CONTENTS

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Preface

v

Part I THE MOLECULAR DESIGN OF LIFE

1

CHAPTER 1 Biochemistry: An Evolving Science

1

1.1 Biochemical Unity Underlies Biological Diversity

1

1.2 DNA Illustrates the Interplay Between Form and Function

4

 

DNA is constructed from four building blocks

4

 

Two single strands of DNA combine to form a double helix

5

 

DNA structure explains heredity and the storage of information

5

1.3 Concepts from Chemistry Explain the Properties of Biological Molecules

6

 

The formation of the DNA double helix as a key example

6

 

The double helix can form from its component strands

6

 

Covalent and noncovalent bonds are important for the structure and stability of biological molecules

6

 

The double helix is an expression of the rules of chemistry

9

 

The laws of thermodynamics govern the behavior of biochemical systems

10

 

Heat is released in the formation of the double helix

12

 

Acid–base reactions are central in many biochemical processes

13

 

Acid–base reactions can disrupt the double helix

14

 

Buffers regulate pH in organisms and in the laboratory

15

1.4 The Genomic Revolution Is Transforming Biochemistry, Medicine, and Other Fields

17

 

Genome sequencing has transformed biochemistry and other fields

17

 

Environmental factors influence human biochemistry

20

 

Genome sequences encode proteins and patterns of expression

21

APPENDIX: Visualizing Molecular Structures I: Small Molecules

22

CHAPTER 2 Protein Composition and Structure

27

2.1 Proteins Are Built from a Repertoire of 20 Amino Acids

29

2.2 Primary Structure: Amino Acids Are Linked by Peptide Bonds to Form Polypeptide Chains

35

 

Proteins have unique amino acid sequences specified by genes

37

 

Polypeptide chains are flexible yet conformationally restricted

38

2.3 Secondary Structure: Polypeptide Chains Can Fold into Regular Structures Such As the Alpha Helix, the Beta Sheet, and Turns and Loops

40

 

The alpha helix is a coiled structure stabilized by intrachain hydrogen bonds

40

 

Beta sheets are stabilized by hydrogen bonding between polypeptide strands

42

 

Polypeptide chains can change direction by making reverse turns and loops

44

 

Fibrous proteins provide structural support for cells and tissues

44

2.4 Tertiary Structure: Water-Soluble Proteins Fold into Compact Structures with Nonpolar Cores

46

2.5 Quaternary Structure: Polypeptide Chains Can Assemble into Multisubunit Structures

48

2.6 The Amino Acid Sequence of a Protein Determines Its Three-Dimensional Structure

49

 

Amino acids have different propensities for forming α helices, β sheets, and turns

51

 

Protein folding is a highly cooperative process

52

 

Proteins fold by progressive stabilization of intermediates rather than by random search

53

 

Prediction of three-dimensional structure from sequence remains a great challenge

54

 

Some proteins are inherently unstructured and can exist in multiple conformations

55

 

Protein misfolding and aggregation are associated with some neurological diseases

56

 

Protein modification and cleavage confer new capabilities

57

APPENDIX: Visualizing Molecular Structures II: Proteins

61

CHAPTER 3 Exploring Proteins and Proteomes

65

The proteome is the functional representation of the genome

66

3.1 The Purification of Proteins Is an Essential First Step in Understanding Their Function

66

 

The assay: How do we recognize the protein that we are looking for?

67

 

Proteins must be released from the cell to be purified

67

 

Proteins can be purified according to solubility, size, charge, and binding affinity

68

 

Proteins can be separated by gel electrophoresis and displayed

71

 

A protein purification scheme can be quantitatively evaluated

75

 

Ultracentrifugation is valuable for separating biomolecules and determining their masses

76

 

Protein purification can be made easier with the use of recombinant DNA technology

78

3.2 Immunology Provides Important Techniques with Which to Investigate Proteins

79

 

Antibodies to specific proteins can be generated

79

 

Monoclonal antibodies with virtually any desired specificity can be readily prepared

80

 

Proteins can be detected and quantified by using an enzyme-linked immunosorbent assay

82

 

Western blotting permits the detection of proteins separated by gel electrophoresis

83

 

Fluorescent markers make the visualization of proteins in the cell possible

84

3.3 Mass Spectrometry Is a Powerful Technique for the Identification of Peptides and Proteins

85

 

Peptides can be sequenced by mass spectrometry

87

 

Proteins can be specifically cleaved into small peptides to facilitate analysis

88

 

Genomic and proteomic methods are complementary

89

 

The amino acid sequence of a protein provides valuable information

90

 

Individual proteins can be identified by mass spectrometry

91

3.4 Peptides Can Be Synthesized by Automated Solid-Phase Methods

92

3.5 Three-Dimensional Protein Structure Can Be Determined by X-ray Crystallography and NMR Spectroscopy

95

 

X-ray crystallography reveals three-dimensional structure in atomic detail

95

 

Nuclear magnetic resonance spectroscopy can reveal the structures of proteins in solution

97

CHAPTER 4 DNA, RNA, and the Flow of Genetic Information

105

4.1 A Nucleic Acid Consists of Four Kinds of Bases Linked to a Sugar–Phosphate Backbone

106

 

RNA and DNA differ in the sugar component and one of the bases

106

 

Nucleotides are the monomeric units of nucleic acids

107

 

DNA molecules are very long and have directionality

108

4.2 A Pair of Nucleic Acid Strands with Complementary Sequences Can Form a Double-Helical Structure

109

 

The double helix is stabilized by hydrogen bonds and van der Waals interactions

109

 

DNA can assume a variety of structural forms

111

 

Z-DNA is a left-handed double helix in which backbone phosphates zigzag

112

 

Some DNA molecules are circular and supercoiled

113

 

Single-stranded nucleic acids can adopt elaborate structures

113

4.3 The Double Helix Facilitates the Accurate Transmission of Hereditary Information

114

 

Differences in DNA density established the validity of the semiconservative replication hypothesis

115

 

The double helix can be reversibly melted

116

4.4 DNA Is Replicated by Polymerases That Take Instructions from Templates

117

 

DNA polymerase catalyzes phosphodiester bridge formation

117

 

The genes of some viruses are made of RNA

118

4.5 Gene Expression Is the Transformation of DNA Information into Functional Molecules

119

 

Several kinds of RNA play key roles in gene expression

119

 

All cellular RNA is synthesized by RNA polymerases

120

 

RNA polymerases take instructions from DNA templates

121

 

Transcription begins near promoter sites and ends at terminator sites

122

 

Transfer RNAs are the adaptor molecules in protein synthesis

123

4.6 Amino Acids Are Encoded by Groups of Three Bases Starting from a Fixed Point

124

 

Major features of the genetic code

125

 

Messenger RNA contains start and stop signals for protein synthesis

126

 

The genetic code is nearly universal

126

4.7 Most Eukaryotic Genes Are Mosaics of Introns and Exons

127

 

RNA processing generates mature RNA

127

 

Many exons encode protein domains

128

CHAPTER 5 Exploring Genes and Genomes

135

5.1 The Exploration of Genes Relies on Key Tools

136

 

Restriction enzymes split DNA into specific fragments

137

 

Restriction fragments can be separated by gel electrophoresis and visualized

137

 

DNA can be sequenced by controlled termination of replication

138

 

DNA probes and genes can be synthesized by automated solid-phase methods

139

 

Selected DNA sequences can be greatly amplified by the polymerase chain reaction

141

 

PCR is a powerful technique in medical diagnostics, forensics, and studies of molecular evolution

142

 

The tools for recombinant DNA technology have been used to identify disease-causing mutations

143

5.2 Recombinant DNA Technology Has Revolutionized All Aspects of Biology

143

 

Restriction enzymes and DNA ligase are key tools in forming recombinant DNA molecules

143

 

Plasmids and λ phage are choice vectors for DNA cloning in bacteria

144

 

Bacterial and yeast artificial chromosomes

147

 

Specific genes can be cloned from digests of genomic DNA

147

 

Complementary DNA prepared from mRNA can be expressed in host cells

149

 

Proteins with new functions can be created through directed changes in DNA

150

 

Recombinant methods enable the exploration of the functional effects of disease-causing mutations

152

5.3 Complete Genomes Have Been Sequenced and Analyzed

152

 

The genomes of organisms ranging from bacteria to multicellular eukaryotes have been sequenced

153

 

The sequence of the human genome has been completed

154

 

Next-generation sequencing methods enable the rapid determination of a complete genome sequence

155

 

Comparative genomics has become a powerful research tool

156

5.4 Eukaryotic Genes Can Be Quantitated and Manipulated with Considerable Precision

157

 

Gene-expression levels can be comprehensively examined

157

 

New genes inserted into eukaryotic cells can be efficiently expressed

159

 

Transgenic animals harbor and express genes introduced into their germ lines

160

 

Gene disruption and genome editing provide clues to gene function and opportunities for new therapies

160

 

RNA interference provides an additional tool for disrupting gene expression

162

 

Tumor-inducing plasmids can be used to introduce new genes into plant cells

163

 

Human gene therapy holds great promise for medicine

164

CHAPTER 6 Exploring Evolution and Bioinformatics

169

6.1 Homologs Are Descended from a Common Ancestor

170

6.2 Statistical Analysis of Sequence Alignments Can Detect Homology

171

 

The statistical significance of alignments can be estimated by shuffling

173

 

Distant evolutionary relationships can be detected through the use of substitution matrices

174

 

Databases can be searched to identify homologous sequences

177

6.3 Examination of Three-Dimensional Structure Enhances Our Understanding of Evolutionary Relationships

177

 

Tertiary structure is more conserved than primary structure

178

 

Knowledge of three-dimensional structures can aid in the evaluation of sequence alignments

179

 

Repeated motifs can be detected by aligning sequences with themselves

180

 

Convergent evolution illustrates common solutions to biochemical challenges

181

 

Comparison of RNA sequences can be a source of insight into RNA secondary structures

182

6.4 Evolutionary Trees Can Be Constructed on the Basis of Sequence Information

183

 

Horizontal gene transfer events may explain unexpected branches of the evolutionary tree

184

6.5 Modern Techniques Make the Experimental Exploration of Evolution Possible

185

 

Ancient DNA can sometimes be amplified and sequenced

185

 

Molecular evolution can be examined experimentally

185

CHAPTER 7 Hemoglobin: Portrait of a Protein in Action

191

7.1 Myoglobin and Hemoglobin Bind Oxygen at Iron Atoms in Heme

192

 

Changes in heme electronic structure upon oxygen binding are the basis for functional imaging studies

193

 

The structure of myoglobin prevents the release of reactive oxygen species

194

 

Human hemoglobin is an assembly of four myoglobin like subunits

195

7.2 Hemoglobin Binds Oxygen Cooperatively

195

 

Oxygen binding markedly changes the quaternary structure of hemoglobin

197

 

Hemoglobin cooperativity can be potentially explained by several models

198

 

Structural changes at the heme groups are transmitted to the α1β1–α2β2 interface

200

 

2,3-Bisphosphoglycerate in red cells is crucial in determining the oxygen affinity of hemoglobin

200

 

Carbon monoxide can disrupt oxygen transport by hemoglobin

201

7.3 Hydrogen Ions and Carbon Dioxide Promote the Release of Oxygen: The Bohr Effect

202

7.4 Mutations in Genes Encoding Hemoglobin Subunits Can Result in Disease

204

 

Sickle-cell anemia results from the aggregation of mutated deoxyhemoglobin molecules

205

 

Thalassemia is caused by an imbalanced production of hemoglobin chains

207

 

The accumulation of free alpha-hemoglobin chains is prevented

207

 

Additional globins are encoded in the human genome

208

APPENDIX: Binding Models Can Be Formulated in Quantitative Terms: The Hill Plot and the Concerted Model

210

CHAPTER 8 Enzymes: Basic Concepts and Kinetics

215

8.1 Enzymes are Powerful and Highly Specific Catalysts

216

 

Many enzymes require cofactors for activity

217

 

Enzymes can transform energy from one form into another

217

8.2 Gibbs Free Energy Is a Useful Thermodynamic Function for Understanding Enzymes

218

 

The free-energy change provides information about the spontaneity but not the rate of a reaction

218

 

The standard free-energy change of a reaction is related to the equilibrium constant

219

 

Enzymes alter only the reaction rate and not the reaction equilibrium

220

8.3 Enzymes Accelerate Reactions by Facilitating the Formation of the Transition State

221

 

The formation of an enzyme–substrate complex is the first step in enzymatic catalysis

222

 

The active sites of enzymes have some common features

223

 

The binding energy between enzyme and substrate is important for catalysis

225

8.4 The Michaelis–Menten Model Accounts for the Kinetic Properties of Many Enzymes

225

 

Kinetics is the study of reaction rates

225

 

The steady-state assumption facilitates a description of enzyme kinetics

226

 

Variations in KM can have physiological consequences

228

 

KM and Vmax values can be determined by several means

228

 

KM and Vmax values are important enzyme characteristics

229

 

kcat/KM is a measure of catalytic efficiency

230

 

Most biochemical reactions include multiple substrates

231

 

Allosteric enzymes do not obey Michaelis–Menten kinetics

233

8.5 Enzymes Can Be Inhibited by Specific Molecules

234

 

The different types of reversible inhibitors are kinetically distinguishable

235

 

Irreversible inhibitors can be used to map the active site

237

 

Penicillin irreversibly inactivates a key enzyme in bacterial cell-wall synthesis

239

 

Transition-state analogs are potent inhibitors of enzymes

240

 

Catalytic antibodies demonstrate the importance of selective binding of the transition state to enzymatic activity

241

8.6 Enzymes Can Be Studied One Molecule at a Time

242

APPENDIX: Enzymes are Classified on the Basis of the Types of Reactions That They Catalyze

245

CHAPTER 9 Catalytic Strategies

251

 

A few basic catalytic principles are used by many enzymes

252

9.1 Proteases Facilitate a Fundamentally Difficult Reaction

253

 

Chymotrypsin possesses a highly reactive serine residue

253

 

Chymotrypsin action proceeds in two steps linked by a covalently bound intermediate

254

 

Serine is part of a catalytic triad that also includes histidine and aspartate

255

 

Catalytic triads are found in other hydrolytic enzymes

258

 

The catalytic triad has been dissected by site-directed mutagenesis

260

 

Cysteine, aspartyl, and metalloproteases are other major classes of peptide-cleaving enzymes

260

 

Protease inhibitors are important drugs

263

9.2 Carbonic Anhydrases Make a Fast Reaction Faster

264

 

Carbonic anhydrase contains a bound zinc ion essential for catalytic activity

265

 

Catalysis entails zinc activation of a water molecule

265

 

A proton shuttle facilitates rapid regeneration of the active form of the enzyme

267

9.3 Restriction Enzymes Catalyze Highly Specific DNA-Cleavage Reactions

269

 

Cleavage is by in-line displacement of 3′-oxygen from phosphorus by magnesium-activated water

269

 

Restriction enzymes require magnesium for catalytic activity

271

 

The complete catalytic apparatus is assembled only within complexes of cognate DNA molecules, ensuring specificity

272

 

Host-cell DNA is protected by the addition of methyl groups to specific bases

274

 

Type II restriction enzymes have a catalytic core in common and are probably related by horizontal gene transfer

275

9.4 Myosins Harness Changes in Enzyme Conformation to Couple ATP Hydrolysis to Mechanical Work

275

 

ATP hydrolysis proceeds by the attack of water on the gamma-phosphoryl group

276

 

Formation of the transition state for ATP hydrolysis is associated with a substantial conformational change

277

 

The altered conformation of myosin persists for a substantial period of time

278

 

Scientists can watch single molecules of myosin move

279

 

Myosins are a family of enzymes containing P-loop structures

280

CHAPTER 10 Regulatory Strategies

285

10.1 Aspartate Transcarbamoylase Is Allosterically Inhibited by the End Product of Its Pathway

286

 

Allosterically regulated enzymes do not follow Michaelis–Menten kinetics

287

 

ATCase consists of separable catalytic and regulatory subunits

287

 

Allosteric interactions in ATCase are mediated by large changes in quaternary structure

288

 

Allosteric regulators modulate the T-to-R equilibrium

291

10.2 Isozymes Provide a Means of Regulation Specific to Distinct Tissues and Developmental Stages

292

10.3 Covalent Modification Is a Means of Regulating Enzyme Activity

293

 

Kinases and phosphatases control the extent of protein phosphorylation

294

 

Phosphorylation is a highly effective means of regulating the activities of target proteins

296

 

Cyclic AMP activates protein kinase A by altering the quaternary structure

297

 

ATP and the target protein bind to a deep cleft in the catalytic subunit of protein kinase A

298

10.4 Many Enzymes Are Activated by Specific Proteolytic Cleavage

299

 

Chymotrypsinogen is activated by specific cleavage of a single peptide bond

299

 

Proteolytic activation of chymotrypsinogen leads to the formation of a substrate-binding site

300

 

The generation of trypsin from trypsinogen leads to the activation of other zymogens

301

 

Some proteolytic enzymes have specific inhibitors

302

 

Blood clotting is accomplished by a cascade of zymogen activations

303

 

Prothrombin requires a vitamin K-dependent modification for activation

304

 

Fibrinogen is converted by thrombin into a fibrin clot

304

 

Vitamin K is required for the formation of γ-carboxyglutamate

306

 

The clotting process must be precisely regulated

307

 

Hemophilia revealed an early step in clotting

308

CHAPTER 11 Carbohydrates

315

11.1 Monosaccharides Are the Simplest Carbohydrates

316

 

Many common sugars exist in cyclic forms

318

 

Pyranose and furanose rings can assume different conformations

320

 

Glucose is a reducing sugar

321

 

Monosaccharides are joined to alcohols and amines through glycosidic bonds

322

 

Phosphorylated sugars are key intermediates in energy generation and biosyntheses

322

11.2 Monosaccharides Are Linked to Form Complex Carbohydrates

323

 

Sucrose, lactose, and maltose are the common disaccharides

323

 

Glycogen and starch are storage forms of glucose

324

 

Cellulose, a structural component of plants, is made of chains of glucose

324

11.3 Carbohydrates Can Be Linked to Proteins to Form Glycoproteins

325

 

Carbohydrates can be linked to proteins through asparagine (N-linked) or through serine or threonine (O-linked) residues

326

 

The glycoprotein erythropoietin is a vital hormone

327

 

Glycosylation functions in nutrient sensing

327

 

Proteoglycans, composed of polysaccharides and protein, have important structural roles

327

 

Proteoglycans are important components of cartilage

328

 

Mucins are glycoprotein components of mucus

329

 

Protein glycosylation takes place in the lumen of the endoplasmic reticulum and in the Golgi complex

330

 

Specific enzymes are responsible for oligosaccharide assembly

331

 

Blood groups are based on protein glycosylation patterns

331

 

Errors in glycosylation can result in pathological conditions

332

 

Oligosaccharides can be “sequenced”

332

11.4 Lectins Are Specific Carbohydrate-Binding Proteins

333

 

Lectins promote interactions between cells

334

 

Lectins are organized into different classes

334

 

Influenza virus binds to sialic acid residues

335

CHAPTER 12 Lipids and Cell Membranes

341

 

Many common features underlie the diversity of biological membranes

342

12.1 Fatty Acids Are Key Constituents of Lipids

342

 

Fatty acid names are based on their parent hydrocarbons

342

 

Fatty acids vary in chain length and degree of unsaturation

343

12.2 There Are Three Common Types of Membrane Lipids

344

 

Phospholipids are the major class of membrane lipids

344

 

Membrane lipids can include carbohydrate moieties

345

 

Cholesterol is a lipid based on a steroid nucleus

346

 

Archaeal membranes are built from ether lipids with branched chains

346

 

A membrane lipid is an amphipathic molecule containing a hydrophilic and a hydrophobic moiety

347

12.3 Phospholipids and Glycolipids Readily Form Bimolecular Sheets in Aqueous Media

348

 

Lipid vesicles can be formed from phospholipids

348

 

Lipid bilayers are highly impermeable to ions and most polar molecules

349

12.4 Proteins Carry Out Most Membrane Processes

350

 

Proteins associate with the lipid bilayer in a variety of ways

351

 

Proteins interact with membranes in a variety of ways

351

 

Some proteins associate with membranes through covalently attached hydrophobic groups

354

 

Transmembrane helices can be accurately predicted from amino acid sequences

354

12.5 Lipids and Many Membrane Proteins Diffuse Rapidly in the Plane of the Membrane

356

 

The fluid mosaic model allows lateral movement but not rotation through the membrane

357

 

Membrane fluidity is controlled by fatty acid composition and cholesterol content

357

 

Lipid rafts are highly dynamic complexes formed between cholesterol and specific lipids

358

 

All biological membranes are asymmetric

358

12.6 Eukaryotic Cells Contain Compartments Bounded by Internal Membranes

359

CHAPTER 13 Membrane Channels and Pumps

367

 

The expression of transporters largely defines the metabolic activities of a given cell type

368

13.1 The Transport of Molecules Across a Membrane May Be Active or Passive

368

 

Many molecules require protein transporters to cross membranes

368

 

Free energy stored in concentration gradients can be quantified

369

13.2 Two Families of Membrane Proteins Use ATP Hydrolysis to Pump Ions and Molecules Across Membranes

370

 

P-type ATPases couple phosphorylation and conformational changes to pump calcium ions across membranes

370

 

Digitalis specifically inhibits the Na+–K+ pump by blocking its dephosphorylation

373

 

P-type ATPases are evolutionarily conserved and play a wide range of roles

374

 

Multidrug resistance highlights a family of membrane pumps with ATP-binding cassette domains

374

13.3 Lactose Permease Is an Archetype of Secondary Transporters That Use One Concentration Gradient to Power the Formation of Another

376

13.4 Specific Channels Can Rapidly Transport Ions Across Membranes

378

 

Action potentials are mediated by transient changes in Na+ and K+ permeability

378

 

Patch-clamp conductance measurements reveal the activities of single channels

379

 

The structure of a potassium ion channel is an archetype for many ion-channel structures

379

 

The structure of the potassium ion channel reveals the basis of ion specificity

380

 

The structure of the potassium ion channel explains its rapid rate of transport

383

 

Voltage gating requires substantial conformational changes in specific ion-channel domains

383

 

A channel can be inactivated by occlusion of the pore: the ball-and-chain model

384

 

The acetylcholine receptor is an archetype for ligand-gated ion channels

385

 

Action potentials integrate the activities of several ion channels working in concert

387

 

Disruption of ion channels by mutations or chemicals can be potentially life-threatening

388

13.5 Gap Junctions Allow Ions and Small Molecules to Flow Between Communicating Cells

389

13.6 Specific Channels Increase the Permeability of Some Membranes to Water

390

CHAPTER 14 Signal-Transduction Pathways

397

 

Signal transduction depends on molecular circuits

398

14.1 Heterotrimeric G Proteins Transmit Signals and Reset Themselves

399

 

Ligand binding to 7TM receptors leads to the activation of heterotrimeric G proteins

400

 

Activated G proteins transmit signals by binding to other proteins

402

 

Cyclic AMP stimulates the phosphorylation of many target proteins by activating protein kinase A

403

 

G proteins spontaneously reset themselves through GTP hydrolysis

403

 

Some 7TM receptors activate the phosphoinositide cascade

404

 

Calcium ion is a widely used second messenger

405

 

Calcium ion often activates the regulatory protein calmodulin

407

14.2 Insulin Signaling: Phosphorylation Cascades Are Central to Many Signal-Transduction Processes

407

 

The insulin receptor is a dimer that closes around a bound insulin molecule

408

 

Insulin binding results in the cross-phosphorylation and activation of the insulin receptor

408

 

The activated insulin-receptor kinase initiates a kinase cascade

409

 

Insulin signaling is terminated by the action of phosphatases

411

14.3 EGF Signaling: Signal-Transduction Pathways Are Poised to Respond

411

 

EGF binding results in the dimerization of the EGF receptor

411

 

The EGF receptor undergoes phosphorylation of its carboxyl-terminal tail

413

 

EGF signaling leads to the activation of Ras, a small G protein

413

 

Activated Ras initiates a protein kinase cascade

414

 

EGF signaling is terminated by protein phosphatases and the intrinsic GTPase activity of Ras

414

14.4 Many Elements Recur with Variation in Different Signal-Transduction Pathways

415

14.5 Defects in Signal-Transduction Pathways Can Lead to Cancer and Other Diseases

416

 

Monoclonal antibodies can be used to inhibit signal-transduction pathways activated in tumors

416

 

Protein kinase inhibitors can be effective anticancer drugs

417

 

Cholera and whooping cough are the result of altered G-protein activity

417

Part II TRANSDUCING AND STORING ENERGY

 

CHAPTER 15 Metabolism: Basic Concepts and Design

423

15.1 Metabolism Is Composed of Many Coupled, Interconnecting Reactions

424

 

Metabolism consists of energy-yielding and energy-requiring reactions

424

 

A thermodynamically unfavorable reaction can be driven by a favorable reaction

425

15.2 ATP Is the Universal Currency of Free Energy in Biological Systems

426

 

ATP hydrolysis is exergonic

426

 

ATP hydrolysis drives metabolism by shifting the equilibrium of coupled reactions

427

 

The high phosphoryl potential of ATP results from structural differences between ATP and its hydrolysis products

429

 

Phosphoryl-transfer potential is an important form of cellular energy transformation

430

15.3 The Oxidation of Carbon Fuels Is an Important Source of Cellular Energy

432

 

Compounds with high phosphoryl-transfer potential can couple carbon oxidation to ATP synthesis

432

 

Ion gradients across membranes provide an important form of cellular energy that can be coupled to ATP synthesis

433

 

Phosphates play a prominent role in biochemical processes

434

 

Energy from foodstuffs is extracted in three stages

434

15.4 Metabolic Pathways Contain Many Recurring Motifs

435

 

Activated carriers exemplify the modular design and economy of metabolism

435

 

Many activated carriers are derived from vitamins

438

 

Key reactions are reiterated throughout metabolism

440

 

Metabolic processes are regulated in three principal ways

442

 

Aspects of metabolism may have evolved from an RNA world

444

CHAPTER 16 Glycolysis and Gluconeogenesis

449

 

Glucose is generated from dietary carbohydrates

450

 

Glucose is an important fuel for most organisms

451

16.1 Glycolysis Is an Energy-Conversion Pathway in Many Organisms

451

 

Hexokinase traps glucose in the cell and begins glycolysis

451

 

Fructose 1,6-bisphosphate is generated from glucose 6-phosphate

453

 

The six-carbon sugar is cleaved into two three-carbon fragments

454

 

Mechanism: Triose phosphate isomerase salvages a three-carbon fragment

455

 

The oxidation of an aldehyde to an acid powers the formation of a compound with high phosphoryl-transfer potential

457

 

Mechanism: Phosphorylation is coupled to the oxidation of glyceraldehyde 3-phosphate by a thioester intermediate

458

 

ATP is formed by phosphoryl transfer from 1,3-bisphosphoglycerate

459

 

Additional ATP is generated with the formation of pyruvate

460

 

Two ATP molecules are formed in the conversion of glucose into pyruvate

461

 

NAD+ is regenerated from the metabolism of pyruvate

462

 

Fermentations provide usable energy in the absence of oxygen

464

 

The binding site for NAD+ is similar in many dehydrogenases

465

 

Fructose is converted into glycolytic intermediates by fructokinase

465

 

Excessive fructose consumption can lead to pathological conditions

466

 

Galactose is converted into glucose 6-phosphate

466

 

Many adults are intolerant of milk because they are deficient in lactase

467

 

Galactose is highly toxic if the transferase is missing

468

16.2 The Glycolytic Pathway Is Tightly Controlled

469

 

Glycolysis in muscle is regulated to meet the need for ATP

469

 

The regulation of glycolysis in the liver illustrates the biochemical versatility of the liver

472

 

A family of transporters enables glucose to enter and leave animal cells

473

 

Aerobic glycolysis is a property of rapidly growing cells

474

 

Cancer and endurance training affect glycolysis in a similar fashion

476

16.3 Glucose Can Be Synthesized from Noncarbohydrate Precursors

476

 

Gluconeogenesis is not a reversal of glycolysis

478

 

The conversion of pyruvate into phosphoenolpyruvate begins with the formation of oxaloacetate

478

 

Oxaloacetate is shuttled into the cytoplasm and converted into phosphoenolpyruvate

480

 

The conversion of fructose 1,6-bisphosphate into fructose 6-phosphate and orthophosphate is an irreversible step

480

 

The generation of free glucose is an important control point

481

 

Six high-transfer-potential phosphoryl groups are spent in synthesizing glucose from pyruvate

481

16.4 Gluconeogenesis and Glycolysis Are Reciprocally Regulated

482

 

Energy charge determines whether glycolysis or gluconeogenesis will be most active

482

 

The balance between glycolysis and gluconeogenesis in the liver is sensitive to blood-glucose concentration

483

 

Substrate cycles amplify metabolic signals and produce heat

485

 

Lactate and alanine formed by contracting muscle are used by other organs

485

 

Glycolysis and gluconeogenesis are evolutionarily intertwined

487

CHAPTER 17 The Citric Acid Cycle

495

 

The citric acid cycle harvests high-energy electrons

496

17.1 The Pyruvate Dehydrogenase Complex Links Glycolysis to the Citric Acid Cycle

497

 

Mechanism: The synthesis of acetyl coenzyme A from pyruvate requires three enzymes and five coenzymes

498

 

Flexible linkages allow lipoamide to move between different active sites

500

17.2 The Citric Acid Cycle Oxidizes Two-Carbon Units

501

 

Citrate synthase forms citrate from oxaloacetate and acetyl coenzyme A

502

 

Mechanism: The mechanism of citrate synthase prevents undesirable reactions

502

 

Citrate is isomerized into isocitrate

504

 

Isocitrate is oxidized and decarboxylated to alpha-ketoglutarate

504

 

Succinyl coenzyme A is formed by the oxidative decarboxylation of alpha-ketoglutarate

505

 

A compound with high phosphoryl-transfer potential is generated from succinyl coenzyme A

505

 

Mechanism: Succinyl coenzyme A synthetase transforms types of biochemical energy

506

 

Oxaloacetate is regenerated by the oxidation of succinate

507

 

The citric acid cycle produces high-transfer-potential electrons, ATP, and CO2

508

17.3 Entry to the Citric Acid Cycle and Metabolism Through It Are Controlled

510

 

The pyruvate dehydrogenase complex is regulated allosterically and by reversible phosphorylation

511

 

The citric acid cycle is controlled at several points

512

 

Defects in the citric acid cycle contribute to the development of cancer

513

17.4 The Citric Acid Cycle Is a Source of Biosynthetic Precursors

514

 

The citric acid cycle must be capable of being rapidly replenished

514

 

The disruption of pyruvate metabolism is the cause of beriberi and poisoning by mercury and arsenic

515

 

The citric acid cycle may have evolved from preexisting pathways

516

17.5 The Glyoxylate Cycle Enables Plants and Bacteria to Grow on Acetate

516

CHAPTER 18 Oxidative Phosphorylation

523

18.1 Eukaryotic Oxidative Phosphorylation Takes Place in Mitochondria

524

 

Mitochondria are bounded by a double membrane

524

 

Mitochondria are the result of an endosymbiotic event

525

18.2 Oxidative Phosphorylation Depends on Electron Transfer

526

 

The electron-transfer potential of an electron is measured as redox potential

526

 

A 1.14-volt potential difference between NADH and molecular oxygen drives electron transport through the chain and favors the formation of a proton gradient

528

18.3 The Respiratory Chain Consists of Four Complexes: Three Proton Pumps and a Physical Link to the Citric Acid Cycle

529

 

Iron–sulfur clusters are common components of the electron transport chain

531

 

The high-potential electrons of NADH enter the respiratory chain at NADH-Q oxidoreductase

532

 

Ubiquinol is the entry point for electrons from FADH2 of flavoproteins

533

 

Electrons flow from ubiquinol to cytochrome c through Q-cytochrome c oxidoreductase

533

 

The Q cycle funnels electrons from a two-electron carrier to a one-electron carrier and pumps protons

535

 

Cytochrome c oxidase catalyzes the reduction of molecular oxygen to water

535

 

Toxic derivatives of molecular oxygen such as superoxide radicals are scavenged by protective enzymes

538

 

Electrons can be transferred between groups that are not in contact

540

 

The conformation of cytochrome c has remained essentially constant for more than a billion years

541

18.4 A Proton Gradient Powers the Synthesis of ATP

541

 

ATP synthase is composed of a proton-conducting unit and a catalytic unit

543

 

Proton flow through ATP synthase leads to the release of tightly bound ATP: The binding-change mechanism

544

 

Rotational catalysis is the world’s smallest molecular motor

546

 

Proton flow around the c ring powers ATP synthesis

546

 

ATP synthase and G proteins have several common features

548

18.5 Many Shuttles Allow Movement Across Mitochondrial Membranes

549

 

Electrons from cytoplasmic NADH enter mitochondria by shuttles

549

 

The entry of ADP into mitochondria is coupled to the exit of ATP by ATP-ADP translocase

550

 

Mitochondrial transporters for metabolites have a common tripartite structure

551

18.6 The Regulation of Cellular Respiration Is Governed Primarily by the Need for ATP

552

 

The complete oxidation of glucose yields about 30 molecules of ATP

552

 

The rate of oxidative phosphorylation is determined by the need for ATP

553

 

ATP synthase can be regulated

554

 

Regulated uncoupling leads to the generation of heat

554

 

Oxidative phosphorylation can be inhibited at many stages

556

 

Mitochondrial diseases are being discovered

557

 

Mitochondria play a key role in apoptosis

557

 

Power transmission by proton gradients is a central motif of bioenergetics

558

CHAPTER 19 The Light Reactions of Photosynthesis

565

 

Photosynthesis converts light energy into chemical energy

566

19.1 Photosynthesis Takes Place in Chloroplasts

567

 

The primary events of photosynthesis take place in thylakoid membranes

567

 

Chloroplasts arose from an endosymbiotic event

568

19.2 Light Absorption by Chlorophyll Induces Electron Transfer

568

 

A special pair of chlorophylls initiate charge separation

569

 

Cyclic electron flow reduces the cytochrome of the reaction center

572

19.3 Two Photosystems Generate a Proton Gradient and NADPH in Oxygenic Photosynthesis

572

 

Photosystem II transfers electrons from water to plastoquinone and generates a proton gradient

572

 

Cytochrome bf links photosystem II to photosystem I

575

 

Photosystem I uses light energy to generate reduced ferredoxin, a powerful reductant

575

 

Ferredoxin–NADP+ reductase converts NADP+ into NADPH

576

19.4 A Proton Gradient across the Thylakoid Membrane Drives ATP Synthesis

578

 

The ATP synthase of chloroplasts closely resembles those of mitochondria and prokaryotes

578

 

The activity of chloroplast ATP synthase is regulated

579

 

Cyclic electron flow through photosystem I leads to the production of ATP instead of NADPH

580

 

The absorption of eight photons yields one O2, two NADPH, and three ATP molecules

581

19.5 Accessory Pigments Funnel Energy into Reaction Centers

581

 

Resonance energy transfer allows energy to move from the site of initial absorbance to the reaction center

582

 

The components of photosynthesis are highly organized

583

 

Many herbicides inhibit the light reactions of photosynthesis

584

19.6 The Ability to Convert Light into Chemical Energy Is Ancient

584

 

Artificial photosynthetic systems may provide clean, renewable energy

585

CHAPTER 20 The Calvin Cycle and the Pentose Phosphate Pathway

589

20.1 The Calvin Cycle Synthesizes Hexoses from Carbon Dioxide and Water

590

 

Carbon dioxide reacts with ribulose 1,5-bisphosphate to form two molecules of 3-phosphoglycerate

591

 

Rubisco activity depends on magnesium and carbamate

592

 

Rubisco activase is essential for rubisco activity

593

 

Rubisco also catalyzes a wasteful oxygenase reaction: Catalytic imperfection

593

 

Hexose phosphates are made from phosphoglycerate, and ribulose 1,5-bisphosphate is regenerated

594

 

Three ATP and two NADPH molecules are used to bring carbon dioxide to the level of a hexose

597

 

Starch and sucrose are the major carbohydrate stores in plants

597

20.2 The Activity of the Calvin Cycle Depends on Environmental Conditions

598

 

Rubisco is activated by light-driven changes in proton and magnesium ion concentrations

598

 

Thioredoxin plays a key role in regulating the Calvin cycle

599

 

The C4 pathway of tropical plants accelerates photosynthesis by concentrating carbon dioxide

599

 

Crassulacean acid metabolism permits growth in arid ecosystems

601

20.3 The Pentose Phosphate Pathway Generates NADPH and Synthesizes Five-Carbon Sugars

601

 

Two molecules of NADPH are generated in the conversion of glucose 6-phosphate into ribulose 5-phosphate

602

 

The pentose phosphate pathway and glycolysis are linked by transketolase and transaldolase

602

 

Mechanism: Transketolase and transaldolase stabilize carbanionic intermediates by different mechanisms

605

20.4 The Metabolism of Glucose 6-Phosphate by the Pentose Phosphate Pathway Is Coordinated with Glycolysis

607

 

The rate of the pentose phosphate pathway is controlled by the level of NADP+

607

 

The flow of glucose 6-phosphate depends on the need for NADPH, ribose 5-phosphate, and ATP

608

 

The pentose phosphate pathway is required for rapid cell growth

610

 

Through the looking-glass: The Calvin cycle and the pentose phosphate pathway are mirror images

610

20.5 Glucose 6-Phosphate Dehydrogenase Plays a Key Role in Protection Against Reactive Oxygen Species

610

 

Glucose 6-phosphate dehydrogenase deficiency causes a drug-induced hemolytic anemia

610

 

A deficiency of glucose 6-phosphate dehydrogenase confers an evolutionary advantage in some circumstances

612

CHAPTER 21 Glycogen Metabolism

617

 

Glycogen metabolism is the regulated release and storage of glucose

618

21.1 Glycogen Breakdown Requires the Interplay of Several Enzymes

619

 

Phosphorylase catalyzes the phosphorolytic cleavage of glycogen to release glucose 1-phosphate

619

 

Mechanism: Pyridoxal phosphate participates in the phosphorolytic cleavage of glycogen

620

 

A debranching enzyme also is needed for the breakdown of glycogen

621

 

Phosphoglucomutase converts glucose 1-phosphate into glucose 6-phosphate

622

 

The liver contains glucose 6-phosphatase, a hydrolytic enzyme absent from muscle

622

21.2 Phosphorylase Is Regulated by Allosteric Interactions and Reversible Phosphorylation

623

 

Liver phosphorylase produces glucose for use by other tissues

623

 

Muscle phosphorylase is regulated by the intracellular energy charge

625

 

Biochemical characteristics of muscle fiber types differ

625

 

Phosphorylation promotes the conversion of phosphorylase b to phosphorylase a

626

 

Phosphorylase kinase is activated by phosphorylation and calcium ions

626

21.3 Epinephrine and Glucagon Signal the Need for Glycogen Breakdown

627

 

G proteins transmit the signal for the initiation of glycogen breakdown

627

 

Glycogen breakdown must be rapidly turned off when necessary

629

 

The regulation of glycogen phosphorylase became more sophisticated as the enzyme evolved

629

21.4 Glycogen Is Synthesized and Degraded by Different Pathways

630

 

UDP-glucose is an activated form of glucose

630

 

Glycogen synthase catalyzes the transfer of glucose from UDP-glucose to a growing chain

630

 

A branching enzyme forms α-1,6 linkages

631

 

Glycogen synthase is the key regulatory enzyme in glycogen synthesis

632

 

Glycogen is an efficient storage form of glucose

632

21.5 Glycogen Breakdown and Synthesis Are Reciprocally Regulated

632

 

Protein phosphatase 1 reverses the regulatory effects of kinases on glycogen metabolism

633

 

Insulin stimulates glycogen synthesis by inactivating glycogen synthase kinase

635

 

Glycogen metabolism in the liver regulates the blood-glucose level

635

 

A biochemical understanding of glycogen-storage diseases is possible

637

CHAPTER 22 Fatty Acid Metabolism

643

 

Fatty acid degradation and synthesis mirror each other in their chemical reactions

644

22.1 Triacylglycerols Are Highly Concentrated Energy Stores

645

 

Dietary lipids are digested by pancreatic lipases

645

 

Dietary lipids are transported in chylomicrons

646

22.2 The Use of Fatty Acids as Fuel Requires Three Stages of Processing

647

 

Triacylglycerols are hydrolyzed by hormone-stimulated lipases

647

 

Free fatty acids and glycerol are released into the blood

648

 

Fatty acids are linked to coenzyme A before they are oxidized

648

 

Carnitine carries long-chain activated fatty acids into the mitochondrial matrix

649

 

Acetyl CoA, NADH, and FADH2 are generated in each round of fatty acid oxidation

650

 

The complete oxidation of palmitate yields 106 molecules of ATP

652

22.3 Unsaturated and Odd-Chain Fatty Acids Require Additional Steps for Degradation

652

 

An isomerase and a reductase are required for the oxidation of unsaturated fatty acids

652

 

Odd-chain fatty acids yield propionyl CoA in the final thiolysis step

654

 

Vitamin B12 contains a corrin ring and a cobalt atom

654

 

Mechanism: Methylmalonyl CoA mutase catalyzes a rearrangement to form succinyl CoA

655

 

Fatty acids are also oxidized in peroxisomes

656

 

Ketone bodies are formed from acetyl CoA when fat breakdown predominates

657

 

Ketone bodies are a major fuel in some tissues

658

 

Animals cannot convert fatty acids into glucose

660

 

Some fatty acids may contribute to the development of pathological conditions

661

 

An isomerase and a reductase are required for the oxidation of unsaturated fatty acids

652

22.4 Fatty Acids Are Synthesized by Fatty Acid Synthase

661

 

Fatty acids are synthesized and degraded by different pathways

661

 

The formation of malonyl CoA is the committed step in fatty acid synthesis

662

 

Intermediates in fatty acid synthesis are attached to an acyl carrier protein

662

 

Fatty acid synthesis consists of a series of condensation, reduction, dehydration, and reduction reactions

662

 

Fatty acids are synthesized by a multifunctional enzyme complex in animals

664

 

The synthesis of palmitate requires 8 molecules of acetyl CoA, 14 molecules of NADPH, and 7 molecules of ATP

666

 

Citrate carries acetyl groups from mitochondria to the cytoplasm for fatty acid synthesis

666

 

Several sources supply NADPH for fatty acid synthesis

667

 

Fatty acid metabolism is altered in tumor cells

667

22.5 The Elongation and Unsaturation of Fatty Acids are Accomplished by Accessory Enzyme Systems

668

 

Membrane-bound enzymes generate unsaturated fatty acids

668

 

Eicosanoid hormones are derived from polyunsaturated fatty acids

669

 

Variations on a theme: Polyketide and nonribosomal peptide synthetases resemble fatty acid synthase

670

22.6 Acetyl CoA Carboxylase Plays a Key Role in Controlling Fatty Acid Metabolism

670

 

Acetyl CoA carboxylase is regulated by conditions in the cell

671

 

Acetyl CoA carboxylase is regulated by a variety of hormones

671

CHAPTER 23 Protein Turnover and Amino Acid Catabolism

681

23.1 Proteins are Degraded to Amino Acids

682

 

The digestion of dietary proteins begins in the stomach and is completed in the intestine

682

 

Cellular proteins are degraded at different rates

682

23.2 Protein Turnover Is Tightly Regulated

683

 

Ubiquitin tags proteins for destruction

683

 

The proteasome digests the ubiquitin-tagged proteins

685

 

The ubiquitin pathway and the proteasome have prokaryotic counterparts

686

 

Protein degradation can be used to regulate biological function

687

23.3 The First Step in Amino Acid Degradation Is the Removal of Nitrogen

687

 

Alpha-amino groups are converted into ammonium ions by the oxidative deamination of glutamate

687

 

Mechanism: Pyridoxal phosphate forms Schiff-base intermediates in aminotransferases

689

 

Aspartate aminotransferase is an archetypal pyridoxal-dependent transaminase

690

 

Blood levels of aminotransferases serve a diagnostic function

691

 

Pyridoxal phosphate enzymes catalyze a wide array of reactions

691

 

Serine and threonine can be directly deaminated

692

 

Peripheral tissues transport nitrogen to the liver

692

23.4 Ammonium Ion Is Converted into Urea in Most Terrestrial Vertebrates

693

 

The urea cycle begins with the formation of carbamoyl phosphate

693

 

Carbamoyl phosphate synthetase is the key regulatory enzyme for urea synthesis

694

 

Carbamoyl phosphate reacts with ornithine to begin the urea cycle

694

 

The urea cycle is linked to gluconeogenesis

696

 

Urea-cycle enzymes are evolutionarily related to enzymes in other metabolic pathways

696

 

Inherited defects of the urea cycle cause hyperammonemia and can lead to brain damage

697

 

Urea is not the only means of disposing of excess nitrogen

698

23.5 Carbon Atoms of Degraded Amino Acids Emerge as Major Metabolic Intermediates

698

 

Pyruvate is an entry point into metabolism for a number of amino acids

699

 

Oxaloacetate is an entry point into metabolism for aspartate and asparagine

700

 

Alpha-ketoglutarate is an entry point into metabolism for five-carbon amino acids

700

 

Succinyl coenzyme A is a point of entry for several nonpolar amino acids

701

 

Methionine degradation requires the formation of a key methyl donor, S-adenosylmethionine

701

 

The branched-chain amino acids yield acetyl CoA, acetoacetate, or propionyl CoA

701

 

Oxygenases are required for the degradation of aromatic amino acids

703

23.6 Inborn Errors of Metabolism Can Disrupt Amino Acid Degradation

705

 

Phenylketonuria is one of the most common metabolic disorders

706

 

Determining the basis of the neurological symptoms of phenylketonuria is an active area of research

706

Part III SYNTHESIZING THE MOLECULES OF LIFE

 

CHAPTER 24 The Biosynthesis of Amino Acids

713

 

Amino acid synthesis requires solutions to three key biochemical problems

714

24.1 Nitrogen Fixation: Microorganisms Use ATP and a Powerful Reductant to Reduce Atmospheric Nitrogen to Ammonia

714

 

The iron–molybdenum cofactor of nitrogenase binds and reduces atmospheric nitrogen

715

 

Ammonium ion is assimilated into an amino acid through glutamate and glutamine

717

24.2 Amino Acids Are Made from Intermediates of the Citric Acid Cycle and Other Major Pathways

719

 

Human beings can synthesize some amino acids but must obtain others from their diet

719

 

Aspartate, alanine, and glutamate are formed by the addition of an amino group to an alpha-ketoacid

720

 

A common step determines the chirality of all amino acids

721

 

The formation of asparagine from aspartate requires an adenylated intermediate

721

 

Glutamate is the precursor of glutamine, proline, and arginine

722

 

3-Phosphoglycerate is the precursor of serine, cysteine, and glycine

722

 

Tetrahydrofolate carries activated one-carbon units at several oxidation levels

723

 

S-Adenosylmethionine is the major donor of methyl groups

724

 

Cysteine is synthesized from serine and homocysteine

726

 

High homocysteine levels correlate with vascular disease

726

 

Shikimate and chorismate are intermediates in the biosynthesis of aromatic amino acids

727

 

Tryptophan synthase illustrates substrate channeling in enzymatic catalysis

729

24.3 Feedback Inhibition Regulates Amino Acid Biosynthesis

730

 

Branched pathways require sophisticated regulation

731

 

The sensitivity of glutamine synthetase to allosteric regulation is altered by covalent modification

732

24.4 Amino Acids Are Precursors of Many Biomolecules

734

 

Glutathione, a gamma-glutamyl peptide, serves as a sulfhydryl buffer and an antioxidant

734

 

Nitric oxide, a short-lived signal molecule, is formed from arginine

735

 

Porphyrins are synthesized from glycine and succinyl coenzyme A

736

 

Porphyrins accumulate in some inherited disorders of porphyrin metabolism

737

CHAPTER 25 Nucleotide Biosynthesis

743

 

Nucleotides can be synthesized by de novo or salvage pathways

744

25.1 The Pyrimidine Ring Is Assembled de Novo or Recovered by Salvage Pathways

744

 

Bicarbonate and other oxygenated carbon compounds are activated by phosphorylation

745

 

The side chain of glutamine can be hydrolyzed to generate ammonia

745

 

Intermediates can move between active sites by channeling

745

 

Orotate acquires a ribose ring from PRPP to form a pyrimidine nucleotide and is converted into uridylate

746

 

Nucleotide mono-, di-, and triphosphates are interconvertible

747

 

CTP is formed by amination of UTP

747

 

Salvage pathways recycle pyrimidine bases

748

25.2 Purine Bases Can Be Synthesized de Novo or Recycled by Salvage Pathways

748

 

The purine ring system is assembled on ribose phosphate

749

 

The purine ring is assembled by successive steps of activation by phosphorylation followed by displacement

749

 

AMP and GMP are formed from IMP

751

 

Enzymes of the purine synthesis pathway associate with one another in vivo

752

 

Salvage pathways economize intracellular energy expenditure

752

25.3 Deoxyribonucleotides Are Synthesized by the Reduction of Ribonucleotides Through a Radical Mechanism

753

 

Mechanism: A tyrosyl radical is critical to the action of ribonucleotide reductase

753

 

Stable radicals other than tyrosyl radical are employed by other ribonucleotide reductases

755

 

Thymidylate is formed by the methylation of deoxyuridylate

755

 

Dihydrofolate reductase catalyzes the regeneration of tetrahydrofolate, a one-carbon carrier

756

 

Several valuable anticancer drugs block the synthesis of thymidylate

757

25.4 Key Steps in Nucleotide Biosynthesis Are Regulated by Feedback Inhibition

758

 

Pyrimidine biosynthesis is regulated by aspartate transcarbamoylase

758

 

The synthesis of purine nucleotides is controlled by feedback inhibition at several sites

758

 

The synthesis of deoxyribonucleotides is controlled by the regulation of ribonucleotide reductase

759

25.5 Disruptions in Nucleotide Metabolism Can Cause Pathological Conditions

760

 

The loss of adenosine deaminase activity results in severe combined immunodeficiency

760

 

Gout is induced by high serum levels of urate

761

 

Lesch–Nyhan syndrome is a dramatic consequence of mutations in a salvage-pathway enzyme

761

 

Folic acid deficiency promotes birth defects such as spina bifida

762

CHAPTER 26 The Biosynthesis of Membrane Lipids and Steroids

767

26.1 Phosphatidate Is a Common Intermediate in the Synthesis of Phospholipids and Triacylglycerols

768

 

The synthesis of phospholipids requires an activated intermediate

769

 

Some phospholipids are synthesized from an activated alcohol

770

 

Phosphatidylcholine is an abundant phospholipid

770

 

Excess choline is implicated in the development of heart disease

771

 

Base-exchange reactions can generate phospholipids

771

 

Sphingolipids are synthesized from ceramide

772

 

Gangliosides are carbohydrate-rich sphingolipids that contain acidic sugars

772

 

Sphingolipids confer diversity on lipid structure and function

773

 

Respiratory distress syndrome and Tay–Sachs disease result from the disruption of lipid metabolism

774

 

Ceramide metabolism stimulates tumor growth

774

 

Phosphatidic acid phosphatase is a key regulatory enzyme in lipid metabolism

775

26.2 Cholesterol Is Synthesized from Acetyl Coenzyme A in Three Stages

776

 

The synthesis of mevalonate, which is activated as isopentenyl pyrophosphate, initiates the synthesis of cholesterol

776

 

Squalene (C30) is synthesized from six molecules of isopentenyl pyrophosphate (C5)

777

 

Squalene cyclizes to form cholesterol

778

26.3 The Complex Regulation of Cholesterol Biosynthesis Takes Place at Several Levels

779

 

Lipoproteins transport cholesterol and triacylglycerols throughout the organism

782

 

Low-density lipoproteins play a central role in cholesterol metabolism

784

 

The absence of the LDL receptor leads to hypercholesterolemia and atherosclerosis

784

 

Mutations in the LDL receptor prevent LDL release and result in receptor destruction

785

 

Cycling of the LDL receptor is regulated

787

 

HDL appears to protect against atherosclerosis

787

 

The clinical management of cholesterol levels can be understood at a biochemical level

788

26.4 Important Derivatives of Cholesterol Include Bile Salts and Steroid Hormones

788

 

Letters identify the steroid rings and numbers identify the carbon atoms

790

 

Steroids are hydroxylated by cytochrome P450 monooxygenases that use NADPH and O2

790

 

The cytochrome P450 system is widespread and performs a protective function

791

 

Pregnenolone, a precursor of many other steroids, is formed from cholesterol by cleavage of its side chain

792

 

Progesterone and corticosteroids are synthesized from pregnenolone

792

 

Androgens and estrogens are synthesized from pregnenolone

792

 

Vitamin D is derived from cholesterol by the ring-splitting activity of light

794

CHAPTER 27 The Integration of Metabolism

801

27.1 Caloric Homeostasis Is a Means of Regulating Body Weight

802

27.2 The Brain Plays a Key Role in Caloric Homeostasis

804

 

Signals from the gastrointestinal tract induce feelings of satiety

804

 

Leptin and insulin regulate long-term control over caloric homeostasis

805

 

Leptin is one of several hormones secreted by adipose tissue

806

 

Leptin resistance may be a contributing factor to obesity

806

 

Dieting is used to combat obesity

807

27.3 Diabetes Is a Common Metabolic Disease Often Resulting from Obesity

807

 

Insulin initiates a complex signal-transduction pathway in muscle

808

 

Metabolic syndrome often precedes type 2 diabetes

809

 

Excess fatty acids in muscle modify metabolism

810

 

Insulin resistance in muscle facilitates pancreatic failure

810

 

Metabolic derangements in type 1 diabetes result from insulin insufficiency and glucagon excess

812

27.4 Exercise Beneficially Alters the Biochemistry of Cells

813

 

Mitochondrial biogenesis is stimulated by muscular activity

813

 

Fuel choice during exercise is determined by the intensity and duration of activity

813

27.5 Food Intake and Starvation Induce Metabolic Changes

816

 

The starved–fed cycle is the physiological response to a fast

816

 

Metabolic adaptations in prolonged starvation minimize protein degradation

818

27.6 Ethanol Alters Energy Metabolism in the Liver

819

 

Ethanol metabolism leads to an excess of NADH

820

 

Excess ethanol consumption disrupts vitamin metabolism

821

CHAPTER 28 DNA Replication, Repair, and Recombination

827

28.1 DNA Replication Proceeds by the Polymerization of Deoxyribonucleoside Triphosphates Along a Template

828

 

DNA polymerases require a template and a primer

829

 

All DNA polymerases have structural features in common

829

 

Two bound metal ions participate in the polymerase reaction

829

 

The specificity of replication is dictated by complementarity of shape between bases

830

 

An RNA primer synthesized by primase enables DNA synthesis to begin

831

 

One strand of DNA is made continuously, whereas the other strand is synthesized in fragments

831

 

DNA ligase joins ends of DNA in duplex regions

832

 

The separation of DNA strands requires specific helicases and ATP hydrolysis

832

28.2 DNA Unwinding and Supercoiling Are Controlled by Topoisomerases

833

 

The linking number of DNA, a topological property, determines the degree of supercoiling

835

 

Topoisomerases prepare the double helix for unwinding

836

 

Type I topoisomerases relax supercoiled structures

836

 

Type II topoisomerases can introduce negative supercoils through coupling to ATP hydrolysis

837

28.3 DNA Replication Is Highly Coordinated

839

 

DNA replication requires highly processive polymerases

839

 

The leading and lagging strands are synthesized in a coordinated fashion

840

 

DNA replication in Escherichia coli begins at a unique site

842

 

DNA synthesis in eukaryotes is initiated at multiple sites

843

 

Telomeres are unique structures at the ends of linear chromosomes

844

 

Telomeres are replicated by telomerase, a specialized polymerase that carries its own RNA template

845

28.4 Many Types of DNA Damage Can Be Repaired

845

 

Errors can arise in DNA replication

846

 

Bases can be damaged by oxidizing agents, alkylating agents, and light

846

 

DNA damage can be detected and repaired by a variety of systems

847

 

The presence of thymine instead of uracil in DNA permits the repair of deaminated cytosine

849

 

Some genetic diseases are caused by the expansion of repeats of three nucleotides

850

 

Many cancers are caused by the defective repair of DNA

850

 

Many potential carcinogens can be detected by their mutagenic action on bacteria

852

28.5 DNA Recombination Plays Important Roles in Replication, Repair, and Other Processes

852

 

RecA can initiate recombination by promoting strand invasion

853

 

Some recombination reactions proceed through Holliday-junction intermediates

854

CHAPTER 29 RNA Synthesis and Processing

859

 

RNA synthesis comprises three stages: Initiation, elongation, and termination

860

29.1 RNA Polymerases Catalyze Transcription

861

 

RNA chains are formed de novo and grow in the 5′-to-3′ direction

862

 

RNA polymerases backtrack and correct errors

863

 

RNA polymerase binds to promoter sites on the DNA template to initiate transcription

864

 

Sigma subunits of RNA polymerase recognize promoter sites

865

 

RNA polymerases must unwind the template double helix for transcription to take place

865

 

Elongation takes place at transcription bubbles that move along the DNA template

866

 

Sequences within the newly transcribed RNA signal termination

866

 

Some messenger RNAs directly sense metabolite concentrations

867

 

The rho protein helps to terminate the transcription of some genes

868

 

Some antibiotics inhibit transcription

869

 

Precursors of transfer and ribosomal RNA are cleaved and chemically modified after transcription in prokaryotes

870

29.2 Transcription in Eukaryotes Is Highly Regulated

871

 

Three types of RNA polymerase synthesize RNA in eukaryotic cells

872

 

Three common elements can be found in the RNA polymerase II promoter region

874

 

The TFIID protein complex initiates the assembly of the active transcription complex

874

 

Multiple transcription factors interact with eukaryotic promoters

875

 

Enhancer sequences can stimulate transcription at start sites thousands of bases away

876

29.3 The Transcription Products of Eukaryotic Polymerases Are Processed

876

 

RNA polymerase I produces three ribosomal RNAs

877

 

RNA polymerase III produces transfer RNA

877

 

The product of RNA polymerase II, the pre-mRNA transcript, acquires a 5′ cap and a 3′ poly(A) tail

878

 

Small regulatory RNAs are cleaved from larger precursors

879

 

RNA editing changes the proteins encoded by mRNA

879

 

Sequences at the ends of introns specify splice sites in mRNA precursors

880

 

Splicing consists of two sequential transesterification reactions

881

 

Small nuclear RNAs in spliceosomes catalyze the splicing of mRNA precursors

882

 

Transcription and processing of mRNA are coupled

883

 

Mutations that affect pre-mRNA splicing cause disease

884

 

Most human pre-mRNAS can be spliced in alternative ways to yield different proteins

885

29.4 The Discovery of Catalytic RNA was Revealing in Regard to Both Mechanism and Evolution

 

886

CHAPTER 30 Protein Synthesis

893

30.1 Protein Synthesis Requires the Translation of Nucleotide Sequences into Amino Acid Sequences

894

 

The synthesis of long proteins requires a low error frequency

894

 

Transfer RNA molecules have a common design

895

 

Some transfer RNA molecules recognize more than one codon because of wobble in base-pairing

897

30.2 Aminoacyl Transfer RNA Synthetases Read the Genetic Code

898

 

Amino acids are first activated by adenylation

898

 

Aminoacyl-tRNA synthetases have highly discriminating amino acid activation sites

899

 

Proofreading by aminoacyl-tRNA synthetases increases the fidelity of protein synthesis

900

 

Synthetases recognize various features of transfer RNA molecules

901

 

Aminoacyl-tRNA synthetases can be divided into two classes

901

30.3 The Ribosome Is the Site of Protein Synthesis

902

 

Ribosomal RNAs (5S, 16S, and 23S rRNA) play a central role in protein synthesis

903

 

Ribosomes have three tRNA-binding sites that bridge the 30s and 50s subunits

905

 

The start signal is usually AUG preceded by several bases that pair with 16S rRNA

905

 

Bacterial protein synthesis is initiated by formylmethionyl transfer RNA

906

 

Formylmethionyl-tRNAf is placed in the P site of the ribosome in the formation of the 70S initiation complex

907

 

Elongation factors deliver aminoacyl-tRNA to the ribosome

907

 

Peptidyl transferase catalyzes peptide-bond synthesis

908

 

The formation of a peptide bond is followed by the GTP-driven translocation of tRNAs and mRNA

909

 

Protein synthesis is terminated by release factors that read stop codons

910

30.4 Eukaryotic Protein Synthesis Differs from Bacterial Protein Synthesis Primarily in Translation Initiation

911

 

Mutations in initiation factor 2 cause a curious pathological condition

913

30.5 A Variety of Antibiotics and Toxins Can Inhibit Protein Synthesis

913

 

Some antibiotics inhibit protein synthesis

914

 

Diphtheria toxin blocks protein synthesis in eukaryotes by inhibiting translocation

914

 

Ricin fatally modifies 28S ribosomal RNA

915

30.6 Ribosomes Bound to the Endoplasmic Reticulum Manufacture Secretory and Membrane Proteins

915

 

Protein synthesis begins on ribosomes that are free in the cytoplasm

916

 

Signal sequences mark proteins for translocation across the endoplasmic reticulum membrane

916

 

Transport vesicles carry cargo proteins to their final destination

918

CHAPTER 31 The Control of Gene Expression in Prokaryotes

925

31.1 Many DNA-Binding Proteins Recognize Specific DNA Sequences

926

 

The helix-turn-helix motif is common to many prokaryotic DNA-binding proteins

927

31.2 Prokaryotic DNA-Binding Proteins Bind Specifically to Regulatory Sites in Operons

927

 

An operon consists of regulatory elements and protein-encoding genes

928

 

The lac repressor protein in the absence of lactose binds to the operator and blocks transcription

929

 

Ligand binding can induce structural changes in regulatory proteins

930

 

The operon is a common regulatory unit in prokaryotes

930

 

Transcription can be stimulated by proteins that contact RNA polymerase

931

31.3 Regulatory Circuits Can Result in Switching Between Patterns of Gene Expression

932

 

The λ repressor regulates its own expression

932

 

A circuit based on the λ repressor and Cro forms a genetic switch

933

 

Many prokaryotic cells release chemical signals that regulate gene expression in other cells

933

 

Biofilms are complex communities of prokaryotes

934

31.4 Gene Expression Can Be Controlled at Posttranscriptional Levels

935

 

Attenuation is a prokaryotic mechanism for regulating transcription through the modulation of nascent RNA secondary structure

935

CHAPTER 32 The Control of Gene Expression in Eukaryotes

941

32.1 Eukaryotic DNA Is Organized into Chromatin

943

 

Nucleosomes are complexes of DNA and histones

943

 

DNA wraps around histone octamers to form nucleosomes

943

32.2 Transcription Factors Bind DNA and Regulate Transcription Initiation

945

 

A range of DNA-binding structures are employed by eukaryotic DNA-binding proteins

945

 

Activation domains interact with other proteins

946

 

Multiple transcription factors interact with eukaryotic regulatory regions

946

 

Enhancers can stimulate transcription in specific cell types

946

 

Induced pluripotent stem cells can be generated by introducing four transcription factors into differentiated cells

947

32.3 The Control of Gene Expression Can Require Chromatin Remodeling

948

 

The methylation of DNA can alter patterns of gene expression

949

 

Steroids and related hydrophobic molecules pass through membranes and bind to DNA-binding receptors

949

 

Nuclear hormone receptors regulate transcription by recruiting coactivators to the transcription complex

950

 

Steroid-hormone receptors are targets for drugs

951

 

Chromatin structure is modulated through covalent modifications of histone tails

952

 

Histone deacetylases contribute to transcriptional repression

953

32.4 Eukaryotic Gene Expression Can Be Controlled at Posttranscriptional Levels

954

 

Genes associated with iron metabolism are translationally regulated in animals

954

 

Small RNAs regulate the expression of many eukaryotic genes

956

Part IV RESPONDING TO ENVIRONMENTAL CHANGES

 

CHAPTER 33 Sensory Systems

961

33.1 A Wide Variety of Organic Compounds Are Detected by Olfaction

962

 

Olfaction is mediated by an enormous family of seven-transmembrane-helix receptors

962

 

Odorants are decoded by a combinatorial mechanism

964

33.2 Taste Is a Combination of Senses That Function by Different Mechanisms

966

 

Sequencing of the human genome led to the discovery of a large family of 7TM bitter receptors

967

 

A heterodimeric 7TM receptor responds to sweet compounds

968

 

Umami, the taste of glutamate and aspartate, is mediated by a heterodimeric receptor related to the sweet receptor

969

 

Salty tastes are detected primarily by the passage of sodium ions through channels

969

 

Sour tastes arise from the effects of hydrogen ions (acids) on channels

969

33.3 Photoreceptor Molecules in the Eye Detect Visible Light

970

 

Rhodopsin, a specialized 7TM receptor, absorbs visible light

970

 

Light absorption induces a specific isomerization of bound 11-cis-retinal

971

 

Light-induced lowering of the calcium level coordinates recovery

972

 

Color vision is mediated by three cone receptors that are homologs of rhodopsin

973

 

Rearrangements in the genes for the green and red pigments lead to “color blindness”

974

33.4 Hearing Depends on the Speedy Detection of Mechanical Stimuli

975

 

Hair cells use a connected bundle of stereocilia to detect tiny motions

975

 

Mechanosensory channels have been identified in Drosophila and vertebrates

976

33.5 Touch Includes the Sensing of Pressure, Temperature, and Other Factors

977

 

Studies of capsaicin reveal a receptor for sensing high temperatures and other painful stimuli

977

CHAPTER 34 The Immune System

981

 

Innate immunity is an evolutionarily ancient defense system

982

 

The adaptive immune system responds by using the principles of evolution

984

34.1 Antibodies Possess Distinct Antigen-Binding and Effector Units

985

34.2 Antibodies Bind Specific Molecules Through Hypervariable Loops

988

 

The immunoglobulin fold consists of a beta-sandwich framework with hypervariable loops

988

 

X-ray analyses have revealed how antibodies bind antigens

989

 

Large antigens bind antibodies with numerous interactions

990

34.3 Diversity Is Generated by Gene Rearrangements

991

 

J (joining) genes and D (diversity) genes increase antibody diversity

991

 

More than 108 antibodies can be formed by combinatorial association and somatic mutation

992

 

The oligomerization of antibodies expressed on the surfaces of immature B cells triggers antibody secretion

993

 

Different classes of antibodies are formed by the hopping of VH genes

994

34.4 Major-Histocompatibility-Complex Proteins Present Peptide Antigens on Cell Surfaces for Recognition by T-Cell Receptors

995

 

Peptides presented by MHC proteins occupy a deep groove flanked by alpha helices

996

 

T-cell receptors are antibody-like proteins containing variable and constant regions

998

 

CD8 on cytotoxic T cells acts in concert with T-cell receptors

998

 

Helper T cells stimulate cells that display foreign peptides bound to class II MHC proteins

1000

 

Helper T cells rely on the T-cell receptor and CD4 to recognize foreign peptides on antigen-presenting cells

1000

 

MHC proteins are highly diverse

1002

 

Human immunodeficiency viruses subvert the immune system by destroying helper T cells

1003

34.5 The Immune System Contributes to the Prevention and the Development of Human Diseases

1004

 

T cells are subjected to positive and negative selection in the thymus

1004

 

Autoimmune diseases result from the generation of immune responses against self-antigens

1005

 

The immune system plays a role in cancer prevention

1005

 

Vaccines are a powerful means to prevent and eradicate disease

1006

CHAPTER 35 Molecular Motors

1011

35.1 Most Molecular-Motor Proteins Are Members of the P-Loop NTPase Superfamily

1012

 

Molecular motors are generally oligomeric proteins with an ATPase core and an extended structure

1012

 

ATP binding and hydrolysis induce changes in the conformation and binding affinity of motor proteins

1014

35.2 Myosins Move Along Actin Filaments

1016

 

Actin is a polar, self-assembling, dynamic polymer

1016

 

Myosin head domains bind to actin filaments

1018

 

Motions of single motor proteins can be directly observed

1018

 

Phosphate release triggers the myosin power stroke

1019

 

Muscle is a complex of myosin and actin

1019

 

The length of the lever arm determines motor velocity

1022

35.3 Kinesin and Dynein Move Along Microtubules

1022

 

Microtubules are hollow cylindrical polymers

1022

 

Kinesin motion is highly processive

1024

35.4 A Rotary Motor Drives Bacterial Motion

1026

 

Bacteria swim by rotating their flagella

1026

 

Proton flow drives bacterial flagellar rotation

1026

 

Bacterial chemotaxis depends on reversal of the direction of flagellar rotation

1028

CHAPTER 36 Drug Development

1033

36.1 The Development of Drugs Presents Huge Challenges

1034

 

Drug candidates must be potent and selective modulators of their targets

1035

 

Drugs must have suitable properties to reach their targets

1036

 

Toxicity can limit drug effectiveness

1040

36.2 Drug Candidates Can Be Discovered by Serendipity, Screening, or Design

1041

 

Serendipitous observations can drive drug development

1041

 

Natural products are a valuable source of drugs and drug leads

1043

 

Screening libraries of synthetic compounds expands the opportunity for identification of drug leads

1044

 

Drugs can be designed on the basis of three-dimensional structural information about their targets

1046

36.3 Analyses of Genomes Hold Great Promise for Drug Discovery

1048

 

Potential targets can be identified in the human proteome

1048

 

Animal models can be developed to test the validity of potential drug targets

1049

 

Potential targets can be identified in the genomes of pathogens

1050

 

Genetic differences influence individual responses to drugs

1050

36.4 The Clinical Development of Drugs Proceeds Through Several Phases

1051

 

Clinical trials are time consuming and expensive

1052

 

The evolution of drug resistance can limit the utility of drugs for infectious agents and cancer

1053

Answers to Problems

A1

Selected Readings

B1

Index

C1