MOLECULAR CELL BIOLOGY EIGHTH EDITIONPDF电子书下载

Part Ⅰ Chemical and Molecular Foundations 1

1 Molecules，Cells，and Model Organisms 1

1.1 The Molecules of Life 5

Proteins Give Cells Structure and Perform Most Cellular Tasks 7

Nucleic Acids Carry Coded Information for Making Proteins at the Right Time and Place 7

Phospholipids Are the Conserved Building Blocks of All Cellular Membranes 9

1.2 Prokaryotic Cell Structure and Function 10

Prokaryotes Comprise Two Kingdoms：Archaea and Eubacteria 10

Escherichia coli Is Widely Used in Biological Research 11

1.3 Eukaryotic Cell Structure and Function 12

The Cytoskeleton Has Many Important Functions 12

The Nucleus Contains the DNA Genome，RNA Synthetic Apparatus，and a Fibrous Matrix 12

Eukaryotic Cells Contain a Large Number of Internal Membrane Structures 14

Mitochondria Are the Principal Sites of ATP Production in Aerobic Cells 18

Chloroplasts Contain Internal Compartments in Which Photosynthesis Takes Place 18

All Eukaryotic Cells Use a Similar Cycle to Regulate Their Division 18

1.4 Unicellular Eukaryotic Model Organisms 19

Yeasts Are Used to Study Fundamental Aspects of Eukaryotic Cell Structure and Function 19

Mutations in Yeast Led to the Identification of Key Cell Cycle Proteins 21

Studies in the Alga Chlamydomonas reinhardtii Led to the Development of a Powerful Technique to Study Brain Function 22

The Parasite That Causes Malaria Has Novel Organelles That Allow It to Undergo a Remarkable Life Cycle 22

1.5 Metazoan Structure，Differentiation，and Model Organisms 24

Multicellularity Requires Cell-Cell and Cell-Matrix Adhesions 24

Epithelia Originated Early in Evolution 24

Tissues Are Organized into Organs 24

Genomics Has Revealed Important Aspects of Metazoan Evolution and Cell Function 24

Embryonic Development Uses a Conserved Set of Master Transcription Factors 25

Planaria Are Used to Study Stem Cells and Tissue Regeneration 27

Invertebrates，Fish，Mice，and Other Organisms Serve as Experimental Systems for Study of Human Development and Disease 28

Genetic Diseases Elucidate Important Aspects of Cell Function 28

The Following Chapters Present Much Experimental Data That Explains How We Know What We Know About Cell Structure and Function 29

2 Chemical Foundations 31

2.1 Covalent Bonds and Noncovalent Interactions 33

The Electronic Structure of an Atom Determines the Number and Geometry of the 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 36

Ionic Interactions Are Attractions Between Oppositely Charged Ions 36

Hydrogen Bonds Are Noncovalent Interactions That Determine the Water Solubility of Uncharged Molecules 37

Van der Waals Interactions Are Weak Attractive Interactions Caused by Transient Dipoles 38

The Hydrophobic Effect Causes Nonpolar Molecules to Adhere to One Another 39

Molecular Complementarity Due to Noncovalent Interactions Leads to a Lock-and-Key Fit Between Biomolecules 40

2.2 Chemical Building Blocks of Cells 41

Amino Acids Differing Only in Their Side Chains Compose Proteins 42

Five Different Nucleotides Are Used to Build Nucleic Acids 45

Monosaccharides Covalently Assemble into Linear and Branched Polysaccharides 46

Phospholipids Associate Noncovalently to Form the Basic Bilayer Structure of Biomembranes 48

2.3 Chemical Reactions and Chemical Equilibrium 51

A Chemical Reaction Is in Equilibrium When the Rates of the Forward and Reverse Reactions Are Equal 52

The Equilibrium Constant Reflects the Extent of a Chemical Reaction 52

Chemical Reactions in Cells Are at Steady State 52

Dissociation Constants of Binding Reactions Reflect the Affinity of Interacting Molecules 53

Biological Fluids Have Characteristic pH Values 54

Hydrogen Ions Are Released by Acids and Taken Up by Bases 55

Buffers Maintain the pH of Intracellular and Extracellular Fluids 55

2.4 Biochemical Energetics 57

Several Forms of Energy Are Important in Biological Systems 57

Cells Can Transform One Type of Energy into Another 58

The Change in Free Energy Determines If a Chemical Reaction Will Occur Spontaneously 58

The ΔG°’ of a Reaction Can Be Calculated from Its Keq 60

The Rate of a Reaction Depends on the Activation Energy Necessary to Energize the Reactants into a Transition State 60

Life Depends on the Coupling of Unfavorable Chemical Reactions with Energetically Favorable Ones 61

Hydrolysis of ATP Releases Substantial Free Energy and Drives Many Cellular Processes 61

ATP Is Generated During Photosynthesis and Respiration 62

NAD+ and FAD Couple Many Biological Oxidation and Reduction Reactions 63

3 Protein Structure and Function 67

3.1 Hierarchical Structure of Proteins 69

The Primary Structure of a Protein Is Its Linear Arrangement of Amino Acids 69

Secondary Structures Are the Core Elements of Protein Architecture 70

Tertiary Structure Is the Overall Folding of a Polypeptide Chain 72

There Are Four Broad Structural Categories of Proteins 72

Different Ways of Depicting the Conformation of Proteins Convey Different Types of Information 74

Structural Motifs Are Regular Combinations of Secondary Structures 75

Domains Are Modules of Tertiary Structure 76

Multiple Polypeptides Assemble into Quaternary Structures and Supramolecular Complexes 78

Comparing Protein Sequences and Structures Provides Insight into Protein Function and Evolution 79

3.2 Protein Folding 81

Planar Peptide Bonds Limit the Shapes into Which Proteins Can Fold 81

The Amino Acid Sequence of a Protein Determines How It Will Fold 81

Folding of Proteins in Vivo Is Promoted by Chaperones 82

Protein Folding Is Promoted by Proline Isomerases 86

Abnormally Folded Proteins Can Form Amyloids That Are Implicated in Diseases 87

3.3 Protein Binding and Enzyme Catalysis 89

Specific Binding of Ligands Underlies the Functions of Most Proteins 89

Enzymes Are Highly Efficient and Specific Catalysts 90

An Enzyme’s Active Site Binds Substrates and Carries Out Catalysis 91

Serine Proteases Demonstrate How an Enzyme’s Active Site Works 92

Enzymes in a Common Pathway Are Often Physically Associated with One Another 96

3.4 Regulating Protein Function 97

Regulated Synthesis and Degradation of Proteins Is a Fundamental Property of Cells 97

The Proteasome Is a Molecular Machine Used to Degrade Proteins 97

Ubiquitin Marks Cytosolic Proteins for Degradation in Proteasomes 99

Noncovalent Binding Permits Allosteric，or Cooperative，Regulation of Proteins 100

Noncovalent Binding of Calcium and GTP Are Widely Used as Allosteric Switches to Control Protein Activity 101

Phosphorylation and Dephosphory lation Covalently Regulate Protein Activity 102

Ubiquitinylation and Deubiquitinylation Covalently Regulate Protein Activity 103

Proteolytic Cleavage Irreversibly Activates or Inactivates Some Proteins 104

Higher-Order Regulation Includes Control of Protein Location 105

3.5 Purifying，Detecting，and Characterizing Proteins 105

Centrifugation Can Separate Particles and Molecules That Differ in Mass or Density 106

Electrophoresis Separates Molecules on the Basis of Their Charge-to-Mass Ratio 107

Liquid Chromatography Resolves Proteins by Mass，Charge，or Affinity 109

Highly Specific Enzyme and Antibody Assays Can Detect Individual Proteins 111

Radioisotopes Are Indispensable Tools for Detecting Biological Molecules 114

Mass Spectrometry Can Determine the Mass and Sequence of Proteins 116

Protein Primary Structure Can Be Determined by Chemical Methods and from Gene Sequences 118

Protein Conformation Is Determined by Sophisticated Physical Methods 119

3.6 Proteomics 122

Proteomics Is the Study of All or a Large Subset of Proteins in a Biological System 122

Advanced Techniques in Mass Spectrometry Are Critical to Proteomic Analysis 123

4 Culturing and Visualizing Cells 129

4.1 Growing and Studying Cells in Culture 130

Culture of Animal Cells Requires Nutrient-Rich Media and Special Solid Surfaces 130

Primary Cell Cultures and Cell Strains Have a Finite Life Span 131

Transformed Cells Can Grow Indefinitely in Culture 132

Flow Cytometry Separates Different Cell Types 132

Growth of Cells in Two-Dimensional and Three-Dimensional Culture Mimics the In Vivo Environment 133

Hybridomas Produce Abundant Monoclonal Antibodies 135

A Wide Variety of Cell Biological Processes Can Be Studied with Cultured Cells 136

Drugs Are Commonly Used in Cell Biological Research 136

4.2 Light Microscopy：Exploring Cell Structure and Visualizing Proteins Within Cells 139

The Resolution of the Conventional Light Microscope Is About 0.2 μm 139

Phase-Contrast and Differential-Interference-Contrast Microscopy Visualize Unstained Live Cells 141

Imaging Subcellular Details Often Requires That Specimens Be Fixed，Sectioned，and Stained 142

Fluorescence Microscopy Can Localize and Quantify Specific Molecules in Live Cells 143

Intracellular Ion Concentrations Can Be Determined with Ion-Sensitive Fluorescent Dyes 143

Immunofluorescence Microscopy Can Detect Specific Proteins in Fixed Cells 144

Tagging with Fluorescent Proteins Allows the Visualization of Specific Proteins in Live Cells 146

Deconvolution and Confocal Microscopy Enhance Visualization of Three-Dimensional Fluorescent Objects 147

Two-Photon Excitation Microscopy Allows Imaging Deep into Tissue Samples 149

TIRF Microscopy Provides Exceptional Imaging in One Focal Plane 150

FRAP Reveals the Dynamics of Cellular Components 151

FRET Measures Distance Between Fluorochromes 152

Super-Resolution Microscopy Can Localize Proteins to Nanometer Accuracy 153

Light-Sheet Microscopy Can Rapidly Image Cells in Living Tissue 155

4.3 Electron Microscopy：High-Resolution Imaging 156

Single Molecules or Structures Can Be Imaged Using a Negative Stain or Metal Shadowing 157

Cells and Tissues Are Cut into Thin Sections for Viewing by Electron Microscopy 158

Immunoelectron Microscopy Localizes Proteins at the Ultrastructural Level 159

Cryoelectron Microscopy Allows Visualization of Specimens Without Fixation or Staining 160

Scanning Electron Microscopy of Metal-Coated Specimens Reveals Surface Features 161

4.4 Isolation of Cell Organelles 161

Disruption of Cells Releases Their Organelles and Other Contents 162

Centrifugation Can Separate Many Types of Organelles 162

Organelle-Specific Antibodies Are Useful in Preparing Highly Purified Organelles 162

Proteomics Reveals the Protein Composition of Organelles 164

Part Ⅱ Biomembranes，Genes，and Gene Regulation 167

5 Fundamental Molecular Genetic Mechanisms 167

5.1 Structure of Nucleic Acids 169

A Nucleic Acid Strand Is a Linear Polymer with End-to-End Directionality 170

Native DNA Is a Double Helix of Complementary Antiparallel Strands 170

DNA Can Undergo Reversible Strand Separation 172

Torsional Stress in DNA Is Relieved by Enzymes 174

Different Types of RNA Exhibit Various Conformations Related to Their Functions 174

5.2 Transcription of Protein-Coding Genes and Formation of Functional mRNA 176

A Template DNA Strand Is Transcribed into a Complementary RNA Chain by RNA Polymerase 176

Organization of Genes Differs in Prokaryotic and Eukaryotic DNA 179

Eukaryotic Precursor mRNAs Are Processed to Form Functional mRNAs 180

Alternative RNA Splicing Increases the Number of Proteins Expressed from a Single Eukaryotic Gene 181

5.3 The Decoding of mRNA by tRNAs 183

Messenger RNA Carries Information from DNA in a Three-Letter Genetic Code 183

The Folded Structure of tRNA Promotes Its Decoding Functions 185

Nonstandard Base Pairing Often Occurs Between Codons and Anticodons 186

Amino Acids Become Activated When Covalently Linked to tRNAs 188

5.4 Stepwise Synthesis of Proteins on Ribosomes 188

Ribosomes Are Protein-Synthesizing Machines 188

Methionyl-tRNA i Met Recognizes the AUG Start Codon 190

Eukaryotic Translation Initiation Usually Occurs at the First AUG Downstream from the 5’ End of an mRNA 191

During Chain Elongation Each Incoming Aminoacyl-tRNA Moves Through Three Ribosomal Sites 193

Translation Is Terminated by Release Factors When a Stop Codon Is Reached 195

Polysomes and Rapid Ribosome Recycling Increase the Efficiency of Translation 195

GTPase-Superfamily Proteins Function in Several Quality-Control Steps of Translation 195

Nonsense Mutations Cause Premature Termination of Protein Synthesis 196

5.5 DNA Replication 197

DNA Polymerases Require a Primer to Initiate Replication 197

Duplex DNA Is Unwound，and Daughter Strands Are Formed at the DNA Replication Fork 199

Several Proteins Participate in DNA Replication 199

DNA Replication Occurs Bidirectionally from Each Origin 201

5.6 DNA Repair and Recombination 203

DNA Polymerases Introduce Copying Errors and Also Correct Them 203

Chemical and Radiation Damage to DNA Can Lead to Mutations 203

High-Fidelity DNA Excision-Repair Systems Recognize and Repair Damage 204

Base Excision Repairs T-G Mismatches and Damaged Bases 205

Mismatch Excision Repairs Other Mismatches and Small Insertions and Deletions 205

Nucleotide Excision Repairs Chemical Adducts that Distort Normal DNA Shape 206

Two Systems Use Recombination to Repair Double-Strand Breaks in DNA 207

Homologous Recombination Can Repair DNA Damage and Generate Genetic Diversity 209

5.7 Viruses：Parasites of the Cellular Genetic System 212

Most Viral Host Ranges Are Narrow 212

Viral Capsids Are Regular Arrays of One or a Few Types of Protein 213

Viruses Can Be Cloned and Counted in Plaque Assays 213

Lytic Viral Growth Cycles Lead to Death of Host Cells 213

Viral DNA Is Integrated into the Host-Cell Genome in Some Nonlytic Viral Growth Cycles 216

6 Molecular Genetic Techniques 223

6.1 Genetic Analysis of Mutations to Identify and Study Genes 224

Recessive and Dominant Mutant Alleles Generally Have Opposite Effects on Gene Function 224

Segregation of Mutations in Breeding Experiments Reveals Their Dominance or Recessivity 225

Conditional Mutations Can Be Used to Study Essential Genes in Yeast 227

Recessive Lethal Mutations in Diploids Can Be Identified by Inbreeding and Maintained in Heterozygotes 228

Complementation Tests Determine Whether Different Recessive Mutations Are in the Same Gene 229

Double Mutants Are Useful in Assessing the Order in Which Proteins Function 230

Genetic Suppression and Synthetic Lethality Can Reveal Interacting or Redundant Proteins 231

Genes Can Be Identified by Their Map Position on the Chromosome 232

6.2 DNA Cloning and Characterization 234

Restriction Enzymes and DNA Ligases Allow Insertion of DNA Fragments into Cloning Vectors 234

Isolated DNA Fragments Can Be Cloned into E.coli Plasmid Vectors 236

Yeast Genomic Libraries Can Be Constructed with Shuttle Vectors and Screened by Functional Complementation 237

cDNA Libraries Represent the Sequences of Protein-Coding Genes 238

The Polymerase Chain Reaction Amplifies a Specific DNA Sequence from a Complex Mixture 239

Cloned DNA Molecules Can Be Sequenced Rapidly by Methods Based on PCR 243

6.3 Using Cloned DNA Fragments to Study Gene Expression 246

Hybridization Techniques Permit Detection of Specific DNA Fragments and mRNAs 246

DNA Microarrays Can Be Used to Evaluate the Expression of Many Genes at One Time 247

Cluster Analysis of Multiple Expression Experiments Identifies Co-regulated Genes 248

E.coli Expression Systems Can Produce Large Quantities of Proteins from Cloned Genes 249

Plasmid Expression Vectors Can Be Designed for Use in Animal Cells 251

6.4 Locating and Identifying Human Disease Genes 254

Monogenic Diseases Show One of Three Patterns of Inheritance 254

DNA Polymorphisms Are Used as Markers for Linkage Mapping of Human Mutations 255

Linkage Studies Can Map Disease Genes with a Resolution of About 1 Centimorgan 256

Further Analysis Is Needed to Locate a Disease Gene in Cloned DNA 257

Many Inherited Diseases Result from Multiple Genetic Defects 257

6.5 Inactivating the Function of Specific Genes in Eukaryotes 259

Normal Yeast Genes Can Be Replaced with Mutant Alleles by Homologous Recombination 260

Genes Can Be Placed Under the Control of an Experimentally Regulated Promoter 260

Specific Genes Can Be Permanently Inactivated in the Germ Line of Mice 261

Somatic Cell Recombination Can Inactivate Genes in Specific Tissues 261

Dominant-Negative Alleles Can Inhibit the Function of Some Genes 262

RNA Interference Causes Gene Inactivation by Destroying the Corresponding mRNA 264

Engineered CRISPR-Cas9 Systems Allow Precise Genome Editing 266

7 Biomembrane Structure 271

7.1 The Lipid Bilayer：Composition and Structural Organization 273

Phospholipids Spontaneously Form Bilayers 273

Phospholipid Bilayers Form a Sealed Compartment Surrounding an Internal Aqueous Space 274

Biomembranes Contain Three Principal Classes of Lipids 276

Most Lipids and Many Proteins Are Laterally Mobile in Biomembranes 278

Lipid Composition Influences the Physical Properties of Membranes 279

Lipid Composition Is Different in the Exoplasmic and Cytosolic Leaflets 281

Cholesterol and Sphingolipids Cluster with Specific Proteins in Membrane Microdomains 282

Cells Store Excess Lipids in Lipid Droplets 283

7.2 Membrane Proteins：Structure and Basic Functions 284

Proteins Interact with Membranes in Three Different Ways 284

Most Transmembrane Proteins Have Membrane-Spanning α Helices 285

Multiple β Strands in Porins Form Membrane-Spanning “Barrels” 288

Covalently Attached Lipids Anchor Some Proteins to Membranes 288

All Transmembrane Proteins and Glycolipids Are Asymmetrically Oriented in the Bilayer 289

Lipid-Binding Motifs Help Target Peripheral Proteins to the Membrane 290

Proteins Can Be Removed from Membranes by Detergents or High-Salt Solutions 290

7.3 Phospholipids，Sphingolipids，and Cholesterol：Synthesis and Intracellular Movement 293

Fatty Acids Are Assembled from Two-Carbon Building Blocks by Several Important Enzymes 293

Small Cytosolic Proteins Facilitate Movement of Fatty Acids 293

Fatty Acids Are Incorporated into Phospholipids Primarily on the ER Membrane 294

Flippases Move Phospholipids from One Membrane Leaflet to the Opposite Leaflet 295

Cholesterol Is Synthesized by Enzymes in the Cytosol and ER Membrane 295

Cholesterol and Phospholipids Are Transported Between Organelles by Several Mechanisms 296

8 Genes，Genomics，and Chromosomes 301

8.1 Eukaryotic Gene Structure 303

Most Eukaryotic Genes Contain Introns and Produce mRNAs Encoding Single Proteins 303

Simple and Complex Transcription Units Are Found in Eukaryotic Genomes 303

Protein-Coding Genes May Be Solitary or Belong to a Gene Family 305

Heavily Used Gene Products Are Encoded by Multiple Copies of Genes 307

Nonprotein-Coding Genes Encode Functional RNAs 308

8.2 Chromosomal Organization of Genes and Noncoding DNA 309

Genomes of Many Organisms Contain Nonfunctional DNA 309

Most Simple-Sequence DNAs Are Concentrated in Specific Chromosomal Locations 310

DNA Fingerprinting Depends on Differences in Length of Simple-Sequence DNAs 311

Unclassified Intergenic DNA Occupies a Significant Portion of the Genome 312

8.3 Transposable （Mobile） DNA Elements 312

Movement of Mobile Elements Involves a DNA or an RNA Intermediate 313

DNA Transposons Are Present in Prokaryotes and Eukaryotes 314

LTR Retrotransposons Behave Like Intracellular Retroviruses 316

Non-LTR Retrotransposons Transpose by a Distinct Mechanism 318

Other Retroposed RNAs Are Found in Genomic DNA 321

Mobile DNA Elements Have Significantly Influenced Evolution 321

8.4 Genomics：Genome-Wide Analysis of Gene Structure and Function 323

Stored Sequences Suggest Functions of Newly Identified Genes and Proteins 324

Comparison of Related Sequences from Different Species Can Give Clues to Evolutionary Relationships Among Proteins 325

Genes Can Be Identified Within Genomic DNA Sequences 326

The Number of Protein-Coding Genes in an Organism’s Genome Is Not Directly Related to Its Biological Complexity 326

8.5 Structural Organization of Eukaryotic Chromosomes 327

Chromatin Exists in Extended and Condensed Forms 328

Modifications of Histone Tails Control Chromatin Condensation and Function 330

Nonhistone Proteins Organize Long Chromatin Loops 335

Additional Nonhistone Proteins Regulate Transcription and Replication 339

8.6 Morphology and Functional Elements of Eukaryotic Chromosomes 341

Chromosome Number，Size，and Shape at Metaphase Are Species-Specific 341

During Metaphase，Chromosomes Can Be Distinguished by Banding Patterns and Chromosome Painting 341

Chromosome Painting and DNA Sequencing Reveal the Evolution of Chromosomes 342

Interphase Polytene Chromosomes Arise by DNA Amplification 343

Three Functional Elements Are Required for Replication and Stable Inheritance of Chromosomes 345

Centromere Sequences Vary Greatly in Length and Complexity 345

Addition of Telomeric Sequences by Telomerase Prevents Shortening of Chromosomes 347

9 Transcriptional Control of Gene Expression 353

9.1 Control of Gene Expression in Bacteria 356

Transcription Initiation by Bacterial RNA Polymerase Requires Association with a Sigma Factor 357

Initiation of lac Operon Transcription Can Be Repressed or Activated 357

Small Molecules Regulate Expression of Many Bacterial Genes via DNA-Binding Repressors and Activators 358

Transcription Initiation from Some Promoters Requires Alternative Sigma Factors 359

Transcription by σ54-RNA Polymerase Is Controlled by Activators That Bind Far from the Promoter 359

Many Bacterial Responses Are Controlled by Two-Component Regulatory Systems 360

Expression of Many Bacterial Operons Is Controlled by Regulation of Transcriptional Elongation 361

9.2 Overview of Eukaryotic Gene Control 363

Regulatory Elements in Eukaryotic DNA Are Found Both Close to and Many Kilobases Away from Transcription Start Sites 364

Three Eukaryotic RNA Polymerases Catalyze Formation of Different RNAs 367

The Largest Subunit in RNA Polymerase Ⅱ Has an Essential Carboxy-Terminal Repeat 370

9.3 RNA Polymerase Ⅱ Promoters and General Transcription Factors 371

RNA Polymerase Ⅱ Initiates Transcription at DNA Sequences Corresponding to the 5’ Cap of mRNAs 371

The TATA Box，Initiators，and CpG Islands Function as Promoters in Eukaryotic DNA 371

General Transcription Factors Position RNA Polymerase Ⅱ at Start Sites and Assist in Initiation 373

Elongation Factors Regulate the Initial Stages of Transcription in the Promoter-Proximal Region 377

9.4 Regulatory Sequences in Protein-Coding Genes and the Proteins Through Which They Function 378

Promoter-Proximal Elements Help Regulate Eukaryotic Genes 378

Distant Enhancers Often Stimulate Transcription by RNA Polymerase Ⅱ 379

Most Eukaryotic Genes Are Regulated by Multiple Transcription-Control Elements 379

DNase Ⅰ Footprinting and EMSA Detect Protein-DNA Interactions 380

Activators Are Composed of Distinct Functional Domains 381

Repressors Are the Functional Converse of Activators 383

DNA-Binding Domains Can Be Classified into Numerous Structural Types 384

Structurally Diverse Activation and Repression Domains Regulate Transcription 386

Transcription Factor Interactions Increase Gene-Control Options 387

Multiprotein Complexes Form on Enhancers 388

9.5 Molecular Mechanisms of Transcription Repression and Activation 390

Formation of Heterochromatin Silences Gene Expression at Telomeres，near Centromeres，and in Other Regions 390

Repressors Can Direct Histone Deacetylation at Specific Genes 393

Activators Can Direct Histone Acetylation at Specific Genes 394

Chromatin-Remodeling Complexes Help Activate or Repress Transcription 395

Pioneer Transcription Factors Initiate the Process of Gene Activation During Cellular Differentiation 395

The Mediator Complex Forms a Molecular Bridge Between Activation Domains and Pol Ⅱ 396

9.6 Regulation of Transcription-Factor Activity 398

DNaⅠse Hypersensitive Sites Reflect the Developmental History of Cellular Differentiation 398

Nuclear Receptors Are Regulated by Extracellular Signals 400

All Nuclear Receptors Share a Common Domain Structure 400

Nuclear-Receptor Response Elements Contain Inverted or Direct Repeats 400

Hormone Binding to a Nuclear Receptor Regulates Its Activity as a Transcription Factor 402

Metazoans Regulate the RNA Polymerase Ⅱ Transition from Initiation to Elongation 402

Termination of Transcription Is Also Regulated 402

9.7 Epigenetic Regulation of Transcription 404

DNA Methylation Represses Transcription 404

Methylation of Specific Histone Lysines Is Linked to Epigenetic Mechanisms of Gene Repression 405

Epigenetic Control by Polycomb and Trithorax Complexes 406

Long Noncoding RNAs Direct Epigenetic Repression in Metazoans 409

9.8 Other Eukaryotic Transcription Systems 412

Transcription Initiation by Pol Ⅰ and Pol Ⅲ Is Analogous to That by Pol Ⅱ 412

10 Post-transcriptional Gene Control 417

10.1 Processing of Eukaryotic Pre-mRNA 419

The 5’ Cap Is Added to Nascent RNAs Shortly After Transcription Initiation 420

A Diverse Set of Proteins with Conserved RNA-Binding Domains Associate with Pre-mRNAs 421

Splicing Occurs at Short，Conserved Sequences in Pre-mRNAs via Two Transesterification Reactions 423

During Splicing，snRNAs Base-Pair with Pre-mRNA 424

Spliceosomes，Assembled from snRNPs and a Pre-mRNA，Carry Out Splicing 426

Chain Elongation by RNA Polymerase Ⅱ Is Coupled to the Presence of RNA-Processing Factors 428

SR Proteins Contribute to Exon Definition in Long Pre-mRNAs 428

Self-Splicing Group Ⅱ Introns Provide Clues to the Evolution of snRNAs 429

3’ Cleavage and Polyadenylation of Pre-mRNAs Are Tightly Coupled 430

Nuclear Exoribonucleases Degrade RNA That Is Processed Out of Pre-mRNAs 432

RNA Processing Solves the Problem of Pervasive Transcription of the Genome in Metazoans 432

10.2 Regulation of Pre-mRNA Processing 435

Alternative Splicing Generates Transcripts with Different Combinations of Exons 435

A Cascade of Regulated RNA Splicing Controls Drosophila Sexual Differentiation 435

Splicing Repressors and Activators Control Splicing at Alternative Sites 437

RNA Editing Alters the Sequences of Some Pre-mRNAs 439

10.3 Transport of mRNA Across the Nuclear Envelope 440

Phosphorylation and Dephosphorylation of SR Proteins Imposes Directionality on mRNP Export Across the Nuclear Pore Complex 441

Balbiani Rings in Insect Larval Salivary Glands Allow Direct Visualization of mRNP Export Through NPCs 442

Pre-mRNAs in Spliceosomes Are Not Exported from the Nucleus 443

HIV Rev Protein Regulates the Transport of Unspliced Viral mRNAs 444

10.4 Cytoplasmic Mechanisms of Post-transcriptional Control 445

Degradation of mRNAs in the Cytoplasm Occurs by Several Mechanisms 445

Adenines in mRNAs and IncRNAs May Be Post-transcriptionally Modified by N6 Methylation 447

Micro-RNAs Repress Translation and Induce Degradation of Specific mRNAs 447

Alternative Polyadenylation Increases miRNA Control Options 450

RNA Interference Induces Degradation of Precisely Complementary mRNAs 450

Cytoplasmic Polyadenylation Promotes Translation of Some mRNAs 451

Protein Synthesis Can Be Globally Regulated 452

Sequence-Specific RNA-Binding Proteins Control Translation of Specific mRNAs 455

Surveillance Mechanisms Prevent Translation of Improperly Processed mRNAs 456

Localization of mRNAs Permits Production of Proteins at Specific Regions Within the Cytoplasm 457

10.5 Processing of rRNA and tRNA 461

Pre-rRNA Genes Function as Nucleolar Organizers 461

Small Nucleolar RNAs Assist in Processing Pre-rRNAs 462

Self-Splicing Group Ⅰ Introns Were the First Examples of Catalytic RNA 466

Pre-tRNAs Undergo Extensive Modification in the Nucleus 466

Nuclear Bodies Are Functionally Specialized Nuclear Domains 468

Part Ⅲ Cellular Organization and Function 473

11 Transmembrane Transport of Ions and Small Molecules 473

11.1 Overview of Transmembrane Transport 474

Only Gases and Small Uncharged Molecules Cross Membranes by Simple Diffusion 474

Three Main Classes of Membrane Proteins Transport Molecules and Ions Across Cellular Membranes 475

11.2 Facilitated Transport of Glucose and Water 477

Uniport Transport Is Faster and More Specific than Simple Diffusion 477

The Low Km of the GLUT1 Uniporter Enables It to Transport Glucose into Most Mammalian Cells 478

The Human Genome Encodes a Family of Sugar-Transporting GLUT Proteins 480

Transport Proteins Can Be Studied Using Artificial Membranes and Recombinant Cells 480

Osmotic Pressure Causes Water to Move Across Membranes 481

Aquaporins Increase the Water Permeability of Cellular Membranes 481

11.3 ATP-Powered Pumps and the Intracellular Ionic Environment 483

There Are Four Main Classes of ATP-Powered Pumps 484

ATP-Powered Ion Pumps Generate and Maintain Ionic Gradients Across Cellular Membranes 485

Muscle Relaxation Depends on Ca 2+ ATPases That Pump Ca 2+ from the Cytosol into the Sarcoplasmic Reticulum 486

The Mechanism of Action of the Ca 2+ Pump Is Known in Detail 486

Calmodulin Regulates the Plasma-Membrane Pumps That Control Cytosolic Ca 2+ Concentrations 489

The Na+/K+ ATPase Maintains the Intracellular Na+ and K+ Concentrations in Animal Cells 489

V-Class H+ ATPases Maintain the Acidity of Lysosomes and Vacuoles 489

ABC Proteins Export a Wide Variety of Drugs and Toxins from the Cell 491

Certain ABC Proteins “Flip” Phospholipids and Other Lipid-Soluble Substrates from One Membrane Leaflet to the Other 493

The ABC Cystic Fibrosis Transmembrane Regulator Is a Chloride Channel，Not a Pump 494

11.4 Nongated Ion Channels and the Resting Membrane Potential 495

Selective Movement of Ions Creates a Transmembrane Electric Gradient 495

The Resting Membrane Potential in Animal Cells Depends Largely on the Outward Flow of K+ Ions Through Open K+ Channels 497

Ion Channels Are Selective for Certain Ions by Virtue of a Molecular “Selectivity Filter” 497

Patch Clamps Permit Measurement of Ion Movements Through Single Channels 500

Novel Ion Channels Can Be Characterized by a Combination of Oocyte Expression and Patch Clamping 501

11.5 Cotransport by Symporters and Antiporters 502

Na+ Entry into Mammalian Cells Is Thermodynamically Favored 502

Na+-Linked Symporters Enable Animal Cells to Import Glucose and Amino Acids Against High Concentration Gradients 503

A Bacterial Na+/Amino Acid Symporter Reveals How Symport Works 504

A Na+-Linked Ca 2+ Antiporter Regulates the Strength of Cardiac Muscle Contraction 504

Several Cotransporters Regulate Cytosolic pH 505

An Anion Antiporter Is Essential for Transport of CO2 by Erythrocytes 506

Numerous Transport Proteins Enable Plant Vacuoles to Accumulate Metabolites and Ions 507

11.6 Transcellular Transport 508

Multiple Transport Proteins Are Needed to Move Glucose and Amino Acids Across Epithelia 508

Simple Rehydration Therapy Depends on the Osmotic Gradient Created by Absorption of Glucose and Na+ 509

Parietal Cells Acidify the Stomach Contents While Maintaining a Neutral Cytosolic pH 509

Bone Resorption Requires the Coordinated Function of a V-Class Proton Pump and a Specific Chloride Channel 510

12 Cellular Energetics 513

12.1 First Step of Harvesting Energy from Glucose：Glycolysis 515

During Glycolysis （Stage Ⅰ），Cytosolic Enzymes Convert Glucose to Pyruvate 516

The Rate of Glycolysis Is Adjusted to Meet the Cell’s Need for ATP 516

Glucose Is Fermented When Oxygen Is Scarce 518

12.2 The Structure and Functions of Mitochondria 520

Mitochondria Are Multifunctional Organelles 520

Mitochondria Have Two Structurally and Functionally Distinct Membranes 520

Mitochondria Contain DNA Located in the Matrix 523

The Size，Structure，and Coding Capacity of mtDNA Vary Considerably Among Organisms 525

Products of Mitochondrial Genes Are Not Exported 526

Mitochondria Evolved from a Single Endosymbiotic Event Involving a Rickettsia-Like Bacterium 527

Mitochondrial Genetic Codes Differ from the Standard Nuclear Code 527

Mutations in Mitochondrial DNA Cause Several Genetic Diseases in Humans 528

Mitochondria Are Dynamic Organelles That Interact Directly with One Another 528

Mitochondria Are Influenced by Direct Contacts with the Endoplasmic Reticulum 529

12.3 The Citric Acid Cycle and Fatty Acid Oxidation 533

In the First Part of Stage Ⅱ，Pyruvate Is Converted to Acetyl CoA and High-Energy Electrons 533

In the Second Part of Stage Ⅱ，the Citric Acid Cycle Oxidizes the Acetyl Group in Acetyl CoA to CO2 and Generates High-Energy Electrons 533

Transporters in the Inner Mitochondrial Membrane Help Maintain Appropriate Cytosolic and Matrix Concentrations of NAD+ and NADH 535

Mitochondrial Oxidation of Fatty Acids Generates ATP 536

Peroxisomal Oxidation of Fatty Acids Generates No ATP 537

12.4 The Electron-Transport Chain and Generation of the Proton-Motive Force 539

Oxidation of NADH and FADH2 Releases a Significant Amount of Energy 539

Electron Transport in Mitochondria Is Coupled to Proton Pumping 539

Electrons Flow “Downhill” Through a Series of Electron Carriers 540

Four Large Multiprotein Complexes Couple Electron Transport to Proton Pumping Across the Inner Mitochondrial Membrane 542

The Reduction Potentials of Electron Carriers in the Electron-Transport Chain Favor Electron Flow from NADH to O2 546

The Multiprotein Complexes of the Electron-Transport Chain Assemble into Supercomplexes 546

Reactive Oxygen Species Are By-Products of Electron Transport 547

Experiments Using Purified Electron-Transport Chain Complexes Established the Stoichiometry of Proton Pumping 549

The Proton-Motive Force in Mitochondria Is Due Largely to a Voltage Gradient Across the Inner Membrane 550

12.5 Harnessing the Proton-Motive Force to Synthesize ATP 551

The Mechanism of ATP Synthesis Is Shared Among Bacteria，Mitochondria，and Chloroplasts 552

ATP Synthase Comprises F 0 and F1 Multiprotein Complexes 553

Rotation of the F1 y Subunit，Driven by Proton Movement Through F0，Powers ATP Synthesis 554

Multiple Protons Must Pass Through ATP Synthase to Synthesize One ATP 555

F 0 c Ring Rotation Is Driven by Protons Flowing Through Transmembrane Channels 556

ATP-ADP Exchange Across the Inner Mitochondrial Membrane Is Powered by the Proton-Motive Force 556

The Rate of Mitochondrial Oxidation Normally Depends on ADP Levels 558

Mitochondria in Brown Fat Use the Proton-Motive Force to Generate Heat 558

12.6 Photosynthesis and Light-Absorbing Pigments 560

Thylakoid Membranes in Chloroplasts Are the Sites of Photosynthesis in Plants 560

Chloroplasts Contain Large DNAs Often Encoding More Than a Hundred Proteins 560

Three of the Four Stages in Photosynthesis Occur Only During Illumination 561

Photosystems Comprise a Reaction Center and Associated Light-Harvesting Complexes 563

Photoelectron Transport from Energized Reaction-Center Chlorophyll a Produces a Charge Separation 564

Internal Antennas and Light-Harvesting Complexes Increase the Efficiency of Photosynthesis 566

12.7 Molecular Analysis of Photosystems 567

The Single Photosystem of Purple Bacteria Generates a Proton-Motive Force but No O2 567

Chloroplasts Contain Two Functionally and Spatially Distinct Photosystems 567

Linear Electron Flow Through Both Plant Photosystems Generates a Proton-Motive Force，O2，and NADPH 568

An Oxygen-Evolving Complex Is Located on the Luminal Surface of the PSII Reaction Center 569

Multiple Mechanisms Protect Cells Against Damage from Reactive Oxygen Species During Photoelectron Transport 570

Cyclic Electron Flow Through PSI Generates a Proton-Motive Force but No NADPH or O2 570

Relative Activities of Photosystems Ⅰ and Ⅱ Are Regulated 571

12.8 CO2 Metabolism During Photosynthesis 573

Rubisco Fixes CO2 in the Chloroplast Stroma 573

Synthesis of Sucrose Using Fixed CO2 Is Completed in the Cytosol 573

Light and Rubisco Activase Stimulate CO2 Fixation 574

Photorespiration Competes with Carbon Fixation and Is Reduced in C4 Plants 576

13 Moving Proteins into Membranes and Organelles 583

13.1 Targeting Proteins To and Across the ER Membrane 585

Pulse-Chase Experiments with Purified ER Membranes Demonstrated That Secreted Proteins Cross the ER Membrane 586

A Hydrophobic N-Terminal Signal Sequence Targets Nascent Secretory Proteins to the ER 586

Cotranslational Translocation Is Initiated by Two GTP-Hydrolyzing Proteins 588

Passage of Growing Polypeptides Through the Translocon Is Driven by Translation 589

ATP Hydrolysis Powers Post-translational Translocation of Some Secretory Proteins in Yeast 591

13.2 Insertion of Membrane Proteins into the ER 593

Several Topological Classes of Integral Membrane Proteins Are Synthesized on the ER 593

Internal Stop-Transfer Anchor and Signal-Anchor Sequences Determine Topology of Single-Pass Proteins 594

Multipass Proteins Have Multiple Internal Topogenic Sequences 597

A Phospholipid Anchor Tethers Some Cell-Surface Proteins to the Membrane 598

The Topology of a Membrane Protein Can Often Be Deduced from Its Sequence 599

13.3 Protein Modifications，Folding，and Quality Control in the ER 601

A Preformed N-Linked Oligosaccharide Is Added to Many Proteins in the Rough ER 601

Oligosaccharide Side Chains May Promote Folding and Stability of Glycoproteins 602

Disulfide Bonds Are Formed and Rearranged by Proteins in the ER Lumen 603

Chaperones and Other ER Proteins Facilitate Folding and Assembly of Proteins 604

Improperly Folded Proteins in the ER Induce Expression of Protein-Folding Catalysts 606

Unassembled or Misfolded Proteins in the ER Are Often Transported to the Cytosol for Degradation 607

13.4 Targeting of Proteins to Mitochondria and Chloroplasts 608

Amphipathic N-Terminal Targeting Sequences Direct Proteins to the Mitochondrial Matrix 609

Mitochondrial Protein Import Requires Outer-Membrane Receptors and Translocons in Both Membranes 610

Studies with Chimeric Proteins Demonstrate Important Features of Mitochondrial Protein Import 612

Three Energy Inputs Are Needed to Import Proteins into Mitochondria 613

Multiple Signals and Pathways Target Proteins to Submitochondrial Compartments 613

Import of Chloroplast Stromal Proteins Is Similar to Import of Mitochondrial Matrix Proteins 617

Proteins Are Targeted to Thylakoids by Mechanisms Related to Bacterial Protein Translocation 617

13.5 Targeting of Peroxisomal Proteins 619

A Cytosolic Receptor Targets Proteins with an SKL Sequence at the C-Terminus to the Peroxisomal Matrix 619

Peroxisomal Membrane and Matrix Proteins Are Incorporated by Different Pathways 621

13.6 Transport Into and Out of the Nucleus 622

Large and Small Molecules Enter and Leave the Nucleus via Nuclear Pore Complexes 622

Nuclear Transport Receptors Escort Proteins Containing Nuclear-Localization Signals into the Nucleus 624

A Second Type of Nuclear Transport Receptor Escorts Proteins Containing Nuclear-Export Signals Out of the Nucleus 625

Most mRNAs Are Exported from the Nucleus by a Ran-Independent Mechanism 627

14 Vesicular Traffic，Secretion，and Endocytosis 631

14.1 Techniques for Studying the Secretory Pathway 634

Transport of a Protein Through the Secretory Pathway Can Be Assayed in Live Cells 634

Yeast Mutants Define Major Stages and Many Components in Vesicular Transport 635

Cell-Free Transport Assays Allow Dissection of Individual Steps in Vesicular Transport 637

14.2 Molecular Mechanisms of Vesicle Budding and Fusion 638

Assembly of a Protein Coat Drives Vesicle Formation and Selection of Cargo Molecules 638

A Conserved Set of GTPase Switch Proteins Controls the Assembly of Different Vesicle Coats 639

Targeting Sequences on Cargo Proteins Make Specific Molecular Contacts with Coat Proteins 641

Rab GTPases Control Docking of Vesicles on Target Membranes 641

Paired Sets of SNARE Proteins Mediate Fusion of Vesicles with Target Membranes 642

Dissociation of SNARE Complexes After Membrane Fusion Is Driven by ATP Hydrolysis 644

14.3 Early Stages of the Secretory Pathway 645

COPII Vesicles Mediate Transport from the ER to the Golgi 645

COPI Vesicles Mediate Retrograde Transport Within the Golgi and from the Golgi to the ER 647

Anterograde Transport Through the Golgi Occurs by Cisternal Maturation 648

14.4 Later Stages of the Secretory Pathway 650

Vesicles Coated with Clathrin and Adapter Proteins Mediate Transport from the trans-Golgi 651

Dynamin Is Required for Pinching Off of Clathrin-Coated Vesicles 652

Mannose 6-Phosphate Residues Target Soluble Proteins to Lysosomes 653

Study of Lysosomal Storage Diseases Revealed Key Components of the Lysosomal Sorting Pathway 655

Protein Aggregation in the trans-Golgi May Function in Sorting Proteins to Regulated Secretory Vesicles 655

Some Proteins Undergo Proteolytic Processing After Leaving the trans-Golgi 656

Several Pathways Sort Membrane Proteins to the Apical or Basolateral Region of Polarized Cells 657

14.5 Receptor-Mediated Endocytosis 659

Cells Take Up Lipids from the Blood in the Form of Large，Well-Defined Lipoprotein Complexes 659

Receptors for Macromolecular Ligands Contain Sorting Signals That Target Them for Endocytosis 660

The Acidic pH of Late Endosomes Causes Most Receptor-Ligand Complexes to Dissociate 662

The Endocytic Pathway Delivers Iron to Cells Without Dissociation of the Transferrin-Transferrin Receptor Complex in Endosomes 663

14.6 Directing Membrane Proteins and Cytosolic Materials to the Lysosome 665

Multivesicular Endosomes Segregate Membrane Proteins Destined for the Lysosomal Membrane from Proteins Destined for Lysosomal Degradation 665

Retroviruses Bud from the Plasma Membrane by a Process Similar to Formation of Multivesicular Endosomes 666

The Autophagic Pathway Delivers Cytosolic Proteins or Entire Organelles to Lysosomes 667

15 Signal Transduction and G protein-Coupled Receptors 673

15.1 Signal Transduction：From Extracellular Signal to Cellular Response 675

Signaling Molecules Can Act Locally or at a Distance 675

Receptors Bind Only a Single Type of Hormone or a Group of Closely Related Hormones 676

Protein Kinases and Phosphatases Are Employed in Many Signaling Pathways 676

GTP-Binding Proteins Are Frequently Used in Signal Transduction Pathways as On/Off Switches 677

Intracellular “Second Messengers” Transmit Signals from Many Receptors 678

Signal Transduction Pathways Can Amplify the Effects of Extracellular Signals 679

15.2 Studying Cell-Surface Receptors and Signal Transduction Proteins 681

The Dissociation Constant Is a Measure of the Affinity of a Receptor for Its Ligand 681

Binding Assays Are Used to Detect Receptors and Determine Their Affinity and Specificity for Ligands 681

Near-Maximal Cellular Response to a Signaling Molecule Usually Does Not Require Activation of All Receptors 682

Sensitivity of a Cell to External Signals Is Determined by the Number of Cell-Surface Receptors and Their Affinity for Ligand 683

Hormone Analogs Are Widely Used as Drugs 683

Receptors Can Be Purified by Affinity Chromatography Techniques 683

Immunoprecipitation Assays and Affinity Techniques Can Be Used to Study the Activity of Signal Transduction Proteins 684

15.3 G Protein-Coupled Receptors：Structure and Mechanism 686

All G Protein-Coupled Receptors Share the Same Basic Structure 686

Ligand-Activated G Protein-Coupled Receptors Catalyze Exchange of GTP for GDP on the α Subunit of a Heterotrimeric G Protein 689

Different G Proteins Are Activated by Different GPCRs and In Turn Regulate Different Effector Proteins 691

15.4 G Protein-Coupled Receptors That Regulate Ion Channels 693

Acetylcholine Receptors in the Heart Muscle Activate a G Protein That Opens K+ Channels 693

Light Activates Rhodopsin in Rod Cells of the Eye 694

Activation of Rhodopsin by Light Leads to Closing of cGMP-Gated Cation Channels 695

Signal Amplification Makes the Rhodopsin Signal Transduction Pathway Exquisitely Sensitive 696

Rapid Termination of the Rhodopsin Signal Transduction Pathway Is Essential for the Temporal Resolution of Vision 697

Rod Cells Adapt to Varying Levels of Ambient Light by Intracellular Trafficking of Arrestin and Transducin 698

15.5 G Protein-Coupled Receptors That Activate or Inhibit Adenylyl Cyclase 699

Adenylyl Cyclase Is Stimulated and Inhibited by Different Receptor-Ligand Complexes 699

Structural Studies Established How Gαs·GTP Binds to and Activates Adenylyl Cyclase 701

cAMP Activates Protein Kinase A by Releasing Inhibitory Subunits 701

Glycogen Metabolism Is Regulated by Hormone-Induced Activation of PKA 702

cAMP-Mediated Activation of PKA Produces Diverse Responses in Different Cell Types 703

Signal Amplification Occurs in the cAMP-PKA Pathway 704

CREB Links cAMP and PKA to Activation of Gene Transcription 704

Anchoring Proteins Localize Effects of cAMP to Specific Regions of the Cell 705

Multiple Mechanisms Suppress Signaling from the GPCR/cAMP/PKA Pathway 706

15.6 G Protein-Coupled Receptors That Trigger Elevations in Cytosolic and Mitochondrial Calcium 708

Calcium Concentrations in the Mitochondrial Matrix，ER，and Cytosol Can Be Measured with Targeted Fluorescent Proteins 709

Activated Phospholipase C Generates Two Key Second Messengers Derived from the Membrane Lipid Phosphatidylinositol 4，5-Bisphosphate 709

The Ca 2+-Calmodulin Complex Mediates Many Cellular Responses to External Signals 713

DAG Activates Protein Kinase C 714

Integration of Ca 2+ and cAMP Second Messengers Regulates Glycogenolysis 714

Signal-Induced Relaxation of Vascular Smooth Muscle Is Mediated by a Ca 2+ -Nitric Oxide-cGMP-Activated Protein Kinase G Pathway 714

16 Signaling Pathways That Control Gene Expression 719

16.1 Receptor Serine Kinases That Activate Smads 722

TGF-β Proteins Are Stored in an Inactive Form in the Extracellular Matrix 722

Three Separate TGF-β Receptor Proteins Participate in Binding TGF-β and Activating Signal Transduction 722

Activated TGF-β Receptors Phosphorylate Smad Transcription Factors 724

The Smad3/Smad4 Complex Activates Expression of Different Genes in Different Cell Types 724

Negative Feedback Loops Regulate TGF-β/Smad Signaling 725

16.2 Cytokine Receptors and the JAK/STAT Signaling Pathway 726

Cytokines Influence the Development of Many Cell Types 727

Binding of a Cytokine to Its Receptor Activates One or More Tightly Bound JAK Protein Tyrosine Kinases 728

Phosphotyrosine Residues Are Binding Surfaces for Multiple Proteins with Conserved Domains 730

SH2 Domains in Action：JAK Kinases Activate STAT Transcription Factors 731

Multiple Mechanisms Down-Regulate Signaling from Cytokine Receptors 731

16.3 Receptor Tyrosine Kinases 734

Binding of Ligand Promotes Dimerization of an RTK and Leads to Activation of Its Intrinsic Tyrosine Kinase 734

Homo- and Hetero-oligomers of Epidermal Growth Factor Receptors Bind Members of the Epidermal Growth Factor Family 735

Activation of the EGF Receptor Results in the Formation of an Asymmetric Active Kinase Dimer 736

Multiple Mechanisms Down-Regulate Signaling from RTKs 737

16.4 The Ras/MAP Kinase Pathway 739

Ras，a GTPase Switch Protein，Operates Downstream of Most RTKs and Cytokine Receptors 739

Genetic Studies in Drosophila Identified Key Signal-Transducing Proteins in the Ras/MAP Kinase Pathway 739

Receptor Tyrosine Kinases Are Linked to Ras by Adapter Proteins 741

Binding of Sos to Inactive Ras Causes a Conformational Change That Triggers an Exchange of GTP for GDP 742

Signals Pass from Activated Ras to a Cascade of Protein Kinases Ending with MAP Kinase 742

Phosphorylation of MAP Kinase Results in a Conformational Change That Enhances Its Catalytic Activity and Promotes Its Dimerization 744

MAP Kinase Regulates the Activity of Many Transcription Factors Controlling Early Response Genes 745

G Protein-Coupled Receptors Transmit Signals to MAP Kinase in Yeast Mating Pathways 746

Scaffold Proteins Separate Multiple MAP Kinase Pathways in Eukaryotic Cells 746

16.5 Phosphoinositide Signaling Pathways 748

Phospholipase Cγ Is Activated by Some RTKs and Cytokine Receptors 749

Recruitment of PI-3 Kinase to Activated Receptors Leads to Synthesis of Three Phosphorylated Phosphatidylinositols 749

Accumulation of PI 3-Phosphates in the Plasma Membrane Leads to Activation of Several Kinases 750

Activated Protein Kinase B Induces Many Cellular Responses 750

The PI-3 Kinase Pathway Is Negatively Regulated by PTEN Phosphatase 751

16.6 Signaling Pathways Controlled by Ubiquitinylation and Protein Degradation：Wnt，Hedgehog，and NF-κB 751

Wnt Signaling Triggers Release of a Transcription Factor from a Cytosolic Protein Complex 752

Concentration Gradients of Wnt Protein Are Essential for Many Steps in Development 753

Hedgehog Signaling Relieves Repression of Target Genes 754

Hedgehog Signaling in Vertebrates Requires Primary Cilia 757

Degradation of an Inhibitor Protein Activates the NF-κB Transcription Factor 757

Polyubiquitin Chains Serve as Scaffolds Linking Receptors to Downstream Proteins in the NF-κB Pathway 760

16.7 Signaling Pathways Controlled by Protein Cleavage：Notch/Delta，SREBP，and Alzheimer’s Disease 761

On Binding Delta，the Notch Receptor Is Cleaved，Releasing a Component Transcription Factor 761

Matrix MetaIloproteases Catalyze Cleavage of Many Signaling Proteins from the Cell Surface 763

Inappropriate Cleavage of Amyloid Precursor Protein Can Lead to Alzheimer’s Disease 763

Regulated Intramembrane Proteolysis of SREBPs Releases a Transcription Factor That Acts to Maintain Phospholipid and Cholesterol Levels 763

16.8 Integration of Cellular Responses to Multiple Signaling Pathways：Insulin Action 766

Insulin and Glucagon Work Together to Maintain a Stable Blood Glucose Level 766

A Rise in Blood Glucose Triggers Insulin Secretion from the β Islet Cells 767

In Fat and Muscle Cells，Insulin Triggers Fusion of Intracellular Vesicles Containing the GLUT4 Glucose Transporter to the Plasma Membrane 767

Insulin Inhibits Glucose Synthesis and Enhances Storage of Glucose as Glycogen 769

Multiple Signal Transduction Pathways Interact to Regulate Adipocyte Differentiation Through PPARγ，the Master Transcriptional Regulator 770

Inflammatory Hormones Cause Derangement of Adipose Cell Function in Obesity 770

17 Cell Organization and Movement Ⅰ：Microfilaments 775

17.1 Microfilaments and Actin Structures 778

Actin Is Ancient，Abundant，and Highly Conserved 778

G-Actin Monomers Assemble into Long，Helical F-Actin Polymers 779

F-Actin Has Structural and Functional Polarity 780

17.2 Dynamics of Actin Filaments 781

Actin Polymerization In Vitro Proceeds in Three Steps 781

Actin Filaments Grow Faster at （+） Ends Than at （-） Ends 782

Actin Filament Treadmilling Is Accelerated by Profilin and Cofilin 784

Thymosin-β4 Provides a Reservoir of Actin for Polymerization 785

Capping Proteins Block Assembly and Disassembly at Actin Filament Ends 785

17.3 Mechanisms of Actin Filament Assembly 786

Formins Assemble Unbranched Filaments 786

The Arp2/3 Complex Nucleates Branched Filament Assembly 787

Intracellular Movements Can Be Powered by Actin Polymerization 789

Microfilaments Function in Endocytosis 790

Toxins That Perturb the Pool of Actin Monomers Are Useful for Studying Actin Dynamics 791

17.4 Organization of Actin-Based Cellular Structures 793

Cross-Linking Proteins Organize Actin Filaments into Bundles or Networks 793

Adapter Proteins Link Actin Filaments to Membranes 793

17.5 Myosins：Actin-Based Motor Proteins 796

Myosins Have Head，Neck，and Tail Domains with Distinct Functions 797

Myosins Make Up a Large Family of Mechanochemical Motor Proteins 798

Conformational Changes in the Myosin Head Couple ATP Hydrolysis to Movement 800

Myosin Heads Take Discrete Steps Along Actin Filaments 802

17.6 Myosin-Powered Movements 803

Myosin Thick Filaments and Actin Thin Filaments in Skeletal Muscle Slide Past Each Other During Contraction 803

Skeletal Muscle Is Structured by Stabilizing and Scaffolding Proteins 805

Contraction of Skeletal Muscle Is Regulated by Ca 2+ and Actin-Binding Proteins 805

Actin and Myosin Ⅱ Form Contractile Bundles in Nonmuscle Cells 807

Myosin-Dependent Mechanisms Regulate Contraction in Smooth Muscle and Nonmuscle Cells 808

Myosin V-Bound Vesicles Are Carried Along Actin Filaments 808

17.7 Cell Migration：Mechanism，Signaling，and Chemotaxis 811

Cell Migration Coordinates Force Generation with Cell Adhesion and Membrane Recycling 811

The Small GTP-Binding Proteins Cdc42，Rac，and Rho Control Actin Organization 813

Cell Migration Involves the Coordinate Regulation of Cdc42，Rac，and Rho 815

Migrating Cells Are Steered by Chemotactic Molecules 816

18 Cell Organization and Movement Ⅱ：Microtubules and Intermediate Filaments 821

18.1 Microtubule Structure and Organization 822

Microtubule Walls Are Polarized Structures Built from αβ-Tubulin Dimers 822

Microtubules Are Assembled from MTOCs to Generate Diverse Configurations 824

18.2 Microtubule Dynamics 827

Individual Microtubules Exhibit Dynamic Instability 827

Localized Assembly and “Search and Capture” Help Organize Microtubules 829

Drugs Affecting Tubulin Polymerization Are Useful Experimentally and in Treatment of Diseases 829

18.3 Regulation of Microtubule Structure and Dynamics 830

Microtubules Are Stabilized by Side-Binding Proteins 830

+TIPs Regulate the Properties and Functions of the Microtubule （+） End 831

Other End-Binding Proteins Regulate Microtubule Disassembly 832

18.4 Kinesins and Dyneins：Microtubule-Based Motor Proteins 833

Organelles in Axons Are Transported Along Microtubules in Both Directions 833

Kinesin-1 Powers Anterograde Transport of Vesicles Down Axons Toward the （+） Ends of Microtubules 835

The Kinesins Form a Large Protein Superfamily with Diverse Functions 835

Kinesin-1 Is a Highly Processive Motor 836

Dynein Motors Transport Organelles Toward the （-） Ends of Microtubules 838

Kinesins and Dyneins Cooperate in the Transport of Organelles Throughout the Cell 841

Tubulin Modifications Distinguish Different Classes of Microtubules and Their Accessibility to Motors 842

18.5 Cilia and Flagella：Microtubule-Based Surface Structures 844

Eukaryotic Cilia and Flagella Contain Long Doublet Microtubules Bridged by Dynein Motors 844

Ciliary and Flagellar Beating Are Produced by Controlled Sliding of Outer Doublet Microtubules 844

Intraflagellar Transport Moves Material Up and Down Cilia and Flagella 845

Primary Cilia Are Sensory Organelles on Interphase Cells 847

Defects in Primary Cilia Underlie Many Diseases 848

18.6 Mitosis 849

Centrosomes Duplicate Early in the Cell Cycle in Preparation for Mitosis 849

Mitosis Can Be Divided into Six Stages 850

The Mitotic Spindle Contains Three Classes of Microtubules 851

Microtubule Dynamics Increase Dramatically in Mitosis 852

Mitotic Asters Are Pushed Apart by Kinesin-5 and Oriented by Dynein 853

Chromosomes Are Captured and Oriented During Prometaphase 853

Duplicated Chromosomes Are Aligned by Motors and Microtubule Dynamics 854

The Chromosomal Passenger Complex Regulates Microtubule Attachment at Kinetochores 855

Anaphase A Moves Chromosomes to Poles by Microtubule Shortening 857

Anaphase B Separates Poles by the Combined Action of Kinesins and Dynein 858

Additional Mechanisms Contribute to Spindle Formation 858

Cytokinesis Splits the Duplicated Cell in Two 859

Plant Cells Reorganize Their Microtubules and Build a New Cell Wall in Mitosis 860

18.7 Intermediate Filaments 861

Intermediate Filaments Are Assembled from Subunit Dimers 861

Intermediate Filaments Are Dynamic 861

Cytoplasmic Intermediate Filament Proteins Are Expressed in a Tissue-Specific Manner 862

Lamins Line the Inner Nuclear Envelope To Provide Organization and Rigidity to the Nucleus 865

Lamins Are Reversibly Disassembled by Phosphorylation During Mitosis 866

18.8 Coordination and Cooperation Between Cytoskeletal Elements 867

Intermediate Filament-Associated Proteins Contribute to Cellular Organization 867

Microfilaments and Microtubules Cooperate to Transport Melanosomes 867

Cdc42 Coordinates Microtubules and Microfilaments During Cell Migration 867

Advancement of Neural Growth Cones Is Coordinated by Microfilaments and Microtubules 868

19 The Eukaryotic Cell Cycle 873

19.1 Overview of the Cell Cycle and Its Control 875

The Cell Cycle Is an Ordered Series of Events Leading to Cell Replication 875

Cyclin-Dependent Kinases Control the Eukaryotic Cell Cycle 876

Several Key Principles Govern the Cell Cycle 876

19.2 Model Organisms and Methods of Studying the Cell Cycle 877

Budding and Fission Yeasts Are Powerful Systems for Genetic Analysis of the Cell Cycle 877

Frog Oocytes and Early Embryos Facilitate Biochemical Characterization of the Cell Cycle Machinery 878

Fruit Flies Reveal the Interplay Between Development and the Cell Cycle 879

The Study of Tissue Culture Cells Uncovers Cell Cycle Regulation in Mammals 880

Researchers Use Multiple Tools to Study the Cell Cycle 881

19.3 Regulation of CDK Activity 882

Cyclin-Dependent Kinases Are Small Protein Kinases That Require a Regulatory Cyclin Subunit for Their Activity 883

Cyclins Determine the Activity of CDKs 884

Cyclin Levels Are Primarily Regulated by Protein Degradation 885

CDKs Are Regulated by Activating and Inhibitory Phosphorylation 886

CDK Inhibitors Control Cyclin-CDK Activity 886

Genetically Engineered CDKs Led to the Discovery of CDK Functions 887

19.4 Commitment to the Cell Cycle and DNA Replication 887

Cells Are Irreversibly Committed to Division at a Cell Cycle Point Called START or the Restriction Point 888

The E2F Transcription Factor and Its Regulator Rb Control the G1-S Phase Transition in Metazoans 889

Extracellular Signals Govern Cell Cycle Entry 889

Degradation of an S Phase CDK Inhibitor Triggers DNA Replication 890

Replication at Each Origin Is Initiated Once and Only Once During the Cell Cycle 892

Duplicated DNA Strands Become Linked During Replication 893

19.5 Entry into Mitosis 895

Precipitous Activation of Mitotic CDKs Initiates Mitosis 896

Mitotic CDKs Promote Nuclear Envelope Breakdown 897

Mitotic CDKs Promote Mitotic Spindle Formation 897

Chromosome Condensation Facilitates Chromosome Segregation 899

19.6 Completion of Mitosis：Chromosome Segregation and Exit from Mitosis 901

Separase-Mediated Cleavage of Cohesins Initiates Chromosome Segregation 901

APC/C Activates Separase Through Securin Ubiquitinylation 901

Mitotic CDK Inactivation Triggers Exit from Mitosis 902

Cytokinesis Creates Two Daughter Cells 903

19.7 Surveillance Mechanisms in Cell Cycle Regulation 904

Checkpoint Pathways Establish Dependencies and Prevent Errors in the Cell Cycle 905

The Growth Checkpoint Pathway Ensures That Cells Enter the Cell Cycle Only After Sufficient Macromolecule Biosynthesis 905

The DNA Damage Response System Halts Cell Cycle Progression When DNA Is Compromised 905

The Spindle Assembly Checkpoint Pathway Prevents Chromosome Segregation Until Chromosomes Are Accurately Attached to the Mitotic Spindle 908

The Spindle Position Checkpoint Pathway Ensures That the Nucleus Is Accurately Partitioned Between Two Daughter Cells 909

19.8 Meiosis：A Special Type of Cell Division 911

Extracellular and Intracellular Cues Regulate Germ Cell Formation 912

Several Key Features Distinguish Meiosis from Mitosis 912

Recombination and a Meiosis-Specific Cohesin Subunit Are Necessary for the Specialized Chromosome Segregation in Meiosis Ⅰ 915

Co-orienting Sister Kinetochores Is Critical for Meiosis I Chromosome Segregation 917

DNA Replication Is Inhibited Between the Two Meiotic Divisions 917

Part Ⅳ Cell Growth and Differentiation 921

20 Integrating Cells into Tissues 921