Molecular cell biology sixth edition【2025|PDF|Epub|mobi|kindle电子书版本百度云盘下载】

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Part Ⅰ Chemical and Molecular Foundations1

1 LIFE BEGINS WITH CELLS1

1.1 The Diversity and Commonality of Cells1

All Cells Are Prokaryotic or Eukaryotic1

Unicellular Organisms Help and Hurt Us4

Viruses Are the Ultimate Parasites6

Changes in Cells Underlie Evolution6

Even Single Cells Can Have Sex7

We Develop from a Single Cell8

Stem Cells，Fundamental to Forming Tissues and Organs，Offer Medical Opportunities8

1.2 The Molecules of a Cell9

Small Molecules Carry Energy，Transmit Signals，and Are Linked into Macromolecules9

Proteins Give Cells Structure and Perform Most Cellular Tasks10

Nucleic Acids Carry Coded Information for Making Proteins at the Right Time and Place11

The Genome Is Packaged into Chromosomes and Replicated During Cell Division12

Mutations May Be Good，Bad，or Indifferent13

1.3 The Work of Cells14

Cells Build and Degrade Numerous Molecules and Structures15

Animal Cells Produce Their Own External Environment and Glues16

Cells Change Shape and Move16

Cells Sense and Send Information16

Cells Regulate Their Gene Expression to Meet Changing Needs17

Cells Grow and Divide18

Cells Die from Aggravated Assault or an Internal Program19

1.4 Investigating Cells and Their Parts20

Cell Biology Reveals the Size，Shape，Location，and Movements of Cell Components20

Biochemistry and Biophysics Reveal the Molecular Structure and Chemistry of Purified Cell Constituents21

Genetics Reveals the Consequences of Damaged Genes22

Genomics Reveals Differences in the Structure and Expression of Entire Genomes23

Developmental Biology Reveals Changes in the Properties of Cells as They Specialize23

Choosing the Right Experimental Organism for the Job25

The Most Successful Biological Studies Use Multiple Approaches27

1.5 A Genome Perspective on Evolution28

Metabolic Proteins，the Genetic Code，and Organelle Structures Are Nearly Universal28

Darwin’s Ideas About the Evolution of Whole Animals Are Relevant to Genes28

Many Genes Controlling Development Are Remarkably Similar in Humans and Other Animals28

Human Medicine Is Informed by Research on Other Organisms29

2 CHEMICAL FOUNDATIONS31

2.1 Covalent Bonds and Noncovalent Interactions32

The Electronic Structure of an Atom Determines the Number and Geometry of Covalent Bonds It Can Make33

Electrons May Be Shared Equally or Unequally in Covalent Bonds34

Covalent Bonds Are Much Stronger and More Stable Than Noncovalent Interactions35

Ionic Interactions Are Attractions between Oppositely Charged Ions36

Hydrogen Bonds Determine the Water Solubility of Uncharged Molecules37

Van der Waals Interactions Are Caused by Transient Dipoles37

The Hydrophobic Effect Causes Nonpolar Molecules to Adhere to One Another38

Molecular Complementarity Mediated via Noncovalent Interactions Permits Tight，Highly Specific Binding of Biomolecules39

2.2 Chemical Building Blocks of Cells40

Amino Acids Differing Only in Their Side Chains Compose Proteins41

Five Different Nucleotides Are Used to Build Nucleic Acids44

Monosaccharides Joined by Glycosidic Bonds Form Linear and Branched Polysaccharides44

Phospholipids Associate Noncovalently to Form the Basic Bilayer Structure of Biomembranes46

2.3 Chemical Equilibrium49

Equilibrium Constants Reflect the Extent of a Chemical Reaction50

Chemical Reactions in Cells Are at Steady State50

Dissociation Constants of Binding Reactions Reflect the Affinity of Interacting Molecules50

Biological Fluids Have Characteristic pH Values51

Hydrogen Ions Are Released by Acids and Taken Up by Bases52

Buffers Maintain the pH of Intracellular and Extracellular Fluids52

2.4 Biochemical Energetics54

Several Forms of Energy Are Important in Biological Systems54

Cells Can Transform One Type of Energy into Another55

The Change in Free Energy Determines the Direction of a Chemical Reaction55

The △G°’ of a Reaction Can Be Calculated from Its Keq56

The Rate of a Reaction Depends on the Activation Energy Necessary to Energize the Reactants into a Transition State56

Life Depends on the Coupling of Unfavorable Chemical Reactions with Energetically Favorable Reactions57

Hydrolysis of ATP Releases Substantial Free Energy and Drives Many Cellular Processes57

ATP Is Generated During Photosynthesis and Respiration59

NAD＋ and FAD Couple Many Biological Oxidation and Reduction Reactions59

3 PROTEIN STRUCTURE AND FUNCTION63

3.1 Hierarchical Structure of Proteins64

The Primary Structure of a Protein Is Its Linear Arrangement of Amino Acids65

Secondary Structures Are the Core Elements of Protein Architecture66

Overall Folding of a Polypeptide Chain Yields Its Tertiary Structure67

Different Ways of Depicting the Conformation of Proteins Convey Different Types of Information68

Structural Motifs Are Regular Combinations of Secondary and Tertiary Structures68

Structural and Functional Domains Are Modules of Tertiary Structure70

Proteins Associate into Multimeric Structures and Macromolecular Assemblies72

Members of Protein Families Have a Common Evolutionary Ancestor72

3.2 Protein Folding74

Planar Peptide Bonds Limit the Shapes into Which Proteins Can Fold74

Information Directing a Protein’s Folding Is Encoded in Its Amino Acid Sequence74

Folding of Proteins in Vivo Is Promoted by Chaperones75

Alternatively Folded Proteins Are Implicated in Diseases77

3.3 Protein Function78

Specific Binding of Ligands Underlies the Functions of Most Proteins78

Enzymes Are Highly Efficient and Specific Catalysts79

An Enzyme’s Active Site Binds Substrates and Carries Out Catalysis80

Serine Proteases Demonstrate How an Enzyme’s Active Site Works81

Enzymes in a Common Pathway Are Often Physically Associated with One Another84

Enzymes Called Molecular Motors Convert Energyinto Motion85

3.4 Regulating Protein Function Ⅰ：Protein Degradation86

Regulated Synthesis and Degradation of Proteins is a Fundamental Property of Cells86

The Proteasome Is a Complex Molecular Machine Used to Degrade Proteins87

Ubiquitin Marks Cytosolic Proteins for Degradation in Proteasomes88

3.5 Regulating Protein Function Ⅱ：Noncovalent and Covalent Modifications88

Noncovalent Binding Permits Allosteric，or Cooperative，Regulation of Proteins89

Noncovalent Binding of Calcium and GTP Are Widely Used As Allosteric Switches to Control Protein Activity90

Phosphorylation and Dephosphorylation Covalently Regulate Protein Activity91

Proteolytic Cleavage Irreversibly Activates or Inactivates Some Proteins91

Higher-Order Regulation Includes Control of Protein Location and Concentration92

3.6 Purifying，Detecting，and Characterizing Proteins92

Centrifugation Can Separate Particles and Molecules That Differ in Mass or Density92

Electrophoresis Separates Molecules on the Basis of Their Charge-to-Mass Ratio94

Liquid Chromatography Resolves Proteins by Mass，Charge，or Binding Affinity96

Highly Specific Enzyme and Antibody Assays Can Detect Individual Proteins98

Radioisotopes Are Indispensable Tools for Detecting Biological Molecules99

Mass Spectrometry Can Determine the Mass and Sequence of Proteins101

Protein Primary Structure Can Be Determined by Chemical Methods and from Gene Sequences103

Protein Conformation Is Determined by Sophisticated Physical Methods103

3.7 Proteomics105

Proteomics Is the Study of All or a Large Subset of Proteins in a Biological System105

Advanced Techniques in Mass Spectrometry Are Critical to Proteomic Analysis106

Part Ⅱ Genetics and Molecular Biology111

4 BASIC MOLECULAR GENETIC MECHANISMS111

4.1 Structure of Nucleic Acids113

A Nucleic Acid Strand Is a Linear Polymer with End-to-End Directionality113

Native DNA Is a Double Helix of Complementary Antiparallel Strands114

DNA Can Undergo Reversible Strand Separation116

Torsional Stress in DNA Is Relieved by Enzymes117

Different Types of RNA Exhibit Various Conformations Related to Their Functions118

4.2 Transcription of Protein-Coding Genes and Formation of Functional mRNA120

A Template DNA Strand Is Transcribed into a Complementary RNA Chain by RNA Polymerase120

Organization of Genes Differs in Prokaryotic and Eukaryotic DNA122

Eukaryotic Precursor mRNAs Are Processed to Form Functional mRNAs123

Alternative RNA Splicing Increases the Number of Proteins Expressed from a Single Eukaryotic Gene125

4.3 The Decoding of mRNA by tRNAs127

Messenger RNA Carries information from DNA in a Three-Letter Genetic Code127

The Folded Structure of tRNA Promotes Its Decoding Functions129

Nonstandard Base Pairing Often Occurs Between Codons and Anticodons130

Amino Acids Become Activated When Covalently Linked to tRNAs131

4.4 Stepwise Synthesis of Proteins on Ribosomes132

Ribosomes Are Protein-Synthesizing Machines132

Methionyl-tRNAiMET Recognizes the AUG Start Codon133

Translation Initiation Usually Occurs at the First AUG from the 5’ End of an mRNA133

During Chain Elongation Each Incoming Aminoacyl-tRNA Moves Through Three Ribosomal Sites135

Translation Is Terminated by Release Factors When a Stop Codon Is Reached137

Polysomes and Rapid Ribosome Recycling Increase the Efficiency of Translation138

4.5 DNA Replication139

DNA Polymerases Require a Primer to Initiate Replication140

Duplex DNA Is Unwound and Daughter Strands Are Formed at the DNA Replication Fork141

Several Proteins Participate in DNA Replication141

DNA Replication Usually Occurs Bidirectionally from Each Origin143

4.6 DNA Repair and Recombination145

DNA Polymerases Introduce Copying Errors and Also Correct Them145

Chemical and Radiation Damage to DNA Can Lead to Mutations145

High-Fidelity DNA Excision-Repair Systems Recognize and Repair Damage147

Base Excision Repairs T·G Mismatches and Damaged Bases147

Mismatch Excision Repairs Other Mismatches and Small Insertions and Deletions147

Nucleotide Excision Repairs Chemical Adducts That Distort Normal DNA Shape148

Two Systems Utilize Recombination to Repair Double-Strand Breaks in DNA149

Homologous Recombination Can Repair DNA Damage and Generate Genetic Diversity150

4.7 Viruses：Parasites of the Cellular Genetic System154

Most Viral Host Ranges Are Narrow154

Viral Capsids Are Regular Arrays of One or a Few Types of Protein154

Viruses Can Be Cloned and Counted in Plaque Assays155

Lytic Viral Growth Cycles Lead to the Death of Host Cells156

Viral DNA Is Integrated into the Host-Cell Genome in Some Nonlytic Viral Growth Cycles158

5 MOLECULAR GENETIC TECHNIQUES165

5.1 Genetic Analysis of Mutations to Identify and Study Genes166

Recessive and Dominant Mutant Alleles Generally Have Opposite Effects on Gene Function166

Segregation of Mutations in Breeding Experiments Reveals Their Dominance or Recessivity167

Conditional Mutations Can Be Used to Study Essential Genes in Yeast170

Recessive Lethal Mutations in Diploids Can Be Identified by Inbreeding and Maintained in Heterozygotes171

Complementation Tests Determine Whether Different Recessive Mutations Are in the Same Gene171

Double Mutants Are Useful in Assessing the Order in Which Proteins Function171

Genetic Suppression and Synthetic Lethality Can Reveal Interacting or Redundant Proteins173

Genes Can Be Identified by Their Map Position on the Chromosome174

5.2 DNA Cloning and Characterization176

Restriction Enzymes and DNA Ligases Allow Insertion of DNA Fragments into Cloning Vectors176

E.coli Plasmid Vectors Are Suitable for Cloning Isolated DNA Fragments178

cDNA Libraries Represent the Sequences of Protein-Coding Genes179

cDNAs Prepared by Reverse Transcription of Cellular mRNAs Can Be Cloned to Generate cDNA Libraries181

DNA Libraries Can Be Screened by Hybridization to an Oligonucleotide Probe181

Yeast Genomic Libraries Can Be Constructed with Shuttle Vectors and Screened by Functional Complementation182

Gel Electrophoresis Allows Separation of Vector DNA from Cloned Fragments184

Cloned DNA Molecules Are Sequenced Rapidly by the Dideoxy Chain-Termination Method187

The Polymerase Chain Reaction Amplifies a Specific DNA Sequence from a Complex Mixture188

5.3 Using Cloned DNA Fragments to Study Gene Expression191

Hybridization Techniques Permit Detection of Specific DNA Fragments and mRNAs191

DNA Microarrays Can Be Used to Evaluate the Expression of Many Genes at One Time192

Cluster Analysis of Multiple Expression Experiments Identifies Co-regulated Genes193

E.coli Expression Systems Can Produce Large Quantities of Proteins from Cloned Genes194

Plasmid Expression Vectors Can Be Designed for Use in Animal Cells196

5.4 Identifying and Locating Human Disease Genes198

Many Inherited Diseases Show One of Three Major Patterns of Inheritance199

DNA Polymorphisms Are Used in Linkage-Mapping Human Mutations200

Linkage Studies Can Map Disease Genes with a Resolution of About 1 Centimorgan201

Further Analysis Is Needed to Locate a Disease Gene in Cloned DNA202

Many Inherited Diseases Result from Multiple Genetic Defects203

5.5 Inactivating the Function of Specific Genes in Eukaryotes204

Normal Yeast Genes Can Be Replaced with Mutant Alleles by Homologous Recombination205

Transcription of Genes Ligated to a Regulated Promoter Can Be Controlled Experimentally206

Specific Genes Can Be Permanently Inactivated in the Germ Line of Mice207

Somatic Cell Recombination Can Inactivate Genes in Specific Tissues208

Dominant-Negative Alleles Can Functionally Inhibit Some Genes209

RNA Interference Causes Gene Inactivation by Destroying the Corresponding mRNA210

6 GENES，GENOMICS，AND CHROMOSOMES215

6.1 Eukaryotic Gene Structure217

Most Eukaryotic Genes Contain Introns and Produce mRNAs Encoding Single Proteins217

Simple and Complex Transcription Units Are Found in Eukaryotic Genomes217

Protein-Coding Genes May Be Solitary or Belong to a Gene Family219

Heavily Used Gene Products Are Encoded by Multiple Copies of Genes221

Nonprotein-Coding Genes Encode Functional RNAs222

6.2 Chromosomal Organization of Genes and Noncoding DNA223

Genomes of Many Organisms Contain Much Nonfunctional DNA223

Most Simple-Sequence DNAs Are Concentrated in Specific Chromosomal Locations224

DNA Fingerprinting Depends on Differences in Length of Simple-Sequence DNAs225

Unclassified Spacer DNA Occupies a Significant Portion of the Genome225

6.3 Transposable（Mobile） DNA Elements226

Movement of Mobile Elements Involves a DNA or an RNA Intermediate226

DNA Transposons Are Present in Prokaryotes and Eukaryotes227

LTR Retrotransposons Behave Like Intracellular Retroviruses229

Non-LTR Retrotransposons Transpose by a Distinct Mechanism230

Other Retrotransposed RNAs Are Found in Genomic DNA234

Mobile DNA Elements Have Significantly Influenced Evolution234

6.4 Organelle DNAs236

Mitochondria Contain Multiple mtDNA Molecules237

mtDNA Is Inherited Cytoplasmically237

The Size，Structure，and Coding Capacity of mtDNA Vary Considerably Between Organisms238

Products of Mitochondrial Genes Are Not Exported240

Mitochondria Evolved from a Single Endosymbiotic Event Involving a Rickettsia-like Bacterium240

Mitochondrial Genetic Codes Differ from the Standard Nuclear Code240

Mutations in Mitochondrial DNA Cause Several Genetic Diseases in Humans240

Chloroplasts Contain Large DNAs Often Encoding More Than a Hundred Proteins242

6.5 Genomics：Genome-wide Analysis of Gene Structure and Expression243

Stored Sequences Suggest Functions of Newly Identified Genes and Proteins243

Comparison of Related Sequences from Different Species Can Give Clues to Evolutionary Relationships Among Proteins244

Genes Can Be Identified Within Genomic DNA Sequences244

The Number of Protein-Coding Genes in an Organism’s Genome Is Not Directly Related to Its Biological Complexity245

Single Nucleotide Polymorphisms and Gene Copy-Number Variation Are Important Determinants of Differences Between Individuals of a Species246

6.6 Structural Organization of Eukaryotic Chromosomes247

Chromatin Exists in Extended and Condensed Forms248

Modifications of Histone Tails Control Chromatin Condensation and Function250

Nonhistone Proteins Provide a Structural Scaffold for Long Chromatin Loops254

Additional Nonhistone Proteins Regulate Transcription and Replication256

6.7 Morphology and Functional Elements of Eukaryotic Chromosomes257

Chromosome Number，Size，and Shape at Metaphase Are Species-Specific257

During Metaphase，Chromosomes Can Be Distinguished by Banding Patterns and Chromosome Painting258

Chromosome Painting and DNA Sequencing Reveal the Evolution of Chromosomes259

Interphase Polytene Chromosomes Arise by DNA Amplification260

Three Functional Elements Are Required for Replication and Stable Inheritance of Chromosomes261

Centromere Sequences Vary Greatly in Length263

Addition of Telomeric Sequences by Telomerase Prevents Shortening of Chromosomes263

7 TRANSCRIPTIONAL CONTROL OF GENE EXPRESSION269

7.1 Control of Gene Expression in Bacteria271

Transcription Initiation by Bacterial RNA Polymerase Requires Association with a Sigma Factor271

Initiation of Iac Operon Transcription Can Be Repressed and Activated271

Small Molecules Regulate Expression of Many Bacterial Genes via DNA-Binding Repressors and Activators273

Transcription Initiation from Some Promoters Requires Alternative Sigma Factors273

Transcription by σ54-RNA Polymerase Is Controlled by Activators That Bind Far from the Promoter274

Many Bacterial Responses Are Controlled by Two-Component Regulatory Systems275

7.2 Overview of Eukaryotic Gene Control and RNA Polymerases276

Regulatory Elements in Eukaryotic DNA Are Found Both Close to and Many Kilobases Away from Transcription Start Sites276

Three Eukaryotic Polymerases Catalyze Formation of Different RNAs278

The Largest Subunit in RNA Polymerase Ⅱ Has an Essential Carboxyl-Terminal Repeat279

RNA Polymerase Ⅱ Initiates Transcription at DNA Sequences Corresponding to the 5’ Cap of mRNAs280

7.3 Regulatory Sequences in Protein-Coding Genes282

The TATA Box，Initiators，and CpG Islands Function as Promoters in Eukaryotic DNA282

Promoter-Proximal Elements Help Regulate Eukaryotic Genes282

Distant Enhancers Often Stimulate Transcription by RNA Polymerase Ⅱ284

Most Eukaryotic Genes Are Regulated by Multiple Transcription-Control Elements285

7.4 Activators and Repressors of Transcription286

Footprinting and Gel-Shift Assays Detect Protein-DNA Interactions286

Activators Are Modular Proteins Composed of Distinct Functional Domains and Promote Transcription288

Repressors Inhibit Transcription and Are the Functional Converse of Activators290

DNA-Binding Domains Can Be Classified into Numerous Structural Types290

Structurally Diverse Activation and Repression Domains Regulate Transcription293

Transcription Factor Interactions Increase Gene-Control Options294

Multiprotein Complexes Form on Enhancers295

7.5 Transcription Initiation by RNA Polymerase Ⅱ296

General Transcription Factors Position RNA Polymerase Ⅱ at Start Sites and Assist in Initiation296

Sequential Assembly of Proteins Forms the Pol Ⅱ Transcription Preinitiation Complex in Vitro297

In Vivo Transcription Initiation by Pol Ⅱ Requires Additional Proteins298

7.6 Molecular Mechanisms of Transcription Repression and Activation299

Formation of Heterochromatin Silences Gene Expression at Telomeres，Near Centromeres，and in Other Regions299

Repressors Can Direct Histone Deacetylation and Methylation at Specific Genes303

Activators Can Direct Histone Acetylation and Methylation at Specific Genes305

Chromatin-Remodeling Factors Help Activate or Repress Transcription306

Histone Modifications Vary Greatly in Their Stabilities307

The Mediator Complex Forms a Molecular Bridge Between Activation Domains and Pol Ⅱ307

Transcription of Many Genes Requires Ordered Binding and Function of Activators and Co-activators308

The Yeast Two-Hybrid System Exploits Activator Flexibility to Detect cDNAs That Encode Interacting Proteins310

7.7 Regulation of Transcription-Factor Activity311

All Nuclear Receptors Share a Common Domain Structure312

Nuclear-Receptor Response Elements Contain Inverted or Direct Repeats313

Hormone Binding to a Nuclear Receptor Regulates Its Activity as a Transcription Factor313

7.8 Regulated Elongation and Termination of Transcription314

Transcription of the HIV Genome Is Regulated by an Antitermination Mechanism315

Promoter-Proximal Pausing of RNA Polymerase Ⅱ Occurs in Some Rapidly Induced Genes316

7.9 Other Eukaryotic Transcription Systems316

Transcription Initiation by Pol Ⅰ and Pol Ⅲ Is Analogous to That by Pol Ⅱ316

Mitochondrial and Chloroplast DNAs Are Transcribed by Organelle-Specific RNA Polymerases317

8 POST-TRANSCRIPTIONAL GENE CONTROL323

8.1 Processing of Eukaryotic Pre-mRNA325

The 5’ Cap Is Added to Nascent RNAs Shortly After Transcription Initiation325

A Diverse Set of Proteins with Conserved RNA-Binding Domains Associate with Pre-mRNAs326

Splicing Occurs at Short，Conserved Sequences in Pre-mRNAs via Two Transesterification Reactions329

During Splicing，snRNAs Base-Pair with Pre-mRNA330

Spliceosomes，Assembled from snRNPs and a Pre-mRNA，Carry Out Splicing330

Chain Elongation by RNA Polymerase Ⅱ Is Coupled to the Presence of RNA-Processing Factors333

SR Proteins Contribute to Exon Definition in Long Pre-mRNAs333

Self-Splicing Group Ⅱ Introns Provide Clues to the Evolution of snRNAs334

3’ Cleavage and Polyadenylation of Pre-mRNAs Are Tightly Coupled335

Nuclear Exonucleases Degrade RNA That Is Processed Out of Pre-mRNAs336

8.2 Regulation of Pre-mRNA Processing337

Alternative Splicing Is the Primary Mechanism for Regulating mRNA Processing337

A Cascade of Regulated RNA Splicing Controls Drosophila Sexual Differentiation338

Splicing Repressors and Activators Control Splicing at Alternative Sites339

RNA Editing Alters the Sequences of Some Pre-mRNAs340

8.3 Transport of mRNA Across the Nuclear Envelope341

Nuclear Pore Complexes Control Import and Exportfrom the Nucleus342

Pre-mRNAs in Spliceosomes Are Not Exported from the Nucleus345

HIV Rev Protein Regulates the Transport of Unspliced Viral mRNAs346

8.4 Cytoplasmic Mechanisms of Post-transcriptional Control347

Micro RNAs Repress Translation of Specific mRNAs347

RNA Interference Induces Degradation of Precisely Complementary mRNAs349

Cytoplasmic Polyadenylation Promotes Translation of Some mRNAs351

Degradation of mRNAs in the Cytoplasm Occurs by Several Mechanisms352

Protein Synthesis Can Be Globally Regulated353

Sequence-Specific RNA-Binding Proteins Control Specific mRNA Translation356

Surveillance Mechanisms Prevent Translation of Improperly Processed mRNAs357

Localization of mRNAs Permits Production of Proteins at Specific Regions Within the Cytoplasm357

8.5 Processing of rRNA and tRNA358

Pre-rRNA Genes Function as Nucleolar Organizers and Are Similar in All Eukaryotes359

Small Nucleolar RNAs Assist in Processing Pre-rRNAs360

Self-Splicing Group I Introns Were the First Examples of Catalytic RNA363

Pre-tRNAs Undergo Extensive Modification in the Nucleus363

Nuclear Bodies Are Functionally Specialized Nuclear Domains364

Part Ⅲ Cell Structure and Function371

9 VISUALIZING，FRACTIONATING，AND CULTURING CELLS371

9.1 Organelles of the Eukaryotic Cell372

The Plasma Membrane Has Many Common Functions in All Cells372

Endosomes Take Up Soluble Macromolecules from the Cell Exterior372

Lysosomes Are Acidic Organelles That Contain a Battery of Degradative Enzymes373

Peroxisomes Degrade Fatty Acids and Toxic Compounds374

The Endoplasmic Reticulum Is a Network of Interconnected Internal Membranes375

The Golgi Complex Processes and Sorts Secreted and Membrane Proteins376

Plant Vacuoles Store Small Molecules and Enable a Cell to Elongate Rapidly377

The Nucleus Contains the DNA Genome，RNA Synthetic Apparatus，and a Fibrous Matrix378

Mitochondria Are the Principal Sites of ATP Production in Aerobic Non photosynthetic Cells378

Chloroplasts Contain Internal Compartments in Which Photosynthesis Takes Place379

9.2 Light Microscopy：Visualizing Cell Structure and Localizing Proteins Within Cells380

The Resolution of the Light Microscope Is About 0.2 μm381

Phase-Contrast and Differential Interference Contrast Microscopy Visualize Unstained Living Cells381

Fluorescence Microscopy Can Localize and Quantify Specific Molecules in Live Cells382

Imaging Subcellular Details Often Requires that the Samples Be Fixed，Sectioned，and Stained384

Immunofluorescence Microscopy Can Detect Specific Proteins in Fixed Cells385

Confocal and Deconvolution Microscopy Enable Visualization of Three-Dimensional Objects386

Graphics and Informatics Have Transformed Modern Microscopy387

9.3 Electron Microscopy：Methods and Applications388

Resolution of Transmission Electron Microscopy is Vastly Greater Than That of Light Microscopy388

Cryoelectron Microscopy Allows Visualization of Particles Without Fixation or Staining389

Electron Microscopy of Metal-Coated Specimens Can Reveal Surface Features of Cells and Their Components390

9.4 Purification of Cell Organelles391

Disruption of Cells Releases Their Organelles and Other Contents391

Centrifugation Can Separate Many Types of Organelles392

Organelle-Specific Antibodies Are Useful in Preparing Highly Purified Organelles393

9.5 Isolation，Culture，and Differentiation of Metazoan Cells394

Flow Cytometry Separates Different Cell Types394

Culture of Animal Cells Requires Nutrient-Rich Media and Special Solid Surfaces395

Primary Cell Cultures Can Be Used to Study Cell Differentiation396

Primary Cell Cultures and Cell Strains Have a Finite Life Span396

Transformed Cells Can Grow Indefinitely in Culture397

Some Cell Lines Undergo Differentiation in Culture398

Hybrid Cells Called Hybridomas Produce Abundant Monoclonal Antibodies400

HAT Medium Is Commonly Used to Isolate Hybrid Cells402

CLASSIC EXPERIMENT 9.1 Separating Organelles407

10 BIOMEMBRANE STRUCTURE409

10.1 Biomembranes：Lipid Composition and Structural Organization411

Phospholipids Spontaneously Form Bilayers411

Phospholipid Bilayers Form a Sealed Compartment Surrounding an Internal Aqueous Space411

Biomembranes Contain Three Principal Classes of Lipids415

Most Lipids and Many Proteins Are Laterally Mobile in Biomembranes416

Lipid Composition Influences the Physical Properties of Membranes418

Lipid Composition Is Different in the Exoplasmic and Cytosolic Leaflets419

Cholesterol and Sphingolipids Cluster with Specific Proteins in Membrane Microdomains420

10.2 Biomembranes：Protein Components and Basic Functions421

Proteins Interact with Membranes in Three Different Ways421

Most Transmembrane Proteins Have Membrane-Spanning α Helices422

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

Covalently Attached Hydrocarbon Chains Anchor Some Proteins to Membranes424

All Transmembrane Proteins and Glycolipids Are Asymmetrically Oriented in the Bilayer426

Lipid-Binding Motifs Help Target Peripheral Proteins to the Membrane427

Proteins Can Be Removed from Membranes by Detergents or High-Salt Solutions427

10.3 Phospholipids，Sphingolipids，and Cholesterol：Synthesis and Intracellular Movement429

Fatty Acids Synthesis Is Mediated by Several Important Enzymes430

Small Cytosolic Proteins Facilitate Movement of Fatty Acids430

Incorporation of Fatty Acids into Membrane Lipids Takes Place on Organelle Membranes431

Flippases Move Phospholipids from One Membrane Leaflet to the Opposite Leaflet431

Cholesterol Is Synthesized by Enzymes in the Cytosol and ER Membrane432

Cholesterol and Phospholipids Are Transported Between Organelles by Several Mechanisms433

11 TRANSMEMBRANE TRANSPORT OF IONS AND SMALL MOLECULES437

11.1 Overview of Membrane Transport438

Only Small Hydrophobic Molecules Cross Membranes by Simple Diffusion438

Membrane Proteins Mediate Transport of Most Molecules and All Ions Across Biomembranes439

11.2 Uniport Transport of Glucose and Water441

Several Features Distinguish Uniport Transport from Simple Diffusion441

GLUT1 Uniporter Transports Glucose into Most Mammalian Cells442

The Human Genome Encodes a Family of Sugar-Transporting GLUT Proteins443

Transport Proteins Can Be Enriched Within Artificial Membranes and Cells443

Osmotic Pressure Causes Water to Move Across Membranes444

Aquaporins Increase the Water Permeability of Cell Membranes444

11.3 ATP-Powered Pumps and the Intracellular Ionic Environment447

Different Classes of Pumps Exhibit Characteristic Structural and Functional Properties447

ATP-Powered Ion Pumps Generate and Maintain Ionic Gradients Across Cellular Membranes448

Muscle Relaxation Depends on Ca 2＋ ATPases That Pump Ca 2＋ from the Cytosol into the Sarcoplasmic Reticulum449

Calmodulin Regulates the Plasma Membrane Ca 2＋ Pumps That Control Cytosolic Ca 2＋Concentrations451

Na＋/K＋ ATPase Maintains the Intracellular Na＋and K＋ Concentrations in Animal Cells452

V-Class H＋ ATPases Maintain the Acidity of Lysosomes and Vacuoles453

Bacterial Permeases Are ABC Proteins That Import a Variety of Nutrients from the Environment454

The Approximately 50 Mammalian ABC Transporters Play Diverse and Important Roles in Cell and Organ Physiology455

Certain ABC Proteins “Flip” Phospholipids and Other Lipid-Soluble Substrates from One Membrane Leaflet to the Opposite Leaflet456

11.4 Nongated Ion Channels and the Resting Membrane Potential458

Selective Movement of Ions Creates a Transmembrane Electric Potential Difference458

The Membrane Potential in Animal Cells Depends Largely on Potassium Ion Movements Through Open Resting K＋ Channels460

Ion Channels Contain a Selectivity Filter Formed from Conserved Transmembrane Segments461

Patch Clamps Permit Measurement of Ion Movements Through Single Channels463

Novel Ion Channels Can Be Characterized by a Combination of Oocyte Expression and Patch Clamping464

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

11.5 Cotransport by Symporters and Antiporters465

Na＋-Linked Symporters Import Amino Acids and Glucose into Animal Cells Against High Concentration Gradients466

Bacterial Symporter Structure Reveals the Mechanism of Substrate Binding467

Na＋-Linked Ca 2＋ Antiporter Exports Ca 2＋ from Cardiac Muscle Cells468

Several Cotransporters Regulate Cytosolic pH468

A Putative Cation Exchange Protein Plays a Key Role in Evolution of Human Skin Pigmentation469

Numerous Transport Proteins Enable Plant Vacuoles to Accumulate Metabolites and Ions469

11.6 Transepithelial Transport470

Multiple Transport Proteins Are Needed to Move Glucose and Amino Acids Across Epithelia471

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 pH472

CLASSIC EXPERIMENT 11.1 Stumbling Upon Active Transport477

12 CELLULAR ENERGETICS479

12.1 First Steps of Glucose and Fatty Acid Catabolism：Glycolysis and the Citric Acid Cycle480

During Glycolysis（Stage Ⅰ），Cytosolic Enzymes Convert Glucose to Pyruvate481

The Rate of Glycolysis Is Adjusted to Meet the Cell’s Need for ATP483

Glucose Is Fermented Under Anaerobic Conditions485

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

Mitochondria Are Dynamic Organelles with Two Structurally and Functionally Distinct Membranes485

In Stage Ⅱ，Pyruvate Is Oxidized to CO2 and High-Energy Electrons Stored in Reduced Coenzymes487

Transporters in the Inner Mitochondrial Membrane Help Maintain Appropriate Cytosolic and Matrix Concentrations of NAD＋ and NADH489

Mitochondrial Oxidation of Fatty Acids Generates ATP491

Peroxisomal Oxidation of Fatty Acids Generates No ATP491

12.2 The Electron Transport Chain and Generation of the Proton-Motive Force493

Stepwise Electron Transport Efficiently Releases the Energy Stored in NADH and FADH2493

Electron Transport in Mitochondria Is Coupled to Proton Pumping493

Electrons Flow from FADH2 and NADH to O2 Through Four Multiprotein Complexes494

Reduction Potentials of Electron Carriers Favor Electron Flow from NADH to O2499

Experiments Using Purified Complexes Established the Stoichiometry of Proton Pumping499

The Q Cycle Increases the Number of Protons Translocated as Electrons Flow Through Complex Ⅲ500

The Proton-Motive Force in Mitochondria Is Due Largely to a Voltage Gradient Across the Inner Membrane502

Toxic By-products of Electron Transport Can Damage Cells502

12.3 Harnessing the Proton-Motive Force for Energy-Requiring Processes503

The Mechanism of ATP Synthesis Is Shared Among Bacteria，Mitochondria，and Chloroplasts505

ATP Synthase Comprises Two Multiprotein Complexes Termed F0 and F1505

Rotation of the F1 γ Subunit，Driven by Proton Movement Through F0，Powers ATP Synthesis506

ATP-ADP Exchange Across the Inner Mitochondrial Membrane Is Powered by the Proton-Motive Force509

Rate of Mitochondrial Oxidation Normally Depends on ADP Levels510

Brown-Fat Mitochondria Use the Proton-Motive Force to Generate Heat510

12.4 Photosynthesis and Light-Absorbing Pigments511

Thylakoid Membranes in Chloroplasts Are the Sites of Photosynthesis in Plants511

Three of the Four Stages in Photosynthesis Occur Only During Illumination511

Each Photon of Light Has a Defined Amount of Energy513

Photosystems Comprise a Reaction Center and Associated Light-Harvesting Complexes514

Photoelectron Transport from Energized Reaction-Center Chlorophyll a Produces a Charge Separation514

Internal Antenna and Light-Harvesting Complexes Increase the Efficiency of Photosynthesis515

12.5 Molecular Analysis of Photosystems517

The Single Photosystem of Purple Bacteria Generates a Proton-Motive Force but No O2517

Linear Electron Flow Through Both Plant Photosystems，PSII and PSI，Generates a Proton-Motive Force，O2，and NADPH519

An Oxygen-Evolving Complex Is Located on the Luminal Surface of the PSII Reaction Center520

Cells Use Multiple Mechanisms to Protect Against Damage from Reactive Oxygen Species During Photoelectron Transport521

Cyclic Electron Flow Through PSI Generates a Proton-Motive Force but No NADPH or O2522

Relative Activities of Photosystems Ⅰ and Ⅱ Are Regulated523

12.6 CO2 Metabolism During Photosynthesis524

Rubisco Fixes CO2 in the Chloroplast Stroma525

Synthesis of Sucrose Using Fixed CO2 Is Completed in the Cytosol525

Light and Rubisco Activase Stimulate CO2 Fixation525

Photorespiration，Which Competes with Photosynthesis，Is Reduced in Plants That Fix CO2 by the C4 Pathway527

13 MOVING PROTEINS INTO MEMBRANES AND ORGANELLES533

13.1 Translocation of Secretory Proteins Across the ER Membrane535

A Hydrophobic N-Terminal Signal Sequence Targets Nascent Secretory Proteins to the ER536

Cotranslational Translocation Is Initiated by Two GTP-Hydrolyzing Proteins537

Passage of Growing Polypeptides Through the Translocon Is Driven by Energy Released During Translation539

ATP Hydrolysis Powers Post-translational Translocation of Some Secretory Proteins in Yeast540

13.2 Insertion of Proteins into the ER Membrane542

Several Topological Classes of Integral Membrane Proteins Are Synthesized on the ER543

Internal Stop-Transfer and Signal-Anchor Sequences Determine Topology of Single-Pass Proteins544

Multipass Proteins Have Multiple Internal Topogenic Sequences546

A Phospholipid Anchor Tethers Some Cell-Surface Proteins to the Membrane547

The Topology of a Membrane Protein Often Can Be Deduced from Its Sequence547

13.3 Protein Modifications，Folding，and Quality Control in the ER549

A Preformed N-Linked Oligosaccharide Is Added to Many Proteins in the Rough ER550

Oligosaccharide Side Chains May Promote Folding and Stability of Glycoproteins552

Disulfide Bonds Are Formed and Rearranged by Proteins in the ER Lumen552

Chaperones and Other ER Proteins Facilitate Folding and Assembly of Proteins552

Improperly Folded Proteins in the ER Induce Expression of Protein-Folding Catalysts555

Unassembled or Misfolded Proteins in the ER Are Often Transported to the Cytosol for Degradation556

13.4 Sorting of Proteins to Mitochondria and Chloroplasts557

Amphipathic N-Terminal Signal Sequences Direct Proteins to the Mitochondrial Matrix558

Mitochondrial Protein Import Requires Outer-Membrane Receptors and Translocons in Both Membranes558

Studies with Chimeric Proteins Demonstrate Important Features of Mitochondrial Import560

Three Energy Inputs Are Needed to Import Proteins into Mitochondria561

Multiple Signals and Pathways Target Proteins to Submitochondrial Compartments561

Targeting of Chloroplast Stromal Proteins Is Similar to Import of Mitochondrial Matrix Proteins565

Proteins Are Targeted to Thylakoids by Mechanisms Related to Translocation Across the Bacterial Inner Membrane565

13.5 Sorting of Peroxisomal Proteins567

Cytosolic Receptor Targets Proteins with an SKL Sequence at the C-Terminus into the Peroxisomal Matrix567

Peroxisomal Membrane and Matrix Proteins Are Incorporated by Different Pathways568

13.6 Transport into and out of the Nucleus569

Large and Small Molecules Enter and Leave the Nucleus via Nuclear Pore Complexes570

Importins Transport Proteins Containing Nuclear- Localization Signals into the Nucleus571

Exportins Transport Proteins Containing Nuclear-ExportSignals out of the Nucleus573

Most mRNAs Are Exported from the Nucleus by a Ran-Independent Mechanism573

14 VESICULAR TRAFFIC，SECRETION，AND ENDOCYTOSIS579

14.1 Techniques for Studying the Secretory Pathway580

Transport of a Protein Through the Secretory Pathway Can Be Assayed in Living Cells582

Yeast Mutants Define Major Stages and Many Components in Vesicular Transport584

Cell-Free Transport Assays Allow Dissection of Individual Steps in Vesicular Transport585

14.2 Molecular Mechanisms of Vesicular Traffic586

Assembly of a Protein Coat Drives Vesicle Formation and Selection of Cargo Molecules586

A Conserved Set of GTPase Switch Proteins Controls Assembly of Different Vesicle Coats587

Targeting Sequences on Cargo Proteins Make Specific Molecular Contacts with Coat Proteins588

Rab GTPases Control Docking of Vesicles on Target Membranes589

Paired Sets of SNARE Proteins Mediate Fusion of Vesicles with Target Membranes591

Dissociation of SNARE Complexes After Membrane Fusion Is Driven by ATP Hydrolysis591

14.3 Early Stages of the Secretory Pathway592

COPII Vesicles Mediate Transport from the ER to the Golgi592

COPI Vesicles Mediate Retrograde Transport within the Golgi and from the Golgi to the ER594

Anterograde Transport Through the Golgi Occurs by Cisternal Maturation595

14.4 Later Stages of the Secretory Pathway597

Vesicles Coated with Clathrin and/or Adapter Proteins Mediate Several Transport Steps598

Dynamin Is Required for Pinching Off of Clathrin Vesicles599

Mannose 6-Phosphate Residues Target Soluble Proteins to Lysosomes600

Study of Lysosomal Storage Diseases Revealed Key Components of the Lysosomal Sorting Pathway602

Protein Aggregation in the trans-Golgi May Function in Sorting Proteins to Regulated Secretory Vesicles602

Some Proteins Undergo Proteolytic Processing After Leaving the trans-Golgi603

Several Pathways Sort Membrane Proteins to the Apical or Basolateral Region of Polarized Cells604

14.5 Receptor-Mediated Endocytosis606

Cells Take Up Lipids from the Blood in the Form of Large，Well-Defined Lipoprotein Complexes606

Receptors for Low-Density Lipoprotein and Other Ligands Contain Sorting Signals That Target Them for Endocytosis608

The Acidic pH of Late Endosomes Causes Most Receptor-Ligand Complexes to Dissociate610

The Endocytic Pathway Delivers Iron to Cells without Dissociation of the Receptor-Transferrin Complex in Endosomes611

14.6 Directing Membrane Proteins and Cytosolic Materials to the Lysosome612

Multivesicular Endosomes Segregate Membrane Proteins Destined for the Lysosomal Membrane from Proteins Destined for Lysosomal Degradation612

Retroviruses Bud from the Plasma Membrane by a Process Similar to Formation of Multivesicular Endosomes614

CLASSIC EXPERIMENT 14.1 Following a Protein Out of the Cell621

15 CELL SIGNALING Ⅰ：SIGNAL TRANSDUCTION AND SHORT-TERM CELLULAR RESPONSES623

15.1 From Extracellular Signal to Cellular Response625

Signaling Cells Produce and Release Signaling Molecules625

Signaling Molecules Can Act Locally or at a Distance625

Binding of Signaling Molecules Activates Receptors on Target Cells626

15.2 Studying Cell-Surface Receptors627

Receptor Proteins Bind Ligands Specifically627

The Dissociation Constant Is a Measure of the Affinity of a Receptor for Its Ligand628

Binding Assays Are Used to Detect Receptors and Determine Their Affinities for Ligands628

Maximal Cellular Response to a Signaling Molecule Usually Does Not Require Activation of All Receptors629

Sensitivity of a Cell to External Signals Is Determined by the Number of Surface Receptors and Their Affinity for Ligand631

Receptors Can Be Purified by Affinity Techniques631

Receptors Are Frequently Expressed from Cloned Genes631

15.3 Highly Conserved Components of Intracellular Signal-Transduction Pathways632

GTP-Binding Proteins Are Frequently Used As On/Off Switches633

Protein Kinases and Phosphatases are Employed in Virtually All Signaling Pathways634

Second Messengers Carry and Amplify Signals from Many Receptors634

15.4 General Elements of G Protein-Coupled Receptor Systems635

G Protein-Coupled Receptors Are a Large and Diverse Family with a Common Structure and Function635

G Protein-Coupled Receptors Activate Exchange of GTP for GDP on the α Subunit of a Trimeric G Protein637

Different G Proteins Are Activated by Different GPCRs and In Turn Regulate Different Effector Proteins639

15.5 G Protein-Coupled Receptors That Regulate Ion Channels640

Acetylcholine Receptors in the Heart Muscle Activate a G Protein That Opens K＋ Channels641

Light Activates Gαt-Coupled Rhodopsins641

Activation of Rhodopsin Induces Closing of cGMP-Gated Cation Channels642

Rod Cells Adapt to Varying Levels of Ambient Light Because of Opsin Phosphorylation and Binding of Arrestin644

15.6 G Protein-Coupled Receptors That Activate or Inhibit Adenylyl Cyclase646

Adenylyl Cyclase Is Stimulated and Inhibited by Different Receptor-Ligand Complexes646

Structural Studies Established How Gαs·GTP Binds to and Activates Adenylyl Cyclase646

cAMP Activates Protein Kinase A by Releasing Catalytic Subunits647

Glycogen Metabolism Is Regulated by Hormone-Induced Activation of Protein Kinase A648

cAMP-Mediated Activation of Protein Kinase A Produces Diverse Responses in Different Cell Types649

Signal Amplification Commonly Occurs in Many Signaling Pathways650

Several Mechanisms Down-Regulate Signaling from G Protein-Coupled Receptors651

Anchoring Proteins Localize Effects of cAMP to Specific Regions of the Cell652

15.7 G Protein-Coupled Receptors That Activate Phospholipase C653

Phosphorylated Derivatives of Inositol Are Important Second Messengers654

Calcium Ion Release from the Endoplasmic Reticulum is Triggered by IP3654

The Ca 2＋/Calmodulin Complex Mediates Many Cellular Responses to External Signals655

Diacylglycerol（DAG） Activates Protein Kinase C，Which Regulates Many Other Proteins656

Signal-Induced Relaxation of Vascular Smooth Muscle Is Mediated by cGMP-Activated Protein Kinase G656

15.8 Integrating Responses of Cells to Environmental Influences657

Integration of Multiple Second Messengers Regulates Glycogenolysis657

Insulin and Glucagon Work Together to Maintain a Stable Blood Glucose Level658

CLASSIC EXPERIMENT 15.1 The Infancy of Signal Transduction—GTP Stimulation of cAMP Synthesis663

16 CELL-SIGNALING Ⅱ：SIGNALING PATHWAYS THAT CONTROL GENE ACTIVITY665

16.1 TGFβ Receptors and the Direct Activation of Smads668

A TGFβ Signaling Molecule Is Formed by Cleavage of an Inactive Precursor668

Radioactive Tagging Was Used to Identify TGFβ Receptors669

Activated TGFβ Receptors Phosphorylate Smad Transcription Factors670

Negative Feedback Loops Regulate TGFβ/Smad Signaling671

Loss of TGFβ Signaling Plays a Key Role in Cancer671

16.2 Cytokine Receptors and the JAK/STAT Pathway672

Cytokines Influence Development of Many Cell Types672

Cytokine Receptors Have Similar Structures and Activate Similar Signaling Pathways673

JAK Kinases Activate STAT Transcription Factors674

Complementation Genetics Revealed That JAK and STAT Proteins Transduce Cytokine Signals677

Signaling from Cytokine Receptors Is Regulated by Negative Signals678

Mutant Erythropoietin Receptor That Cannot Be Turned Off Leads to Increased Numbers of Erythrocytes679

16.3 Receptor Tyrosine Kinases679

Ligand Binding Leads to Phosphorylation and Activation of Intrinsic Kinase in RTKs680

Overexpression of HER2，a Receptor Tyrosine Kinase，Occurs in Some Breast Cancers680

Conserved Domains Are Important for Binding Signal-Transduction Proteins to Activated Receptors682

Down-regulation of RTK Signaling Occurs by Endocytosis and Lysosomal Degradation683

16.4 Activation of Ras and MAP Kinase Pathways684

Ras，a GTPase Switch Protein，Cycles Between Active and Inactive States685

Receptor Tyrosine Kinases Are Linked to Ras by Adapter Proteins685

Genetic Studies in Drosophila Identified Key Signal-Transducing Proteins in the Ras/MAP Kinase Pathway685

Binding of Sos Protein to Inactive Ras Causes a Conformational Change That Activates Ras687

Signals Pass from Activated Ras to a Cascade of Protein Kinases688

MAP Kinase Regulates the Activity of Many Transcription Factors Controlling Early-Response Genes690

G Protein-Coupled Receptors Transmit Signals to MAP Kinase in Yeast Mating Pathways691

Scaffold Proteins Separate Multiple MAP Kinase Pathways in Eukaryotic Cells692

The Ras/MAP Kinase Pathway Can Induce Diverse Cellular Responses693

16.5 Phosphoinositides as Signal Transducers694

Phospholipase Cγ Is Activated by Some RTKs and Cytokine Receptors694

Recruitment of PI-3 Kinase to Hormone-Stimulated Receptors Leads to Synthesis of Phosphorylated Phosphatidylinositols694

Accumulation of PI 3-Phosphates in the Plasma Membrane Leads to Activation of Several Kinases695

Activated Protein Kinase B Induces Many Cellular Responses696

The PI-3 Kinase Pathway Is Negatively Regulated by PTEN Phosphatase697

16.6 Activation of Gene Transcription by Seven-Spanning Cell-Surface Receptors697

CREB Links cAMP and Protein Kinase A to Activation of Gene Transcription698

GPCR-Bound Arrestin Activates Several Kinase Cascades698

Wnt Signals Trigger Release of a Transcription Factor from Cytosolic Protein Complex699

Hedgehog Signaling Relieves Repression of Target Genes700

16.7 Pathways That Involve Signal-Induced Protein Cleavage703

Degradation of an Inhibitor Protein Activates the NF-κB Transcription Factors703

Ligand-Activated Notch Is Cleaved Twice，Releasing a Transcription Factor705

Matrix Metal loproteases Catalyze Cleavage of Many Signaling Proteins from the Cell Surface706

Inappropriate Cleavage of Amyloid Precursor Protein Can Lead to Alzheimer’s Disease706

Regulated Intramembrane Proteolysis of SREBP Releases a Transcription Factor That Acts to Maintain Phospholipid and Cholesterol Levels707

17 CELL ORGANIZATION AND MOVEMENT Ⅰ：MICROFILAMENTS713

17.1 Microfilaments and Actin Structures716

Actin Is Ancient，Abundant，and Highly Conserved717

G-Actin Monomers Assemble into Long，Helical F-Actin Polymers717

F-Actin Has Structural and Functional Polarity718

17.2 Dynamics of Actin Filaments718

Actin Polymerization in Vitro Proceeds in Three Steps719

Actin Filaments Grow Faster at（＋） Ends Than at（-） Ends720

Actin Filament Treadmilling Is Accelerated by Profilin and Cofilin721

Thymosin-β4 Provides a Reservoir of Actin for Polymerization722

Capping Proteins Block Assembly and Disassembly at Actin Filament Ends722

17.3 Mechanisms of Actin Filament Assembly723

Formins Assemble Unbranched Filaments723

The Arp2/3 Complex Nucleates Branched Filament Assembly724

Intracellular Movements Can Be Powered by Actin Polymerization726

Toxins That Perturb the Pool of Actin Monomers Are Useful for Studying Actin Dynamics726

17.4 Organization of Actin-Based Cellular Structures728

Cross-Linking Proteins Organize Actin Filaments into Bundles or Networks728

Adaptor Proteins Link Actin Filaments to Membranes728

17.5 Myosins：Actin-Based Motor Proteins731

Myosins Have Head，Neck，and Tail Domains with Distinct Functions732

Myosins Make Up a Large Family of Mechanochemical Motor Proteins733

Conformational Changes in the Myosin Head Couple ATP Hydrolysis to Movement736

Myosin Heads Take Discrete Steps Along Actin Filaments736

Myosin V Walks Hand Over Hand Down an Actin Filament737

17.6 Myosin-Powered Movements738

Myosin Thick Filaments and Actin Thin Filaments in Skeletal Muscle Slide Past One Another During Contraction738

Skeletal Muscle Is Structured by Stabilizing and Scaffolding Proteins740

Contraction of Skeletal Muscle Is Regulated by Ca 2＋ and Actin-Binding Proteins740

Actin and Myosin Ⅱ Form Contractile Bundles in Nonmuscle Cells741

Myosin-Dependent Mechanisms Regulate Contraction in Smooth Muscle and Nonmuscle Cells742

Myosin-V-Bound Vesicles Are Carried Along Actin Filaments743

17.7 Cell Migration：Signaling and Chemotaxis745

Cell Migration Coordinates Force Generation with Cell Adhesion and Membrane Recycling745

The Small GTP-Binding Proteins Cdc42，Rac，and Rho Control Actin Organization747

Cell Migration Involves the Coordinate Regulation of Cdc42，Rac，and Rho748

Migrating Cells Are Steered by Chemotactic Molecules750

Chemotactic Gradients Induce Altered Phosphoinositide Levels Between the Front and Back of a Cell750

CLASSIC EXPERIMENT 17.1 Looking at Muscle Contraction755

18 CELL ORGANIZATION AND MOVEMENT Ⅱ：MICROTUBULES AND INTERMEDIATE FILAMENTS757

18.1 Microtubule Structure and Organization758

Microtubule Walls Are Polarized Structures Built from αβ-Tubulin Dimers758

Microtubules Are Assembled from MTOCs to Generate Diverse Organizations760

18.2 Microtubule Dynamics762

Microtubules Are Dynamic Structures Due to Kinetic Differences at Their Ends763

Individual Microtubules Exhibit Dynamic Instability763

Localized Assembly and “Search-and-Capture” Help Organize Microtubules766

Drugs Affecting Tubulin Polymerization Are Useful Experimentally and to Treat Diseases766

18.3 Regulation of Microtubule Structure and Dynamics767

Microtubules Are Stabilized by Side- and End-Binding Proteins767

Microtubules Are Disassembled by End Binding and Severing Proteins768

18.4 Kinesins and Dyneins：Microtubule- Based Motor Proteins769

Organelles in Axons Are Transported Along Microtubules in Both Directions769

Kinesin-1 Powers Anterograde Transport of Vesicles Down Axons Toward the（＋） End of Microtubules770

Kinesins Form a Large Protein Family with Diverse Functions771

Kinesin-1 Is a Highly Processive Motor772

Dynein Motors Transport Organelles Toward the（-）End of Microtubules774

Kinesins and Dyneins Cooperate in the Transport of Organelles Throughout the Cell775

18.5 Cilia and Flagella：Microtubule-Based Surface Structures777

Eukaryotic Cilia and Flagella Contain Long Doublet Microtubules Bridged by Dynein Motors777

Ciliary and Flagellar Beating Are Produced by Controlled Sliding of Outer Doublet Microtubules778

Intraflagellar Transport Moves Material Up and Down Cilia and Flagella779

Defects in Intraflagellar Transport Cause Disease by Affecting Sensory Primary Cilia780

18.6 Mitosis781

Mitosis Can Be Divided into Six Phases782

Centrosomes Duplicate Early in the Cell Cycle in Preparation for Mitosis783

The Mitotic Spindle Contains Three Classes of Microtubules784

Microtubule Dynamics Increases Dramatically in Mitosis784

Microtubules Treadmill During Mitosis785

The Kinetochore Captures and Helps Transport Chromosomes786

Duplicated Chromosomes Are Aligned by Motors and Treadmilling Microtubules788

Anaphase A Moves Chromosomes to Poles by Microtubule Shortening789

Anaphase B Separates Poles by the Combined Action of Kinesins and Dynein789

Additional Mechanisms Contribute to Spindle Formation789

Cytokinesis Splits the Duplicated Cell in Two789

Plant Cells Reorganize Their Microtubules and Build a New Cell Wall in Mitosis790

18.7 Intermediate Filaments791

Intermediate Filaments Are Assembled from Subunit Dimers792

Intermediate Filaments Proteins Are Expressed in a Tissue-Specific Manner792

Intermediate Filaments Are Dynamic795

Defects in Lamins and Keratins Cause Many Diseases795

18.8 Coordination and Cooperation between Cytoskeletal Elements796

Intermediate Filament-Associated Proteins Contribute to Cellular Organization796

Microfilaments and Microtubules Cooperate to Transport Melanosomes796

Cdc42 Coordinates Microtubules and Microfilaments During Cell Migration797

19 INTEGRATING CELLS INTO TISSUES801

19.1 Cell-Cell and Cell-Matrix Adhesion：An Overview803

Cell-Adhesion Molecules Bind to One Another and to Intracellular Proteins803

The Extracellular Matrix Participates in Adhesion，Signaling，and Other Functions805

The Evolution of Multifaceted Adhesion Molecules Enabled the Evolution of Diverse Animal Tissues807

19.2 Cell-Cell and Cell-ECM Junctions and Their Adhesion Molecules808

Epithelial Cells Have Distinct Apical，Lateral，and Basal Surfaces808

Three Types of Junctions Mediate Many Cell-Cell and Cell-ECM Interactions809

Cadherins Mediate Cell-Cell Adhesions in Adherens Junctions and Desmosomes810

Tight Junctions Seal Off Body Cavities and Restrict Diffusion of Membrane Components814

Integrins Mediate Cell-ECM Adhesions in Epithelial Cells816

Gap Junctions Composed of Connexins Allow Small Molecules to Pass Directly Between Adjacent Cells817

19.3 The Extracellular Matrix Ⅰ：The Basal Lamina820

The Basal Lamina Provides a Foundation for Assembly of Cells into Tissues820

Laminin，a Multiadhesive Matrix Protein，Helps Cross-link Components of the Basal Lamina821

Sheet-Forming Type Ⅳ Collagen Is a Major Structural Component of the Basal Lamina821

Perlecan，a Proteoglycan，Cross-links Components of the Basal Lamina and Cell-Surface Receptors824

19.4 The Extracellular Matrix Ⅱ：Connective and Other Tissues825

Fibrillar Collagens Are the Major Fibrous Proteins in the ECM of Connective Tissues825

Fibrillar Collagen Is Secreted and Assembled into Fibrils Outside of the Cell826

Type Ⅰ and Ⅱ Collagens Associate with Nonfibrillar Collagens to Form Diverse Structures826

Proteoglycans and Their Constituent GAGs Play Diverse Roles in the ECM827

Hyaluronan Resists Compression，Facilitates Cell Migration，and Gives Cartilage Its Gel-like Properties829

Fibronectins Interconnect Cells and Matrix，Influencing Cell Shape，Differentiation，and Movement830

19.5 Adhesive Interactions in Motile and Nonmotile Cells833

Integrins Relay Signals Between Cells and Their Three-Dimensional Environment833

Regulation of Integrin-Mediated Adhesion and Signaling Controls Cell Movement834

Connections Between the ECM and Cytoskeleton Are Defective in Muscular Dystrophy835

IgCAMs Mediate Cell-Cell Adhesion in Neuronal and Other Tissues836

Leukocyte Movement into Tissues Is Orchestrated by a Precisely Timed Sequence of Adhesive Interactions837

19.6 Plant Tissues839

The Plant Cell Wall Is a Laminate of Cellulose Fibrils in a Matrix of Glycoproteins840

Loosening of the Cell Wall Permits Plant Cell Growth840

Plasmodesmata Directly Connect the Cytosols of Adjacent Cells in Higher Plants840

Only a Few Adhesive Molecules Have Been Identified in Plants841

Part Ⅳ Cell Growth and Development847

20 REGULATING THE EUKARYOTIC CELL CYCLE847

20.1 Overview of the Cell Cycle and Its Control849

The Cell Cycle Is an Ordered Series of Events Leading to Cell Replication849

Regulated Protein Phosphorylation and Degradation Control Passage Through the Cell Cycle849

Diverse Experimental Systems Have Been Used to Identify and Isolate Cell-Cycle Control Proteins851

20.2 Control of Mitosis by Cyclins and MPF Activity853

Maturation-Promoting Factor（MPF） Stimulates Meiotic Maturation in Oocytes and Mitosis in Somatic Cells854

Mitotic Cyclin Was First Identified in Early Sea Urchin Embryos856

Cyclin B Levels and Kinase Activity of Mitosis-Promoting Factor（MPF） Change Together in Cycling Xenopus Egg Extracts856

Anaphase-Promoting Complex（APC/C） Controls Degradation of Mitotic Cyclins and Exit from Mitosis858

20.3 Cyclin-Dependent Kinase Regulation During Mitosis859

MPF Components Are Conserved Between Lower and Higher Eukaryotes860

Phosphorylation of the CDK Subunit Regulates the Kinase Activity of MPF861

Conformational Changes Induced by Cyclin Binding and Phosphorylation Increase MPF Activity862

20.4 Molecular Mechanisms for Regulating Mitotic Events864

Phosphorylation of Nuclear Lamins and Other Proteins Promotes Early Mitotic Events864

Unlinking of Sister Chromatids Initiates Anaphase867

Chromosome Decondensation and Reassembly of the Nuclear Envelope Depend on Dephosphorylation of MPF Substrates870

20.5 Cyclin-CDK and Ubiquitin-Protein Ligase Control of S phase872

A Cyclin-Dependent Kinase（CDK） Is Critical for S-Phase Entry in S.cerevisiae872

Three G1 Cyclins Associate with S.cerevisiae CDK to Form S-Phase-Promoting Factors874

Degradation of the S-Phase Inhibitor Triggers DNA Replication876

Multiple Cyclins Regulate the Kinase Activity of S.cerevisiae CDK During Different Cell-Cycle Phases877

Replication at Each Origin Is Initiated Only Once During the Cell Cycle877

20.6 Cell-Cycle Control in Mammalian Cells879

Mammalian Restriction Point Is Analogous to START in Yeast Cells880

Multiple CDKs and Cyclins Regulate Passage of Mammalian Cells Through the Cell Cycle881

Regulated Expression of Two Classes of Genes Returns G0 Mammalian Cells to the Cell Cycle881

Passage Through the Restriction Point Depends on Phosphorylation of the Tumor-Suppressor Rb Protein882

Cyclin A Is Required for DNA Synthesis and CDK1 for Entry into Mitosis883

Two Types of Cyclin-CDK Inhibitors Contribute to Cell-Cycle Control in Mammals883

20.7 Checkpoints in Cell-Cycle Regulation884

The Presence of Unreplicated DNA Prevents Entry into Mitosis888

Improper Assembly of the Mitotic Spindle Prevents the Initiation of Anaphase888

Proper Segregation of Daughter Chromosomes Is Monitored by the Mitotic Exit Network889

Cell-Cycle Arrest of Cells with Damaged DNA Depends on Tumor Suppressors891

20.8 Meiosis：A Special Type of Cell Division892

Key Features Distinguish Meiosis from Mitosis892

Repression of G1 Cyclins and a Meiosis-Specific Protein Kinase Promote Premeiotic S Phase895

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