THIRD EDITIO N

Principles of Biochemistr y

David L Nelso n

Michael M . Cox

Preface ii i

I Foundations of Biochemistry 11

The Molecular Logic of Life 3

2 Cells 20

3 Biomolecules 53

4 Water 82

II Structure and Catalysis 11 35

Amino Acids, Peptides, and Proteins 11 5

6 The Three-Dimensional Structure of Proteins 15 9

7

Protein Function 203

8 Enzymes 243

9 Carbohydrates and Glycobiology 29 3

10

Nucleotides and Nucleic Acids 32 5

11

Lipids 36 3

12

Biological Membranes and Transport 38 9

13

Biosignaling 43 7

III Bioenergetics and Metabolism 48 514

Principles of Bioenergetics 49 0

15 Glycolysis and the Catabolism of Hexoses 52 7

16 The Citric Acid Cycle 567

17 Oxidation of Fatty Acids 59 8

18 Amino Acid Oxidation and the Production of Urea 62 3

19 Oxidative Phosphorylation and Photophosphorylation 65 9

20 Carbohydrate Biosynthesis 72 2

21

Lipid Biosynthesis 770

22

Biosynthesis of Amino Acids, Nucleotides, and Related Molecules 81 8

23

Integration and Hormonal Regulation of Mammalian Metabolism 86 9

IV Information Pathways 90 524 Genes and Chromosomes 90 7

25 DNA Metabolism 93 1

26 RNA Metabolism 97 9

27 Protein Metabolism 102 0

28 Regulation of Gene Expression 107 2

29 Recombinant DNA Technology 111 9

Appendix A Common Abbreviations in the Biochemical Research Literature AP- 1

Appendix B Abbreviated Solutions to Problems AP- 4Glossary G- 1

Illustration Credits IC- 1Index I-1

Preface iii

Major Structural Features of Eukaryotic Cells 2 9The Plasma Membrane Contains Transporters and Receptors 3 0

Foundations of Biochemistry

1

Endocytosis and Exocytosis Carry Traffic across the PlasmaMembrane 3 1

1 The Molecular Logic of Life 3

The Endoplasmic Reticulum Organizes the Synthesis of Proteins andLipids 32

The Chemical Unity of Diverse Living Organisms 3

The Golgi Complex Processes and Sorts Proteins 3 3Biochemistry Explains Diverse Forms of Life in Unifying Chemical

Lyosomes Are the Sites of Degradative Reactions 3 3Terms 4

Vacuoles of Plant Cells Play Several Important Roles 3 4All Macromolecules Are Constructed from a Few Simple

Peroxisomes Destroy Hydrogen Peroxide, and Glyoxysomes Conver tCompounds 5 Fats to Carbohydrates 34Energy Production and Consumption in Metabolism 6

The Nucleus Contains the Genome 35Organisms Are Never at Equilibrium with Their Surroundings 6

Mitochondria Are the Power Plants of Aerobic Eukaryoti cMolecular Composition Reflects a Dynamic Steady State 6

Cells 3 6Organisms Transform Energy and Matter from Their

Chloroplasts Convert Solar Energy into Chemical Energy 3 7Surroundings 7

Mitochondria and Chloroplasts Probably Evolved fro mThe Flow of Electrons Provides Energy for Organisms 8

Endosymbiotic Bacteria 3 8Energy Coupling Links Reactions in Biology 9

The Cytoskeleton Stabilizes Cell Shape, Organizes the Cytoplasm ,Enzymes Promote Sequences of Chemical Reactions 11

and Produces Motion 3 9

Metabolism Is Regulated to Achieve Balance and Economy 12

The Cytoplasm Is Crowded, Highly Ordered, and Dynamic 4 2

Biological Information Transfer 13

Study of Cellular Components 42

Genetic Continuity Is Vested in DNA Molecules 13

Organelles Can Be Isolated by Centrifugation 42

The Structure of DNA Allows for Its Repair and Replication with

In Vitro Studies May Overlook Important Interactions amon gNear-Perfect Fidelity 14

Molecules 4 2

Changes in the Hereditary Instructions Allow Evolution 14

Evolution of Multicellular Organisms and Cellula rMolecular Anatomy Reveals Evolutionary Relationships 15

Differentiation 44The Linear Sequence in DNA Encodes Proteins with Three-

Viruses : Parasites of Cells 4 6Dimensional Structures 1 6

Noncovalent Interactions Stabilize Three-Dimensional

Summary 48

Further Reading 49

Problems 5 0Structures 1 7

The Physical Roots of the Biochemical World 1 8

Further Reading 19

v. 1

2 Cells 20

>sh~ a

> s~

ti:

Cellular Dimensions 21 A a

I1

n

Cells and Tissues Used in Biochemical Studies 22

v

f:

`-' {

Evolution and Structure of Prokaryotic Cells 24

+

,=:&rEscherichia co/i Is the Best-Studied Prokaryotic Cell 26

i -, ,

\ 12,-N'./iEvolution of Eukaryotic Cells 27

~i`, < y

1 \

Yom: _

Eukaryotic Cells Evolved from Prokaryotes in Several Stages 28

"

lIL 'Early Eukaryotic Cells Gave Rise to Diverse Protists 29

page 13

4 Water 82.y.

Weak Interactions in Aqueous Systems 8 2tit. Hydrogen Bonding Gives Water Its Unusual Properties 8 2

Water Forms Hydrogen Bonds with Polar Solutes 8 5

Water Interacts Electrostatically with Charged Solutes 8 6

Entropy Increases as Crystalline Substances Dissolve 8 7

•

Nonpolar Gases Are Poorly Soluble in Water 8 8

Nonpolar Compounds Force Energetically Unfavorable Changes i nt.?3 the Structure of Water 8 8

Van der Waals Interactions Are Weak Interatomic Attractions 9 0

page 62

Weak Interactions Are Crucial to Macromolecular Structure an dFunction 90

Solutes Affect the Colligative Properties of Aqueous Solutions 9 2

Box 4-1 Touch Response in Plants: An Osmotic Event 9 4

Ionization of Water, Weak Acids, and Weak Bases 9 5

3 Biomolecules 53

Pure Water Is Slightly Ionized 95

The Ionization of Water Is Expressed by an EquilibriumChemical Composition and Bonding 53

Constant 9 6Biomolecules Are Compounds of Carbon 54

Box 4-2 The /on Product of Water: Two IllustrativeFunctional Groups Determine Chemical Properties 56

Problems 9 7

Three-Dimensional Structure : Configuration and

The pH Scale Designates the H + and OH- Concentrations 97

Conformation 57

Weak Acids and Bases Have Characteristic Dissociatio n

The Configuration of a Molecule Is Changed Only by Breaking a

Constants 98

Bond 58

Titration Curves Reveal the pK a of Weak Acids 9 9

Molecular Conformation Is Changed by Rotation About Single

Buffering against pH Changes in Biological Systems 10 1Bonds 60

Buffers Are Mixtures of Weak Acids and Their ConjugateBox 3-1 Louis Pasteur and Optical Activity: In Vino, Veritas 61

Bases 102Configuration and Conformation Define Biomolecular

A Simple Expression Relates pH, pK, and Buffe rStructures 62

Concentration 10 2Interactions between Biomolecules Are Stereospecific 63

Box 4-3 Solving Problems Using the Henderson-Hasselbalc h

Chemical Reactivity 64

Equation 103

Bond Strength Is Related to the Properties of the Bonded

Weak Acids or Bases Buffer Cells and Tissues against p H

Atoms 64

Changes 104

Five General Types of Chemical Transformations Occur in

n Box 4-4 Blood, Lungs, and Buffer: The Bicarbonate Buffer

Cells 65

System 105

All Oxidation-Reduction Reactions Involve Electron Transfer 65

Water as a Reactant 10 6Carbon-Carbon Bonds Are Cleaved and Formed by Nucleophili c

Substitution Reactions 66

The Fitness of the Aqueous Environment for Living

Electron Transfers within a Molecule Produce Internal

Organisms 107

Rearrangements 67

Summary 107

Further Reading 10 8

Group Transfer Reactions Activate Metabolic Intermediates 68

Problems 109

Biopolymers Are Formed by Condensations 6 9

Macromolecules and Their Monomeric Subunits 69

II Structure and Catalysis 11 3Macromolecules Are the Major Constituents of Cells 6 9

Macromolecules Are Composed of Monomeric Subunits 70

5 Amino Acids, Peptides, and Proteins 11 5

Monomeric Subunits Have Simple Structures 70

Amino Acids 11 6

Subunit Condensation Creates Order and Requires Energy 72

Amino Acids Share Common Structural Features 11 6

Cells Have a Structural Hierarchy 72

The Amino Acid Residues in Proteins Are L Stereoisomers 11 7

Prebiotic Evolution 74

Amino Acids Can Be Classified by R Group 11 8. Box 5-1 Absorption of Light by Molecules : The Lambert-Bee r

Biomolecules First Arose by Chemical Evolution 74

Law 12 1Chemical Evolution Can Be Simulated in the Laboratory 7 4

RNA or Related Precursors May Have Been the First Genes and

Nonstandard Amino Acids Also Have Important Functions 12 1

Catalysts 75

Amino Acids Can Act as Acids and Bases 12 3

Biological Evolution Began More Than Three and a Half Billion

Amino Acids Have Characteristic Titration Curves 12 3

Years Ago 76

Titration Curves Predict the Electric Charge of Amino Acids 125

Summary 78

Further Reading 78

Amino Acids Differ in Their Acid-Base Properties 12 5

Problems 80

Peptides and Proteins 126

Peptides Are Chains of Amino Acids 126

Protein Motifs Are the Basis for Protein Structura l

Peptides Can Be Distinguished by Their Ionization Behavior 127

Classification 18 5

Biologically Active Peptides and Polypeptides Occur in a Vast

Protein Quaternary Structures Range from Simple Dimers to Larg e

Range of Sizes 127

Complexes 18 8

Polypeptides Have Characteristic Amino Acid Compositions 128

There Are Limits to the Size of Proteins 19 1

Some Proteins Contain Chemical Groups Other Than Amino

Protein Denaturation and Folding 19 1Acids 129

Loss of Protein Structure Results in Loss of Function 192There Are Several Levels of Protein Structure 129

Amino Acid Sequence Determines Tertiary Structure 19 2

Working with Proteins 130

Polypeptides Fold Rapidly by a Stepwise Process 19 3

Proteins Can Be Separated and Purified 130

* Box 6-4 Death by Misfolding: The Prion Diseases 196

Proteins Can Be Separated and Characterized

Some Proteins Undergo Assisted Folding 19 6by Electrophoresis 13 4

Unseparated Proteins Can Be Quantified 136

Summary 199

Further Reading 200Problems 200

The Covalent Structure of Proteins 13 7

The Function of a Protein Depends on Its Amino Acid

7 Protein Function 203Sequence 13 8

The Amino Acid Sequences of Numerous Proteins Have Been

Reversible Binding of a Protein to a Ligand : Oxygen-Bindin g

Determined 138

Proteins 204

• Box 5-2 Protein Homology among Species 139 Oxygen Can Be Bound to a Herne Prosthetic Group 20 4

Short Polypeptides Are Sequenced Using Automated

Myoglobin Has a Single Binding Site for Oxygen 20 6

Procedures 141

Protein-Ligand Interactions Can Be Described Quantitatively 20 6

Large Proteins Must Be Sequenced in Smaller Segments 142

Protein Structure Affects How Ligands Bind 20 9

Amino Acid Sequences Can Also Be Deduced by Other

Oxygen Is Transported in Blood by Hemoglobin 21 0Methods 145

Hemoglobin Subunits Are Structurally Similar to Myoglobin 21 0Box 5-3 Investigating Proteins with Mass Spectrometry 146

Hemoglobin Undergoes a Structural Change on Bindin gAmino Acid Sequences Provide Important Biochemical

Oxygen 21 2Information 150

Hemoglobin Binds Oxygen Cooperatively 214Small Peptides and Proteins Can Be Chemically Synthesized 150

Cooperative Ligand Binding Can Be Described Quantitatively 21 5

Summary 152

Further Reading 153

Two Models Suggest Mechanisms for Cooperative Binding 21 5

Problems 154

Hemoglobin Also Transports H ' and C0 2 216Oxygen Binding to Hemoglobin Is Regulated by

2,3-Bisphosphoglycerate 21 86 The Three-Dimensional Structure of Proteins 159

Sickle-Cell Anemia Is a Molecular Disease of Hemoglobin 21 9Overview of Protein Structure 159

A Protein's Conformation Is Stabilized Largely by Weak

Complementary Interactions between Proteins and Ligands :The Immune System and Immunoglobulins 22 1

Interactions 160

The Immune Response Features a Specialized Array of Cells andThe Peptide Bond Is Rigid and Planar 161

Proteins 22 2

Protein Secondary Structure 163

Self Is Distinguished from Nonself by the Display of Peptides o nThe a Helix Is a Common Protein Secondary Structure 163

Cell Surfaces 223

• Box 6-1 Knowing the Right Hand from the Left 165 Molecular Interactions at Cell Surfaces Trigger the Immun e

Amino Acid Sequence Affects a Helix Stability 165

Response 22 5

The ß Conformation Organizes Polypeptide Chains into

Antibodies Have Two Identical Antigen Binding Sites 228

Sheets 166

ß Turns Are Common in Proteins 16 8

Common Secondary Structures Have Characteristic Bond Anglesand Amino Acid Content 16 9

Protein Tertiary and Quaternary Structures 170

Aa. 'IfFibrous Proteins Are Adapted for a Structural Function 170

%AO! }

• Box 6-2 Permanent Waving Is Biochemical Engineering 172 ,Structural Diversity Reflects Functional Diversity in Globula r

Proteins 175

Myoglobin Provided Early Clues about the Complexity of GlobularProtein Structure 17 5

• Box 6-3 Methods for Determining the Three-Dimensiona lStructure of a Protein 178

Globular Proteins Have a Variety of Tertiary Structures 18 2

Analysis of Many Globular Proteins Reveals Common Structural

page 20 9

Patterns 183

Antibodies Bind Tightly and Specifically to Antigen 230

• Box 8-2 Kinetic Tests for Determining InhibitionThe Antibody-Antigen Interaction Is the Basis for a Variety of

Mechanisms 26 7Important Analytical Procedures 231

Irreversible Inhibition Is an Important Tool in Enzyme Researc hand Pharmacology 26 8

Protein Interactions Modulated by Chemical Energy : Actin,

Enzyme Activity Is Affected by pH 26 9Myosin, and Molecular Motors 23 3The Major Proteins of Muscle Are Myosin and Actin 233

Examples of Enzymatic Reactions 26 9Additional Proteins Organize the Thin and Thick Filaments into

x Box 8-3 Evidence for Enzyme-Transition StateOrdered Structures 235

Complementarity 27 0Myosin Thick Filaments Slide along Actin Thin Filaments 237

Reaction Mechanisms Illustrate Principles 27 2

Summary 238

Further Reading 239

Regulatory Enzymes 278Problems 240

Allosteric Enzymes Undergo Conformational Changes in Respons eto Modulator Binding 27 8

8 Enzymes 243

The Regulatory Step in Many Pathways Is Catalyzed by a nAn Introduction to Enzymes 244

Allosteric Enzyme 28 0Most Enzymes Are Proteins 244

The Kinetic Properties of Allosteric Enzymes Diverge fro mEnzymes Are Classified by the Reactions They Catalyze 246

Michaelis Menten Behavior 280Some Regulatory Enzymes Undergo Reversible Covalen t

How Enzymes Work 246

Modification 28 1Enzymes Affect Reaction Rates, Not Equilibria 247

Phosphoryl Groups Affect the Structure and Catalytic Activity ofReaction Rates and Equilibria Have Precise Thermodynamic

Proteins 28 2Definitions 249

Multiple Phosphorylations Allow Exquisite Regulator yA Few Principles Explain the Catalytic Power and Specificity of

Control 28 4Enzymes 250

Some Types of Regulation Require Proteolytic Cleavage of a nWeak Interactions between Enzyme and Substrate Are Optimized

Enzyme Precursor 28 6in the Transition State 251

Some Regulatory Enzymes Use Multiple Regulator yBinding Energy Contributes to Reaction Specificity and

Mechanisms 28 7Catalysis 253

Summary 288

Further Reading 289Specific Catalytic Groups Contribute to Catalysis 255

Problems 29 0Enzyme Kinetics As an Approach to Understanding

Mechanism 257

9 Carbohydrates and Glycobiology 29 3Substrate Concentration Affects the Rate of Enzyme-Catalyzed

Monosaccharides and Disaccharides 294Reactions 257

The Two Families of Monosaccharides Are Aldoses an dThe Relationship between Substrate Concentration and Reaction

Ketoses 294Rate Can Be Expressed Quantitatively 259

Monosaccharides Have Asymmetric Centers 29 5n Box 8-1 Transformations of the Michaelis-Menten Equation : The

The Common Monosaccharides Have Cyclic Structures 297Double-Reciprocal Plot 26 1Kinetic Parameters Are Used to Compare Enzyme Activities 261

Organisms Contain a Variety of Hexose Derivatives 299

Many Enzymes Catalyze Reactions with Two or More

Monosaccharides Are Reducing Agents 30 1

Substrates 264

Disaccharides Contain a Glycosidic Bond 30 1

Pre-Steady State Kinetics Can Provide Evidence for Specific

Polysaccharides 30 3Reaction Steps 265

Starch and Glycogen Are Stored Fuels 30 4Enzymes Are Subject to Inhibition 265

Cellulose and Chitin Are Structural Homopolysaccharides 30 6Reversible Inhibition Can Be Competitive, Uncompetitive, or

Bacterial Cell Walls Contain Peptidoglycans 307Mixed 266

Glycosaminoglycans Are Components of the Extracellula rMatrix 308

Glycoconjugates: Proteoglycans, Glycoproteins, an dGlycolipids 31 1

lb"

Proteoglycans Are Glycosaminoglycan-Containing Macromolecule s•,~

of the Cell Surface and Extracellular Matrix 31 1f r

,06 ,~: .

'

Glycoproteins Are Information-Rich Conjugates Containing

~

Oligosaccharides 31 3~Glycolipids and Lipopolysaccharides Are Membran e

WIP , n,

Components 31 4I

Oligosaccharide-Lectin Interactions Mediate Many Biologica lProcesses 31 5

`4 Analysis of Carbohydrates 31 8k

Summary 320

Further Reading 32 1page 233

Problems 322

10 Nucleotides and Nucleic Acids 325 • •Some Basics 325

•

0O••

~•

i ••••-0 0

Nucleotides and Nucleic Acids Have Characteristic Bases and

•

Y

•

•i •

•• !•Pentoses 325

•

•00

Phosphodiester Bonds Link Successive Nucleotides in Nucleic

• •!~•!~ •!~ •!! 00400! •!N,•!! •!!!

00-

Acids 329

•i! •i!i •i!i •e!i •* •i!i • !i .iii •i!iThe Properties of Nucleotide Bases Affect the Three-Dimensional

S •ö!•0: 4 • 1 . • • i •g i •~~• •~~~ •iiiStructure of Nucleic Acids 331

+

• +~•

•4)

••

:

•

Nucleic Acid Structure 332

• •

•••e ••

• 5

••DNA Stores Genetic Information 333

••

•~••

••`•DNA Molecules Have Distinctive Base Compositions 334

page 41 1DNA Is a Double Helix 33 5DNA Can Occur in Different Three-Dimensional Forms 33 7Certain DNA Sequences Adopt Unusual Structures 33 9Messenger RNAs Code for Polypeptide Chains 341

Vitamins E and K and the Lipid Quinones Are Oxidation-Reductio nMany RNAs Have More Complex Three-Dimensional

Cofactors 38 2Structures 342

Dolichols Activate Sugar Precursors for Biosynthesis 38 2Nucleic Acid Chemistry 345

Separation and Analysis of Lipids 38 3Double-Helical DNA and RNA Can Be Denatured 34 5Nucleic Acids from Different Species Can Form Hybrids 347

Lipid Extraction Requires Organic Solvents 38 4Adsorption Chromatography Separates Lipids of Differen t

Nucleotides and Nucleic Acids Undergo Nonenzymatic

Polarity 384Transformations 348

Gas-Liquid Chromatography Resolves Mixtures of Volatile Lipi dSome Bases of DNA Are Methylated 351

Derivatives 385The Sequences of Long DNA Strands Can Be Determined 351

Specific Hydrolysis Aids in Determination of Lipid Structure 385The Chemical Synthesis of DNA Has Been Automated 354

Mass Spectrometry Reveals Complete Lipid Structure 386Other Functions of Nucleotides 354

Summary 386

Further Reading 387Nucleotides Carry Chemical Energy in Cells 354

Problems 388Adenine Nucleotides Are Components of Many Enzyme

Cofactors 356

12 Biological Membranes and Transport 38 9Some Nucleotides Are Regulatory Molecules 358

The Molecular Constituents of Membranes 39 0Summary 359

Further Reading 360

Each Type of Membrane Has Characteristic Lipids an dProblems 361

Proteins 39 0

11 Lipids 363

The Supramolecular Architecture of Membranes 39 1A Lipid Bilayer Is the Basic Structural Element o f

Storage Lipids 363

Membranes 39 2Fatty Acids Are Hydrocarbon Derivatives 363

Membrane Lipids Are in Constant Motion 394Triacylglycerols Are Fatty Acid Esters of Glycerol 366

Membrane Proteins Diffuse Laterally in the Bilayer 39 5Triacylglycerols Provide Stored Energy and Insulation 366

n Box 12-1 Looking at Membranes 396n Box 11-1 Sperm Whales: Fatheads of the Deep 367

Some Membrane Proteins Span the Lipid Bilayer 396Many Foods Contain Triacylglycerols 368

Peripheral Membrane Proteins Are Easily Solubilized 39 8Waxes Serve as Energy Stores and Water Repellents 368

Covalently Attached Lipids Anchor Some Peripheral Membran eStructural Lipids in Membranes 369

Proteins 40 0

Glycerophospholipids Are Derivatives of Phosphatidic Acid 369

Integral Proteins Are Held in the Membrane by Hydrophobi cInteractions with Lipids 400

Some Phospholipids Have Ether Linked Fatty Acids 371

The Topology of an Integral Membrane Protein Can Sometimes B eSphingolipids Are Derivatives of Sphingosine 372

Predicted from Its Sequence 40 2Sphingolipids at Cell Surfaces Are Sites of Biological

Integral Proteins Mediate Cell-Cell Interactions an dRecognition 373

Adhesion 40 4Phospholipids and Sphingolipids Are Degraded in Lysosomes 374

Membrane Fusion Is Central to Many Biological Processes 40 5n Box 11-2 Inherited Human Diseases Resulting from Abnorma l

Accumulations of Membrane Lipids 375

Solute Transport across Membranes 408Sterols Have Four Fused Carbon Rings 376

Passive Transport Is Facilitated by Membrane Proteins 40 8Aquaporins Form Hydrophilic Transmembrane Channels for th e

Lipids as Signals, Cofactors, and Pigments 376

Passage of Water 41 0Phosphatidylinositols Act as Intracellular Signals 377

The Glucose Transporter of Erythrocytes Mediates Passiv eEicosanoids Carry Messages to Nearby Cells 378

Transport 41 1Steroid Hormones Carry Messages between Tissues 379

Chloride and Bicarbonate Are Cotransported across the Erythrocyt eVitamins A and D Are Hormone Precursors 380

Membrane 413

The ß-Adrenergic Receptor Is Desensitized byQ

S

Phosphorylation 45 4

+

Cyclic AMP Acts as a Second Messenger for a Number o f10

•

Regulatory Molecules 45 4v-';=--

Two Second Messengers Are Derived fro m

0•"C I•ml

s‘ iL ,

t .3 wA

riot

Phosphatidylinositols 45 6

~i . mort fowl

y*la ;

~rt

Calcium Is a Second Messenger in Many Signa laril owl ti n 9 iI mpg Ion ion ! w

it slit

. Transductions 45 711'n

Oki 03r! 111r_ ,

laz*„Sensory Transduction in Vision, Olfaction, and Gustation 45 8

VI)

Light Hyperpolarizes Rod and Cone Cells of the Vertebrat eI_

Eye 458

page 418

Light Triggers Conformational Changes in the Recepto rRhodopsin 46 0

Excited Rhodopsin Acts through the G Protein Transducin t oReduce the cGMP Concentration 46 0

n Box 12-2 Defective Glucose and Water Transport in Two Forms

Signal Amplification Occurs in Rod and Cone Cells 46 0

of Diabetes 414

The Visual Signal Is Terminated Quickly 46 1

Active Transport Results in Solute Movement against a

Rhodopsin Is Desensitized by Phosphorylation 46 2

Concentration or Electrochemical Gradient 415

Cone Cells Specialize in Color Vision 46 2

There Are at Least Four General Types of Transport ATPases 416

n Box 13-2 Color Blindness: John Dalton's Experiment from

n Box 12-3 A Defective /on Channel Causes Cystic Fibrosis 418

the Grave 463

A P-Type ATPase Catalyzes Active Cotransport of Na'

Vertebrate Olfaction and Gustation Use Mechanisms Similar to th e

and K` 420

Visual System 46 3

ATP-Driven Ca' Pumps Maintain a Low Concentration of Calcium

G Protein-Coupled Serpentine Receptor Systems Share Severa l

in the Cytosol 421

Features 465

Ion Gradients Provide the Energy for Secondary Active

Disruption of G-Protein Signaling Causes Disease 46 6

Transport 422

Phosphorylation as a Regulatory Mechanism 467Ion Selective Channels Allow Rapid Movement of Ions across

Localization of Protein Kinases and Phosphatases Affects th eMembranes 424

Specificity for Target Proteins 46 7The Structure of a K ' Channel Shows the Basis for Its Io n

Specificity 424

Regulation of Transcription by Steroid Hormones 46 8

The Acetylcholine Receptor Is a Ligand-Gated Ion Channel 426

Regulation of the Cell Cycle by Protein Kinases 469The Neuronal Na' Channel Is a Voltage-Gated Ion Channel 428

The Cell Cycle Has Four Stages 46 9Ion-Channel Function Is Measured Electrically 429

Levels of Cyclin-Dependent Protein Kinases Oscillate 469Defective Ion Channels Can Have Striking Physiological

CDKs Regulate Cell Division by Phosphorylating Critica lConsequences 430

Proteins 47 3Porins Are Transmembrane Channels for Small Molecules 430

Oncogenes, Tumor Suppressor Genes, and Programmed Cel l

Summary 432

Further Reading 433

Death 474Problems 434

Oncogenes Are Mutant Forms of the Genes for Proteins tha tRegulate the Cell Cycle 47 4

13 Biosignaling 437

Defects in Tumor Suppressor Genes Remove Normal Restraints o n

Molecular Mechanisms of Signal Transduction 437

Cell Division 47 5

n Box 13-1 Scatchard Analysis Quantifies the Receptor-Ligand

Apoptosis Is Programmed Cell Suicide 476

Interaction 439

Summary 478

Further Reading 479

Gated Ion Channels 441

Problems 481

Ion Channels Underlie Electrical Signaling in Excitable Cells 44 1

The Nicotinic Acetylcholine Receptor Is a Ligand-Gated Ion

III Bioenergetics and Metabolism 485Channel 44 3

Voltage-Gated Ion Channels Produce Neuronal Action

14 Principles of Bioenergetics 490Potentials 444

Neurons Have Receptor Channels That Respond to a Variety of

Bioenergetics and Thermodynamics 491

Neurotransmitters 445

Biological Energy Transformations Obey the Laws ofThermodynamics 49 1

Receptor Enzymes 445

n Box 14-1 Entropy: The Advantages of Being Disorganized 492The Insulin Receptor Is a Tyrosine-Specific Protein Kinase 445

Cells Require Sources of Free Energy 49 3Guanylyl Cyclase Is a Receptor Enzyme That Generates the Second

The Standard Free-Energy Change Is Directly Related to th eMessenger cGMP 448

Equilibrium Constant 494G Protein-Coupled Receptors and Second Messengers 449

Actual Free-Energy Changes Depend on Reactant and Product

The ß-Adrenergic Receptor System Acts through the Second

Concentrations 49 6Messenger cAMP 449

Standard Free-Energy Changes Are Additive 498

Phosphoryl Group Transfers and ATP 499

Other Monosaccharides Enter the Glycolytic Pathway at Severa lThe Free-Energy Change for ATP Hydrolysis Is Large

Points 549and Negative 500

Dietary Polysaccharides and Disaccharides Are Hydrolyzed t on Box 14-2 The Free Energy of Hydrolysis of ATP within Cells: The

Monosaccharides 550

Real Cost of Doing Metabolic Business 501

Regulation of Carbohydrate Catabolism 55 1Other Phosphorylated Compounds and Thioesters Also Have Large

Regulatory Enzymes Act as Metabolic Valves 55 1Free Energies of Hydrolysis 502

Glycolysis and Gluconeogenesis Are Coordinately Regulated 553ATP Provides Energy by Group Transfers, Not by Simpl eHydrolysis 504

Phosphofructokinase-1 Is under Complex Allosteri cRegulation 554

ATP Donates Phosphoryl, Pyrophosphoryl, and Adenyly lGroups 506

Hexokinase Is Allosterically Inhibited by Its Reaction Product 555

Assembly of Informational Macromolecules Requires Energy 508

NI Box 15-3 Isozymes: Different Proteins, Same Reaction 556

ATP Energizes Active Transport and Muscle Contraction 508

Pyruvate Kinase Is Inhibited by ATP 556

• Box 14-3 Firefly Flashes: Glowing Reports of ATP 509

Glycogen Phosphorylase Is Regulated Allostericall y

Transphosphorylations between Nucleotides Occurand Hormonally 55 7

in All Cell Types 510

The Pentose Phosphate Pathway of Glucose Oxidation 55 8Inorganic Polyphosphate Is a Potential Phosphoryl

n Box 15-4 Glucose 6-Phosphate Dehydrogenase Deficiency:Group Donor 511

Why Pythagoras Wouldn't Eat Falafel 560

Biochemical and Chemical Equations Are Not Identical 511

Summary 561

Further Reading 56 2Biological Oxidation-Reduction Reactions 512

Problems 56 3The Flow of Electrons Can Do Biological Work 512

Oxidation-Reductions Can Be Described as Half-Reactions 513

16 The Citric Acid Cycle 56 7

Biological Oxidations Often Involve Dehydrogenation 514

Production of Acetate 568

Reduction Potentials Measure Affinity for Electrons 515

Pyruvate Is Oxidized to Acetyl-CoA and CO 2 568

Standard Reduction Potentials Can Be Used to Calculate the

The Pyruvate Dehydrogenase Complex Requires FiveFree-Energy Change 516

Coenzymes 569

Cellular Oxidation of Glucose to Carbon Dioxide Requires

The Pyruvate Dehydrogenase Complex Consists of Three Distinc tSpecialized Electron Carriers 517

Enzymes 570

A Few Types of Coenzymes and Proteins Serve as Universal

Intermediates Remain Bound to the Enzyme Surface 57 0

Electron Carriers 518

Reactions of the Citric Acid Cycle 57 1NADH and NADPH Act with Dehydrogenases as Soluble Electron

The Citric Acid Cycle Has Eight Steps 573Carriers 518 Box

Flavin Nucleotides Are Tightly Bound in Flavoproteins 520

•

16-1 Synthases and Synthetases ; Ligases and Lyases ;Kinases, Phosphatases, and Phosphorylases : Yes, the Names

Summary 522

Further Reading 523

Are Confusing! 576

Problems 524

The Energy of Oxidations in the Cycle Is EfficientlyConserved 579

15 Glycolysis and the Catabolism of Hexoses 527

n Box 16-2 Citrate: A Symmetrical Molecule That Reacts

Glycolysis 527

Asymmetrically 580

An Overview : Glycolysis Has Two Phases 528

Why Is the Oxidation of Acetate So Complicated? 58 1

The Preparatory Phase of Glycolysis Requires ATP 532

Citric Acid Cycle Components Are Important Biosyntheti c

The Payoff Phase of Glycolysis Produces ATP and NADH 535

Intermediates 583

•Overall Balance Sheet Shows a Net Gain of ATP 540

Box 16-3 Citrate Synthase, Soda Pop, and the Worl dThe Food Supply 583Intermediates Are Channeled between Glycolytic Enzymes 540

Anaplerotic Reactions Replenish Citric Acid Cycl eGlycolysis Is under Tight Regulation 541

Intermediates 584Glucose Catabolism Is Deranged in Cancerous Tissue 54 1

Fates of Pyruvate under Aerobic and AnaerobicConditions 542

Pyruvate Is the Terminal Electron Acceptor in Lactic Aci dFermentation 542

n Box 15-1 Glycolysis at Limiting Concentrations of Oxygen:Athletes, Alligators, and Coelacanths 543

n Box 15-2 Brewing Beer 544

'e:.

Ethanol Is the Reduced Product in Alcohol Fermentation 544

'`

$ +Thiamine Pyrophosphate Carries "Active Aldehyde" Groups 545

11 . 1Microbial Fermentations Yield Other End Products of Commercia l

Value 546,er

4 >

Feeder Pathways for Glycolysis 54 7Glycogen and Starch Are Degraded by Phosphorolysis 547

page 509

~''

Biotin in Pyruvate Carboxylase Carries CO 2 Groups 585

Extrahepatic Tissues Use Ketone Bodies as Fuels 61 7

Regulation of the Citric Acid Cycle 586

Ketone Bodies Are Overproduced in Diabetes and durin g

Production of Acetyl-CoA by the Pyruvate Dehydrogenase Complex

Starvation 61 7

Is Regulated by Allosteric and Covalent Mechanisms 586

Summary 618

Further Reading 61 9The Citric Acid Cycle Is Regulated at Its Three Exergonic

Problems 62 0Steps 58 7

The Glyoxylate Cycle 588

18 Amino Acid Oxidation and the Productio nThe Glyoxylate Cycle Produces Four-Carbon Compounds

of Urea 623from Acetate 589

Metabolic Fates of Amino Groups 62 4

The Citric Acid and Glyoxylate Cycles Are Coordinately

Dietary Protein Is Enzymatically Degraded to Amino Acids 62 6Regulated 590

Pyridoxal Phosphate Participates in the Transfer of a-Amin oGroups to a-Ketoglutarate 62 8

Summary 592

Further Reading 592Problems 594

n Box 18-1 Assays for Tissue Damage 63 1

Glutamate Releases Ammonia in the Liver 63 1

17 Oxidation of Fatty Acids 598

Glutamine Transports Ammonia in the Bloodstream 63 2

Digestion, Mobilization, and Transport of Fats 599

Alanine Transports Ammonia from Muscles to the Liver 63 2

Dietary Fats Are Absorbed in the Small Intestine 599

Ammonia Is Toxic to Animals 63 3

Hormones Trigger Mobilization of Stored Triacylglycerols 601

Nitrogen Excretion and the Urea Cycle 63 4

Fatty Acids Are Activated and Transported into

Urea Is Produced from Ammonia in Five Enzymatic Steps 63 5Mitochondria 602

The Citric Acid and Urea Cycles Can Be Linked 63 6

ß Oxidation 604

The Activity of the Urea Cycle Is Regulated at Two Levels 63 6

The ß Oxidation of Saturated Fatty Acids Has Four Basic

Pathway Interconnections Reduce the Energetic Cost of Urea

Steps 604

Synthesis 63 7

The Four Steps Are Repeated to Yield Acetyl-CoA and ATP 605

Genetic Defects in the Urea Cycle Can Be Life-Threatening 63 7

n Box 17-1 Fat Bears Carry Out ß Oxidation in Their Sleep 606

Natural Habitat Determines the Pathway for Nitroge n

Acetyl-CoA Can Be Further Oxidized in the Citric

Excretion 638

Acid Cycle 607

Pathways of Amino Acid Degradation 63 9

Oxidation of Unsaturated Fatty Acids Requires Two Additional

Several Enzyme Cofactors Play Important Roles in Amino Aci dReactions 607

Catabolism 640Complete Oxidation of Odd-Number Fatty Acids Requires Three

Ten Amino Acids Are Degraded to Acetyl-CoA 64 3Extra Reactions 608

Phenylalanine Catabolism Is Genetically Defective in Som en Box 17-2 Coenzyme 8 12 : A Radical Solution to a Perplexing

People 64 6Problem 610

Five Amino Acids Are Converted to a-Ketoglutarate 64 8Fatty Acid Oxidation Is Tightly Regulated 612

Four Amino Acids Are Converted to Succinyl-CoA 65 0Peroxisomes Also Carry Out ß Oxidation 612

Branched-Chain Amino Acids Are Not Degraded in the Liver 65 1Plant Peroxisomes and Glyoxysomes Use Acetyl-CoA from

n Box 18-2 Scientific Sleuths Solve a Murder Mystery 654ß Oxidation as a Biosynthetic Precursor 613

Asparagine and Aspartate Are Degraded to Oxaloacetate 653The ß-Oxidation Enzymes of Different Organelles Have Diverged

Some Amino Acids Can Be Converted to Glucose, Others to Keton eduring Evolution 614

Bodies 654Omega Oxidation Occurs in the Endoplasmic Reticulum 61 4

Genetic Defects in Fatty Acyl-CoA Dehydrogenases Cause Serious

Summary 654

Further Reading 655

Disease 615

Problems 65 6

Ketone Bodies 61 5

Ketone Bodies Formed in the Liver Are Exported to Other

19 Oxidative Phosphorylation an dOrgans 616

Photophosphorylation 65 9Oxidative Phosphorylation 66 0

Electon-Transfer Reactions in Mitochondria 66 0

,., .. "

Electrons Are Funneled to Universal Electron Acceptors 66 1

Electons Pass through a Series of Membrane-Bound Carriers 66 2

Electron Carriers Function in Multienzyme Complexes 66 6

44101

The Energy of Electron Transfer Is Efficiently Conserved in aProton Gradient 67 2ja:

9

6

Plant Mitochondria Have Alternative Mechanisms for Oxidizin g

w

NADH 673

n Box 19-1 Alternative Respiratory Pathways and Hot, Stinking

Plants 674

ATP Synthesis 67 5page 629

ATP Synthase Has Two Functional Domains, F e and F 1 678~jy

ATP Is Stabilized Relative to ADP on the Surface of F 1 678

ly

1r

r

p

The Proton Gradient Drives the Release of ATP from the Enzyme

r=

~ . .

Surface 679

, .

;

. .'

A i .Each ß Subunit of ATP Synthase Can Assume Three Different

;,

%

Conformations 680

f_

f

w ;

.1-Rotational Catalysis Is Key to the Binding-Change Mechanism for

: `=ter.

•. rATP Synthesis 682

v

'Chemiosmotic Coupling Allows Nonintegral Stoichiometries of 0 2

~ 'Consumption and ATP Synthesis 683

±~ =N C

'`The Proton-Motive Force Energizes Active Transport 68 4

Shuttle Systems Are Required for Mitochondrial Oxidation of

page 68 1Cytosolic NADH 68 5

Regulation of Oxidative Phosphorylation 68 6

Oxidative Phosphorylation Is Regulated by Cellula rEnergy Needs 68 7

Uncoupled Mitochondria in Brown Fat Produce Heat 687

20 Carbohydrate Biosynthesis 722ATP-Producing Pathways Are Coordinately Regulated 688

Gluconeogenesis 723Mutations in Mitochondria) Genes Cause Human Disease 688

Conversion of Pyruvate to Phosphoenolpyruvate Requires Tw oMitochondria Probably Evolved from Endosymbiotic Bacteria 690

Exergonic Reactions 72 6

Photosynthesis : Harvesting Light Energy 691

Conversion of Fructose 1,6-Bisphosphate to Fructose 6-Phosphat eIs the Second Bypass 72 8

General Features of Photophosphorylation 691

Conversion of Glucose 6-Phosphate to Free Glucose Is the Thir dPhotosynthesis in Plants Takes Place in Chloroplasts 692

Bypass 72 8Light Drives Electron Flow in Chloroplasts 692

Gluconeogenesis is Expensive 72 9

Light Absorption 693

Citric Acid Cycle Intermediates and Many Amino Acids Are

Chlorophylls Absorb Light Energy for Photosynthesis 693

Glucogenic 73 0

Accessory Pigments Extend the Range of Light Absorption 696

Futile Cycles in Carbohydrate Metabolism Consume ATP 73 0

Chlorophyll Funnels Absorbed Energy to Reaction Centers by

Gluconeogenesis and Glycolysis Are Reciprocally Regulated 73 1

Exciton Transfer 697

Gluconeogenesis Converts Fats and Proteins to Glucose i nGerminating Seeds 73 3

The Central Photochemical Event : Light-DrivenElectron Flow 699

Biosynthesis of Glycogen, Starch, Sucrose, and Othe r

Bacteria Have One of Two Types of Single Photochemical Reaction

Carbohydrates 735

LCenters 699

UDP-Glucose Is the Substrate for Glycogen Synthesis 73 6

Kinetic and Thermodynamic Factors Prevent Energy Dissipation by

Glycogen Synthase and Glycogen Phosphorylase Are Reciprocall y

Internal Conversion 702

Regulated 73 8

In Higher Plants, Two Reaction Centers Act in Tandem 702

ADP-Glucose Is the Substrate for Starch Synthesis in Plants an d

Spatial Separation of Photosystems I and II Prevents Exciton

Glycogen Synthesis in Bacteria 73 9

Larceny 705

UDP-Glucose Is the Substrate for Sucrose Synthesi s

The Cytochrome b6 f Complex Links Photosystems II and I 706

in Plants 74 1

Cyanobacteria Use the Cytochrome b 6 f Complex and Cytochrome c6

Lactose Synthesis Is Regulated in a Unique Way 74 2

in Both Oxidative Phosphorylation and

UDP-Glucose is an intermediate in the Formation of Glucuronat ePhotophosphorylation 706

and Vitamin C 74 3

Water Is Split by the Oxygen-Evolving Complex 707

Sugar Nucleotides Are Precursors in Bacterial Cell Wal lSynthesis 74 4

ATP Synthesis by Photophosphorylation 708

n Box 20-1 Penicillin and d-Lactamase : The Magic Bullet versu sA Proton Gradient Couples Electron Flow and Phosphorylation 708

the Bulletproof Vest 746The Approximate Stoichiometry of Photophosphorylation Has Bee n

Established 709

Photosynthetic Carbohydrate Synthesis 746

Cyclic Electron Flow Produces ATP but Not NADPH or 0 2 710

Carbon Dioxide Assimilation Occurs in Three Stages 74 8

The ATP Synthase of Chloroplasts Is Like That of

Each Triose Phosphate Synthesized from CO 2 Costs Six NADP H

Mitochondria 710

and Nine ATP 75 4

Chloroplasts Probably Evolved from Endosymbiotic

A Transport System Exports Triose Phosphates from the Chloroplas t

Cyanobacteria 711

and Imports Phosphate 75 5

Diverse Photosynthetic Organisms Use Hydrogen Donors Other

Regulation of Carbohydrate Metabolism in Plants 75 7Than Water 711

Rubisco Is Subject to Both Positive and Negative Regulation 75 7In Halophilic Bacteria, a Single Protein Absorbs Light and Pumps

Certain Enzymes of the Calvin Cycle Are Indirectly Activate dProtons to Drive ATP Synthesis 712

by Light 758

Summary 714

Further Reading 715

The Use of Triose Phosphates for Sucrose and Starch Synthesis Is

i 1Problems 718

Tightly Regulated in Plants 759

Plasmalogen Synthesis Requires Formation of an Ether-Linkedd

~.

'',I

Fatty Alcohol 79 6V. 1 ,

,,'

,

Sphingolipid and Glycerophospholipid Synthesis Share Precursor s,

1st)

'

and Some Mechanisms 798

,/' ,

Polar Lipids Are Targeted to Specific Cell Membranes 79 8

y .. .

' a",

Biosynthesis of Cholesterol, Steroids, and Isoprenoids 799,),„

-J>

,

Cholesterol Is Made from Acetyl-CoA in Four Stages 79 9*,'~iE

F

r

_

s ,' •'

Cholesterol Has Several Fates 804

Cholesterol and Other Lipids Are Carried on Plasm aLipoproteins 804

• Box 21-3 Apolipoprotein E Alleles Predict Incidence ofpage 805

Alzheimer's Disease 808

Cholesteryl Esters Enter Cells by Receptor-Mediate dEndocytosis 80 9

Cholesterol Biosynthesis Is Regulated by Several Factors 81 0

Photorespiration Results from Rubisco's Oxygenase Activity 760

Steroid Hormones Are Formed by Side Chain Cleavage an d

Some Plants Have a Mechanism to Minimize Photorespiration 761

Oxidation of Cholesterol 81 2

Summary 763

Further Reading 765

Intermediates in Cholesterol Biosynthesis Have Many Alternativ e

Problems 766

Fates 81 2

Summary 814

Further Reading 81521 Lipid Biosynthesis 770

Problems 816

Biosynthesis of Fatty Acids and Eicosanoids 770

22 Biosynthesis of Amino Acids, Nucleotides, an dMalonyl-CoA Is Formed from Acetyl-CoA and Bicarbonate 770

Related Molecules 81 8Fatty Acids Are Synthesized by a Repeating Reaction

Sequence 772

Overview of Nitrogen Metabolism 81 9

The Fatty Acid Synthase Complex Has Seven Different

The Nitrogen Cycle Maintains a Pool of Biologically Availabl e

Active Sites 772

Nitrogen 81 9

Fatty Acid Synthase Receives the Acetyl and Malonyl Groups 774

Nitrogen Is Fixed by Enzymes of the Nitrogenase Complex 82 0

The Fatty Acid Synthase Reactions Are Repeated to Form

Ammonia Is Incorporated into Biomolecules through Glutamat e

Palmitate 776

and Glutamine 823

The Fatty Acid Synthase of Some Organisms Is Composed of

Glutamine Synthetase Is a Primary Regulatory Point in Nitroge n

Multifunctional Proteins 777

Metabolism 824

Fatty Acid Synthesis Occurs in the Cytosol of Many Organisms but

Several Classes of Reactions Play Special Roles in th e

in the Chloroplasts of Plants 778

Biosynthesis of Amino Acids and Nucleotides 82 6

Acetate Is Shuttled out of Mitochondria as Citrate 779

Biosynthesis of Amino Acids 82 6Fatty Acid Biosynthesis Is Tightly Regulated 780

a-Ketoglutarate Gives Rise to Glutamate, Glutamine, Proline, an dLong-Chain Saturated Fatty Acids Are Synthesized from Palmitate

Arginine 829781

Serine, Glycine, and Cysteine Are Derived fro mSome Fatty Acids Are Desaturated 781

3-Phosphoglycerate 82 9

n

Box 21-1 Mixed-Function Oxidases, Oxygenases, and Three Nonessential and Six Essential Amino Acids Are Synthesized

Cytochrome P-450 782

from Oxaloacetate and Pyruvate 83 1

Eicosanoids Are Formed from 20-Carbon Polyunsaturated Fatty

Chorismate Is a Key Intermediate in the Synthesis of Tryptophan ,

Acids 784

Phenylalanine, and Tyrosine 83 4

n

Box 21-2 Cyclooxygenase lsozymes and the Search fora Better Histidine Biosynthesis Uses Precursors of Purin eAspirin : Relief is in (the Active) Site 786

Biosynthesis 83 9

Biosynthesis of Triacylglycerols 786

Amino Acid Biosynthesis Is under Allosteric Regulation 83 9

Triacylglycerols and Glycerophospholipids Are Synthesized from

Molecules Derived from Amino Acids 84 0the Same Precursors 788

Glycine Is a Precursor of Porphyrins 84 0Triacylglycerol Biosynthesis in Animals Is Regulated by

n Box 22-1 Biochemistry of Kings and Vampires 84 1Hormones 790

Degradation of Herne Yields Bile Pigments 84 2

Biosynthesis of Membrane Phospholipids 791

Amino Acids Are Required for the Biosynthesis of Creatine an d

There Are Two Strategies for Attaching Head Groups 791

Glutathione 842

Phospholipid Synthesis in E. coli Employs

a-Amino Acids Are Found Primarily in Bacteria 843

CDP-Diacylglycerol 792

Aromatic Amino Acids Are Precursors of Many Plan t

Eukaryotes Synthesize Anionic Phospholipids from CDP-

Substances 843

Diacylglycerol 794

Amino Acids Are Converted to Biological Amines b y

Eukaryotic Pathways to Phosphatidylserine,

Decarboxylation 84 4

Phosphatidylethanolamine, and Phosphatidylcholine Are

• Box 22-2 Curing African Sleeping Sickness with a Biochemica lInterrelated 794

Trojan Horse 846

Arginine Is the Precursor for Biological Synthesis of Nitric

IV Information Pathways

90 5Oxide 848

Biosynthesis and Degradation of Nucleotides 848

24 Genes and Chromosomes 907De Novo Purine Synthesis Begins with PRPP 849

Chromosomal Elements 90 8Purine Nucleotide Biosynthesis Is Regulated by Feedback

Genes Are Segments of DNA That Code for Polypeptide Chainsinhibition 852

and RNAs 908Pyrimidine Nucleotides Are Made from Aspartate, PRPP, and

Eukaryotic Chromosomes Are Very Complex 909Carbamoyl Phosphate 853

Many Eukaryotic Genes Contain Intervening Nontranscribe dPyrimidine Nucleotide Biosynthesis Is Regulated by Feedback

Sequences (Introns) 91 0Inhibition 85 5

Nucleoside Monophosphates Are Converted to Nucleoside

The Size and Sequence Structure of DNA Molecules 91 1

Triphosphates 855

Viral DNA Molecules Are Relatively Small 91 1

Ribonucleotides Are the Precursors of Deoxyribonucleotides 856

Bacteria Contain Chromosomes and Extrachromosomal DNA 91 2

Thymidylate Is Derived from dCDP and dUMP 860

Eukaryotic Cells Contain More DNA Than Do Prokaryotes 91 4

Degradation of Purines and Pyrimidines Produces Uric Acid and

Organelles of Eukaryotic Cells Also Contain DNA 91 5

Urea, Respectively 861

DNA Supercoiling 91 5Purine and Pyrimidine Bases Are Recycled by Salvage

Most Cellular DNA Is Underwound 91 7Pathways 86 2

Overproduction of Uric Acid Causes Gout 863

DNA Underwinding Is Defined by Topological Linkin gNumber 918

Many Chemotherapeutic Agents Target Enzymes in the Nucleotide

Topoisomerases Catalyze Changes in the Linking Numbe rBiosynthetic Pathways 863

of DNA 92 1Summary 865

Further Reading 866

DNA Compaction Requires a Special Form of Supercoiling 922Problems 867

Chromatin and Nucleoid Structure 92 3

23 Integration and Hormonal Regulation of

Histones Are Small, Basic Proteins 92 4

Mammalian Metabolism 869

Nucleosomes Are the Fundamental Organizational Units of

Tissue-Specific Metabolism : The Division of Labor 869

Chromatin 92 4

Nucleosomes Are Packed into Successively Higher-Orde rThe Liver Processes and Distributes Nutrients 870

Structures 92 6Adipose Tissue Stores and Supplies Fatty Acids 873

Bacterial DNA Is Also Highly Organized 92 7Muscle Uses ATP for Mechanical Work 874

The Brain Uses Energy for Transmission of Electrical

Summary 928

Further Reading 92 9

Impulses 876

Problems 930

Blood Carries Oxygen, Metabolites, and Hormones 877

25 DNA Metabolism 93 1Hormonal Regulation of Fuel Metabolism 878

A Word about Terminology 93 3Epinephrine Signals Impending Activity 87 8

Glucagon Signals Low Blood Glucose 879

DNA Replication 93 3

During Fasting and Starvation, Metabolism Shifts to Provide Fuel

DNA Replication Is Governed by a Set of Fundamenta lRules 933

for the Brain 880

Insulin Signals High Blood Glucose 882

DNA Is Degraded by Nucleases 93 6

Cortisol Signals Stress, Including Low Blood Glucose 882

DNA Is Synthesized by DNA Polymerases 936

!

Diabetes Is a Defect in Insulin Production or Action 883

Replication Is Very Accurate 938

E. col/ Has at Least Five DNA Polymerases 93 9Hormones: Diverse Structures for Diverse Functions 88 4

Hormone Discovery and Purification Requires a Bioassay 88 4

n Box 23-1 How is a Hormone Discovered? The Arduous Pathwayto Purified insulin 885

Hormones Act through Specific High-Affinity Cellula rReceptors 887

. :

Hormones Are Chemically Diverse 88 9

What Regulates the Regulators? 89 3

Long-Term Regulation of Body Mass 896

Leptin Was Predicted by the Lipostat Theory 896

Many Factors Regulate Feeding Behavior and Energ yExpenditure 898

Leptin Triggers a Regulatory Cascade 89 8

The Leptin System May Have Evolved to Regulate the Starvatio nResponse 89 9

Summary 900

Further Reading 90 1Problems 902

page 904

1

DNA Replication Requires Many Enzymes and

RNA Catalyzes Splicing 99 2Protein Factors 942

Eukaryotic mRNAs Undergo Additional Processing 99 7Replication of the E. coll Chromosome Proceeds in Stages 942

Multiple Products Are Derived from One Gene by Differential RN AReplication in Eukaryotic Cells Is More Complex 948

Processing 99 9

DNA Repair 949

Ribosomal RNAs and tRNAs Also Undergo Processing 1000

Mutations Are Linked to Cancer 949

Some Events in RNA Metabolism Are Catalyze d

All Cells Have Multiple DNA Repair Systems 950

by RNA Enzymes 1003

n Box 25-1 DNA Repair and Cancer 953

Cellular mRNAs Are Degraded at Different Rates 1005

The Interaction of Replication Forks with DNA Damage Leads to

Polynucleotide Phosphorylase Makes Random RNA-lik ePolymers 1006

Recombination or Error-Prone Repair 958

DNA Recombination 959

RNA-Dependent Synthesis of RNA and DNA 1007

Homologous Genetic Recombination Has Multiple Functions 960Reverse Transcriptase Produces DNA from Viral RNA 100 7

Recombination during Meiosis Is Initiated with Double-Strand

Retroviruses Cause Cancer and AIDS 100 9

Breaks 962

n Box 26-2 FightingA/DS with Inhibitors of H/V Reverse

Recombination Requires Specific Enzymes 963

Transcriptase 101 0

TAll Aspects of DNA Metabolism Come Together to Repair Stalled

Evolutionaryosons ,

Origi nRetrov i

101 0ruses, and Introns May Have a Commo n

Replication Forks 967Telomerase Is a Specialized Reverse Transcriptase 1012

Site-Specific Recombination Results in Precise DN ARearrangements 967

Some Viral RNAs Are Replicated by RNA-Directed RN A

Complete Chromosome Replication Can Require Site-Specific

Polymerase 101 3

Recombination 970

RNA Synthesis Offers Important Clues to Biochemica l

Transposable Genetic Elements Move from One LocationEvolution 101 4

to Another 970

Summary 1017

Further Reading 101 7Immunoglobulin Genes Are Assembled by Recombination 973

Problems 1019

Summary 975

Further Reading 976

27 Protein Metabolism 1020Problems 977

The Genetic Code 1020

26 RNA Metabolism 979

The Genetic Code Was Cracked Using Artificial mRN ATemplates 1022

DNA-Dependent Synthesis of RNA 980

n Box 27-1 Translational Frameshifting and RNA Editing : mRNAsRNA Is Synthesized by RNA Polymerases 980

That Change Horses in Midstream 1026RNA Synthesis Is Initiated at Promoters 983

Wobble Allows Some tRNAs to Recognize More tha nTranscription Is Regulated 984

One Codon 102 8n Box 26-1 RNA Polymerase Leaves Its Footprint on a

n Box 27-2 Natural Variations in the Genetic Code 1030Promoter 985

Overlapping Genes in Different Reading Frames Are Found i nSpecific Sequences Signal Termination of RNA Synthesis 986

Some Viral DNAs 1032Eukaryotic Cells Have Three Kinds of Nuclear RNA

Polymerases 986

Protein Synthesis 1034

RNA Polymerase II Requires Many Other Proteins for Its

The Ribosome Is a Complex Supramolecular Machine 1035

Activity 987

Transfer RNAs Have Characteristic Structural Features 1037

DNA-Dependent RNA Polymerase Can Be Selectively

Stage 1 : Aminoacyl-tRNA Synthetases Attach the Correct Amin oInhibited 990

Acids to Their tRNAs 1039

RNA Processing 990

Stage 2 : A Specific Amino Acid Initiates Protein Synthesis 1044

The Introns Transcribed into RNA Are Removed by Splicing 991

Stage 3 : Peptide Bonds Are Formed in the Elongation Stage 104 7Stage 4 : Termination of Polypeptide Synthesis Requires a Specia l

Signal 1050n Box 27-3 Induced Variation in the Genetic Code: Nonsense

Suppression 105 1§,~

Stage 5 : Newly Suppressed Polypeptide Chains Undergo Foldin gand Processing 1053

.' .'

kTl ,

Itir

'

Protein Synthesis Is Inhibited by Many Antibiotics an dA • ce

► ,

4

Toxins 1054i . : 11 1

r~~!►. T

4

Protein Targeting and Degradation 1056..:.r

IR

>

Posttranslational Modification of Many Eukaryotic Proteins Begin s')

b%

AA

F

in the Endoplasmic Reticulum 1057lwo'vi

Glycosylation Plays a Key Role in Protein Targeting 1058Ir

S ;

Proteins Are Targeted to Mitochondria and Chloroplasts by Simila rPathways 106 1

page 1043

Signal Sequences for Nuclear Transport Are Not Cleaved 1063

Bacteria Also Use Signal Sequences for Protein Targeting 106 4Cells Import Proteins by Receptor-Mediated Endocytosis 1065

_

.iw

ia.

Protein Degradation Is Mediated by Specialized Systems in All

.viv.Cells 1066

.-

dl►. .

Summary 1067

Further Reading 106 8Problems 1069

. ,1

28 Regulation of Gene Expression 107 2Principles of Gene Regulation 1074

,RNA Polymerase Binds to DNA at Promoters 107 4

Transcription Initiation Is Regulated by Proteins That Bin dto or near Promoters 1074

page 114 5Most Prokaryotic Genes Are Regulated in Units Called

Operons 107 7

The lac Operon Is Subject to Negative Regulation 1078

Regulatory Proteins Have Discrete DNA-Binding Domains 108 0

Regulatory Proteins Also Have Protein-Protein Interaction

Cloning Vectors Allow Amplification of Inserted DN ADomains 1084

Segments 1124

Regulation of Gene Expression in Prokaryotes 1085

Isolating a Gene from a Cellular Chromosome 112 8The /ac Operon Is Subject to Positive Regulation 1086

Cloning a Gene Often Requires a DNA Library 112 8The ara Operon Undergoes Both Positive and Negative Regulation

Specific DNA Sequences Can Be Amplified 112 9by a Single Regulatory Protein 1088

Hybridization Allows the Detection of Specific Sequences 113 1Many Genes for Amino Acid Biosynthesis Are Regulated by

n Box 29-1 A Potent Weapon in Forensic Medicine 1132Transcription Attenuation 1091

DNA Microarrays Provide Compact Libraries for Studying Gene sInduction of the SOS Response Requires the Destruction of

and Their Expression 113 4Repressor Proteins 109 4

Synthesis of Ribosomal Proteins Is Coordinated with rRNA

Applications of Recombinant DNA Technology 113 5

Synthesis 1095

Cloned Genes Can Be Expressed 113 5

Some Genes Are Regulated by Genetic Recombination 1097

Cloned Genes Can Be Altered 113 6

Regulation of Gene Expression in Eukaryotes 1099

Yeast Is an Important Eukaryotic Host for Recombinan tDNA 1138

Transcriptionally Active Chromatin Is Structurally Distinct from

Very Large DNA Segments Can Be Cloned in Yeast Artificia lInactive Chromatin 1100Chromosomes 113 8

Modifications Increase the Accessibility of DNA 1100

n Box 29-2 The Human Genome and Human Gene Therapy 1140Chromatin Is Remodeled by Acetylation and Nucleosomal

Cloning in Plants Is Aided by a Bacterial Plant Parasite 114 0Displacements 1100

Many Eukaryotic Promoters Are Positively Regulated 1101

Cloning in Animal Cells Points the Way to Human Gen eTherapy 114 5

DNA-Binding Transactivators and Coactivators Facilitate Assembly

Recombinant DNA Technology Yields New Product sof the General Transcription Factors 1102

and Choices 114 7Three Classes of Proteins Are Involved in Transcriptiona l

Activation 1102

Summary 1148

Further Reading 114 9

The Genes Required for Galactose Metabolism in Yeast Are

Problems 1150

Subject to Both Positive and Negative Regulation 110 4

DNA-Binding Transactivators Have a Modular Structure 1106

Appendix A Common Abbreviations in th e

Eukaryotic Gene Expression Can Be Regulated by Intercellular and

Biochemical Research Literature AP- 1Intracellular Signals 110 6

Regulation Can Occur through Phosphorylation of Nuclear

Appendix B Abbreviated Solutions to Problems AP- 4Transcription Factors 1108

Many Eukaryotic mRNAs Are Subject to Translational

Illustration Credits IC-1Repression 1108

Development Is Controlled by Cascades of Regulatory

Glossary G-1Proteins 1109

Index 1- 1Summary 1115

Further Reading 111 6Problems 1117

29 Recombinant DNA Technology 111 9DNA Cloning : The Basics 111 9

Restriction Endonucleases and DNA Ligase Yield Recombinan tDNA 1120