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Part Ⅰ Chemical and Molecular Foundations1

1 Molecules，Cells，and Model Organisms1

1.1 The Molecules of Life5

Proteins Give Cells Structure and Perform Most Cellular Tasks7

Nucleic Acids Carry Coded Information for Making Proteins at the Right Time and Place7

Phospholipids Are the Conserved Building Blocks of All Cellular Membranes9

1.2 Prokaryotic Cell Structure and Function10

Prokaryotes Comprise Two Kingdoms：Archaea and Eubacteria10

Escherichia coli Is Widely Used in Biological Research11

1.3 Eukaryotic Cell Structure and Function12

The Cytoskeleton Has Many Important Functions12

The Nucleus Contains the DNA Genome，RNA Synthetic Apparatus，and a Fibrous Matrix12

Eukaryotic Cells Contain a Large Number of Internal Membrane Structures14

Mitochondria Are the Principal Sites of ATP Production in Aerobic Cells18

Chloroplasts Contain Internal Compartments in Which Photosynthesis Takes Place18

All Eukaryotic Cells Use a Similar Cycle to Regulate Their Division18

1.4 Unicellular Eukaryotic Model Organisms19

Yeasts Are Used to Study Fundamental Aspects of Eukaryotic Cell Structure and Function19

Mutations in Yeast Led to the Identification of Key Cell Cycle Proteins21

Studies in the Alga Chlamydomonas reinhardtii Led to the Development of a Powerful Technique to Study Brain Function22

The Parasite That Causes Malaria Has Novel Organelles That Allow It to Undergo a Remarkable Life Cycle22

1.5 Metazoan Structure，Differentiation，and Model Organisms24

Multicellularity Requires Cell-Cell and Cell-Matrix Adhesions24

Epithelia Originated Early in Evolution24

Tissues Are Organized into Organs24

Genomics Has Revealed Important Aspects of Metazoan Evolution and Cell Function24

Embryonic Development Uses a Conserved Set of Master Transcription Factors25

Planaria Are Used to Study Stem Cells and Tissue Regeneration27

Invertebrates，Fish，Mice，and Other Organisms Serve as Experimental Systems for Study of Human Development and Disease28

Genetic Diseases Elucidate Important Aspects of Cell Function28

The Following Chapters Present Much Experimental Data That Explains How We Know What We Know About Cell Structure and Function29

2 Chemical Foundations31

2.1 Covalent Bonds and Noncovalent Interactions33

The Electronic Structure of an Atom Determines the Number and Geometry of the 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 Interactions36

Ionic Interactions Are Attractions Between Oppositely Charged Ions36

Hydrogen Bonds Are Noncovalent Interactions That Determine the Water Solubility of Uncharged Molecules37

Van der Waals Interactions Are Weak Attractive Interactions Caused by Transient Dipoles38

The Hydrophobic Effect Causes Nonpolar Molecules to Adhere to One Another39

Molecular Complementarity Due to Noncovalent Interactions Leads to a Lock-and-Key Fit Between Biomolecules40

2.2 Chemical Building Blocks of Cells41

Amino Acids Differing Only in Their Side Chains Compose Proteins42

Five Different Nucleotides Are Used to Build Nucleic Acids45

Monosaccharides Covalently Assemble into Linear and Branched Polysaccharides46

Phospholipids Associate Noncovalently to Form the Basic Bilayer Structure of Biomembranes48

2.3 Chemical Reactions and Chemical Equilibrium51

A Chemical Reaction Is in Equilibrium When the Rates of the Forward and Reverse Reactions Are Equal52

The Equilibrium Constant Reflects the Extent of a Chemical Reaction52

Chemical Reactions in Cells Are at Steady State52

Dissociation Constants of Binding Reactions Reflect the Affinity of Interacting Molecules53

Biological Fluids Have Characteristic pH Values54

Hydrogen Ions Are Released by Acids and Taken Up by Bases55

Buffers Maintain the pH of Intracellular and Extracellular Fluids55

2.4 Biochemical Energetics57

Several Forms of Energy Are Important in Biological Systems57

Cells Can Transform One Type of Energy into Another58

The Change in Free Energy Determines If a Chemical Reaction Will Occur Spontaneously58

The ΔG°’ of a Reaction Can Be Calculated from Its Keq60

The Rate of a Reaction Depends on the Activation Energy Necessary to Energize the Reactants into a Transition State60

Life Depends on the Coupling of Unfavorable Chemical Reactions with Energetically Favorable Ones61

Hydrolysis of ATP Releases Substantial Free Energy and Drives Many Cellular Processes61

ATP Is Generated During Photosynthesis and Respiration62

NAD+ and FAD Couple Many Biological Oxidation and Reduction Reactions63

3 Protein Structure and Function67

3.1 Hierarchical Structure of Proteins69

The Primary Structure of a Protein Is Its Linear Arrangement of Amino Acids69

Secondary Structures Are the Core Elements of Protein Architecture70

Tertiary Structure Is the Overall Folding of a Polypeptide Chain72

There Are Four Broad Structural Categories of Proteins72

Different Ways of Depicting the Conformation of Proteins Convey Different Types of Information74

Structural Motifs Are Regular Combinations of Secondary Structures75

Domains Are Modules of Tertiary Structure76

Multiple Polypeptides Assemble into Quaternary Structures and Supramolecular Complexes78

Comparing Protein Sequences and Structures Provides Insight into Protein Function and Evolution79

3.2 Protein Folding81

Planar Peptide Bonds Limit the Shapes into Which Proteins Can Fold81

The Amino Acid Sequence of a Protein Determines How It Will Fold81

Folding of Proteins in Vivo Is Promoted by Chaperones82

Protein Folding Is Promoted by Proline Isomerases86

Abnormally Folded Proteins Can Form Amyloids That Are Implicated in Diseases87

3.3 Protein Binding and Enzyme Catalysis89

Specific Binding of Ligands Underlies the Functions of Most Proteins89

Enzymes Are Highly Efficient and Specific Catalysts90

An Enzyme’s Active Site Binds Substrates and Carries Out Catalysis91

Serine Proteases Demonstrate How an Enzyme’s Active Site Works92

Enzymes in a Common Pathway Are Often Physically Associated with One Another96

3.4 Regulating Protein Function97

Regulated Synthesis and Degradation of Proteins Is a Fundamental Property of Cells97

The Proteasome Is a Molecular Machine Used to Degrade Proteins97

Ubiquitin Marks Cytosolic Proteins for Degradation in Proteasomes99

Noncovalent Binding Permits Allosteric，or Cooperative，Regulation of Proteins100

Noncovalent Binding of Calcium and GTP Are Widely Used as Allosteric Switches to Control Protein Activity101

Phosphorylation and Dephosphory lation Covalently Regulate Protein Activity102

Ubiquitinylation and Deubiquitinylation Covalently Regulate Protein Activity103

Proteolytic Cleavage Irreversibly Activates or Inactivates Some Proteins104

Higher-Order Regulation Includes Control of Protein Location105

3.5 Purifying，Detecting，and Characterizing Proteins105

Centrifugation Can Separate Particles and Molecules That Differ in Mass or Density106

Electrophoresis Separates Molecules on the Basis of Their Charge-to-Mass Ratio107

Liquid Chromatography Resolves Proteins by Mass，Charge，or Affinity109

Highly Specific Enzyme and Antibody Assays Can Detect Individual Proteins111

Radioisotopes Are Indispensable Tools for Detecting Biological Molecules114

Mass Spectrometry Can Determine the Mass and Sequence of Proteins116

Protein Primary Structure Can Be Determined by Chemical Methods and from Gene Sequences118

Protein Conformation Is Determined by Sophisticated Physical Methods119

3.6 Proteomics122

Proteomics Is the Study of All or a Large Subset of Proteins in a Biological System122

Advanced Techniques in Mass Spectrometry Are Critical to Proteomic Analysis123

4 Culturing and Visualizing Cells129

4.1 Growing and Studying Cells in Culture130

Culture of Animal Cells Requires Nutrient-Rich Media and Special Solid Surfaces130

Primary Cell Cultures and Cell Strains Have a Finite Life Span131

Transformed Cells Can Grow Indefinitely in Culture132

Flow Cytometry Separates Different Cell Types132

Growth of Cells in Two-Dimensional and Three-Dimensional Culture Mimics the In Vivo Environment133

Hybridomas Produce Abundant Monoclonal Antibodies135

A Wide Variety of Cell Biological Processes Can Be Studied with Cultured Cells136

Drugs Are Commonly Used in Cell Biological Research136

4.2 Light Microscopy：Exploring Cell Structure and Visualizing Proteins Within Cells139

The Resolution of the Conventional Light Microscope Is About 0.2 μm139

Phase-Contrast and Differential-Interference-Contrast Microscopy Visualize Unstained Live Cells141

Imaging Subcellular Details Often Requires That Specimens Be Fixed，Sectioned，and Stained142

Fluorescence Microscopy Can Localize and Quantify Specific Molecules in Live Cells143

Intracellular Ion Concentrations Can Be Determined with Ion-Sensitive Fluorescent Dyes143

Immunofluorescence Microscopy Can Detect Specific Proteins in Fixed Cells144

Tagging with Fluorescent Proteins Allows the Visualization of Specific Proteins in Live Cells146

Deconvolution and Confocal Microscopy Enhance Visualization of Three-Dimensional Fluorescent Objects147

Two-Photon Excitation Microscopy Allows Imaging Deep into Tissue Samples149

TIRF Microscopy Provides Exceptional Imaging in One Focal Plane150

FRAP Reveals the Dynamics of Cellular Components151

FRET Measures Distance Between Fluorochromes152

Super-Resolution Microscopy Can Localize Proteins to Nanometer Accuracy153

Light-Sheet Microscopy Can Rapidly Image Cells in Living Tissue155

4.3 Electron Microscopy：High-Resolution Imaging156

Single Molecules or Structures Can Be Imaged Using a Negative Stain or Metal Shadowing157

Cells and Tissues Are Cut into Thin Sections for Viewing by Electron Microscopy158

Immunoelectron Microscopy Localizes Proteins at the Ultrastructural Level159

Cryoelectron Microscopy Allows Visualization of Specimens Without Fixation or Staining160

Scanning Electron Microscopy of Metal-Coated Specimens Reveals Surface Features161

4.4 Isolation of Cell Organelles161

Disruption of Cells Releases Their Organelles and Other Contents162

Centrifugation Can Separate Many Types of Organelles162

Organelle-Specific Antibodies Are Useful in Preparing Highly Purified Organelles162

Proteomics Reveals the Protein Composition of Organelles164

Part Ⅱ Biomembranes，Genes，and Gene Regulation167

5 Fundamental Molecular Genetic Mechanisms167

5.1 Structure of Nucleic Acids169

A Nucleic Acid Strand Is a Linear Polymer with End-to-End Directionality170

Native DNA Is a Double Helix of Complementary Antiparallel Strands170

DNA Can Undergo Reversible Strand Separation172

Torsional Stress in DNA Is Relieved by Enzymes174

Different Types of RNA Exhibit Various Conformations Related to Their Functions174

5.2 Transcription of Protein-Coding Genes and Formation of Functional mRNA176

A Template DNA Strand Is Transcribed into a Complementary RNA Chain by RNA Polymerase176

Organization of Genes Differs in Prokaryotic and Eukaryotic DNA179

Eukaryotic Precursor mRNAs Are Processed to Form Functional mRNAs180

Alternative RNA Splicing Increases the Number of Proteins Expressed from a Single Eukaryotic Gene181

5.3 The Decoding of mRNA by tRNAs183

Messenger RNA Carries Information from DNA in a Three-Letter Genetic Code183

The Folded Structure of tRNA Promotes Its Decoding Functions185

Nonstandard Base Pairing Often Occurs Between Codons and Anticodons186

Amino Acids Become Activated When Covalently Linked to tRNAs188

5.4 Stepwise Synthesis of Proteins on Ribosomes188

Ribosomes Are Protein-Synthesizing Machines188

Methionyl-tRNA i Met Recognizes the AUG Start Codon190

Eukaryotic Translation Initiation Usually Occurs at the First AUG Downstream from the 5’ End of an mRNA191

During Chain Elongation Each Incoming Aminoacyl-tRNA Moves Through Three Ribosomal Sites193

Translation Is Terminated by Release Factors When a Stop Codon Is Reached195

Polysomes and Rapid Ribosome Recycling Increase the Efficiency of Translation195

GTPase-Superfamily Proteins Function in Several Quality-Control Steps of Translation195

Nonsense Mutations Cause Premature Termination of Protein Synthesis196

5.5 DNA Replication197

DNA Polymerases Require a Primer to Initiate Replication197

Duplex DNA Is Unwound，and Daughter Strands Are Formed at the DNA Replication Fork199

Several Proteins Participate in DNA Replication199

DNA Replication Occurs Bidirectionally from Each Origin201

5.6 DNA Repair and Recombination203

DNA Polymerases Introduce Copying Errors and Also Correct Them203

Chemical and Radiation Damage to DNA Can Lead to Mutations203

High-Fidelity DNA Excision-Repair Systems Recognize and Repair Damage204

Base Excision Repairs T-G Mismatches and Damaged Bases205

Mismatch Excision Repairs Other Mismatches and Small Insertions and Deletions205

Nucleotide Excision Repairs Chemical Adducts that Distort Normal DNA Shape206

Two Systems Use Recombination to Repair Double-Strand Breaks in DNA207

Homologous Recombination Can Repair DNA Damage and Generate Genetic Diversity209

5.7 Viruses：Parasites of the Cellular Genetic System212

Most Viral Host Ranges Are Narrow212

Viral Capsids Are Regular Arrays of One or a Few Types of Protein213

Viruses Can Be Cloned and Counted in Plaque Assays213

Lytic Viral Growth Cycles Lead to Death of Host Cells213

Viral DNA Is Integrated into the Host-Cell Genome in Some Nonlytic Viral Growth Cycles216

6 Molecular Genetic Techniques223

6.1 Genetic Analysis of Mutations to Identify and Study Genes224

Recessive and Dominant Mutant Alleles Generally Have Opposite Effects on Gene Function224

Segregation of Mutations in Breeding Experiments Reveals Their Dominance or Recessivity225

Conditional Mutations Can Be Used to Study Essential Genes in Yeast227

Recessive Lethal Mutations in Diploids Can Be Identified by Inbreeding and Maintained in Heterozygotes228

Complementation Tests Determine Whether Different Recessive Mutations Are in the Same Gene229

Double Mutants Are Useful in Assessing the Order in Which Proteins Function230

Genetic Suppression and Synthetic Lethality Can Reveal Interacting or Redundant Proteins231

Genes Can Be Identified by Their Map Position on the Chromosome232

6.2 DNA Cloning and Characterization234

Restriction Enzymes and DNA Ligases Allow Insertion of DNA Fragments into Cloning Vectors234

Isolated DNA Fragments Can Be Cloned into E.coli Plasmid Vectors236

Yeast Genomic Libraries Can Be Constructed with Shuttle Vectors and Screened by Functional Complementation237

cDNA Libraries Represent the Sequences of Protein-Coding Genes238

The Polymerase Chain Reaction Amplifies a Specific DNA Sequence from a Complex Mixture239

Cloned DNA Molecules Can Be Sequenced Rapidly by Methods Based on PCR243

6.3 Using Cloned DNA Fragments to Study Gene Expression246

Hybridization Techniques Permit Detection of Specific DNA Fragments and mRNAs246

DNA Microarrays Can Be Used to Evaluate the Expression of Many Genes at One Time247

Cluster Analysis of Multiple Expression Experiments Identifies Co-regulated Genes248

E.coli Expression Systems Can Produce Large Quantities of Proteins from Cloned Genes249

Plasmid Expression Vectors Can Be Designed for Use in Animal Cells251

6.4 Locating and Identifying Human Disease Genes254

Monogenic Diseases Show One of Three Patterns of Inheritance254

DNA Polymorphisms Are Used as Markers for Linkage Mapping of Human Mutations255

Linkage Studies Can Map Disease Genes with a Resolution of About 1 Centimorgan256

Further Analysis Is Needed to Locate a Disease Gene in Cloned DNA257

Many Inherited Diseases Result from Multiple Genetic Defects257

6.5 Inactivating the Function of Specific Genes in Eukaryotes259

Normal Yeast Genes Can Be Replaced with Mutant Alleles by Homologous Recombination260

Genes Can Be Placed Under the Control of an Experimentally Regulated Promoter260

Specific Genes Can Be Permanently Inactivated in the Germ Line of Mice261

Somatic Cell Recombination Can Inactivate Genes in Specific Tissues261

Dominant-Negative Alleles Can Inhibit the Function of Some Genes262

RNA Interference Causes Gene Inactivation by Destroying the Corresponding mRNA264

Engineered CRISPR-Cas9 Systems Allow Precise Genome Editing266

7 Biomembrane Structure271

7.1 The Lipid Bilayer：Composition and Structural Organization273

Phospholipids Spontaneously Form Bilayers273

Phospholipid Bilayers Form a Sealed Compartment Surrounding an Internal Aqueous Space274

Biomembranes Contain Three Principal Classes of Lipids276

Most Lipids and Many Proteins Are Laterally Mobile in Biomembranes278

Lipid Composition Influences the Physical Properties of Membranes279

Lipid Composition Is Different in the Exoplasmic and Cytosolic Leaflets281

Cholesterol and Sphingolipids Cluster with Specific Proteins in Membrane Microdomains282

Cells Store Excess Lipids in Lipid Droplets283

7.2 Membrane Proteins：Structure and Basic Functions284

Proteins Interact with Membranes in Three Different Ways284

Most Transmembrane Proteins Have Membrane-Spanning α Helices285

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

Covalently Attached Lipids Anchor Some Proteins to Membranes288

All Transmembrane Proteins and Glycolipids Are Asymmetrically Oriented in the Bilayer289

Lipid-Binding Motifs Help Target Peripheral Proteins to the Membrane290

Proteins Can Be Removed from Membranes by Detergents or High-Salt Solutions290

7.3 Phospholipids，Sphingolipids，and Cholesterol：Synthesis and Intracellular Movement293

Fatty Acids Are Assembled from Two-Carbon Building Blocks by Several Important Enzymes293

Small Cytosolic Proteins Facilitate Movement of Fatty Acids293

Fatty Acids Are Incorporated into Phospholipids Primarily on the ER Membrane294

Flippases Move Phospholipids from One Membrane Leaflet to the Opposite Leaflet295

Cholesterol Is Synthesized by Enzymes in the Cytosol and ER Membrane295

Cholesterol and Phospholipids Are Transported Between Organelles by Several Mechanisms296

8 Genes，Genomics，and Chromosomes301

8.1 Eukaryotic Gene Structure303

Most Eukaryotic Genes Contain Introns and Produce mRNAs Encoding Single Proteins303

Simple and Complex Transcription Units Are Found in Eukaryotic Genomes303

Protein-Coding Genes May Be Solitary or Belong to a Gene Family305

Heavily Used Gene Products Are Encoded by Multiple Copies of Genes307

Nonprotein-Coding Genes Encode Functional RNAs308

8.2 Chromosomal Organization of Genes and Noncoding DNA309

Genomes of Many Organisms Contain Nonfunctional DNA309

Most Simple-Sequence DNAs Are Concentrated in Specific Chromosomal Locations310

DNA Fingerprinting Depends on Differences in Length of Simple-Sequence DNAs311

Unclassified Intergenic DNA Occupies a Significant Portion of the Genome312

8.3 Transposable （Mobile） DNA Elements312

Movement of Mobile Elements Involves a DNA or an RNA Intermediate313

DNA Transposons Are Present in Prokaryotes and Eukaryotes314

LTR Retrotransposons Behave Like Intracellular Retroviruses316

Non-LTR Retrotransposons Transpose by a Distinct Mechanism318

Other Retroposed RNAs Are Found in Genomic DNA321

Mobile DNA Elements Have Significantly Influenced Evolution321

8.4 Genomics：Genome-Wide Analysis of Gene Structure and Function323

Stored Sequences Suggest Functions of Newly Identified Genes and Proteins324

Comparison of Related Sequences from Different Species Can Give Clues to Evolutionary Relationships Among Proteins325

Genes Can Be Identified Within Genomic DNA Sequences326

The Number of Protein-Coding Genes in an Organism’s Genome Is Not Directly Related to Its Biological Complexity326

8.5 Structural Organization of Eukaryotic Chromosomes327

Chromatin Exists in Extended and Condensed Forms328

Modifications of Histone Tails Control Chromatin Condensation and Function330

Nonhistone Proteins Organize Long Chromatin Loops335

Additional Nonhistone Proteins Regulate Transcription and Replication339

8.6 Morphology and Functional Elements of Eukaryotic Chromosomes341

Chromosome Number，Size，and Shape at Metaphase Are Species-Specific341

During Metaphase，Chromosomes Can Be Distinguished by Banding Patterns and Chromosome Painting341

Chromosome Painting and DNA Sequencing Reveal the Evolution of Chromosomes342

Interphase Polytene Chromosomes Arise by DNA Amplification343

Three Functional Elements Are Required for Replication and Stable Inheritance of Chromosomes345

Centromere Sequences Vary Greatly in Length and Complexity345

Addition of Telomeric Sequences by Telomerase Prevents Shortening of Chromosomes347

9 Transcriptional Control of Gene Expression353

9.1 Control of Gene Expression in Bacteria356

Transcription Initiation by Bacterial RNA Polymerase Requires Association with a Sigma Factor357

Initiation of lac Operon Transcription Can Be Repressed or Activated357

Small Molecules Regulate Expression of Many Bacterial Genes via DNA-Binding Repressors and Activators358

Transcription Initiation from Some Promoters Requires Alternative Sigma Factors359

Transcription by σ54-RNA Polymerase Is Controlled by Activators That Bind Far from the Promoter359

Many Bacterial Responses Are Controlled by Two-Component Regulatory Systems360

Expression of Many Bacterial Operons Is Controlled by Regulation of Transcriptional Elongation361

9.2 Overview of Eukaryotic Gene Control363

Regulatory Elements in Eukaryotic DNA Are Found Both Close to and Many Kilobases Away from Transcription Start Sites364

Three Eukaryotic RNA Polymerases Catalyze Formation of Different RNAs367

The Largest Subunit in RNA Polymerase Ⅱ Has an Essential Carboxy-Terminal Repeat370

9.3 RNA Polymerase Ⅱ Promoters and General Transcription Factors371

RNA Polymerase Ⅱ Initiates Transcription at DNA Sequences Corresponding to the 5’ Cap of mRNAs371

The TATA Box，Initiators，and CpG Islands Function as Promoters in Eukaryotic DNA371

General Transcription Factors Position RNA Polymerase Ⅱ at Start Sites and Assist in Initiation373

Elongation Factors Regulate the Initial Stages of Transcription in the Promoter-Proximal Region377

9.4 Regulatory Sequences in Protein-Coding Genes and the Proteins Through Which They Function378

Promoter-Proximal Elements Help Regulate Eukaryotic Genes378

Distant Enhancers Often Stimulate Transcription by RNA Polymerase Ⅱ379

Most Eukaryotic Genes Are Regulated by Multiple Transcription-Control Elements379

DNase Ⅰ Footprinting and EMSA Detect Protein-DNA Interactions380

Activators Are Composed of Distinct Functional Domains381

Repressors Are the Functional Converse of Activators383

DNA-Binding Domains Can Be Classified into Numerous Structural Types384

Structurally Diverse Activation and Repression Domains Regulate Transcription386

Transcription Factor Interactions Increase Gene-Control Options387

Multiprotein Complexes Form on Enhancers388

9.5 Molecular Mechanisms of Transcription Repression and Activation390

Formation of Heterochromatin Silences Gene Expression at Telomeres，near Centromeres，and in Other Regions390

Repressors Can Direct Histone Deacetylation at Specific Genes393

Activators Can Direct Histone Acetylation at Specific Genes394

Chromatin-Remodeling Complexes Help Activate or Repress Transcription395

Pioneer Transcription Factors Initiate the Process of Gene Activation During Cellular Differentiation395

The Mediator Complex Forms a Molecular Bridge Between Activation Domains and Pol Ⅱ396

9.6 Regulation of Transcription-Factor Activity398

DNaⅠse Hypersensitive Sites Reflect the Developmental History of Cellular Differentiation398

Nuclear Receptors Are Regulated by Extracellular Signals400

All Nuclear Receptors Share a Common Domain Structure400

Nuclear-Receptor Response Elements Contain Inverted or Direct Repeats400

Hormone Binding to a Nuclear Receptor Regulates Its Activity as a Transcription Factor402

Metazoans Regulate the RNA Polymerase Ⅱ Transition from Initiation to Elongation402

Termination of Transcription Is Also Regulated402

9.7 Epigenetic Regulation of Transcription404

DNA Methylation Represses Transcription404

Methylation of Specific Histone Lysines Is Linked to Epigenetic Mechanisms of Gene Repression405

Epigenetic Control by Polycomb and Trithorax Complexes406

Long Noncoding RNAs Direct Epigenetic Repression in Metazoans409

9.8 Other Eukaryotic Transcription Systems412

Transcription Initiation by Pol Ⅰ and Pol Ⅲ Is Analogous to That by Pol Ⅱ412

10 Post-transcriptional Gene Control417

10.1 Processing of Eukaryotic Pre-mRNA419

The 5’ Cap Is Added to Nascent RNAs Shortly After Transcription Initiation420

A Diverse Set of Proteins with Conserved RNA-Binding Domains Associate with Pre-mRNAs421

Splicing Occurs at Short，Conserved Sequences in Pre-mRNAs via Two Transesterification Reactions423

During Splicing，snRNAs Base-Pair with Pre-mRNA424

Spliceosomes，Assembled from snRNPs and a Pre-mRNA，Carry Out Splicing426

Chain Elongation by RNA Polymerase Ⅱ Is Coupled to the Presence of RNA-Processing Factors428

SR Proteins Contribute to Exon Definition in Long Pre-mRNAs428

Self-Splicing Group Ⅱ Introns Provide Clues to the Evolution of snRNAs429

3’ Cleavage and Polyadenylation of Pre-mRNAs Are Tightly Coupled430

Nuclear Exoribonucleases Degrade RNA That Is Processed Out of Pre-mRNAs432

RNA Processing Solves the Problem of Pervasive Transcription of the Genome in Metazoans432

10.2 Regulation of Pre-mRNA Processing435

Alternative Splicing Generates Transcripts with Different Combinations of Exons435

A Cascade of Regulated RNA Splicing Controls Drosophila Sexual Differentiation435

Splicing Repressors and Activators Control Splicing at Alternative Sites437

RNA Editing Alters the Sequences of Some Pre-mRNAs439

10.3 Transport of mRNA Across the Nuclear Envelope440

Phosphorylation and Dephosphorylation of SR Proteins Imposes Directionality on mRNP Export Across the Nuclear Pore Complex441

Balbiani Rings in Insect Larval Salivary Glands Allow Direct Visualization of mRNP Export Through NPCs442

Pre-mRNAs in Spliceosomes Are Not Exported from the Nucleus443

HIV Rev Protein Regulates the Transport of Unspliced Viral mRNAs444

10.4 Cytoplasmic Mechanisms of Post-transcriptional Control445

Degradation of mRNAs in the Cytoplasm Occurs by Several Mechanisms445

Adenines in mRNAs and IncRNAs May Be Post-transcriptionally Modified by N6 Methylation447

Micro-RNAs Repress Translation and Induce Degradation of Specific mRNAs447

Alternative Polyadenylation Increases miRNA Control Options450

RNA Interference Induces Degradation of Precisely Complementary mRNAs450

Cytoplasmic Polyadenylation Promotes Translation of Some mRNAs451

Protein Synthesis Can Be Globally Regulated452

Sequence-Specific RNA-Binding Proteins Control Translation of Specific mRNAs455

Surveillance Mechanisms Prevent Translation of Improperly Processed mRNAs456

Localization of mRNAs Permits Production of Proteins at Specific Regions Within the Cytoplasm457

10.5 Processing of rRNA and tRNA461

Pre-rRNA Genes Function as Nucleolar Organizers461

Small Nucleolar RNAs Assist in Processing Pre-rRNAs462

Self-Splicing Group Ⅰ Introns Were the First Examples of Catalytic RNA466

Pre-tRNAs Undergo Extensive Modification in the Nucleus466

Nuclear Bodies Are Functionally Specialized Nuclear Domains468

Part Ⅲ Cellular Organization and Function473

11 Transmembrane Transport of Ions and Small Molecules473

11.1 Overview of Transmembrane Transport474

Only Gases and Small Uncharged Molecules Cross Membranes by Simple Diffusion474

Three Main Classes of Membrane Proteins Transport Molecules and Ions Across Cellular Membranes475

11.2 Facilitated Transport of Glucose and Water477

Uniport Transport Is Faster and More Specific than Simple Diffusion477

The Low Km of the GLUT1 Uniporter Enables It to Transport Glucose into Most Mammalian Cells478

The Human Genome Encodes a Family of Sugar-Transporting GLUT Proteins480

Transport Proteins Can Be Studied Using Artificial Membranes and Recombinant Cells480

Osmotic Pressure Causes Water to Move Across Membranes481

Aquaporins Increase the Water Permeability of Cellular Membranes481

11.3 ATP-Powered Pumps and the Intracellular Ionic Environment483

There Are Four Main Classes of ATP-Powered Pumps484

ATP-Powered Ion Pumps Generate and Maintain Ionic Gradients Across Cellular Membranes485

Muscle Relaxation Depends on Ca 2+ ATPases That Pump Ca 2+ from the Cytosol into the Sarcoplasmic Reticulum486

The Mechanism of Action of the Ca 2+ Pump Is Known in Detail486

Calmodulin Regulates the Plasma-Membrane Pumps That Control Cytosolic Ca 2+ Concentrations489

The Na+/K+ ATPase Maintains the Intracellular Na+ and K+ Concentrations in Animal Cells489

V-Class H+ ATPases Maintain the Acidity of Lysosomes and Vacuoles489

ABC Proteins Export a Wide Variety of Drugs and Toxins from the Cell491

Certain ABC Proteins “Flip” Phospholipids and Other Lipid-Soluble Substrates from One Membrane Leaflet to the Other493

The ABC Cystic Fibrosis Transmembrane Regulator Is a Chloride Channel，Not a Pump494

11.4 Nongated Ion Channels and the Resting Membrane Potential495

Selective Movement of Ions Creates a Transmembrane Electric Gradient495

The Resting Membrane Potential in Animal Cells Depends Largely on the Outward Flow of K+ Ions Through Open K+ Channels497

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

Patch Clamps Permit Measurement of Ion Movements Through Single Channels500

Novel Ion Channels Can Be Characterized by a Combination of Oocyte Expression and Patch Clamping501

11.5 Cotransport by Symporters and Antiporters502

Na+ Entry into Mammalian Cells Is Thermodynamically Favored502

Na+-Linked Symporters Enable Animal Cells to Import Glucose and Amino Acids Against High Concentration Gradients503

A Bacterial Na+/Amino Acid Symporter Reveals How Symport Works504

A Na+-Linked Ca 2+ Antiporter Regulates the Strength of Cardiac Muscle Contraction504

Several Cotransporters Regulate Cytosolic pH505

An Anion Antiporter Is Essential for Transport of CO2 by Erythrocytes506

Numerous Transport Proteins Enable Plant Vacuoles to Accumulate Metabolites and Ions507

11.6 Transcellular Transport508

Multiple Transport Proteins Are Needed to Move Glucose and Amino Acids Across Epithelia508

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 pH509

Bone Resorption Requires the Coordinated Function of a V-Class Proton Pump and a Specific Chloride Channel510

12 Cellular Energetics513

12.1 First Step of Harvesting Energy from Glucose：Glycolysis515

During Glycolysis （Stage Ⅰ），Cytosolic Enzymes Convert Glucose to Pyruvate516

The Rate of Glycolysis Is Adjusted to Meet the Cell’s Need for ATP516

Glucose Is Fermented When Oxygen Is Scarce518

12.2 The Structure and Functions of Mitochondria520

Mitochondria Are Multifunctional Organelles520

Mitochondria Have Two Structurally and Functionally Distinct Membranes520

Mitochondria Contain DNA Located in the Matrix523

The Size，Structure，and Coding Capacity of mtDNA Vary Considerably Among Organisms525

Products of Mitochondrial Genes Are Not Exported526

Mitochondria Evolved from a Single Endosymbiotic Event Involving a Rickettsia-Like Bacterium527

Mitochondrial Genetic Codes Differ from the Standard Nuclear Code527

Mutations in Mitochondrial DNA Cause Several Genetic Diseases in Humans528

Mitochondria Are Dynamic Organelles That Interact Directly with One Another528

Mitochondria Are Influenced by Direct Contacts with the Endoplasmic Reticulum529

12.3 The Citric Acid Cycle and Fatty Acid Oxidation533

In the First Part of Stage Ⅱ，Pyruvate Is Converted to Acetyl CoA and High-Energy Electrons533

In the Second Part of Stage Ⅱ，the Citric Acid Cycle Oxidizes the Acetyl Group in Acetyl CoA to CO2 and Generates High-Energy Electrons533

Transporters in the Inner Mitochondrial Membrane Help Maintain Appropriate Cytosolic and Matrix Concentrations of NAD+ and NADH535

Mitochondrial Oxidation of Fatty Acids Generates ATP536

Peroxisomal Oxidation of Fatty Acids Generates No ATP537

12.4 The Electron-Transport Chain and Generation of the Proton-Motive Force539

Oxidation of NADH and FADH2 Releases a Significant Amount of Energy539

Electron Transport in Mitochondria Is Coupled to Proton Pumping539

Electrons Flow “Downhill” Through a Series of Electron Carriers540

Four Large Multiprotein Complexes Couple Electron Transport to Proton Pumping Across the Inner Mitochondrial Membrane542

The Reduction Potentials of Electron Carriers in the Electron-Transport Chain Favor Electron Flow from NADH to O2546

The Multiprotein Complexes of the Electron-Transport Chain Assemble into Supercomplexes546

Reactive Oxygen Species Are By-Products of Electron Transport547

Experiments Using Purified Electron-Transport Chain Complexes Established the Stoichiometry of Proton Pumping549

The Proton-Motive Force in Mitochondria Is Due Largely to a Voltage Gradient Across the Inner Membrane550

12.5 Harnessing the Proton-Motive Force to Synthesize ATP551

The Mechanism of ATP Synthesis Is Shared Among Bacteria，Mitochondria，and Chloroplasts552

ATP Synthase Comprises F 0 and F1 Multiprotein Complexes553

Rotation of the F1 y Subunit，Driven by Proton Movement Through F0，Powers ATP Synthesis554

Multiple Protons Must Pass Through ATP Synthase to Synthesize One ATP555

F 0 c Ring Rotation Is Driven by Protons Flowing Through Transmembrane Channels556

ATP-ADP Exchange Across the Inner Mitochondrial Membrane Is Powered by the Proton-Motive Force556

The Rate of Mitochondrial Oxidation Normally Depends on ADP Levels558

Mitochondria in Brown Fat Use the Proton-Motive Force to Generate Heat558

12.6 Photosynthesis and Light-Absorbing Pigments560

Thylakoid Membranes in Chloroplasts Are the Sites of Photosynthesis in Plants560

Chloroplasts Contain Large DNAs Often Encoding More Than a Hundred Proteins560

Three of the Four Stages in Photosynthesis Occur Only During Illumination561

Photosystems Comprise a Reaction Center and Associated Light-Harvesting Complexes563

Photoelectron Transport from Energized Reaction-Center Chlorophyll a Produces a Charge Separation564

Internal Antennas and Light-Harvesting Complexes Increase the Efficiency of Photosynthesis566

12.7 Molecular Analysis of Photosystems567

The Single Photosystem of Purple Bacteria Generates a Proton-Motive Force but No O2567

Chloroplasts Contain Two Functionally and Spatially Distinct Photosystems567

Linear Electron Flow Through Both Plant Photosystems Generates a Proton-Motive Force，O2，and NADPH568

An Oxygen-Evolving Complex Is Located on the Luminal Surface of the PSII Reaction Center569

Multiple Mechanisms Protect Cells Against Damage from Reactive Oxygen Species During Photoelectron Transport570

Cyclic Electron Flow Through PSI Generates a Proton-Motive Force but No NADPH or O2570

Relative Activities of Photosystems Ⅰ and Ⅱ Are Regulated571

12.8 CO2 Metabolism During Photosynthesis573

Rubisco Fixes CO2 in the Chloroplast Stroma573

Synthesis of Sucrose Using Fixed CO2 Is Completed in the Cytosol573

Light and Rubisco Activase Stimulate CO2 Fixation574

Photorespiration Competes with Carbon Fixation and Is Reduced in C4 Plants576

13 Moving Proteins into Membranes and Organelles583

13.1 Targeting Proteins To and Across the ER Membrane585

Pulse-Chase Experiments with Purified ER Membranes Demonstrated That Secreted Proteins Cross the ER Membrane586

A Hydrophobic N-Terminal Signal Sequence Targets Nascent Secretory Proteins to the ER586

Cotranslational Translocation Is Initiated by Two GTP-Hydrolyzing Proteins588

Passage of Growing Polypeptides Through the Translocon Is Driven by Translation589

ATP Hydrolysis Powers Post-translational Translocation of Some Secretory Proteins in Yeast591

13.2 Insertion of Membrane Proteins into the ER593

Several Topological Classes of Integral Membrane Proteins Are Synthesized on the ER593

Internal Stop-Transfer Anchor and Signal-Anchor Sequences Determine Topology of Single-Pass Proteins594

Multipass Proteins Have Multiple Internal Topogenic Sequences597

A Phospholipid Anchor Tethers Some Cell-Surface Proteins to the Membrane598

The Topology of a Membrane Protein Can Often Be Deduced from Its Sequence599

13.3 Protein Modifications，Folding，and Quality Control in the ER601

A Preformed N-Linked Oligosaccharide Is Added to Many Proteins in the Rough ER601

Oligosaccharide Side Chains May Promote Folding and Stability of Glycoproteins602

Disulfide Bonds Are Formed and Rearranged by Proteins in the ER Lumen603

Chaperones and Other ER Proteins Facilitate Folding and Assembly of Proteins604

Improperly Folded Proteins in the ER Induce Expression of Protein-Folding Catalysts606

Unassembled or Misfolded Proteins in the ER Are Often Transported to the Cytosol for Degradation607

13.4 Targeting of Proteins to Mitochondria and Chloroplasts608

Amphipathic N-Terminal Targeting Sequences Direct Proteins to the Mitochondrial Matrix609

Mitochondrial Protein Import Requires Outer-Membrane Receptors and Translocons in Both Membranes610

Studies with Chimeric Proteins Demonstrate Important Features of Mitochondrial Protein Import612

Three Energy Inputs Are Needed to Import Proteins into Mitochondria613

Multiple Signals and Pathways Target Proteins to Submitochondrial Compartments613

Import of Chloroplast Stromal Proteins Is Similar to Import of Mitochondrial Matrix Proteins617

Proteins Are Targeted to Thylakoids by Mechanisms Related to Bacterial Protein Translocation617

13.5 Targeting of Peroxisomal Proteins619

A Cytosolic Receptor Targets Proteins with an SKL Sequence at the C-Terminus to the Peroxisomal Matrix619

Peroxisomal Membrane and Matrix Proteins Are Incorporated by Different Pathways621

13.6 Transport Into and Out of the Nucleus622

Large and Small Molecules Enter and Leave the Nucleus via Nuclear Pore Complexes622

Nuclear Transport Receptors Escort Proteins Containing Nuclear-Localization Signals into the Nucleus624

A Second Type of Nuclear Transport Receptor Escorts Proteins Containing Nuclear-Export Signals Out of the Nucleus625

Most mRNAs Are Exported from the Nucleus by a Ran-Independent Mechanism627

14 Vesicular Traffic，Secretion，and Endocytosis631

14.1 Techniques for Studying the Secretory Pathway634

Transport of a Protein Through the Secretory Pathway Can Be Assayed in Live Cells634

Yeast Mutants Define Major Stages and Many Components in Vesicular Transport635

Cell-Free Transport Assays Allow Dissection of Individual Steps in Vesicular Transport637

14.2 Molecular Mechanisms of Vesicle Budding and Fusion638

Assembly of a Protein Coat Drives Vesicle Formation and Selection of Cargo Molecules638

A Conserved Set of GTPase Switch Proteins Controls the Assembly of Different Vesicle Coats639

Targeting Sequences on Cargo Proteins Make Specific Molecular Contacts with Coat Proteins641

Rab GTPases Control Docking of Vesicles on Target Membranes641

Paired Sets of SNARE Proteins Mediate Fusion of Vesicles with Target Membranes642

Dissociation of SNARE Complexes After Membrane Fusion Is Driven by ATP Hydrolysis644

14.3 Early Stages of the Secretory Pathway645

COPII Vesicles Mediate Transport from the ER to the Golgi645

COPI Vesicles Mediate Retrograde Transport Within the Golgi and from the Golgi to the ER647

Anterograde Transport Through the Golgi Occurs by Cisternal Maturation648

14.4 Later Stages of the Secretory Pathway650

Vesicles Coated with Clathrin and Adapter Proteins Mediate Transport from the trans-Golgi651

Dynamin Is Required for Pinching Off of Clathrin-Coated Vesicles652

Mannose 6-Phosphate Residues Target Soluble Proteins to Lysosomes653

Study of Lysosomal Storage Diseases Revealed Key Components of the Lysosomal Sorting Pathway655

Protein Aggregation in the trans-Golgi May Function in Sorting Proteins to Regulated Secretory Vesicles655

Some Proteins Undergo Proteolytic Processing After Leaving the trans-Golgi656

Several Pathways Sort Membrane Proteins to the Apical or Basolateral Region of Polarized Cells657

14.5 Receptor-Mediated Endocytosis659

Cells Take Up Lipids from the Blood in the Form of Large，Well-Defined Lipoprotein Complexes659

Receptors for Macromolecular Ligands Contain Sorting Signals That Target Them for Endocytosis660

The Acidic pH of Late Endosomes Causes Most Receptor-Ligand Complexes to Dissociate662

The Endocytic Pathway Delivers Iron to Cells Without Dissociation of the Transferrin-Transferrin Receptor Complex in Endosomes663

14.6 Directing Membrane Proteins and Cytosolic Materials to the Lysosome665

Multivesicular Endosomes Segregate Membrane Proteins Destined for the Lysosomal Membrane from Proteins Destined for Lysosomal Degradation665

Retroviruses Bud from the Plasma Membrane by a Process Similar to Formation of Multivesicular Endosomes666

The Autophagic Pathway Delivers Cytosolic Proteins or Entire Organelles to Lysosomes667

15 Signal Transduction and G protein-Coupled Receptors673

15.1 Signal Transduction：From Extracellular Signal to Cellular Response675

Signaling Molecules Can Act Locally or at a Distance675

Receptors Bind Only a Single Type of Hormone or a Group of Closely Related Hormones676

Protein Kinases and Phosphatases Are Employed in Many Signaling Pathways676

GTP-Binding Proteins Are Frequently Used in Signal Transduction Pathways as On/Off Switches677

Intracellular “Second Messengers” Transmit Signals from Many Receptors678

Signal Transduction Pathways Can Amplify the Effects of Extracellular Signals679

15.2 Studying Cell-Surface Receptors and Signal Transduction Proteins681

The Dissociation Constant Is a Measure of the Affinity of a Receptor for Its Ligand681

Binding Assays Are Used to Detect Receptors and Determine Their Affinity and Specificity for Ligands681

Near-Maximal Cellular Response to a Signaling Molecule Usually Does Not Require Activation of All Receptors682

Sensitivity of a Cell to External Signals Is Determined by the Number of Cell-Surface Receptors and Their Affinity for Ligand683

Hormone Analogs Are Widely Used as Drugs683

Receptors Can Be Purified by Affinity Chromatography Techniques683

Immunoprecipitation Assays and Affinity Techniques Can Be Used to Study the Activity of Signal Transduction Proteins684

15.3 G Protein-Coupled Receptors：Structure and Mechanism686

All G Protein-Coupled Receptors Share the Same Basic Structure686

Ligand-Activated G Protein-Coupled Receptors Catalyze Exchange of GTP for GDP on the α Subunit of a Heterotrimeric G Protein689

Different G Proteins Are Activated by Different GPCRs and In Turn Regulate Different Effector Proteins691

15.4 G Protein-Coupled Receptors That Regulate Ion Channels693

Acetylcholine Receptors in the Heart Muscle Activate a G Protein That Opens K+ Channels693

Light Activates Rhodopsin in Rod Cells of the Eye694

Activation of Rhodopsin by Light Leads to Closing of cGMP-Gated Cation Channels695

Signal Amplification Makes the Rhodopsin Signal Transduction Pathway Exquisitely Sensitive696

Rapid Termination of the Rhodopsin Signal Transduction Pathway Is Essential for the Temporal Resolution of Vision697

Rod Cells Adapt to Varying Levels of Ambient Light by Intracellular Trafficking of Arrestin and Transducin698

15.5 G Protein-Coupled Receptors That Activate or Inhibit Adenylyl Cyclase699

Adenylyl Cyclase Is Stimulated and Inhibited by Different Receptor-Ligand Complexes699

Structural Studies Established How Gαs·GTP Binds to and Activates Adenylyl Cyclase701

cAMP Activates Protein Kinase A by Releasing Inhibitory Subunits701

Glycogen Metabolism Is Regulated by Hormone-Induced Activation of PKA702

cAMP-Mediated Activation of PKA Produces Diverse Responses in Different Cell Types703

Signal Amplification Occurs in the cAMP-PKA Pathway704

CREB Links cAMP and PKA to Activation of Gene Transcription704

Anchoring Proteins Localize Effects of cAMP to Specific Regions of the Cell705

Multiple Mechanisms Suppress Signaling from the GPCR/cAMP/PKA Pathway706

15.6 G Protein-Coupled Receptors That Trigger Elevations in Cytosolic and Mitochondrial Calcium708

Calcium Concentrations in the Mitochondrial Matrix，ER，and Cytosol Can Be Measured with Targeted Fluorescent Proteins709

Activated Phospholipase C Generates Two Key Second Messengers Derived from the Membrane Lipid Phosphatidylinositol 4，5-Bisphosphate709

The Ca 2+-Calmodulin Complex Mediates Many Cellular Responses to External Signals713

DAG Activates Protein Kinase C714

Integration of Ca 2+ and cAMP Second Messengers Regulates Glycogenolysis714

Signal-Induced Relaxation of Vascular Smooth Muscle Is Mediated by a Ca 2+ -Nitric Oxide-cGMP-Activated Protein Kinase G Pathway714

16 Signaling Pathways That Control Gene Expression719

16.1 Receptor Serine Kinases That Activate Smads722

TGF-β Proteins Are Stored in an Inactive Form in the Extracellular Matrix722

Three Separate TGF-β Receptor Proteins Participate in Binding TGF-β and Activating Signal Transduction722

Activated TGF-β Receptors Phosphorylate Smad Transcription Factors724

The Smad3/Smad4 Complex Activates Expression of Different Genes in Different Cell Types724

Negative Feedback Loops Regulate TGF-β/Smad Signaling725

16.2 Cytokine Receptors and the JAK/STAT Signaling Pathway726

Cytokines Influence the Development of Many Cell Types727

Binding of a Cytokine to Its Receptor Activates One or More Tightly Bound JAK Protein Tyrosine Kinases728

Phosphotyrosine Residues Are Binding Surfaces for Multiple Proteins with Conserved Domains730

SH2 Domains in Action：JAK Kinases Activate STAT Transcription Factors731

Multiple Mechanisms Down-Regulate Signaling from Cytokine Receptors731

16.3 Receptor Tyrosine Kinases734

Binding of Ligand Promotes Dimerization of an RTK and Leads to Activation of Its Intrinsic Tyrosine Kinase734

Homo- and Hetero-oligomers of Epidermal Growth Factor Receptors Bind Members of the Epidermal Growth Factor Family735

Activation of the EGF Receptor Results in the Formation of an Asymmetric Active Kinase Dimer736

Multiple Mechanisms Down-Regulate Signaling from RTKs737

16.4 The Ras/MAP Kinase Pathway739

Ras，a GTPase Switch Protein，Operates Downstream of Most RTKs and Cytokine Receptors739

Genetic Studies in Drosophila Identified Key Signal-Transducing Proteins in the Ras/MAP Kinase Pathway739

Receptor Tyrosine Kinases Are Linked to Ras by Adapter Proteins741

Binding of Sos to Inactive Ras Causes a Conformational Change That Triggers an Exchange of GTP for GDP742

Signals Pass from Activated Ras to a Cascade of Protein Kinases Ending with MAP Kinase742

Phosphorylation of MAP Kinase Results in a Conformational Change That Enhances Its Catalytic Activity and Promotes Its Dimerization744

MAP Kinase Regulates the Activity of Many Transcription Factors Controlling Early Response Genes745

G Protein-Coupled Receptors Transmit Signals to MAP Kinase in Yeast Mating Pathways746

Scaffold Proteins Separate Multiple MAP Kinase Pathways in Eukaryotic Cells746

16.5 Phosphoinositide Signaling Pathways748

Phospholipase Cγ Is Activated by Some RTKs and Cytokine Receptors749

Recruitment of PI-3 Kinase to Activated Receptors Leads to Synthesis of Three Phosphorylated Phosphatidylinositols749

Accumulation of PI 3-Phosphates in the Plasma Membrane Leads to Activation of Several Kinases750

Activated Protein Kinase B Induces Many Cellular Responses750

The PI-3 Kinase Pathway Is Negatively Regulated by PTEN Phosphatase751

16.6 Signaling Pathways Controlled by Ubiquitinylation and Protein Degradation：Wnt，Hedgehog，and NF-κB751

Wnt Signaling Triggers Release of a Transcription Factor from a Cytosolic Protein Complex752

Concentration Gradients of Wnt Protein Are Essential for Many Steps in Development753

Hedgehog Signaling Relieves Repression of Target Genes754

Hedgehog Signaling in Vertebrates Requires Primary Cilia757

Degradation of an Inhibitor Protein Activates the NF-κB Transcription Factor757

Polyubiquitin Chains Serve as Scaffolds Linking Receptors to Downstream Proteins in the NF-κB Pathway760

16.7 Signaling Pathways Controlled by Protein Cleavage：Notch/Delta，SREBP，and Alzheimer’s Disease761

On Binding Delta，the Notch Receptor Is Cleaved，Releasing a Component Transcription Factor761

Matrix MetaIloproteases Catalyze Cleavage of Many Signaling Proteins from the Cell Surface763

Inappropriate Cleavage of Amyloid Precursor Protein Can Lead to Alzheimer’s Disease763

Regulated Intramembrane Proteolysis of SREBPs Releases a Transcription Factor That Acts to Maintain Phospholipid and Cholesterol Levels763

16.8 Integration of Cellular Responses to Multiple Signaling Pathways：Insulin Action766

Insulin and Glucagon Work Together to Maintain a Stable Blood Glucose Level766

A Rise in Blood Glucose Triggers Insulin Secretion from the β Islet Cells767

In Fat and Muscle Cells，Insulin Triggers Fusion of Intracellular Vesicles Containing the GLUT4 Glucose Transporter to the Plasma Membrane767

Insulin Inhibits Glucose Synthesis and Enhances Storage of Glucose as Glycogen769

Multiple Signal Transduction Pathways Interact to Regulate Adipocyte Differentiation Through PPARγ，the Master Transcriptional Regulator770

Inflammatory Hormones Cause Derangement of Adipose Cell Function in Obesity770

17 Cell Organization and Movement Ⅰ：Microfilaments775

17.1 Microfilaments and Actin Structures778

Actin Is Ancient，Abundant，and Highly Conserved778

G-Actin Monomers Assemble into Long，Helical F-Actin Polymers779

F-Actin Has Structural and Functional Polarity780

17.2 Dynamics of Actin Filaments781

Actin Polymerization In Vitro Proceeds in Three Steps781

Actin Filaments Grow Faster at （+） Ends Than at （-） Ends782

Actin Filament Treadmilling Is Accelerated by Profilin and Cofilin784

Thymosin-β4 Provides a Reservoir of Actin for Polymerization785

Capping Proteins Block Assembly and Disassembly at Actin Filament Ends785

17.3 Mechanisms of Actin Filament Assembly786

Formins Assemble Unbranched Filaments786

The Arp2/3 Complex Nucleates Branched Filament Assembly787

Intracellular Movements Can Be Powered by Actin Polymerization789

Microfilaments Function in Endocytosis790

Toxins That Perturb the Pool of Actin Monomers Are Useful for Studying Actin Dynamics791

17.4 Organization of Actin-Based Cellular Structures793

Cross-Linking Proteins Organize Actin Filaments into Bundles or Networks793

Adapter Proteins Link Actin Filaments to Membranes793

17.5 Myosins：Actin-Based Motor Proteins796

Myosins Have Head，Neck，and Tail Domains with Distinct Functions797

Myosins Make Up a Large Family of Mechanochemical Motor Proteins798

Conformational Changes in the Myosin Head Couple ATP Hydrolysis to Movement800

Myosin Heads Take Discrete Steps Along Actin Filaments802

17.6 Myosin-Powered Movements803

Myosin Thick Filaments and Actin Thin Filaments in Skeletal Muscle Slide Past Each Other During Contraction803

Skeletal Muscle Is Structured by Stabilizing and Scaffolding Proteins805

Contraction of Skeletal Muscle Is Regulated by Ca 2+ and Actin-Binding Proteins805

Actin and Myosin Ⅱ Form Contractile Bundles in Nonmuscle Cells807

Myosin-Dependent Mechanisms Regulate Contraction in Smooth Muscle and Nonmuscle Cells808

Myosin V-Bound Vesicles Are Carried Along Actin Filaments808

17.7 Cell Migration：Mechanism，Signaling，and Chemotaxis811

Cell Migration Coordinates Force Generation with Cell Adhesion and Membrane Recycling811

The Small GTP-Binding Proteins Cdc42，Rac，and Rho Control Actin Organization813

Cell Migration Involves the Coordinate Regulation of Cdc42，Rac，and Rho815

Migrating Cells Are Steered by Chemotactic Molecules816

18 Cell Organization and Movement Ⅱ：Microtubules and Intermediate Filaments821

18.1 Microtubule Structure and Organization822

Microtubule Walls Are Polarized Structures Built from αβ-Tubulin Dimers822

Microtubules Are Assembled from MTOCs to Generate Diverse Configurations824

18.2 Microtubule Dynamics827

Individual Microtubules Exhibit Dynamic Instability827

Localized Assembly and “Search and Capture” Help Organize Microtubules829

Drugs Affecting Tubulin Polymerization Are Useful Experimentally and in Treatment of Diseases829

18.3 Regulation of Microtubule Structure and Dynamics830

Microtubules Are Stabilized by Side-Binding Proteins830

+TIPs Regulate the Properties and Functions of the Microtubule （+） End831

Other End-Binding Proteins Regulate Microtubule Disassembly832

18.4 Kinesins and Dyneins：Microtubule-Based Motor Proteins833

Organelles in Axons Are Transported Along Microtubules in Both Directions833

Kinesin-1 Powers Anterograde Transport of Vesicles Down Axons Toward the （+） Ends of Microtubules835

The Kinesins Form a Large Protein Superfamily with Diverse Functions835

Kinesin-1 Is a Highly Processive Motor836

Dynein Motors Transport Organelles Toward the （-） Ends of Microtubules838

Kinesins and Dyneins Cooperate in the Transport of Organelles Throughout the Cell841

Tubulin Modifications Distinguish Different Classes of Microtubules and Their Accessibility to Motors842

18.5 Cilia and Flagella：Microtubule-Based Surface Structures844

Eukaryotic Cilia and Flagella Contain Long Doublet Microtubules Bridged by Dynein Motors844

Ciliary and Flagellar Beating Are Produced by Controlled Sliding of Outer Doublet Microtubules844

Intraflagellar Transport Moves Material Up and Down Cilia and Flagella845

Primary Cilia Are Sensory Organelles on Interphase Cells847

Defects in Primary Cilia Underlie Many Diseases848

18.6 Mitosis849

Centrosomes Duplicate Early in the Cell Cycle in Preparation for Mitosis849

Mitosis Can Be Divided into Six Stages850

The Mitotic Spindle Contains Three Classes of Microtubules851

Microtubule Dynamics Increase Dramatically in Mitosis852

Mitotic Asters Are Pushed Apart by Kinesin-5 and Oriented by Dynein853

Chromosomes Are Captured and Oriented During Prometaphase853

Duplicated Chromosomes Are Aligned by Motors and Microtubule Dynamics854

The Chromosomal Passenger Complex Regulates Microtubule Attachment at Kinetochores855

Anaphase A Moves Chromosomes to Poles by Microtubule Shortening857

Anaphase B Separates Poles by the Combined Action of Kinesins and Dynein858

Additional Mechanisms Contribute to Spindle Formation858

Cytokinesis Splits the Duplicated Cell in Two859

Plant Cells Reorganize Their Microtubules and Build a New Cell Wall in Mitosis860

18.7 Intermediate Filaments861

Intermediate Filaments Are Assembled from Subunit Dimers861

Intermediate Filaments Are Dynamic861

Cytoplasmic Intermediate Filament Proteins Are Expressed in a Tissue-Specific Manner862

Lamins Line the Inner Nuclear Envelope To Provide Organization and Rigidity to the Nucleus865

Lamins Are Reversibly Disassembled by Phosphorylation During Mitosis866

18.8 Coordination and Cooperation Between Cytoskeletal Elements867

Intermediate Filament-Associated Proteins Contribute to Cellular Organization867

Microfilaments and Microtubules Cooperate to Transport Melanosomes867

Cdc42 Coordinates Microtubules and Microfilaments During Cell Migration867

Advancement of Neural Growth Cones Is Coordinated by Microfilaments and Microtubules868

19 The Eukaryotic Cell Cycle873

19.1 Overview of the Cell Cycle and Its Control875

The Cell Cycle Is an Ordered Series of Events Leading to Cell Replication875

Cyclin-Dependent Kinases Control the Eukaryotic Cell Cycle876

Several Key Principles Govern the Cell Cycle876

19.2 Model Organisms and Methods of Studying the Cell Cycle877

Budding and Fission Yeasts Are Powerful Systems for Genetic Analysis of the Cell Cycle877

Frog Oocytes and Early Embryos Facilitate Biochemical Characterization of the Cell Cycle Machinery878

Fruit Flies Reveal the Interplay Between Development and the Cell Cycle879

The Study of Tissue Culture Cells Uncovers Cell Cycle Regulation in Mammals880

Researchers Use Multiple Tools to Study the Cell Cycle881

19.3 Regulation of CDK Activity882

Cyclin-Dependent Kinases Are Small Protein Kinases That Require a Regulatory Cyclin Subunit for Their Activity883

Cyclins Determine the Activity of CDKs884

Cyclin Levels Are Primarily Regulated by Protein Degradation885

CDKs Are Regulated by Activating and Inhibitory Phosphorylation886

CDK Inhibitors Control Cyclin-CDK Activity886

Genetically Engineered CDKs Led to the Discovery of CDK Functions887

19.4 Commitment to the Cell Cycle and DNA Replication887

Cells Are Irreversibly Committed to Division at a Cell Cycle Point Called START or the Restriction Point888

The E2F Transcription Factor and Its Regulator Rb Control the G1-S Phase Transition in Metazoans889

Extracellular Signals Govern Cell Cycle Entry889

Degradation of an S Phase CDK Inhibitor Triggers DNA Replication890

Replication at Each Origin Is Initiated Once and Only Once During the Cell Cycle892

Duplicated DNA Strands Become Linked During Replication893

19.5 Entry into Mitosis895

Precipitous Activation of Mitotic CDKs Initiates Mitosis896

Mitotic CDKs Promote Nuclear Envelope Breakdown897

Mitotic CDKs Promote Mitotic Spindle Formation897

Chromosome Condensation Facilitates Chromosome Segregation899

19.6 Completion of Mitosis：Chromosome Segregation and Exit from Mitosis901

Separase-Mediated Cleavage of Cohesins Initiates Chromosome Segregation901

APC/C Activates Separase Through Securin Ubiquitinylation901

Mitotic CDK Inactivation Triggers Exit from Mitosis902

Cytokinesis Creates Two Daughter Cells903

19.7 Surveillance Mechanisms in Cell Cycle Regulation904

Checkpoint Pathways Establish Dependencies and Prevent Errors in the Cell Cycle905

The Growth Checkpoint Pathway Ensures That Cells Enter the Cell Cycle Only After Sufficient Macromolecule Biosynthesis905

The DNA Damage Response System Halts Cell Cycle Progression When DNA Is Compromised905

The Spindle Assembly Checkpoint Pathway Prevents Chromosome Segregation Until Chromosomes Are Accurately Attached to the Mitotic Spindle908

The Spindle Position Checkpoint Pathway Ensures That the Nucleus Is Accurately Partitioned Between Two Daughter Cells909

19.8 Meiosis：A Special Type of Cell Division911

Extracellular and Intracellular Cues Regulate Germ Cell Formation912

Several Key Features Distinguish Meiosis from Mitosis912

Recombination and a Meiosis-Specific Cohesin Subunit Are Necessary for the Specialized Chromosome Segregation in Meiosis Ⅰ915

Co-orienting Sister Kinetochores Is Critical for Meiosis I Chromosome Segregation917

DNA Replication Is Inhibited Between the Two Meiotic Divisions917

Part Ⅳ Cell Growth and Differentiation921

20 Integrating Cells into Tissues921