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Part Ⅰ Chemical and Molecular Foundations 1

1 LIFE BEGINS WITH CELLS 1

1.1 The Diversity and Commonality of Cells 1

All Cells Are Prokaryotic or Eukaryotic 1

Unicellular Organisms Help and Hurt Us 4

Viruses Are the Ultimate Parasites 6

Changes in Cells Underlie Evolution 6

Even Single Cells Can Have Sex 7

We Develop from a Single Cell 8

Stem Cells，Fundamental to Forming Tissues and Organs，Offer Medical Opportunities 8

1.2 The Molecules of a Cell 9

Small Molecules Carry Energy，Transmit Signals，and Are Linked into Macromolecules 9

Proteins Give Cells Structure and Perform Most Cellular Tasks 10

Nucleic Acids Carry Coded Information for Making Proteins at the Right Time and Place 11

The Genome Is Packaged into Chromosomes and Replicated During Cell Division 12

Mutations May Be Good，Bad，or Indifferent 13

1.3 The Work of Cells 14

Cells Build and Degrade Numerous Molecules and Structures 15

Animal Cells Produce Their Own External Environment and Glues 16

Cells Change Shape and Move 16

Cells Sense and Send Information 16

Cells Regulate Their Gene Expression to Meet Changing Needs 17

Cells Grow and Divide 18

Cells Die from Aggravated Assault or an Internal Program 19

1.4 Investigating Cells and Their Parts 20

Cell Biology Reveals the Size，Shape，Location，and Movements of Cell Components 20

Biochemistry and Biophysics Reveal the Molecular Structure and Chemistry of Purified Cell Constituents 21

Genetics Reveals the Consequences of Damaged Genes 22

Genomics Reveals Differences in the Structure and Expression of Entire Genomes 23

Developmental Biology Reveals Changes in the Properties of Cells as They Specialize 23

Choosing the Right Experimental Organism for the Job 25

The Most Successful Biological Studies Use Multiple Approaches 27

1.5 A Genome Perspective on Evolution 28

Metabolic Proteins，the Genetic Code，and Organelle Structures Are Nearly Universal 28

Darwin’s Ideas About the Evolution of Whole Animals Are Relevant to Genes 28

Many Genes Controlling Development Are Remarkably Similar in Humans and Other Animals 28

Human Medicine Is Informed by Research on Other Organisms 29

2 CHEMICAL FOUNDATIONS 31

2.1 Covalent Bonds and Noncovalent Interactions 32

The Electronic Structure of an Atom Determines the Number and Geometry of Covalent Bonds It Can Make 33

Electrons May Be Shared Equally or Unequally in Covalent Bonds 34

Covalent Bonds Are Much Stronger and More Stable Than Noncovalent Interactions 35

Ionic Interactions Are Attractions between Oppositely Charged Ions 36

Hydrogen Bonds Determine the Water Solubility of Uncharged Molecules 37

Van der Waals Interactions Are Caused by Transient Dipoles 37

The Hydrophobic Effect Causes Nonpolar Molecules to Adhere to One Another 38

Molecular Complementarity Mediated via Noncovalent Interactions Permits Tight，Highly Specific Binding of Biomolecules 39

2.2 Chemical Building Blocks of Cells 40

Amino Acids Differing Only in Their Side Chains Compose Proteins 41

Five Different Nucleotides Are Used to Build Nucleic Acids 44

Monosaccharides Joined by Glycosidic Bonds Form Linear and Branched Polysaccharides 44

Phospholipids Associate Noncovalently to Form the Basic Bilayer Structure of Biomembranes 46

2.3 Chemical Equilibrium 49

Equilibrium Constants Reflect the Extent of a Chemical Reaction 50

Chemical Reactions in Cells Are at Steady State 50

Dissociation Constants of Binding Reactions Reflect the Affinity of Interacting Molecules 50

Biological Fluids Have Characteristic pH Values 51

Hydrogen Ions Are Released by Acids and Taken Up by Bases 52

Buffers Maintain the pH of Intracellular and Extracellular Fluids 52

2.4 Biochemical Energetics 54

Several Forms of Energy Are Important in Biological Systems 54

Cells Can Transform One Type of Energy into Another 55

The Change in Free Energy Determines the Direction of a Chemical Reaction 55

The △G°’ of a Reaction Can Be Calculated from Its Keq 56

The Rate of a Reaction Depends on the Activation Energy Necessary to Energize the Reactants into a Transition State 56

Life Depends on the Coupling of Unfavorable Chemical Reactions with Energetically Favorable Reactions 57

Hydrolysis of ATP Releases Substantial Free Energy and Drives Many Cellular Processes 57

ATP Is Generated During Photosynthesis and Respiration 59

NAD＋ and FAD Couple Many Biological Oxidation and Reduction Reactions 59

3 PROTEIN STRUCTURE AND FUNCTION 63

3.1 Hierarchical Structure of Proteins 64

The Primary Structure of a Protein Is Its Linear Arrangement of Amino Acids 65

Secondary Structures Are the Core Elements of Protein Architecture 66

Overall Folding of a Polypeptide Chain Yields Its Tertiary Structure 67

Different Ways of Depicting the Conformation of Proteins Convey Different Types of Information 68

Structural Motifs Are Regular Combinations of Secondary and Tertiary Structures 68

Structural and Functional Domains Are Modules of Tertiary Structure 70

Proteins Associate into Multimeric Structures and Macromolecular Assemblies 72

Members of Protein Families Have a Common Evolutionary Ancestor 72

3.2 Protein Folding 74

Planar Peptide Bonds Limit the Shapes into Which Proteins Can Fold 74

Information Directing a Protein’s Folding Is Encoded in Its Amino Acid Sequence 74

Folding of Proteins in Vivo Is Promoted by Chaperones 75

Alternatively Folded Proteins Are Implicated in Diseases 77

3.3 Protein Function 78

Specific Binding of Ligands Underlies the Functions of Most Proteins 78

Enzymes Are Highly Efficient and Specific Catalysts 79

An Enzyme’s Active Site Binds Substrates and Carries Out Catalysis 80

Serine Proteases Demonstrate How an Enzyme’s Active Site Works 81

Enzymes in a Common Pathway Are Often Physically Associated with One Another 84

Enzymes Called Molecular Motors Convert Energyinto Motion 85

3.4 Regulating Protein Function Ⅰ：Protein Degradation 86

Regulated Synthesis and Degradation of Proteins is a Fundamental Property of Cells 86

The Proteasome Is a Complex Molecular Machine Used to Degrade Proteins 87

Ubiquitin Marks Cytosolic Proteins for Degradation in Proteasomes 88

3.5 Regulating Protein Function Ⅱ：Noncovalent and Covalent Modifications 88

Noncovalent Binding Permits Allosteric，or Cooperative，Regulation of Proteins 89

Noncovalent Binding of Calcium and GTP Are Widely Used As Allosteric Switches to Control Protein Activity 90

Phosphorylation and Dephosphorylation Covalently Regulate Protein Activity 91

Proteolytic Cleavage Irreversibly Activates or Inactivates Some Proteins 91

Higher-Order Regulation Includes Control of Protein Location and Concentration 92

3.6 Purifying，Detecting，and Characterizing Proteins 92

Centrifugation Can Separate Particles and Molecules That Differ in Mass or Density 92

Electrophoresis Separates Molecules on the Basis of Their Charge-to-Mass Ratio 94

Liquid Chromatography Resolves Proteins by Mass，Charge，or Binding Affinity 96

Highly Specific Enzyme and Antibody Assays Can Detect Individual Proteins 98

Radioisotopes Are Indispensable Tools for Detecting Biological Molecules 99

Mass Spectrometry Can Determine the Mass and Sequence of Proteins 101

Protein Primary Structure Can Be Determined by Chemical Methods and from Gene Sequences 103

Protein Conformation Is Determined by Sophisticated Physical Methods 103

3.7 Proteomics 105

Proteomics Is the Study of All or a Large Subset of Proteins in a Biological System 105

Advanced Techniques in Mass Spectrometry Are Critical to Proteomic Analysis 106

Part Ⅱ Genetics and Molecular Biology 111

4 BASIC MOLECULAR GENETIC MECHANISMS 111

4.1 Structure of Nucleic Acids 113

A Nucleic Acid Strand Is a Linear Polymer with End-to-End Directionality 113

Native DNA Is a Double Helix of Complementary Antiparallel Strands 114

DNA Can Undergo Reversible Strand Separation 116

Torsional Stress in DNA Is Relieved by Enzymes 117

Different Types of RNA Exhibit Various Conformations Related to Their Functions 118

4.2 Transcription of Protein-Coding Genes and Formation of Functional mRNA 120

A Template DNA Strand Is Transcribed into a Complementary RNA Chain by RNA Polymerase 120

Organization of Genes Differs in Prokaryotic and Eukaryotic DNA 122

Eukaryotic Precursor mRNAs Are Processed to Form Functional mRNAs 123

Alternative RNA Splicing Increases the Number of Proteins Expressed from a Single Eukaryotic Gene 125

4.3 The Decoding of mRNA by tRNAs 127

Messenger RNA Carries information from DNA in a Three-Letter Genetic Code 127

The Folded Structure of tRNA Promotes Its Decoding Functions 129

Nonstandard Base Pairing Often Occurs Between Codons and Anticodons 130

Amino Acids Become Activated When Covalently Linked to tRNAs 131

4.4 Stepwise Synthesis of Proteins on Ribosomes 132

Ribosomes Are Protein-Synthesizing Machines 132

Methionyl-tRNAiMET Recognizes the AUG Start Codon 133

Translation Initiation Usually Occurs at the First AUG from the 5’ End of an mRNA 133

During Chain Elongation Each Incoming Aminoacyl-tRNA Moves Through Three Ribosomal Sites 135

Translation Is Terminated by Release Factors When a Stop Codon Is Reached 137

Polysomes and Rapid Ribosome Recycling Increase the Efficiency of Translation 138

4.5 DNA Replication 139

DNA Polymerases Require a Primer to Initiate Replication 140

Duplex DNA Is Unwound and Daughter Strands Are Formed at the DNA Replication Fork 141

Several Proteins Participate in DNA Replication 141

DNA Replication Usually Occurs Bidirectionally from Each Origin 143

4.6 DNA Repair and Recombination 145

DNA Polymerases Introduce Copying Errors and Also Correct Them 145

Chemical and Radiation Damage to DNA Can Lead to Mutations 145

High-Fidelity DNA Excision-Repair Systems Recognize and Repair Damage 147

Base Excision Repairs T·G Mismatches and Damaged Bases 147

Mismatch Excision Repairs Other Mismatches and Small Insertions and Deletions 147

Nucleotide Excision Repairs Chemical Adducts That Distort Normal DNA Shape 148

Two Systems Utilize Recombination to Repair Double-Strand Breaks in DNA 149

Homologous Recombination Can Repair DNA Damage and Generate Genetic Diversity 150

4.7 Viruses：Parasites of the Cellular Genetic System 154

Most Viral Host Ranges Are Narrow 154

Viral Capsids Are Regular Arrays of One or a Few Types of Protein 154

Viruses Can Be Cloned and Counted in Plaque Assays 155

Lytic Viral Growth Cycles Lead to the Death of Host Cells 156

Viral DNA Is Integrated into the Host-Cell Genome in Some Nonlytic Viral Growth Cycles 158

5 MOLECULAR GENETIC TECHNIQUES 165

5.1 Genetic Analysis of Mutations to Identify and Study Genes 166

Recessive and Dominant Mutant Alleles Generally Have Opposite Effects on Gene Function 166

Segregation of Mutations in Breeding Experiments Reveals Their Dominance or Recessivity 167

Conditional Mutations Can Be Used to Study Essential Genes in Yeast 170

Recessive Lethal Mutations in Diploids Can Be Identified by Inbreeding and Maintained in Heterozygotes 171

Complementation Tests Determine Whether Different Recessive Mutations Are in the Same Gene 171

Double Mutants Are Useful in Assessing the Order in Which Proteins Function 171

Genetic Suppression and Synthetic Lethality Can Reveal Interacting or Redundant Proteins 173

Genes Can Be Identified by Their Map Position on the Chromosome 174

5.2 DNA Cloning and Characterization 176

Restriction Enzymes and DNA Ligases Allow Insertion of DNA Fragments into Cloning Vectors 176

E.coli Plasmid Vectors Are Suitable for Cloning Isolated DNA Fragments 178

cDNA Libraries Represent the Sequences of Protein-Coding Genes 179

cDNAs Prepared by Reverse Transcription of Cellular mRNAs Can Be Cloned to Generate cDNA Libraries 181

DNA Libraries Can Be Screened by Hybridization to an Oligonucleotide Probe 181

Yeast Genomic Libraries Can Be Constructed with Shuttle Vectors and Screened by Functional Complementation 182

Gel Electrophoresis Allows Separation of Vector DNA from Cloned Fragments 184

Cloned DNA Molecules Are Sequenced Rapidly by the Dideoxy Chain-Termination Method 187

The Polymerase Chain Reaction Amplifies a Specific DNA Sequence from a Complex Mixture 188

5.3 Using Cloned DNA Fragments to Study Gene Expression 191

Hybridization Techniques Permit Detection of Specific DNA Fragments and mRNAs 191

DNA Microarrays Can Be Used to Evaluate the Expression of Many Genes at One Time 192

Cluster Analysis of Multiple Expression Experiments Identifies Co-regulated Genes 193

E.coli Expression Systems Can Produce Large Quantities of Proteins from Cloned Genes 194

Plasmid Expression Vectors Can Be Designed for Use in Animal Cells 196

5.4 Identifying and Locating Human Disease Genes 198

Many Inherited Diseases Show One of Three Major Patterns of Inheritance 199

DNA Polymorphisms Are Used in Linkage-Mapping Human Mutations 200

Linkage Studies Can Map Disease Genes with a Resolution of About 1 Centimorgan 201

Further Analysis Is Needed to Locate a Disease Gene in Cloned DNA 202

Many Inherited Diseases Result from Multiple Genetic Defects 203

5.5 Inactivating the Function of Specific Genes in Eukaryotes 204

Normal Yeast Genes Can Be Replaced with Mutant Alleles by Homologous Recombination 205

Transcription of Genes Ligated to a Regulated Promoter Can Be Controlled Experimentally 206

Specific Genes Can Be Permanently Inactivated in the Germ Line of Mice 207

Somatic Cell Recombination Can Inactivate Genes in Specific Tissues 208

Dominant-Negative Alleles Can Functionally Inhibit Some Genes 209

RNA Interference Causes Gene Inactivation by Destroying the Corresponding mRNA 210

6 GENES，GENOMICS，AND CHROMOSOMES 215

6.1 Eukaryotic Gene Structure 217

Most Eukaryotic Genes Contain Introns and Produce mRNAs Encoding Single Proteins 217

Simple and Complex Transcription Units Are Found in Eukaryotic Genomes 217

Protein-Coding Genes May Be Solitary or Belong to a Gene Family 219

Heavily Used Gene Products Are Encoded by Multiple Copies of Genes 221

Nonprotein-Coding Genes Encode Functional RNAs 222

6.2 Chromosomal Organization of Genes and Noncoding DNA 223

Genomes of Many Organisms Contain Much Nonfunctional DNA 223

Most Simple-Sequence DNAs Are Concentrated in Specific Chromosomal Locations 224

DNA Fingerprinting Depends on Differences in Length of Simple-Sequence DNAs 225

Unclassified Spacer DNA Occupies a Significant Portion of the Genome 225

6.3 Transposable（Mobile） DNA Elements 226

Movement of Mobile Elements Involves a DNA or an RNA Intermediate 226

DNA Transposons Are Present in Prokaryotes and Eukaryotes 227

LTR Retrotransposons Behave Like Intracellular Retroviruses 229

Non-LTR Retrotransposons Transpose by a Distinct Mechanism 230

Other Retrotransposed RNAs Are Found in Genomic DNA 234

Mobile DNA Elements Have Significantly Influenced Evolution 234

6.4 Organelle DNAs 236

Mitochondria Contain Multiple mtDNA Molecules 237

mtDNA Is Inherited Cytoplasmically 237

The Size，Structure，and Coding Capacity of mtDNA Vary Considerably Between Organisms 238

Products of Mitochondrial Genes Are Not Exported 240

Mitochondria Evolved from a Single Endosymbiotic Event Involving a Rickettsia-like Bacterium 240

Mitochondrial Genetic Codes Differ from the Standard Nuclear Code 240

Mutations in Mitochondrial DNA Cause Several Genetic Diseases in Humans 240

Chloroplasts Contain Large DNAs Often Encoding More Than a Hundred Proteins 242

6.5 Genomics：Genome-wide Analysis of Gene Structure and Expression 243

Stored Sequences Suggest Functions of Newly Identified Genes and Proteins 243

Comparison of Related Sequences from Different Species Can Give Clues to Evolutionary Relationships Among Proteins 244

Genes Can Be Identified Within Genomic DNA Sequences 244

The Number of Protein-Coding Genes in an Organism’s Genome Is Not Directly Related to Its Biological Complexity 245

Single Nucleotide Polymorphisms and Gene Copy-Number Variation Are Important Determinants of Differences Between Individuals of a Species 246

6.6 Structural Organization of Eukaryotic Chromosomes 247

Chromatin Exists in Extended and Condensed Forms 248

Modifications of Histone Tails Control Chromatin Condensation and Function 250

Nonhistone Proteins Provide a Structural Scaffold for Long Chromatin Loops 254

Additional Nonhistone Proteins Regulate Transcription and Replication 256

6.7 Morphology and Functional Elements of Eukaryotic Chromosomes 257

Chromosome Number，Size，and Shape at Metaphase Are Species-Specific 257

During Metaphase，Chromosomes Can Be Distinguished by Banding Patterns and Chromosome Painting 258

Chromosome Painting and DNA Sequencing Reveal the Evolution of Chromosomes 259

Interphase Polytene Chromosomes Arise by DNA Amplification 260

Three Functional Elements Are Required for Replication and Stable Inheritance of Chromosomes 261

Centromere Sequences Vary Greatly in Length 263

Addition of Telomeric Sequences by Telomerase Prevents Shortening of Chromosomes 263

7 TRANSCRIPTIONAL CONTROL OF GENE EXPRESSION 269

7.1 Control of Gene Expression in Bacteria 271

Transcription Initiation by Bacterial RNA Polymerase Requires Association with a Sigma Factor 271

Initiation of Iac Operon Transcription Can Be Repressed and Activated 271

Small Molecules Regulate Expression of Many Bacterial Genes via DNA-Binding Repressors and Activators 273

Transcription Initiation from Some Promoters Requires Alternative Sigma Factors 273

Transcription by σ54-RNA Polymerase Is Controlled by Activators That Bind Far from the Promoter 274

Many Bacterial Responses Are Controlled by Two-Component Regulatory Systems 275

7.2 Overview of Eukaryotic Gene Control and RNA Polymerases 276

Regulatory Elements in Eukaryotic DNA Are Found Both Close to and Many Kilobases Away from Transcription Start Sites 276

Three Eukaryotic Polymerases Catalyze Formation of Different RNAs 278

The Largest Subunit in RNA Polymerase Ⅱ Has an Essential Carboxyl-Terminal Repeat 279

RNA Polymerase Ⅱ Initiates Transcription at DNA Sequences Corresponding to the 5’ Cap of mRNAs 280

7.3 Regulatory Sequences in Protein-Coding Genes 282

The TATA Box，Initiators，and CpG Islands Function as Promoters in Eukaryotic DNA 282

Promoter-Proximal Elements Help Regulate Eukaryotic Genes 282

Distant Enhancers Often Stimulate Transcription by RNA Polymerase Ⅱ 284

Most Eukaryotic Genes Are Regulated by Multiple Transcription-Control Elements 285

7.4 Activators and Repressors of Transcription 286

Footprinting and Gel-Shift Assays Detect Protein-DNA Interactions 286

Activators Are Modular Proteins Composed of Distinct Functional Domains and Promote Transcription 288

Repressors Inhibit Transcription and Are the Functional Converse of Activators 290

DNA-Binding Domains Can Be Classified into Numerous Structural Types 290

Structurally Diverse Activation and Repression Domains Regulate Transcription 293

Transcription Factor Interactions Increase Gene-Control Options 294

Multiprotein Complexes Form on Enhancers 295

7.5 Transcription Initiation by RNA Polymerase Ⅱ 296

General Transcription Factors Position RNA Polymerase Ⅱ at Start Sites and Assist in Initiation 296

Sequential Assembly of Proteins Forms the Pol Ⅱ Transcription Preinitiation Complex in Vitro 297

In Vivo Transcription Initiation by Pol Ⅱ Requires Additional Proteins 298

7.6 Molecular Mechanisms of Transcription Repression and Activation 299

Formation of Heterochromatin Silences Gene Expression at Telomeres，Near Centromeres，and in Other Regions 299

Repressors Can Direct Histone Deacetylation and Methylation at Specific Genes 303

Activators Can Direct Histone Acetylation and Methylation at Specific Genes 305

Chromatin-Remodeling Factors Help Activate or Repress Transcription 306

Histone Modifications Vary Greatly in Their Stabilities 307

The Mediator Complex Forms a Molecular Bridge Between Activation Domains and Pol Ⅱ 307

Transcription of Many Genes Requires Ordered Binding and Function of Activators and Co-activators 308

The Yeast Two-Hybrid System Exploits Activator Flexibility to Detect cDNAs That Encode Interacting Proteins 310

7.7 Regulation of Transcription-Factor Activity 311

All Nuclear Receptors Share a Common Domain Structure 312

Nuclear-Receptor Response Elements Contain Inverted or Direct Repeats 313

Hormone Binding to a Nuclear Receptor Regulates Its Activity as a Transcription Factor 313

7.8 Regulated Elongation and Termination of Transcription 314

Transcription of the HIV Genome Is Regulated by an Antitermination Mechanism 315

Promoter-Proximal Pausing of RNA Polymerase Ⅱ Occurs in Some Rapidly Induced Genes 316

7.9 Other Eukaryotic Transcription Systems 316

Transcription Initiation by Pol Ⅰ and Pol Ⅲ Is Analogous to That by Pol Ⅱ 316

Mitochondrial and Chloroplast DNAs Are Transcribed by Organelle-Specific RNA Polymerases 317

8 POST-TRANSCRIPTIONAL GENE CONTROL 323

8.1 Processing of Eukaryotic Pre-mRNA 325

The 5’ Cap Is Added to Nascent RNAs Shortly After Transcription Initiation 325

A Diverse Set of Proteins with Conserved RNA-Binding Domains Associate with Pre-mRNAs 326

Splicing Occurs at Short，Conserved Sequences in Pre-mRNAs via Two Transesterification Reactions 329

During Splicing，snRNAs Base-Pair with Pre-mRNA 330

Spliceosomes，Assembled from snRNPs and a Pre-mRNA，Carry Out Splicing 330

Chain Elongation by RNA Polymerase Ⅱ Is Coupled to the Presence of RNA-Processing Factors 333

SR Proteins Contribute to Exon Definition in Long Pre-mRNAs 333

Self-Splicing Group Ⅱ Introns Provide Clues to the Evolution of snRNAs 334

3’ Cleavage and Polyadenylation of Pre-mRNAs Are Tightly Coupled 335

Nuclear Exonucleases Degrade RNA That Is Processed Out of Pre-mRNAs 336

8.2 Regulation of Pre-mRNA Processing 337

Alternative Splicing Is the Primary Mechanism for Regulating mRNA Processing 337

A Cascade of Regulated RNA Splicing Controls Drosophila Sexual Differentiation 338

Splicing Repressors and Activators Control Splicing at Alternative Sites 339

RNA Editing Alters the Sequences of Some Pre-mRNAs 340

8.3 Transport of mRNA Across the Nuclear Envelope 341

Nuclear Pore Complexes Control Import and Exportfrom the Nucleus 342

Pre-mRNAs in Spliceosomes Are Not Exported from the Nucleus 345

HIV Rev Protein Regulates the Transport of Unspliced Viral mRNAs 346

8.4 Cytoplasmic Mechanisms of Post-transcriptional Control 347

Micro RNAs Repress Translation of Specific mRNAs 347

RNA Interference Induces Degradation of Precisely Complementary mRNAs 349

Cytoplasmic Polyadenylation Promotes Translation of Some mRNAs 351

Degradation of mRNAs in the Cytoplasm Occurs by Several Mechanisms 352

Protein Synthesis Can Be Globally Regulated 353

Sequence-Specific RNA-Binding Proteins Control Specific mRNA Translation 356

Surveillance Mechanisms Prevent Translation of Improperly Processed mRNAs 357

Localization of mRNAs Permits Production of Proteins at Specific Regions Within the Cytoplasm 357

8.5 Processing of rRNA and tRNA 358

Pre-rRNA Genes Function as Nucleolar Organizers and Are Similar in All Eukaryotes 359

Small Nucleolar RNAs Assist in Processing Pre-rRNAs 360

Self-Splicing Group I Introns Were the First Examples of Catalytic RNA 363

Pre-tRNAs Undergo Extensive Modification in the Nucleus 363

Nuclear Bodies Are Functionally Specialized Nuclear Domains 364

Part Ⅲ Cell Structure and Function 371

9 VISUALIZING，FRACTIONATING，AND CULTURING CELLS 371

9.1 Organelles of the Eukaryotic Cell 372

The Plasma Membrane Has Many Common Functions in All Cells 372

Endosomes Take Up Soluble Macromolecules from the Cell Exterior 372

Lysosomes Are Acidic Organelles That Contain a Battery of Degradative Enzymes 373

Peroxisomes Degrade Fatty Acids and Toxic Compounds 374

The Endoplasmic Reticulum Is a Network of Interconnected Internal Membranes 375

The Golgi Complex Processes and Sorts Secreted and Membrane Proteins 376

Plant Vacuoles Store Small Molecules and Enable a Cell to Elongate Rapidly 377

The Nucleus Contains the DNA Genome，RNA Synthetic Apparatus，and a Fibrous Matrix 378

Mitochondria Are the Principal Sites of ATP Production in Aerobic Non photosynthetic Cells 378

Chloroplasts Contain Internal Compartments in Which Photosynthesis Takes Place 379

9.2 Light Microscopy：Visualizing Cell Structure and Localizing Proteins Within Cells 380

The Resolution of the Light Microscope Is About 0.2 μm 381

Phase-Contrast and Differential Interference Contrast Microscopy Visualize Unstained Living Cells 381

Fluorescence Microscopy Can Localize and Quantify Specific Molecules in Live Cells 382

Imaging Subcellular Details Often Requires that the Samples Be Fixed，Sectioned，and Stained 384

Immunofluorescence Microscopy Can Detect Specific Proteins in Fixed Cells 385

Confocal and Deconvolution Microscopy Enable Visualization of Three-Dimensional Objects 386

Graphics and Informatics Have Transformed Modern Microscopy 387

9.3 Electron Microscopy：Methods and Applications 388

Resolution of Transmission Electron Microscopy is Vastly Greater Than That of Light Microscopy 388

Cryoelectron Microscopy Allows Visualization of Particles Without Fixation or Staining 389

Electron Microscopy of Metal-Coated Specimens Can Reveal Surface Features of Cells and Their Components 390

9.4 Purification of Cell Organelles 391

Disruption of Cells Releases Their Organelles and Other Contents 391

Centrifugation Can Separate Many Types of Organelles 392

Organelle-Specific Antibodies Are Useful in Preparing Highly Purified Organelles 393

9.5 Isolation，Culture，and Differentiation of Metazoan Cells 394

Flow Cytometry Separates Different Cell Types 394

Culture of Animal Cells Requires Nutrient-Rich Media and Special Solid Surfaces 395

Primary Cell Cultures Can Be Used to Study Cell Differentiation 396

Primary Cell Cultures and Cell Strains Have a Finite Life Span 396

Transformed Cells Can Grow Indefinitely in Culture 397

Some Cell Lines Undergo Differentiation in Culture 398

Hybrid Cells Called Hybridomas Produce Abundant Monoclonal Antibodies 400

HAT Medium Is Commonly Used to Isolate Hybrid Cells 402

CLASSIC EXPERIMENT 9.1 Separating Organelles 407

10 BIOMEMBRANE STRUCTURE 409

10.1 Biomembranes：Lipid Composition and Structural Organization 411

Phospholipids Spontaneously Form Bilayers 411

Phospholipid Bilayers Form a Sealed Compartment Surrounding an Internal Aqueous Space 411

Biomembranes Contain Three Principal Classes of Lipids 415

Most Lipids and Many Proteins Are Laterally Mobile in Biomembranes 416

Lipid Composition Influences the Physical Properties of Membranes 418

Lipid Composition Is Different in the Exoplasmic and Cytosolic Leaflets 419

Cholesterol and Sphingolipids Cluster with Specific Proteins in Membrane Microdomains 420

10.2 Biomembranes：Protein Components and Basic Functions 421

Proteins Interact with Membranes in Three Different Ways 421

Most Transmembrane Proteins Have Membrane-Spanning α Helices 422

Multiple β Strands in Porins Form Membrane-Spanning “Barrels” 424

Covalently Attached Hydrocarbon Chains Anchor Some Proteins to Membranes 424

All Transmembrane Proteins and Glycolipids Are Asymmetrically Oriented in the Bilayer 426

Lipid-Binding Motifs Help Target Peripheral Proteins to the Membrane 427

Proteins Can Be Removed from Membranes by Detergents or High-Salt Solutions 427

10.3 Phospholipids，Sphingolipids，and Cholesterol：Synthesis and Intracellular Movement 429

Fatty Acids Synthesis Is Mediated by Several Important Enzymes 430

Small Cytosolic Proteins Facilitate Movement of Fatty Acids 430

Incorporation of Fatty Acids into Membrane Lipids Takes Place on Organelle Membranes 431

Flippases Move Phospholipids from One Membrane Leaflet to the Opposite Leaflet 431

Cholesterol Is Synthesized by Enzymes in the Cytosol and ER Membrane 432

Cholesterol and Phospholipids Are Transported Between Organelles by Several Mechanisms 433

11 TRANSMEMBRANE TRANSPORT OF IONS AND SMALL MOLECULES 437

11.1 Overview of Membrane Transport 438

Only Small Hydrophobic Molecules Cross Membranes by Simple Diffusion 438

Membrane Proteins Mediate Transport of Most Molecules and All Ions Across Biomembranes 439

11.2 Uniport Transport of Glucose and Water 441

Several Features Distinguish Uniport Transport from Simple Diffusion 441

GLUT1 Uniporter Transports Glucose into Most Mammalian Cells 442

The Human Genome Encodes a Family of Sugar-Transporting GLUT Proteins 443

Transport Proteins Can Be Enriched Within Artificial Membranes and Cells 443

Osmotic Pressure Causes Water to Move Across Membranes 444

Aquaporins Increase the Water Permeability of Cell Membranes 444

11.3 ATP-Powered Pumps and the Intracellular Ionic Environment 447

Different Classes of Pumps Exhibit Characteristic Structural and Functional Properties 447

ATP-Powered Ion Pumps Generate and Maintain Ionic Gradients Across Cellular Membranes 448

Muscle Relaxation Depends on Ca 2＋ ATPases That Pump Ca 2＋ from the Cytosol into the Sarcoplasmic Reticulum 449

Calmodulin Regulates the Plasma Membrane Ca 2＋ Pumps That Control Cytosolic Ca 2＋Concentrations 451

Na＋/K＋ ATPase Maintains the Intracellular Na＋and K＋ Concentrations in Animal Cells 452

V-Class H＋ ATPases Maintain the Acidity of Lysosomes and Vacuoles 453

Bacterial Permeases Are ABC Proteins That Import a Variety of Nutrients from the Environment 454

The Approximately 50 Mammalian ABC Transporters Play Diverse and Important Roles in Cell and Organ Physiology 455

Certain ABC Proteins “Flip” Phospholipids and Other Lipid-Soluble Substrates from One Membrane Leaflet to the Opposite Leaflet 456

11.4 Nongated Ion Channels and the Resting Membrane Potential 458

Selective Movement of Ions Creates a Transmembrane Electric Potential Difference 458

The Membrane Potential in Animal Cells Depends Largely on Potassium Ion Movements Through Open Resting K＋ Channels 460

Ion Channels Contain a Selectivity Filter Formed from Conserved Transmembrane Segments 461

Patch Clamps Permit Measurement of Ion Movements Through Single Channels 463

Novel Ion Channels Can Be Characterized by a Combination of Oocyte Expression and Patch Clamping 464

Na＋ Entry into Mammalian Cells Has a Negative Change in Free Energy（△G） 464

11.5 Cotransport by Symporters and Antiporters 465

Na＋-Linked Symporters Import Amino Acids and Glucose into Animal Cells Against High Concentration Gradients 466

Bacterial Symporter Structure Reveals the Mechanism of Substrate Binding 467

Na＋-Linked Ca 2＋ Antiporter Exports Ca 2＋ from Cardiac Muscle Cells 468

Several Cotransporters Regulate Cytosolic pH 468

A Putative Cation Exchange Protein Plays a Key Role in Evolution of Human Skin Pigmentation 469

Numerous Transport Proteins Enable Plant Vacuoles to Accumulate Metabolites and Ions 469

11.6 Transepithelial Transport 470

Multiple Transport Proteins Are Needed to Move Glucose and Amino Acids Across Epithelia 471

Simple Rehydration Therapy Depends on the Osmotic Gradient Created by Absorption of Glucose and Na＋ 471

Parietal Cells Acidify the Stomach Contents While Maintaining a Neutral Cytosolic pH 472

CLASSIC EXPERIMENT 11.1 Stumbling Upon Active Transport 477

12 CELLULAR ENERGETICS 479

12.1 First Steps of Glucose and Fatty Acid Catabolism：Glycolysis and the Citric Acid Cycle 480

During Glycolysis（Stage Ⅰ），Cytosolic Enzymes Convert Glucose to Pyruvate 481

The Rate of Glycolysis Is Adjusted to Meet the Cell’s Need for ATP 483

Glucose Is Fermented Under Anaerobic Conditions 485

Under Aerobic Conditions，Mitochondria Efficiently Oxidize Pyruvate and Generate ATP（Stages Ⅱ-Ⅳ） 485

Mitochondria Are Dynamic Organelles with Two Structurally and Functionally Distinct Membranes 485

In Stage Ⅱ，Pyruvate Is Oxidized to CO2 and High-Energy Electrons Stored in Reduced Coenzymes 487

Transporters in the Inner Mitochondrial Membrane Help Maintain Appropriate Cytosolic and Matrix Concentrations of NAD＋ and NADH 489

Mitochondrial Oxidation of Fatty Acids Generates ATP 491

Peroxisomal Oxidation of Fatty Acids Generates No ATP 491

12.2 The Electron Transport Chain and Generation of the Proton-Motive Force 493

Stepwise Electron Transport Efficiently Releases the Energy Stored in NADH and FADH2 493

Electron Transport in Mitochondria Is Coupled to Proton Pumping 493

Electrons Flow from FADH2 and NADH to O2 Through Four Multiprotein Complexes 494

Reduction Potentials of Electron Carriers Favor Electron Flow from NADH to O2 499

Experiments Using Purified Complexes Established the Stoichiometry of Proton Pumping 499

The Q Cycle Increases the Number of Protons Translocated as Electrons Flow Through Complex Ⅲ 500

The Proton-Motive Force in Mitochondria Is Due Largely to a Voltage Gradient Across the Inner Membrane 502

Toxic By-products of Electron Transport Can Damage Cells 502

12.3 Harnessing the Proton-Motive Force for Energy-Requiring Processes 503

The Mechanism of ATP Synthesis Is Shared Among Bacteria，Mitochondria，and Chloroplasts 505

ATP Synthase Comprises Two Multiprotein Complexes Termed F0 and F1 505

Rotation of the F1 γ Subunit，Driven by Proton Movement Through F0，Powers ATP Synthesis 506

ATP-ADP Exchange Across the Inner Mitochondrial Membrane Is Powered by the Proton-Motive Force 509

Rate of Mitochondrial Oxidation Normally Depends on ADP Levels 510

Brown-Fat Mitochondria Use the Proton-Motive Force to Generate Heat 510

12.4 Photosynthesis and Light-Absorbing Pigments 511

Thylakoid Membranes in Chloroplasts Are the Sites of Photosynthesis in Plants 511

Three of the Four Stages in Photosynthesis Occur Only During Illumination 511

Each Photon of Light Has a Defined Amount of Energy 513

Photosystems Comprise a Reaction Center and Associated Light-Harvesting Complexes 514

Photoelectron Transport from Energized Reaction-Center Chlorophyll a Produces a Charge Separation 514

Internal Antenna and Light-Harvesting Complexes Increase the Efficiency of Photosynthesis 515

12.5 Molecular Analysis of Photosystems 517

The Single Photosystem of Purple Bacteria Generates a Proton-Motive Force but No O2 517

Linear Electron Flow Through Both Plant Photosystems，PSII and PSI，Generates a Proton-Motive Force，O2，and NADPH 519

An Oxygen-Evolving Complex Is Located on the Luminal Surface of the PSII Reaction Center 520

Cells Use Multiple Mechanisms to Protect Against Damage from Reactive Oxygen Species During Photoelectron Transport 521

Cyclic Electron Flow Through PSI Generates a Proton-Motive Force but No NADPH or O2 522

Relative Activities of Photosystems Ⅰ and Ⅱ Are Regulated 523

12.6 CO2 Metabolism During Photosynthesis 524

Rubisco Fixes CO2 in the Chloroplast Stroma 525

Synthesis of Sucrose Using Fixed CO2 Is Completed in the Cytosol 525

Light and Rubisco Activase Stimulate CO2 Fixation 525

Photorespiration，Which Competes with Photosynthesis，Is Reduced in Plants That Fix CO2 by the C4 Pathway 527

13 MOVING PROTEINS INTO MEMBRANES AND ORGANELLES 533

13.1 Translocation of Secretory Proteins Across the ER Membrane 535

A Hydrophobic N-Terminal Signal Sequence Targets Nascent Secretory Proteins to the ER 536

Cotranslational Translocation Is Initiated by Two GTP-Hydrolyzing Proteins 537

Passage of Growing Polypeptides Through the Translocon Is Driven by Energy Released During Translation 539

ATP Hydrolysis Powers Post-translational Translocation of Some Secretory Proteins in Yeast 540

13.2 Insertion of Proteins into the ER Membrane 542

Several Topological Classes of Integral Membrane Proteins Are Synthesized on the ER 543

Internal Stop-Transfer and Signal-Anchor Sequences Determine Topology of Single-Pass Proteins 544

Multipass Proteins Have Multiple Internal Topogenic Sequences 546

A Phospholipid Anchor Tethers Some Cell-Surface Proteins to the Membrane 547

The Topology of a Membrane Protein Often Can Be Deduced from Its Sequence 547

13.3 Protein Modifications，Folding，and Quality Control in the ER 549

A Preformed N-Linked Oligosaccharide Is Added to Many Proteins in the Rough ER 550

Oligosaccharide Side Chains May Promote Folding and Stability of Glycoproteins 552

Disulfide Bonds Are Formed and Rearranged by Proteins in the ER Lumen 552

Chaperones and Other ER Proteins Facilitate Folding and Assembly of Proteins 552

Improperly Folded Proteins in the ER Induce Expression of Protein-Folding Catalysts 555

Unassembled or Misfolded Proteins in the ER Are Often Transported to the Cytosol for Degradation 556

13.4 Sorting of Proteins to Mitochondria and Chloroplasts 557

Amphipathic N-Terminal Signal Sequences Direct Proteins to the Mitochondrial Matrix 558

Mitochondrial Protein Import Requires Outer-Membrane Receptors and Translocons in Both Membranes 558

Studies with Chimeric Proteins Demonstrate Important Features of Mitochondrial Import 560

Three Energy Inputs Are Needed to Import Proteins into Mitochondria 561

Multiple Signals and Pathways Target Proteins to Submitochondrial Compartments 561

Targeting of Chloroplast Stromal Proteins Is Similar to Import of Mitochondrial Matrix Proteins 565

Proteins Are Targeted to Thylakoids by Mechanisms Related to Translocation Across the Bacterial Inner Membrane 565

13.5 Sorting of Peroxisomal Proteins 567

Cytosolic Receptor Targets Proteins with an SKL Sequence at the C-Terminus into the Peroxisomal Matrix 567

Peroxisomal Membrane and Matrix Proteins Are Incorporated by Different Pathways 568

13.6 Transport into and out of the Nucleus 569

Large and Small Molecules Enter and Leave the Nucleus via Nuclear Pore Complexes 570

Importins Transport Proteins Containing Nuclear- Localization Signals into the Nucleus 571

Exportins Transport Proteins Containing Nuclear-ExportSignals out of the Nucleus 573

Most mRNAs Are Exported from the Nucleus by a Ran-Independent Mechanism 573

14 VESICULAR TRAFFIC，SECRETION，AND ENDOCYTOSIS 579

14.1 Techniques for Studying the Secretory Pathway 580

Transport of a Protein Through the Secretory Pathway Can Be Assayed in Living Cells 582

Yeast Mutants Define Major Stages and Many Components in Vesicular Transport 584

Cell-Free Transport Assays Allow Dissection of Individual Steps in Vesicular Transport 585

14.2 Molecular Mechanisms of Vesicular Traffic 586

Assembly of a Protein Coat Drives Vesicle Formation and Selection of Cargo Molecules 586

A Conserved Set of GTPase Switch Proteins Controls Assembly of Different Vesicle Coats 587

Targeting Sequences on Cargo Proteins Make Specific Molecular Contacts with Coat Proteins 588

Rab GTPases Control Docking of Vesicles on Target Membranes 589

Paired Sets of SNARE Proteins Mediate Fusion of Vesicles with Target Membranes 591

Dissociation of SNARE Complexes After Membrane Fusion Is Driven by ATP Hydrolysis 591

14.3 Early Stages of the Secretory Pathway 592

COPII Vesicles Mediate Transport from the ER to the Golgi 592

COPI Vesicles Mediate Retrograde Transport within the Golgi and from the Golgi to the ER 594

Anterograde Transport Through the Golgi Occurs by Cisternal Maturation 595

14.4 Later Stages of the Secretory Pathway 597

Vesicles Coated with Clathrin and/or Adapter Proteins Mediate Several Transport Steps 598

Dynamin Is Required for Pinching Off of Clathrin Vesicles 599

Mannose 6-Phosphate Residues Target Soluble Proteins to Lysosomes 600

Study of Lysosomal Storage Diseases Revealed Key Components of the Lysosomal Sorting Pathway 602

Protein Aggregation in the trans-Golgi May Function in Sorting Proteins to Regulated Secretory Vesicles 602

Some Proteins Undergo Proteolytic Processing After Leaving the trans-Golgi 603

Several Pathways Sort Membrane Proteins to the Apical or Basolateral Region of Polarized Cells 604

14.5 Receptor-Mediated Endocytosis 606

Cells Take Up Lipids from the Blood in the Form of Large，Well-Defined Lipoprotein Complexes 606

Receptors for Low-Density Lipoprotein and Other Ligands Contain Sorting Signals That Target Them for Endocytosis 608

The Acidic pH of Late Endosomes Causes Most Receptor-Ligand Complexes to Dissociate 610

The Endocytic Pathway Delivers Iron to Cells without Dissociation of the Receptor-Transferrin Complex in Endosomes 611

14.6 Directing Membrane Proteins and Cytosolic Materials to the Lysosome 612

Multivesicular Endosomes Segregate Membrane Proteins Destined for the Lysosomal Membrane from Proteins Destined for Lysosomal Degradation 612

Retroviruses Bud from the Plasma Membrane by a Process Similar to Formation of Multivesicular Endosomes 614

CLASSIC EXPERIMENT 14.1 Following a Protein Out of the Cell 621

15 CELL SIGNALING Ⅰ：SIGNAL TRANSDUCTION AND SHORT-TERM CELLULAR RESPONSES 623

15.1 From Extracellular Signal to Cellular Response 625

Signaling Cells Produce and Release Signaling Molecules 625

Signaling Molecules Can Act Locally or at a Distance 625

Binding of Signaling Molecules Activates Receptors on Target Cells 626

15.2 Studying Cell-Surface Receptors 627

Receptor Proteins Bind Ligands Specifically 627

The Dissociation Constant Is a Measure of the Affinity of a Receptor for Its Ligand 628

Binding Assays Are Used to Detect Receptors and Determine Their Affinities for Ligands 628

Maximal Cellular Response to a Signaling Molecule Usually Does Not Require Activation of All Receptors 629

Sensitivity of a Cell to External Signals Is Determined by the Number of Surface Receptors and Their Affinity for Ligand 631

Receptors Can Be Purified by Affinity Techniques 631

Receptors Are Frequently Expressed from Cloned Genes 631

15.3 Highly Conserved Components of Intracellular Signal-Transduction Pathways 632

GTP-Binding Proteins Are Frequently Used As On/Off Switches 633

Protein Kinases and Phosphatases are Employed in Virtually All Signaling Pathways 634

Second Messengers Carry and Amplify Signals from Many Receptors 634

15.4 General Elements of G Protein-Coupled Receptor Systems 635

G Protein-Coupled Receptors Are a Large and Diverse Family with a Common Structure and Function 635

G Protein-Coupled Receptors Activate Exchange of GTP for GDP on the α Subunit of a Trimeric G Protein 637

Different G Proteins Are Activated by Different GPCRs and In Turn Regulate Different Effector Proteins 639

15.5 G Protein-Coupled Receptors That Regulate Ion Channels 640

Acetylcholine Receptors in the Heart Muscle Activate a G Protein That Opens K＋ Channels 641

Light Activates Gαt-Coupled Rhodopsins 641

Activation of Rhodopsin Induces Closing of cGMP-Gated Cation Channels 642

Rod Cells Adapt to Varying Levels of Ambient Light Because of Opsin Phosphorylation and Binding of Arrestin 644

15.6 G Protein-Coupled Receptors That Activate or Inhibit Adenylyl Cyclase 646

Adenylyl Cyclase Is Stimulated and Inhibited by Different Receptor-Ligand Complexes 646

Structural Studies Established How Gαs·GTP Binds to and Activates Adenylyl Cyclase 646

cAMP Activates Protein Kinase A by Releasing Catalytic Subunits 647

Glycogen Metabolism Is Regulated by Hormone-Induced Activation of Protein Kinase A 648

cAMP-Mediated Activation of Protein Kinase A Produces Diverse Responses in Different Cell Types 649

Signal Amplification Commonly Occurs in Many Signaling Pathways 650

Several Mechanisms Down-Regulate Signaling from G Protein-Coupled Receptors 651

Anchoring Proteins Localize Effects of cAMP to Specific Regions of the Cell 652

15.7 G Protein-Coupled Receptors That Activate Phospholipase C 653

Phosphorylated Derivatives of Inositol Are Important Second Messengers 654

Calcium Ion Release from the Endoplasmic Reticulum is Triggered by IP3 654

The Ca 2＋/Calmodulin Complex Mediates Many Cellular Responses to External Signals 655

Diacylglycerol（DAG） Activates Protein Kinase C，Which Regulates Many Other Proteins 656

Signal-Induced Relaxation of Vascular Smooth Muscle Is Mediated by cGMP-Activated Protein Kinase G 656

15.8 Integrating Responses of Cells to Environmental Influences 657

Integration of Multiple Second Messengers Regulates Glycogenolysis 657

Insulin and Glucagon Work Together to Maintain a Stable Blood Glucose Level 658

CLASSIC EXPERIMENT 15.1 The Infancy of Signal Transduction—GTP Stimulation of cAMP Synthesis 663

16 CELL-SIGNALING Ⅱ：SIGNALING PATHWAYS THAT CONTROL GENE ACTIVITY 665

16.1 TGFβ Receptors and the Direct Activation of Smads 668

A TGFβ Signaling Molecule Is Formed by Cleavage of an Inactive Precursor 668

Radioactive Tagging Was Used to Identify TGFβ Receptors 669

Activated TGFβ Receptors Phosphorylate Smad Transcription Factors 670

Negative Feedback Loops Regulate TGFβ/Smad Signaling 671

Loss of TGFβ Signaling Plays a Key Role in Cancer 671

16.2 Cytokine Receptors and the JAK/STAT Pathway 672

Cytokines Influence Development of Many Cell Types 672

Cytokine Receptors Have Similar Structures and Activate Similar Signaling Pathways 673

JAK Kinases Activate STAT Transcription Factors 674

Complementation Genetics Revealed That JAK and STAT Proteins Transduce Cytokine Signals 677

Signaling from Cytokine Receptors Is Regulated by Negative Signals 678

Mutant Erythropoietin Receptor That Cannot Be Turned Off Leads to Increased Numbers of Erythrocytes 679

16.3 Receptor Tyrosine Kinases 679

Ligand Binding Leads to Phosphorylation and Activation of Intrinsic Kinase in RTKs 680

Overexpression of HER2，a Receptor Tyrosine Kinase，Occurs in Some Breast Cancers 680

Conserved Domains Are Important for Binding Signal-Transduction Proteins to Activated Receptors 682

Down-regulation of RTK Signaling Occurs by Endocytosis and Lysosomal Degradation 683

16.4 Activation of Ras and MAP Kinase Pathways 684

Ras，a GTPase Switch Protein，Cycles Between Active and Inactive States 685

Receptor Tyrosine Kinases Are Linked to Ras by Adapter Proteins 685

Genetic Studies in Drosophila Identified Key Signal-Transducing Proteins in the Ras/MAP Kinase Pathway 685

Binding of Sos Protein to Inactive Ras Causes a Conformational Change That Activates Ras 687

Signals Pass from Activated Ras to a Cascade of Protein Kinases 688

MAP Kinase Regulates the Activity of Many Transcription Factors Controlling Early-Response Genes 690

G Protein-Coupled Receptors Transmit Signals to MAP Kinase in Yeast Mating Pathways 691

Scaffold Proteins Separate Multiple MAP Kinase Pathways in Eukaryotic Cells 692

The Ras/MAP Kinase Pathway Can Induce Diverse Cellular Responses 693

16.5 Phosphoinositides as Signal Transducers 694

Phospholipase Cγ Is Activated by Some RTKs and Cytokine Receptors 694

Recruitment of PI-3 Kinase to Hormone-Stimulated Receptors Leads to Synthesis of Phosphorylated Phosphatidylinositols 694

Accumulation of PI 3-Phosphates in the Plasma Membrane Leads to Activation of Several Kinases 695

Activated Protein Kinase B Induces Many Cellular Responses 696

The PI-3 Kinase Pathway Is Negatively Regulated by PTEN Phosphatase 697

16.6 Activation of Gene Transcription by Seven-Spanning Cell-Surface Receptors 697

CREB Links cAMP and Protein Kinase A to Activation of Gene Transcription 698

GPCR-Bound Arrestin Activates Several Kinase Cascades 698

Wnt Signals Trigger Release of a Transcription Factor from Cytosolic Protein Complex 699

Hedgehog Signaling Relieves Repression of Target Genes 700

16.7 Pathways That Involve Signal-Induced Protein Cleavage 703

Degradation of an Inhibitor Protein Activates the NF-κB Transcription Factors 703

Ligand-Activated Notch Is Cleaved Twice，Releasing a Transcription Factor 705

Matrix Metal loproteases Catalyze Cleavage of Many Signaling Proteins from the Cell Surface 706

Inappropriate Cleavage of Amyloid Precursor Protein Can Lead to Alzheimer’s Disease 706

Regulated Intramembrane Proteolysis of SREBP Releases a Transcription Factor That Acts to Maintain Phospholipid and Cholesterol Levels 707

17 CELL ORGANIZATION AND MOVEMENT Ⅰ：MICROFILAMENTS 713

17.1 Microfilaments and Actin Structures 716

Actin Is Ancient，Abundant，and Highly Conserved 717

G-Actin Monomers Assemble into Long，Helical F-Actin Polymers 717

F-Actin Has Structural and Functional Polarity 718

17.2 Dynamics of Actin Filaments 718

Actin Polymerization in Vitro Proceeds in Three Steps 719

Actin Filaments Grow Faster at（＋） Ends Than at（-） Ends 720

Actin Filament Treadmilling Is Accelerated by Profilin and Cofilin 721

Thymosin-β4 Provides a Reservoir of Actin for Polymerization 722

Capping Proteins Block Assembly and Disassembly at Actin Filament Ends 722

17.3 Mechanisms of Actin Filament Assembly 723

Formins Assemble Unbranched Filaments 723

The Arp2/3 Complex Nucleates Branched Filament Assembly 724

Intracellular Movements Can Be Powered by Actin Polymerization 726

Toxins That Perturb the Pool of Actin Monomers Are Useful for Studying Actin Dynamics 726

17.4 Organization of Actin-Based Cellular Structures 728

Cross-Linking Proteins Organize Actin Filaments into Bundles or Networks 728

Adaptor Proteins Link Actin Filaments to Membranes 728

17.5 Myosins：Actin-Based Motor Proteins 731

Myosins Have Head，Neck，and Tail Domains with Distinct Functions 732

Myosins Make Up a Large Family of Mechanochemical Motor Proteins 733

Conformational Changes in the Myosin Head Couple ATP Hydrolysis to Movement 736

Myosin Heads Take Discrete Steps Along Actin Filaments 736

Myosin V Walks Hand Over Hand Down an Actin Filament 737

17.6 Myosin-Powered Movements 738

Myosin Thick Filaments and Actin Thin Filaments in Skeletal Muscle Slide Past One Another During Contraction 738

Skeletal Muscle Is Structured by Stabilizing and Scaffolding Proteins 740

Contraction of Skeletal Muscle Is Regulated by Ca 2＋ and Actin-Binding Proteins 740

Actin and Myosin Ⅱ Form Contractile Bundles in Nonmuscle Cells 741

Myosin-Dependent Mechanisms Regulate Contraction in Smooth Muscle and Nonmuscle Cells 742

Myosin-V-Bound Vesicles Are Carried Along Actin Filaments 743

17.7 Cell Migration：Signaling and Chemotaxis 745

Cell Migration Coordinates Force Generation with Cell Adhesion and Membrane Recycling 745

The Small GTP-Binding Proteins Cdc42，Rac，and Rho Control Actin Organization 747

Cell Migration Involves the Coordinate Regulation of Cdc42，Rac，and Rho 748

Migrating Cells Are Steered by Chemotactic Molecules 750

Chemotactic Gradients Induce Altered Phosphoinositide Levels Between the Front and Back of a Cell 750

CLASSIC EXPERIMENT 17.1 Looking at Muscle Contraction 755

18 CELL ORGANIZATION AND MOVEMENT Ⅱ：MICROTUBULES AND INTERMEDIATE FILAMENTS 757

18.1 Microtubule Structure and Organization 758

Microtubule Walls Are Polarized Structures Built from αβ-Tubulin Dimers 758

Microtubules Are Assembled from MTOCs to Generate Diverse Organizations 760

18.2 Microtubule Dynamics 762

Microtubules Are Dynamic Structures Due to Kinetic Differences at Their Ends 763

Individual Microtubules Exhibit Dynamic Instability 763

Localized Assembly and “Search-and-Capture” Help Organize Microtubules 766

Drugs Affecting Tubulin Polymerization Are Useful Experimentally and to Treat Diseases 766

18.3 Regulation of Microtubule Structure and Dynamics 767

Microtubules Are Stabilized by Side- and End-Binding Proteins 767

Microtubules Are Disassembled by End Binding and Severing Proteins 768

18.4 Kinesins and Dyneins：Microtubule- Based Motor Proteins 769

Organelles in Axons Are Transported Along Microtubules in Both Directions 769

Kinesin-1 Powers Anterograde Transport of Vesicles Down Axons Toward the（＋） End of Microtubules 770

Kinesins Form a Large Protein Family with Diverse Functions 771

Kinesin-1 Is a Highly Processive Motor 772

Dynein Motors Transport Organelles Toward the（-）End of Microtubules 774

Kinesins and Dyneins Cooperate in the Transport of Organelles Throughout the Cell 775

18.5 Cilia and Flagella：Microtubule-Based Surface Structures 777

Eukaryotic Cilia and Flagella Contain Long Doublet Microtubules Bridged by Dynein Motors 777

Ciliary and Flagellar Beating Are Produced by Controlled Sliding of Outer Doublet Microtubules 778

Intraflagellar Transport Moves Material Up and Down Cilia and Flagella 779

Defects in Intraflagellar Transport Cause Disease by Affecting Sensory Primary Cilia 780

18.6 Mitosis 781

Mitosis Can Be Divided into Six Phases 782

Centrosomes Duplicate Early in the Cell Cycle in Preparation for Mitosis 783

The Mitotic Spindle Contains Three Classes of Microtubules 784

Microtubule Dynamics Increases Dramatically in Mitosis 784

Microtubules Treadmill During Mitosis 785

The Kinetochore Captures and Helps Transport Chromosomes 786

Duplicated Chromosomes Are Aligned by Motors and Treadmilling Microtubules 788

Anaphase A Moves Chromosomes to Poles by Microtubule Shortening 789

Anaphase B Separates Poles by the Combined Action of Kinesins and Dynein 789

Additional Mechanisms Contribute to Spindle Formation 789

Cytokinesis Splits the Duplicated Cell in Two 789

Plant Cells Reorganize Their Microtubules and Build a New Cell Wall in Mitosis 790

18.7 Intermediate Filaments 791

Intermediate Filaments Are Assembled from Subunit Dimers 792

Intermediate Filaments Proteins Are Expressed in a Tissue-Specific Manner 792

Intermediate Filaments Are Dynamic 795

Defects in Lamins and Keratins Cause Many Diseases 795

18.8 Coordination and Cooperation between Cytoskeletal Elements 796

Intermediate Filament-Associated Proteins Contribute to Cellular Organization 796

Microfilaments and Microtubules Cooperate to Transport Melanosomes 796

Cdc42 Coordinates Microtubules and Microfilaments During Cell Migration 797

19 INTEGRATING CELLS INTO TISSUES 801

19.1 Cell-Cell and Cell-Matrix Adhesion：An Overview 803

Cell-Adhesion Molecules Bind to One Another and to Intracellular Proteins 803

The Extracellular Matrix Participates in Adhesion，Signaling，and Other Functions 805

The Evolution of Multifaceted Adhesion Molecules Enabled the Evolution of Diverse Animal Tissues 807

19.2 Cell-Cell and Cell-ECM Junctions and Their Adhesion Molecules 808

Epithelial Cells Have Distinct Apical，Lateral，and Basal Surfaces 808

Three Types of Junctions Mediate Many Cell-Cell and Cell-ECM Interactions 809

Cadherins Mediate Cell-Cell Adhesions in Adherens Junctions and Desmosomes 810

Tight Junctions Seal Off Body Cavities and Restrict Diffusion of Membrane Components 814

Integrins Mediate Cell-ECM Adhesions in Epithelial Cells 816

Gap Junctions Composed of Connexins Allow Small Molecules to Pass Directly Between Adjacent Cells 817

19.3 The Extracellular Matrix Ⅰ：The Basal Lamina 820

The Basal Lamina Provides a Foundation for Assembly of Cells into Tissues 820

Laminin，a Multiadhesive Matrix Protein，Helps Cross-link Components of the Basal Lamina 821

Sheet-Forming Type Ⅳ Collagen Is a Major Structural Component of the Basal Lamina 821

Perlecan，a Proteoglycan，Cross-links Components of the Basal Lamina and Cell-Surface Receptors 824

19.4 The Extracellular Matrix Ⅱ：Connective and Other Tissues 825

Fibrillar Collagens Are the Major Fibrous Proteins in the ECM of Connective Tissues 825

Fibrillar Collagen Is Secreted and Assembled into Fibrils Outside of the Cell 826

Type Ⅰ and Ⅱ Collagens Associate with Nonfibrillar Collagens to Form Diverse Structures 826

Proteoglycans and Their Constituent GAGs Play Diverse Roles in the ECM 827

Hyaluronan Resists Compression，Facilitates Cell Migration，and Gives Cartilage Its Gel-like Properties 829

Fibronectins Interconnect Cells and Matrix，Influencing Cell Shape，Differentiation，and Movement 830

19.5 Adhesive Interactions in Motile and Nonmotile Cells 833

Integrins Relay Signals Between Cells and Their Three-Dimensional Environment 833

Regulation of Integrin-Mediated Adhesion and Signaling Controls Cell Movement 834

Connections Between the ECM and Cytoskeleton Are Defective in Muscular Dystrophy 835

IgCAMs Mediate Cell-Cell Adhesion in Neuronal and Other Tissues 836

Leukocyte Movement into Tissues Is Orchestrated by a Precisely Timed Sequence of Adhesive Interactions 837

19.6 Plant Tissues 839

The Plant Cell Wall Is a Laminate of Cellulose Fibrils in a Matrix of Glycoproteins 840

Loosening of the Cell Wall Permits Plant Cell Growth 840

Plasmodesmata Directly Connect the Cytosols of Adjacent Cells in Higher Plants 840

Only a Few Adhesive Molecules Have Been Identified in Plants 841

Part Ⅳ Cell Growth and Development 847

20 REGULATING THE EUKARYOTIC CELL CYCLE 847

20.1 Overview of the Cell Cycle and Its Control 849

The Cell Cycle Is an Ordered Series of Events Leading to Cell Replication 849

Regulated Protein Phosphorylation and Degradation Control Passage Through the Cell Cycle 849

Diverse Experimental Systems Have Been Used to Identify and Isolate Cell-Cycle Control Proteins 851

20.2 Control of Mitosis by Cyclins and MPF Activity 853

Maturation-Promoting Factor（MPF） Stimulates Meiotic Maturation in Oocytes and Mitosis in Somatic Cells 854

Mitotic Cyclin Was First Identified in Early Sea Urchin Embryos 856

Cyclin B Levels and Kinase Activity of Mitosis-Promoting Factor（MPF） Change Together in Cycling Xenopus Egg Extracts 856

Anaphase-Promoting Complex（APC/C） Controls Degradation of Mitotic Cyclins and Exit from Mitosis 858

20.3 Cyclin-Dependent Kinase Regulation During Mitosis 859

MPF Components Are Conserved Between Lower and Higher Eukaryotes 860

Phosphorylation of the CDK Subunit Regulates the Kinase Activity of MPF 861

Conformational Changes Induced by Cyclin Binding and Phosphorylation Increase MPF Activity 862

20.4 Molecular Mechanisms for Regulating Mitotic Events 864

Phosphorylation of Nuclear Lamins and Other Proteins Promotes Early Mitotic Events 864

Unlinking of Sister Chromatids Initiates Anaphase 867

Chromosome Decondensation and Reassembly of the Nuclear Envelope Depend on Dephosphorylation of MPF Substrates 870

20.5 Cyclin-CDK and Ubiquitin-Protein Ligase Control of S phase 872

A Cyclin-Dependent Kinase（CDK） Is Critical for S-Phase Entry in S.cerevisiae 872

Three G1 Cyclins Associate with S.cerevisiae CDK to Form S-Phase-Promoting Factors 874

Degradation of the S-Phase Inhibitor Triggers DNA Replication 876

Multiple Cyclins Regulate the Kinase Activity of S.cerevisiae CDK During Different Cell-Cycle Phases 877

Replication at Each Origin Is Initiated Only Once During the Cell Cycle 877

20.6 Cell-Cycle Control in Mammalian Cells 879

Mammalian Restriction Point Is Analogous to START in Yeast Cells 880

Multiple CDKs and Cyclins Regulate Passage of Mammalian Cells Through the Cell Cycle 881

Regulated Expression of Two Classes of Genes Returns G0 Mammalian Cells to the Cell Cycle 881

Passage Through the Restriction Point Depends on Phosphorylation of the Tumor-Suppressor Rb Protein 882

Cyclin A Is Required for DNA Synthesis and CDK1 for Entry into Mitosis 883

Two Types of Cyclin-CDK Inhibitors Contribute to Cell-Cycle Control in Mammals 883

20.7 Checkpoints in Cell-Cycle Regulation 884

The Presence of Unreplicated DNA Prevents Entry into Mitosis 888

Improper Assembly of the Mitotic Spindle Prevents the Initiation of Anaphase 888

Proper Segregation of Daughter Chromosomes Is Monitored by the Mitotic Exit Network 889

Cell-Cycle Arrest of Cells with Damaged DNA Depends on Tumor Suppressors 891

20.8 Meiosis：A Special Type of Cell Division 892

Key Features Distinguish Meiosis from Mitosis 892

Repression of G1 Cyclins and a Meiosis-Specific Protein Kinase Promote Premeiotic S Phase 895

Recombination and a Meiosis-Specific Cohesin Subunit Are Necessary for the Specialized Chromosome Segregation in Meiosis