H 6 Transcription And

CONTROL OF GENE EXPRESSION, 105

Structure of RNA, 105 RNA Polymerase, 106 Gene Notation, 106 Bacterial RNA Synthesis, 106 Control of Bacterial Gene Expression, 109 lac, an Inducible Operon, 111 trp, a Repressible Operon, 116 Eukaryotic RNA Synthesis, 118 Messenger RNA Processing, 118 Control of Eukaryotic Gene Expression, 119

Glucocorticoids Cross the Cell Membrane to Activate Transcription, 121 Summary, 125 Further Reading, 125 Review Questions, 126 Answers to Review Questions, 127

7 RECOMBINANT DNA AND GENETIC ENGINEERING, 129

DNA Cloning, 129 Creating the Clone, 130

Introduction of Foreign DNA Molecules into Bacteria, 130 Selection of cDNA Clones, 134 Genomic DNA Clones, 139 Uses of DNA Clones, 143 DNA Sequencing, 143 Southern Blotting, 146 In situ Hybridization, 147 Northern Blotting, 148 Production of Mammalian Proteins in

Bacteria, 149 Protein Engineering, 149 Polymerase Chain Reaction, 150 Identifying the Gene Responsible for a

Disease, 152 Reverse Genetics, 152 Transgenic Animals, 157 Ethics of DNA Testing for Inherited

Disease, 157 Summary, 158 Further Reading, 159 Review Questions, 159 Answers to Review Questions, 160

8 MANUFACTURING PROTEIN, 163

Attachment of an Amino Acid to Its tRNA, 163

Transfer RNA, the Anticodon, and the Wobble, 164 TheRibosome, 165 Bacterial Protein Synthesis, 168

Ribosome-Binding Site, 168 Chain Initiation, 169 The 70S Initiation Complex, 171 Elongation of the Protein Chain, 171 The Polyribosome, 173 Termination of Protein Synthesis, 174 The Ribosome Is Recycled, 175 Eukaryotic Protein Synthesis Is a Little More Complex, 175 Antibiotics and Protein Synthesis, 176 Summary, 178 Further Reading, 179 Review Questions, 179 Answers to Review Questions, 180

H 9 PROTEIN STRUCTURE, 183

Naming Proteins, 184 Polymers of Amino Acids, 184

The Amino Acid Building Blocks, 184 The Unique Properties of Each Amino Acid, 188 Other Amino Acids Are Found in

Nature, 191 The Three-Dimensional Structures of Proteins, 192 Hydrogen Bonds, 195 Electrostatic Interactions, 199 van der Waals Forces, 199 Hydrophobic Interactions, 199 Disulfide Bonds, 199 Tertiary Structure: Domains and

Motifs, 200 Quaternary Structure: Assemblies of Protein

Subunits, 204 Prosthetic Groups, 205 The Primary Structure Contains all the Information Necessary to Specify Higher-Level Structures, 206 Summary, 209 Further Reading, 209 Review Questions, 210 Answers to Review Questions, 211

H 10 INTRACELLULAR PROTEIN TRAFFICKING, 213

Three Modes of Intracellular Protein Transport, 213 Targeting Sequences, 215 Retention, 215 Transport to and from the Nucleus, 215 The Nuclear Pore Complex, 216 Gated Transport Through the Nuclear

Pore, 216 GTPases and the GDP/GTP Cycle, 218 GTPases in Nuclear Transport, 218 Transport Across Membranes, 221 Transport to Mitochondria, 221 Chaperones and Protein Folding, 221 Transport to Peroxisomes, 221 Synthesis on the Rough Endoplasmic

Reticulum, 223 Glycosylation: The Endoplasmic Reticulum and Golgi System, 225 Vesicular Trafficking Between Intracellular Compartments, 226 The Principle of Fission and Fusion, 226 Vesicle Formation, 228 Coatomer-Coated Vesicles, 228 Clathrin-Coated Vesicles, 229 The Trans-Golgi Network and Protein

Secretion, 229 Targeting Proteins to the Lysosome, 230 Fusion, 231 Summary, 232 Further Reading, 233 Review Questions, 233 Answers to Review Questions, 234

H 11 HOW PROTEINS WORK, 237

How Proteins Bind Other Molecules, 237 Dynamic Protein Structures, 238 Allosteric Effects, 238 Chemical Changes That Shift the Preferred Shape of a Protein, 240 Enzymes Are Protein Catalysts, 241

The Initial Velocity of an Enzyme

Reaction, 242 Effect of Substrate Concentration on

Initial Velocity, 244 The Effect of Enzyme Concentration, 245 The Specificity Constant, 247 Enzyme Catalysis, 247 Cofactors and Prosthetic Groups, 249 Enzymes Can Be Regulated, 251 Summary, 254 Further Reading, 254 Review Questions, 255 Answers to Review Questions, 256

12 ENERGY TRADING WITHIN THE CELL, 257

Cellular Energy Currencies, 258 Reduced Nicotinamide Adenine

Dinucleotide (NADH), 259 Nucleoside Triphosphates (ATP plus

GTP, CTP, TTP, and UTP), 259 The Hydrogen Ion Gradient Across the

Mitochondrial Membrane, 261 The Sodium Gradient Across the Plasma Membrane, 262 Energy Currencies Are Interconvertible, 263 Exchange Mechanisms Convert Between the Four Energy Currencies, 263 Electron Transport Chain, 265 ATP Synthase, 269 Sodium/Potassium ATPase, 270 ADP/ATP Exchanger, 271 Photosynthesis, 271 All Carriers Can Change Direction, 275 Summary, 278 Further Reading, 278 Review Questions, 278 Answers to Review Questions, 279

13 METABOLISM, 281

The Krebs Cycle: The Central Switching Yard of Metabolism, 283

From Glucose to Pyruvate: Glycolysis, 284 Glycolysis Without Oxygen, 286 Glycogen Can Provide Glucose for

Glycolysis, 288 Glucose May Be Oxidized to Produce Pentose Sugars, 289 From Fats to Acetyl-CoA: p Oxidation, 290 Amino Acids as Another Source of

Metabolic Energy, 292 Making Glucose: Gluconeogenesis, 295 Making Glycogen: Glycogenesis, 298 Making Fatty Acids and Glycerides, 300 Synthesis of Amino Acids, 300 Carbon Fixation in Plants, 302 Control of Energy Production, 303 Feedback and Feedforward, 303 Negative Feedback Control of

Glycolysis, 304 Feedforward Control in Muscle Cells, 304 Summary, 306 Further Reading, 306 Review Questions, 307 Answers to Review Questions, 308

H 14 IONS AND VOLTAGES, 309

The Potassium Gradient and the Resting Voltage, 309

Potassium Channels Make the Plasma Membrane Permeable to Potassium Ions, 310

Concentration Gradients and Electrical Voltage Can Balance, 311 The Chloride Gradient, 314 General Properties of Channels, 314 General Properties of Carriers, 316 The Glucose Carrier, 316 The Sodium-Calcium Exchanger, 317 Carriers with an Enzymatic Action: The Calcium ATPase, 318 Summary, 322 Further Reading, 322

Review Questions, 322 Answers to Review Questions, 324

H 15 THE ACTION POTENTIAL, 325

The Calcium Action Potential in Sea Urchin Eggs, 325

Effect of Egg Transmembrane Voltage on

Sperm Fusion, 325 The Voltage-Gated Calcium

Channel, 327 The Calcium Action Potential, 328 The Voltage-Gated Sodium Channel in Nerve Cells, 330

The Voltage-Gated Sodium Channel, 330 Electrical Transmission down a Nerve

Cell Axon, 332 Myelination and Rapid Action Potential Transmission, 334 Summary, 337 Further Reading, 338 Review Questions, 338 Answers to Review Questions, 339

H 16 INTRACELLULAR SIGNALING, 341

Calcium, 341

Calcium Can Enter from the Extracellular

Medium, 341 Calcium Can Be Released from the

Endoplasmic Reticulum, 344 Processes Activated by Cytosolic

Calcium Are Extremely Diverse, 348 Return of Calcium to Resting Levels, 350 Cyclic Adenosine Monophosphate, 350 Cyclic Guanosine Monophosphate, 353 Multiple Messengers, 353 Biochemical Signaling, 353

Receptor Tyrosine Kinases and the MAP

Kinase Cascade, 353 Growth Factors Can Trigger a Calcium

Signal, 356 Protein Kinase B and the Glucose Transporter: How Insulin Works, 356

Crosstalk—Signaling Pathways or Signaling Webs?, 357 Summary, 359 Further Reading, 360 Review Questions, 360 Answers to Review Questions, 361

H 17 INTERCELLULAR COMMUNICATION, 363

Classifying Transmitters and Receptors, 363 Ionotropic Cell Surface Receptors, 364 Metabotropic Cell Surface

Receptors, 365 Intracellular Receptors, 365 Intercellular Communication in Action: The Gastrocnemius Muscle, 365 Telling the Muscle to Contract:

The Action of Motoneurones, 367 Controlling the Blood Supply: Paracrine

Transmitters, 368 New Blood Vessels in Growing Muscle, 371 Synapses Between Neurons, 372 Summary, 376 Further Reading, 377 Review Questions, 377 Answers to Review Questions, 378

H 18 MECHANICAL MOLECULES, 381

The Cytoskeleton is Both Strong and

Motile, 381 Microtubules, 381 Microtubule-Based Motility, 386 Cilia and Flagella, 386 Intracellular Transport, 389 Microfilaments, 390

Muscle Contraction, 393 Cell Locomotion, 395 Cytoplasmic Streaming, 395 Intermediate Filaments, 396

Anchoring Cell Junctions, 396 Summary, 398

Further Reading, 398

Review Questions, 398

Answers to Review Questions, 400

0 19 CELL CYCLE AND CONTROL OF CELL NUMBER, 401

Stages of Mitosis, 402 Meiosis and Fertilization, 404 Meiosis, 405

Fertilization and Inheritance, 406 Dominant Genetic Disease, 408 Crossing Over and Linkage, 408 Control of the Cell Division Cycle, 408 Molecular Regulation of the G2/M (Interphase/Mitosis) Cell Cycle Control Point, 410 What About the G1/S Control Point?, 412 Apoptosis, 415

Instructed Death: Death Domain

Receptors, 416 Default Death: Absence of Growth

Factors, 416 The Sick Are Left to Die:

Stress-Activated Apoptosis, 417 Summary, 419 Further Reading, 420 Review Questions, 420 Answers to Review Questions, 421

Ü 20 CASE STUDY: CYSTIC FIBROSIS, 423

Introduction, 423

Cystic Fibrosis is a Severe Genetic

Disease, 423 The Fundamental Lesion in Cystic Fibrosis

Lies in Chloride Transport, 424 Homing in on the CF Gene, 425 Cloning the Gene for CF, 426 The CFTR Gene Codes for a Chloride Ion

Channel, 426 Gene Therapy for CF, 427 Diagnostic Tests for CF, 431

The Future, 432

Summary, 433

Further Reading, 433

Review Questions, 434

Answers to Review Questions, 435

APPENDIX: CHANNELS AND CARRIERS, 437

GLOSSARY, 441

INDEX, 501

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