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Chapter 1 Cells and Genomes1

THE UNIVERSAL FEATURES OF CELLS ON EARTH2

All Cells Store Their Hereditary Information in the Same Linear Chemical Code：DNA2

All Cells Replicate Their Hereditary Information by Templated Polymerization3

All Cells Transcribe Portions of Their Hereditary Information into the Same Intermediary Form：RNA4

All Cells Use Proteins as Catalysts5

All Cells Translate RNA into Protein in the Same Way6

Each Protein Is Encoded by a Specific Gene7

Life Requires Free Energy8

All Cells Function as Biochemical Factories Dealing with the Same Basic Molecular Building Blocks8

All Cells Are Enclosed in a Plasma Membrane Across Which Nutrients and Waste Materials Must Pass8

A Living Cell Can Exist with Fewer Than 500 Genes9

Summary10

THE DIVERSITY OF GENOMES AND THE TREE OF LIFE10

Cells Can Be Powered by a Variety of Free-Energy Sources10

Some Cells Fix Nitrogen and Carbon Dioxide for Others12

The Greatest Biochemical Diversity Exists Among Prokaryotic Cells12

The Tree of Life Has Three Primary Branches：Bacteria，Archaea，and Eukaryotes14

Some Genes Evolve Rapidly； Others Are Highly Conserved15

Most Bacteria and Archaea Have 1000-6000 Genes16

New Genes Are Generated from Preexisting Genes16

Gene Duplications Give Rise to Families of Related Genes Within a Single Cell17

Genes Can Be Transferred Between Organisms，Both in the Laboratory and in Nature18

Sex Results in Horizontal Exchanges of Genetic Information Within a Species19

The Function of a Gene Can Often Be Deduced from Its Sequence20

More Than 200 Gene Families Are Common to All Three Primary Branches of the Tree of Life20

Mutations Reveal the Functions of Genes21

Molecular Biology Began with a Spotlight on E.coli22

Summary22

GENETIC INFORMATION IN EUKARYOTES23

Eukaryotic Cells May Have Originated as Predators24

Modern Eukaryotic Cells Evolved from a Symbiosis25

Eukaryotes Have Hybrid Genomes27

Eukaryotic Genomes Are Big28

Eukaryotic Genomes Are Rich in Regulatory DNA29

The Genome Defines the Program of Multicellular Development29

Many Eukaryotes Live as Solitary Cells30

A Yeast Serves as a Minimal Model Eukaryote30

The Expression Levels of All the Genes of An Organism Can Be Monitored Simultaneously32

Arabidopsis Has Been Chosen Out of 300，000 Species As a Model Plant32

The World of Animal Cells Is Represented By a Worm，a Fly，a Fish，a Mouse，and a Human33

Studies in Drosophila Provide a Key to Vertebrate Development33

The Vertebrate Genome Is a Product of Repeated Duplications34

The Frog and the Zebrafish Provide Accessible Models for Vertebrate Development35

The Mouse Is the Predominant Mammalian Model Organism35

Humans Report on Their Own Peculiarities36

We Are All Different in Detail38

To Understand Cells and Organisms Will Require Mathematics，Computers，and Quantitative Information38

Summary39

Problems39

References41

Chapter 2 Cell Chemistry and Bioenergetics43

THE CHEMICAL COMPONENTS OF A CELL43

Water Is Held Together by Hydrogen Bonds44

Four Types of Noncovalent Attractions Help Bring Molecules Together in Cells44

Some Polar Molecules Form Acids and Bases in Water45

A Cell Is Formed from Carbon Compounds47

Cells Contain Four Major Families of Small Organic Molecules47

The Chemistry of Cells Is Dominated by Macromolecules with Remarkable Properties47

Noncovalent Bonds Specify Both the Precise Shape of a Macromolecule and Its Binding to Other Molecules49

Summary50

CATALYSIS AND THE USE OF ENERGY BY CELLS51

Cell Metabolism Is Organized by Enzymes51

Biological Order Is Made Possible by the Release of Heat Energy from Cells52

Cells Obtain Energy by the Oxidation of Organic Molecules54

Oxidation and Reduction Involve Electron Transfers55

Enzymes Lower the Activation-Energy Barriers That Block Chemical Reactions57

Enzymes Can Drive Substrate Molecules Along Specific Reaction Pathways58

How Enzymes Find Their Substrates：The Enormous Rapidity of Molecular Motions59

The Free-Energy Change for a Reaction，△G，Determines Whether It Can Occur Spontaneously60

The Concentration of Reactants Influences the Free-Energy Change and a Reaction’s Direction61

The Standard Free-Energy Change，△G°，Makes It Possible to Compare the Energetics of Different Reactions61

The Equilibrium Constant and △G° Are Readily Derived from Each Other62

The Free-Energy Changes of Coupled Reactions Are Additive63

Activated Carrier Molecules Are Essential for Biosynthesis63

The Formation of an Activated Carrier Is Coupled to an Energetically Favorable Reaction64

ATP Is the Most Widely Used Activated Carrier Molecule65

Energy Stored in ATP Is Often Harnessed to Join Two Molecules Together65

NADH and NADPH Are Important Electron Carriers67

There Are Many Other Activated Carrier Molecules in Cells68

The Synthesis of Biological Polymers Is Driven by ATP Hydrolysis70

Summary73

HOW CELLS OBTAIN ENERGY FROM FOOD73

Glycolysis Is a Central ATP-Producing Pathway74

Fermentations Produce ATP in the Absence of Oxygen75

Glycolysis Illustrates How Enzymes Couple Oxidation to Energy Storage76

Organisms Store Food Molecules in Special Reservoirs78

Most Animal Cells Derive Their Energy from Fatty Acids Between Meals81

Sugars and Fats Are Both Degraded to Acetyl CoA in Mitochondria81

The Citric Acid Cycle Generates NADH by Oxidizing Acetyl Groups to CO282

Electron Transport Drives the Synthesis of the Majority of the ATP in Most Cells84

Amino Acids and Nucleotides Are Part of the Nitrogen Cycle85

Metabolism Is Highly Organized and Regulated87

Summary88

Problems88

References108

Chapter 3 Proteins109

THE SHAPE AND STRUCTURE OF PROTEINS109

The Shape of a Protein Is Specified by Its Amino Acid Sequence109

Proteins Fold into a Conformation of Lowest Energy114

The α Helix and the β Sheet Are Common Folding Patterns115

Protein Domains Are Modular Units from Which Larger Proteins Are Built117

Few of the Many Possible Polypeptide Chains Will Be Useful to Cells118

Proteins Can Be Classified into Many Families119

Some Protein Domains Are Found in Many Different Proteins121

Certain Pairs of Domains Are Found Together in Many Proteins122

The Human Genome Encodes a Complex Set of Proteins，Revealing That Much Remains Unknown122

Larger Protein Molecules Often Contain More Than One Polypeptide Chain123

Some Globular Proteins Form Long Helical Filaments123

Many Protein Molecules Have Elongated，Fibrous Shapes124

Proteins Contain a Surprisingly Large Amount of Intrinsically Disordered Polypeptide Chain125

Covalent Cross-Linkages Stabilize Extracellular Proteins127

Protein Molecules Often Serve as Subunits for the Assembly of Large Structures127

Many Structures in Cells Are Capable of Self-Assembly128

Assembly Factors Often Aid the Formation of Complex Biological Structures130

Amyloid Fibrils Can Form from Many Proteins130

Amyloid Structures Can Perform Useful Functions in Cells132

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

Summary134

PROTEIN FUNCTION134

All Proteins Bind to Other Molecules134

The Surface Conformation of a Protein Determines Its Chemistry135

Sequence Comparisons Between Protein Family Members Highlight Crucial Ligand-Binding Sites136

Proteins Bind to Other Proteins Through Several Types of Interfaces137

Antibody Binding Sites Are Especially Versatile138

The Equilibrium Constant Measures Binding Strength138

Enzymes Are Powerful and Highly Specific Catalysts140

Substrate Binding Is the First Step in Enzyme Catalysis141

Enzymes Speed Reactions by Selectively Stabilizing Transition States141

Enzymes Can Use Simultaneous Acid and Base Catalysis144

Lysozyme Illustrates How an Enzyme Works144

Tightly Bound Small Molecules Add Extra Functions to Proteins146

Multienzyme Complexes Help to Increase the Rate of Cell Metabolism148

The Cell Regulates the Catalytic Activities of Its Enzymes149

Allosteric Enzymes Have Two or More Binding Sites That Interact151

Two Ligands Whose Binding Sites Are Coupled Must Reciprocally Affect Each Other’s Binding151

Symmetric Protein Assemblies Produce Cooperative Allosteric Transitions152

Many Changes in Proteins Are Driven by Protein Phosphorylation153

A Eukaryotic Cell Contains a Large Collection of Protein Kinases and Protein Phosphatases154

The Regulation of the Src Protein Kinase Reveals How a Protein Can Function as a Microprocessor155

Proteins That Bind and Hydrolyze GTP Are Ubiquitous Cell Regulators156

Regulatory Proteins GAP and GEF Control the Activity of GTP-Binding Proteins by Determining Whether GTP or GDP-Is Bound157

Proteins Can Be Regulated by the Covalent Addition of Other Proteins157

An Elaborate Ubiquitin-Conjugating System Is Used to Mark Proteins158

Protein Complexes with Interchangeable Parts Make Efficient Use of Genetic Information159

A GTP-Binding Protein Shows How Large Protein Movements Can Be Generated160

Motor Proteins Produce Large Movements in Cells161

Membrane-Bound Transporters Harness Energy to Pump Molecules Through Membranes163

Proteins Often Form Large Complexes That Function as Protein Machines164

Scaffolds Concentrate Sets of Interacting Proteins164

Many Proteins Are Controlled by Covalent Modifications That Direct Them to Specific Sites Inside the Cell165

A Complex Network of Protein Interactions Underlies Cell Function166

Summary169

Problems170

References172

Chapter 4 DNA，Chromosomes，and Genomes175

THE STRUCTURE AND FUNCTION OF DNA175

A DNA Molecule Consists of Two Complementary Chains of Nucleotides175

The Structure of DNA Provides a Mechanism for Heredity177

In Eukaryotes，DNA Is Enclosed in a Cell Nucleus178

Summary179

CHROMOSOMAL DNA AND ITS PACKAGING IN THE CHROMATIN FIBER179

EukarYotic DNA Is Packaged into a Set of Chromosomes180

Chromosomes Contain Long Strings of Genes182

The Nucleotide Sequence of the Human Genome Shows How Our Genes Are Arranged183

Each DNA Molecule That Forms a Linear Chromosome Must Contain a Centromere，Two Telomeres，and Replication Origins185

DNA Molecules Are Highly Condensed in Chromosomes187

Nucleosomes Are a Basic Unit of Eukaryotic Chromosome Structure187

The Structure of the Nucleosome Core Particle Reveals How DNA Is Packaged188

Nucleosomes Have a Dynamic Structure，and Are Frequently Subjected to Changes Catalyzed by ATP-Dependent Chromatin Remodeling Complexes190

Nucleosomes Are Usually Packed Together into a Compact Chromatin Fiber191

Summary193

CHROMATIN STRUCTURE AND FUNCTION194

Heterochromatin Is Highly Organized and Restricts Gene Expression194

The Heterochromatic State Is Self-Propagating194

The Core Histones Are Covalently Modified at Many Different Sites196

Chromatin Acquires Additional Variety Through the Site-Specific Insertion of a Small Set of Histone Variants198

Covalent Modifications and Histone Variants Act in Concert to Control Chromosome Functions198

A Complex of Reader and Writer Proteins Can Spread Specific Chromatin Modifications Along a Chromosome199

Barrier DNA Sequences Block the Spread of Reader-Writer Complexes and thereby Separate Neighboring Chromatin Domains202

The Chromatin in Centromeres Reveals How Histone Variants Can Create Special Structures203

Some Chromatin Structures Can Be Directly Inherited204

Experiments with Frog Embryos Suggest that both Activating and Repressive Chromatin Structures Can Be Inherited Epigenetically205

Chromatin Structures Are Important for Eukaryotic Chromosome Function206

Summary207

THE GLOBAL STRUCTURE OF CHROMOSOMES207

Chromosomes Are Folded into Large Loops of Chromatin207

Polytene Chromosomes Are Uniquely Useful for Visualizing Chromatin Structures208

There Are Multiple Forms of Chromatin210

Chromatin Loops Decondense When the Genes Within Them Are Expressed211

Chromatin Can Move to Specific Sites Within the Nucleus to Alter Gene Expression212

Networks of Macromolecules Form a Set of Distinct Biochemical Environments inside the Nucleus213

Mitotic Chromosomes Are Especially Highly Condensed214

Summary216

HOW GENOMES EVOLVE216

Genome Comparisons Reveal Functional DNA Sequences by their Conservation Throughout Evolution217

Genome Alterations Are Caused by Failures of the Normal Mechanisms for Copying and Maintaining DNA，as well as by Transposable DNA Elements217

The Genome Sequences of Two Species Differ in Proportion to the Length of Time Since They Have Separately Evolved218

Phylogenetic Trees Constructed from a Comparison of DNA Sequences Trace the Relationships of All Organisms219

A Comparison of Human and Mouse Chromosomes Shows How the Structures of Genomes Diverge221

The Size of a Vertebrate Genome Reflects the Relative Rates of DNA Addition and DNA Loss in a Lineage222

We Can Infer the Sequence of Some Ancient Genomes223

Multispecies Sequence Comparisons Identify Conserved DNA Sequences of Unknown Function224

Changes in Previously Conserved Sequences Can Help Decipher Critical Steps in Evolution226

Mutations in the DNA Sequences That Control Gene Expression Have Driven Many of the Evolutionary Changes in Vertebrates227

Gene Duplication Also Provides an Important Source of Genetic Novelty During Evolution227

Duplicated Genes Diverge228

The Evolution of the Globin Gene Family Shows How DNA Duplications Contribute to the Evolution of Organisms229

Genes Encoding New Proteins Can Be Created by the Recombination of Exons230

Neutral Mutations Often Spread to Become Fixed in a Population，with a Probability That Depends on Population Size230

A Great Deal Can Be Learned from Analyses of the Variation Among Humans232

Summary234

Problems234

References236

Chapter 5 DNA Replication，Repair，and Recombination237

THE MAINTENANCE OF DNA SEQUENCES237

Mutation Rates Are Extremely Low237

Low Mutation Rates Are Necessary for Life as We Know It238

Summary239

DNA REPLICATION MECHANISMS239

Base-Pairing Underlies DNA Replication and DNA Repair239

The DNA Replication Fork Is Asymmetrical240

The High Fidelity of DNA Replication Requires Several Proofreading Mechanisms242

Only DNA Replication in the 5’-to-3’Direction Allows Efficient Error Correction244

A Special Nucleotide-Polymerizing Enzyme Synthesizes Short RNA Primer Molecules on the Lagging Strand245

Special Proteins Help to Open Up the DNA Double Helix in Front of the Replication Fork246

A Sliding Ring Holds a Moving DNA Polymerase Onto the DNA246

The Proteins at a Replication Fork Cooperate to Form a Replication Machine249

A Strand-Directed Mismatch Repair System Removes Replication Errors That Escape from the Replication Machine250

DNA Topoisomerases Prevent DNA Tangling During Replication251

DNA Replication Is Fundamentally Similar in Eukaryotes and Bacteria253

Summary254

THE INITIATION AND COMPLETION OF DNA REPLICATION IN CHROMOSOMES254

DNA Synthesis Begins at Replication Origins254

Bacterial Chromosomes Typically Have a Single Origin of DNA Replication255

Eukaryotic Chromosomes Contain Multiple Origins of Replication256

In Eukaryotes，DNA Replication Takes Place During Only One Part of the Cell Cycle258

Different Regions on the Same Chromosome Replicate at Distinct Times in S Phase258

A Large Multisubunit Complex Binds to Eukaryotic Origins of Replication259

Features of the Human Genome That Specify Origins of Replication Remain to Be Discovered260

New Nucleosomes Are Assembled Behind the Replication Fork261

Telomerase Replicates the Ends of Chromosomes262

Telomeres Are Packaged Into Specialized Structures That Protect the Ends of Chromosomes263

Telomere Length Is Regulated by Cells and Organisms264

Summary265

DNA REPAIR266

Without DNA Repair，Spontaneous DNA Damage Would Rapidly Change DNA Sequences267

The DNA Double Helix Is Readily Repaired268

DNA Damage Can Be Removed by More Than One Pathway269

Coupling Nucleotide Excision Repair to Transcription Ensures That the Cell’s Most Important DNA Is Efficiently Repaired271

The Chemistry of the DNA Bases Facilitates Damage Detection271

Special Translesion DNA Polymerases Are Used in Emergencies273

Double-Strand Breaks Are Efficiently Repaired273

DNA Damage Delays Progression of the Cell Cycle276

Summary276

HOMOLOGOUS RECOMBINATION276

Homologous Recombination Has Common Features in All Cells277

DNA Base-Pairing Guides Homologous Recombination277

Homologous Recombination Can Flawlessly Repair Double-Strand Breaks in DNA278

Strand Exchange Is Carried Out by the RecA/Rad51 Protein279

Homologous Recombination Can Rescue Broken DNA Replication Forks280

Cells Carefully Regulate the Use of Homologous Recombination in DNA Repair280

Homologous Recombination Is Crucial for Meiosis282

Meiotic Recombination Begins with a Programmed Double-Strand Break282

Holliday Junctions Are Formed During Meiosis284

Homologous Recombination Produces Both Crossovers and Non-Crossovers During Meiosis284

Homologous Recombination Often Results in Gene Conversion286

Summary286

TRANSPOSITION AND CONSERVATIVE SITE-SPECIFIC RECOMBINATION287

Through Transposition，Mobile Genetic Elements Can Insert Into Any DNA Sequence288

DNA-Only Transposons Can Move by a Cut-and-Paste Mechanism288

Some Viruses Use a Transposition Mechanism to Move Themselves Into Host-Cell Chromosomes290

Retroviral-like Retrotransposons Resemble Retroviruses，but Lack a Protein Coat291

A Large Fraction of the Human Genome Is Composed of Nonretroviral Retrotransposons291

Different Transposable Elements Predominate in Different Organisms292

Genome Sequences Reveal the Approximate Times at Which Transposable Elements Have Moved292

Conservative Site-Specific Recombination Can Reversibly Rearrange DNA292

Conservative Site-Specific Recombination Can Be Used to Turn Genes On or Off294

Bacterial Conservative Site-Specific Recombinases Have Become Powerful Tools for Cell and Developmental Biologists294

Summary295

Problems296

References298

Chapter 6 How Cells Read the Genome：From DNA to Protein299

FROM DNA TO RNA301

RNA Molecules Are Single-Stranded302

Transcription Produces RNA Complementary to One Strand of DNA302

RNA Polymerases Carry Out Transcription303

Cells Produce Different Categories of RNA Molecules305

Signals Encoded in DNA Tell RNA Polymerase Where to Startand Stop306

Transcription Start and Stop Signals Are Heterogeneous in Nucleotide Sequence307

Transcription Initiation in Eukaryotes Requires Many Proteins309

RNA Polymerase Ⅱ Requires a Set of General Transcription Factors310

Polymerase Ⅱ Also Requires Activator，Mediator，and Chromatin-Modifying Proteins312

Transcription Elongation in Eukaryotes Requires AccessoryProteins313

Transcription Creates Superhelical Tension314

Transcription Elongation in Eukaryotes Is Tightly Coupled to RNA Processing315

RNA Capping Is the First Modification of Eukaryotic Pre-mRNAs316

RNA Splicing Removes Intron Sequences from Newly Transcribed Pre-mRNAs317

Nucleotide Sequences Signal Where Splicing Occurs319

RNA Splicing Is Performed by the Spliceosome319

The Spliceosome Uses ATP Hydrolysis to Produce a Complex Series of RNA-RNA Rearrangements321

Other Properties of Pre-mRNA and Its Synthesis Help to Explain the Choice of Proper Splice Sites321

Chromatin Structure Affects RNA Splicing323

RNA Splicing Shows Remarkable Plasticity323

Spliceosome-Catalyzed RNA Splicing Probably Evolved from Self-splicing Mechanisms324

RNA-Processing Enzymes Generate the 3’End of Eukaryotic mRNAs324

Mature Eukaryotic mRNAs Are Selectively Exported from the Nucleus325

Noncoding RNAs Are Also Synthesized and Processed in the Nucleus327

The Nucleolus Is a Ribosome-Producing Factory329

The Nucleus Contains a Variety of Subnuclear Aggregates331

Summary333

FROM RNA TO PROTEIN333

An mRNA Sequence Is Decoded in Sets of Three Nucleotides334

tRNA Molecules Match Amino Acids to Codons in mRNA334

tRNAs Are Covalently Modified Before They Exit from the Nucleus336

Specific Enzymes Couple Each Amino Acid to Its Appropriate tRNA Molecule336

Editing by tRNA Synthetases Ensures Accuracy338

Amino Acids Are Added to the C-terminal End of a Growing Polypeptide Chain339

The RNA Message Is Decoded in Ribosomes340

Elongation Factors Drive Translation Forward and Improve Its Accuracy343

Many Biological Processes Overcome the Inherent Limitations of Complementary Base-Pairing345

Accuracy in Translation Requires an Expenditure of Free Energy345

The Ribosome Is a Ribozyme346

Nucleotide Sequences in mRNA Signal Where to Start Protein Synthesis347

Stop Codons Mark the End of Translation348

Proteins Are Made on Polyribosomes349

There Are Minor Variations in the Standard Genetic Code349

Inhibitors of Prokaryotic Protein Synthesis Are Useful as Antibiotics351

Quality Control Mechanisms Act to Prevent Translation of Damaged mRNAs351

Some Proteins Begin to Fold While Still Being Synthesized353

Molecular Chaperones Help Guide the Folding of Most Proteins354

Cells Utilize Several Types of Chaperones355

Exposed Hydrophobic Regions Provide Critical Signals for Protein Quality Control357

The Proteasome Is a Compartmentalized Protease with Sequestered Active Sites357

Many Proteins Are Controlled by Regulated Destruction359

There Are Many Steps From DNA to Protein361

Summary362

THE RNA WORLD AND THE ORIGINS OF LIFE362

Single-Stranded RNA Molecules Can Fold into Highly Elaborate Structures363

RNA Can Both Store Information and Catalyze Chemical Reactions364

How Did Protein Synthesis Evolve？365

All Present-Day Cells Use DNA as Their Hereditary Material365

Summary366

Problems366

References368

Chapter 7 Control of Gene Expression369

AN OVERVIEW OF GENE CONTROL369

The Different Cell Types of a Multicellular Organism Contain the Same DNA369

Different Cell Types Synthesize Different Sets of RNAs and Proteins370

External Signals Can Cause a Cell to Change the Expression of Its Genes372

Gene Expression Can Be Regulated at Many of the Steps in the Pathway from DNA to RNA to Protein372

Summary373

CONTROL OF TRANSCRIPTION BY SEQUENCE-SPECIFIC DNA-BINDING PROTEINS373

The Sequence of Nucleotides in the DNA Double Helix Can Be Read by Proteins373

Transcription Regulators Contain Structural Motifs That Can Read DNA Sequences374

Dimerization of Transcription Regulators Increases Their Affinity and Specificity for DNA375

Transcription Regulators Bind Cooperatively to DNA378

Nucleosome Structure Promotes Cooperative Binding of Transcription Regulators379

Summary380

TRANSCRIPTION REGULATORS SWITCH GENES ON AND OFF380

The Tryptophan Repressor Switches Genes Off380

Repressors Turn Genes Off and Activators Turn Them On381

An Activator and a Repressor Control the Lac Operon382

DNA Looping Can Occur During Bacterial Gene Regulation383

Complex Switches Control Gene Transcription in Eukaryotes384

A Eukaryotic Gene Control Region Consists of a Promoter Plus Many cis-Regulatory Sequences384

Eukaryotic Transcription Regulators Work in Groups385

Activator Proteins Promote the Assembly of RNA Polymerase at the Start Point of Transcription386

Eukaryotic Transcription Activators Direct the Modification of Local Chromatin Structure386

Transcription Activators Can Promote Transcription by Releasing RNA Polymerase from Promoters388

Transcription Activators Work Synergistically388

Eukaryotic Transcription Repressors Can Inhibit Transcription in Several Ways389

Insulator DNA Sequences Prevent Eukaryotic Transcription Regulators from Influencing Distant Genes391

Summary392

MOLECULAR GENETIC MECHANISMS THAT CREATE AND MAINTAIN SPECIALIZED CELL TYPES392

Complex Genetic Switches That Regulate Drosophila Development Are Built Up from Smaller Molecules392

The Drosophila Eve Gene Is Regulated by Combinatorial Controls394

Transcription Regulators Are Brought Into Play by Extracellular Signals395

Combinatorial Gene Control Creates Many Different Cell Types396

Specialized Cell Types Can Be Experimentally Reprogrammed to Become Pluripotent Stem Cells398

Combinations of Master Transcription Regulators Specify Cell Types by Controlling the Expression of Many Genes398

Specialized Cells Must Rapidly Turn Sets of Genes On and Off399

Differentiated Cells Maintain Their Identity400

Transcription Circuits Allow the Cell to Carry Out Logic Operations402

Summary404

MECHANISMS THAT REINFORCE CELL MEMORY IN PLANTS AND ANIMALS404

Patterns of DNA Methylation Can Be Inherited When Vertebrate Cells Divide404

CG-Rich Islands Are Associated with Many Genes in Mammals405

Genomic Imprinting Is Based on DNA Methylation407

Chromosome-Wide Alterations in Chromatin Structure Can Be Inherited409

Epigenetic Mechanisms Ensure That Stable Patterns of Gene Expression Can Be Transmitted to Daughter Cells411

Summary413

POST-TRANSCRIPTIONAL CONTROLS413

Transcription Attenuation Causes the Premature Termination of Some RNA Molecules414

Riboswitches Probably Represent Ancient Forms of Gene Control414

Alternative RNA Splicing Can Produce Different Forms of a Protein from the Same Gene415

The Definition of a Gene Has Been Modified Since the Discoveryof Alternative RNA Splicing416

A Change in the Site of RNA Transcript Cleavage and Poly-A Addition Can Change the C-terminus of a Protein417

RNA Editing Can Change the Meaning of the RNA Message418

RNA Transport from the Nucleus Can Be Regulated419

Some mRNAs Are Localized to Specific Regions of the Cytosol421

The 5’and 3’Untranslated Regions of mRNAs Control Their Translation422

The Phosphorylation of an Initiation Factor Regulates Protein Synthesis Globally423

Initiation at AUG Codons Upstream of the Translation Start Can Regulate Eukaryotic Translation Initiation424

Internal Ribosome Entry Sites Provide Opportunities for Translational Control425

Changes in mRNA Stability Can Regulate Gene Expression426

Regulation of mRNA Stability Involves P-bodies and Stress Granules427

Summary428

REGULATION OF GENE EXPRESSION BY NONCODING RNAs429

Small Noncoding RNA Transcripts Regulate Many Animal and Plant Genes Through RNA Interference429

miRNAs Regulate mRNA Translation and Stability429

RNA Interference Is Also Used as a Cell Defense Mechanism431

RNA Interference Can Direct Heterochromatin Formation432

piRNAs Protect the Germ Line from Transposable Elements433

RNA Interference Has Become a Powerful Experimental Tool433

Bacteria Use Small Noncoding RNAs to Protect Themselves from Viruses433

Long Noncoding RNAs Have Diverse Functions in the Cell435

Summary436

Problems436

References438

Chapter 8 Analyzing Cells，Molecules，and Systems439

ISOLATING CELLS AND GROWING THEM IN CULTURE440

Cells Can Be Isolated from Tissues440

Cells Can Be Grown in Culture440

Eukaryotic Cell Lines Are a Widely Used Source of Homogeneous Cells442

Hybridoma Cell Lines Are Factories That Produce Monoclonal Antibodies444

Summary445

PURIFYING PROTEINS445

Cells Can Be Separated into Their Component Fractions445

Cell Extracts Provide Accessible Systems to Study Cell Functions447

Proteins Can Be Separated by Chromatography448

Immunoprecipitation Is a Rapid Affiinity Purification Method449

Genetically Engineered Tags Provide an Easy Way to Purify Proteins450

Purified Cell-free Systems Are Required for the Precise Dissection of Molecular Functions451

Summary451

ANALYZING PROTEINS452

Proteins Can Be Separated by SDS Polyacrylamide-Gel Electrophoresis452

Two-Dimensional Gel Electrophoresis Provides Greater Protein Separation452

Specific Proteins Can Be Detected by Blotting with Antibodies454

Hydrodynamic Measurements Reveal the Size and Shape of a Protein Complex455

Mass Spectrometry Provides a Highly Sensitive Method for Identifying Unknown Proteins455

Sets of Interacting Proteins Can Be Identified by Biochemical Methods457

Optical Methods Can Monitor Protein Interactions458

Protein Function Can Be Selectively Disrupted With Small Molecules459

Protein Structure Can Be Determined Using X-Ray Diffraction460

NMR Can Be Used to Determine Protein Structure in Solution461

Protein Sequence and Structure Provide Clues About Protein Function462

Summary463

ANALYZING AND MANIPULATING DNA463

Restriction Nucleases Cut Large DNA Molecules into Specific Fragments464

Gel Electrophoresis Separates DNA Molecules of Different Sizes465

Purified DNA Molecules Can Be Specifically Labeled with Radioisotopes or Chemical Markers in vitro467

Genes Can Be Cloned Using Bacteria467

An Entire Genome Can Be Represented in a DNA Library469

Genomic and cDNA Libraries Have Different Advantages and Drawbacks471

Hybridization Provides a Powerful，But Simple Way to Detect Specific Nucleotide Sequences472

Genes Can Be Cloned in vitro Using PCR473

PCR Is Also Used for Diagnostic and Forensic Applications474

Both DNA and RNA Can Be Rapidly Sequenced477

To Be Useful，Genome Sequences Must Be Annotated477

DNA Cloning Allows Any Protein to be Produced in Large Amounts483

Summary484

STUDYING GENE EXPRESSION AND FUNCTION485

Classical Genetics Begins by Disrupting a Cell Process by Random Mutagenesis485

Genetic Screens Identify Mutants with Specific Abnormalities488

Mutations Can Cause Loss or Gain of Protein Function489

Complementation Tests Reveal Whether Two Mutations Are in the Same Gene or Different Genes490

Gene Products Can Be Ordered in Pathways by Epistasis Analysis490

Mutations Responsible for a Phenotype Can Be Identified Through DNA Analysis491

Rapid and Cheap DNA Sequencing Has Revolutionized Human Genetic Studies491

Linked Blocks of Polymorphisms Have Been Passed Down from Our Ancestors492

Polymorphisms Can Aid the Search for Mutations Associated with Disease493

Genomics Is Accelerating the Discovery of Rare Mutations That Predispose Us to Serious Disease493

Reverse Genetics Begins with a Known Gene and Determines Which Cell Processes Require Its Function494

Animals and Plants Can Be Genetically Altered495

The Bacterial CRISPR System Has Been Adapted to Edit Genomes in a Wide Variety of Species497

Large Collections of Engineered Mutations Provide a Tool for Examining the Function of Every Gene in an Organism498

RNA Interference Is a Simple and Rapid Way to Test Gene Function499

Reporter Genes Reveal When and Where a Gene Is Expressed501

In situ Hybridization Can Reveal the Location of mRNAs and Noncoding RNAs502

Expression of Individual Genes Can Be Measured Using Quantitative RT-PCR502

Analysis of mRNAs by Microarray or RNA-seq Provides a Snapshot of Gene Expression503

Genome-wide Chromatin Immunoprecipitation Identifies Sites on the Genome Occupied by Transcription Regulators505

Ribosome Profiling Reveals Which mRNAs Are Being Translated in the Cell505

Recombinant DNA Methods Have Revolutionized Human Health506

Transgenic Plants Are Important for Agriculture507

Summary508

MATHEMATICAL ANALYSIS OF CELL FUNCTIONS509

Regulatory Networks Depend on Molecular Interactions509

Differential Equations Help Us Predict Transient Behavior512

Both Promoter Activity and Protein Degradation Affect the Rate of Change of Protein Concentration513

The Time Required to Reach Steady State Depends on Protein Lifetime514

Quantitative Methods Are Similar for Transcription Repressors and Activators514

Negative Feedback Is a Powerful Strategy in Cell Regulation515

Delayed Negative Feedback Can Induce Oscillations516

DNA Binding By a Repressor or an Activator Can Be Cooperative516

Positive Feedback Is Important for Switchlike Responses and Bistability518

Robustness Is an Important Characteristic of Biological Networks520

Two Transcription Regulators That Bind to the Same Gene Promoter Can Exert Combinatorial Control520

An Incoherent Feed-forward Interaction Generates Pulses522

A Coherent Feed-forward Interaction Detects Persistent Inputs522

The Same Network Can Behave Differently in Different Cells Due to Stochastic Effects523

Several Computational Approaches Can Be Used to Model the Reactions in Cells524

Statistical Methods Are Critical For the Analysis of Biological Data524

Summary525

Problems525

References528

Chapter 9 Visualizing Cells529

LOOKING AT CELLS IN THE LIGHT MICROSCOPE529

The Light Microscope Can Resolve Details 0.2 μm Apart530

Photon Noise Creates Additional Limits to Resolution When Light Levels Are Low532

Living Cells Are Seen Clearly in a Phase-Contrast or a Differential-Interference-Contrast Microscope533

Images Can Be Enhanced and Analyzed by Digital Techniques534

Intact Tissues Are Usually Fixed and Sectioned Before Microscopy535

Specific Molecules Can Be Located in Cells by Fluorescence Microscopy536

Antibodies Can Be Used to Detect Specific Molecules539

Imaging of Complex Three-Dimensional Objects Is Possible with the Optical Microscope540

The Confocal Microscope Produces Optical Sections by Excluding Out-of-Focus Light540

Individual Proteins Can Be Fluorescently Tagged in Living Cells and Organisms542

Protein Dynamics Can Be Followed in Living Cells543

Light-Emitting Indicators Can Measure Rapidly Changing Intracellular Ion Concentrations546

Single Molecules Can Be Visualized by Total Internal Reflection Fluorescence Microscopy547

Individual Molecules Can Be Touched，Imaged，and Moved Using Atomic Force Microscopy548

Superresolution Fluorescence Techniques Can Overcome Diffraction-Limited Resolution549

Superresolution Can Also be Achieved Using Single-Molecule Localization Methods551

Summary554

LOOKING AT CELLS AND MOLECULES IN THE ELECTRON MICROSCOPE554

The Electron Microscope Resolves the Fine Structure of the Cell554

Biological Specimens Require Special Preparation for Electron Microscopy555

Specific Macromolecules Can Be Localized by Immunogold Electron Microscopy556

Different Views of a Single Object Can Be Combined to Give a Three-Dimensional Reconstruction557

Images of Surfaces Can Be Obtained by Scanning Electron Microscopy558

Negative Staining and Cryoelectron Microscopy Both Allow Macromolecules to Be Viewed at High Resolution559

Multiple Images Can Be Combined to Increase Resolution561

Summary562

Problems563

References564

Chapter 10 Membrane Structure565

THE LIPID BILAYER566

Phosphoglycerides，Sphingolipids，and Sterols Are the Major Lipids in Cell Membranes566

Phospholipids Spontaneously Form Bilayers568

The Lipid Bilayer Is a Two-dimensional Fluid569

The Fluidity of a Lipid Bilayer Depends on Its Composition571

Despite Their Fluidity，Lipid Bilayers Can Form Domains of Different Compositions572

Lipid Droplets Are Surrounded by a Phospholipid Monolayer573

The Asymmetry of the Lipid Bilayer Is Functionally Important573

Glycolipids Are Found on the Surface of All Eukaryotic Plasma Membranes575

Summary576

MEMBRANE PROTEINS576

Membrane Proteins Can Be Associated with the Lipid Bilayer in Various Ways576

Lipid Anchors Control the Membrane Localization of Some Signaling Proteins577

In Most Transmembrane Proteins，the Polypeptide Chain Crosses the Lipid Bilayer in an α-Helical Conformation579

Transmembrane α Helices Often Interact with One Another580

Some β Barrels Form Large Channels580

Many Membrane Proteins Are Glycosylated582

Membrane Proteins Can Be Solubilized and Purified in Detergents583

Bacteriorhodopsin Is a Light-driven Proton（H＋）Pump That Traverses the Lipid Bilayer as Seven α Helices586

Membrane Proteins Often Function as Large Complexes588

Many Membrane Proteins Diffuse in the Plane of the Membrane588

Cells Can Confine Proteins and Lipids to Specific Domains Within a Membrane590

The Cortical Cytoskeleton Gives Membranes Mechanical Strength and Restricts Membrane Protein Diffusion591

Membrane-bending Proteins Deform Bilayers593

Summary594

Problems595

References596

Chapter 11 Membrane Transport of Small Molecules and the Electrical Properties of Membranes597

PRINCIPLES OF MEMBRANE TRANSPORT597

Protein-Free Lipid Bilayers Are Impermeable to Ions598

There Are Two Main Classes of Membrane Transport Proteins：Transporters and Channels598

Active Transport Is Mediated by Transporters Coupled to an Energy Source599

Summary600

TRANSPORTERS AND ACTIVE MEMBRANE TRANSPORT600

Active Transport Can Be Driven by Ion-Concentration Gradients601

Transporters in the Plasma Membrane Regulate Cytosolic pH604

An Asymmetric Distribution of Transporters in Epithelial Cells Underlies the Transcellular Transport of Solutes605

There Are Three Classes of ATP-Driven Pumps606

A P-type ATPase Pumps Ca2＋ into the Sarcoplasmic Reticulum in Muscle Cells606

The Plasma Membrane Na＋-K＋ Pump Establishes Na＋ and K＋ Gradients Across the Plasma Membrane607

ABC Transporters Constitute the Largest Family of Membrane Transport Proteins609

Summary611

CHANNELS AND THE ELECTRICAL PROPERTIES OF MEMBRANES611

Aquaporins Are Permeable to Water But Impermeable to Ions612

Ion Channels Are Ion-Selective and Fluctuate Between Open and Closed States613

The Membrane Potential in Animal Cells Depends Mainly on K＋Leak Channels and the K＋ Gradient Across the Plasma Membrane615

The Resting Potential Decays Only Slowly When the Na＋-K＋ Pump Is Stopped615

The Three-Dimensional Structure of a Bacterial K＋ Channel Shows How an Ion Channel Can Work617

Mechanosensitive Channels Protect Bacterial Cells Against Extreme Osmotic Pressures619

The Function of a Neuron Depends on Its Elongated Structure620

Voltage-Gated Cation Channels Generate Action Potentials in Electrically Excitable Cells621

The Use of Channelrhodopsins Has Revolutionized the Study of Neural Circuits623

Myelination Increases the Speed and Efficiency of Action Potential Propagation in Nerve Cells625

Patch-Clamp Recording Indicates That Individual Ion Channels Open in an All-or-Nothing Fashion626

Voltage-Gated Cation Channels Are Evolutionarily and Structurally Related626

Different Neuron Types Display Characteristic Stable Firing Properties627

Transmitter-Gated Ion Channels Convert Chemical Signals into Electrical Ones at Chemical Synapses627

Chemical Synapses Can Be Excitatory or Inhibitory629

The Acetylcholine Receptors at the Neuromuscular Junction Are Excitatory Transmitter-Gated Cation Channels630

Neurons Contain Many Types of Transmitter-Gated Channels631

Many Psychoactive Drugs Act at Synapses631

Neuromuscular Transmission Involves the Sequential Activation of Five Different Sets of Ion Channels632

Single Neurons Are Complex Computation Devices633

Neuronal Computation Requires a Combination of at Least Three Kinds of K＋ Channels634

Long-Term Potentiation（LTP）in the Mammalian Hippocampus Depends on Ca2＋ Entry Through NMDA-Receptor Channels636

Summary637

Problems638

References640

Chapter 12 Intracellular Compartments and Protein Sorting641

THE COMPARTMENTALIZATION OF CELLS641

All Eukaryotic Cells Have the Same Basic Set of Membrane-enclosed Organelles641

Evolutionary Origins May Help Explain the Topological Relationships of Organelles643

Proteins Can Move Between Compartments in Different Ways645

Signal Sequences and Sorting Receptors Direct Proteins to the Correct Cell Address647

Most Organelles Cannot Be Constructed De Novo：They Require Information in the Organelle Itself648

Summary649

THE TRANSPORT OF MOLECULES BETWEEN THE NUCLEUS AND THE CYTOSOL649

Nuclear Pore Complexes Perforate the Nuclear Envelope649

Nuclear Localization Signals Direct Nuclear Proteins to the Nucleus650

Nuclear Import Receptors Bind to Both Nuclear Localization Signals and NPC Proteins652

Nuclear Export Works Like Nuclear Import，But in Reverse652

The Ran GTPase Imposes Directionality on Transport Through NPCs653

Transport Through NPCs Can Be Regulated by Controlling Access to the Transport Machinery654

During Mitosis the Nuclear Envelope Disassembles656

Summary657

THE TRANSPORT OF PROTEINS INTO MITOCHONDRIA AND CHLOROPLASTS658

Translocation into Mitochondria Depends on Signal Sequences and Protein Translocators659

Mitochondrial Precursor Proteins Are Imported as Unfolded Polypeptide Chains660

ATP Hydrolysis and a Membrane Potential Drive Protein Import Into the Matrix Space661

Bacteria and Mitochondria Use Similar Mechanisms to Insert Porins into their Outer Membrane662

Transport Into the Inner Mitochondrial Membrane and Intermembrane Space Occurs Via Several Routes663

Two Signal Sequences Direct Proteins to the Thylakoid Membrane in Chloroplasts664

Summary666

PEROXISOMES666

Peroxisomes Use Molecular Oxygen and Hydrogen Peroxide to Perform Oxidation Reactions666

A Short Signal Sequence Directs the Import of Proteins into Peroxisomes667

Summary669

THE ENDOPLASMIC RETICULUM669

The ER Is Structurally and Functionally Diverse670

Signal Sequences Were First Discovered in Proteins Imported into the Rough ER672

A Signal-Recognition Particle（SRP）Directs the ER Signal Sequence to a Specific Receptor in the Rough ER Membrane673

The Polypeptide Chain Passes Through an Aqueous Channel in the Translocator675

Translocation Across the ER Membrane Does Not Always Require Ongoing Polypeptide Chain Elongation677

In Single-Pass Transmembrane Proteins，a Single Internal ER Signal Sequence Remains in the Lipid Bilayer as a Membrane-spanning α Helix677

Combinations of Start-Transfer and Stop-Transfer Signals Determine the Topology of Multipass Transmembrane Proteins679

ER Tail-anchored Proteins Are Integrated into the ER Membrane by a Special Mechanism682

Translocated Polypeptide Chains Fold and Assemble in the Lumen of the Rough ER682

Most Proteins Synthesized in the Rough ER Are Glycosylated by the Addition of a Common N-Linked Oligosaccharide683

Oligosaccharides Are Used as Tags to Mark the State of Protein Folding685

Improperly Folded Proteins Are Exported from the ER and Degraded in the Cytosol685

Misfolded Proteins in the ER Activate an Unfolded Protein Response686

Some Membrane Proteins Acquire a Covalently Attached Glycosylphosphatidylinositol（GPI）Anchor688

The ER Assembles Most Lipid Bilayers689

Summary691

Problems692

References694

Chapter 13 Intracellular Membrane Traffic695

THE MOLECULAR MECHANISMS OF MEMBRANE TRANSPORT AND THE MAINTENANCE OF COMPARTMENTAL DIVERSITY697

There Are Various Types of Coated Vesicles697

The Assembly of a Clathrin Coat Drives Vesicle Formation697

Adaptor Proteins Select Cargo into Clathrin-Coated Vesicles698

Phosphoinositides Mark Organelles and Membrane Domains700

Membrane-Bending Proteins Help Deform the Membrane During Vesicle Formation701

Cytoplasmic Proteins Regulate the Pinching-Off and Uncoating of Coated Vesicles701

Monomeric GTPases Control Coat Assembly703

Not All Transport Vesicles Are Spherical704

Rab Proteins Guide Transport Vesicles to Their Target Membrane705

Rab Cascades Can Change the Identity of an Organelle707

SNAREs Mediate Membrane Fusion708

Interacting SNAREs Need to Be Pried Apart Before They Can Function Again709

Summary710

TRANSPORT FROM THE ER THROUGH THE GOLGI APPARATUS710

Proteins Leave the ER in COPII-Coated Transport Vesicles711

Only Proteins That Are Properly Folded and Assembled Can Leave the ER712

Vesicular Tubular Clusters Mediate Transport from the ER to the Golgi Apparatus712

The Retrieval Pathway to the ER Uses Sorting Signals713

Many Proteins Are Selectively Retained in the Compartments in Which They Function714

The Golgi Apparatus Consists of an Ordered Series of Compartments715

Oligosaccharide Chains Are Processed in the Golgi Apparatus716

Proteoglycans Are Assembled in the Golgi Apparatus718

What Is the Purpose of Glycosylation？719

Transport Through the Golgi Apparatus May Occur by Cisternal Maturation720

Golgi Matrix Proteins Help Organize the Stack721

Summary722

TRANSPORT FROM THE TRANS GOLGI NETWORK TO LYSOSOMES722

Lysosomes Are the Principal Sites of Intracellular Digestion722

Lysosomes Are Heterogeneous723

Plant and Fungal Vacuoles Are Remarkably Versatile Lysosomes724

Multiple Pathways Deliver Materials to Lysosomes725

Autophagy Degrades Unwanted Proteins and Organelles726

A Mannose 6-Phosphate Receptor Sorts Lysosomal Hydrolases in the Trans Golgi Network727

Defects in the GIcNAc Phosphotransferase Cause a Lysosomal Storage Disease in Humans728

Some Lysosomes and Multivesicular Bodies Undergo Exocytosis729

Summary729

TRANSPORT INTO THE CELL FROM THE PLASMA MEMBRANE：ENDOCYTOSIS730

Pinocytic Vesicles Form from Coated Pits in the Plasma Membrane731

Not All Pinocytic Vesicles Are Clathrin-Coated731

Cells Use Receptor-Mediated Endocytosis to Import Selected Extracellular Macromolecules732

Specific Proteins Are Retrieved from Early Endosomes and Returned to the Plasma Membrane734

Plasma Membrane Signaling Receptors are Down-Regulated by Degradation in Lysosomes735

Early Endosomes Mature into Late Endosomes735

ESCRT Protein Complexes Mediate the Formation of Intralumenal Vesicles in Multivesicular Bodies736

Recycling Endosomes Regulate Plasma Membrane Composition737

Specialized Phagocytic Cells Can Ingest Large Particles738

Summary740

TRANSPORT FROM THE TRANS GOLGI NETWORK TO THE CELL EXTERIOR：EXOCYTOSIS741

Many Proteins and Lipids Are Carried Automatically from the Trans Golgi Network（TGN）to the Cell Surface741

Secretory Vesicles Bud from the Trans Golgi Network742

Precursors of Secretory Proteins Are Proteolytically Processed During the Formation of Secretory Vesicles743

Secretory Vesicles Wait Near the Plasma Membrane Until Signaled to Release Their Contents744

For Rapid Exocytosis，Synaptic Vesicles Are Primed at the Presynaptic Plasma Membrane744

Synaptic Vesicles Can Form Directly from Endocytic Vesicles746

Secretory Vesicle Membrane Components Are Quickly Removed from the Plasma Membrane746

Some Regulated Exocytosis Events Serve to Enlarge the Plasma Membrane748

Polarized Cells Direct Proteins from the Trans Golgi Network to the Appropriate Domain of the Plasma Membrane748

Summary750

Problems750

References752

Chapter 14 Energy Conversion：Mitochondria and Chloroplasts753

THE MITOCHONDRION755

The Mitochondrion Has an Outer Membrane and an Inner Membrane757

The Inner Membrane Cristae Contain the Machine for Electron Transport and ATP Synthesis758

The Citric Acid Cycle in the Matrix Produces NADH758

Mitochondria Have Many Essential Roles in Cellular Metabolism759

A Chemiosmotic Process Couples Oxidation Energy to ATP Production761

The Energy Derived from Oxidation Is Stored as an Electrochemical Gradient762

Summary763

THE PROTON PUMPS OF THE ELECTRON-TRANSPORT CHAIN763

The Redox Potential Is a Measure of Electron Affinities763

Electron Transfers Release Large Amounts of Energy764

Transition Metal Ions and Quinones Accept and Release Electrons Readily764

NADH Transfers Its Electrons to Oxygen Through Three Large Enzyme Complexes Embedded in the Inner Membrane766

The NADH Dehydrogenase Complex Contains Separate Modules for Electron Transport and Proton Pumping768

Cytochrome c Reductase Takes Up and Releases Protons on the Opposite Side of the Crista Membrane，Thereby Pumping Protons768

The Cytochrome c Oxidase Complex Pumps Protons and Reduces O2 Using a Catalytic Iron-Copper Center770

The Respiratory Chain Forms a Supercomplex in the Crista Membrane772

Protons Can Move Rapidly Through Proteins Along Predefined Pathways773

Summary774

ATP PRODUCTION IN MITOCHONDRIA774

The Large Negative Value of △G for ATP Hydrolysis Makes ATP Useful to the Cell774

The ATP Synthase Is a Nanomachine that Produces ATP by Rotary Catalysis776

Proton-driven Turbines Are of Ancient Origin777

Mitochondrial Cristae Help to Make ATP Synthesis Efficient778

Special Transport Proteins Exchange ATP and ADP Through the Inner Membrane779

Chemismotic Mechanisms First Arose in Bacteria780

Summary782

CHLOROPLASTS AND PHOTOSYNTHESIS782

Chloroplasts Resemble Mitochondria But Have a Separate Thylakoid Compartment782

Chloroplasts Capture Energy from Sunlight and Use It to Fix Carbon783

Carbon Fixation Uses ATP and NADPH to Convert CO2 into Sugars784

Sugars Generated by Carbon Fixation Can Be Stored as Starch or Consumed to Produce ATP785

The Thylakoid Membranes of Chloroplasts Contain the Protein Complexes Required for Photosynthesis and ATP Generation786

Chlorophyll-Protein Complexes Can Transfer Either Excitation Energy or Electrons787

A Photosystem Consists of an Antenna Complex and a Reaction Center788

The Thylakoid Membrane Contains Two Different Photosystems Working in Series789

Photosystem Ⅱ Uses a Manganese Cluster to Withdraw Electrons From Water790

The Cytochrome b6-f Complex Connects Photosystem Ⅱ to Photosystem I791

Photosystem I Carries Out the Second Charge-Separation Step in the Z Scheme792

The Chloroplast ATP Synthase Uses the Proton Gradient Generated by the Photosynthetic Light Reactions to Produce ATP793

All Photosynthetic Reaction Centers Have Evolved From a Common Ancestor793

The Proton-Motive Force for ATP Production in Mitochondria and Chloroplasts Is Essentially the Same794

Chemiosmotic Mechanisms Evolved in Stages794

By Providing an Inexhaustible Source of Reducing Power，Photosynthetic Bacteria Overcame a Major Evolutionary Obstacle796

The Photosynthetic Electron-Transport Chains of Cyanobacteria Produced Atmospheric Oxygen and Permitted New Life-Forms796

Summary798

THE GENETIC SYSTEMS OF MITOCHONDRIA AND CHLOROPLASTS800

The Genetic Systems of Mitochondria and Chloroplasts Resemble Those of Prokaryotes800

Over Time，Mitochondria and Chloroplasts Have Exported Most of Their Genes to the Nucleus by Gene Transfer801

The Fission and Fusion of Mitochondria Are Topologically Complex Processes802

Animal Mitochondria Contain the Simplest Genetic Systems Known803

Mitochondria Have a Relaxed Codon Usage and Can Have a Variant Genetic Code804

Chloroplasts and Bacteria Share Many Striking Similarities806

Organelle Genes Are Maternally Inherited in Animals and Plants807

Mutations in Mitochondrial DNA Can Cause Severe Inherited Diseases807

The Accumulation of Mitochondrial DNA Mutations Is a Contributor to Aging808

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

Summary809

Problems809

References811

Chapter 15 Cell Signaling813

PRINCIPLES OF CELL SIGNALING813

Extracellular Signals Can Act Over Short or Long Distances814

Extracellular Signal Molecules Bind to Specific Receptors815

Each Cell Is Programmed to Respond to Specific Combinations of Extracellular Signals816

There Are Three Major Classes of Cell-Surface Receptor Proteins818

Cell-Surface Receptors Relay Signals Via Intracellular Signaling Molecules819

Intracellular Signals Must Be Specific and Precise in a Noisy Cytoplasm820

Intracellular Signaling Complexes Form at Activated Receptors822

Modular Interaction Domains Mediate Interactions Between Intracellular Signaling Proteins822

The Relationship Between Signal and Response Varies in Different Signaling Pathways824

The Speed of a Response Depends on the Turnover of Signaling Molecules825

Cells Can Respond Abruptly to a Gradually Increasing Signal827

Positive Feedback Can Generate an All-or-None Response828

Negative Feedback is a Common Motif in Signaling Systems829

Cells Can Adjust Their Sensitivity to a Signal830

Summary831

SIGNALING THROUGH G-PROTEIN-COUPLED RECEPTORS832

Trimeric G Proteins Relay Signals From GPCRs832

Some G Proteins Regulate the Production of Cyclic AMP833

Cyclic-AMP-Dependent Protein Kinase（PKA）Mediates Most of the Effects of Cyclic AMP834

Some G Proteins Signal Via Phospholipids836

Ca2＋ Functions as a Ubiquitous Intracellular Mediator838

Feedback Generates Ca2＋ Waves and Oscillations838

Ca2＋/Calmodulin-Dependent Protein Kinases Mediate Many Responses to Ca2＋ Signals840

Some G Proteins Directly Regulate Ion Channels843

Smell and Vision Depend on GPCRs That Regulate Ion Channels843

Nitric Oxide Is a Gaseous Signaling Mediator That Passes Between Cells846

Second Messengers and Enzymatic Cascades Amplify Signals848

GPCR Desensitization Depends on Receptor Phosphorylation848

Summary849

SIGNALING THROUGH ENZYME-COUPLED RECEPTORS850

Activated Receptor Tyrosine Kinases（RTKs）Phosphorylate Themselves850

Phosphorylated Tyrosines on RTKs Serve as Docking Sites for Intracellular Signaling Proteins852

Proteins with SH2 Domains Bind to Phosphorylated Tyrosines852

The GTPase Ras Mediates Signaling by Most RTKs854

Ras Activates a MAP Kinase Signaling Module855

Scaffold Proteins Help Prevent Cross-talk Between Parallel MAP Kinase Modules857

Rho Family GTPases Functionally Couple Cell-Surface Receptors to the Cytoskeleton858

PI 3-Kinase Produces Lipid Docking Sites in the Plasma Membrane859

The PI-3-Kinase-Akt Signaling Pathway Stimulates Animal Cells to Survive and Grow860

RTKs and GPCRs Activate Overlapping Signaling Pathways861

Some Enzyme-Coupled Receptors Associate with Cytoplasmic Tyrosine Kinases862

Cytokine Receptors Activate the JAK-STAT Signaling Pathway863

Protein Tyrosine Phosphatases Reverse Tyrosine Phosphorylations864

Signal Proteins of the TGFβ Superfamily Act Through Receptor Serine/Threonine Kinases and Smads865

Summary866

ALTERNATIVE SIGNALING ROUTES IN GENE REGULATION867

The Receptor Notch Is a Latent Transcription Regulatory Protein867

Wnt Proteins Bind to Frizzled Receptors and Inhibit the Degradation of β-Catenin868

Hedgehog Proteins Bind to Patched，Relieving Its Inhibition of Smoothened871

Many Stressful and Inflammatory Stimuli Act Through an NFkB-Dependent Signaling Pathway873

Nuclear Receptors Are Ligand-Modulated Transcription Regulators874

Circadian Clocks Contain Negative Feedback Loops That Control Gene Expression876

Three Proteins in a Test Tube Can Reconstitute a Cyanobacterial Circadian Clock878

Summary879

SIGNALING IN PLANTS880

Multicellularity and Cell Communication Evolved Independently in Plants and Animals880

Receptor Serine/Threonine Kinases Are the Largest Class of Cell-Surface Receptors in Plants881

Ethylene Blocks the Degradation of Specific Transcription Regulatory Proteins in the Nucleus881

Regulated Positioning of Auxin Transporters Patterns Plant Growth882

Phytochromes Detect Red Light，and Cryptochromes Detect Blue Light883

Summary885

Problems886

References887

Chapter 16 The Cytoskeleton889

FUNCTION AND ORIGIN OF THE CYTOSKELETON889

Cytoskeletal Filaments Adapt to Form Dynamic or Stable Structures890

The Cytoskeleton Determines Cellular Organization and Polarity892

Filaments Assemble from Protein Subunits That Impart Specific Physical and Dynamic Properties893

Accessory Proteins and Motors Regulate Cytoskeletal Filaments894

Bacterial Cell Organization and Division Depend on Homologs of Eukaryotic Cytoskeletal Proteins896

Summary898

ACTIN AND ACTIN-BINDING PROTEINS898

Actin Subunits Assemble Head-to-Tail to Create Flexible，Polar Filaments898

Nucleation Is the Rate-Limiting Step in the Formation of Actin Filaments899

Actin Filaments Have Two Distinct Ends That Grow at Different Rates900

ATP Hydrolysis Within Actin Filaments Leads to Treadmilling at Steady State901

The Functions of Actin Filaments Are Inhibited by Both Polymer-stabilizing and Polymer-destabilizing Chemicals904

Actin-Binding Proteins Influence Filament Dynamics and Organization904

Monomer Availability Controls Actin Filament Assembly906

Actin-Nucleating Factors Accelerate Polymerization and Generate Branched or Straight Filaments906

Actin-Filament-Binding Proteins Alter Filament Dynamics907

Severing Proteins Regulate Actin Filament Depolymerization909

Higher-Order Actin Filament Arrays Influence Cellular Mechanical Properties and Signaling911

Bacteria Can Hijack the Host Actin Cytoskeleton913

Summary914

MYOSIN AND ACTIN915

Actin-Based Motor Proteins Are Members of the Myosin Superfamily915

Myosin Generates Force by Coupling ATP Hydrolysis to Conformational Changes916

Sliding of Myosin Ⅱ Along Actin Filaments Causes Muscles to Contract916

A Sudden Rise in Cytosolic Ca2＋ Concentration Initiates Muscle Contraction920

Heart Muscle Is a Precisely Engineered Machine923

Actin and Myosin Perform a Variety of Functions in Non-Muscle Cells923

Summary925

MICROTUBULES925

Microtubules Are Hollow Tubes Made of Protofilaments926

Microtubules Undergo Dynamic Instability927

Microtubule Functions Are Inhibited by Both Polymer-stabilizing and Polymer-destabilizing Drugs929

A Protein Complex Containing γ-Tubulin Nucleates Microtubules929

Microtubules Emanate from the Centrosome in Animal Cells930

Microtubule-Binding Proteins Modulate Filament Dynamics and Organization932

Microtubule Plus-End-Binding Proteins Modulate Microtubule Dynamics and Attachments932

Tubulin-Sequestering and Microtubule-Severing Proteins Destabilize Microtubules935

Two Types of Motor Proteins Move Along Microtubules936

Microtubules and Motors Move Organelles and Vesicles938

Construction of Complex Microtubule Assemblies Requires Microtubule Dynamics and Motor Proteins940

Motile Cilia and Flagella Are Built from Microtubules and Dyneins941

Primary Cilia Perform Important Signaling Functions in Animal Cells942

Summary943

INTERMEDIATE FILAMENTS AND SEPTINS944

Intermediate Filament Structure Depends on the Lateral Bundling and Twisting of Coiled-Coils945

Intermediate Filaments Impart Mechanical Stability to Animal Cells946

Linker Proteins Connect Cytoskeletal Filaments and Bridge the Nuclear Envelope948

Septins Form Filaments That Regulate Cell Polarity949

Summary950

CELL POLARIZATION AND MIGRATION951

Many Cells Can Crawl Across a Solid Substratum951

Actin Polymerization Drives Plasma Membrane Protrusion951

Lamellipodia Contain All of the Machinery Required for Cell Motility953

Myosin Contraction and Cell Adhesion Allow Cells to Pull Themselves Forward954

Cell Polarization Is Controlled by Members of the Rho Protein Family955

Extracellular Signals Can Activate the Three Rho Protein Family Members958

External Signals Can Dictate the Direction of Cell Migration958

Communication Among Cytoskeletal Elements Coordinates Whole-Cell Polarization and Locomotion959

Summary960

Problems960

References962

Chapter 17 The Cell Cycle963

OVERVIEW OF THE CELL CYCLE963

The Eukaryotic Cell Cycle Usually Consists of Four Phases964