Table of contents for The world of the cell / Wayne M. Becker ... [et al.].

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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 

Library of Congress Subject Headings for this publication:

Cytology.
Molecular biology.
Cell Physiology.
Molecular Biology.