MOLECULAR BIOLOGY OF THE CELL SIXHTH EDITIONPDF电子书下载

Chapter 1 Cells and Genomes 1

THE UNIVERSAL FEATURES OF CELLS ON EARTH 2

All Cells Store Their Hereditary Information in the Same Linear Chemical Code：DNA 2

All Cells Replicate Their Hereditary Information by Templated Polymerization 3

All Cells Transcribe Portions of Their Hereditary Information into the Same Intermediary Form：RNA 4

All Cells Use Proteins as Catalysts 5

All Cells Translate RNA into Protein in the Same Way 6

Each Protein Is Encoded by a Specific Gene 7

Life Requires Free Energy 8

All Cells Function as Biochemical Factories Dealing with the Same Basic Molecular Building Blocks 8

All Cells Are Enclosed in a Plasma Membrane Across Which Nutrients and Waste Materials Must Pass 8

A Living Cell Can Exist with Fewer Than 500 Genes 9

Summary 10

THE DIVERSITY OF GENOMES AND THE TREE OF LIFE 10

Cells Can Be Powered by a Variety of Free-Energy Sources 10

Some Cells Fix Nitrogen and Carbon Dioxide for Others 12

The Greatest Biochemical Diversity Exists Among Prokaryotic Cells 12

The Tree of Life Has Three Primary Branches：Bacteria，Archaea，and Eukaryotes 14

Some Genes Evolve Rapidly； Others Are Highly Conserved 15

Most Bacteria and Archaea Have 1000-6000 Genes 16

New Genes Are Generated from Preexisting Genes 16

Gene Duplications Give Rise to Families of Related Genes Within a Single Cell 17

Genes Can Be Transferred Between Organisms，Both in the Laboratory and in Nature 18

Sex Results in Horizontal Exchanges of Genetic Information Within a Species 19

The Function of a Gene Can Often Be Deduced from Its Sequence 20

More Than 200 Gene Families Are Common to All Three Primary Branches of the Tree of Life 20

Mutations Reveal the Functions of Genes 21

Molecular Biology Began with a Spotlight on E.coli 22

Summary 22

GENETIC INFORMATION IN EUKARYOTES 23

Eukaryotic Cells May Have Originated as Predators 24

Modern Eukaryotic Cells Evolved from a Symbiosis 25

Eukaryotes Have Hybrid Genomes 27

Eukaryotic Genomes Are Big 28

Eukaryotic Genomes Are Rich in Regulatory DNA 29

The Genome Defines the Program of Multicellular Development 29

Many Eukaryotes Live as Solitary Cells 30

A Yeast Serves as a Minimal Model Eukaryote 30

The Expression Levels of All the Genes of An Organism Can Be Monitored Simultaneously 32

Arabidopsis Has Been Chosen Out of 300，000 Species As a Model Plant 32

The World of Animal Cells Is Represented By a Worm，a Fly，a Fish，a Mouse，and a Human 33

Studies in Drosophila Provide a Key to Vertebrate Development 33

The Vertebrate Genome Is a Product of Repeated Duplications 34

The Frog and the Zebrafish Provide Accessible Models for Vertebrate Development 35

The Mouse Is the Predominant Mammalian Model Organism 35

Humans Report on Their Own Peculiarities 36

We Are All Different in Detail 38

To Understand Cells and Organisms Will Require Mathematics，Computers，and Quantitative Information 38

Summary 39

Problems 39

References 41

Chapter 2 Cell Chemistry and Bioenergetics 43

THE CHEMICAL COMPONENTS OF A CELL 43

Water Is Held Together by Hydrogen Bonds 44

Four Types of Noncovalent Attractions Help Bring Molecules Together in Cells 44

Some Polar Molecules Form Acids and Bases in Water 45

A Cell Is Formed from Carbon Compounds 47

Cells Contain Four Major Families of Small Organic Molecules 47

The Chemistry of Cells Is Dominated by Macromolecules with Remarkable Properties 47

Noncovalent Bonds Specify Both the Precise Shape of a Macromolecule and Its Binding to Other Molecules 49

Summary 50

CATALYSIS AND THE USE OF ENERGY BY CELLS 51

Cell Metabolism Is Organized by Enzymes 51

Biological Order Is Made Possible by the Release of Heat Energy from Cells 52

Cells Obtain Energy by the Oxidation of Organic Molecules 54

Oxidation and Reduction Involve Electron Transfers 55

Enzymes Lower the Activation-Energy Barriers That Block Chemical Reactions 57

Enzymes Can Drive Substrate Molecules Along Specific Reaction Pathways 58

How Enzymes Find Their Substrates：The Enormous Rapidity of Molecular Motions 59

The Free-Energy Change for a Reaction，△G，Determines Whether It Can Occur Spontaneously 60

The Concentration of Reactants Influences the Free-Energy Change and a Reaction’s Direction 61

The Standard Free-Energy Change，△G°，Makes It Possible to Compare the Energetics of Different Reactions 61

The Equilibrium Constant and △G° Are Readily Derived from Each Other 62

The Free-Energy Changes of Coupled Reactions Are Additive 63

Activated Carrier Molecules Are Essential for Biosynthesis 63

The Formation of an Activated Carrier Is Coupled to an Energetically Favorable Reaction 64

ATP Is the Most Widely Used Activated Carrier Molecule 65

Energy Stored in ATP Is Often Harnessed to Join Two Molecules Together 65

NADH and NADPH Are Important Electron Carriers 67

There Are Many Other Activated Carrier Molecules in Cells 68

The Synthesis of Biological Polymers Is Driven by ATP Hydrolysis 70

Summary 73

HOW CELLS OBTAIN ENERGY FROM FOOD 73

Glycolysis Is a Central ATP-Producing Pathway 74

Fermentations Produce ATP in the Absence of Oxygen 75

Glycolysis Illustrates How Enzymes Couple Oxidation to Energy Storage 76

Organisms Store Food Molecules in Special Reservoirs 78

Most Animal Cells Derive Their Energy from Fatty Acids Between Meals 81

Sugars and Fats Are Both Degraded to Acetyl CoA in Mitochondria 81

The Citric Acid Cycle Generates NADH by Oxidizing Acetyl Groups to CO2 82

Electron Transport Drives the Synthesis of the Majority of the ATP in Most Cells 84

Amino Acids and Nucleotides Are Part of the Nitrogen Cycle 85

Metabolism Is Highly Organized and Regulated 87

Summary 88

Problems 88

References 108

Chapter 3 Proteins 109

THE SHAPE AND STRUCTURE OF PROTEINS 109

The Shape of a Protein Is Specified by Its Amino Acid Sequence 109

Proteins Fold into a Conformation of Lowest Energy 114

The α Helix and the β Sheet Are Common Folding Patterns 115

Protein Domains Are Modular Units from Which Larger Proteins Are Built 117

Few of the Many Possible Polypeptide Chains Will Be Useful to Cells 118

Proteins Can Be Classified into Many Families 119

Some Protein Domains Are Found in Many Different Proteins 121

Certain Pairs of Domains Are Found Together in Many Proteins 122

The Human Genome Encodes a Complex Set of Proteins，Revealing That Much Remains Unknown 122

Larger Protein Molecules Often Contain More Than One Polypeptide Chain 123

Some Globular Proteins Form Long Helical Filaments 123

Many Protein Molecules Have Elongated，Fibrous Shapes 124

Proteins Contain a Surprisingly Large Amount of Intrinsically Disordered Polypeptide Chain 125

Covalent Cross-Linkages Stabilize Extracellular Proteins 127

Protein Molecules Often Serve as Subunits for the Assembly of Large Structures 127

Many Structures in Cells Are Capable of Self-Assembly 128

Assembly Factors Often Aid the Formation of Complex Biological Structures 130

Amyloid Fibrils Can Form from Many Proteins 130

Amyloid Structures Can Perform Useful Functions in Cells 132

Many Proteins Contain Low-complexity Domains that Can Form “Reversible Amyloids” 132

Summary 134

PROTEIN FUNCTION 134

All Proteins Bind to Other Molecules 134

The Surface Conformation of a Protein Determines Its Chemistry 135

Sequence Comparisons Between Protein Family Members Highlight Crucial Ligand-Binding Sites 136

Proteins Bind to Other Proteins Through Several Types of Interfaces 137

Antibody Binding Sites Are Especially Versatile 138

The Equilibrium Constant Measures Binding Strength 138

Enzymes Are Powerful and Highly Specific Catalysts 140

Substrate Binding Is the First Step in Enzyme Catalysis 141

Enzymes Speed Reactions by Selectively Stabilizing Transition States 141

Enzymes Can Use Simultaneous Acid and Base Catalysis 144

Lysozyme Illustrates How an Enzyme Works 144

Tightly Bound Small Molecules Add Extra Functions to Proteins 146

Multienzyme Complexes Help to Increase the Rate of Cell Metabolism 148

The Cell Regulates the Catalytic Activities of Its Enzymes 149

Allosteric Enzymes Have Two or More Binding Sites That Interact 151

Two Ligands Whose Binding Sites Are Coupled Must Reciprocally Affect Each Other’s Binding 151

Symmetric Protein Assemblies Produce Cooperative Allosteric Transitions 152

Many Changes in Proteins Are Driven by Protein Phosphorylation 153

A Eukaryotic Cell Contains a Large Collection of Protein Kinases and Protein Phosphatases 154

The Regulation of the Src Protein Kinase Reveals How a Protein Can Function as a Microprocessor 155

Proteins That Bind and Hydrolyze GTP Are Ubiquitous Cell Regulators 156

Regulatory Proteins GAP and GEF Control the Activity of GTP-Binding Proteins by Determining Whether GTP or GDP-Is Bound 157

Proteins Can Be Regulated by the Covalent Addition of Other Proteins 157

An Elaborate Ubiquitin-Conjugating System Is Used to Mark Proteins 158

Protein Complexes with Interchangeable Parts Make Efficient Use of Genetic Information 159

A GTP-Binding Protein Shows How Large Protein Movements Can Be Generated 160

Motor Proteins Produce Large Movements in Cells 161

Membrane-Bound Transporters Harness Energy to Pump Molecules Through Membranes 163

Proteins Often Form Large Complexes That Function as Protein Machines 164

Scaffolds Concentrate Sets of Interacting Proteins 164

Many Proteins Are Controlled by Covalent Modifications That Direct Them to Specific Sites Inside the Cell 165

A Complex Network of Protein Interactions Underlies Cell Function 166

Summary 169

Problems 170

References 172

Chapter 4 DNA，Chromosomes，and Genomes 175

THE STRUCTURE AND FUNCTION OF DNA 175

A DNA Molecule Consists of Two Complementary Chains of Nucleotides 175

The Structure of DNA Provides a Mechanism for Heredity 177

In Eukaryotes，DNA Is Enclosed in a Cell Nucleus 178

Summary 179

CHROMOSOMAL DNA AND ITS PACKAGING IN THE CHROMATIN FIBER 179

EukarYotic DNA Is Packaged into a Set of Chromosomes 180

Chromosomes Contain Long Strings of Genes 182

The Nucleotide Sequence of the Human Genome Shows How Our Genes Are Arranged 183

Each DNA Molecule That Forms a Linear Chromosome Must Contain a Centromere，Two Telomeres，and Replication Origins 185

DNA Molecules Are Highly Condensed in Chromosomes 187

Nucleosomes Are a Basic Unit of Eukaryotic Chromosome Structure 187

The Structure of the Nucleosome Core Particle Reveals How DNA Is Packaged 188

Nucleosomes Have a Dynamic Structure，and Are Frequently Subjected to Changes Catalyzed by ATP-Dependent Chromatin Remodeling Complexes 190

Nucleosomes Are Usually Packed Together into a Compact Chromatin Fiber 191

Summary 193

CHROMATIN STRUCTURE AND FUNCTION 194

Heterochromatin Is Highly Organized and Restricts Gene Expression 194

The Heterochromatic State Is Self-Propagating 194

The Core Histones Are Covalently Modified at Many Different Sites 196

Chromatin Acquires Additional Variety Through the Site-Specific Insertion of a Small Set of Histone Variants 198

Covalent Modifications and Histone Variants Act in Concert to Control Chromosome Functions 198

A Complex of Reader and Writer Proteins Can Spread Specific Chromatin Modifications Along a Chromosome 199

Barrier DNA Sequences Block the Spread of Reader-Writer Complexes and thereby Separate Neighboring Chromatin Domains 202

The Chromatin in Centromeres Reveals How Histone Variants Can Create Special Structures 203

Some Chromatin Structures Can Be Directly Inherited 204

Experiments with Frog Embryos Suggest that both Activating and Repressive Chromatin Structures Can Be Inherited Epigenetically 205

Chromatin Structures Are Important for Eukaryotic Chromosome Function 206

Summary 207

THE GLOBAL STRUCTURE OF CHROMOSOMES 207

Chromosomes Are Folded into Large Loops of Chromatin 207

Polytene Chromosomes Are Uniquely Useful for Visualizing Chromatin Structures 208

There Are Multiple Forms of Chromatin 210

Chromatin Loops Decondense When the Genes Within Them Are Expressed 211

Chromatin Can Move to Specific Sites Within the Nucleus to Alter Gene Expression 212

Networks of Macromolecules Form a Set of Distinct Biochemical Environments inside the Nucleus 213

Mitotic Chromosomes Are Especially Highly Condensed 214

Summary 216

HOW GENOMES EVOLVE 216

Genome Comparisons Reveal Functional DNA Sequences by their Conservation Throughout Evolution 217

Genome Alterations Are Caused by Failures of the Normal Mechanisms for Copying and Maintaining DNA，as well as by Transposable DNA Elements 217

The Genome Sequences of Two Species Differ in Proportion to the Length of Time Since They Have Separately Evolved 218

Phylogenetic Trees Constructed from a Comparison of DNA Sequences Trace the Relationships of All Organisms 219

A Comparison of Human and Mouse Chromosomes Shows How the Structures of Genomes Diverge 221

The Size of a Vertebrate Genome Reflects the Relative Rates of DNA Addition and DNA Loss in a Lineage 222

We Can Infer the Sequence of Some Ancient Genomes 223

Multispecies Sequence Comparisons Identify Conserved DNA Sequences of Unknown Function 224

Changes in Previously Conserved Sequences Can Help Decipher Critical Steps in Evolution 226

Mutations in the DNA Sequences That Control Gene Expression Have Driven Many of the Evolutionary Changes in Vertebrates 227

Gene Duplication Also Provides an Important Source of Genetic Novelty During Evolution 227

Duplicated Genes Diverge 228

The Evolution of the Globin Gene Family Shows How DNA Duplications Contribute to the Evolution of Organisms 229

Genes Encoding New Proteins Can Be Created by the Recombination of Exons 230

Neutral Mutations Often Spread to Become Fixed in a Population，with a Probability That Depends on Population Size 230

A Great Deal Can Be Learned from Analyses of the Variation Among Humans 232

Summary 234

Problems 234

References 236

Chapter 5 DNA Replication，Repair，and Recombination 237

THE MAINTENANCE OF DNA SEQUENCES 237

Mutation Rates Are Extremely Low 237

Low Mutation Rates Are Necessary for Life as We Know It 238

Summary 239

DNA REPLICATION MECHANISMS 239

Base-Pairing Underlies DNA Replication and DNA Repair 239

The DNA Replication Fork Is Asymmetrical 240

The High Fidelity of DNA Replication Requires Several Proofreading Mechanisms 242

Only DNA Replication in the 5’-to-3’Direction Allows Efficient Error Correction 244

A Special Nucleotide-Polymerizing Enzyme Synthesizes Short RNA Primer Molecules on the Lagging Strand 245

Special Proteins Help to Open Up the DNA Double Helix in Front of the Replication Fork 246

A Sliding Ring Holds a Moving DNA Polymerase Onto the DNA 246

The Proteins at a Replication Fork Cooperate to Form a Replication Machine 249

A Strand-Directed Mismatch Repair System Removes Replication Errors That Escape from the Replication Machine 250

DNA Topoisomerases Prevent DNA Tangling During Replication 251

DNA Replication Is Fundamentally Similar in Eukaryotes and Bacteria 253

Summary 254

THE INITIATION AND COMPLETION OF DNA REPLICATION IN CHROMOSOMES 254

DNA Synthesis Begins at Replication Origins 254

Bacterial Chromosomes Typically Have a Single Origin of DNA Replication 255

Eukaryotic Chromosomes Contain Multiple Origins of Replication 256

In Eukaryotes，DNA Replication Takes Place During Only One Part of the Cell Cycle 258

Different Regions on the Same Chromosome Replicate at Distinct Times in S Phase 258

A Large Multisubunit Complex Binds to Eukaryotic Origins of Replication 259

Features of the Human Genome That Specify Origins of Replication Remain to Be Discovered 260

New Nucleosomes Are Assembled Behind the Replication Fork 261

Telomerase Replicates the Ends of Chromosomes 262

Telomeres Are Packaged Into Specialized Structures That Protect the Ends of Chromosomes 263

Telomere Length Is Regulated by Cells and Organisms 264

Summary 265

DNA REPAIR 266

Without DNA Repair，Spontaneous DNA Damage Would Rapidly Change DNA Sequences 267

The DNA Double Helix Is Readily Repaired 268

DNA Damage Can Be Removed by More Than One Pathway 269

Coupling Nucleotide Excision Repair to Transcription Ensures That the Cell’s Most Important DNA Is Efficiently Repaired 271

The Chemistry of the DNA Bases Facilitates Damage Detection 271

Special Translesion DNA Polymerases Are Used in Emergencies 273

Double-Strand Breaks Are Efficiently Repaired 273

DNA Damage Delays Progression of the Cell Cycle 276

Summary 276

HOMOLOGOUS RECOMBINATION 276

Homologous Recombination Has Common Features in All Cells 277

DNA Base-Pairing Guides Homologous Recombination 277

Homologous Recombination Can Flawlessly Repair Double-Strand Breaks in DNA 278

Strand Exchange Is Carried Out by the RecA/Rad51 Protein 279

Homologous Recombination Can Rescue Broken DNA Replication Forks 280

Cells Carefully Regulate the Use of Homologous Recombination in DNA Repair 280

Homologous Recombination Is Crucial for Meiosis 282

Meiotic Recombination Begins with a Programmed Double-Strand Break 282

Holliday Junctions Are Formed During Meiosis 284

Homologous Recombination Produces Both Crossovers and Non-Crossovers During Meiosis 284

Homologous Recombination Often Results in Gene Conversion 286

Summary 286

TRANSPOSITION AND CONSERVATIVE SITE-SPECIFIC RECOMBINATION 287

Through Transposition，Mobile Genetic Elements Can Insert Into Any DNA Sequence 288

DNA-Only Transposons Can Move by a Cut-and-Paste Mechanism 288

Some Viruses Use a Transposition Mechanism to Move Themselves Into Host-Cell Chromosomes 290

Retroviral-like Retrotransposons Resemble Retroviruses，but Lack a Protein Coat 291

A Large Fraction of the Human Genome Is Composed of Nonretroviral Retrotransposons 291

Different Transposable Elements Predominate in Different Organisms 292

Genome Sequences Reveal the Approximate Times at Which Transposable Elements Have Moved 292

Conservative Site-Specific Recombination Can Reversibly Rearrange DNA 292

Conservative Site-Specific Recombination Can Be Used to Turn Genes On or Off 294

Bacterial Conservative Site-Specific Recombinases Have Become Powerful Tools for Cell and Developmental Biologists 294

Summary 295

Problems 296

References 298

Chapter 6 How Cells Read the Genome：From DNA to Protein 299

FROM DNA TO RNA 301

RNA Molecules Are Single-Stranded 302

Transcription Produces RNA Complementary to One Strand of DNA 302

RNA Polymerases Carry Out Transcription 303

Cells Produce Different Categories of RNA Molecules 305

Signals Encoded in DNA Tell RNA Polymerase Where to Startand Stop 306

Transcription Start and Stop Signals Are Heterogeneous in Nucleotide Sequence 307

Transcription Initiation in Eukaryotes Requires Many Proteins 309

RNA Polymerase Ⅱ Requires a Set of General Transcription Factors 310

Polymerase Ⅱ Also Requires Activator，Mediator，and Chromatin-Modifying Proteins 312

Transcription Elongation in Eukaryotes Requires AccessoryProteins 313

Transcription Creates Superhelical Tension 314

Transcription Elongation in Eukaryotes Is Tightly Coupled to RNA Processing 315

RNA Capping Is the First Modification of Eukaryotic Pre-mRNAs 316

RNA Splicing Removes Intron Sequences from Newly Transcribed Pre-mRNAs 317

Nucleotide Sequences Signal Where Splicing Occurs 319

RNA Splicing Is Performed by the Spliceosome 319

The Spliceosome Uses ATP Hydrolysis to Produce a Complex Series of RNA-RNA Rearrangements 321

Other Properties of Pre-mRNA and Its Synthesis Help to Explain the Choice of Proper Splice Sites 321

Chromatin Structure Affects RNA Splicing 323

RNA Splicing Shows Remarkable Plasticity 323

Spliceosome-Catalyzed RNA Splicing Probably Evolved from Self-splicing Mechanisms 324

RNA-Processing Enzymes Generate the 3’End of Eukaryotic mRNAs 324

Mature Eukaryotic mRNAs Are Selectively Exported from the Nucleus 325

Noncoding RNAs Are Also Synthesized and Processed in the Nucleus 327

The Nucleolus Is a Ribosome-Producing Factory 329

The Nucleus Contains a Variety of Subnuclear Aggregates 331

Summary 333

FROM RNA TO PROTEIN 333

An mRNA Sequence Is Decoded in Sets of Three Nucleotides 334

tRNA Molecules Match Amino Acids to Codons in mRNA 334

tRNAs Are Covalently Modified Before They Exit from the Nucleus 336

Specific Enzymes Couple Each Amino Acid to Its Appropriate tRNA Molecule 336

Editing by tRNA Synthetases Ensures Accuracy 338

Amino Acids Are Added to the C-terminal End of a Growing Polypeptide Chain 339

The RNA Message Is Decoded in Ribosomes 340

Elongation Factors Drive Translation Forward and Improve Its Accuracy 343

Many Biological Processes Overcome the Inherent Limitations of Complementary Base-Pairing 345

Accuracy in Translation Requires an Expenditure of Free Energy 345

The Ribosome Is a Ribozyme 346

Nucleotide Sequences in mRNA Signal Where to Start Protein Synthesis 347

Stop Codons Mark the End of Translation 348

Proteins Are Made on Polyribosomes 349

There Are Minor Variations in the Standard Genetic Code 349

Inhibitors of Prokaryotic Protein Synthesis Are Useful as Antibiotics 351

Quality Control Mechanisms Act to Prevent Translation of Damaged mRNAs 351

Some Proteins Begin to Fold While Still Being Synthesized 353

Molecular Chaperones Help Guide the Folding of Most Proteins 354

Cells Utilize Several Types of Chaperones 355

Exposed Hydrophobic Regions Provide Critical Signals for Protein Quality Control 357

The Proteasome Is a Compartmentalized Protease with Sequestered Active Sites 357

Many Proteins Are Controlled by Regulated Destruction 359

There Are Many Steps From DNA to Protein 361

Summary 362

THE RNA WORLD AND THE ORIGINS OF LIFE 362

Single-Stranded RNA Molecules Can Fold into Highly Elaborate Structures 363

RNA Can Both Store Information and Catalyze Chemical Reactions 364

How Did Protein Synthesis Evolve？ 365

All Present-Day Cells Use DNA as Their Hereditary Material 365

Summary 366

Problems 366

References 368

Chapter 7 Control of Gene Expression 369

AN OVERVIEW OF GENE CONTROL 369

The Different Cell Types of a Multicellular Organism Contain the Same DNA 369

Different Cell Types Synthesize Different Sets of RNAs and Proteins 370

External Signals Can Cause a Cell to Change the Expression of Its Genes 372

Gene Expression Can Be Regulated at Many of the Steps in the Pathway from DNA to RNA to Protein 372

Summary 373

CONTROL OF TRANSCRIPTION BY SEQUENCE-SPECIFIC DNA-BINDING PROTEINS 373

The Sequence of Nucleotides in the DNA Double Helix Can Be Read by Proteins 373

Transcription Regulators Contain Structural Motifs That Can Read DNA Sequences 374

Dimerization of Transcription Regulators Increases Their Affinity and Specificity for DNA 375

Transcription Regulators Bind Cooperatively to DNA 378

Nucleosome Structure Promotes Cooperative Binding of Transcription Regulators 379

Summary 380

TRANSCRIPTION REGULATORS SWITCH GENES ON AND OFF 380

The Tryptophan Repressor Switches Genes Off 380

Repressors Turn Genes Off and Activators Turn Them On 381

An Activator and a Repressor Control the Lac Operon 382

DNA Looping Can Occur During Bacterial Gene Regulation 383

Complex Switches Control Gene Transcription in Eukaryotes 384

A Eukaryotic Gene Control Region Consists of a Promoter Plus Many cis-Regulatory Sequences 384

Eukaryotic Transcription Regulators Work in Groups 385

Activator Proteins Promote the Assembly of RNA Polymerase at the Start Point of Transcription 386

Eukaryotic Transcription Activators Direct the Modification of Local Chromatin Structure 386

Transcription Activators Can Promote Transcription by Releasing RNA Polymerase from Promoters 388

Transcription Activators Work Synergistically 388

Eukaryotic Transcription Repressors Can Inhibit Transcription in Several Ways 389

Insulator DNA Sequences Prevent Eukaryotic Transcription Regulators from Influencing Distant Genes 391

Summary 392

MOLECULAR GENETIC MECHANISMS THAT CREATE AND MAINTAIN SPECIALIZED CELL TYPES 392

Complex Genetic Switches That Regulate Drosophila Development Are Built Up from Smaller Molecules 392

The Drosophila Eve Gene Is Regulated by Combinatorial Controls 394

Transcription Regulators Are Brought Into Play by Extracellular Signals 395

Combinatorial Gene Control Creates Many Different Cell Types 396

Specialized Cell Types Can Be Experimentally Reprogrammed to Become Pluripotent Stem Cells 398

Combinations of Master Transcription Regulators Specify Cell Types by Controlling the Expression of Many Genes 398

Specialized Cells Must Rapidly Turn Sets of Genes On and Off 399

Differentiated Cells Maintain Their Identity 400

Transcription Circuits Allow the Cell to Carry Out Logic Operations 402

Summary 404

MECHANISMS THAT REINFORCE CELL MEMORY IN PLANTS AND ANIMALS 404

Patterns of DNA Methylation Can Be Inherited When Vertebrate Cells Divide 404

CG-Rich Islands Are Associated with Many Genes in Mammals 405

Genomic Imprinting Is Based on DNA Methylation 407

Chromosome-Wide Alterations in Chromatin Structure Can Be Inherited 409

Epigenetic Mechanisms Ensure That Stable Patterns of Gene Expression Can Be Transmitted to Daughter Cells 411

Summary 413

POST-TRANSCRIPTIONAL CONTROLS 413

Transcription Attenuation Causes the Premature Termination of Some RNA Molecules 414

Riboswitches Probably Represent Ancient Forms of Gene Control 414

Alternative RNA Splicing Can Produce Different Forms of a Protein from the Same Gene 415

The Definition of a Gene Has Been Modified Since the Discoveryof Alternative RNA Splicing 416

A Change in the Site of RNA Transcript Cleavage and Poly-A Addition Can Change the C-terminus of a Protein 417

RNA Editing Can Change the Meaning of the RNA Message 418

RNA Transport from the Nucleus Can Be Regulated 419

Some mRNAs Are Localized to Specific Regions of the Cytosol 421

The 5’and 3’Untranslated Regions of mRNAs Control Their Translation 422

The Phosphorylation of an Initiation Factor Regulates Protein Synthesis Globally 423

Initiation at AUG Codons Upstream of the Translation Start Can Regulate Eukaryotic Translation Initiation 424

Internal Ribosome Entry Sites Provide Opportunities for Translational Control 425

Changes in mRNA Stability Can Regulate Gene Expression 426

Regulation of mRNA Stability Involves P-bodies and Stress Granules 427

Summary 428

REGULATION OF GENE EXPRESSION BY NONCODING RNAs 429

Small Noncoding RNA Transcripts Regulate Many Animal and Plant Genes Through RNA Interference 429

miRNAs Regulate mRNA Translation and Stability 429

RNA Interference Is Also Used as a Cell Defense Mechanism 431

RNA Interference Can Direct Heterochromatin Formation 432

piRNAs Protect the Germ Line from Transposable Elements 433

RNA Interference Has Become a Powerful Experimental Tool 433

Bacteria Use Small Noncoding RNAs to Protect Themselves from Viruses 433

Long Noncoding RNAs Have Diverse Functions in the Cell 435

Summary 436

Problems 436

References 438

Chapter 8 Analyzing Cells，Molecules，and Systems 439

ISOLATING CELLS AND GROWING THEM IN CULTURE 440

Cells Can Be Isolated from Tissues 440

Cells Can Be Grown in Culture 440

Eukaryotic Cell Lines Are a Widely Used Source of Homogeneous Cells 442

Hybridoma Cell Lines Are Factories That Produce Monoclonal Antibodies 444

Summary 445

PURIFYING PROTEINS 445

Cells Can Be Separated into Their Component Fractions 445

Cell Extracts Provide Accessible Systems to Study Cell Functions 447

Proteins Can Be Separated by Chromatography 448

Immunoprecipitation Is a Rapid Affiinity Purification Method 449

Genetically Engineered Tags Provide an Easy Way to Purify Proteins 450

Purified Cell-free Systems Are Required for the Precise Dissection of Molecular Functions 451

Summary 451

ANALYZING PROTEINS 452

Proteins Can Be Separated by SDS Polyacrylamide-Gel Electrophoresis 452

Two-Dimensional Gel Electrophoresis Provides Greater Protein Separation 452

Specific Proteins Can Be Detected by Blotting with Antibodies 454

Hydrodynamic Measurements Reveal the Size and Shape of a Protein Complex 455

Mass Spectrometry Provides a Highly Sensitive Method for Identifying Unknown Proteins 455

Sets of Interacting Proteins Can Be Identified by Biochemical Methods 457

Optical Methods Can Monitor Protein Interactions 458

Protein Function Can Be Selectively Disrupted With Small Molecules 459

Protein Structure Can Be Determined Using X-Ray Diffraction 460

NMR Can Be Used to Determine Protein Structure in Solution 461

Protein Sequence and Structure Provide Clues About Protein Function 462

Summary 463

ANALYZING AND MANIPULATING DNA 463

Restriction Nucleases Cut Large DNA Molecules into Specific Fragments 464

Gel Electrophoresis Separates DNA Molecules of Different Sizes 465

Purified DNA Molecules Can Be Specifically Labeled with Radioisotopes or Chemical Markers in vitro 467

Genes Can Be Cloned Using Bacteria 467

An Entire Genome Can Be Represented in a DNA Library 469

Genomic and cDNA Libraries Have Different Advantages and Drawbacks 471

Hybridization Provides a Powerful，But Simple Way to Detect Specific Nucleotide Sequences 472

Genes Can Be Cloned in vitro Using PCR 473

PCR Is Also Used for Diagnostic and Forensic Applications 474

Both DNA and RNA Can Be Rapidly Sequenced 477

To Be Useful，Genome Sequences Must Be Annotated 477

DNA Cloning Allows Any Protein to be Produced in Large Amounts 483

Summary 484

STUDYING GENE EXPRESSION AND FUNCTION 485

Classical Genetics Begins by Disrupting a Cell Process by Random Mutagenesis 485

Genetic Screens Identify Mutants with Specific Abnormalities 488

Mutations Can Cause Loss or Gain of Protein Function 489

Complementation Tests Reveal Whether Two Mutations Are in the Same Gene or Different Genes 490

Gene Products Can Be Ordered in Pathways by Epistasis Analysis 490

Mutations Responsible for a Phenotype Can Be Identified Through DNA Analysis 491

Rapid and Cheap DNA Sequencing Has Revolutionized Human Genetic Studies 491

Linked Blocks of Polymorphisms Have Been Passed Down from Our Ancestors 492

Polymorphisms Can Aid the Search for Mutations Associated with Disease 493

Genomics Is Accelerating the Discovery of Rare Mutations That Predispose Us to Serious Disease 493

Reverse Genetics Begins with a Known Gene and Determines Which Cell Processes Require Its Function 494

Animals and Plants Can Be Genetically Altered 495

The Bacterial CRISPR System Has Been Adapted to Edit Genomes in a Wide Variety of Species 497

Large Collections of Engineered Mutations Provide a Tool for Examining the Function of Every Gene in an Organism 498

RNA Interference Is a Simple and Rapid Way to Test Gene Function 499

Reporter Genes Reveal When and Where a Gene Is Expressed 501

In situ Hybridization Can Reveal the Location of mRNAs and Noncoding RNAs 502

Expression of Individual Genes Can Be Measured Using Quantitative RT-PCR 502

Analysis of mRNAs by Microarray or RNA-seq Provides a Snapshot of Gene Expression 503

Genome-wide Chromatin Immunoprecipitation Identifies Sites on the Genome Occupied by Transcription Regulators 505

Ribosome Profiling Reveals Which mRNAs Are Being Translated in the Cell 505

Recombinant DNA Methods Have Revolutionized Human Health 506

Transgenic Plants Are Important for Agriculture 507

Summary 508

MATHEMATICAL ANALYSIS OF CELL FUNCTIONS 509

Regulatory Networks Depend on Molecular Interactions 509

Differential Equations Help Us Predict Transient Behavior 512

Both Promoter Activity and Protein Degradation Affect the Rate of Change of Protein Concentration 513

The Time Required to Reach Steady State Depends on Protein Lifetime 514

Quantitative Methods Are Similar for Transcription Repressors and Activators 514

Negative Feedback Is a Powerful Strategy in Cell Regulation 515

Delayed Negative Feedback Can Induce Oscillations 516

DNA Binding By a Repressor or an Activator Can Be Cooperative 516

Positive Feedback Is Important for Switchlike Responses and Bistability 518

Robustness Is an Important Characteristic of Biological Networks 520

Two Transcription Regulators That Bind to the Same Gene Promoter Can Exert Combinatorial Control 520

An Incoherent Feed-forward Interaction Generates Pulses 522

A Coherent Feed-forward Interaction Detects Persistent Inputs 522

The Same Network Can Behave Differently in Different Cells Due to Stochastic Effects 523

Several Computational Approaches Can Be Used to Model the Reactions in Cells 524

Statistical Methods Are Critical For the Analysis of Biological Data 524

Summary 525

Problems 525

References 528

Chapter 9 Visualizing Cells 529

LOOKING AT CELLS IN THE LIGHT MICROSCOPE 529

The Light Microscope Can Resolve Details 0.2 μm Apart 530

Photon Noise Creates Additional Limits to Resolution When Light Levels Are Low 532

Living Cells Are Seen Clearly in a Phase-Contrast or a Differential-Interference-Contrast Microscope 533

Images Can Be Enhanced and Analyzed by Digital Techniques 534

Intact Tissues Are Usually Fixed and Sectioned Before Microscopy 535

Specific Molecules Can Be Located in Cells by Fluorescence Microscopy 536

Antibodies Can Be Used to Detect Specific Molecules 539

Imaging of Complex Three-Dimensional Objects Is Possible with the Optical Microscope 540

The Confocal Microscope Produces Optical Sections by Excluding Out-of-Focus Light 540

Individual Proteins Can Be Fluorescently Tagged in Living Cells and Organisms 542

Protein Dynamics Can Be Followed in Living Cells 543

Light-Emitting Indicators Can Measure Rapidly Changing Intracellular Ion Concentrations 546

Single Molecules Can Be Visualized by Total Internal Reflection Fluorescence Microscopy 547

Individual Molecules Can Be Touched，Imaged，and Moved Using Atomic Force Microscopy 548

Superresolution Fluorescence Techniques Can Overcome Diffraction-Limited Resolution 549

Superresolution Can Also be Achieved Using Single-Molecule Localization Methods 551

Summary 554

LOOKING AT CELLS AND MOLECULES IN THE ELECTRON MICROSCOPE 554

The Electron Microscope Resolves the Fine Structure of the Cell 554

Biological Specimens Require Special Preparation for Electron Microscopy 555

Specific Macromolecules Can Be Localized by Immunogold Electron Microscopy 556

Different Views of a Single Object Can Be Combined to Give a Three-Dimensional Reconstruction 557

Images of Surfaces Can Be Obtained by Scanning Electron Microscopy 558

Negative Staining and Cryoelectron Microscopy Both Allow Macromolecules to Be Viewed at High Resolution 559

Multiple Images Can Be Combined to Increase Resolution 561

Summary 562

Problems 563

References 564

Chapter 10 Membrane Structure 565

THE LIPID BILAYER 566

Phosphoglycerides，Sphingolipids，and Sterols Are the Major Lipids in Cell Membranes 566

Phospholipids Spontaneously Form Bilayers 568

The Lipid Bilayer Is a Two-dimensional Fluid 569

The Fluidity of a Lipid Bilayer Depends on Its Composition 571

Despite Their Fluidity，Lipid Bilayers Can Form Domains of Different Compositions 572

Lipid Droplets Are Surrounded by a Phospholipid Monolayer 573

The Asymmetry of the Lipid Bilayer Is Functionally Important 573

Glycolipids Are Found on the Surface of All Eukaryotic Plasma Membranes 575

Summary 576

MEMBRANE PROTEINS 576

Membrane Proteins Can Be Associated with the Lipid Bilayer in Various Ways 576

Lipid Anchors Control the Membrane Localization of Some Signaling Proteins 577

In Most Transmembrane Proteins，the Polypeptide Chain Crosses the Lipid Bilayer in an α-Helical Conformation 579

Transmembrane α Helices Often Interact with One Another 580

Some β Barrels Form Large Channels 580

Many Membrane Proteins Are Glycosylated 582

Membrane Proteins Can Be Solubilized and Purified in Detergents 583

Bacteriorhodopsin Is a Light-driven Proton（H＋）Pump That Traverses the Lipid Bilayer as Seven α Helices 586

Membrane Proteins Often Function as Large Complexes 588

Many Membrane Proteins Diffuse in the Plane of the Membrane 588

Cells Can Confine Proteins and Lipids to Specific Domains Within a Membrane 590

The Cortical Cytoskeleton Gives Membranes Mechanical Strength and Restricts Membrane Protein Diffusion 591

Membrane-bending Proteins Deform Bilayers 593

Summary 594

Problems 595

References 596

Chapter 11 Membrane Transport of Small Molecules and the Electrical Properties of Membranes 597

PRINCIPLES OF MEMBRANE TRANSPORT 597

Protein-Free Lipid Bilayers Are Impermeable to Ions 598

There Are Two Main Classes of Membrane Transport Proteins：Transporters and Channels 598

Active Transport Is Mediated by Transporters Coupled to an Energy Source 599

Summary 600

TRANSPORTERS AND ACTIVE MEMBRANE TRANSPORT 600

Active Transport Can Be Driven by Ion-Concentration Gradients 601

Transporters in the Plasma Membrane Regulate Cytosolic pH 604

An Asymmetric Distribution of Transporters in Epithelial Cells Underlies the Transcellular Transport of Solutes 605

There Are Three Classes of ATP-Driven Pumps 606

A P-type ATPase Pumps Ca2＋ into the Sarcoplasmic Reticulum in Muscle Cells 606

The Plasma Membrane Na＋-K＋ Pump Establishes Na＋ and K＋ Gradients Across the Plasma Membrane 607

ABC Transporters Constitute the Largest Family of Membrane Transport Proteins 609

Summary 611

CHANNELS AND THE ELECTRICAL PROPERTIES OF MEMBRANES 611

Aquaporins Are Permeable to Water But Impermeable to Ions 612

Ion Channels Are Ion-Selective and Fluctuate Between Open and Closed States 613

The Membrane Potential in Animal Cells Depends Mainly on K＋Leak Channels and the K＋ Gradient Across the Plasma Membrane 615

The Resting Potential Decays Only Slowly When the Na＋-K＋ Pump Is Stopped 615

The Three-Dimensional Structure of a Bacterial K＋ Channel Shows How an Ion Channel Can Work 617

Mechanosensitive Channels Protect Bacterial Cells Against Extreme Osmotic Pressures 619

The Function of a Neuron Depends on Its Elongated Structure 620

Voltage-Gated Cation Channels Generate Action Potentials in Electrically Excitable Cells 621

The Use of Channelrhodopsins Has Revolutionized the Study of Neural Circuits 623

Myelination Increases the Speed and Efficiency of Action Potential Propagation in Nerve Cells 625

Patch-Clamp Recording Indicates That Individual Ion Channels Open in an All-or-Nothing Fashion 626

Voltage-Gated Cation Channels Are Evolutionarily and Structurally Related 626

Different Neuron Types Display Characteristic Stable Firing Properties 627

Transmitter-Gated Ion Channels Convert Chemical Signals into Electrical Ones at Chemical Synapses 627

Chemical Synapses Can Be Excitatory or Inhibitory 629

The Acetylcholine Receptors at the Neuromuscular Junction Are Excitatory Transmitter-Gated Cation Channels 630

Neurons Contain Many Types of Transmitter-Gated Channels 631

Many Psychoactive Drugs Act at Synapses 631

Neuromuscular Transmission Involves the Sequential Activation of Five Different Sets of Ion Channels 632

Single Neurons Are Complex Computation Devices 633

Neuronal Computation Requires a Combination of at Least Three Kinds of K＋ Channels 634

Long-Term Potentiation（LTP）in the Mammalian Hippocampus Depends on Ca2＋ Entry Through NMDA-Receptor Channels 636

Summary 637

Problems 638

References 640

Chapter 12 Intracellular Compartments and Protein Sorting 641

THE COMPARTMENTALIZATION OF CELLS 641

All Eukaryotic Cells Have the Same Basic Set of Membrane-enclosed Organelles 641

Evolutionary Origins May Help Explain the Topological Relationships of Organelles 643

Proteins Can Move Between Compartments in Different Ways 645

Signal Sequences and Sorting Receptors Direct Proteins to the Correct Cell Address 647

Most Organelles Cannot Be Constructed De Novo：They Require Information in the Organelle Itself 648

Summary 649

THE TRANSPORT OF MOLECULES BETWEEN THE NUCLEUS AND THE CYTOSOL 649

Nuclear Pore Complexes Perforate the Nuclear Envelope 649

Nuclear Localization Signals Direct Nuclear Proteins to the Nucleus 650

Nuclear Import Receptors Bind to Both Nuclear Localization Signals and NPC Proteins 652

Nuclear Export Works Like Nuclear Import，But in Reverse 652

The Ran GTPase Imposes Directionality on Transport Through NPCs 653

Transport Through NPCs Can Be Regulated by Controlling Access to the Transport Machinery 654

During Mitosis the Nuclear Envelope Disassembles 656

Summary 657

THE TRANSPORT OF PROTEINS INTO MITOCHONDRIA AND CHLOROPLASTS 658

Translocation into Mitochondria Depends on Signal Sequences and Protein Translocators 659

Mitochondrial Precursor Proteins Are Imported as Unfolded Polypeptide Chains 660

ATP Hydrolysis and a Membrane Potential Drive Protein Import Into the Matrix Space 661

Bacteria and Mitochondria Use Similar Mechanisms to Insert Porins into their Outer Membrane 662

Transport Into the Inner Mitochondrial Membrane and Intermembrane Space Occurs Via Several Routes 663

Two Signal Sequences Direct Proteins to the Thylakoid Membrane in Chloroplasts 664

Summary 666

PEROXISOMES 666

Peroxisomes Use Molecular Oxygen and Hydrogen Peroxide to Perform Oxidation Reactions 666

A Short Signal Sequence Directs the Import of Proteins into Peroxisomes 667

Summary 669

THE ENDOPLASMIC RETICULUM 669

The ER Is Structurally and Functionally Diverse 670

Signal Sequences Were First Discovered in Proteins Imported into the Rough ER 672

A Signal-Recognition Particle（SRP）Directs the ER Signal Sequence to a Specific Receptor in the Rough ER Membrane 673

The Polypeptide Chain Passes Through an Aqueous Channel in the Translocator 675

Translocation Across the ER Membrane Does Not Always Require Ongoing Polypeptide Chain Elongation 677

In Single-Pass Transmembrane Proteins，a Single Internal ER Signal Sequence Remains in the Lipid Bilayer as a Membrane-spanning α Helix 677

Combinations of Start-Transfer and Stop-Transfer Signals Determine the Topology of Multipass Transmembrane Proteins 679

ER Tail-anchored Proteins Are Integrated into the ER Membrane by a Special Mechanism 682

Translocated Polypeptide Chains Fold and Assemble in the Lumen of the Rough ER 682

Most Proteins Synthesized in the Rough ER Are Glycosylated by the Addition of a Common N-Linked Oligosaccharide 683

Oligosaccharides Are Used as Tags to Mark the State of Protein Folding 685

Improperly Folded Proteins Are Exported from the ER and Degraded in the Cytosol 685

Misfolded Proteins in the ER Activate an Unfolded Protein Response 686

Some Membrane Proteins Acquire a Covalently Attached Glycosylphosphatidylinositol（GPI）Anchor 688

The ER Assembles Most Lipid Bilayers 689

Summary 691

Problems 692

References 694

Chapter 13 Intracellular Membrane Traffic 695

THE MOLECULAR MECHANISMS OF MEMBRANE TRANSPORT AND THE MAINTENANCE OF COMPARTMENTAL DIVERSITY 697

There Are Various Types of Coated Vesicles 697

The Assembly of a Clathrin Coat Drives Vesicle Formation 697

Adaptor Proteins Select Cargo into Clathrin-Coated Vesicles 698

Phosphoinositides Mark Organelles and Membrane Domains 700

Membrane-Bending Proteins Help Deform the Membrane During Vesicle Formation 701

Cytoplasmic Proteins Regulate the Pinching-Off and Uncoating of Coated Vesicles 701

Monomeric GTPases Control Coat Assembly 703

Not All Transport Vesicles Are Spherical 704

Rab Proteins Guide Transport Vesicles to Their Target Membrane 705

Rab Cascades Can Change the Identity of an Organelle 707

SNAREs Mediate Membrane Fusion 708

Interacting SNAREs Need to Be Pried Apart Before They Can Function Again 709

Summary 710

TRANSPORT FROM THE ER THROUGH THE GOLGI APPARATUS 710

Proteins Leave the ER in COPII-Coated Transport Vesicles 711

Only Proteins That Are Properly Folded and Assembled Can Leave the ER 712

Vesicular Tubular Clusters Mediate Transport from the ER to the Golgi Apparatus 712

The Retrieval Pathway to the ER Uses Sorting Signals 713

Many Proteins Are Selectively Retained in the Compartments in Which They Function 714

The Golgi Apparatus Consists of an Ordered Series of Compartments 715

Oligosaccharide Chains Are Processed in the Golgi Apparatus 716

Proteoglycans Are Assembled in the Golgi Apparatus 718

What Is the Purpose of Glycosylation？ 719

Transport Through the Golgi Apparatus May Occur by Cisternal Maturation 720

Golgi Matrix Proteins Help Organize the Stack 721

Summary 722

TRANSPORT FROM THE TRANS GOLGI NETWORK TO LYSOSOMES 722

Lysosomes Are the Principal Sites of Intracellular Digestion 722

Lysosomes Are Heterogeneous 723

Plant and Fungal Vacuoles Are Remarkably Versatile Lysosomes 724

Multiple Pathways Deliver Materials to Lysosomes 725

Autophagy Degrades Unwanted Proteins and Organelles 726

A Mannose 6-Phosphate Receptor Sorts Lysosomal Hydrolases in the Trans Golgi Network 727

Defects in the GIcNAc Phosphotransferase Cause a Lysosomal Storage Disease in Humans 728

Some Lysosomes and Multivesicular Bodies Undergo Exocytosis 729

Summary 729

TRANSPORT INTO THE CELL FROM THE PLASMA MEMBRANE：ENDOCYTOSIS 730

Pinocytic Vesicles Form from Coated Pits in the Plasma Membrane 731

Not All Pinocytic Vesicles Are Clathrin-Coated 731

Cells Use Receptor-Mediated Endocytosis to Import Selected Extracellular Macromolecules 732

Specific Proteins Are Retrieved from Early Endosomes and Returned to the Plasma Membrane 734

Plasma Membrane Signaling Receptors are Down-Regulated by Degradation in Lysosomes 735

Early Endosomes Mature into Late Endosomes 735

ESCRT Protein Complexes Mediate the Formation of Intralumenal Vesicles in Multivesicular Bodies 736

Recycling Endosomes Regulate Plasma Membrane Composition 737

Specialized Phagocytic Cells Can Ingest Large Particles 738

Summary 740

TRANSPORT FROM THE TRANS GOLGI NETWORK TO THE CELL EXTERIOR：EXOCYTOSIS 741

Many Proteins and Lipids Are Carried Automatically from the Trans Golgi Network（TGN）to the Cell Surface 741

Secretory Vesicles Bud from the Trans Golgi Network 742

Precursors of Secretory Proteins Are Proteolytically Processed During the Formation of Secretory Vesicles 743

Secretory Vesicles Wait Near the Plasma Membrane Until Signaled to Release Their Contents 744

For Rapid Exocytosis，Synaptic Vesicles Are Primed at the Presynaptic Plasma Membrane 744

Synaptic Vesicles Can Form Directly from Endocytic Vesicles 746

Secretory Vesicle Membrane Components Are Quickly Removed from the Plasma Membrane 746

Some Regulated Exocytosis Events Serve to Enlarge the Plasma Membrane 748

Polarized Cells Direct Proteins from the Trans Golgi Network to the Appropriate Domain of the Plasma Membrane 748

Summary 750

Problems 750

References 752

Chapter 14 Energy Conversion：Mitochondria and Chloroplasts 753

THE MITOCHONDRION 755

The Mitochondrion Has an Outer Membrane and an Inner Membrane 757

The Inner Membrane Cristae Contain the Machine for Electron Transport and ATP Synthesis 758

The Citric Acid Cycle in the Matrix Produces NADH 758

Mitochondria Have Many Essential Roles in Cellular Metabolism 759

A Chemiosmotic Process Couples Oxidation Energy to ATP Production 761

The Energy Derived from Oxidation Is Stored as an Electrochemical Gradient 762

Summary 763

THE PROTON PUMPS OF THE ELECTRON-TRANSPORT CHAIN 763

The Redox Potential Is a Measure of Electron Affinities 763

Electron Transfers Release Large Amounts of Energy 764

Transition Metal Ions and Quinones Accept and Release Electrons Readily 764

NADH Transfers Its Electrons to Oxygen Through Three Large Enzyme Complexes Embedded in the Inner Membrane 766

The NADH Dehydrogenase Complex Contains Separate Modules for Electron Transport and Proton Pumping 768

Cytochrome c Reductase Takes Up and Releases Protons on the Opposite Side of the Crista Membrane，Thereby Pumping Protons 768

The Cytochrome c Oxidase Complex Pumps Protons and Reduces O2 Using a Catalytic Iron-Copper Center 770

The Respiratory Chain Forms a Supercomplex in the Crista Membrane 772

Protons Can Move Rapidly Through Proteins Along Predefined Pathways 773

Summary 774

ATP PRODUCTION IN MITOCHONDRIA 774

The Large Negative Value of △G for ATP Hydrolysis Makes ATP Useful to the Cell 774

The ATP Synthase Is a Nanomachine that Produces ATP by Rotary Catalysis 776

Proton-driven Turbines Are of Ancient Origin 777

Mitochondrial Cristae Help to Make ATP Synthesis Efficient 778

Special Transport Proteins Exchange ATP and ADP Through the Inner Membrane 779

Chemismotic Mechanisms First Arose in Bacteria 780

Summary 782

CHLOROPLASTS AND PHOTOSYNTHESIS 782

Chloroplasts Resemble Mitochondria But Have a Separate Thylakoid Compartment 782

Chloroplasts Capture Energy from Sunlight and Use It to Fix Carbon 783

Carbon Fixation Uses ATP and NADPH to Convert CO2 into Sugars 784

Sugars Generated by Carbon Fixation Can Be Stored as Starch or Consumed to Produce ATP 785

The Thylakoid Membranes of Chloroplasts Contain the Protein Complexes Required for Photosynthesis and ATP Generation 786

Chlorophyll-Protein Complexes Can Transfer Either Excitation Energy or Electrons 787

A Photosystem Consists of an Antenna Complex and a Reaction Center 788

The Thylakoid Membrane Contains Two Different Photosystems Working in Series 789

Photosystem Ⅱ Uses a Manganese Cluster to Withdraw Electrons From Water 790

The Cytochrome b6-f Complex Connects Photosystem Ⅱ to Photosystem I 791

Photosystem I Carries Out the Second Charge-Separation Step in the Z Scheme 792

The Chloroplast ATP Synthase Uses the Proton Gradient Generated by the Photosynthetic Light Reactions to Produce ATP 793

All Photosynthetic Reaction Centers Have Evolved From a Common Ancestor 793

The Proton-Motive Force for ATP Production in Mitochondria and Chloroplasts Is Essentially the Same 794

Chemiosmotic Mechanisms Evolved in Stages 794

By Providing an Inexhaustible Source of Reducing Power，Photosynthetic Bacteria Overcame a Major Evolutionary Obstacle 796

The Photosynthetic Electron-Transport Chains of Cyanobacteria Produced Atmospheric Oxygen and Permitted New Life-Forms 796

Summary 798

THE GENETIC SYSTEMS OF MITOCHONDRIA AND CHLOROPLASTS 800

The Genetic Systems of Mitochondria and Chloroplasts Resemble Those of Prokaryotes 800

Over Time，Mitochondria and Chloroplasts Have Exported Most of Their Genes to the Nucleus by Gene Transfer 801

The Fission and Fusion of Mitochondria Are Topologically Complex Processes 802

Animal Mitochondria Contain the Simplest Genetic Systems Known 803

Mitochondria Have a Relaxed Codon Usage and Can Have a Variant Genetic Code 804

Chloroplasts and Bacteria Share Many Striking Similarities 806

Organelle Genes Are Maternally Inherited in Animals and Plants 807

Mutations in Mitochondrial DNA Can Cause Severe Inherited Diseases 807

The Accumulation of Mitochondrial DNA Mutations Is a Contributor to Aging 808

Why Do Mitochondria and Chloroplasts Maintain a Costly Separate System for DNA Transcription and Translation？ 808

Summary 809

Problems 809

References 811

Chapter 15 Cell Signaling 813

PRINCIPLES OF CELL SIGNALING 813

Extracellular Signals Can Act Over Short or Long Distances 814

Extracellular Signal Molecules Bind to Specific Receptors 815

Each Cell Is Programmed to Respond to Specific Combinations of Extracellular Signals 816

There Are Three Major Classes of Cell-Surface Receptor Proteins 818

Cell-Surface Receptors Relay Signals Via Intracellular Signaling Molecules 819

Intracellular Signals Must Be Specific and Precise in a Noisy Cytoplasm 820

Intracellular Signaling Complexes Form at Activated Receptors 822

Modular Interaction Domains Mediate Interactions Between Intracellular Signaling Proteins 822

The Relationship Between Signal and Response Varies in Different Signaling Pathways 824

The Speed of a Response Depends on the Turnover of Signaling Molecules 825

Cells Can Respond Abruptly to a Gradually Increasing Signal 827

Positive Feedback Can Generate an All-or-None Response 828

Negative Feedback is a Common Motif in Signaling Systems 829

Cells Can Adjust Their Sensitivity to a Signal 830

Summary 831

SIGNALING THROUGH G-PROTEIN-COUPLED RECEPTORS 832

Trimeric G Proteins Relay Signals From GPCRs 832

Some G Proteins Regulate the Production of Cyclic AMP 833

Cyclic-AMP-Dependent Protein Kinase（PKA）Mediates Most of the Effects of Cyclic AMP 834

Some G Proteins Signal Via Phospholipids 836

Ca2＋ Functions as a Ubiquitous Intracellular Mediator 838

Feedback Generates Ca2＋ Waves and Oscillations 838

Ca2＋/Calmodulin-Dependent Protein Kinases Mediate Many Responses to Ca2＋ Signals 840

Some G Proteins Directly Regulate Ion Channels 843

Smell and Vision Depend on GPCRs That Regulate Ion Channels 843

Nitric Oxide Is a Gaseous Signaling Mediator That Passes Between Cells 846

Second Messengers and Enzymatic Cascades Amplify Signals 848

GPCR Desensitization Depends on Receptor Phosphorylation 848

Summary 849

SIGNALING THROUGH ENZYME-COUPLED RECEPTORS 850

Activated Receptor Tyrosine Kinases（RTKs）Phosphorylate Themselves 850

Phosphorylated Tyrosines on RTKs Serve as Docking Sites for Intracellular Signaling Proteins 852

Proteins with SH2 Domains Bind to Phosphorylated Tyrosines 852

The GTPase Ras Mediates Signaling by Most RTKs 854

Ras Activates a MAP Kinase Signaling Module 855

Scaffold Proteins Help Prevent Cross-talk Between Parallel MAP Kinase Modules 857

Rho Family GTPases Functionally Couple Cell-Surface Receptors to the Cytoskeleton 858

PI 3-Kinase Produces Lipid Docking Sites in the Plasma Membrane 859

The PI-3-Kinase-Akt Signaling Pathway Stimulates Animal Cells to Survive and Grow 860

RTKs and GPCRs Activate Overlapping Signaling Pathways 861

Some Enzyme-Coupled Receptors Associate with Cytoplasmic Tyrosine Kinases 862

Cytokine Receptors Activate the JAK-STAT Signaling Pathway 863

Protein Tyrosine Phosphatases Reverse Tyrosine Phosphorylations 864

Signal Proteins of the TGFβ Superfamily Act Through Receptor Serine/Threonine Kinases and Smads 865

Summary 866

ALTERNATIVE SIGNALING ROUTES IN GENE REGULATION 867

The Receptor Notch Is a Latent Transcription Regulatory Protein 867

Wnt Proteins Bind to Frizzled Receptors and Inhibit the Degradation of β-Catenin 868

Hedgehog Proteins Bind to Patched，Relieving Its Inhibition of Smoothened 871

Many Stressful and Inflammatory Stimuli Act Through an NFkB-Dependent Signaling Pathway 873

Nuclear Receptors Are Ligand-Modulated Transcription Regulators 874

Circadian Clocks Contain Negative Feedback Loops That Control Gene Expression 876

Three Proteins in a Test Tube Can Reconstitute a Cyanobacterial Circadian Clock 878

Summary 879

SIGNALING IN PLANTS 880

Multicellularity and Cell Communication Evolved Independently in Plants and Animals 880

Receptor Serine/Threonine Kinases Are the Largest Class of Cell-Surface Receptors in Plants 881

Ethylene Blocks the Degradation of Specific Transcription Regulatory Proteins in the Nucleus 881

Regulated Positioning of Auxin Transporters Patterns Plant Growth 882

Phytochromes Detect Red Light，and Cryptochromes Detect Blue Light 883

Summary 885

Problems 886

References 887

Chapter 16 The Cytoskeleton 889

FUNCTION AND ORIGIN OF THE CYTOSKELETON 889

Cytoskeletal Filaments Adapt to Form Dynamic or Stable Structures 890

The Cytoskeleton Determines Cellular Organization and Polarity 892

Filaments Assemble from Protein Subunits That Impart Specific Physical and Dynamic Properties 893

Accessory Proteins and Motors Regulate Cytoskeletal Filaments 894

Bacterial Cell Organization and Division Depend on Homologs of Eukaryotic Cytoskeletal Proteins 896

Summary 898

ACTIN AND ACTIN-BINDING PROTEINS 898

Actin Subunits Assemble Head-to-Tail to Create Flexible，Polar Filaments 898

Nucleation Is the Rate-Limiting Step in the Formation of Actin Filaments 899

Actin Filaments Have Two Distinct Ends That Grow at Different Rates 900

ATP Hydrolysis Within Actin Filaments Leads to Treadmilling at Steady State 901

The Functions of Actin Filaments Are Inhibited by Both Polymer-stabilizing and Polymer-destabilizing Chemicals 904

Actin-Binding Proteins Influence Filament Dynamics and Organization 904

Monomer Availability Controls Actin Filament Assembly 906

Actin-Nucleating Factors Accelerate Polymerization and Generate Branched or Straight Filaments 906

Actin-Filament-Binding Proteins Alter Filament Dynamics 907

Severing Proteins Regulate Actin Filament Depolymerization 909

Higher-Order Actin Filament Arrays Influence Cellular Mechanical Properties and Signaling 911

Bacteria Can Hijack the Host Actin Cytoskeleton 913

Summary 914

MYOSIN AND ACTIN 915

Actin-Based Motor Proteins Are Members of the Myosin Superfamily 915

Myosin Generates Force by Coupling ATP Hydrolysis to Conformational Changes 916

Sliding of Myosin Ⅱ Along Actin Filaments Causes Muscles to Contract 916

A Sudden Rise in Cytosolic Ca2＋ Concentration Initiates Muscle Contraction 920

Heart Muscle Is a Precisely Engineered Machine 923

Actin and Myosin Perform a Variety of Functions in Non-Muscle Cells 923

Summary 925

MICROTUBULES 925

Microtubules Are Hollow Tubes Made of Protofilaments 926

Microtubules Undergo Dynamic Instability 927

Microtubule Functions Are Inhibited by Both Polymer-stabilizing and Polymer-destabilizing Drugs 929

A Protein Complex Containing γ-Tubulin Nucleates Microtubules 929

Microtubules Emanate from the Centrosome in Animal Cells 930

Microtubule-Binding Proteins Modulate Filament Dynamics and Organization 932

Microtubule Plus-End-Binding Proteins Modulate Microtubule Dynamics and Attachments 932

Tubulin-Sequestering and Microtubule-Severing Proteins Destabilize Microtubules 935

Two Types of Motor Proteins Move Along Microtubules 936

Microtubules and Motors Move Organelles and Vesicles 938

Construction of Complex Microtubule Assemblies Requires Microtubule Dynamics and Motor Proteins 940

Motile Cilia and Flagella Are Built from Microtubules and Dyneins 941

Primary Cilia Perform Important Signaling Functions in Animal Cells 942

Summary 943

INTERMEDIATE FILAMENTS AND SEPTINS 944

Intermediate Filament Structure Depends on the Lateral Bundling and Twisting of Coiled-Coils 945

Intermediate Filaments Impart Mechanical Stability to Animal Cells 946

Linker Proteins Connect Cytoskeletal Filaments and Bridge the Nuclear Envelope 948

Septins Form Filaments That Regulate Cell Polarity 949

Summary 950

CELL POLARIZATION AND MIGRATION 951

Many Cells Can Crawl Across a Solid Substratum 951

Actin Polymerization Drives Plasma Membrane Protrusion 951

Lamellipodia Contain All of the Machinery Required for Cell Motility 953

Myosin Contraction and Cell Adhesion Allow Cells to Pull Themselves Forward 954

Cell Polarization Is Controlled by Members of the Rho Protein Family 955

Extracellular Signals Can Activate the Three Rho Protein Family Members 958

External Signals Can Dictate the Direction of Cell Migration 958

Communication Among Cytoskeletal Elements Coordinates Whole-Cell Polarization and Locomotion 959

Summary 960

Problems 960

References 962

Chapter 17 The Cell Cycle 963

OVERVIEW OF THE CELL CYCLE 963

The Eukaryotic Cell Cycle Usually Consists of Four Phases 964