Lehninger principles of biochemistry
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2008
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| 100 | 1 | |a Nelson, David L. |d 1942- |e Verfasser |0 (DE-588)133943070 |4 aut | |
| 245 | 1 | 0 | |a Lehninger principles of biochemistry |c David L. Nelson ; Michael M. Cox |
| 246 | 1 | 3 | |a Principles of biochemistry |
| 250 | |a 5. ed., 1. print. | ||
| 264 | 1 | |a New York |b Freeman |c 2008 | |
| 300 | |a Getr. Zählung |b Ill., graph. Darst. | ||
| 336 | |b txt |2 rdacontent | ||
| 337 | |b n |2 rdamedia | ||
| 338 | |b nc |2 rdacarrier | ||
| 500 | |a Früher u.d.T.: Lehninger, Albert L.: Principles of biochemistry.- Erg. bildet: Osgood, Marcy: The absolute, ultimate guide to Lehninger principles of biochemistry, 5. ed. | ||
| 650 | 4 | |a Biochemie - Lehrbuch | |
| 650 | 4 | |a Biochemistry | |
| 650 | 0 | 7 | |a Biochemie |0 (DE-588)4006777-4 |2 gnd |9 rswk-swf |
| 650 | 0 | 7 | |a Physiologische Chemie |0 (DE-588)4076124-1 |2 gnd |9 rswk-swf |
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| 700 | 1 | |a Cox, Michael M. |e Verfasser |0 (DE-588)113617615 |4 aut | |
| 700 | 1 | |a Lehninger, Albert L. |d 1917-1986 |e Sonstige |0 (DE-588)132539519 |4 oth | |
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Datensatz im Suchindex
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| DE-BY-TUM_katkey | 1637856 |
| DE-BY-TUM_media_number | 040050760488 040050760477 040030237562 040020776665 040050760433 040020776654 040050760444 040050760455 040030237551 040050760411 040050760466 040050760422 040050760499 040050760400 |
| _version_ | 1816712804689772544 |
| adam_text | Contents in Brief
Contents
Preface
via
1
The Foundations of Biochemistry
1
1
STRUCTURE AND CATALYSIS
41
2
Water
43
3
Amino
Acids, Peptides, and Proteins
71
4
The Three-Dimensionat Structure of Proteins
113
5
Protein Function
1S3
6
Enzymes
183
7
Carbohydrates and Glycobiology
235
8
Nudeotides and Nucleic Acids
271
9
ONA-Based information Technologies
303
10
Lipids
343
11
Biological Membranes and Transport
371
12 Biosignaimg
417
II BIOENERGETiCS
AND METABOLISM
485
13
Bioenergetics and Biochemical Reaction Types
489
14
Glycolysis, Gluconeogenesis, and the Pentose
Phosphate Pathway
527
15
Principles of Metabolic Regulation
569
16
The Citric Acid Cycle
615
17
Fatty Acid Catabolism
647
18
Amino
Acid Oxidation and the Production of Urea
673
19
Oxidative Phosphorylation and Photophosphorylation
707
20
Carbohydrate Biosynthesis in Plants and Bacteria
773
21
Lipid
Biosynthesis
805
22
Biosynthesis of
Amino
Acids, Nudeotides, and
Related Moiecuies
851
23
Hormonal Regulation and integration of
Mammalian Metabolism
901
III INFORMATION PATHWAYS
945
24
Genes and Chromosomes
947
25
DNA Metabolism
975
26
RNA
Metabolism
1021
27
Protein Metabolism
1065
28
Regulation of Gene Expression
1115
Appendix A Common Abbreviations ¡n the Biochemical
Research Literature A-1
Appendix
В
Abbreviated Solutions to Problems AS-
1
Glossary G-l
Credits C-1
IndexH
1
The Foundations of Biochemistry
__________
1.1
Cellular Foundations
Cells Are the Structural and Functional
Units of All Living Organisms
Cellular Dimensions Are Limited by Diffusion
There Are Three Distinct Domains of Life
Escherichìa coli
Is the Most-Studied Bacterium
Eukaryotic Cells Have a Variety of Membranous
Organelles, Which Can Be Isolated for Study
The Cytoplasm Is Organized by the Cytoskeleton
and Is Highly Dynamic
Cells Build Supramolecular Structures
In Vitro Studies May Overlook Important
Interactions among Molecules
1.2
Chemical Foundations
Biomolecules Are Compounds of Carbon with
a Variety of Functional Groups
Cells Contain a Universal Set of Small Molecules
Box
1 -1
Molecular Weight, Molecular Mass, and
Their Correct Units
Macromolecules Are the Major
Constituents of Cells
Three-Dimensional Structure Is Described
by Configuration and Conformation
Box
1-2
Louis Pasteur and Optical Activity: In Vino, Veritas
Interactions between Biomolecules
Are Stereospeciflc
1.3
Physical Foundations
Living Organisms Exist in a Dynamic
Steady State, Never at Equilibrium with
Their Surroundings
Organisms Transform Energy and Matter
from Their Surroundings
Box
1 -3
Entropy: The Advantages of Being Disorganized
The Flow of Electrons Provides Energy
for Organisms
Creating and Maintaining Order Requires Work
and Energy
Energy Coupling Links Reactions in Biology
Keą
and AG° Are Measures of a Reaction s
Tendency to Proceed Spontaneously
Enzymes Promote Sequences of Chemical Reactions
Metabolism Is Regulated to Achieve Balance
and Economy
1.4
Genetic Foundations
Genetic Continuity Is Vested in Single
DNA
Molecules
The Structure of
DNA
Allows for Its Replication
and Repair with Near-Perfect Fidelity
The linear Sequence in
DNA
Encodes Proteins with
Three-Dimensional Structures
2
з
3
4
б
9
10
11
n
13
14
14
15
17
18
19
20
20
21
22
22
22
24
25
26
27
27
28
29
j
xv
|
TxvQ Contents
Changes in the Hereditary Instructions
Allow Evolution
Biornolecules First Arose
Ъу
Chemical Evolution
RNA
or Related Precursors May Have Been the
First Genes and Catalysts
Biological Evolution Began More Than
Three and a Half Billion Years Ago
The First Cell Probably Used Inorganic Fuels
Eukaryotic Cells Evolved from Simpler
Precursors in Several Stages
Molecular Anatomy Reveals Evolutionary
Relationships
Functional Genomics Shows the Allocations of
Genes to Specific Cellular Processes
Genomic Comparisons Have Increasing
Importance in Human Biology and Medicine
STRUCTURE AND CATALYSIS
2.2
taniiation of Water, Weak adds, and Weak Bases
Pure Water Is Slightly Ionized
The Ionization of Water Is Expressed by an
Equilibrium Constant
The
pH
Scale Designates the H+ and OH
Concentrations
Weak Acids and Bases Have Characteristic
Acid Dissociation Constants
Titration
Curves Reveal the pi?a of Weak Adds
23
Buffers Are Mixtures of Weak Acids and Their
Conjugate Bases
The Henderson-Hasselbalch Equation Relates
pH,
pKa, and Buffer Concentration
Weak Acids or Bases Buffer Cells and
Tissues against
pH
Changes
Untreated Diabetes Produces
Life-Threatening Acidosis
Box
2-1
Medicine: On Being One s Own Rabbit
(Don t Try This at Home!)
29
30
31
32
32
33
33
35
35
2.Ί
Weak
Interactions
in Aqueous Systems
Hydrogen Bonding Gives Water Its
Unusual Properties
Water Forms Hydrogen Bonds with Polar Solutes
Water Interacts Electrostatically with
Charged Solutes
Entropy Increases as Crystalline
Substances Dissolve
Nonpolar
Gases Are Poorly Soluble in Water
Nonpolar
Compounds Force Energetically
Unfavorable Changes in the Structure of Water
van
der Waals
Interactions Are Weak Interatomic
Attractions
Weak Interactions Are Crucial to Macromolecular
Structure and Function
Solutes Affect the Colligative Properties of
Aqueous Solutions
43
45
46
47
47
47
60
51
54
54
55
56
57
58
59
60
61
63
64
Amino
Acids Share Common Structural Features
The
Amino
Acid Residues in Proteins Are
L
Stereoisomers
Amino
Acids Can Be Classified by
R
Group
Box
3-1
Methods: Absorption of Light by Molecules:
The Lambert-Beer Law
Uncommon
Amino
Acids Also Have
Important Functions
Amino
Acids Can Act as Acids and Bases
Amino
Acids Have Characteristic
Titration
Curves
Titration
Curves Predict the Electric
Charge of
Amino
Acids
Amino
Acids Differ in Their Acid-Base Properties
3.2
Peptsdes
and Proteins
Peptides Are Chains of
Amino
Acids
Peptides Can Be Distinguished by Their
Ionization Behavior
Biologically Active Peptides and Polypeptides
Occur in a Vast Range of Sizes and
Compositions
Some Proteins Contain Chemical Groups
Other Than
Amino
Acids
Proteins Can Be Separated and Purified
Proteins Can Be Separated and Characterized by
Electrophoresis
Unseparated Proteins Can Be Quantified
3.4
The Stracttire of Proteins: Primary Structure
The Function of a Protein Depends on Its
Amino
Acid Sequence
The
Amino
Acid Sequences of Millions of
Proteins Have Been Determined
Short Polypeptides Are Sequenced with
Automated Procedures
Large Proteins Must Be Sequenced in Smaller
Segments
Amino
Acid Sequences Can Also Be Deduced by
Other Methods
Box
3-2
Methods: Investigating Proteins with
MassSpectrometry
Small Peptides and Proteins Can Be Chemically
Synthesized
Ammo Acid Sequences Provide Important
Biochemical Information
Protein Sequences Can Elucidate the History of
Life on Earth
B©x
3-3
Consensus
Séquences
and Sequence Logos
72
74
74
76
77
78
79
80
81
82
82
83
84
85
85
88
91
93
93
94
95
98
98
100
102
102
103
Contents
4
ТЬ©І¥Є©-ИіЖКо©іпіаі
Stridore
of Pretefes
11
4.1
Oweraew of Protein Structure
A Protein s Conformation Is Stabilized Largely by
Weak Interactions
The
Peptide
Bond Is Rigid and Planar
The a Helix Is a Common Protein Secondary
Structure
Box
4-1
Methods: Knowing the Right Hand from the Left
Amino
Acid Sequence Affects Stability of the
α
Helix
The
β
Conformation Organizes Polypeptide
Chains into Sheets
β
Turns Are Common in Proteins
Common Secondary Structures Have
Characteristic Dihedral Angles
Common Secondary Structures Can Be
Assessed by Circular Dichroism
Fibrous Proteins Are Adapted for a
Structural Function
Box
4-2
Permanent Waving Is Biochemical Engineering
Box
4-3
Medicine: Why Sailors, Explorers, and College
Students Should Eat Their Fresh Fruits and Vegetables
Box
4-4
The Protein Data Bank
Structural Diversity Reflects Functional Diversity
in Globular Proteins
114
115
117
118
119
120
121
121
122
123
125
126
129
129
Myoglobin Provided Early Clues about the Complexity
of Globular Protein Structure
Globular Proteins Have a Variety of
Tertiary Structures
Box
4-5
Methods: Methods for Determining the
Three-Dimensional Structure of a Protein
Protein Motifs Are the Basis for Protein
Structural Classification
Protein Quaternary Structures Range from Simple
Dimers to Large Complexes
Loss of Protein Structure Results in
Loss of Function
Amino
Acid Sequence Determines
Tertiary Structure
Polypeptides Fold Rapidly by a Stepwise Process
Some Proteins Undergo Assisted Folding
Defects in Protein Folding May Be the Molecular
Basis for a Wide Range of Human Genetic
Disorders
Box
4-6
Medicine: Death by Misfolding: The Prion Diseases
129
131
132
136
138
140
141
142
143
145
147
Oxygen Can Bind to
a Heme
Prosthetic Group
Myoglobin Has a Single Binding Site for Oxygen
Protein-Ligand Interactions Can Be Described
Quantitatively
1Б4
165
166
Protein Structure Affects How Ligands Bind
Hemoglobin Transports Oxygen in Blood
Hemoglobin Subunits Are Structurally Similar to
Myoglobin
Hemoglobin Undergoes a Structural Change on
Binding Oxygen
Hemoglobin Binds Oxygen Cooperatively
Cooperative Ligand Binding Can Be Described
Quantitatively
Box
5-1
Medicine: Carbon Monoxide: A Stealthy Killer
Two Models Suggest Mechanisms for
Cooperative Binding
Hemoglobin Also Transports H+ and CO2
Oxygen Binding to Hemoglobin Is Regulated by
2,3-Bisphosphoglycerate
Sickle-Cell Anemia Is a Molecular Disease
of Hemoglobin
158
158
159
160
160
162
163
165
165
167
168
The Immune Response Features a Specialized
Array of Cells and Proteins
170
Antibodies Have Two Identical Antigen-Binding Sites
171
Antibodies Bind Tightly and Specifically to Antigen
173
The Antibody-Antigen Interaction Is the Basis for a
Variety of Important Analytical Procedures
173
The Major Proteins of Muscle Are Myosin and Actin
175
Additional Proteins Organize the Thin and Thick
Filaments into Ordered Structures
176
Myosin Thick Filaments Slide along
Actin Thin Filaments
178
Most Enzymes Are Proteins
Enzymes Are Classified by the Reactions
They Catalyze
184
184
186
186
188
188
189
191
192
Substrate Concentration Affects the Rate of
Enzyme-Catalyzed Reactions
194
The Relationship between Substrate Concentration
and Reaction Rate Can Be Expressed
Quantitatively
195
Enzymes Affect Reaction Rates, Not Equilibria
Reaction Rates and Equilibria Have Precise
Thermodynamic Definitions
A Few Principles Explain the Catalytic Power and
Specificity of Enzymes
Weak Interactions between Enzyme and
Substrate Are Optimized in the Transition State
Binding Energy Contributes to Reaction
Specificity and Catalysis
Specific Catalytic Groups Contribute to Catalysis
! xviii :
Contents
Box
6-1
Transformations of the Michaelis-Menten Equation:
The Double-Reciprocal Plot
Kinetic Parameters Are Used to Compare Enzyme
Activities
Many Enzymes Catalyze Reactions with Two or
More Substrates
Pre-Steady State Kinetics Can Provide
Evidence for Specific Reaction Steps
Enzymes Are Subject to Reversible or
Irreversible Inhibition
Box
6-2
Kinetic Tests for Determining inhibition
Mechanisms
Enzyme Activity Depends on
pH
6.4
Exampies of Enzymatic Reactions
The Chymotrypsin Mechanism Involves Acylation
and Deacylation of
a Ser
Residue
Box
6-3
Evidence for Enzyme-Transition State
Complementarity
Hexokinase Undergoes Induced Pit on
Substrate Binding
The Enolase Reaction Mechanism Requires
Metal Ions
Lysozyme Uses Two Successive Nucleophffic
Displacement Reactions
An Understanding of Enzyme Mechanism Drives
Important Advances in Medicine
6.5
Regulatory Enzymes
Allosteric Enzymes Undergo Conformational
Changes in Response to Modulator Binding
In Many Pathways, Regulated Steps Are
Catalyzed by Allosteric Enzymes
The Kinetic Properties of Allosteric Enzymes
Diverge from Michaelis-Menten Behavior
Some Enzymes are Regulated by Reversible
Covalent Modification
Phosphoryl Groups Affect the Structure and
Catalytic Activity of Enzymes
Multiple Phosphorylations Allow Exquisite
Regulatory Control
Some Enzymes and Other Proteins Are Regulated
by Proteolytic Cleavage of an Enzyme Precursor
Some Regulatory Enzymes Use Several Regulatory
Mechanisms
197
197
200
201
201
202
204
205
205
210
212
213
213
216
220
220
221
222
223
224
225
226
227
7.1
Monesaccharides and Disaccharides
235
The Two Families of Monosaccharides Are
Aldoses and Ketoses
236
Monosaccharides Have Asymmetric Centers
236
The Common Monosaccharides Have Cyclic
Structures
238
Organisms Contain a Variety of Hexose Derivatives
240
Monosaccharides Are Reducing Agents
241
Box
7-1
Mediane:
Blood Glucose Measurements in the
Diagnosis and Treatment of Diabetes
241
Disaccharides Contain a Glycosidic Bond
243
72
t
Some Homopolysaccharides Are Stored
Forms of Fuel
Some Homopolysaccharides Serve
Structural Roles
Steric Factors and Hydrogen Bonding Influence
Homopolysaccharide Folding
Bacterial and Algal Cell Walls Contain Structural
Heteropolysaccharides
Glycosaminoglycans Are Heteropolysaccharides
of the Extracellular Matrix
73
Glycoconjugates: PrateoglycanSjGiycoproteins,
and Giycoiipids
Proteoglycans Are Glycosaminoglycan-Containing
Macromolecules of the Cell Surface and
Extracellular Matrix
Glycoproteins Have Covalently Attached
Oligosaccharides
Giycoiipids and Lipopolysaccharides Are
Membrane Components
7.4
Carbohydrates as informational Molecules:
The Sugar Code
Lectins Are Proteins That Read the Sugar
Code and Mediate Many Biological Processes
Lectin-Carbohydrate Interactions Are Highly
Specific and Often Polyvalent
7.5
Working with Carbohydrates
245
246
247
249
249
252
252
255
256
257
258
261
263
8.1
Some Basics
271
Nucleotides and Nucleic Acids Have
Characteristic Bases and Pentoses
271
Phosphodiester Bonds Link Successive
Nucleotides in Nucleic Acids
274
The Properties of Nucleotide Bases Affect the
Three-Dimensional Structure of Nucleic Acids
276
8.2
Nucleic Add Structure
277
DNA
Is a Double Helix that Stores Genetic
Information
278
DNA
Can Occur in Different Three-Dimensional
Forms
280
Certain
DNA
Sequences Adopt Unusual Structures
281
Messenger RNAs Code for Polypeptide Chains
283
Many RNAs Have More Complex Three-Dimensional
Structures
284
83
Nucleic Add Chemistry
287
Double-Helical
DNA
and
RNA
Can Be Denatured
287
Nucleic Acids from Different Species Can
Form Hybrids
288
Nucleotides and Nucleic Acids Undergo
Nonenzymatic Transformations
289
Some Bases of
DNA Are
Methylated
292
The Sequences of Long
DNA
Strands Can Be
Determined
292
The Chemical Synthesis of
DNA
Has Been
Automated
294
Contents
Nucleotides Carry Chemical Energy in
СеДѕ
Adenine
Nucleotides Are Components of Many
Enzyme Cofactors
Some Nucleotides Are Regulatory Molecules
296
297
298
9.1
DNå
Cloning: The Basics
304
Restriction Endonucleases and
DNA
Ligase
Yield
Recombinant
DNA 304
Cloning Vectors Allow Amplification of Inserted
DNA
Segments
307
Specific
DNA
Sequences Are Detectable by
Hybridization
310
Expression of Cloned Genes Produces
Large Quantities of Protein
312
Alterations in Cloned Genes Produce Modified
Proteins
312
Terminal Tags Provide Binding Sites for Affinity
Purification
313
9.2
From Genes to Genomes
315
DNA
Libraries Provide Specialized Catalogs of
Genetic Information
315
The Polymerase Chain Reaction Amplifies Specific
DNA
Sequences
317
Genome Sequences Provide the Ultimate
Genetic Libraries
317
Box
9-1
A Potent Weapon in Forensic Medicine
319
93
From Genomes to Proteomes
324
Sequence or Structural Relationships
Provide Information on Protein Function
324
Cellular Expression Patterns Can Reveal the
Cellular Function of a Gene
325
Detection of Protein-Protein Interactions Helps to
Define Cellular and Molecular Function
328
9.4
Genome Alterations and New Products
of Biotechnology
330
A Bacterial Plant Parasite Aids Cloning in Plants
330
Manipulation of Animal Cell Genomes Provides
Information on Chromosome Structure and
Gene Expression
332
Box
9-2
/Weácme:
The Human Genome and Human
Gene Therapy
335
New Technologies Promise to Expedite the
Discovery of New Pharmaceuticals
335
Recombinant
DNA
Technology Yields New
Products and Challenges
337
10.1
Storage Lipids
343
Fatty Acids Are Hydrocarbon Derivatives
343
Triacylglycerols Are Fatty Acid Esters of Glycerol
346
Triacylglyeerols Provide Stored Energy
and Insulation
346
Glycerophospholipids Are Derivatives of
Phosphatidic Acid
Some Glycerophospholipids Have Ether-Linked
Fatty Acids
Chloroplaste
Contain Galactolipids and Sulfolipids
Archaea Contain Unique Membrane Lipids
Sphingolipids Are Derivatives of Sphingosine
Sphingolipids at Cell Surfaces Are Sites of
Biological Recognition
Phospholipids and Sphingolipids Are Degraded
in Lysosomes
Sterols Have Four Fused Carbon Rings
Box
10-2
Medicine: Abnormal Accumulations of
Membrane Lipids: Some Inherited Human Diseases
Box
10-1
Sperm Whales: Fatheads of the Deep
347
Partial
Hydrogénation
of Cooking Oils Produces
Trans Fatty Acids
347
Waxes Serve as Energy Stores and Water Repellents
349
ЗбО
360
362
352
362
354
355
355
356
357
357
358
359
359
360
361
362
362
363
363
364
365
365
365
365
Phosphatidylinositols and Sphingosine Derivatives
Act as Intracellular Signals
Eicosanoids Carry Messages to Nearby Cells
Steroid Hormones Carry Messages between Tissues
Vascular Plants Produce Thousands of Volatile
Signals
Vitamins A and
D
Are Hormone Precursors
Vitamins
E
and
К
and the
Lipid
Quiñones
Are
Oxidation-Reduction Cofactors
Dolichols Activate Sugar Precursors for
Biosynthesis
Many Natural Pigments Are
Lipidie
Conjugated Dienes
Lipid
Extraction Requires Organic Solvents
Adsorption Chromatography Separates Lipids
of Different Polarity
Gas-Liquid Chromatography Resolves Mixtures
of Volatile
Lipid
Derivatives
Specific Hydrolysis Aids in Determination of
Lipid
Structure
Mass Spectrometry Reveals Complete
Lipid
Structure
Lipidomics Seeks to Catalog All Lipids and
Their Functions
Each Type of Membrane Has Characteristic
Lipids and Proteins
All Biological Membranes Share Some
Fundamental Properties
A Lipid
Bilayer Is the Basic Structural
Element of Membranes
Three Types of Membrane Proteins Differ in
Their Association with the Membrane
Many Membrane Proteins Span the
lipid
Bilayer
Integral Proteins Are Held in the Membrane by
Hydrophobie
Interactions with
Lipiđs
372
373
374
375
375
376
Contents
The Topology of an Integral Membrane Protein Can
Sometimes Be Predicted from Its Sequence
378
Covalently Attached Iipids Anchor Some
Membrane Proteins
379
381
381
383
384
385
387
388
Acyl Groups in the Bilayer Interior Are Ordered
to Varying Degrees
Transbilayer Movement of Iipids Requires Catalysis
Lipids and Proteins Diffuse Laterally in the Bilayer
SphingoĽpids
and Cholesterol Cluster Together in
Membrane Rafts
Box
11 -1
Methods: Atomic Force Microscopy to Visualize
Membrane Proteins
Membrane Curvature and Fusion Are Central to
Many Biological Processes
Integral Proteins of the Plasma Membrane Are
Involved in Surface Adhesion, Signaling, and
Other Cellular Processes
Passive Transport Is Facilitated by Membrane
Proteins
Transporters Can Be Grouped into Superfamilies
Based on Their Structures
The Glucose Transporter of Erythrocytes Mediates
Passive Transport
The Chloride-Bicarbonate Exchanger Catalyzes
Electroneutral Cotransport of Anions across
the Plasma Membrane
Box
11-2
Medicine: Defective Glucose and Water Transport
in Two Forms of Diabetes
Active Transport Results in Solute Movement
against a Concentration or Electrochemical
Gradient
P
-Туре
ATPases Undergo Phosphorylation during
Their Catalytic Cycles
F-Type ATPases Are Reversible, ATP-Driven
Proton Pumps
ABC Transporters Use ATP to Drive the Active
Transport of a Wide Variety of Substrates
Ion Gradients Provide the Energy for Secondary
Active Transport
Box
11 -3
Medicine: A Defective Ion Channelin Cystic Fibrosis
401
Aquaporins Form Hydrophilic
Transmembrane
Channels for the Passage of Water
Ion-Selective Channels Allow Rapid Movement of
Ions across Membranes
Ion-Channel Function Is Measured Electrically
The Structure of a K+ Channel Reveals the
Basis for Its Specificity
Gated Ion Channels Are Central in
Neuronal
Function
Defective Ion Channels Can Have Severe
Physiological Consequences
390
391
391
393
394
395
396
399
400
400
404
406
407
407
410
The
ß-Adrenergic
Receptor System
Acts through the Second Messenger cAMP
Box
12-2
Medicine:
G
Proteins: Binary Switches in
Health and Disease
Several Mechanisms Cause Termination of the
ß-Adrenergic
Response
The /3-Adrenergic Receptor Is Desensitized by
Phosphorylation and by Association with
Arrestin
Cyclic AMP Acts as a Second Messenger for
Many Regulatory Molecules
Diacylglycerol, Inositol Trisphosphate, and Ca2+
Have Related Roles as Second Messengers
Box
12-3
Methods: FRET: Biochemistry Visualized in a
Living Cell
Calcium Is a Second Messenger That May Be
Localized in Space and Time
11
1
Ε,ο,
Stimulation of the Insulin Receptor Initiates a
Cascade of Protein Phosphorylation Reactions
The Membrane Phospholipid PIP3 Functions at a
Branch in Insulin Signaling
The JAK-STAT Signaling System Also Involves
Tyrosine Kinase Activity
Cross Talk among Signaling Systems Is
Common and Complex
Protein Modules Bind Phosphorylated
Tyr, Ser,
or
Thr Residues in Partner Proteins
Membrane Rafts and Caveolae Segregate
Signaling Proteins
Ion Channels Underlie Electrical Signaling in
Excitable Cells
Voltage-Gated Ion Channels Produce
Neuronal
Action Potentials
The Acetylcholine Receptor Is a
Ligand-Gated Ion Channel
Neurons Have Receptor Channels That
Respond to Different
Neurotransmitters
Toxins Target Ion Channels
410 12
J
Signaling In
423
425
430
430
431
432
434
436
439
439
441
443
444
446
449
449
451
453
453
454
12
J
inîêgrins:
Bidirectional
Celi
Adhesion Receptors
455
12.1
General Features of Signal
ïransdticîi«
Box
12-1
Mđhuds:
Scatenar«!
analysis Quantifies the
Reteptor-Ligarof interaction
421
Bacterial Signaling Entails Phosphorylation in a
Two-Component System
457
Signaling Systems of Plants Have Some of the
Sanie
Components Used by Microbes and Mammals
458
Plants Detect
Ethylene
through a Two-Component
System and
а МАРК
Cascade
460
Receptorluce Protein Kioases Transduce Signals from
Peptìdes
and Brassinosteroids
460
Contents
The Visual System
Uses Classic GPCR Mechanisms
Excited Rhodopsin Acts through the
G
Protein
Transducin to Reduce the cGMP Concentration
The Visual Signal Is Quickly Terminated
Cone Cells Specialize in Color Vision
Vertebrate
Olfaction
and Gustation Use
Mechanisms
Similar
to the Visual System
Box
12-4
Medicine: Color Blindness: John Dalton s
Experiment from the Grave
GPCRs of the Sensory Systems Share Several
Features with GPCRs of Hormone Signaling
Systems
462
463
464
465
465
466
467
12.11
1
The Cell Cycle Has Four Stages
469
Levels of Cyclin-Dependent Protem Kinases Oscillate
469
CDKs Regulate Cell Division by Phosphorylating
Critical Proteins
472
473
474
475
477
Oncogenes Are Mutant Forms of the Genes for
Proteins That Regulate the Cell Cycle
Defects in Certain Genes Remove Normal
Restraints on
СеБ
Drasion
Box
12-5
Medicine: Development of Protein
Kinase Inhibitors for Cancer Treatment
Apoptosis Is Programmed Cell Suicide
Biological Energy Transformations Obey the
Laws of Thermodynamics
Cells Require Sources of Free Energy
Standard Free-Energy Change Is Directly
Related to the Equilibrium Constant
Actual Free-Energy Changes Depend on
Reactant and Product Concentrations
Standard Free-Energy Changes Are Additive
13.2
Chemical Logic and Common
Biochemical and Chemical Equations Are
Not Identical
The Free-Energy Change for ATP Hydrolysis Is
Large and Negative
Other Phosphorylated Compounds and Thioesters
Also Have Large Free Energies of Hydrolysis
ATP Provides Energy by Group Transfers, Not by
Simple Hydrolysis
ATP Donates Phosphoryl, Pyrophospiioryl, and
Adenylyl Groups
Assembly of Informational Macramolecules
Requires Energy
490
491
491
493
494
500
501
501
504
506
507
508
Box
13-1
Firefly Flashes: Glowing Reports of ATP
ATP Energizes Active Transport and
Muscle Contraction
Transphosphorylations between Nucleotides
Occur in All Cell Types
Inorganic Polyphosphate Is a Potential
Phosphoryl Group Donor
The Flow of Electrons Can Do Biological Work
Oxidation-Reductions Can Be Described as
Half-Reactions
Biological Oxidations Often Involve Dehydrogenation
Reduction Potentials Measure Affinity for Electrons
Standard Reduction Potentials Can Be Used to
Calculate Free-Energy Change
Cellular Oxidation of Glucose to Carbon Dioxide
Requires Specialized Electron Carriers
A Few Types of Coenzymes and Proteins Serve as
Universal Electron Carriers
NADH and NADPH Act with Dehydrogenases as
Soluble Electron Carriers
Dietary Deficiency of Niacin, the Vitamin Form of
NAD and NADP, Causes Pellagra
Flavin Nucleotides Are Tightly Boimd in
Flavoproteins
509
509
510
511
512
512
512
513
514
515
516
516
516
519
519
An Overview: Glycolysis Has Two Phases
528
The Preparatory Phase of Glycolysis Requires ATP
531
The Payoff Phase of Glycolysis Yields ATP and NADH
535
The Overall Balance Sheet Shows a Net Gain of ATP
538
Glycolysis Is under Tight Regulation
539
Glucose Uptake Is Deficient in Type
1
Diabetes Mellitus
539
Box
14-1
Medicine: High Rate of Glycolysis in Tumors Suggests
Targets for Chemotherapy and Facilitates Diagnosis
540
543
544
545
546
546
547
548
549
549
Dietary Polysaccharides and Disaccharides
Undergo Hydrolysis to Monosaceharides
Endogenous Glycogen and Starch Are
Degraded by Phosphorolysis
Other Monosaceharides Enter the Glycolytic
Pathway at Several Points
Pyruvate Is the Terminal Electron Acceptor in
Lactic Acid Fermentation
Ethanol
Is the Reduced Product in
Ethanol
Fermentation
Box
14-2
Athletes, Alligators, and Coeiacanths:
Glycolysis at Limiting Concentrations of Oxygen
Box
14-3
Ethanol
Fermentations:
Brewing Beer and Producing Biofuels
Thiamme
Pyrophosphate
Carries
Active
Acetaldehyde
Groups
xii
xxii Contents
Fermentations
Are Used to Produce Some Common
Foods and Industrial Chemicals
Conversion of Pyruvate to Phosphoenolpyruvate
Requires Two Exergonic Reactions
Conversion of Fructose 1,6-Bisphosphate to
Fructose 6-Phosphate Is the Second Bypass
Conversion of Glucose 6-Phosphate to
Glucose Is the Third Bypass
Gluconeogenesis Is Energetically Expensive, but
Essential
Citric Acid Cycle Intermediates and Some
Amino
Acids Are Glucogenic
Mammals Cannot Convert Fatty Acids to Glucose
Glycolysis and Gluconeogenesis Are Reciprocally
Regulated
14.5
Pentose Phosphate Pathway of Glucose Oxidation
Box
14-4
Medicine: Why Pythagoras Wouldn t Eat Falafel:
Glucose 6-Phosphate Dehydrogenase Deficiency
The Oxidative Phase Produces Pentose
Phosphates and NADPH
The Nonoxidative Phase Recycles Pentose
Phosphates to Glucose 6-Phosphate
Wernicke-Korsakoff Syndrome Is Exacerbated by a
Defect in Transketolase
Glucose 6-Phosphate Is Partitioned between
Glycolysis and the Pentose Phosphate Pathway
550
551
553
556
556
556
557
557
557
558
559
559
560
563
563
15.1
Regulation of Metabolic Pathways
570
Cells and Organisms Maintain a Dynamic
Steady State
571
Both the Amount and the Catalytic
Activity of an Enzyme Can Be Regulated
571
Reactions Far from Equilibrium in Cells Are
Common Points of Regulation
574
Adeninę Nucleotides
Play Special Roles in
Metabolic Regulation
575
15.2
analysis of Metabolic Control
577
The Contribution of Each Enzyme to Flux through
a Pathway Is Experimentally Measurable
578
The Control Coefficient Quantifies the Effect of a
Change in Enzyme Activity on Metabolite Flux
through a Pathway
578
Box
15-1
Methods: Metabolic Control Analysis:
Quantitative Aspects
579
The Elasticity Coefficient Is Related to an Enzyme s
Responsiveness to Changes in Metabolite or
Regulator Concentrations
580
The Response Coefficient Expresses the Effect of an
Outside Controller on Flux through a Pathway
581
Metabolic Control Analysis Has Been Applied to
Carbohydrate Metabolism, with Surprising
Results
681
Metabolic Control Analysis Suggests a General
Method for Increasing Flux through a Pathway
582
Hexokinase Isozymes of Muscle and Liver Are
Affected Differently by Their Product,
Glucose 6-Phosphate
Box
15-2
Isozymes: Different Proteins That Catalyze
the Same Reaction
Hexokinase IV (Glucokinase) and Glucose
6-Phosphatase Are Transcriptionally Regulated
Phosphofructokinase-l and Fructose
1
,6-Bisphosphatase Are Reciprocally Regulated
Fructose 2,6-Bisphosphate Is a Potent Allosteric
Regulator of PFK-1 and FBPase-1
Xylulose 5-Phosphate Is a Key Regulator of
Carbohydrate and Fat Metabolism
The Glycolytic Enzyme Pyruvate Kinase Is
Allosterically Inhibited by ATP
The Gluconeogenic Conversion of Pyruvate to
Phosphoenol Pyruvate Is Under Multiple
Types of Regulation
Transcriptional Regulation of Glycolysis and
Gluconeogenesis Changes the Number of
Enzyme Molecules
Box
15-3
Medicine: Genetic Mutations That Lead to
Rare Forms of Diabetes
15.4
The Metabolism of Glycogen in Animals
Glycogen Breakdown Is Catalyzed by Glycogen
Phosphorylase
Glucose 1-Phosphate Can Enter Glycolysis or, in
Liver, Replenish Blood Glucose
The Sugar Nucleotide UDP-Glucose Donates
Glucose for Glycogen Synthesis
Box
15-4
Carl and
Gerty
Cori:
Pioneers in Glycogen
Metabolism and Disease
Glycogenin Primes the Initial Sugar Residues in
Glycogen
15.5
Coordinated Regulation of Glycogen Synthesis
and Breakdown
Glycogen Phosphorylase Is Regulated
Allosterically and Hormonally
Glycogen Synthase Is Also Regulated by
Phosphorylation and Dephosphorylation
Glycogen Synthase Kinase
3
Mediates Some of the
Actions of Insulin
Phosphoprotein Phosphatase
1
Is Central to
Glycogen Metabolism
Allosteric and Hormonal Signals Coordinate
Carbohydrate Metabolism Globally
Carbohydrate and
Lipid
Metabolism Are Integrated
by Hormonal and Allosteric Mechanisms
583
584
585
585
587
588
588
590
590
593
594
595
596
596
598
601
602
603
605
606
606
606
608
16.1
Production of Acetyi-CoA (Activated acetate}
616
Pyruvate Is Oxidized to
Aceţyl-CoA
and COg
616
The Pyruvate Dehydrogenase Complex Requires
Five Goenzymes
617
Contents
The Pyruvate Dehydrogenase Complex Consists
of Three Distinct Enzymes
In Substrate Channeling, Intermediates Never
Leave the Enzyme Surface
The Citric Acid Cycle Has Eight Steps
Box
16-1
Moonlighting Enzymes:
Proteins with More Than One Job
Box
16-2
Synthases and Synthetases;
Ligases
and Lyases;
Kinases, Phosphatases, and Phosphorylases: Yes, the
Names Are Confusing!
Box
16-3
Citrate: A Symmetric Molecule That Reacts
Asymmetrically
The Energy of Oxidations in the Cycle Is Efficiently
Conserved
Why Is the Oxidation of Acetate So Complicated?
Citric Acid Cycle Components Are Important
Biosynthetic Intermediates
Anaplerotic Reactions Replenish Citric Acid Cycle
Intermediates
Box
16-4
Citrate Synthase, Soda Pop, and the
World Food Supply
Biotin in Pyruvate Carboxylase Carries COg Groups
16.3
Regulation of the Citric add Cycle
Production of Acetyl-CoA by the Pyruvate
Dehydrogenase Complex Is Regulated by
Allosteric and Covalent Mechanisms
The Citric Acid Cycle Is Regulated at Its Three
Exergonic Steps
Substrate Channeling through Multienzyme
Complexes May Occur in the Citric Acid Cycle
Some Mutations in Enzymes of the Citric Acid
Cycle Lead to Cancer
16.4
The Glyoxylate Cycle
The Glyoxylate Cycle Produces Pour-Carbon
Compounds from Acetate
The Citric Acid and Glyoxylate Cycles Are
Coordinately Regulated
618
619
620
621
624
627
629
630
631
631
631
633
633
635
636
636
637
637
638
638
639
17.1
Digestion, Mobilization, and Transport of Fats
Dietary Fats Are Absorbed in the Small Intestine
Hormones Trigger Mobilization of Stored
Triacylglycerols
Patty Acids Are Activated and Transported into
Mitochondria
17.2
Oxidation of Fatty Acids
The
β
Oxidation of Saturated Fatty Acids Has
Four Basic Steps
The Four
jß-Oxidation
Steps Are Repeated to Yield
Aceiyl-CoA and ATP
Box
17-1
Fat Bears Carry Out
β
Oxidation in Their Sleep
Acetyl-CoA Can Be Further Oxidized in the
Citric Acid Cycle
Oxidation of Unsaturated Fatty Acids Requires
Two Additional Reactions
648
649
650
652
653
654
655
655
656
Complete Oxidation of Odd-Number Fatty
Acids Requires Three Extra Reactions
Box
17-2
Coenzyme B12: A Radical Solution to a
Perplexing Problem
Fatty Acid Oxidation Is Tightly Regulated
Transcription Factors Turn on the Synthesis of
Proteins for
Lipid
Catabolism
Genetic Defects in Fatty Acyl-CoA
Dehydrogenases Cause Serious Disease
Peroxisomes Also Carry Out
β
Oxidation
Plant Peroxisomes and Glyoxysomes Use
Acetyl-CoA from
β
Oxidation as a
Biosynthetic Precursor
The /3-Oxidation Enzymes of Different
Organelies
Have Diverged during Evolution
The
ω
Oxidation of Fatty Acids Occurs in the
Endoplasmic Reticulum
Phytanic Acid Undergoes a Oxidation in
Peroxisomes
Ketone
Bodies, Formed in the Liver, Are
Exported to Other Organs as Fuel
Ketone
Bodies Are Overproduced in
Diabetes and during Starvation
657
658
660
660
661
662
662
663
664
664
666
666
667
18.1
Metabolic
Fates of
Amino
Groups
Dietary Protein Is Enzymatically Degraded to
Amino
Acids
Pyridoxal Phosphate Participates in the Transfer of
α
-Amino
Groups to a-Ketoglutarate
Glutamate
Releases Its
Amino
Group As
Ammonia in the Liver
Box
18-1
Medicine: Assays for Tissue Damage
Glutaminę
Transports Ammonia in the
Bloodstream
Alaninę
Transports Ammonia from Skeletal
Muscles to the liver
Ammonia Is Toxic to Animals
18.
e
Urea Is Produced from Ammonia in Five
Enzymatic Steps
The Citric Acid and Urea Cycles Can
Be linked
The Activity of the Urea Cycle Is Regulated at
Two Levels
Pathway Interconnections Reduce the Energetic
Cost of Urea Synthesis
Genetic Defects in the Urea Cycle Can Be
Life-Threatening
Some
Amino
Acids Are Converted to Glucose,
Others to
Ketone
Bodies
Several Enzyme Cofactors Play Important
Roles in
Amino
Acid Catabolism
Six
Amino
Acids Are Degraded to Pyruvate
Seven
Amino
Acids Are Degraded to Acetyl-CoA
674
674
677
677
678
680
681
681
682
682
684
685
686
686
687
688
689
692
Contents
19.1
Electron-Transfer Reactions in Mitochondria
Electrons Are
Funneled
to Universal Electron
Acceptors
Electrons Pass through a Series of
Membrane-Bound Carriers
Electron Carriers Function in Multienzyme
Complexes
Mitochondrial Complexes May Associate in
Respirasomes
The Energy of Electron Transfer Is Efficiently
Conserved in a Proton Gradient
Reactive Oxygen Species Are Generated during
Oxidative Phosphorylation
Plant; Mitochondria Have Alternative
Mechanisms for Oxidizing NADH
Box
19-1
Hot, Stinking Plants and Alternative
Respiratory Pathways
ATP Synthase Has Two Functional Domains,
Fo and Px
ATP Is Stabilized Relative to ADP on the
Surface of Fj
The Proton Gradient Drives the Release of
ATP from the Enzyme Surface
Each
β
Subunit
of ATP Synthase Can Assume
Three Different Conformations
Rotational Catalysis Is Key to the Binding-Change
Mechanism for ATP Synthesis
Chemiosmotic Coupling Allows
Nonintegral
Stoichiometries of O2 Consumption and
ATP Synthesis
The Proton-Motive Force Energizes
Active Transport
Shuttle Systems Indirectly Convey Cytosolic
NADH into Mitochondria for Oxidation
Oxidative Phosphorylation Is Regulated by
Cellular Energy Needs
An Inhibitory Protein Prevents ATP Hydrolysis
during Hypoxia
Hypoxia Leads to
ROS
Production and Several
Adaptive Responses
696
698
699
Phenylalanine Catabolism Is Genetically
Defective in Some People
Five
Amino
Acids Are Converted to
a-Ketoglutarate
Four
Amino
Acids Are Converted to Succmyl-CoA
Box
18-2
Medicine: Scientific Sleuths Solve a
Murder Mystery
700
Branched-Chain
Amino
Acids Are Not
Degraded in the Liver
701
Asparagine and Aspartate Are Degraded to
Oxaloacetate
701
ATP-Produeing Pathways Are
Coordinately Regulated
734
709
710
712
718
718
720
721
722
723
725
725
726
726
728
729
730
731
732
733
733
733
19.4
Mitochondria In Thertnogenesis, Steroid
Synthesis, and
Apopîesis
735
Uncoupled Mitochondria in Brown Adipose
Tissue Produce Heat
736
Mitochondrial P-450
Oxygenases Catalyze Steroid
Hydroxylations
736
Mitochondria Are Central to the Initiation of
Apoptosis
737
19.5
Mitochondrial Genes:Their Origin and the
Effects of Mutations
738
Mitochondria Evolved from Endosymbiotic Bacteria
739
Mutations in Mitochondrial
DNA
Accumulate
throughout the Life of the Organism
739
Some Mutations in Mitochondrial Genomes
Cause Disease
740
Diabetes Can Result from Defects in the
Mitochondria of Pancreatic
β
Cells
741
PHOTOSYNTHESIS: HARVESTING LIGHT ENERGY
19.6
General Features of Photophosphorylation
Photosynthesis in Plants Takes Place in
Chloroplasts
Light Drives Electron Flow in Chloroplasts
19.7
Light Absorption
Chlorophylls Absorb Light Energy for
Photosynthesis
Accessory Pigments Extend the Range of Light
Absorption
Chlorophyll Funnels the Absorbed Energy to
Reaction Centers by Exciton Transfer
19.8
The Central Photochemical Event:
Light-Driven Electron Flow
Bacteria Have One of Two Types of Single
Photochemical Reaction Center
Kinetic and Thermodynamic Factors Prevent
the Dissipation of Energy by Internal
Conversion
In Plants, Two Reaction Centers Act in Tandem
Antenna ChlorophyUs Are Tightly Integrated with
Electron Carriers
The Cytochrome b6
ƒ
Complex Links
Photosystems
II and I
CycUc Electron Flow between
PSI
and the
Cytochrome b6
ƒ
Complex Increases the
Production of ATP Relative to NADPH
State Transitions Change the Distribution of LHCII
between the Two
Photosystems
Water Is Split by the Oxygen-Evolving Complex
■ 3.9
ATP Synthesis by Photophosphorylation
A Proton Gradient Couples Electron Flow and
Phosphorylation
The Approximate Stoichiometry of
Photophosphorylation Has Been Established
The ATP Synthase of Chloroplasts Is Like That
of Mitochondria
742
743
743
744
746
747
747
749
749
761
762
754
755
766
756
766
759
769
760
760
Contents
і
xxv
J
Chloroplaste
Evolved from Ancient
Photosynthetic Bacteria
761
In Halobacterium, a Single Protein Absorbs Light
and Pumps Protons to Drive ATP Synthesis
762
esss
773
Plastids Are Organelles Unique to Plant
Cells and Algae
774
Carbon Dioxide Assimilation Occurs in
Three Stages
775
Synthesis of Each
Triose
Phosphate from CO2
Requires Six NADPH and Nine ATP
782
A Transport System Exports
Triose
Phosphates
from the
Chloroplast
and Imports Phosphate
783
Pour Enzymes of the Calvin Cycle Are Indirectly
Activated by Light
784
20.2
Photorespiration
and the C4 and CAM Pathways
786
Photorespiration Results from Rubisco s
Oxygenase Activity
786
The Salvage of Phosphoglycolate Is Costly
787
In C4 Plants, CO2 Fixation and Rubisco Activity
Are Spatially Separated
789
In CAM Plants, CO2 Capture and Rubisco Action
Are Temporally Separated
791
20.3
ADP-Glucose Is the Substrate for Starch Synthesis in
Plant Plastids and for Glycogen Synthesis in
Bacteria
UDP-Glucose Is the Substrate for Sucrose
Synthesis in the Cytosol of Leaf Cells
Conversion of
Triose
Phosphates to Sucrose and
Starch Is Tightly Regulated
20.4
Synthesis of Ceil Wail Polysaccharides:
Plant
Celluiose
and Bacterial Peptidogiycan
Cellulose Is Synthesized by Supramolecular
Structures in the Plasma Membrane
Iipid-Linked Oligosaccharides Are Precursors for
Bacterial Cell Wall Synthesis
20.5
Integration of Carbohydrate Metabolism in the
Plant Cell
Gluconeogenesis Converts Fats and Proteins to
Glucose in Germinating Seeds
Pools of Common Intermediates Link Pathways in
Different Organelles
791
792
792
794
795
796
797
798
799
21.1
Biosynthesis of Fatty Adds and Eicosanoids
805
Malonyl-CoA Is Formed from Acetyl-CoA and
Bicarbonate
805
Fatty Acid Synthesis Proceeds in a Repeating
Reaction Sequence
806
The Mammalian Fatty Acid Synthase Has
Multiple Active Sites
808
Fatty Acid Synthase Receives the
Acetyl
and
Malonyl Groups
808
The Fatty Acid Synthase Reactions Are
Repeated to Form Palmitate
811
Fatty Acid Synthesis Occurs in the Cytosol of Many
Organisms but in the Chloroplasts of Plants
811
Acetate Is Shuttled out of Mitochondria as Citrate
813
Fatty Acid Biosynthesis Is Tightly Regulated
814
Long-Chain Saturated Fatty Acids Are Synthesized
from Palmitate
814
Desaturation of Fatty Acids Requires a
Mixed-Function
Oxidase
815
60x21-1
Mixed-Function
Oxidases,
Oxygenases, and
Cytochrome P-450
816
Eicosanoids Are Formed from 20-Carbon
Polyunsaturated
ř^atty
Acids
817
21.2
Biosynthesis of Triacylglycerols
820
Triacylglycerols and Glycerophospholipids Are
Synthesized from the Same Precursors
820
Triacylglycerol Biosynthesis in Animals Is Regulated
by Hormones
821
Adipose Tissue Generates Glycerol 3-Phosphate by
Glyceroneogenesis
822
Thiazolidinediones Treat Type
2
Diabetes
by Increasing Glyceroneogenesis
824
21.3
Biosynthesis of Membrane Phospholipids
824
Cells Have Two Strategies for Attaching Phospholipid
Head Groups
824
Phospholipid Synthesis in
E. coli
Employs
CDP-Diacylglycerol
825
Eukaryotes Synthesize
Anionie
Phospholipids from
CDP-Diacylglycerol
827
Eukaryotic Pathways to Phosphatidylserine,
Phosphatidylethanolamine, and
Phosphatidylcholine Are Interrelated
827
Plasmalogen
Synthesis Requires Formation of an
Ether-Linked Fatty Alcohol
829
Sphingolipid and Glycerophospholipid Synthesis
Share Precursors and Some Mechanisms
829
Polar Lipids Are Targeted to Specific
Cellular Membranes
830
21.4
Biosynthesis of Cholesterol, Steroids,
and ¡soprenoids
831
Cholesterol Is Made from Acetyl-CoA in
Four Stages
832
Cholesterol Has Several Fates
836
Cholesterol and Other Lipids Are Carried on Plasma
Lipoprotéine
836
Box
21-2
Medicine: ApoE
Alíeles
Predict Incidence of
Alzheimer s Disease
839
Cholesteryl Esters Enter
СеДѕ
by
Receptor-Mediated Endocytosis
840
Cholesterol Biosynthesis Is Regulated at
Several Levels
841
Box
21-3
Medicine: The
Lipid
Hypothesis and
the Development of Statins
842
j^xxvij
Contents
Steroid
Hormones
Are Formed by Side-Chain
Cleavage and Oxidation of Cholesterol
Intermediates in Cholesterol Biosynthesis Have
Many Alternative Fates
844
845
22.1
Overview of Nitrogen Metabolism
852
The Nitrogen Cycle Maintains a Pool of
Biologically Available Nitrogen
852
Nitrogen Is Fixed by Enzymes of the
Nitrogenase Complex
852
Box
22-1
Unusual Lifestyles of the Obscure but Abundant
853
Ammonia Is Incorporated into Biomolecules
through
Glutamate
and
Glutaminę
857
Glutaminę
Synthetase Is a Primary Regulatory
Point in Nitrogen Metabolism
857
Several Classes of Reactions Play Special
Roles in the Biosynthesis of
Amino
Acids and Nucleotides
859
22.2
Biosynthesis of
Amino
Acids
860
a-Ketoglutarate Gives Rise to
Glutamate,
Glutaminę,
Proline,
and
Arginine.
861
Serine, Glycine, and
Cysteine
Are Derived from
S-Phosphoglycerate
863
Three Nonessential and Six Essential
Amino
Acids Are Synthesized from Oxaloacetate and
Pyruvate
865
Chorismate Is a Key Intermediate in the Synthesis
of Tryptophan, Phenylalanine, and Tyrosine
865
Histidine Biosynthesis Uses Precursors of
Purine
Biosynthesis
869
Amino
Acid Biosynthesis Is under
Allosteric Regulation
872
22.3
Molecules Derived from
Amino
Acids
873
Glycine
Is a Precursor of Porphyrins
873
Box
22-2
Medicine: On Kings and Vampires
875
Heme
Is the Source of
ВДе
Pigments
875
Amino
Acids Are Precursors of Greatine and
Glutathione
876
D-
Amino
Acids Are Found Primarily in Bacteria
877
Aromatic
Amino
Acids Are Precursors of Many
Plant Substances
878
Biological Amines Are Products of
Amino
Acid
Deearboxylation
878
Box
22-3
Medicine: Curing African Sleeping Sickness with
a Biochemical Trojan Horse
880
Arginine
Is the Precursor for Biological
Synthesis of Nitric Oxide
882
22.4
Biosynthesis and Degradation of Nucleotides
882
De Novo
Purine Nucleotide
Synthesis
Begins with PRPP
883
Purine
Nucleotide Biosynthesis Is Regulated by
Feedback Inhibition
885
Pyrimidine Nucleotides Are Made from Aspartate,
PRPP, and Carbamoyl Phosphate
886
Pyriniidine Nucleotide Biosynthesis Is
Regulated by Feedback Inhibition
887
Nucleoside
Monophosphates
Are Converted to
Nucleoside Triphosphates
888
Ribonucleotides Are the Precursors of
Deoxyribonucleotides
888
Thymidylate Is Derived from dCDP and dUMP
890
Degradation of
Purines
and Pyrimidines Produces
Uric Acid and Urea, Respectively
892
Purine
and Pyrimidine Bases Are Recycled by
Salvage Pathways
893
Excess Uric Acid Causes Gout
893
Many Chemotherapeutic Agents Target Enzymes
in the Nucleotide Biosynthetic Pathways
894
wias
ж
23.1
Hormones: Diverse Structures for
Diverse Functions
The Detection and Purification of Hormones
Requires a Bioassay
Box
23-1
Medicine: How Is a Hormone Discovered?
The Arduous Path to Purified Insulin
Hormones Act through Specific High-Affinity
Cellular Receptors
Hormones Are Chemically Diverse
Hormone Release Is Regulated by a Hierarchy of
Neuronal
and Hormonal Signals
23.2
Tissue-Specific Metabolism: The Division of Labor
The Liver Processes and Distributes Nutrients
Adipose Tissues Store and Supply Fatty Acids
Brown Adipose Tissue Is Thermogenic
Muscles Use ATP for Mechanical Work
The Brain Uses Energy for Transmission of
Electrical Impulses
Blood Carries Oxygen, Metabolites, and Hormones
23.3
Hormonal Regulation of Fuel Metabolism
Insulin Counters High Blood Glucose
Pancreatic
β
Cells Secrete Insulin in Response to
Changes in Blood Glucose
Glucagon Counters Low Blood Glucose
During Fasting and Starvation, Metabolism
Shifts to Provide Fuel for the Brain
Epinephrine Signals Impending Activity
Cortisol
Signals Stress, Including Low
Blood Glucose
Diabetes Mellitus Arises from Defects in
Insulin Production or Action
Adipose Tissue Has Important
Endocrine Functions
Leptin Stimulates Production of Anorexigenic
Peptide
Hormones
Leptin Triggers a Signaling Cascade That
Regulates Gene Expression
The Leptin System May Have Evolved to
Regulate the Starvation Response
902
903
904
906
909
912
912
916
917
918
920
920
922
922
923
925
926
928
929
929
930
930
932
933
934
Contents
Insulin
Acts in the Arcuate Nucleus to
Regulate Eating and Energy Conservation
Adiponectin Acts through AMPK to Increase
Insulin Sensitivity
Diet Regulates the Expression of Genes
Central to Maintaining Body Mass
Short-Term Eating Behavior Is Influenced by
Ghrelin and PYY3_36
23,5
Obesity, the Metabolic Syndrome, and
In Type
2
Diabetes the Tissues Become
Insensitive to Insulin
Type
2
Diabetes Is Managed with Diet,
Exercise, and Medication
1
Chromosomal Elements
Genes Are Segments of
DNA
That Code for
Polypeptide Chains and RNAs
DNA
Molecules Are Much Longer Than the
Cellular or Viral Packages That
Contam
Them
Eukaryotic Genes and Chromosomes Are
Very Complex
Most Cellular
DNA
Is Underwoimd
DNA
Underwinding Is Defined by Topological
Linking Number
Topoisomerases Catalyze Changes in the
Linking Number of
DNA
Box
24-1
Medicine: Curing Disease by Inhibiting
Topoisomerases
DNA
Compaction Requires a Special Form of
Supercoiling
243
The Structure of Chromosomes
Chromatin Consists of
DNA
and Proteins
Histones Are Small, Basic Proteins
Nucleosomes Are the Fundamental
Organizational Units of Chromatin
Box
24-2
Medicine: Epigenetics, Nucleosome
Structure, and Histone Variants
Nucleosomes Are Packed into Successively
Higher-Order Structures
Condensed Chromosome Structures Are
Maintained by SMC Proteins
Bacterial
DNA
Is Also Highly Organized
934
934
936
937
938
938
939
945
947
947
948
952
954
955
956
968
960
961
962
962
963
964
966
966
969
970
25.1
Жћ
Replication
977
DNA
Replication Follows a Set of
Fundamental Rules
977
DNA
Is Degraded by Nucleases
979
DNA
Is Synthesized by
DNA
Polymerases
979
Replication Is Very Accurate
980
E. coli
Has at Least Five
DNA
Polymerases
982
DNA
Replication Requires Many Enzymes and
Protein Factors
984
Replication of the
E. coli
Chromosome
Proceeds in Stages
985
Replication in Eukaryotic Cells Is Both
Similar and More Complex
991
Viral
DNA
Polymerases Provide Targets for
Antiviral Therapy
992
25.2 DNA
Repair
993
Mutations Are Linked to Cancer
993
All Cells Have Multiple
DNA
Repair Systems
993
The Interaction of Replication Forks with
DNA
Damage Can Lead to Error-Prone Translesion
DNA
Synthesis
1001
Box
25-1
Medicine:
DNA
Repair and Cancer
1003
25.3 DNA
Recombination
1003
Homologous Genetic Recombination Has
Several Functions
1004
Recombination during Meiosis Is Initiated with
Double-Strand Breaks
1005
Recombination Requires a Host of Enzymes and
Other Proteins
1007
All Aspects of
DNA
Metabolism Come Together to
Repair Stalled Replication Forks
1009
Site-Specific Recombination Results in Precise
DNA
Rearrangements
1010
Complete Chromosome Replication Can Require
Site-Specific Recombination
1012
Transposable Genetic Elements Move from One
Location to Another
1013
Immunoglobulin Genes Assemble by
Recombination
1014
26.1
DN
А
-Dependent Synthesis of
RNÂ
1022
RNA
Is Synthesized by
RNA
Polymerases
1022
RNA
Synthesis Begins at Promoters
1025
Box
26-1
Methods:
RNA Polymerase
Leaves Its
Footprint on a Promoter
1026
Transcription Is Regulated at Several Levels
1028
Specific Sequences Signal Termination of
RNA
Synthesis
1029
Eukaryotic Cells Have Three Kinds of Nuclear
RNA
Polymerases
1030
RNA
Polymerase II Requires Many Other
Protein Factors for Its Activity
1030
DNA-Dependent
RNA
Polymerase
Undergoes Selective Inhibition
1033
26.2
RNA
Processing
1033
Eukaryotic mRNAs Are Capped at the
5
End
1034
Both
Introns
and Exons Are Transcribed from
DNA
into
RNA
1035
RNA
Catalyzes the Splicing of
Introns
1036
Eukaryotic mRNAs Have a Distinctive
3
End Structure
1039
A Gene Can Give Rise to Multiple Products by
Differential
RNA
Processing
1040
|xxviiïj
Contents
Ribosomal RNAs and tRNAs
Also
Undergo
Processing
1042
Special-Function RNAs Undergo Several
Types of Processing
1045
RNA
Enzymes Are the Catalysts of Some
Events in
RNA
Metabolism
1045
Cellular mRNAs Are Degraded at Different Rates
1048
Polynucleotide Phosphorylase Makes Random
RNA-like Polymers
1049
26.3
RNA-Dependent Synthesis of RMA and
DNA 1050
Reverse Transcriptase Produces
DNA
from
Viral
RNA
1050
Some Retroviruses Cause Cancer and AIDS
1051
Many
Transposons,
Retroviruses, and
Introns
May Have a Common Evolutionary Origin
1052
Box
26-2
Medicine: Fighting AIDS with Inhibitors of
HIV
Reverse Transcriptase
1053
Telomerase Is a Specialized Reverse Transcriptase
1053
Some Viral RNAs Are Replicated by
Stage
5:
Newly Synthesized Polypeptide Chains
Undergo Folding and Processing
Protein Synthesis Is Inhibited by Many
Antibiotics and Toxins
1096
1098
RNA-Dependent
RNA Polymerase
RNA
Synthesis Offers Important Clues to
Biochemical Evolution
Box
26-3
Methods: The SELEX Method for Generating
RNA
Polymers with New Functions
Box
26-4
An Expanding
RNA
Universe Filled with
TUF
RNAs
1056
1056
1058
1060
27.1
The Genetic Code
The Genetic Code Was Cracked Using Artificial
mRNA Templates
Box
27-1
Exceptions That Prove the Rule:
Natural Variations in the Genetic Code
Wobble Allows Some tRNAs to Recognize
More than One Codon
Translational Frameshifting and
RNA
Editing
Affect How the Code Is Read
27.2
Protein Synthesis
Protein Biosynthesis Takes Place in Five Stages
The Ribosome Is a Complex Supramolecular
Machine
Box
27-2
From an
RNA
World to a Protein World
Transfer RNAs Have Characteristic
Structural Features
Stage
1:
Aminoacyl-tRNA Synthetases Attach the
Correct
Amino
Acids to Their tRNAs
Box
27-3
Natural and Unnatural Expansion of the
Genetic Code
Stage
2:
À
Specific
Amino
Acid Initiates
Protein Synthesis
Stage
3:
Peptide
Bonds Are Formed in the
Elongation Stage
Box
27-4
Induced Variation in the Genetic Code:
Nonsense Suppression
Stage
4:
Termination of Polypeptiae Synthesis
Requires a Special Signal
1065
1066
1070
1070
1072
1075
1075
1076
1078
1079
1081
1085
1088
1091
1094
1094
Posttranslational Modification of Many
Eukaryotic Proteins Begins in the
Endoplasmic Reticulum
Glycosylation Plays a Key Role in
Protein Targeting
Signal Sequences for Nuclear Transport Are,
Not Cleaved
Bacteria Also Use Signal Sequences for
Protein Targeting
Cells Import Proteins by Receptor-Mediated
Endocytosis
Protein Degradation Is Mediated by Specialized
Systems in All Cells
1100
1101
1104
1104
1106
1107
28.1
Principies
of Gene Regulation
1116
RNA
Polymerase Binds to
DNA
at Promoters
1116
Transcription Initiation Is Regulated by Proteins
That Bind to or near Promoters
1117
Many Bacterial Genes Are Clustered and
Regulated in
Opérons
1118
The lac Operon Is Subject to Negative Regulation
1119
Regulatory Proteins Have Discrete DNA-Binding
Domains
1121
Regulatory Proteins Also Have Protein-Protein
Interaction Domains
1124
28.2
Regulation of Gene
Expression
in Bacteria
1126
The lac Operon Undergoes Positive Regulation
1126
Many Genes for
Amino
Acid Biosynthetic Enzymes
Are Regulated by Transcription Attenuation
1127
Induction of the SOS Response Requires
Destruction of
Repressor
Proteins
1130
Synthesis of Ribosomal Proteins Is Coordinated
with rRNA Synthesis
1131
The Function of Some mRNAs Is Regulated by
Small RNAs in
Cis
or in Trans
1132
Some Genes Are Regulated by
Genetic Recombination
1134
28.3
Regulation of Gene Expression in Eukaryotes
1136
TranscriptionaQy Active Chramatin Is Structurally
Distinct from Inactive Chromatin
1136
Chramatin Is Remodeled by Acetylation and
Nucleosomal Displacement/Repositioning
1137
Many Eukaryotic Promoters Are
Positively Regulated
1138
DNA-Binding Activators and Coactivators
Facilitate Assembly of the General
Transcription Factors
П38
The Genes of
Galactose
Metabolism in Yeast
Are Subject to Both Positive and Negative
Regulation
1141
Transcription Activators Have a Modular Structure
1142
Contents
Eukaryotic Gene Expression
Can Be Regulated by
Appendix
A Common Abbreviations in the
Intercellular and Mracellular Signals
1143
Biochemical Research Literature A-1
Regulation Can Result from Phosphorylation of
,. , , . „ , ,
Nuclear Inscription Factors
1144
Appendix
В
Abbreviated Solutions to Problems AS-1
Many Eukaryotic mRNAs Are Subject to Glossary G-
?
Translational Repression
1144
Credits C-l
Posttranscriptional Gene
Süencing
Is Mediated by Indpx I
1
RNA
Interference
1145
RNA-Mediated Regulation of Gene Expression
Takes Many Forms in Eukaryotes
1146
Development Is Controlled by Cascades of
Regulatory Proteins
1146
Box
28-1
Of Fins, Wings, Beaks, and Things
1152
|
| adam_txt |
Contents in Brief
Contents
Preface
via
1
The Foundations of Biochemistry
1
1
STRUCTURE AND CATALYSIS
41
2
Water
43
3
Amino
Acids, Peptides, and Proteins
71
4
The Three-Dimensionat Structure of Proteins
113
5
Protein Function
1S3
6
Enzymes
183
7
Carbohydrates and Glycobiology
235
8
Nudeotides and Nucleic Acids
271
9
ONA-Based information Technologies
303
10
Lipids
343
11
Biological Membranes and Transport
371
12 Biosignaimg
417
II BIOENERGETiCS
AND METABOLISM
485
13
Bioenergetics and Biochemical Reaction Types
489
14
Glycolysis, Gluconeogenesis, and the Pentose
Phosphate Pathway
527
15
Principles of Metabolic Regulation
569
16
The Citric Acid Cycle
615
17
Fatty Acid Catabolism
647
18
Amino
Acid Oxidation and the Production of Urea
673
19
Oxidative Phosphorylation and Photophosphorylation
707
20
Carbohydrate Biosynthesis in Plants and Bacteria
773
21
Lipid
Biosynthesis
805
22
Biosynthesis of
Amino
Acids, Nudeotides, and
Related Moiecuies
851
23
Hormonal Regulation and integration of
Mammalian Metabolism
901
III INFORMATION PATHWAYS
945
24
Genes and Chromosomes
947
25
DNA Metabolism
975
26
RNA
Metabolism
1021
27
Protein Metabolism
1065
28
Regulation of Gene Expression
1115
Appendix A Common Abbreviations ¡n the Biochemical
Research Literature A-1
Appendix
В
Abbreviated Solutions to Problems AS-
1
Glossary G-l
Credits C-1
IndexH
1
The Foundations of Biochemistry
_
1.1
Cellular Foundations
Cells Are the Structural and Functional
Units of All Living Organisms
Cellular Dimensions Are Limited by Diffusion
There Are Three Distinct Domains of Life
Escherichìa coli
Is the Most-Studied Bacterium
Eukaryotic Cells Have a Variety of Membranous
Organelles, Which Can Be Isolated for Study
The Cytoplasm Is Organized by the Cytoskeleton
and Is Highly Dynamic
Cells Build Supramolecular Structures
In Vitro Studies May Overlook Important
Interactions among Molecules
1.2
Chemical Foundations
Biomolecules Are Compounds of Carbon with
a Variety of Functional Groups
Cells Contain a Universal Set of Small Molecules
Box
1 -1
Molecular Weight, Molecular Mass, and
Their Correct Units
Macromolecules Are the Major
Constituents of Cells
Three-Dimensional Structure Is Described
by Configuration and Conformation
Box
1-2
Louis Pasteur and Optical Activity: In Vino, Veritas
Interactions between Biomolecules
Are Stereospeciflc
1.3
Physical Foundations
Living Organisms Exist in a Dynamic
Steady State, Never at Equilibrium with
Their Surroundings
Organisms Transform Energy and Matter
from Their Surroundings
Box
1 -3
Entropy: The Advantages of Being Disorganized
The Flow of Electrons Provides Energy
for Organisms
Creating and Maintaining Order Requires Work
and Energy
Energy Coupling Links Reactions in Biology
Keą
and AG° Are Measures of a Reaction's
Tendency to Proceed Spontaneously
Enzymes Promote Sequences of Chemical Reactions
Metabolism Is Regulated to Achieve Balance
and Economy
1.4
Genetic Foundations
Genetic Continuity Is Vested in Single
DNA
Molecules
The Structure of
DNA
Allows for Its Replication
and Repair with Near-Perfect Fidelity
The linear Sequence in
DNA
Encodes Proteins with
Three-Dimensional Structures
2
з
3
4
б
9
10
11
n
13
14
14
15
17
18
19
20
20
21
22
22
22
24
25
26
27
27
28
29
j
xv
|
TxvQ Contents
Changes in the Hereditary Instructions
Allow Evolution
Biornolecules First Arose
Ъу
Chemical Evolution
RNA
or Related Precursors May Have Been the
First Genes and Catalysts
Biological Evolution Began More Than
Three and a Half Billion Years Ago
The First Cell Probably Used Inorganic Fuels
Eukaryotic Cells Evolved from Simpler
Precursors in Several Stages
Molecular Anatomy Reveals Evolutionary
Relationships
Functional Genomics Shows the Allocations of
Genes to Specific Cellular Processes
Genomic Comparisons Have Increasing
Importance in Human Biology and Medicine
STRUCTURE AND CATALYSIS
2.2
taniiation of Water, Weak adds, and Weak Bases
Pure Water Is Slightly Ionized
The Ionization of Water Is Expressed by an
Equilibrium Constant
The
pH
Scale Designates the H+ and OH"
Concentrations
Weak Acids and Bases Have Characteristic
Acid Dissociation Constants
Titration
Curves Reveal the pi?a of Weak Adds
23
Buffers Are Mixtures of Weak Acids and Their
Conjugate Bases
The Henderson-Hasselbalch Equation Relates
pH,
pKa, and Buffer Concentration
Weak Acids or Bases Buffer Cells and
Tissues against
pH
Changes
Untreated Diabetes Produces
Life-Threatening Acidosis
Box
2-1
Medicine: On Being One's Own Rabbit
(Don't Try This at Home!)
29
30
31
32
32
33
33
35
35
2.Ί
Weak
Interactions
in Aqueous Systems
Hydrogen Bonding Gives Water Its
Unusual Properties
Water Forms Hydrogen Bonds with Polar Solutes
Water Interacts Electrostatically with
Charged Solutes
Entropy Increases as Crystalline
Substances Dissolve
Nonpolar
Gases Are Poorly Soluble in Water
Nonpolar
Compounds Force Energetically
Unfavorable Changes in the Structure of Water
van
der Waals
Interactions Are Weak Interatomic
Attractions
Weak Interactions Are Crucial to Macromolecular
Structure and Function
Solutes Affect the Colligative Properties of
Aqueous Solutions
43
45
46
47
47
47
60
51
54
54
55
56
57
58
59
60
61
63
64
Amino
Acids Share Common Structural Features
The
Amino
Acid Residues in Proteins Are
L
Stereoisomers
Amino
Acids Can Be Classified by
R
Group
Box
3-1
Methods: Absorption of Light by Molecules:
The Lambert-Beer Law
Uncommon
Amino
Acids Also Have
Important Functions
Amino
Acids Can Act as Acids and Bases
Amino
Acids Have Characteristic
Titration
Curves
Titration
Curves Predict the Electric
Charge of
Amino
Acids
Amino
Acids Differ in Their Acid-Base Properties
3.2
Peptsdes
and Proteins
Peptides Are Chains of
Amino
Acids
Peptides Can Be Distinguished by Their
Ionization Behavior
Biologically Active Peptides and Polypeptides
Occur in a Vast Range of Sizes and
Compositions
Some Proteins Contain Chemical Groups
Other Than
Amino
Acids
Proteins Can Be Separated and Purified
Proteins Can Be Separated and Characterized by
Electrophoresis
Unseparated Proteins Can Be Quantified
3.4
The Stracttire of Proteins: Primary Structure
The Function of a Protein Depends on Its
Amino
Acid Sequence
The
Amino
Acid Sequences of Millions of
Proteins Have Been Determined
Short Polypeptides Are Sequenced with
Automated Procedures
Large Proteins Must Be Sequenced in Smaller
Segments
Amino
Acid Sequences Can Also Be Deduced by
Other Methods
Box
3-2
Methods: Investigating Proteins with
MassSpectrometry
Small Peptides and Proteins Can Be Chemically
Synthesized
Ammo Acid Sequences Provide Important
Biochemical Information
Protein Sequences Can Elucidate the History of
Life on Earth
B©x
3-3
Consensus
Séquences
and Sequence Logos
72
74
74
76
77
78
79
80
81
82
82
83
84
85
85
88
91
93
93
94
95
98
98
100
102
102
103
Contents
4
ТЬ©І¥Є©-ИіЖКо©іпіаі
Stridore
of Pretefes
11
4.1
Oweraew of Protein Structure
A Protein's Conformation Is Stabilized Largely by
Weak Interactions
The
Peptide
Bond Is Rigid and Planar
The a Helix Is a Common Protein Secondary
Structure
Box
4-1
Methods: Knowing the Right Hand from the Left
Amino
Acid Sequence Affects Stability of the
α
Helix
The
β
Conformation Organizes Polypeptide
Chains into Sheets
β
Turns Are Common in Proteins
Common Secondary Structures Have
Characteristic Dihedral Angles
Common Secondary Structures Can Be
Assessed by Circular Dichroism
Fibrous Proteins Are Adapted for a
Structural Function
Box
4-2
Permanent Waving Is Biochemical Engineering
Box
4-3
Medicine: Why Sailors, Explorers, and College
Students Should Eat Their Fresh Fruits and Vegetables
Box
4-4
The Protein Data Bank
Structural Diversity Reflects Functional Diversity
in Globular Proteins
114
115
117
118
119
120
121
121
122
123
125
126
129
129
Myoglobin Provided Early Clues about the Complexity
of Globular Protein Structure
Globular Proteins Have a Variety of
Tertiary Structures
Box
4-5
Methods: Methods for Determining the
Three-Dimensional Structure of a Protein
Protein Motifs Are the Basis for Protein
Structural Classification
Protein Quaternary Structures Range from Simple
Dimers to Large Complexes
Loss of Protein Structure Results in
Loss of Function
Amino
Acid Sequence Determines
Tertiary Structure
Polypeptides Fold Rapidly by a Stepwise Process
Some Proteins Undergo Assisted Folding
Defects in Protein Folding May Be the Molecular
Basis for a Wide Range of Human Genetic
Disorders
Box
4-6
Medicine: Death by Misfolding: The Prion Diseases
129
131
132
136
138
140
141
142
143
145
147
Oxygen Can Bind to
a Heme
Prosthetic Group
Myoglobin Has a Single Binding Site for Oxygen
Protein-Ligand Interactions Can Be Described
Quantitatively
1Б4
165
166
Protein Structure Affects How Ligands Bind
Hemoglobin Transports Oxygen in Blood
Hemoglobin Subunits Are Structurally Similar to
Myoglobin
Hemoglobin Undergoes a Structural Change on
Binding Oxygen
Hemoglobin Binds Oxygen Cooperatively
Cooperative Ligand Binding Can Be Described
Quantitatively
Box
5-1
Medicine: Carbon Monoxide: A Stealthy Killer
Two Models Suggest Mechanisms for
Cooperative Binding
Hemoglobin Also Transports H+ and CO2
Oxygen Binding to Hemoglobin Is Regulated by
2,3-Bisphosphoglycerate
Sickle-Cell Anemia Is a Molecular Disease
of Hemoglobin
158
158
159
160
160
162
163
165
165
167
168
The Immune Response Features a Specialized
Array of Cells and Proteins
170
Antibodies Have Two Identical Antigen-Binding Sites
171
Antibodies Bind Tightly and Specifically to Antigen
173
The Antibody-Antigen Interaction Is the Basis for a
Variety of Important Analytical Procedures
173
The Major Proteins of Muscle Are Myosin and Actin
175
Additional Proteins Organize the Thin and Thick
Filaments into Ordered Structures
176
Myosin Thick Filaments Slide along
Actin Thin Filaments
178
Most Enzymes Are Proteins
Enzymes Are Classified by the Reactions
They Catalyze
184
184
186
186
188
188
189
191
192
Substrate Concentration Affects the Rate of
Enzyme-Catalyzed Reactions
194
The Relationship between Substrate Concentration
and Reaction Rate Can Be Expressed
Quantitatively
195
Enzymes Affect Reaction Rates, Not Equilibria
Reaction Rates and Equilibria Have Precise
Thermodynamic Definitions
A Few Principles Explain the Catalytic Power and
Specificity of Enzymes
Weak Interactions between Enzyme and
Substrate Are Optimized in the Transition State
Binding Energy Contributes to Reaction
Specificity and Catalysis
Specific Catalytic Groups Contribute to Catalysis
! xviii :
Contents
Box
6-1
Transformations of the Michaelis-Menten Equation:
The Double-Reciprocal Plot
Kinetic Parameters Are Used to Compare Enzyme
Activities
Many Enzymes Catalyze Reactions with Two or
More Substrates
Pre-Steady State Kinetics Can Provide
Evidence for Specific Reaction Steps
Enzymes Are Subject to Reversible or
Irreversible Inhibition
Box
6-2
Kinetic Tests for Determining inhibition
Mechanisms
Enzyme Activity Depends on
pH
6.4
Exampies of Enzymatic Reactions
The Chymotrypsin Mechanism Involves Acylation
and Deacylation of
a Ser
Residue
Box
6-3
Evidence for Enzyme-Transition State
Complementarity
Hexokinase Undergoes Induced Pit on
Substrate Binding
The Enolase Reaction Mechanism Requires
Metal Ions
Lysozyme Uses Two Successive Nucleophffic
Displacement Reactions
An Understanding of Enzyme Mechanism Drives
Important Advances in Medicine
6.5
Regulatory Enzymes
Allosteric Enzymes Undergo Conformational
Changes in Response to Modulator Binding
In Many Pathways, Regulated Steps Are
Catalyzed by Allosteric Enzymes
The Kinetic Properties of Allosteric Enzymes
Diverge from Michaelis-Menten Behavior
Some Enzymes are Regulated by Reversible
Covalent Modification
Phosphoryl Groups Affect the Structure and
Catalytic Activity of Enzymes
Multiple Phosphorylations Allow Exquisite
Regulatory Control
Some Enzymes and Other Proteins Are Regulated
by Proteolytic Cleavage of an Enzyme Precursor
Some Regulatory Enzymes Use Several Regulatory
Mechanisms
197
197
200
201
201
202
204
205
205
210
212
213
213
216
220
220
221
222
223
224
225
226
227
7.1
Monesaccharides and Disaccharides
235
The Two Families of Monosaccharides Are
Aldoses and Ketoses
236
Monosaccharides Have Asymmetric Centers
236
The Common Monosaccharides Have Cyclic
Structures
238
Organisms Contain a Variety of Hexose Derivatives
240
Monosaccharides Are Reducing Agents
241
Box
7-1
Mediane:
Blood Glucose Measurements in the
Diagnosis and Treatment of Diabetes
241
Disaccharides Contain a Glycosidic Bond
243
72
t
Some Homopolysaccharides Are Stored
Forms of Fuel
Some Homopolysaccharides Serve
Structural Roles
Steric Factors and Hydrogen Bonding Influence
Homopolysaccharide Folding
Bacterial and Algal Cell Walls Contain Structural
Heteropolysaccharides
Glycosaminoglycans Are Heteropolysaccharides
of the Extracellular Matrix
73
Glycoconjugates: PrateoglycanSjGiycoproteins,
and Giycoiipids
Proteoglycans Are Glycosaminoglycan-Containing
Macromolecules of the Cell Surface and
Extracellular Matrix
Glycoproteins Have Covalently Attached
Oligosaccharides
Giycoiipids and Lipopolysaccharides Are
Membrane Components
7.4
Carbohydrates as informational Molecules:
The Sugar Code
Lectins Are Proteins That Read the Sugar
Code and Mediate Many Biological Processes
Lectin-Carbohydrate Interactions Are Highly
Specific and Often Polyvalent
7.5
Working with Carbohydrates
245
246
247
249
249
252
252
255
256
257
258
261
263
8.1
Some Basics
271
Nucleotides and Nucleic Acids Have
Characteristic Bases and Pentoses
271
Phosphodiester Bonds Link Successive
Nucleotides in Nucleic Acids
274
The Properties of Nucleotide Bases Affect the
Three-Dimensional Structure of Nucleic Acids
276
8.2
Nucleic Add Structure
277
DNA
Is a Double Helix that Stores Genetic
Information
278
DNA
Can Occur in Different Three-Dimensional
Forms
280
Certain
DNA
Sequences Adopt Unusual Structures
281
Messenger RNAs Code for Polypeptide Chains
283
Many RNAs Have More Complex Three-Dimensional
Structures
284
83
Nucleic Add Chemistry
287
Double-Helical
DNA
and
RNA
Can Be Denatured
287
Nucleic Acids from Different Species Can
Form Hybrids
288
Nucleotides and Nucleic Acids Undergo
Nonenzymatic Transformations
289
Some Bases of
DNA Are
Methylated
292
The Sequences of Long
DNA
Strands Can Be
Determined
292
The Chemical Synthesis of
DNA
Has Been
Automated
294
Contents
Nucleotides Carry Chemical Energy in
СеДѕ
Adenine
Nucleotides Are Components of Many
Enzyme Cofactors
Some Nucleotides Are Regulatory Molecules
296
297
298
9.1
DNå
Cloning: The Basics
304
Restriction Endonucleases and
DNA
Ligase
Yield
Recombinant
DNA 304
Cloning Vectors Allow Amplification of Inserted
DNA
Segments
307
Specific
DNA
Sequences Are Detectable by
Hybridization
310
Expression of Cloned Genes Produces
Large Quantities of Protein
312
Alterations in Cloned Genes Produce Modified
Proteins
312
Terminal Tags Provide Binding Sites for Affinity
Purification
313
9.2
From Genes to Genomes
315
DNA
Libraries Provide Specialized Catalogs of
Genetic Information
315
The Polymerase Chain Reaction Amplifies Specific
DNA
Sequences
317
Genome Sequences Provide the Ultimate
Genetic Libraries
317
Box
9-1
A Potent Weapon in Forensic Medicine
319
93
From Genomes to Proteomes
324
Sequence or Structural Relationships
Provide Information on Protein Function
324
Cellular Expression Patterns Can Reveal the
Cellular Function of a Gene
325
Detection of Protein-Protein Interactions Helps to
Define Cellular and Molecular Function
328
9.4
Genome Alterations and New Products
of Biotechnology
330
A Bacterial Plant Parasite Aids Cloning in Plants
330
Manipulation of Animal Cell Genomes Provides
Information on Chromosome Structure and
Gene Expression
332
Box
9-2
/Weácme:
The Human Genome and Human
Gene Therapy
335
New Technologies Promise to Expedite the
Discovery of New Pharmaceuticals
335
Recombinant
DNA
Technology Yields New
Products and Challenges
337
10.1
Storage Lipids
343
Fatty Acids Are Hydrocarbon Derivatives
343
Triacylglycerols Are Fatty Acid Esters of Glycerol
346
Triacylglyeerols Provide Stored Energy
and Insulation
346
Glycerophospholipids Are Derivatives of
Phosphatidic Acid
Some Glycerophospholipids Have Ether-Linked
Fatty Acids
Chloroplaste
Contain Galactolipids and Sulfolipids
Archaea Contain Unique Membrane Lipids
Sphingolipids Are Derivatives of Sphingosine
Sphingolipids at Cell Surfaces Are Sites of
Biological Recognition
Phospholipids and Sphingolipids Are Degraded
in Lysosomes
Sterols Have Four Fused Carbon Rings
Box
10-2
Medicine: Abnormal Accumulations of
Membrane Lipids: Some Inherited Human Diseases
Box
10-1
Sperm Whales: Fatheads of the Deep
347
Partial
Hydrogénation
of Cooking Oils Produces
Trans Fatty Acids
347
Waxes Serve as Energy Stores and Water Repellents
349
ЗбО
360
362
352
362
354
355
355
356
357
357
358
359
359
360
361
362
362
363
363
364
365
365
365
365
Phosphatidylinositols and Sphingosine Derivatives
Act as Intracellular Signals
Eicosanoids Carry Messages to Nearby Cells
Steroid Hormones Carry Messages between Tissues
Vascular Plants Produce Thousands of Volatile
Signals
Vitamins A and
D
Are Hormone Precursors
Vitamins
E
and
К
and the
Lipid
Quiñones
Are
Oxidation-Reduction Cofactors
Dolichols Activate Sugar Precursors for
Biosynthesis
Many Natural Pigments Are
Lipidie
Conjugated Dienes
Lipid
Extraction Requires Organic Solvents
Adsorption Chromatography Separates Lipids
of Different Polarity
Gas-Liquid Chromatography Resolves Mixtures
of Volatile
Lipid
Derivatives
Specific Hydrolysis Aids in Determination of
Lipid
Structure
Mass Spectrometry Reveals Complete
Lipid
Structure
Lipidomics Seeks to Catalog All Lipids and
Their Functions
Each Type of Membrane Has Characteristic
Lipids and Proteins
All Biological Membranes Share Some
Fundamental Properties
A Lipid
Bilayer Is the Basic Structural
Element of Membranes
Three Types of Membrane Proteins Differ in
Their Association with the Membrane
Many Membrane Proteins Span the
lipid
Bilayer
Integral Proteins Are Held in the Membrane by
Hydrophobie
Interactions with
Lipiđs
372
373
374
375
375
376
Contents
The Topology of an Integral Membrane Protein Can
Sometimes Be Predicted from Its Sequence
378
Covalently Attached Iipids Anchor Some
Membrane Proteins
379
381
381
383
384
385
387
388
Acyl Groups in the Bilayer Interior Are Ordered
to Varying Degrees
Transbilayer Movement of Iipids Requires Catalysis
Lipids and Proteins Diffuse Laterally in the Bilayer
SphingoĽpids
and Cholesterol Cluster Together in
Membrane Rafts
Box
11 -1
Methods: Atomic Force Microscopy to Visualize
Membrane Proteins
Membrane Curvature and Fusion Are Central to
Many Biological Processes
Integral Proteins of the Plasma Membrane Are
Involved in Surface Adhesion, Signaling, and
Other Cellular Processes
Passive Transport Is Facilitated by Membrane
Proteins
Transporters Can Be Grouped into Superfamilies
Based on Their Structures
The Glucose Transporter of Erythrocytes Mediates
Passive Transport
The Chloride-Bicarbonate Exchanger Catalyzes
Electroneutral Cotransport of Anions across
the Plasma Membrane
Box
11-2
Medicine: Defective Glucose and Water Transport
in Two Forms of Diabetes
Active Transport Results in Solute Movement
against a Concentration or Electrochemical
Gradient
P
-Туре
ATPases Undergo Phosphorylation during
Their Catalytic Cycles
F-Type ATPases Are Reversible, ATP-Driven
Proton Pumps
ABC Transporters Use ATP to Drive the Active
Transport of a Wide Variety of Substrates
Ion Gradients Provide the Energy for Secondary
Active Transport
Box
11 -3
Medicine: A Defective Ion Channelin Cystic Fibrosis
401
Aquaporins Form Hydrophilic
Transmembrane
Channels for the Passage of Water
Ion-Selective Channels Allow Rapid Movement of
Ions across Membranes
Ion-Channel Function Is Measured Electrically
The Structure of a K+ Channel Reveals the
Basis for Its Specificity
Gated Ion Channels Are Central in
Neuronal
Function
Defective Ion Channels Can Have Severe
Physiological Consequences
390
391
391
393
394
395
396
399
400
400
404
406
407
407
410
The
ß-Adrenergic
Receptor System
Acts through the Second Messenger cAMP
Box
12-2
Medicine:
G
Proteins: Binary Switches in
Health and Disease
Several Mechanisms Cause Termination of the
ß-Adrenergic
Response
The /3-Adrenergic Receptor Is Desensitized by
Phosphorylation and by Association with
Arrestin
Cyclic AMP Acts as a Second Messenger for
Many Regulatory Molecules
Diacylglycerol, Inositol Trisphosphate, and Ca2+
Have Related Roles as Second Messengers
Box
12-3
Methods: FRET: Biochemistry Visualized in a
Living Cell
Calcium Is a Second Messenger That May Be
Localized in Space and Time
11
1
Ε,ο,
Stimulation of the Insulin Receptor Initiates a
Cascade of Protein Phosphorylation Reactions
The Membrane Phospholipid PIP3 Functions at a
Branch in Insulin Signaling
The JAK-STAT Signaling System Also Involves
Tyrosine Kinase Activity
Cross Talk among Signaling Systems Is
Common and Complex
Protein Modules Bind Phosphorylated
Tyr, Ser,
or
Thr Residues in Partner Proteins
Membrane Rafts and Caveolae Segregate
Signaling Proteins
Ion Channels Underlie Electrical Signaling in
Excitable Cells
Voltage-Gated Ion Channels Produce
Neuronal
Action Potentials
The Acetylcholine Receptor Is a
Ligand-Gated Ion Channel
Neurons Have Receptor Channels That
Respond to Different
Neurotransmitters
Toxins Target Ion Channels
410 12
J
Signaling In
423
425
430
430
431
432
434
436
439
439
441
443
444
446
449
449
451
453
453
454
12
J
inîêgrins:
Bidirectional
Celi
Adhesion Receptors
455
12.1
General Features of Signal
ïransdticîi«
Box
12-1
Mđhuds:
Scatenar«!
analysis Quantifies the
Reteptor-Ligarof interaction
421
Bacterial Signaling Entails Phosphorylation in a
Two-Component System
457
Signaling Systems of Plants Have Some of the
Sanie
Components Used by Microbes and Mammals
458
Plants Detect
Ethylene
through a Two-Component
System and
а МАРК
Cascade
460
Receptorluce Protein Kioases Transduce Signals from
Peptìdes
and Brassinosteroids
460
Contents
The Visual System
Uses Classic GPCR Mechanisms
Excited Rhodopsin Acts through the
G
Protein
Transducin to Reduce the cGMP Concentration
The Visual Signal Is Quickly Terminated
Cone Cells Specialize in Color Vision
Vertebrate
Olfaction
and Gustation Use
Mechanisms
Similar
to the Visual System
Box
12-4
Medicine: Color Blindness: John Dalton's
Experiment from the Grave
GPCRs of the Sensory Systems Share Several
Features with GPCRs of Hormone Signaling
Systems
462
463
464
465
465
466
467
12.11
1
The Cell Cycle Has Four Stages
469
Levels of Cyclin-Dependent Protem Kinases Oscillate
469
CDKs Regulate Cell Division by Phosphorylating
Critical Proteins
472
473
474
475
477
Oncogenes Are Mutant Forms of the Genes for
Proteins That Regulate the Cell Cycle
Defects in Certain Genes Remove Normal
Restraints on
СеБ
Drasion
Box
12-5
Medicine: Development of Protein
Kinase Inhibitors for Cancer Treatment
Apoptosis Is Programmed Cell Suicide
Biological Energy Transformations Obey the
Laws of Thermodynamics
Cells Require Sources of Free Energy
Standard Free-Energy Change Is Directly
Related to the Equilibrium Constant
Actual Free-Energy Changes Depend on
Reactant and Product Concentrations
Standard Free-Energy Changes Are Additive
13.2
Chemical Logic and Common
Biochemical and Chemical Equations Are
Not Identical
The Free-Energy Change for ATP Hydrolysis Is
Large and Negative
Other Phosphorylated Compounds and Thioesters
Also Have Large Free Energies of Hydrolysis
ATP Provides Energy by Group Transfers, Not by
Simple Hydrolysis
ATP Donates Phosphoryl, Pyrophospiioryl, and
Adenylyl Groups
Assembly of Informational Macramolecules
Requires Energy
490
491
491
493
494
500
501
501
504
506
507
508
Box
13-1
Firefly Flashes: Glowing Reports of ATP
ATP Energizes Active Transport and
Muscle Contraction
Transphosphorylations between Nucleotides
Occur in All Cell Types
Inorganic Polyphosphate Is a Potential
Phosphoryl Group Donor
The Flow of Electrons Can Do Biological Work
Oxidation-Reductions Can Be Described as
Half-Reactions
Biological Oxidations Often Involve Dehydrogenation
Reduction Potentials Measure Affinity for Electrons
Standard Reduction Potentials Can Be Used to
Calculate Free-Energy Change
Cellular Oxidation of Glucose to Carbon Dioxide
Requires Specialized Electron Carriers
A Few Types of Coenzymes and Proteins Serve as
Universal Electron Carriers
NADH and NADPH Act with Dehydrogenases as
Soluble Electron Carriers
Dietary Deficiency of Niacin, the Vitamin Form of
NAD and NADP, Causes Pellagra
Flavin Nucleotides Are Tightly Boimd in
Flavoproteins
509
509
510
511
512
512
512
513
514
515
516
516
516
519
519
An Overview: Glycolysis Has Two Phases
528
The Preparatory Phase of Glycolysis Requires ATP
531
The Payoff Phase of Glycolysis Yields ATP and NADH
535
The Overall Balance Sheet Shows a Net Gain of ATP
538
Glycolysis Is under Tight Regulation
539
Glucose Uptake Is Deficient in Type
1
Diabetes Mellitus
539
Box
14-1
Medicine: High Rate of Glycolysis in Tumors Suggests
Targets for Chemotherapy and Facilitates Diagnosis
540
543
544
545
546
546
547
548
549
549
Dietary Polysaccharides and Disaccharides
Undergo Hydrolysis to Monosaceharides
Endogenous Glycogen and Starch Are
Degraded by Phosphorolysis
Other Monosaceharides Enter the Glycolytic
Pathway at Several Points
Pyruvate Is the Terminal Electron Acceptor in
Lactic Acid Fermentation
Ethanol
Is the Reduced Product in
Ethanol
Fermentation
Box
14-2
Athletes, Alligators, and Coeiacanths:
Glycolysis at Limiting Concentrations of Oxygen
Box
14-3
Ethanol
Fermentations:
Brewing Beer and Producing Biofuels
Thiamme
Pyrophosphate
Carries
"Active
Acetaldehyde"
Groups
xii
xxii Contents
Fermentations
Are Used to Produce Some Common
Foods and Industrial Chemicals
Conversion of Pyruvate to Phosphoenolpyruvate
Requires Two Exergonic Reactions
Conversion of Fructose 1,6-Bisphosphate to
Fructose 6-Phosphate Is the Second Bypass
Conversion of Glucose 6-Phosphate to
Glucose Is the Third Bypass
Gluconeogenesis Is Energetically Expensive, but
Essential
Citric Acid Cycle Intermediates and Some
Amino
Acids Are Glucogenic
Mammals Cannot Convert Fatty Acids to Glucose
Glycolysis and Gluconeogenesis Are Reciprocally
Regulated
14.5
Pentose Phosphate Pathway of Glucose Oxidation
Box
14-4
Medicine: Why Pythagoras Wouldn't Eat Falafel:
Glucose 6-Phosphate Dehydrogenase Deficiency
The Oxidative Phase Produces Pentose
Phosphates and NADPH
The Nonoxidative Phase Recycles Pentose
Phosphates to Glucose 6-Phosphate
Wernicke-Korsakoff Syndrome Is Exacerbated by a
Defect in Transketolase
Glucose 6-Phosphate Is Partitioned between
Glycolysis and the Pentose Phosphate Pathway
550
551
553
556
556
556
557
557
557
558
559
559
560
563
563
15.1
Regulation of Metabolic Pathways
570
Cells and Organisms Maintain a Dynamic
Steady State
571
Both the Amount and the Catalytic
Activity of an Enzyme Can Be Regulated
571
Reactions Far from Equilibrium in Cells Are
Common Points of Regulation
574
Adeninę Nucleotides
Play Special Roles in
Metabolic Regulation
575
15.2
analysis of Metabolic Control
577
The Contribution of Each Enzyme to Flux through
a Pathway Is Experimentally Measurable
578
The Control Coefficient Quantifies the Effect of a
Change in Enzyme Activity on Metabolite Flux
through a Pathway
578
Box
15-1
Methods: Metabolic Control Analysis:
Quantitative Aspects
579
The Elasticity Coefficient Is Related to an Enzyme's
Responsiveness to Changes in Metabolite or
Regulator Concentrations
580
The Response Coefficient Expresses the Effect of an
Outside Controller on Flux through a Pathway
581
Metabolic Control Analysis Has Been Applied to
Carbohydrate Metabolism, with Surprising
Results
681
Metabolic Control Analysis Suggests a General
Method for Increasing Flux through a Pathway
582
Hexokinase Isozymes of Muscle and Liver Are
Affected Differently by Their Product,
Glucose 6-Phosphate
Box
15-2
Isozymes: Different Proteins That Catalyze
the Same Reaction
Hexokinase IV (Glucokinase) and Glucose
6-Phosphatase Are Transcriptionally Regulated
Phosphofructokinase-l and Fructose
1
,6-Bisphosphatase Are Reciprocally Regulated
Fructose 2,6-Bisphosphate Is a Potent Allosteric
Regulator of PFK-1 and FBPase-1
Xylulose 5-Phosphate Is a Key Regulator of
Carbohydrate and Fat Metabolism
The Glycolytic Enzyme Pyruvate Kinase Is
Allosterically Inhibited by ATP
The Gluconeogenic Conversion of Pyruvate to
Phosphoenol Pyruvate Is Under Multiple
Types of Regulation
Transcriptional Regulation of Glycolysis and
Gluconeogenesis Changes the Number of
Enzyme Molecules
Box
15-3
Medicine: Genetic Mutations That Lead to
Rare Forms of Diabetes
15.4
The Metabolism of Glycogen in Animals
Glycogen Breakdown Is Catalyzed by Glycogen
Phosphorylase
Glucose 1-Phosphate Can Enter Glycolysis or, in
Liver, Replenish Blood Glucose
The Sugar Nucleotide UDP-Glucose Donates
Glucose for Glycogen Synthesis
Box
15-4
Carl and
Gerty
Cori:
Pioneers in Glycogen
Metabolism and Disease
Glycogenin Primes the Initial Sugar Residues in
Glycogen
15.5
Coordinated Regulation of Glycogen Synthesis
and Breakdown
Glycogen Phosphorylase Is Regulated
Allosterically and Hormonally
Glycogen Synthase Is Also Regulated by
Phosphorylation and Dephosphorylation
Glycogen Synthase Kinase
3
Mediates Some of the
Actions of Insulin
Phosphoprotein Phosphatase
1
Is Central to
Glycogen Metabolism
Allosteric and Hormonal Signals Coordinate
Carbohydrate Metabolism Globally
Carbohydrate and
Lipid
Metabolism Are Integrated
by Hormonal and Allosteric Mechanisms
583
584
585
585
587
588
588
590
590
593
594
595
596
596
598
601
602
603
605
606
606
606
608
16.1
Production of Acetyi-CoA (Activated acetate}
616
Pyruvate Is Oxidized to
Aceţyl-CoA
and COg
616
The Pyruvate Dehydrogenase Complex Requires
Five Goenzymes
617
Contents
The Pyruvate Dehydrogenase Complex Consists
of Three Distinct Enzymes
In Substrate Channeling, Intermediates Never
Leave the Enzyme Surface
The Citric Acid Cycle Has Eight Steps
Box
16-1
Moonlighting Enzymes:
Proteins with More Than One Job
Box
16-2
Synthases and Synthetases;
Ligases
and Lyases;
Kinases, Phosphatases, and Phosphorylases: Yes, the
Names Are Confusing!
Box
16-3
Citrate: A Symmetric Molecule That Reacts
Asymmetrically
The Energy of Oxidations in the Cycle Is Efficiently
Conserved
Why Is the Oxidation of Acetate So Complicated?
Citric Acid Cycle Components Are Important
Biosynthetic Intermediates
Anaplerotic Reactions Replenish Citric Acid Cycle
Intermediates
Box
16-4
Citrate Synthase, Soda Pop, and the
World Food Supply
Biotin in Pyruvate Carboxylase Carries COg Groups
16.3
Regulation of the Citric add Cycle
Production of Acetyl-CoA by the Pyruvate
Dehydrogenase Complex Is Regulated by
Allosteric and Covalent Mechanisms
The Citric Acid Cycle Is Regulated at Its Three
Exergonic Steps
Substrate Channeling through Multienzyme
Complexes May Occur in the Citric Acid Cycle
Some Mutations in Enzymes of the Citric Acid
Cycle Lead to Cancer
16.4
The Glyoxylate Cycle
The Glyoxylate Cycle Produces Pour-Carbon
Compounds from Acetate
The Citric Acid and Glyoxylate Cycles Are
Coordinately Regulated
618
619
620
621
624
627
629
630
631
631
631
633
633
635
636
636
637
637
638
638
639
17.1
Digestion, Mobilization, and Transport of Fats
Dietary Fats Are Absorbed in the Small Intestine
Hormones Trigger Mobilization of Stored
Triacylglycerols
Patty Acids Are Activated and Transported into
Mitochondria
17.2
Oxidation of Fatty Acids
The
β
Oxidation of Saturated Fatty Acids Has
Four Basic Steps
The Four
jß-Oxidation
Steps Are Repeated to Yield
Aceiyl-CoA and ATP
Box
17-1
Fat Bears Carry Out
β
Oxidation in Their Sleep
Acetyl-CoA Can Be Further Oxidized in the
Citric Acid Cycle
Oxidation of Unsaturated Fatty Acids Requires
Two Additional Reactions
648
649
650
652
653
654
655
655
656
Complete Oxidation of Odd-Number Fatty
Acids Requires Three Extra Reactions
Box
17-2
Coenzyme B12: A Radical Solution to a
Perplexing Problem
Fatty Acid Oxidation Is Tightly Regulated
Transcription Factors Turn on the Synthesis of
Proteins for
Lipid
Catabolism
Genetic Defects in Fatty Acyl-CoA
Dehydrogenases Cause Serious Disease
Peroxisomes Also Carry Out
β
Oxidation
Plant Peroxisomes and Glyoxysomes Use
Acetyl-CoA from
β
Oxidation as a
Biosynthetic Precursor
The /3-Oxidation Enzymes of Different
Organelies
Have Diverged during Evolution
The
ω
Oxidation of Fatty Acids Occurs in the
Endoplasmic Reticulum
Phytanic Acid Undergoes a Oxidation in
Peroxisomes
Ketone
Bodies, Formed in the Liver, Are
Exported to Other Organs as Fuel
Ketone
Bodies Are Overproduced in
Diabetes and during Starvation
657
658
660
660
661
662
662
663
664
664
666
666
667
18.1
Metabolic
Fates of
Amino
Groups
Dietary Protein Is Enzymatically Degraded to
Amino
Acids
Pyridoxal Phosphate Participates in the Transfer of
α
-Amino
Groups to a-Ketoglutarate
Glutamate
Releases Its
Amino
Group As
Ammonia in the Liver
Box
18-1
Medicine: Assays for Tissue Damage
Glutaminę
Transports Ammonia in the
Bloodstream
Alaninę
Transports Ammonia from Skeletal
Muscles to the liver
Ammonia Is Toxic to Animals
18.
e
Urea Is Produced from Ammonia in Five
Enzymatic Steps
The Citric Acid and Urea Cycles Can
Be linked
The Activity of the Urea Cycle Is Regulated at
Two Levels
Pathway Interconnections Reduce the Energetic
Cost of Urea Synthesis
Genetic Defects in the Urea Cycle Can Be
Life-Threatening
Some
Amino
Acids Are Converted to Glucose,
Others to
Ketone
Bodies
Several Enzyme Cofactors Play Important
Roles in
Amino
Acid Catabolism
Six
Amino
Acids Are Degraded to Pyruvate
Seven
Amino
Acids Are Degraded to Acetyl-CoA
674
674
677
677
678
680
681
681
682
682
684
685
686
686
687
688
689
692
Contents
19.1
Electron-Transfer Reactions in Mitochondria
Electrons Are
Funneled
to Universal Electron
Acceptors
Electrons Pass through a Series of
Membrane-Bound Carriers
Electron Carriers Function in Multienzyme
Complexes
Mitochondrial Complexes May Associate in
Respirasomes
The Energy of Electron Transfer Is Efficiently
Conserved in a Proton Gradient
Reactive Oxygen Species Are Generated during
Oxidative Phosphorylation
Plant; Mitochondria Have Alternative
Mechanisms for Oxidizing NADH
Box
19-1
Hot, Stinking Plants and Alternative
Respiratory Pathways
ATP Synthase Has Two Functional Domains,
Fo and Px
ATP Is Stabilized Relative to ADP on the
Surface of Fj
The Proton Gradient Drives the Release of
ATP from the Enzyme Surface
Each
β
Subunit
of ATP Synthase Can Assume
Three Different Conformations
Rotational Catalysis Is Key to the Binding-Change
Mechanism for ATP Synthesis
Chemiosmotic Coupling Allows
Nonintegral
Stoichiometries of O2 Consumption and
ATP Synthesis
The Proton-Motive Force Energizes
Active Transport
Shuttle Systems Indirectly Convey Cytosolic
NADH into Mitochondria for Oxidation
Oxidative Phosphorylation Is Regulated by
Cellular Energy Needs
An Inhibitory Protein Prevents ATP Hydrolysis
during Hypoxia
Hypoxia Leads to
ROS
Production and Several
Adaptive Responses
696
698
699
Phenylalanine Catabolism Is Genetically
Defective in Some People
Five
Amino
Acids Are Converted to
a-Ketoglutarate
Four
Amino
Acids Are Converted to Succmyl-CoA
Box
18-2
Medicine: Scientific Sleuths Solve a
Murder Mystery
700
Branched-Chain
Amino
Acids Are Not
Degraded in the Liver
701
Asparagine and Aspartate Are Degraded to
Oxaloacetate
701
ATP-Produeing Pathways Are
Coordinately Regulated
734
709
710
712
718
718
720
721
722
723
725
725
726
726
728
729
730
731
732
733
733
733
19.4
Mitochondria In Thertnogenesis, Steroid
Synthesis, and
Apopîesis
735
Uncoupled Mitochondria in Brown Adipose
Tissue Produce Heat
736
Mitochondrial P-450
Oxygenases Catalyze Steroid
Hydroxylations
736
Mitochondria Are Central to the Initiation of
Apoptosis
737
19.5
Mitochondrial Genes:Their Origin and the
Effects of Mutations
738
Mitochondria Evolved from Endosymbiotic Bacteria
739
Mutations in Mitochondrial
DNA
Accumulate
throughout the Life of the Organism
739
Some Mutations in Mitochondrial Genomes
Cause Disease
740
Diabetes Can Result from Defects in the
Mitochondria of Pancreatic
β
Cells
741
PHOTOSYNTHESIS: HARVESTING LIGHT ENERGY
19.6
General Features of Photophosphorylation
Photosynthesis in Plants Takes Place in
Chloroplasts
Light Drives Electron Flow in Chloroplasts
19.7
Light Absorption
Chlorophylls Absorb Light Energy for
Photosynthesis
Accessory Pigments Extend the Range of Light
Absorption
Chlorophyll Funnels the Absorbed Energy to
Reaction Centers by Exciton Transfer
19.8
The Central Photochemical Event:
Light-Driven Electron Flow
Bacteria Have One of Two Types of Single
Photochemical Reaction Center
Kinetic and Thermodynamic Factors Prevent
the Dissipation of Energy by Internal
Conversion
In Plants, Two Reaction Centers Act in Tandem
Antenna ChlorophyUs Are Tightly Integrated with
Electron Carriers
The Cytochrome b6
ƒ
Complex Links
Photosystems
II and I
CycUc Electron Flow between
PSI
and the
Cytochrome b6
ƒ
Complex Increases the
Production of ATP Relative to NADPH
State Transitions Change the Distribution of LHCII
between the Two
Photosystems
Water Is Split by the Oxygen-Evolving Complex
■ 3.9
ATP Synthesis by Photophosphorylation
A Proton Gradient Couples Electron Flow and
Phosphorylation
The Approximate Stoichiometry of
Photophosphorylation Has Been Established
The ATP Synthase of Chloroplasts Is Like That
of Mitochondria
742
743
743
744
746
747
747
749
749
761
762
754
755
766
756
766
759
769
760
760
Contents
і
xxv
'J
Chloroplaste
Evolved from Ancient
Photosynthetic Bacteria
761
In Halobacterium, a Single Protein Absorbs Light
and Pumps Protons to Drive ATP Synthesis
762
esss
773
Plastids Are Organelles Unique to Plant
Cells and Algae
774
Carbon Dioxide Assimilation Occurs in
Three Stages
775
Synthesis of Each
Triose
Phosphate from CO2
Requires Six NADPH and Nine ATP
782
A Transport System Exports
Triose
Phosphates
from the
Chloroplast
and Imports Phosphate
783
Pour Enzymes of the Calvin Cycle Are Indirectly
Activated by Light
784
20.2
Photorespiration
and the C4 and CAM Pathways
786
Photorespiration Results from Rubisco's
Oxygenase Activity
786
The Salvage of Phosphoglycolate Is Costly
787
In C4 Plants, CO2 Fixation and Rubisco Activity
Are Spatially Separated
789
In CAM Plants, CO2 Capture and Rubisco Action
Are Temporally Separated
791
20.3
ADP-Glucose Is the Substrate for Starch Synthesis in
Plant Plastids and for Glycogen Synthesis in
Bacteria
UDP-Glucose Is the Substrate for Sucrose
Synthesis in the Cytosol of Leaf Cells
Conversion of
Triose
Phosphates to Sucrose and
Starch Is Tightly Regulated
20.4
Synthesis of Ceil Wail Polysaccharides:
Plant
Celluiose
and Bacterial Peptidogiycan
Cellulose Is Synthesized by Supramolecular
Structures in the Plasma Membrane
Iipid-Linked Oligosaccharides Are Precursors for
Bacterial Cell Wall Synthesis
20.5
Integration of Carbohydrate Metabolism in the
Plant Cell
Gluconeogenesis Converts Fats and Proteins to
Glucose in Germinating Seeds
Pools of Common Intermediates Link Pathways in
Different Organelles
791
792
792
794
795
796
797
798
799
21.1
Biosynthesis of Fatty Adds and Eicosanoids
805
Malonyl-CoA Is Formed from Acetyl-CoA and
Bicarbonate
805
Fatty Acid Synthesis Proceeds in a Repeating
Reaction Sequence
806
The Mammalian Fatty Acid Synthase Has
Multiple Active Sites
808
Fatty Acid Synthase Receives the
Acetyl
and
Malonyl Groups
808
The Fatty Acid Synthase Reactions Are
Repeated to Form Palmitate
811
Fatty Acid Synthesis Occurs in the Cytosol of Many
Organisms but in the Chloroplasts of Plants
811
Acetate Is Shuttled out of Mitochondria as Citrate
813
Fatty Acid Biosynthesis Is Tightly Regulated
814
Long-Chain Saturated Fatty Acids Are Synthesized
from Palmitate
814
Desaturation of Fatty Acids Requires a
Mixed-Function
Oxidase
815
60x21-1
Mixed-Function
Oxidases,
Oxygenases, and
Cytochrome P-450
816
Eicosanoids Are Formed from 20-Carbon
Polyunsaturated
ř^atty
Acids
817
21.2
Biosynthesis of Triacylglycerols
820
Triacylglycerols and Glycerophospholipids Are
Synthesized from the Same Precursors
820
Triacylglycerol Biosynthesis in Animals Is Regulated
by Hormones
821
Adipose Tissue Generates Glycerol 3-Phosphate by
Glyceroneogenesis
822
Thiazolidinediones Treat Type
2
Diabetes
by Increasing Glyceroneogenesis
824
21.3
Biosynthesis of Membrane Phospholipids
824
Cells Have Two Strategies for Attaching Phospholipid
Head Groups
824
Phospholipid Synthesis in
E. coli
Employs
CDP-Diacylglycerol
825
Eukaryotes Synthesize
Anionie
Phospholipids from
CDP-Diacylglycerol
827
Eukaryotic Pathways to Phosphatidylserine,
Phosphatidylethanolamine, and
Phosphatidylcholine Are Interrelated
827
Plasmalogen
Synthesis Requires Formation of an
Ether-Linked Fatty Alcohol
829
Sphingolipid and Glycerophospholipid Synthesis
Share Precursors and Some Mechanisms
829
Polar Lipids Are Targeted to Specific
Cellular Membranes
830
21.4
Biosynthesis of Cholesterol, Steroids,
and ¡soprenoids
831
Cholesterol Is Made from Acetyl-CoA in
Four Stages
832
Cholesterol Has Several Fates
836
Cholesterol and Other Lipids Are Carried on Plasma
Lipoprotéine
836
Box
21-2
Medicine: ApoE
Alíeles
Predict Incidence of
Alzheimer's Disease
839
Cholesteryl Esters Enter
СеДѕ
by
Receptor-Mediated Endocytosis
840
Cholesterol Biosynthesis Is Regulated at
Several Levels
841
Box
21-3
Medicine: The
Lipid
Hypothesis and
the Development of Statins
842
j^xxvij
Contents
Steroid
Hormones
Are Formed by Side-Chain
Cleavage and Oxidation of Cholesterol
Intermediates in Cholesterol Biosynthesis Have
Many Alternative Fates
844
845
22.1
Overview of Nitrogen Metabolism
852
The Nitrogen Cycle Maintains a Pool of
Biologically Available Nitrogen
852
Nitrogen Is Fixed by Enzymes of the
Nitrogenase Complex
852
Box
22-1
Unusual Lifestyles of the Obscure but Abundant
853
Ammonia Is Incorporated into Biomolecules
through
Glutamate
and
Glutaminę
857
Glutaminę
Synthetase Is a Primary Regulatory
Point in Nitrogen Metabolism
857
Several Classes of Reactions Play Special
Roles in the Biosynthesis of
Amino
Acids and Nucleotides
859
22.2
Biosynthesis of
Amino
Acids
860
a-Ketoglutarate Gives Rise to
Glutamate,
Glutaminę,
Proline,
and
Arginine.
861
Serine, Glycine, and
Cysteine
Are Derived from
S-Phosphoglycerate
863
Three Nonessential and Six Essential
Amino
Acids Are Synthesized from Oxaloacetate and
Pyruvate
865
Chorismate Is a Key Intermediate in the Synthesis
of Tryptophan, Phenylalanine, and Tyrosine
865
Histidine Biosynthesis Uses Precursors of
Purine
Biosynthesis
869
Amino
Acid Biosynthesis Is under
Allosteric Regulation
872
22.3
Molecules Derived from
Amino
Acids
873
Glycine
Is a Precursor of Porphyrins
873
Box
22-2
Medicine: On Kings and Vampires
875
Heme
Is the Source of
ВДе
Pigments
875
Amino
Acids Are Precursors of Greatine and
Glutathione
876
D-
Amino
Acids Are Found Primarily in Bacteria
877
Aromatic
Amino
Acids Are Precursors of Many
Plant Substances
878
Biological Amines Are Products of
Amino
Acid
Deearboxylation
878
Box
22-3
Medicine: Curing African Sleeping Sickness with
a Biochemical Trojan Horse
880
Arginine
Is the Precursor for Biological
Synthesis of Nitric Oxide
882
22.4
Biosynthesis and Degradation of Nucleotides
882
De Novo
Purine Nucleotide
Synthesis
Begins with PRPP
883
Purine
Nucleotide Biosynthesis Is Regulated by
Feedback Inhibition
885
Pyrimidine Nucleotides Are Made from Aspartate,
PRPP, and Carbamoyl Phosphate
886
Pyriniidine Nucleotide Biosynthesis Is
Regulated by Feedback Inhibition
887
Nucleoside
Monophosphates
Are Converted to
Nucleoside Triphosphates
888
Ribonucleotides Are the Precursors of
Deoxyribonucleotides
888
Thymidylate Is Derived from dCDP and dUMP
890
Degradation of
Purines
and Pyrimidines Produces
Uric Acid and Urea, Respectively
892
Purine
and Pyrimidine Bases Are Recycled by
Salvage Pathways
893
Excess Uric Acid Causes Gout
893
Many Chemotherapeutic Agents Target Enzymes
in the Nucleotide Biosynthetic Pathways
894
wias
ж
23.1
Hormones: Diverse Structures for
Diverse Functions
The Detection and Purification of Hormones
Requires a Bioassay
Box
23-1
Medicine: How Is a Hormone Discovered?
The Arduous Path to Purified Insulin
Hormones Act through Specific High-Affinity
Cellular Receptors
Hormones Are Chemically Diverse
Hormone Release Is Regulated by a Hierarchy of
Neuronal
and Hormonal Signals
23.2
Tissue-Specific Metabolism: The Division of Labor
The Liver Processes and Distributes Nutrients
Adipose Tissues Store and Supply Fatty Acids
Brown Adipose Tissue Is Thermogenic
Muscles Use ATP for Mechanical Work
The Brain Uses Energy for Transmission of
Electrical Impulses
Blood Carries Oxygen, Metabolites, and Hormones
23.3
Hormonal Regulation of Fuel Metabolism
Insulin Counters High Blood Glucose
Pancreatic
β
Cells Secrete Insulin in Response to
Changes in Blood Glucose
Glucagon Counters Low Blood Glucose
During Fasting and Starvation, Metabolism
Shifts to Provide Fuel for the Brain
Epinephrine Signals Impending Activity
Cortisol
Signals Stress, Including Low
Blood Glucose
Diabetes Mellitus Arises from Defects in
Insulin Production or Action
Adipose Tissue Has Important
Endocrine Functions
Leptin Stimulates Production of Anorexigenic
Peptide
Hormones
Leptin Triggers a Signaling Cascade That
Regulates Gene Expression
The Leptin System May Have Evolved to
Regulate the Starvation Response
902
903
904
906
909
912
912
916
917
918
920
920
922
922
923
925
926
928
929
929
930
930
932
933
934
Contents
Insulin
Acts in the Arcuate Nucleus to
Regulate Eating and Energy Conservation
Adiponectin Acts through AMPK to Increase
Insulin Sensitivity
Diet Regulates the Expression of Genes
Central to Maintaining Body Mass
Short-Term Eating Behavior Is Influenced by
Ghrelin and PYY3_36
23,5
Obesity, the Metabolic Syndrome, and
In Type
2
Diabetes the Tissues Become
Insensitive to Insulin
Type
2
Diabetes Is Managed with Diet,
Exercise, and Medication
1
Chromosomal Elements
Genes Are Segments of
DNA
That Code for
Polypeptide Chains and RNAs
DNA
Molecules Are Much Longer Than the
Cellular or Viral Packages That
Contam
Them
Eukaryotic Genes and Chromosomes Are
Very Complex
Most Cellular
DNA
Is Underwoimd
DNA
Underwinding Is Defined by Topological
Linking Number
Topoisomerases Catalyze Changes in the
Linking Number of
DNA
Box
24-1
Medicine: Curing Disease by Inhibiting
Topoisomerases
DNA
Compaction Requires a Special Form of
Supercoiling
243
The Structure of Chromosomes
Chromatin Consists of
DNA
and Proteins
Histones Are Small, Basic Proteins
Nucleosomes Are the Fundamental
Organizational Units of Chromatin
Box
24-2
Medicine: Epigenetics, Nucleosome
Structure, and Histone Variants
Nucleosomes Are Packed into Successively
Higher-Order Structures
Condensed Chromosome Structures Are
Maintained by SMC Proteins
Bacterial
DNA
Is Also Highly Organized
934
934
936
937
938
938
939
945
947
947
948
952
954
955
956
968
960
961
962
962
963
964
966
966
969
970
25.1
Жћ
Replication
977
DNA
Replication Follows a Set of
Fundamental Rules
977
DNA
Is Degraded by Nucleases
979
DNA
Is Synthesized by
DNA
Polymerases
979
Replication Is Very Accurate
980
E. coli
Has at Least Five
DNA
Polymerases
982
DNA
Replication Requires Many Enzymes and
Protein Factors
984
Replication of the
E. coli
Chromosome
Proceeds in Stages
985
Replication in Eukaryotic Cells Is Both
Similar and More Complex
991
Viral
DNA
Polymerases Provide Targets for
Antiviral Therapy
992
25.2 DNA
Repair
993
Mutations Are Linked to Cancer
993
All Cells Have Multiple
DNA
Repair Systems
993
The Interaction of Replication Forks with
DNA
Damage Can Lead to Error-Prone Translesion
DNA
Synthesis
1001
Box
25-1
Medicine:
DNA
Repair and Cancer
1003
25.3 DNA
Recombination
1003
Homologous Genetic Recombination Has
Several Functions
1004
Recombination during Meiosis Is Initiated with
Double-Strand Breaks
1005
Recombination Requires a Host of Enzymes and
Other Proteins
1007
All Aspects of
DNA
Metabolism Come Together to
Repair Stalled Replication Forks
1009
Site-Specific Recombination Results in Precise
DNA
Rearrangements
1010
Complete Chromosome Replication Can Require
Site-Specific Recombination
1012
Transposable Genetic Elements Move from One
Location to Another
1013
Immunoglobulin Genes Assemble by
Recombination
1014
26.1
DN
А
-Dependent Synthesis of
RNÂ
1022
RNA
Is Synthesized by
RNA
Polymerases
1022
RNA
Synthesis Begins at Promoters
1025
Box
26-1
Methods:
RNA Polymerase
Leaves Its
Footprint on a Promoter
1026
Transcription Is Regulated at Several Levels
1028
Specific Sequences Signal Termination of
RNA
Synthesis
1029
Eukaryotic Cells Have Three Kinds of Nuclear
RNA
Polymerases
1030
RNA
Polymerase II Requires Many Other
Protein Factors for Its Activity
1030
DNA-Dependent
RNA
Polymerase
Undergoes Selective Inhibition
1033
26.2
RNA
Processing
1033
Eukaryotic mRNAs Are Capped at the
5'
End
1034
Both
Introns
and Exons Are Transcribed from
DNA
into
RNA
1035
RNA
Catalyzes the Splicing of
Introns
1036
Eukaryotic mRNAs Have a Distinctive
3'
End Structure
1039
A Gene Can Give Rise to Multiple Products by
Differential
RNA
Processing
1040
|xxviiïj
Contents
Ribosomal RNAs and tRNAs
Also
Undergo
Processing
1042
Special-Function RNAs Undergo Several
Types of Processing
1045
RNA
Enzymes Are the Catalysts of Some
Events in
RNA
Metabolism
1045
Cellular mRNAs Are Degraded at Different Rates
1048
Polynucleotide Phosphorylase Makes Random
RNA-like Polymers
1049
26.3
RNA-Dependent Synthesis of RMA and
DNA 1050
Reverse Transcriptase Produces
DNA
from
Viral
RNA
1050
Some Retroviruses Cause Cancer and AIDS
1051
Many
Transposons,
Retroviruses, and
Introns
May Have a Common Evolutionary Origin
1052
Box
26-2
Medicine: Fighting AIDS with Inhibitors of
HIV
Reverse Transcriptase
1053
Telomerase Is a Specialized Reverse Transcriptase
1053
Some Viral RNAs Are Replicated by
Stage
5:
Newly Synthesized Polypeptide Chains
Undergo Folding and Processing
Protein Synthesis Is Inhibited by Many
Antibiotics and Toxins
1096
1098
RNA-Dependent
RNA Polymerase
RNA
Synthesis Offers Important Clues to
Biochemical Evolution
Box
26-3
Methods: The SELEX Method for Generating
RNA
Polymers with New Functions
Box
26-4
An Expanding
RNA
Universe Filled with
TUF
RNAs
1056
1056
1058
1060
27.1
The Genetic Code
The Genetic Code Was Cracked Using Artificial
mRNA Templates
Box
27-1
Exceptions That Prove the Rule:
Natural Variations in the Genetic Code
Wobble Allows Some tRNAs to Recognize
More than One Codon
Translational Frameshifting and
RNA
Editing
Affect How the Code Is Read
27.2
Protein Synthesis
Protein Biosynthesis Takes Place in Five Stages
The Ribosome Is a Complex Supramolecular
Machine
Box
27-2
From an
RNA
World to a Protein World
Transfer RNAs Have Characteristic
Structural Features
Stage
1:
Aminoacyl-tRNA Synthetases Attach the
Correct
Amino
Acids to Their tRNAs
Box
27-3
Natural and Unnatural Expansion of the
Genetic Code
Stage
2:
À
Specific
Amino
Acid Initiates
Protein Synthesis
Stage
3:
Peptide
Bonds Are Formed in the
Elongation Stage
Box
27-4
Induced Variation in the Genetic Code:
Nonsense Suppression
Stage
4:
Termination of Polypeptiae Synthesis
Requires a Special Signal
1065
1066
1070
1070
1072
1075
1075
1076
1078
1079
1081
1085
1088
1091
1094
1094
Posttranslational Modification of Many
Eukaryotic Proteins Begins in the
Endoplasmic Reticulum
Glycosylation Plays a Key Role in
Protein Targeting
Signal Sequences for Nuclear Transport Are,
Not Cleaved
Bacteria Also Use Signal Sequences for
Protein Targeting
Cells Import Proteins by Receptor-Mediated
Endocytosis
Protein Degradation Is Mediated by Specialized
Systems in All Cells
1100
1101
1104
1104
1106
1107
28.1
Principies
of Gene Regulation
1116
RNA
Polymerase Binds to
DNA
at Promoters
1116
Transcription Initiation Is Regulated by Proteins
That Bind to or near Promoters
1117
Many Bacterial Genes Are Clustered and
Regulated in
Opérons
1118
The lac Operon Is Subject to Negative Regulation
1119
Regulatory Proteins Have Discrete DNA-Binding
Domains
1121
Regulatory Proteins Also Have Protein-Protein
Interaction Domains
1124
28.2
Regulation of Gene
Expression
in Bacteria
1126
The lac Operon Undergoes Positive Regulation
1126
Many Genes for
Amino
Acid Biosynthetic Enzymes
Are Regulated by Transcription Attenuation
1127
Induction of the SOS Response Requires
Destruction of
Repressor
Proteins
1130
Synthesis of Ribosomal Proteins Is Coordinated
with rRNA Synthesis
1131
The Function of Some mRNAs Is Regulated by
Small RNAs in
Cis
or in Trans
1132
Some Genes Are Regulated by
Genetic Recombination
1134
28.3
Regulation of Gene Expression in Eukaryotes
1136
TranscriptionaQy Active Chramatin Is Structurally
Distinct from Inactive Chromatin
1136
Chramatin Is Remodeled by Acetylation and
Nucleosomal Displacement/Repositioning
1137
Many Eukaryotic Promoters Are
Positively Regulated
1138
DNA-Binding Activators and Coactivators
Facilitate Assembly of the General
Transcription Factors
П38
The Genes of
Galactose
Metabolism in Yeast
Are Subject to Both Positive and Negative
Regulation
1141
Transcription Activators Have a Modular Structure
1142
Contents
Eukaryotic Gene Expression
Can Be Regulated by
Appendix
A Common Abbreviations in the
Intercellular and Mracellular Signals
1143
Biochemical Research Literature A-1
Regulation Can Result from Phosphorylation of
,. , , . „ , ,
Nuclear Inscription Factors
1144
Appendix
В
Abbreviated Solutions to Problems AS-1
Many Eukaryotic mRNAs Are Subject to Glossary G-
?
Translational Repression
1144
Credits C-l
Posttranscriptional Gene
Süencing
Is Mediated by Indpx I
1
RNA
Interference
1145
RNA-Mediated Regulation of Gene Expression
Takes Many Forms in Eukaryotes
1146
Development Is Controlled by Cascades of
Regulatory Proteins
1146
Box
28-1
Of Fins, Wings, Beaks, and Things
1152 |
| any_adam_object | 1 |
| any_adam_object_boolean | 1 |
| author | Nelson, David L. 1942- Cox, Michael M. |
| author_GND | (DE-588)133943070 (DE-588)113617615 (DE-588)132539519 |
| author_facet | Nelson, David L. 1942- Cox, Michael M. |
| author_role | aut aut |
| author_sort | Nelson, David L. 1942- |
| author_variant | d l n dl dln m m c mm mmc |
| building | Verbundindex |
| bvnumber | BV023260737 |
| callnumber-first | Q - Science |
| callnumber-label | QD415 |
| callnumber-raw | QD415 |
| callnumber-search | QD415 |
| callnumber-sort | QD 3415 |
| callnumber-subject | QD - Chemistry |
| classification_rvk | WD 4000 WD 4010 |
| classification_tum | CHE 800f |
| ctrlnum | (OCoLC)254583916 (DE-599)BVBBV023260737 |
| dewey-full | 572 |
| dewey-hundreds | 500 - Natural sciences and mathematics |
| dewey-ones | 572 - Biochemistry |
| dewey-raw | 572 |
| dewey-search | 572 |
| dewey-sort | 3572 |
| dewey-tens | 570 - Biology |
| discipline | Biologie Chemie |
| discipline_str_mv | Biologie Chemie |
| edition | 5. ed., 1. print. |
| format | Book |
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| genre | (DE-588)4123623-3 Lehrbuch gnd-content |
| genre_facet | Lehrbuch |
| id | DE-604.BV023260737 |
| illustrated | Illustrated |
| index_date | 2024-07-02T20:31:55Z |
| indexdate | 2024-11-25T17:26:05Z |
| institution | BVB |
| isbn | 9781429208925 9780716771081 071677108X |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-016445946 |
| oclc_num | 254583916 |
| open_access_boolean | |
| owner | DE-20 DE-355 DE-BY-UBR DE-29T DE-19 DE-BY-UBM DE-703 DE-M49 DE-BY-TUM DE-83 DE-91G DE-BY-TUM |
| owner_facet | DE-20 DE-355 DE-BY-UBR DE-29T DE-19 DE-BY-UBM DE-703 DE-M49 DE-BY-TUM DE-83 DE-91G DE-BY-TUM |
| physical | Getr. Zählung Ill., graph. Darst. |
| publishDate | 2008 |
| publishDateSearch | 2008 |
| publishDateSort | 2008 |
| publisher | Freeman |
| record_format | marc |
| spellingShingle | Nelson, David L. 1942- Cox, Michael M. Lehninger principles of biochemistry Biochemie - Lehrbuch Biochemistry Biochemie (DE-588)4006777-4 gnd Physiologische Chemie (DE-588)4076124-1 gnd CD-ROM (DE-588)4139307-7 gnd |
| subject_GND | (DE-588)4006777-4 (DE-588)4076124-1 (DE-588)4139307-7 (DE-588)4123623-3 |
| title | Lehninger principles of biochemistry |
| title_alt | Principles of biochemistry |
| title_auth | Lehninger principles of biochemistry |
| title_exact_search | Lehninger principles of biochemistry |
| title_exact_search_txtP | Lehninger principles of biochemistry |
| title_full | Lehninger principles of biochemistry David L. Nelson ; Michael M. Cox |
| title_fullStr | Lehninger principles of biochemistry David L. Nelson ; Michael M. Cox |
| title_full_unstemmed | Lehninger principles of biochemistry David L. Nelson ; Michael M. Cox |
| title_short | Lehninger principles of biochemistry |
| title_sort | lehninger principles of biochemistry |
| topic | Biochemie - Lehrbuch Biochemistry Biochemie (DE-588)4006777-4 gnd Physiologische Chemie (DE-588)4076124-1 gnd CD-ROM (DE-588)4139307-7 gnd |
| topic_facet | Biochemie - Lehrbuch Biochemistry Biochemie Physiologische Chemie CD-ROM Lehrbuch |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=016445946&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
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