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DETAILED CONTENTS About the Authors iii Preface v Acknowledgments viii Chapter 1 A Preview of the Cell 01 The Cell Theory: A Brief History 01 The Emergence of Modern Cell Biology 03 The Cytological Strand Deals with Cellular Structure 05 The Biochemical Strand Covers the Chemistry of Biological Structure and Function 08 The Genetic Strand Focuses on Information Flow 09 ¿Facts¿ and the Scientific Method 0012 PerspectiveSummary of Key Points 0013 Making Connections 00 Problem Set 0013 Suggested Reading 0015 Box 1A: Units of Measurement in Cell Biology 02 Box 1B: Further Insights: Biology, ¿Facts,¿ and the Scientific Method 0010 Chapter 2 The Chemistry of the Cell 0016 The Importance of Carbon 0017 Carbon-Containing Molecules Are Stable 0018 Carbon-Containing Molecules Are Diverse 0019 Carbon-Containing Molecules Can Form Stereoisomers 0019 The Importance of Water 0020 Water Molecules Are Polar 0021 Water Molecules Are Cohesive 0021 Water Has a High Temperature-Stabilizing Capacity 0021 Water Is an Excellent Solvent 0022 The Importance of Selectively Permeable Membranes 0023 A Membrane Is a Lipid Bilayer with Proteins Embedded in It 0024 Membranes Are Selectively Permeable 0025 The Importance of Synthesis by Polymerization 0025 Macromolecules Are Responsible for Most of the Form and Function in Living Systems 0026 Cells Contain Three Different Kinds of Macromolecules 0026 Macromolecules Are Synthesized by Stepwise Polymerization of Monomers 0028 The Importance of Self-Assembly 0029 Many Proteins Self-Assemble 0030 Molecular Chaperones Assist the Assembly of Some Proteins 0032 Noncovalent Bonds and Interactions Are Important in the Folding of Macromolecules 0033 Self-Assembly Also Occurs in Other Cellular Structures 0033 The Tobacco Mosaic Virus Is a Case Study in Self-Assembly 0034 Self-Assembly Has Limits 0035 Hierarchical Assembly Provides Advantages for the Cell 0035 PerspectiveSummary of Key Points 0037 Making Connections 00 Problem Set 0037 Suggested Reading 0039 Box 2A: Further Insights: Tempus Fugit and the Fine Art of Watchmaking 0036 Chapter 3 The Macromolecules of the Cell 0040 Proteins 0040 The Monomers Are Amino Acids 0041 The Polymers Are Polypeptides and Proteins 0042 Several Kinds of Bonds and Interactions Are Important in Protein Folding and Stability 0044 Disulfide Bonds 00 Protein Structure Depends on Amino Acid Sequence and Interactions 0046 Nucleic Acids 0053 The Monomers Are Nucleotides 0054 The Polymers Are DNA and RNA 0056 A DNA Molecule Is a Double-Stranded Helix 0058 Polysaccharides 0061 The Monomers Are Monosaccharides 0061 The Polymers Are Storage and Structural Polysaccharides 0062 Polysaccharide Structure Depends on the Kinds of Glycosidic Bonds Involved 0065 Lipids 0066 Fatty Acids Are the Building Blocks of Several Classes of Lipids 0066 Triacylglycerols Are Storage Lipids 0067 Phospholipids Are Important in Membrane Structure 0068 Glycolipids Are Specialized Membrane Components 0069 Steroids Are Lipids with a Variety of Functions 0069 Terpenes Are Formed from Isoprene 0070 PerspectiveSummary of Key Points 0070 Making Connections 00 Problem Set 0071 Suggested Reading 0073 Box 3A: Further Insights: On the Trail of the Double Helix 0058 Chapter 4 Cells and Organelles 7400 Properties and Strategies of Cells 7400 All Organisms Are Eukaryotes, Eubacteria, or Archaea 740 Cells Come in Many Sizes and Shapes Limitations on Cell Size 7500 Eukaryotic Cells Use Organelles to Compartmentalize Cellular Function 7600 Bacteria, Archaea,Prokaryotes and Eukaryotes Differ from Each Other in Many Ways 7600 Cell Specialization Demonstrates the Unity and Diversity of Biology 8000 The Eukaryotic Cell in Overview: Pictures at an Exhibition 8100 The Plasma Membrane Defines Cell Boundaries and Retains Contents 8100 The Nucleus Is the Cell¿s Information Center of the Eukaryotic Cell 8200 Intracellular Membranes and Organelles Define Compartments 8300 The Cytoplasm of Eukaryotic Cells Contains the Cytosol and Cytoskeleton 9500 The Extracellular Matrix and the Cell Wall Are the ¿Outside¿ of the Cell 9700 Viruses, Viroids, and Prions: Agents That Invade Cells 9800 A Virus Consists of a DNA or RNA Core Surrounded by a Protein Coat 9800 Viroids Are Small, Circular RNA Molecules 9900 Prions Are ¿Proteinaceous Infective Particles¿ 9900 Perspective Summary of Key Points 101000 Making Connections 000 Problem Set 101000 Suggested Reading 103000 Box 4A: Human Applications: Organelles and Human Diseases 8400 Box 4B: Further Insights: Discovering Organelles: The Importance of Centrifuges and Chance Observations 9200 Chapter 5 Bioenergetics: The Flow of Energy in the Cell 105000 The Importance of Energy 105000 Cells Need Energy to Drive Six Different Kinds of Changes 106000 Most Organisms Obtain Energy Either from Sunlight or from Organic Food Moleculesthe Oxidation of Chemical Compounds 108000 Energy Flows Through the Biosphere Continuously 108000 The Flow of Energy Through the Biosphere Is Accompanied by a Flow of Matter 109000 Bioenergetics 110000 To Understand Energy Flow, We Need to Understand Systems, Heat, and Work 110000 The First Law of Thermodynamics Tells Us That Energy Is Conserved 112000 The Second Law of Thermodynamics Tells Us That Reactions Have Directionality 112000 Entropy and Free Energy Are Two Alternative Means of Assessing Thermodynamic Spontaneity 114000 Understanding ?G 118000 The Equilibrium Constant Is a Measure of Directionality 119000 ?G Can Be Calculated Readily 119000 The Standard Free Energy Change Is ?G Measured Under Standard Conditions 120000 Summing Up: The Meaning of ?G? and ?G?? 121000 Free Energy Change: Sample Calculations 122000 Life and the Steady State: Reactions That Move Toward Equilibrium Without Ever Getting There 123000 PerspectiveSummary of Key Points 123000 Making Connections 000 Problem Set 124000 Suggested Reading 126000 Box 5A: Further Insights: Jumping Beans and Free Energy 116000 Chapter 6 Enzymes: The Catalysts of Life 127000 Activation Energy and the Metastable State 127000 Before a Chemical Reaction Can Occur, the Activation Energy Barrier Must Be Overcome 128000 The Metastable State Is a Result of the Activation Barrier 128000 Catalysts Overcome the Activation Energy Barrier 129000 Enzymes as Biological Catalysts 129000 Most Enzymes Are Proteins 129000 Substrate Binding, Activation, and Reaction Occur at the Active Site 134000 Enzyme Kinetics 136000 Most Enzymes Display Michaelis-Menten Kinetics 137000 What Is the Meaning of Vmax and Km? 137000 Why aAre Km and Vmax Important to Cell Biologists? 139000 The Double-Reciprocal Plot Is a Useful Means of Linearizing Kinetic Data 140000 Determining Km and Vmax: An Example 141000 Enzyme Inhibitors Act Irreversibly or Reversibly 142000 Enzyme Regulation 143000 Allosteric Enzymes Are Regulated by Molecules Other than Reactants and Products 144000 Allosteric Enzymes Exhibit Cooperative Interactions Between Subunits 146000 Enzymes Can Also Be Regulated by the Addition or Removal of Chemical Groups 146000 RNA Molecules as Enzymes: Ribozymes 000147 PerspectiveSummary of Key Points 000149 Making Connections 000 Problem Set 000150 Suggested Reading 000153 Box 6A: Further Insights: Monkeys and Peanuts 000138 Chapter 7 Membranes: Their Structure, Function, and Chemistry 000154 The Functions of Membranes 000155 Membranes Define Boundaries and Serve as Permeability Barriers 000155 Membranes Are Sites of Specific Proteins and Therefore of Specific Functions 000155 Membrane Proteins Regulate the Transport of Solutes 000156 Membrane Proteins Detect and Transmit Electrical and Chemical Signals 000156 Membrane Proteins Mediate Cell Adhesion and Cell-to-Cell Communication 000156 Models of Membrane Structure: An Experimental Perspective 000156 Overton and Langmuir: Lipids Are Important Components of Membranes 000157 Gorter and Grendel: The Basis of Membrane Structure Is a Lipid Bilayer 000157 Davson and Danielli: Membranes Also Contain Proteins 000158 Robertson: All Membranes Share a Common Underlying Structure 000158 Further Research Revealed Major Shortcomings of the Davson-Danielli Model 000159 Singer and Nicolson: A Membrane Consists of a Mosaic of Proteins in a Fluid Lipid Bilayer 000160 Unwin and Henderson: Most Membrane Proteins Contain Transmembrane Segments 000160 Recent Findings Further Refine Our Understanding of Membrane Structure 000161 Membrane Lipids: The ¿Fluid¿ Part of the Model 000162 Membranes Contain Several Major Classes of Lipids 000162 Thin-Layer Chromatography Is an Important Technique for Lipid Analysis 000164 Fatty Acids Are Essential to Membrane Structure and Function 000165 Membrane Asymmetry: Most Lipids Are Distributed Unequally Between the Two Monolayers 000165 The Lipid Bilayer Is Fluid 000167 Membranes Function Properly Only in the Fluid State 000168 Most Organisms Can Regulate Membrane Fluidity 000170 Lipid Rafts Are Localized Regions of Membrane Lipids That Are Involved in Cell Signaling 000171 Membrane Proteins: The ¿Mosaic¿ Part of the Model 000171 The Membrane Consists of a Mosaic of Proteins: Evidence from Freeze-Fracture Microscopy 000171 Membranes Contain Integral, Peripheral, and Lipid-Anchored Proteins 000173 Proteins Can Be Separated by SDS¿Polyacrylamide Gel Electrophoresis 000176 Determining the Three-Dimensional Structure of Membrane Proteins Is Proving to Be Increasingly Feasible 000176 Molecular Biology Has Contributed Greatly to Our Understanding of Membrane Proteins 000178 Membrane Proteins Have a Variety of Functions 000179 Membrane Proteins Are Oriented Asymmetrically Across the Lipid Bilayer 000179 Many Membrane Proteins Are Glycosylated 000182 Membrane Proteins Vary in Their Mobility 000183 PerspectiveSummary of Key Points 000187 Making Connections 000 Problem Set 000187 Suggested Reading 000190 Box 7A: Experimental Techniques: Revolutionizing the Study of Membrane Proteins: The Impact of Molecular Biology 000180 Chapter 8 Transport Across Membranes: Overcoming the Permeability Barrier 000191 Cells and Transport Processes 000191 Solutes Cross Membranes by Simple Diffusion, Facilitated Diffusion, and Active Transport 000192 The Movement of a Solute Across a Membrane Is Determined by Its Concentration Gradient or Its Electrochemical Potential 000193 The Erythrocyte Plasma Membrane Provides Examples of Transport Mechanisms 000193 Simple Diffusion: Unassisted Movement Down the Gradient 000193 Diffusion Always Moves Solutes Toward Equilibrium 000194 Osmosis Is the Diffusion of Water Across a Differentially Selectively Permeable Membrane 000195 Simple Diffusion Is Limited to Small, Nonpolar Molecules 000195 The Rate of Simple Diffusion Is Directly Proportional to the Concentration Gradient 000198 Facilitated Diffusion: Protein-Mediated Movement Down the Gradient 000199 Carrier Proteins and Channel Proteins Facilitate Diffusion by Different Mechanisms 000199 Carrier Proteins Alternate Between Two Conformational States 000200 Carrier Proteins Are Analogous to Enzymes in Their Specificity and Kinetics 000200 Carrier Proteins Transport Either One or Two Solutes 000200 The Erythrocyte Glucose Transporter and Anion Exchange Protein Are Examples of Carrier Proteins 000201 Channel Proteins Facilitate Diffusion by Forming Hydrophilic Transmembrane Channels 000202 Active Transport: Protein-Mediated Movement Up the Gradient 000203 The Coupling of Active Transport to an Energy Source May Be Direct or Indirect 000204 Direct Active Transport Depends on Four Types of Transport ATPases 000205 Indirect Active Transport Is Driven by Ion Gradients 000206 Examples of Active Transport 000207 Direct Active Transport: The Na+/K+ Pump Maintains Electrochemical Ion Gradients 000207 Indirect Active Transport: Sodium Symport Drives the Uptake of Glucose 000210 The Bacteriorhodopsin Proton Pump Uses Light Energy to Transport Protons 000210 The Energetics of Transport 000212 For Uncharged Solutes, the ?G of Transport Depends Only on the Concentration Gradient 000213 For Charged Solutes, the ?G of Transport Depends on the Electrochemical Potential 000214 Beyond Ions and Small Molecules: Secretion and Uptake of Macromolecules and Particles 000215 Perspective Summary of Key Points 000216 Making Connections 000 Problem Set 000216 Suggested Reading 000219 Box 8A: Further Insights: Osmosis: The Special Case of Water Diffusion of Water Across a Selectively Permeable Membrane 000196 Box 8B: Human Applications: Membrane Transport, Cystic Fibrosis, and the Prospects for Gene Therapy 000208 Chapter 9 Chemotrophic Energy Metabolism: Glycolysis and Fermentation 000221 Metabolic Pathways 000221 ATP: The Universal Energy Coupler 000222 ATP Contains Two Energy-Rich Phosphoanhydride Bonds 000222 ATP Hydrolysis Is Highly Exergonic Because of Charge Repulsion and Resonance Stabilization 000222 ATP Is an Important Intermediate in Cellular Energy Metabolism 000224 Chemotrophic Energy Metabolism 000225 Biological Oxidations Usually Involve the Removal of Both Electrons and Protons and Are Highly Exergonic 000225 Coenzymes Such as Serve as Electron Acceptors in Biological Oxidations 000226 Most Chemotrophs Meet Their Energy Needs by Oxidizing Organic Food Molecules 000227 Glucose Is One of the Most Important Oxidizable Substrates in Energy Metabolism 000227 The Oxidation of Glucose Is Highly Exergonic 000228 Glucose Catabolism Yields Much More Energy in the Presence of Oxygen than in Its Absence 000228 Based on Their Need for Oxygen, Organisms Are Aerobic, Anaerobic, or Facultative 000228 Glycolysis and Fermentation: ATP Generation Without the Involvement of Oxygen 000229 Glycolysis Generates ATP by Catabolizing Glucose to Pyruvate 000229 The Fate of Pyruvate Depends on Whether or Not Oxygen Is Available 000232 In the Absence of Oxygen, Pyruvate Undergoes Fermentation to Regenerate 000232 Fermentation Taps Only a Small Fraction of the Substrate¿s Free Energy of the Substrate but Conserves That Energy Efficiently as ATP 000234 Alternative Substrates for Glycolysis 000234 Other Sugars and Glycerol Are Also Catabolized by the Glycolytic Pathway 000234 Polysaccharides Are Cleaved to Form Sugar Phosphates That Also Enter the Glycolytic Pathway 000236 Gluconeogenesis 000236 The Regulation of Glycolysis and Gluconeogenesis 000238 Key Enzymes in the Glycolytic and Gluconeogenic Pathways Are Subject to Allosteric Regulation 000238 Fructose-2,6-Bisphosphate Is an Important Regulator of Glycolysis and Gluconeogenesis 000239 Novel Roles for Glycolytic Enzymes 000 PerspectiveSummary of Key Points 000243 Making Connections 000 Problem Set 000244 Suggested Reading 000247 Box 9A: Further Insights: ¿What Happens to the Sugar?¿ 000240 Chapter 10 Chemotrophic Energy Metabolism: Aerobic Respiration 000248 Cellular Respiration: Maximizing ATP Yields 000248 Aerobic Respiration Yields Much More Energy than Fermentation Does 000249 Respiration Includes Glycolysis, Pyruvate Oxidation, the TCA Cycle, Electron Transport, and ATP Synthesis 000250 The Mitochondrion: Where the Action Takes Place 000250 Mitochondria Are Often Present Where the ATP Needs Are Greatest 000250 Are Mitochondria Interconnected Networks Rather than Discrete Organelles? 000251 The Outer and Inner Membranes Define Two Separate Compartments and Three Regions 000252 Mitochondrial Functions Occur in or on Specific Membranes and Compartments 000253 In Prokaryotes Bacteria, Respiratory Functions Are Localized to the Plasma Membrane and the Cytoplasm 000254 The Tricarboxylic Acid Cycle: Oxidation in the Round 000255 Pyruvate Is Converted to Acetyl Coenzyme A by Oxidative Decarboxylation 000255 The TCA Cycle Begins with the Entry of Acetate as Acetyl CoA 000256 Two Oxidative Decarboxylations then Form NADH and Release CO2 000NADH Is Formed and Is Released in Two Oxidative Reactions of the TCA Cycle 256 Direct Generation of GTP (or ATP) Occurs at One Step in the TCA Cycle 000258 The Final Oxidative Reactions of the TCA Cycle Generate and NADH 000258 Summing Up: The Products of the TCA Cycle aAre ATP, NADH, and FADH2 000258 Several TCA Cycle Enzymes Are Subject to Allosteric Regulation 000259 The TCA Cycle Also Plays a Central Role in the Catabolism of Fats and Proteins 000261 The TCA Cycle Serves as a Source of Precursors for Anabolic Pathways 000262 The Glyoxylate Cycle Converts Acetyl CoA to Carbohydrates 000262 Electron Transport: Electron Flow from Coenzymes to Oxygen 000265 The Electron Transport System Conveys Electrons from Reduced Coenzymes to Oxygen 000265 The Electron Transport System Consists of Five Different Kinds of Carriers 000265 The Electron Carriers Function in a Sequence Determined by Their Reduction Potentials 000267 Most of the Carriers Are Organized into Four Large Respiratory Complexes 000268 The Respiratory Complexes Move Freely Within the Inner Membrane 000271 The Electrochemical Proton Gradient: Key to Energy Coupling 000271 Electron Transport and ATP Synthesis Are Coupled Events 000271 The Chemiosmotic Model: The ¿Missing Link¿ Is a Proton Gradient 000272 Coenzyme Oxidation Pumps Enough Protons to Form 3 ATP per NADH and 2 ATP per FADH2 000272 The Chemiosmotic Model Is Affirmed by an Impressive Array of Evidence 000273 1. Electron Transport Causes Protons to Be Pumped Out of the Mitochondrial Matrix 000273 2. Components of the Electron Transport System Are Asymmetrically Oriented Within the Inner Mitochondrial Membrane 000273 3. Membrane Vesicles Containing Complexes I, III, or IV Establish Proton Gradients 000273 4. Oxidative Phosphorylation Requires a Membrane-Enclosed Compartment 000274 5. Uncoupling Agents Abolish Both the Proton Gradient and ATP Synthesis 000274 6. The Proton Gradient Has Enough Energy to Drive ATP Synthesis 000274 7. Artificial Proton Gradients Can Drive ATP Synthesis in the Absence of Electron Transport 000274 ATP Synthesis: Putting It All Together 000275 F1 Particles Have ATP Synthase Activity 000275 The FoF1 Complex: Proton Translocation Through Fo Drives ATP Synthesis by F1 000276 ATP Synthesis by FoF1 Involves Physical Rotation of the Gamma Subunit 000276 The Chemiosmotic Model Involves Dynamic Transmembrane Proton Traffic 000279 Aerobic Respiration: Summing It All Up 000279 The Maximum ATP Yield of Aerobic Respiration Is 36¿38 ATPs per Glucose 000279 Aerobic Respiration Is a Highly Efficient Process 000281 PerspectiveSummary of Key Points 000283 Making Connections 000 Problem Set 000284 Suggested Reading 000287 Box 10A: Further Insights: The Glyoxylate Cycle, Glyoxysomes, and Seed Germination 000263 Chapter 11 Phototrophic Energy Metabolism: Photosynthesis 000288 The Energy Transduction Reactions Convert Solar Energy to Chemical Energy 000 The Carbon Assimilation Reactions Fix Carbon by Reducing Carbon Dioxide 000 The Chloroplast Is the Photosynthetic Organelle in Eukaryotic Cells 00 An Overview of Photosynthesis 288 The Chloroplast: A Photosynthetic Organelle 290 Chloroplasts Are Composed of Three Membrane Systems 290 Photosynthetic Energy Transduction I: Light Harvesting 000291 Chlorophyll Is Life¿s Primary Link to Sunlight 000295 Accessory Pigments Further Expand Access to Solar Energy 000296 Light-Gathering Molecules Are Organized into Photosystems and Light-Harvesting Complexes 000296 Oxygenic Phototrophs Have Two Types of Photosystems 000296 Photosynthetic Energy Transduction II: Photoreduction (NADPH Synthesis) in Oxygenic Phototrophs 000297 Photosystem II Transfers Electrons from Water to a Plastoquinone 000298 The Cytochrome b6/f Complex Transfers Electrons from a Plastoquinol to Plastocyanin 000299 Photosystem I Transfers Electrons from Plastocyanin to Ferredoxin 000299 Ferredoxin NADP+ Reductase Catalyzes the Reduction of NADP+ 000300 Photosynthetic Energy Transduction III: Photophosphorylation (ATP Synthesis) in Oxygenic Phototrophs 000300 The ATP Synthase Complex Couples Transport of Protons Across the Thylakoid Membrane to ATP Synthesis 000300 Cyclic Photophosphorylation Allows a Photosynthetic Cell to Balance NADPH and ATP Synthesis to Meet Its Precise Energy Needs 000301 A Summary of Tthe Complete Energy Transduction System 000302 A Photosynthetic Reaction Center from a Purple Bacterium 302 Photosynthetic Carbon Assimilation I: The Calvin Cycle 000303 Carbon Dioxide Enters the Calvin Cycle by Carboxylation of Ribulose-1,5-Bisphosphate 000303 3-Phosphoglycerate Is Reduced to Form Glyceraldehyde-3-Phosphate 000305 Regeneration of Ribulose-1,5-Bisphosphate Allows Continuous Carbon Assimilation 000305 The Complete Calvin Cycle and Its Relation to Photosynthetic Energy Transduction 000305 Regulation of the Calvin Cycle 000 The Calvin Cycle Is Highly Regulated to Ensure Maximum Efficiency 000306 Regulation of Rubisco Carbon Fixation by Rubisco Activase 000307 Photosynthetic Energy Transduction and the Calvin Cycle 307 Photosynthetic Carbon Assimilation II: Carbohydrate Synthesis 000308 Glyceraldehyde-3-Phosphate and Dihydroxyacetone Phosphate Are Combined to Form Glucose-1-PhosphateGlucose-1-Phosphate Is Synthesized from Triose Phosphates 000308 The Biosynthesis of Sucrose Occurs in the Cytosol 000309 The Biosynthesis of Starch Occurs in the Chloroplast Stroma 000309 Photosynthesis Also Produces Reduced Nitrogen and Sulfur Compounds 000 Other Photosynthetic Assimilation Pathways 309 Rubisco¿s Oxygenase Activity Decreases Photosynthetic Efficiency 000309 The Glycolate Pathway Returns Reduced Carbon from Phosphoglycolate to the Calvin Cycle 000310 C4 Plants Minimize Photorespiration by Confining Rubisco to Cells Containing High Concentrations of CO2 000312 CAM Plants Minimize Photorespiration and Water Loss by Opening Their Stomata Only at Night 000314 PerspectiveSummary of Key Points 000315 Making Connections 000 Problem Set 000315 Suggested Reading 000317 Box 11A: Further Insights: The Endosymbiont Theory and the Evolution of Mitochondria and Chloroplasts from Ancient Bacteria 000292 Box 11B: Further Insights: A Photosynthetic Reaction Center from a Purple Bacterium 000 Chapter 12 Intracellular Compartments: The Endoplasmic Reticulum, Golgi Complex, Endosomes, Lysosomes, The Endomembrane System and Peroxisomes 000318 The Endoplasmic Reticulum 000318 The Two Basic Kinds of Endoplasmic Reticulum Differ in Structure and Function 000320 Rough ER Is Involved in the Biosynthesis and Processing of Proteins 000320 Smooth ER Is Involved in Drug Detoxification, Carbohydrate Metabolism, and Steroid BiosynthesisOther Cellular Processes 000321 The ER Plays a Central Role in the Biosynthesis of Membranes 000327 The Golgi Complex 000328 The Golgi Complex Consists of a Series of Membrane-Bounded Cisternae 000328 Two Models Depict the Flow of Lipids and Proteins Through the Golgi Complex 000330 Roles of the ER and Golgi Complex in Protein Glycosylation 000331 Roles of the ER and Golgi Complex in Protein Trafficking 000333 ER-Specific Proteins Contain Retention and Retrieval Tags 000335 Golgi Complex Proteins May Be Sorted According to the Lengths of Their Membrane-Spanning Domains 000335 Targeting of Soluble Lysosomal Proteins to Endosomes and Lysosomes Is a Model for Protein Sorting in the TGN 000335 Secretory Pathways Transport Molecules to the Exterior of the Cell 000337 Exocytosis and Endocytosis: Transporting Material Across the Plasma Membrane 000338 Exocytosis Releases Intracellular Molecules to the Extracellular Medium 000338 Endocytosis Imports Extracellular Molecules by Forming Vesicles from the Plasma Membrane 000339 Coated Vesicles in Cellular Transport Processes 000344 Clathrin-Coated Vesicles Are Surrounded by Lattices Composed of Clathrin and Adaptor Protein 000345 The Assembly of Clathrin Coats Drives the Formation of Vesicles from the Plasma Membrane and TGN 000347 COPI- and COPII-Coated Vesicles Connect Travel Between the ER and Golgi Complex Cisternae 000347 SNARE Proteins Mediate Fusion Between Vesicles and Target Membranes Following Tethering 000348 Lysosomes and Cellular Digestion 000349 Lysosomes Isolate Digestive Enzymes from the Rest of the Cell 000349 Lysosomes Develop from Endosomes 000350 Lysosomal Enzymes Are Important for Several Different Digestive Processes 000351 Lysosomal Storage Diseases Are Usually Characterized by the Accumulation of Indigestible Material 000353 The Plant Vacuole: A Multifunctional Organelle 000353 Peroxisomes 000354 The Discovery of Peroxisomes Depended on Innovations in Equilibrium Density Centrifugation 000354 Most Peroxisomal Functions Are Linked to Hydrogen Peroxide Metabolism 000355 Plant Cells Contain Types of Peroxisomes Not Found in Animal Cells 000357 Peroxisome Biogenesis Occurs by Division of Preexisting Peroxisomes 000357 PerspectiveSummary of Key Points 000359 Making Connections 000 Problem Set 000360 Suggested Reading 000362 Box 12A: Experimental Techniques: Centrifugation: An Indispensable Technique of Cell Biology 000322 Box 12B: Human Applications: Cholesterol, the LDL Receptor, and Receptor-Mediated Endocytosis 000342 Chapter 13 Signal Transduction Mechanisms: I. Electrical Signals in Nerve Cells 000363 The Nervous SystemNeurons 000363 Neurons Are Specially Adapted for the Transmission of Electrical Signals 000364 Understanding Membrane Potential 000365 The Resting Membrane Potential Depends on Differing Concentrations of Ions Inside and Outside the Neuron 000366 The Nernst Equation Describes the Relationship Between Membrane Potential and Ion Concentration 000367 Ions Trapped Inside the Cell Have Important Effects on Resting Membrane Potential 368 Steady-State Concentrations of Common Ions Affect Resting Membrane Potential 000368 The Goldman Equation Describes the Combined Effects of Ions on Membrane Potential 000368 Electrical Excitability 000370 Ion Channels Act Like Gates for the Movement of Ions Through the Membrane 000370 Patch Clamping and Molecular Biological Techniques Allow the Activity of Single Ion Channels to Be Monitored 000371 Specific Domains of Voltage-Gated Channels Act as Sensors and Inactivators 000372 The Action Potential 000373 Action Potentials Propagate Electrical Signals Along an Axon 000374 Action Potentials Involve Rapid Changes in the Membrane Potential of the Axon 000375 Action Potentials Result from the Rapid Movement of Ions Through Axonal Membrane Channels 000375 Action Potentials Are Propagated Along the Axon Without Losing Strength 000377 The Myelin Sheath Acts Like an Electrical Insulator Surrounding the Axon 000379 Synaptic Transmission 000380 Neurotransmitters Relay Signals Across Nerve Synapses 000381 Elevated Calcium Levels Stimulate Secretion of Neurotransmitters from Presynaptic Neurons 000382 Secretion of Neurotransmitters Requires the Docking and Fusion of Vesicles with the Plasma Membrane 000383 Neurotransmitters Are Detected by Specific Receptors on Postsynaptic Neurons 000385 Neurotransmitters Must Be Inactivated Shortly After Their Release 000386 Integration and Processing of Nerve Signals 000386 Neurons Can Integrate Signals from Other Neurons Through Both Temporal and Spatial Summation 000387 Neurons Can Integrate Both Excitatory and Inhibitory Signals from Other Neurons 000387 PerspectiveSummary of Key Points 000388 Making Connections 000 Problem Set 000389 Suggested Reading 000390 Box 13A: Human Applications: Poisoned Arrows, Snake Bites, and Nerve Gases 000387 Chapter 14 Signal Transduction Mechanisms: II. Messengers and Receptors 392000 Chemical Signals and Cellular Receptors 392000 Different Types of Chemical Signals Can Be Received by Cells 392000 Receptor Binding Involves Specific Interactions Between Ligands and Their Receptors 393000 Receptor Binding Activates a Sequence of Signal Transduction Events Within the Cell 395000 G Protein-Linked Receptors 396000 Seven-Membrane Spanning Receptors Act via G Proteins 396000 Cyclic AMP Is a Second Messenger Whose Production Is RegulatedUsed by One Class of Some G Proteins 396000 Disruption of G Protein Signaling Causes Several Human Diseases 399000 Many G Proteins Use Inositol Trisphosphate and Diacylglycerol as Second Messengers 399000 The Release of Calcium Ions Is a Key Event in Many Signaling Processes 400000 Nitric Oxide Couples G Protein-Linked Receptor Stimulation in Endothelial Cells to Relaxation of Smooth Muscle Cells in Blood Vessels 404000 The ?? Subunits of G Proteins Can Also Transduce Signals 000 Protein Kinase-Associated Receptors 405000 Growth Factors Often Bind Protein-Kinase Associated Receptors 000 Receptor Tyrosine Kinases Aggregate and Undergo Autophosphorylation 405000 Receptor Tyrosine Kinases Initiate a Signal Transduction Cascade Involving Ras and MAP Kinase 406000 Receptor Tyrosine Kinases Activate a Variety of Other Signaling Pathways 410000 Scaffolding Complexes Can Facilitate Cell Signaling 000 Dominant Negative Mutant Receptors Are Important Tools for Studying Receptor Function 000 Growth Factors as Messengers 411 Disruption of Growth Factor Signaling Through Receptor Tyrosine Kinases Can Have Dramatic Effects on Embryonic Development 411 Other Growth Factors Transduce Their Signals via Receptor Serine/Threonine Kinases 412000 Disruption of Growth Factor Signaling Can Lead to Cancer 000 Growth Factor Receptor Pathways Share Common Themes 413000 Disruption of Growth Factor Signaling Can Lead to Cancer 413 The Endocrine and Paracrine Hormone Systems 414 Hormonal Signaling 000 Hormonal Signals Can Be Classified by the Distance They Travel toand by Their Chemical PropertiesTarget Cells 414000 Control of Glucose Metabolism Is a Good Example of Endocrine Regulation 000 Insulin Affects Several Signaling Pathways to Regulate Resting Glucose Levels 000 Hormones Control Many Physiological Functions 414 Animal Hormones Can Be Classified by Their Chemical Properties 414 Adrenergic Hormones and Receptors Are a Good Example of Endocrine Regulation 415 Prostaglandins Are a Good Example of Paracrine Regulation 419 Cell Signals and Apoptosis 419000 Apoptosis Is Triggered by Death Signals or Withdrawal of Survival Factors 420000 PerspectiveSummary of Key Points 422000 Making Connections 000 Problem Set 423000 Suggested Reading 424000 Box 14A: Experimental Techniques: Using Genetic Model Systems to Study Cell Signaling 408000 Chapter 15 Cytoskeletal Systems 000425 The Major Structural Elements of the Cytoskeleton 000425 Eukaryotes Have Three Basic Types of Cytoskeletal Elements 000 Prokaryotes Have Cytoskeletal Systems That Are Structurally Similar to Those in Eukaryotes 000 The Cytoskeleton Is Dynamically Assembled and Disassembled 000 Techniques for Studying the Cytoskeleton 427 Modern Microscopy Techniques Have Revolutionized the Study of the Cytoskeleton 427 Drugs and Mutations Can Be Used to Disrupt Cytoskeletal Structures 427 Microtubules 000427 Two Types of Microtubules Are Responsible for Many Functions in the Cell 000427 Tubulin Heterodimers Are the Protein Building Blocks of Microtubules 000429 Microtubules Can Form as Singles, Doubles, or Triplets 000 Microtubules Form by the Addition of Tubulin Dimers at Their Ends 000430 Addition of Tubulin Dimers Occurs More Quickly at the Plus Ends of Microtubules 000431 Drugs Can Affect the Assembly of Microtubules 000 GTP Hydrolysis Contributes to the Dynamic Instability of Microtubules 000432 Microtubules Originate from Microtubule-Microtubule Organizing Centers Within the Cell 000432 MTOCs Organize and Polarize the Microtubules Within Cells 000434 Microtubule Stability Within Cells Is Highly Tightly Regulated in Cells by a Variety of Microtubule-Binding Proteins 000435 Drugs Can Affect the Assembly of Microtubules 435 Microtubules Are Regulated Along Their Length by Microtubule-Associated Proteins 436 Microfilaments 000437 Actin Is the Protein Building Block of Microfilaments 000437 Different Types of Actin and Actin-Related Proteins Are Found in Cells 000438 G-Actin Monomers Polymerize into F-Actin Microfilaments 000438 Cells Can Dynamically Regulate How and Where Actin Is Assembled 439 Specific Proteins and Drugs Affect Polymerization Dynamics at the Ends of Microfilaments 000439 Cells Can Dynamically Assemble actin into a Variety of Structures 000 Actin-Binding Proteins Regulate the Polymerization, Length, and Organization of Microfilaments 000 Cell Signaling Regulates Where and When Actin-Based Structures Assemble 000 Inositol Phospholipids Regulate Molecules That Affect Actin Polymerization 440 Actin Branching Is Controlled by the Arp2/3 Complex 441 Rho, Rac, and Cdc42 Regulate Actin Polymerization 443 Actin-Binding Proteins Regulate Interactions Between Microfilaments 444 Bundled Actin Filaments Form the Core of Microvilli 444 A Variety of Proteins Link Actin to Membranes 445 Intermediate Filaments 000446 Intermediate Filament Proteins Are Tissue Specific-Specific 000446 Intermediate Filaments Assemble from Fibrous Subunits 000448 Intermediate Filaments Confer Mechanical Strength on Tissues 000448 The Cytoskeleton Is a Mechanically Integrated Structure 000449 PerspectiveSummary of Key Points 000450 Making Connections 000 Problem Set 000450 Suggested Reading 000451 Box 15A: Human Applications: Infectious Microorganisms Can Move Within Cells Using Actin ¿Tails¿ 000442 Chapter 16 Cellular Movement: Motility and Contractility 000453 Motile Systems 000453 Intracellular Microtubule-Based Movement: Kinesin and Dynein 000454 MT Motor ProteinsMAPs Move Organelles Along Microtubules During Axonal Transport 000454 Kinesins Motor Proteins Move Along Microtubules by Hydrolyzing ATP 000455 Kinesins Are a Large Family of Proteins with Varying Structures and Functions 000456 Dyneins Can Be Grouped into Two Major Classes: Axonemal and Cytoplasmic Dyneins 000456 Microtubule Motors Are Involved in Shaping the Endomembrane System and Vesicle Transport 000 Motor MAPs Are Involved in the Transport of Intracellular Vesicles 457 Microtubule-Based Motility: Cilia and Flagella 000457 Cilia and Flagella Are Common Motile Appendages of Eukaryotic Cells 000457 Cilia and Flagella Consist of an Axoneme Connected to a Basal Body 000459 Microtubule Sliding Within the Axoneme Causes Cilia and Flagella to Bend 000460 Actin-Based Cell Movement: The Myosins 000461 Myosins Have Are a Large Family of Actin-Based Motors with Diverse Roles in Cell Motility 000461 SomeMany Myosins Move Along Actin Filaments in Short Steps 000462 Filament-Based Movement in Muscle 000463 Skeletal Muscle Cells Are Made of Thin and Thick Filaments 000463 Sarcomeres Contain Ordered Arrays of Actin, Myosin, and Accessory Proteins 000464 The Sliding-Filament Model Explains Muscle Contraction 000467 Cross-Bridges Hold Filaments Together, and ATP Powers Their Movement 000467 The Regulation of Muscle Contraction Depends on Calcium 000470 The Coordinated Contraction of Cardiac Muscle Cells Involves Electrical Coupling 000472 Smooth Muscle Is More Similar to Nonmuscle Cells than to Skeletal Muscle 000473 Actin-Based Motility in Nonmuscle Cells 000475 Cell Migration via Lamellipodia Involves Cycles of Protrusion, Attachment, Translocation, and Detachment 000475 Amoeboid Movement Involves Cycles of Gelation and Solation of the Actin Cytoskeleton 000477 Cytoplasmic Streaming Moves Components Within the Cytoplasm of Some Cells 000477 Chemotaxis Is a Directional Movement in Response to a Graded Chemical Stimulus 000478 Amoeboid Movement Involves Cycles of Gelation and Solation of the Actin Cytoskeleton 000 Actin-Based Motors Move Components Within the Cytoplasm of Some Cells 000 PerspectiveSummary of Key Points 000478 Making Connections 000 Problem Set 000479 Suggested Reading 000480 Box 16A: Human Applications: Cytoskeletal Motor Proteins and Human Disease 000463 Chapter 17 Beyond the Cell: Extracellular Structures, Cell Adhesion, and Cell Junctions, and Extracellular Structures 000482 Cell-Cell Recognition and Adhesion 000 Transmembrane Proteins Mediate Cell-Cell Adhesion 000 Carbohydrate Groups Are Important in Cell-Cell Recognition and Adhesion 000 Cell-Cell Junctions 000 Adhesive Junctions Link Adjoining Cells to Each Other 000 Tight Junctions Prevent the Movement of Molecules Across Cell Layers 000 Gap Junctions Allow Direct Electrical and Chemical Communication Between Cells 000 The Extracellular Matrix of Animal Cells 000482 Collagens Are Responsible for the Strength of the Extracellular Matrix 000483 A Precursor Called Procollagen Forms Many Types of Tissue-Specific Collagens 000484 Elastins Impart Elasticity and Flexibility to the Extracellular Matrix 000484 Collagen and Elastin Fibers Are Embedded in a Matrix of Proteoglycans 000486 Free Hyaluronate Lubricates Joints and Facilitates Cell Migration 000487 Proteoglycans and Adhesive Glycoproteins Anchor Cells to the Extracellular Matrix 000487 Fibronectins Bind Cells to the ECM and Guide Cellular Movement 000487 Laminins Bind Cells to the Basal Lamina 000489 Integrins Are Cell Surface Receptors tThat Bind ECM Constituents 000489 The Glycocalyx Is a Carbohydrate-Rich Zone at the Periphery of Animal Cells 000492 Cell¿Cell Recognition and Adhesion 492 Transmembrane Proteins Mediate Cell¿Cell Adhesion 493 Carbohydrate Groups Are Important in Cell¿Cell Recognition and Adhesion 494 Cell Junctions 496 Adhesive Junctions Link Adjoining Cells to Each Other 496 Tight Junctions Prevent the Movement of Molecules Across Cell Layers 499 Gap Junctions Allow Direct Electrical and Chemical Communication Between Cells 501 The Plant Cell Surface 000501 Cell Walls Provide a Structural Framework and Serve as a Permeability Barrier 000501 The Plant Cell Wall Is a Network of Cellulose Microfibrils, Polysaccharides, and Glycoproteins 000502 Cell Walls Are Synthesized in Several Discrete Stages 000504 Plasmodesmata Permit Direct Cell-Cell Communication Through the Cell Wall 000504 PerspectiveSummary of Key Points 000506 Making Connections 000 Problem Set 000507 Suggested Reading 000508 Box 17A: Human Applications: Food Poisoning and ¿Bad Bugs¿: The Cell Surface Connection 000498 Chapter 18 The Structural Basis of Cellular Information: DNA, Chromosomes, and the Nucleus 000510 The Chemical Nature of the Genetic Material 000511 Miescher¿s Discovery of DNA Led to Conflicting Proposals Concerning the Chemical Nature of Genes 000511 Avery Showed That DNA Is the Genetic Material of Bacteria 000512 Hershey and Chase Showed That DNA Is the Genetic Material of Viruses 000513 Chargaff¿s Rules Reveal That A = T and G = C 000513 DNA Structure 000517 Watson and Crick Discovered That DNA Is a Double Helix 000517 DNA Can Be Interconverted Between Relaxed and Supercoiled Forms 000519 The Two Strands of a DNA Double Helix Can Be Separated Experimentally by Denaturation and Rejoined by Renaturation 000521 The Organization of DNA in Genomes 000523 Genome Size Generally Increases with an Organism¿s Complexity 000523 Restriction Enzymes Endonucleases Cleave DNA Molecules at Specific Sites 000524 Rapid Procedures Exist for DNA Sequencing 000526 The Genomes of Numerous Many Organisms Have Been Sequenced 000529 The Field of Bioinformatics Has Emerged to Decipher Genomes, Transcriptomes, and Proteomes 000529 Tiny Differences in Genome Sequence Distinguish People from One Another 000 Repeated DNA Sequences Partially Explain the Large Size of Eukaryotic Genomes 000530 DNA Packaging 000533 Prokaryotes Bacteria Package DNA in Bacterial Chromosomes and Plasmids 000533 Eukaryotes Package DNA in Chromatin and Chromosomes 000535 Nucleosomes Are the Basic Unit of Chromatin Structure 000536 A Histone Octamer Forms the Nucleosome Core 000537 Nucleosomes Are Packed Together to Form Chromatin Fibers and Chromosomes 000538 Eukaryotes Also Package Some of Their DNA in Mitochondria and Chloroplasts 000540 The Nucleus 000541 A Double-Membrane Nuclear Envelope Surrounds the Nucleus 000541 Molecules Enter and Exit the Nucleus Through Nuclear Pores 000544 The Nuclear Matrix and Nuclear Lamina Are Supporting Structures of the Nucleus 000547 Chromatin Fibers Are Dispersed Within the Nucleus in a Nonrandom Fashion 000548 The Nucleolus Is Involved in Ribosome Formation 000548 PerspectiveSummary of Key Points 000550 Making Connections 000 Problem Set 000551 Suggested Reading 000553 Box 18A: Further Insights: Phages: Model Systems for Studying Genes 000515 Box 18B: Further Insights: A Closer Look at Restriction Enzymes Endonucleases 000526 Box 18C: Experimental Techniques: DNA Fingerprinting 000534 Chapter 19 The Cell Cycle, DNA Replication, and Mitosis 000554 An Overview of the Cell Cycle 000554 DNA Replication 000556 Equilibrium Density Centrifugation Shows That DNA Replication Is Semiconservative 000556 DNA Replication Is Usually Bidirectional 000558 Replication Licensing Ensures That DNA Molecules Are Duplicated Only Once Before Each Cell Division 000 Eukaryotic DNA Replication Involves Multiple Replicons 559 DNA Polymerases Catalyze the Elongation of DNA Chains 000561 DNA Is Synthesized as Discontinuous Segments That Are Joined Together by DNA Ligase 000563 Proofreading Is Performed by the 3?? 5? Exonuclease Activity of DNA Polymerase 000566 RNA Primers Initiate DNA Replication 000566 Unwinding the DNA Double Helix Requires DNA Helicases, Topoisomerases, and Single-Stranded DNA Binding Proteins 000567 Putting It All Together: DNA Replication in Summary 000568 Telomeres Solve the DNA End-Replication Problem 000570 Eukaryotic DNA Is Licensed for Replication 000571 DNA Damage and Repair 000572 DNA Damage Can Occur Spontaneously or in Response to Mutagens 000573 Translesion Synthesis and Excision Repair Correct Mutations Involving Abnormal Nucleotides 000574 Mismatch Repair Corrects Mutations That Involve Noncomplementary Base Pairs 000575 Damage Repair Helps Explain Why DNA Contains Thymine Instead of Uracil 000575 Double-Strand DNA Breaks Are Repaired by Nonhomologous End-Joining or Homologous Recombination 000576 Nuclear and Cell Division 000576 Mitosis Is Subdivided into Prophase, Prometaphase, Metaphase, Anaphase, and Telophase 000576 The Mitotic Spindle Is Responsible for Chromosome Movements During Mitosis 000581 Cytokinesis Divides the Cytoplasm 000584 Cell Division Is Sometimes Asymmetric 000 Regulation of the Cell Cycle 000586 The Length of the Cell Cycle Varies Among Different Cell Types 000586 Progression Through the Cell Cycle Is Controlled at Several Key Transition Points 000587 Studies Involving Cell Fusion and Cell Cycle Mutants Led to the Identification of Molecules That Control the Cell Cycle 000588 Progression Through the Cell Cycle Is Controlled by Cyclin-Dependent Kinases (Cdks) 000589 Mitotic Cdk-Cyclin Drives Progression Through the G2-M Transition by Phosphorylating Key Proteins Involved in the Early Stages of Mitosis 000589 The Anaphase-Promoting Complex Coordinates Key Mitotic Events by Targeting Specific Proteins for Destruction 000 Mitotic Cdk-Cyclin Contributes to Activation of the Anaphase-Promoting Complex 592 G1 Cdk-Cyclin Regulates Progression Through the Restriction Point by Phosphorylating the Rb Protein 000593 Checkpoint Pathways Monitor for Chromosome-to-Spindle Attachments, Completion of DNA Replication, and DNA Damage 000594 Putting It All Together: The Cell- Cycle Regulation Machine 000595 Growth Factors and Cell Proliferation 000596 Stimulatory Growth Factors Activate the Ras Pathway 000596 Stimulatory Growth Factors Can Also Activate the PI3K-Akt Pathway 000597 Inhibitory Growth Factors Act Through Cdk Inhibitors 000598 PerspectiveSummary of Key Points 000599 Making Connections 000 Problem Set 000600 Suggested Reading 000602 Box 19A: Experimental Techniques: The PCR Revolution 000564 Chapter 20 Sexual Reproduction, Meiosis, and Genetic Recombination 000604 Sexual Reproduction 000604 Sexual Reproduction Produces Genetic Variety by Bringing Together Chromosomes from Two Different Parents 000604 Diploid Cells May Be Homozygous or Heterozygous for Each Gene 000605 Gametes Are Haploid Cells Specialized for Sexual Reproduction 000606 Meiosis 000606 The Life Cycles of Sexual Organisms Have Diploid and Haploid Phases 000607 Meiosis Converts One Diploid Cell into Four Haploid Cells 000608 Meiosis I Produces Two Haploid Cells That Have Chromosomes Composed of Sister Chromatids 000609 Meiosis II Resembles a Mitotic Division 000611 Sperm and Egg Cells Are Generated by Meiosis Accompanied by Cell Differentiation 000615 Meiosis Generates Genetic Diversity 000617 Genetic Variability: Segregation and Assortment of Alleles 000617 Information Specifying Recessive Traits Can Be Present Without Being Displayed 000618 The Law of Segregation States That the Alleles of Each Gene Separate from Each Other During Gamete Formation 000619 The Law of Independent Assortment States That the Alleles of Each Gene Separate Independently of the Alleles of Other Genes 000619 Early Microscopic Evidence Suggested That Chromosomes Might Carry Genetic Information 000620 Chromosome Behavior Explains the Laws of Segregation and Independent Assortment 000620 The DNA Molecules of Homologous Chromosomes Have Similar Base Sequences 000621 Genetic Variability: Recombination and Crossing Over 000622 Chromosomes Contain Groups of Linked Genes That Are Usually Inherited Together 000623 Homologous Chromosomes Exchange Segments During Crossing Over 000623 Gene Locations Can Be Mapped by Measuring Recombination Frequencies 000624 Genetic Recombination in Bacteria and Viruses 000625 Co-infection of Bacterial Cells with Related Bacteriophages Can Lead to Genetic Recombination 000625 Transformation and Transduction Involve Recombination with Free DNA or DNA Brought into Bacterial Cells by Bacteriophages 000626 Conjugation Is a Modified Sexual Activity That Facilitates Genetic Recombination in Bacteria 000627 Molecular Mechanism of Homologous Recombination 000629 DNA Breakage- and- Exchange Underlies Homologous Recombination 000629 Homologous Recombination Can Lead to Gene Conversion 000630 Homologous Recombination Is Initiated by Single-Strand DNA Exchanges (Holliday Junctions) 000631 The Synaptonemal Complex Facilitates Homologous Recombination During Meiosis 000633 Homologous Recombination Is Used Experimentally to Knock Out Specific Genes 000 Recombinant DNA Technology and Gene Cloning 000633 The Discovery of Restriction Enzymes Paved the Way for Recombinant DNA Technology 000634 DNA Cloning Techniques Permit Individual Gene Sequences to Be Produced in Large Quantities 000635 Genomic and cDNA Libraries Are Both Useful for DNA Cloning 000639 Large DNA Segments Can Be Cloned in YACs and BACs 000640 PCR Is Widely Used to Clone Genes from Sequenced Genomes 000 Genetic Engineering 000641 Genetic Engineering Can Produce Valuable Proteins That Are Otherwise Difficult to Obtain 000641 The Ti Plasmid Is a Useful Vector for Introducing Foreign Genes into Plants 000641 Genetic Modification Can Improve the Traits of Food Crops 000642 Concerns Have Been Raised aAbout the Safety and Environmental Risks of GM Crops 000643 Gene Therapies Are Being Developed for the Treatment of Human Diseases 000643 PerspectiveSummary of Key Points 000645 Making Connections 000 Problem Set 000646 Suggested Reading 000648 Box 20A: Experimental Techniques: Supermouse, an Early Transgenic Triumph 000644 Chapter 21 Gene Expression: I. The Genetic Code and Transcription 000649 The Directional Flow of Genetic Information 000649 The Genetic Code 000650 Experiments on Neurospora Revealed That Genes Can Code for Enzymes 000650 Most Genes Code for the Amino Acid Sequences of Polypeptide Chains 000651 The Genetic Code Is a Triplet Code 000655 The Genetic Code Is Degenerate and Nonoverlapping 000657 Messenger RNA Guides the Synthesis of Polypeptide Chains 000657 The Codon Dictionary Was Established Using Synthetic RNA Polymers and Triplets 000659 Of the 64 Possible Codons in Messenger RNA, 61 Code for Amino Acids 000659 The Genetic Code Is (Nearly) Universal 000660 Transcription in Prokaryotic Bacterial Cells 000661 Transcription Is Catalyzed by RNA Polymerase, Which Synthesizes RNA Using DNA as a Template 000661 Transcription Involves Four Stages: Binding, Initiation, Elongation, and Termination 000661 Transcription in Eukaryotic Cells 000665 RNA Polymerases I, II, and III Carry Out Transcription in the Eukaryotic Nucleus 000666 Three Classes of Promoters Are Found in Eukaryotic Nuclear Genes, One for Each Type of RNA Polymerase 000666 General Transcription Factors Are Involved in the Transcription of All Nuclear Genes 000668 Elongation, Termination, and RNA Cleavage Are Involved in Completing Eukaryotic RNA Synthesis 000669 RNA Processing 000670 Ribosomal RNA Processing Involves Cleavage of Multiple rRNAs from a Common Precursor 000670 Transfer RNA Processing Involves Removal, Addition, and Chemical Modification of Nucleotides 000671 Messenger RNA Processing in Eukaryotes Involves Capping, Addition of Poly(A), and Removal of Introns 000673 Spliceosomes Remove Introns from Pre-mRNA 000676 Some Introns Are Self-Splicing 000677 The Existence of Introns Permits Alternative Splicing and Exon Shuffling 000 Why Do Eukaryotic Genes Have Introns? 000678 RNA Editing Allows mRNA the Coding Sequences of mRNA to Be Altered 000679 Key Aspects of mRNA Metabolism 000680 Most mRNA Molecules Have a Relatively Short Life Span 000680 The Existence of mRNA Allows Amplification of Genetic Information 000680 PerspectiveSummary of Key Points 000680 Making Connections 000 Problem Set 000681 Suggested Reading 000683 Box 21A: Further Insights: Reverse Transcription, Retroviruses, and Retrotransposons 000652 Box 21B: Experimental Techniques: Identifying Protein-Binding Sites on DNA 000664 Chapter 22 Gene Expression: II. Protein Synthesis and Sorting 000684 Translation: The Cast of Characters 000684 The Ribosome Carries Out Polypeptide Synthesis 000684 Transfer RNA Molecules Bring Amino Acids to the Ribosome 000686 Aminoacyl-tRNA Synthetases Link Amino Acids to the Correct Transfer RNAs 000688 Messenger RNA Brings Polypeptide Coding-Coding Information to the Ribosome 000690 Protein Factors Are Required for the Initiation, Elongation, and Termination of Polypeptide Chains 000690 The Mechanism of Translation 000690 The Initiation of Translation Requires Initiation Factors, Ribosomal Subunits, mRNA, and Initiator tRNA 000692 Chain Elongation Involves Sequential Cycles of Aminoacyl tRNA Binding, Peptide Bond Formation, and Translocation 000693 Termination of Polypeptide Synthesis Is Triggered by Release Factors That Recognize Stop Codons 000696 Polypeptide Folding Is Facilitated by Molecular Chaperones 000696 Protein Synthesis Typically Utilizes a Substantial Fraction of a Cell¿s Energy Budget 000696 A Summary of Translation 000698 Mutations and Translation 000698 Suppressor tRNAs Overcome the Effects of Some Mutations 000698 Nonsense-Mediated Decay and Nonstop Decay Are Mechanisms for Promoting Promote the Destruction of Defective mRNAs 000699 Posttranslational Processing 000700 Protein Targeting and Sorting 000702 Cotranslational Import Allows Some Polypeptides to Enter the ER as They Are Being Synthesized 000704 The Signal Recognition Particle (SRP) Binds the Ribosome-mRNA-Polypeptide Complex to the ER Membrane 000 Protein Folding and Quality Control Take Place Within the ER 000 Proteins Released into the ER Lumen Are Routed to the Golgi Complex, Secretory Vesicles, Lysosomes, or Back to the ER 000 Stop-Transfer Sequences Mediate the Insertion of Integral Membrane Proteins 000 Posttranslational Import Allows Some Polypeptides to Enter Organelles After They Have Been Synthesized 000708 PerspectiveSummary of Key Points 000711 Making Connections 000 Problem Set 000712 Suggested Reading 000714 Box 22A: Human Applications: Protein-Folding Diseases 000697 Box 22B: Further Insights: A Mutation Primer 000700 Chapter 23 The Regulation of Gene Expression 000715 Bacterial Gene Regulation in Prokaryotes 000715 Catabolic and Anabolic Pathways Are Regulated Through Induction and Repression Respectively 000715 The Genes Involved in Lactose Catabolism Are Organized into an Inducible Operon 000717 The lac Repressor Is an Allosteric Protein Whose Binding to DNA Is Controlled by Lactose 000717 Studies of Mutant Bacteria Revealed How the lac Operon Is Organized 000718 The Genes Involved in Tryptophan Synthesis Are Organized into a Repressible Operon 000721 The lac and trp Operons Illustrate the Negative Control of Transcription 000722 Catabolite Repression Illustrates the Positive Control of Transcription 000723 Inducible Operons Are Often Under Dual Control 000724 Sigma Factors Determine Which Sets of Genes Can Be Expressed 000724 Attenuation Allows Transcription to Be Regulated After the Initiation Step 000724 Riboswitches Allow Transcription and Translation to Be Controlled by Small Molecule Interactions with RNA 000726 Eukaryotic Gene Regulation: Genomic Control 000727 Multicellular Eukaryotes Are Composed of Numerous Specialized Cell Types 000728 Eukaryotic Gene Expression Is Regulated at Five Main Levels 000728 As a General Rule, the Cells of a Multicellular Organism All Contain the Same Set of Genes 000728 Gene Amplification and Deletion Can Alter the Genome 000729 DNA Rearrangements Can Alter the Genome 000731 Chromosome Puffs Provide Visual Evidence That Chromatin Decondensation Is Involved in Genomic Control 000733 DNase I Sensitivity Provides Further Evidence for the Role of Chromatin Decondensation in Genomic Control 000734 DNA Methylation Is Associated with Inactive Regions of the Genome 000735 Changes in Histones, HMG Proteins, and the Nuclear Matrix Are and Associated Chromatin Proteins Can Alter Genome Activitywith Active Regions of the Genome 000736 Eukaryotic Gene Regulation: Transcriptional Control 000737 Different Sets of Genes Are Transcribed in Different Cell Types 000737 DNA Microarrays Allow the Expression of Thousands of Genes to Be Monitored Simultaneously 000738 Proximal Control Elements Lie Close to the Promoter 000739 Enhancers and Silencers Are Located at Variable Distances from the Promoter 000740 Coactivators Mediate the Interaction Between Regulatory Transcription Factors and the RNA Polymerase Complex 000741 Multiple DNA Control Elements and Transcription Factors Act in Combination 000742 Several Common Structural Motifs Allow Regulatory Transcription Factors to Bind to DNA and Activate Transcription 000742 DNA Response Elements Coordinate the Expression of Nonadjacent Genes 000745 Steroid Hormone Receptors Are Transcription Factors That Bind to Hormone Response Elements 000745 CREBs and STATs Are Examples of Transcription Factors Activated by Phosphorylation 000747 The Heat-Shock Response Element Coordinates the Expression of Genes Activated by Elevated Temperatures 000748 Homeotic Genes Code for Transcription Factors That Regulate Embryonic Development 000748 Eukaryotic Gene Regulation: Posttranscriptional Control 000750 Control of RNA Processing and Nuclear Export Follows Transcription 000750 Translation Rates Can Be Controlled by Initiation Factors and Translational Repressors 000751 Translation Can Also Be Controlled by Regulation of mRNA DegradationHalf-Life 000752 RNA Interference Utilizes Short Small RNAs to Silence the Expression of Genes Containing Complementary Base Sequences 000753 MicroRNAs Produced by Normal Cellular Genes Silence the Translation of Developmentally Important Messenger RNAs 000754 Posttranslational Control Involves Modifications of Protein Structure, Function, and Degradation 000755 Ubiquitin Targets Proteins for Degradation by Proteasomes 000755 A Summary of Eukaryotic Gene Regulation 000757 PerspectiveSummary of Key Points 000757 Making Connections 000 Problem Set 000758 Suggested Reading 000760 Box 23A: Further Insights Experimental Techniques: Dolly: A Lamb with No Father 000730 Chapter 24 Cancer Cells 000762 Uncontrolled Cell Proliferation 000762 Tumors Are Produced by Uncontrolled Cell Proliferation in Which the Balance Between Cell Division and Cell Differentiation Is Disrupted 000762 Cancer Cell Proliferation Is Anchorage-Independent and Insensitive to Population Density 000763 Cancer Cells Are Immortalized by Mechanisms That Maintain Telomere Length 000764 Abnormalities Defects in Signaling Pathways, Cell Cycle Controls, and Apoptosis Contribute to Uncontrolled Proliferation 000765 How Cancers Spreads 000765 Angiogenesis Is Required for Tumors to Grow Beyond a Few Millimeters in Diameter 000765 Blood Vessel Growth Is Controlled by a Balance Between Angiogenesis Activators and Inhibitors 000766 Spreading of Cancer by Invasion and Metastasis Is a Complex, Multistep Process 000767 Changes in Cell Adhesion, Motility, and Protease Production Allow Cancer Cells to Invade Surrounding Tissues and Vessels 000767 Relatively Few Cancer Cells Survive the Voyage Through the Bloodstream and Establish Metastases 000768 Blood-Flow Patterns and Organ-Specific Factors Determine Where Cancer Cells Metastasize 000769 The Immune System Can Inhibit the Development Growth and Spread of Metastases 000769 What Causes Cancer? 000770 Epidemiological Data Have Allowed Many Causes of Cancer to Be Identified 000770 Many Chemicals Can Cause Cancer, Often After Metabolic Activation in the Liver 000771 DNA Mutations Triggered by Chemical Carcinogens Lead to Cancer 000771 Cancer Arises Through a Multistep Process Involving Initiation, Promotion, and Tumor Progression 000772 Ionizing and Ultraviolet Radiation Also Cause DNA Mutations That Lead to Cancer 000774 Viruses and Other Infectious Agents Are Responsible for Trigger the Development of Some Cancers 000775 Oncogenes and Tumor Suppressor Genes 000775 Oncogenes Are Genes Whose Presence Can Trigger the Development of Cancer 000776 Proto-oncogenes Are Converted into Oncogenes by Several Distinct Mechanisms 000776 Most Oncogenes Code for Components of Growth Growth-Signaling Pathways 000778 Tumor Suppressor Genes Are Genes Whose Loss or Inactivation Can Lead to Cancer 000781 The RB Tumor Suppressor Gene Was Discovered by Studying Families with Hereditary Retinoblastoma 000782 The p53 Tumor Suppressor Gene Is the Most Frequently Mutated Gene in Human Cancers 000783 The APC Tumor Suppressor Gene Codes for a Protein That Inhibits the Wnt Signaling Pathway 000784 Human Cancers Develop by the Stepwise Accumulation of Mutations Involving Oncogenes and Tumor Suppressor Genes 000785 Genetic Instability Facilitates the Accumulation of Mutations in Cancer CellsSome Tumor Suppressor Genes Produce Proteins Involved in DNA Repair or Chromosome Sorting 000786 Epigenetic Alterations in Gene Expression Influence the Properties of Cancel Cells 000 Summing Up: The Hallmarks of Cancer 000788 Diagnosis, Screening, and Treatment 000789 Cancer Is Diagnosed by Microscopic Examination of Tissue Specimens 000789 Screening Techniques for Early Detection Can Prevent Many Cancer Deaths 000790 Surgery, Radiation, and Chemotherapy Are Standard Treatments for Cancer 000791 Immunotherapies Exploit the Ability of the Immune System to Recognize Cancer Cells 000791 Herceptin and Gleevec Are Cancer Drugs That Act Through Molecular Targeting 000792 Molecular and Genetic Testing May Allow Cancer Treatments to Be Tailored to Individual Patients 000 Anti-angiogenic Therapies Act by Attacking a Tumor¿s Blood Supply 000792 PerspectiveSummary of Key Points 000794 Making Connections 000 Problem Set 000795 Suggested Reading 000795 Box 24A: Human Applications: Children of the Moon 000787 Box 24B: Experimental Techniques: Monoclonal Antibodies and Cancer Treatment 000793 Appendix Principles and Techniques of Microscopy A-01 Optical Principles of Microscopy A-1 The Illuminating Wavelength Sets a Limit on How Small an Object Can Be Seen A-1 Resolution Refers to the Ability to Distinguish Adjacent Objects as Separate from One Another A-3 The Practical Limit of Resolution Is Roughly 200 nm for Light Microscopy and 2 nm for Electron Microscopy A-4 The Light Microscope A-5 Compound Microscopes Use Several Lenses in Combination A-5 Phase-Contrast Microscopy Detects Differences in Refractive Index and Thickness A-6 Differential Interference Contrast (DIC) Microscopy Utilizes a Split Light Beam to Detect Phase Differences A-7 Fluorescence Microscopy Can Deteect the Presence of Specific Molecules or Ions Within Cells A-8 Confocal Microscopy Minimizes Blurring by Excluding Out-of-Focus Light from an Image A-10 Digital Video Microscopy Can Record Enhanced Time-Lapse Images A-13 Optical Methods Can Be Used to Measure the Movements and Properties of Proteins and Other Macromolecules A-15 Sample Preparation Techniques for Light Microscopy A-17 Specimen Preparation Often Involves Fixation, Sectioning, and Staining A-17 The Electron Microscope A-18 Transmission Electron Microscopy Forms an Image from Electrons that Pass Through the Specimen A-18 Scanning Electron Microscopy Reveals the Surface Architecture of Cells and Organelles A-19 Sample Preparation Techniques for Electron Microscopy A-21 Ultrathin Sectioning and Staining Are Common Preparation Techniques for Transmission Electron Microscopy A-21 Radioisotopes and Antibodies Can Localize Molecules in Electron Micrographs A-22 Correlative Microscopy Can Be Used to Bridge the Gap Between Light and Electron Microscopy A-22 Negative Staining Can Highlight Small Objects in Relief Against a Stained Background A-23 Shadowing Techniques Use Metal Vapor Sprayed Across a Specimen¿s Surface A-23 Freeze Fracturing and Freeze Etching Are Useful for Examining the Interior of Membranes A-24 Stereo Electron Microscopy Allows Specimens to Be Viewed in Three Dimensions A-26 Specimen Preparation for Scanning Electron Microscopy Involves Fixation but Not Sectioning A-26 Other Imaging Methods A-27 Scanning Probe Microscopy Reveals the Surface Features of Individual Molecules A-27 X-Ray Diffraction Allows the Three-Dimensional Structure of Macromolecules to Be Determined A-28 CryoEM Bridges the Gap Between X-Ray Crystallography and Electron Microscopy A-28 Suggested Reading A-30 Glossary G-I Photo, Illustration, and Text Credits C-1 Index I-1
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