stationary Phases 99
D. Electrophoresis Separates Molecules According to
Box 6-1 Pathways of Discovery: Linus Pauling and
Charge and Size 102
Structural Biochemistry 132
E. Ultracentrifugation Separates Molecules by Mass 104 Box 6-2 Biochemistry in Health and Disease: Collagen
Diseases 139
3 Protein Sequencing 106
Box 6-3 Perspectives in Biochemistry: Thermostable
A. The First Step Is to Separate Subunits 106 Proteins 159
B. The Polypeptide Chains Are Cleaved 110 Box 6-4 Perspectives in Biochemistry: Protein Structure
C. Edman Degradation Removes a Peptide’s First Prediction and Protein Design 165
Amino Acid Residue 110
D. Mass Spectrometry Determines the Molecular
Masses of Peptides 113
7 Protein Function: Myoglobin and
E. Reconstructed Protein Sequences Are Stored in Databases 114
Hemoglobin, Muscle Contraction, and
4 Protein Evolution 116 Antibodies 176
A. Protein Sequences Reveal Evolutionary Relationships 117
B. Proteins Evolve by the Duplication of Genes or Gene 1 Oxygen Binding to Myoglobin
Segments 119
and Hemoglobin 177
A. Myoglobin Is a Monomeric Oxygen-
Box 5-1 Pathways of Discovery: Frederick Sanger and
Binding Protein 177
Protein Sequencing 108
B. Hemoglobin Is a Tetramer with Two
Conformations 181
6 Proteins: Three-Dimensional
C. Oxygen Binds Cooperatively to
Structure 127 Hemoglobin 184
D. Hemoglobin’s Two Conformations Exhibit Different Affinities for
1 Secondary Structure 128 Oxygen 186
A. The Planar Peptide Group Limits Polypeptide E. Mutations May Alter Hemoglobin’s Structure and
Conformations 128 Function 193
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