Part Ⅰ Chemical and Molecular Foundations 1
1 Molecules，Cells，and Model Organisms 1
1.1 The Molecules of Life 5
Proteins Give Cells Structure and Perform Most Cellular Tasks 7
Nucleic Acids Carry Coded Information for Making Proteins at the Right Time and Place 7
Phospholipids Are the Conserved Building Blocks of All Cellular Membranes 9
1.2 Prokaryotic Cell Structure and Function 10
Prokaryotes Comprise Two Kingdoms：Archaea and Eubacteria 10
Escherichia coli Is Widely Used in Biological Research 11
1.3 Eukaryotic Cell Structure and Function 12
The Cytoskeleton Has Many Important Functions 12
The Nucleus Contains the DNA Genome，RNA Synthetic Apparatus，and a Fibrous Matrix 12
Eukaryotic Cells Contain a Large Number of Internal Membrane Structures 14
Mitochondria Are the Principal Sites of ATP Production in Aerobic Cells 18
Chloroplasts Contain Internal Compartments in Which Photosynthesis Takes Place 18
All Eukaryotic Cells Use a Similar Cycle to Regulate Their Division 18
1.4 Unicellular Eukaryotic Model Organisms 19
Yeasts Are Used to Study Fundamental Aspects of Eukaryotic Cell Structure and Function 19
Mutations in Yeast Led to the Identification of Key Cell Cycle Proteins 21
Studies in the Alga Chlamydomonas reinhardtii Led to the Development of a Powerful Technique to Study Brain Function 22
The Parasite That Causes Malaria Has Novel Organelles That Allow It to Undergo a Remarkable Life Cycle 22
1.5 Metazoan Structure，Differentiation，and Model Organisms 24
Multicellularity Requires Cell-Cell and Cell-Matrix Adhesions 24
Epithelia Originated Early in Evolution 24
Tissues Are Organized into Organs 24
Genomics Has Revealed Important Aspects of Metazoan Evolution and Cell Function 24
Embryonic Development Uses a Conserved Set of Master Transcription Factors 25
Planaria Are Used to Study Stem Cells and Tissue Regeneration 27
Invertebrates，Fish，Mice，and Other Organisms Serve as Experimental Systems for Study of Human Development and Disease 28
Genetic Diseases Elucidate Important Aspects of Cell Function 28
The Following Chapters Present Much Experimental Data That Explains How We Know What We Know About Cell Structure and Function 29
2 Chemical Foundations 31
2.1 Covalent Bonds and Noncovalent Interactions 33
The Electronic Structure of an Atom Determines the Number and Geometry of the Covalent Bonds It Can Make 33
Electrons May Be Shared Equally or Unequally in Covalent Bonds 34
Covalent Bonds Are Much Stronger and More Stable Than Noncovalent Interactions 36
Ionic Interactions Are Attractions Between Oppositely Charged Ions 36
Hydrogen Bonds Are Noncovalent Interactions That Determine the Water Solubility of Uncharged Molecules 37
Van der Waals Interactions Are Weak Attractive Interactions Caused by Transient Dipoles 38
The Hydrophobic Effect Causes Nonpolar Molecules to Adhere to One Another 39
Molecular Complementarity Due to Noncovalent Interactions Leads to a Lock-and-Key Fit Between Biomolecules 40
2.2 Chemical Building Blocks of Cells 41
Amino Acids Differing Only in Their Side Chains Compose Proteins 42
Five Different Nucleotides Are Used to Build Nucleic Acids 45
Monosaccharides Covalently Assemble into Linear and Branched Polysaccharides 46
Phospholipids Associate Noncovalently to Form the Basic Bilayer Structure of Biomembranes 48
2.3 Chemical Reactions and Chemical Equilibrium 51
A Chemical Reaction Is in Equilibrium When the Rates of the Forward and Reverse Reactions Are Equal 52
The Equilibrium Constant Reflects the Extent of a Chemical Reaction 52
Chemical Reactions in Cells Are at Steady State 52
Dissociation Constants of Binding Reactions Reflect the Affinity of Interacting Molecules 53
Biological Fluids Have Characteristic pH Values 54
Hydrogen Ions Are Released by Acids and Taken Up by Bases 55
Buffers Maintain the pH of Intracellular and Extracellular Fluids 55
2.4 Biochemical Energetics 57
Several Forms of Energy Are Important in Biological Systems 57
Cells Can Transform One Type of Energy into Another 58
The Change in Free Energy Determines If a Chemical Reaction Will Occur Spontaneously 58
The ΔG°’ of a Reaction Can Be Calculated from Its Keq 60
The Rate of a Reaction Depends on the Activation Energy Necessary to Energize the Reactants into a Transition State 60
Life Depends on the Coupling of Unfavorable Chemical Reactions with Energetically Favorable Ones 61
Hydrolysis of ATP Releases Substantial Free Energy and Drives Many Cellular Processes 61
ATP Is Generated During Photosynthesis and Respiration 62
NAD+ and FAD Couple Many Biological Oxidation and Reduction Reactions 63
3 Protein Structure and Function 67
3.1 Hierarchical Structure of Proteins 69
The Primary Structure of a Protein Is Its Linear Arrangement of Amino Acids 69
Secondary Structures Are the Core Elements of Protein Architecture 70
Tertiary Structure Is the Overall Folding of a Polypeptide Chain 72
There Are Four Broad Structural Categories of Proteins 72
Different Ways of Depicting the Conformation of Proteins Convey Different Types of Information 74
Structural Motifs Are Regular Combinations of Secondary Structures 75
Domains Are Modules of Tertiary Structure 76
Multiple Polypeptides Assemble into Quaternary Structures and Supramolecular Complexes 78
Comparing Protein Sequences and Structures Provides Insight into Protein Function and Evolution 79
3.2 Protein Folding 81
Planar Peptide Bonds Limit the Shapes into Which Proteins Can Fold 81
The Amino Acid Sequence of a Protein Determines How It Will Fold 81
Folding of Proteins in Vivo Is Promoted by Chaperones 82
Protein Folding Is Promoted by Proline Isomerases 86
Abnormally Folded Proteins Can Form Amyloids That Are Implicated in Diseases 87
3.3 Protein Binding and Enzyme Catalysis 89
Specific Binding of Ligands Underlies the Functions of Most Proteins 89
Enzymes Are Highly Efficient and Specific Catalysts 90
An Enzyme’s Active Site Binds Substrates and Carries Out Catalysis 91
Serine Proteases Demonstrate How an Enzyme’s Active Site Works 92
Enzymes in a Common Pathway Are Often Physically Associated with One Another 96
3.4 Regulating Protein Function 97
Regulated Synthesis and Degradation of Proteins Is a Fundamental Property of Cells 97
The Proteasome Is a Molecular Machine Used to Degrade Proteins 97
Ubiquitin Marks Cytosolic Proteins for Degradation in Proteasomes 99
Noncovalent Binding Permits Allosteric，or Cooperative，Regulation of Proteins 100
Noncovalent Binding of Calcium and GTP Are Widely Used as Allosteric Switches to Control Protein Activity 101
Phosphorylation and Dephosphory lation Covalently Regulate Protein Activity 102
Ubiquitinylation and Deubiquitinylation Covalently Regulate Protein Activity 103
Proteolytic Cleavage Irreversibly Activates or Inactivates Some Proteins 104
Higher-Order Regulation Includes Control of Protein Location 105
3.5 Purifying，Detecting，and Characterizing Proteins 105
Centrifugation Can Separate Particles and Molecules That Differ in Mass or Density 106
Electrophoresis Separates Molecules on the Basis of Their Charge-to-Mass Ratio 107
Liquid Chromatography Resolves Proteins by Mass，Charge，or Affinity 109
Highly Specific Enzyme and Antibody Assays Can Detect Individual Proteins 111
Radioisotopes Are Indispensable Tools for Detecting Biological Molecules 114
Mass Spectrometry Can Determine the Mass and Sequence of Proteins 116
Protein Primary Structure Can Be Determined by Chemical Methods and from Gene Sequences 118
Protein Conformation Is Determined by Sophisticated Physical Methods 119
3.6 Proteomics 122
Proteomics Is the Study of All or a Large Subset of Proteins in a Biological System 122
Advanced Techniques in Mass Spectrometry Are Critical to Proteomic Analysis 123
4 Culturing and Visualizing Cells 129
4.1 Growing and Studying Cells in Culture 130
Culture of Animal Cells Requires Nutrient-Rich Media and Special Solid Surfaces 130
Primary Cell Cultures and Cell Strains Have a Finite Life Span 131
Transformed Cells Can Grow Indefinitely in Culture 132
Flow Cytometry Separates Different Cell Types 132
Growth of Cells in Two-Dimensional and Three-Dimensional Culture Mimics the In Vivo Environment 133
Hybridomas Produce Abundant Monoclonal Antibodies 135
A Wide Variety of Cell Biological Processes Can Be Studied with Cultured Cells 136
Drugs Are Commonly Used in Cell Biological Research 136
4.2 Light Microscopy：Exploring Cell Structure and Visualizing Proteins Within Cells 139
The Resolution of the Conventional Light Microscope Is About 0.2 μm 139
Phase-Contrast and Differential-Interference-Contrast Microscopy Visualize Unstained Live Cells 141
Imaging Subcellular Details Often Requires That Specimens Be Fixed，Sectioned，and Stained 142
Fluorescence Microscopy Can Localize and Quantify Specific Molecules in Live Cells 143
Intracellular Ion Concentrations Can Be Determined with Ion-Sensitive Fluorescent Dyes 143
Immunofluorescence Microscopy Can Detect Specific Proteins in Fixed Cells 144
Tagging with Fluorescent Proteins Allows the Visualization of Specific Proteins in Live Cells 146
Deconvolution and Confocal Microscopy Enhance Visualization of Three-Dimensional Fluorescent Objects 147
Two-Photon Excitation Microscopy Allows Imaging Deep into Tissue Samples 149
TIRF Microscopy Provides Exceptional Imaging in One Focal Plane 150
FRAP Reveals the Dynamics of Cellular Components 151
FRET Measures Distance Between Fluorochromes 152
Super-Resolution Microscopy Can Localize Proteins to Nanometer Accuracy 153
Light-Sheet Microscopy Can Rapidly Image Cells in Living Tissue 155
4.3 Electron Microscopy：High-Resolution Imaging 156
Single Molecules or Structures Can Be Imaged Using a Negative Stain or Metal Shadowing 157
Cells and Tissues Are Cut into Thin Sections for Viewing by Electron Microscopy 158
Immunoelectron Microscopy Localizes Proteins at the Ultrastructural Level 159
Cryoelectron Microscopy Allows Visualization of Specimens Without Fixation or Staining 160
Scanning Electron Microscopy of Metal-Coated Specimens Reveals Surface Features 161
4.4 Isolation of Cell Organelles 161
Disruption of Cells Releases Their Organelles and Other Contents 162
Centrifugation Can Separate Many Types of Organelles 162
Organelle-Specific Antibodies Are Useful in Preparing Highly Purified Organelles 162
Proteomics Reveals the Protein Composition of Organelles 164
Part Ⅱ Biomembranes，Genes，and Gene Regulation 167
5 Fundamental Molecular Genetic Mechanisms 167
5.1 Structure of Nucleic Acids 169
A Nucleic Acid Strand Is a Linear Polymer with End-to-End Directionality 170
Native DNA Is a Double Helix of Complementary Antiparallel Strands 170
DNA Can Undergo Reversible Strand Separation 172
Torsional Stress in DNA Is Relieved by Enzymes 174
Different Types of RNA Exhibit Various Conformations Related to Their Functions 174
5.2 Transcription of Protein-Coding Genes and Formation of Functional mRNA 176
A Template DNA Strand Is Transcribed into a Complementary RNA Chain by RNA Polymerase 176
Organization of Genes Differs in Prokaryotic and Eukaryotic DNA 179
Eukaryotic Precursor mRNAs Are Processed to Form Functional mRNAs 180
Alternative RNA Splicing Increases the Number of Proteins Expressed from a Single Eukaryotic Gene 181
5.3 The Decoding of mRNA by tRNAs 183
Messenger RNA Carries Information from DNA in a Three-Letter Genetic Code 183
The Folded Structure of tRNA Promotes Its Decoding Functions 185
Nonstandard Base Pairing Often Occurs Between Codons and Anticodons 186
Amino Acids Become Activated When Covalently Linked to tRNAs 188
5.4 Stepwise Synthesis of Proteins on Ribosomes 188
Ribosomes Are Protein-Synthesizing Machines 188
Methionyl-tRNA i Met Recognizes the AUG Start Codon 190
Eukaryotic Translation Initiation Usually Occurs at the First AUG Downstream from the 5’ End of an mRNA 191
During Chain Elongation Each Incoming Aminoacyl-tRNA Moves Through Three Ribosomal Sites 193
Translation Is Terminated by Release Factors When a Stop Codon Is Reached 195
Polysomes and Rapid Ribosome Recycling Increase the Efficiency of Translation 195
GTPase-Superfamily Proteins Function in Several Quality-Control Steps of Translation 195
Nonsense Mutations Cause Premature Termination of Protein Synthesis 196
5.5 DNA Replication 197
DNA Polymerases Require a Primer to Initiate Replication 197
Duplex DNA Is Unwound，and Daughter Strands Are Formed at the DNA Replication Fork 199
Several Proteins Participate in DNA Replication 199
DNA Replication Occurs Bidirectionally from Each Origin 201
5.6 DNA Repair and Recombination 203
DNA Polymerases Introduce Copying Errors and Also Correct Them 203
Chemical and Radiation Damage to DNA Can Lead to Mutations 203
High-Fidelity DNA Excision-Repair Systems Recognize and Repair Damage 204
Base Excision Repairs T-G Mismatches and Damaged Bases 205
Mismatch Excision Repairs Other Mismatches and Small Insertions and Deletions 205
Nucleotide Excision Repairs Chemical Adducts that Distort Normal DNA Shape 206
Two Systems Use Recombination to Repair Double-Strand Breaks in DNA 207
Homologous Recombination Can Repair DNA Damage and Generate Genetic Diversity 209
5.7 Viruses：Parasites of the Cellular Genetic System 212
Most Viral Host Ranges Are Narrow 212
Viral Capsids Are Regular Arrays of One or a Few Types of Protein 213
Viruses Can Be Cloned and Counted in Plaque Assays 213
Lytic Viral Growth Cycles Lead to Death of Host Cells 213
Viral DNA Is Integrated into the Host-Cell Genome in Some Nonlytic Viral Growth Cycles 216
6 Molecular Genetic Techniques 223
6.1 Genetic Analysis of Mutations to Identify and Study Genes 224
Recessive and Dominant Mutant Alleles Generally Have Opposite Effects on Gene Function 224
Segregation of Mutations in Breeding Experiments Reveals Their Dominance or Recessivity 225
Conditional Mutations Can Be Used to Study Essential Genes in Yeast 227
Recessive Lethal Mutations in Diploids Can Be Identified by Inbreeding and Maintained in Heterozygotes 228
Complementation Tests Determine Whether Different Recessive Mutations Are in the Same Gene 229
Double Mutants Are Useful in Assessing the Order in Which Proteins Function 230
Genetic Suppression and Synthetic Lethality Can Reveal Interacting or Redundant Proteins 231
Genes Can Be Identified by Their Map Position on the Chromosome 232
6.2 DNA Cloning and Characterization 234
Restriction Enzymes and DNA Ligases Allow Insertion of DNA Fragments into Cloning Vectors 234
Isolated DNA Fragments Can Be Cloned into E.coli Plasmid Vectors 236
Yeast Genomic Libraries Can Be Constructed with Shuttle Vectors and Screened by Functional Complementation 237
cDNA Libraries Represent the Sequences of Protein-Coding Genes 238
The Polymerase Chain Reaction Amplifies a Specific DNA Sequence from a Complex Mixture 239
Cloned DNA Molecules Can Be Sequenced Rapidly by Methods Based on PCR 243
6.3 Using Cloned DNA Fragments to Study Gene Expression 246
Hybridization Techniques Permit Detection of Specific DNA Fragments and mRNAs 246
DNA Microarrays Can Be Used to Evaluate the Expression of Many Genes at One Time 247
Cluster Analysis of Multiple Expression Experiments Identifies Co-regulated Genes 248
E.coli Expression Systems Can Produce Large Quantities of Proteins from Cloned Genes 249
Plasmid Expression Vectors Can Be Designed for Use in Animal Cells 251
6.4 Locating and Identifying Human Disease Genes 254
Monogenic Diseases Show One of Three Patterns of Inheritance 254
DNA Polymorphisms Are Used as Markers for Linkage Mapping of Human Mutations 255
Linkage Studies Can Map Disease Genes with a Resolution of About 1 Centimorgan 256
Further Analysis Is Needed to Locate a Disease Gene in Cloned DNA 257
Many Inherited Diseases Result from Multiple Genetic Defects 257
6.5 Inactivating the Function of Specific Genes in Eukaryotes 259
Normal Yeast Genes Can Be Replaced with Mutant Alleles by Homologous Recombination 260
Genes Can Be Placed Under the Control of an Experimentally Regulated Promoter 260
Specific Genes Can Be Permanently Inactivated in the Germ Line of Mice 261
Somatic Cell Recombination Can Inactivate Genes in Specific Tissues 261
Dominant-Negative Alleles Can Inhibit the Function of Some Genes 262
RNA Interference Causes Gene Inactivation by Destroying the Corresponding mRNA 264
Engineered CRISPR-Cas9 Systems Allow Precise Genome Editing 266
7 Biomembrane Structure 271
7.1 The Lipid Bilayer：Composition and Structural Organization 273
Phospholipids Spontaneously Form Bilayers 273
Phospholipid Bilayers Form a Sealed Compartment Surrounding an Internal Aqueous Space 274
Biomembranes Contain Three Principal Classes of Lipids 276
Most Lipids and Many Proteins Are Laterally Mobile in Biomembranes 278
Lipid Composition Influences the Physical Properties of Membranes 279
Lipid Composition Is Different in the Exoplasmic and Cytosolic Leaflets 281
Cholesterol and Sphingolipids Cluster with Specific Proteins in Membrane Microdomains 282
Cells Store Excess Lipids in Lipid Droplets 283
7.2 Membrane Proteins：Structure and Basic Functions 284
Proteins Interact with Membranes in Three Different Ways 284
Most Transmembrane Proteins Have Membrane-Spanning α Helices 285
Multiple β Strands in Porins Form Membrane-Spanning “Barrels” 288
Covalently Attached Lipids Anchor Some Proteins to Membranes 288
All Transmembrane Proteins and Glycolipids Are Asymmetrically Oriented in the Bilayer 289
Lipid-Binding Motifs Help Target Peripheral Proteins to the Membrane 290
Proteins Can Be Removed from Membranes by Detergents or High-Salt Solutions 290
7.3 Phospholipids，Sphingolipids，and Cholesterol：Synthesis and Intracellular Movement 293
Fatty Acids Are Assembled from Two-Carbon Building Blocks by Several Important Enzymes 293
Small Cytosolic Proteins Facilitate Movement of Fatty Acids 293
Fatty Acids Are Incorporated into Phospholipids Primarily on the ER Membrane 294
Flippases Move Phospholipids from One Membrane Leaflet to the Opposite Leaflet 295
Cholesterol Is Synthesized by Enzymes in the Cytosol and ER Membrane 295
Cholesterol and Phospholipids Are Transported Between Organelles by Several Mechanisms 296
8 Genes，Genomics，and Chromosomes 301
8.1 Eukaryotic Gene Structure 303
Most Eukaryotic Genes Contain Introns and Produce mRNAs Encoding Single Proteins 303
Simple and Complex Transcription Units Are Found in Eukaryotic Genomes 303
Protein-Coding Genes May Be Solitary or Belong to a Gene Family 305
Heavily Used Gene Products Are Encoded by Multiple Copies of Genes 307
Nonprotein-Coding Genes Encode Functional RNAs 308
8.2 Chromosomal Organization of Genes and Noncoding DNA 309
Genomes of Many Organisms Contain Nonfunctional DNA 309
Most Simple-Sequence DNAs Are Concentrated in Specific Chromosomal Locations 310
DNA Fingerprinting Depends on Differences in Length of Simple-Sequence DNAs 311
Unclassified Intergenic DNA Occupies a Significant Portion of the Genome 312
8.3 Transposable （Mobile） DNA Elements 312
Movement of Mobile Elements Involves a DNA or an RNA Intermediate 313
DNA Transposons Are Present in Prokaryotes and Eukaryotes 314
LTR Retrotransposons Behave Like Intracellular Retroviruses 316
Non-LTR Retrotransposons Transpose by a Distinct Mechanism 318
Other Retroposed RNAs Are Found in Genomic DNA 321
Mobile DNA Elements Have Significantly Influenced Evolution 321
8.4 Genomics：Genome-Wide Analysis of Gene Structure and Function 323
Stored Sequences Suggest Functions of Newly Identified Genes and Proteins 324
Comparison of Related Sequences from Different Species Can Give Clues to Evolutionary Relationships Among Proteins 325
Genes Can Be Identified Within Genomic DNA Sequences 326
The Number of Protein-Coding Genes in an Organism’s Genome Is Not Directly Related to Its Biological Complexity 326
8.5 Structural Organization of Eukaryotic Chromosomes 327
Chromatin Exists in Extended and Condensed Forms 328
Modifications of Histone Tails Control Chromatin Condensation and Function 330
Nonhistone Proteins Organize Long Chromatin Loops 335
Additional Nonhistone Proteins Regulate Transcription and Replication 339
8.6 Morphology and Functional Elements of Eukaryotic Chromosomes 341
Chromosome Number，Size，and Shape at Metaphase Are Species-Specific 341
During Metaphase，Chromosomes Can Be Distinguished by Banding Patterns and Chromosome Painting 341
Chromosome Painting and DNA Sequencing Reveal the Evolution of Chromosomes 342
Interphase Polytene Chromosomes Arise by DNA Amplification 343
Three Functional Elements Are Required for Replication and Stable Inheritance of Chromosomes 345
Centromere Sequences Vary Greatly in Length and Complexity 345
Addition of Telomeric Sequences by Telomerase Prevents Shortening of Chromosomes 347
9 Transcriptional Control of Gene Expression 353
9.1 Control of Gene Expression in Bacteria 356
Transcription Initiation by Bacterial RNA Polymerase Requires Association with a Sigma Factor 357
Initiation of lac Operon Transcription Can Be Repressed or Activated 357
Small Molecules Regulate Expression of Many Bacterial Genes via DNA-Binding Repressors and Activators 358
Transcription Initiation from Some Promoters Requires Alternative Sigma Factors 359
Transcription by σ54-RNA Polymerase Is Controlled by Activators That Bind Far from the Promoter 359
Many Bacterial Responses Are Controlled by Two-Component Regulatory Systems 360
Expression of Many Bacterial Operons Is Controlled by Regulation of Transcriptional Elongation 361
9.2 Overview of Eukaryotic Gene Control 363
Regulatory Elements in Eukaryotic DNA Are Found Both Close to and Many Kilobases Away from Transcription Start Sites 364
Three Eukaryotic RNA Polymerases Catalyze Formation of Different RNAs 367
The Largest Subunit in RNA Polymerase Ⅱ Has an Essential Carboxy-Terminal Repeat 370
9.3 RNA Polymerase Ⅱ Promoters and General Transcription Factors 371
RNA Polymerase Ⅱ Initiates Transcription at DNA Sequences Corresponding to the 5’ Cap of mRNAs 371
The TATA Box，Initiators，and CpG Islands Function as Promoters in Eukaryotic DNA 371
General Transcription Factors Position RNA Polymerase Ⅱ at Start Sites and Assist in Initiation 373
Elongation Factors Regulate the Initial Stages of Transcription in the Promoter-Proximal Region 377
9.4 Regulatory Sequences in Protein-Coding Genes and the Proteins Through Which They Function 378
Promoter-Proximal Elements Help Regulate Eukaryotic Genes 378
Distant Enhancers Often Stimulate Transcription by RNA Polymerase Ⅱ 379
Most Eukaryotic Genes Are Regulated by Multiple Transcription-Control Elements 379
DNase Ⅰ Footprinting and EMSA Detect Protein-DNA Interactions 380
Activators Are Composed of Distinct Functional Domains 381
Repressors Are the Functional Converse of Activators 383
DNA-Binding Domains Can Be Classified into Numerous Structural Types 384
Structurally Diverse Activation and Repression Domains Regulate Transcription 386
Transcription Factor Interactions Increase Gene-Control Options 387
Multiprotein Complexes Form on Enhancers 388
9.5 Molecular Mechanisms of Transcription Repression and Activation 390
Formation of Heterochromatin Silences Gene Expression at Telomeres，near Centromeres，and in Other Regions 390
Repressors Can Direct Histone Deacetylation at Specific Genes 393
Activators Can Direct Histone Acetylation at Specific Genes 394
Chromatin-Remodeling Complexes Help Activate or Repress Transcription 395
Pioneer Transcription Factors Initiate the Process of Gene Activation During Cellular Differentiation 395
The Mediator Complex Forms a Molecular Bridge Between Activation Domains and Pol Ⅱ 396
9.6 Regulation of Transcription-Factor Activity 398
DNaⅠse Hypersensitive Sites Reflect the Developmental History of Cellular Differentiation 398
Nuclear Receptors Are Regulated by Extracellular Signals 400
All Nuclear Receptors Share a Common Domain Structure 400
Nuclear-Receptor Response Elements Contain Inverted or Direct Repeats 400
Hormone Binding to a Nuclear Receptor Regulates Its Activity as a Transcription Factor 402
Metazoans Regulate the RNA Polymerase Ⅱ Transition from Initiation to Elongation 402
Termination of Transcription Is Also Regulated 402
9.7 Epigenetic Regulation of Transcription 404
DNA Methylation Represses Transcription 404
Methylation of Specific Histone Lysines Is Linked to Epigenetic Mechanisms of Gene Repression 405
Epigenetic Control by Polycomb and Trithorax Complexes 406
Long Noncoding RNAs Direct Epigenetic Repression in Metazoans 409
9.8 Other Eukaryotic Transcription Systems 412
Transcription Initiation by Pol Ⅰ and Pol Ⅲ Is Analogous to That by Pol Ⅱ 412
10 Post-transcriptional Gene Control 417
10.1 Processing of Eukaryotic Pre-mRNA 419
The 5’ Cap Is Added to Nascent RNAs Shortly After Transcription Initiation 420
A Diverse Set of Proteins with Conserved RNA-Binding Domains Associate with Pre-mRNAs 421
Splicing Occurs at Short，Conserved Sequences in Pre-mRNAs via Two Transesterification Reactions 423
During Splicing，snRNAs Base-Pair with Pre-mRNA 424
Spliceosomes，Assembled from snRNPs and a Pre-mRNA，Carry Out Splicing 426
Chain Elongation by RNA Polymerase Ⅱ Is Coupled to the Presence of RNA-Processing Factors 428
SR Proteins Contribute to Exon Definition in Long Pre-mRNAs 428
Self-Splicing Group Ⅱ Introns Provide Clues to the Evolution of snRNAs 429
3’ Cleavage and Polyadenylation of Pre-mRNAs Are Tightly Coupled 430
Nuclear Exoribonucleases Degrade RNA That Is Processed Out of Pre-mRNAs 432
RNA Processing Solves the Problem of Pervasive Transcription of the Genome in Metazoans 432
10.2 Regulation of Pre-mRNA Processing 435
Alternative Splicing Generates Transcripts with Different Combinations of Exons 435
A Cascade of Regulated RNA Splicing Controls Drosophila Sexual Differentiation 435
Splicing Repressors and Activators Control Splicing at Alternative Sites 437
RNA Editing Alters the Sequences of Some Pre-mRNAs 439
10.3 Transport of mRNA Across the Nuclear Envelope 440
Phosphorylation and Dephosphorylation of SR Proteins Imposes Directionality on mRNP Export Across the Nuclear Pore Complex 441
Balbiani Rings in Insect Larval Salivary Glands Allow Direct Visualization of mRNP Export Through NPCs 442
Pre-mRNAs in Spliceosomes Are Not Exported from the Nucleus 443
HIV Rev Protein Regulates the Transport of Unspliced Viral mRNAs 444
10.4 Cytoplasmic Mechanisms of Post-transcriptional Control 445
Degradation of mRNAs in the Cytoplasm Occurs by Several Mechanisms 445
Adenines in mRNAs and IncRNAs May Be Post-transcriptionally Modified by N6 Methylation 447
Micro-RNAs Repress Translation and Induce Degradation of Specific mRNAs 447
Alternative Polyadenylation Increases miRNA Control Options 450
RNA Interference Induces Degradation of Precisely Complementary mRNAs 450
Cytoplasmic Polyadenylation Promotes Translation of Some mRNAs 451
Protein Synthesis Can Be Globally Regulated 452
Sequence-Specific RNA-Binding Proteins Control Translation of Specific mRNAs 455
Surveillance Mechanisms Prevent Translation of Improperly Processed mRNAs 456
Localization of mRNAs Permits Production of Proteins at Specific Regions Within the Cytoplasm 457
10.5 Processing of rRNA and tRNA 461
Pre-rRNA Genes Function as Nucleolar Organizers 461
Small Nucleolar RNAs Assist in Processing Pre-rRNAs 462
Self-Splicing Group Ⅰ Introns Were the First Examples of Catalytic RNA 466
Pre-tRNAs Undergo Extensive Modification in the Nucleus 466
Nuclear Bodies Are Functionally Specialized Nuclear Domains 468
Part Ⅲ Cellular Organization and Function 473
11 Transmembrane Transport of Ions and Small Molecules 473
11.1 Overview of Transmembrane Transport 474
Only Gases and Small Uncharged Molecules Cross Membranes by Simple Diffusion 474
Three Main Classes of Membrane Proteins Transport Molecules and Ions Across Cellular Membranes 475
11.2 Facilitated Transport of Glucose and Water 477
Uniport Transport Is Faster and More Specific than Simple Diffusion 477
The Low Km of the GLUT1 Uniporter Enables It to Transport Glucose into Most Mammalian Cells 478
The Human Genome Encodes a Family of Sugar-Transporting GLUT Proteins 480
Transport Proteins Can Be Studied Using Artificial Membranes and Recombinant Cells 480
Osmotic Pressure Causes Water to Move Across Membranes 481
Aquaporins Increase the Water Permeability of Cellular Membranes 481
11.3 ATP-Powered Pumps and the Intracellular Ionic Environment 483
There Are Four Main Classes of ATP-Powered Pumps 484
ATP-Powered Ion Pumps Generate and Maintain Ionic Gradients Across Cellular Membranes 485
Muscle Relaxation Depends on Ca 2+ ATPases That Pump Ca 2+ from the Cytosol into the Sarcoplasmic Reticulum 486
The Mechanism of Action of the Ca 2+ Pump Is Known in Detail 486
Calmodulin Regulates the Plasma-Membrane Pumps That Control Cytosolic Ca 2+ Concentrations 489
The Na+/K+ ATPase Maintains the Intracellular Na+ and K+ Concentrations in Animal Cells 489
V-Class H+ ATPases Maintain the Acidity of Lysosomes and Vacuoles 489
ABC Proteins Export a Wide Variety of Drugs and Toxins from the Cell 491
Certain ABC Proteins “Flip” Phospholipids and Other Lipid-Soluble Substrates from One Membrane Leaflet to the Other 493
The ABC Cystic Fibrosis Transmembrane Regulator Is a Chloride Channel，Not a Pump 494
11.4 Nongated Ion Channels and the Resting Membrane Potential 495
Selective Movement of Ions Creates a Transmembrane Electric Gradient 495
The Resting Membrane Potential in Animal Cells Depends Largely on the Outward Flow of K+ Ions Through Open K+ Channels 497
Ion Channels Are Selective for Certain Ions by Virtue of a Molecular “Selectivity Filter” 497
Patch Clamps Permit Measurement of Ion Movements Through Single Channels 500
Novel Ion Channels Can Be Characterized by a Combination of Oocyte Expression and Patch Clamping 501
11.5 Cotransport by Symporters and Antiporters 502
Na+ Entry into Mammalian Cells Is Thermodynamically Favored 502
Na+-Linked Symporters Enable Animal Cells to Import Glucose and Amino Acids Against High Concentration Gradients 503
A Bacterial Na+/Amino Acid Symporter Reveals How Symport Works 504
A Na+-Linked Ca 2+ Antiporter Regulates the Strength of Cardiac Muscle Contraction 504
Several Cotransporters Regulate Cytosolic pH 505
An Anion Antiporter Is Essential for Transport of CO2 by Erythrocytes 506
Numerous Transport Proteins Enable Plant Vacuoles to Accumulate Metabolites and Ions 507
11.6 Transcellular Transport 508
Multiple Transport Proteins Are Needed to Move Glucose and Amino Acids Across Epithelia 508
Simple Rehydration Therapy Depends on the Osmotic Gradient Created by Absorption of Glucose and Na+ 509
Parietal Cells Acidify the Stomach Contents While Maintaining a Neutral Cytosolic pH 509
Bone Resorption Requires the Coordinated Function of a V-Class Proton Pump and a Specific Chloride Channel 510
12 Cellular Energetics 513
12.1 First Step of Harvesting Energy from Glucose：Glycolysis 515
During Glycolysis （Stage Ⅰ），Cytosolic Enzymes Convert Glucose to Pyruvate 516
The Rate of Glycolysis Is Adjusted to Meet the Cell’s Need for ATP 516
Glucose Is Fermented When Oxygen Is Scarce 518
12.2 The Structure and Functions of Mitochondria 520
Mitochondria Are Multifunctional Organelles 520
Mitochondria Have Two Structurally and Functionally Distinct Membranes 520
Mitochondria Contain DNA Located in the Matrix 523
The Size，Structure，and Coding Capacity of mtDNA Vary Considerably Among Organisms 525
Products of Mitochondrial Genes Are Not Exported 526
Mitochondria Evolved from a Single Endosymbiotic Event Involving a Rickettsia-Like Bacterium 527
Mitochondrial Genetic Codes Differ from the Standard Nuclear Code 527
Mutations in Mitochondrial DNA Cause Several Genetic Diseases in Humans 528
Mitochondria Are Dynamic Organelles That Interact Directly with One Another 528
Mitochondria Are Influenced by Direct Contacts with the Endoplasmic Reticulum 529
12.3 The Citric Acid Cycle and Fatty Acid Oxidation 533
In the First Part of Stage Ⅱ，Pyruvate Is Converted to Acetyl CoA and High-Energy Electrons 533
In the Second Part of Stage Ⅱ，the Citric Acid Cycle Oxidizes the Acetyl Group in Acetyl CoA to CO2 and Generates High-Energy Electrons 533
Transporters in the Inner Mitochondrial Membrane Help Maintain Appropriate Cytosolic and Matrix Concentrations of NAD+ and NADH 535
Mitochondrial Oxidation of Fatty Acids Generates ATP 536
Peroxisomal Oxidation of Fatty Acids Generates No ATP 537
12.4 The Electron-Transport Chain and Generation of the Proton-Motive Force 539
Oxidation of NADH and FADH2 Releases a Significant Amount of Energy 539
Electron Transport in Mitochondria Is Coupled to Proton Pumping 539
Electrons Flow “Downhill” Through a Series of Electron Carriers 540
Four Large Multiprotein Complexes Couple Electron Transport to Proton Pumping Across the Inner Mitochondrial Membrane 542
The Reduction Potentials of Electron Carriers in the Electron-Transport Chain Favor Electron Flow from NADH to O2 546
The Multiprotein Complexes of the Electron-Transport Chain Assemble into Supercomplexes 546
Reactive Oxygen Species Are By-Products of Electron Transport 547
Experiments Using Purified Electron-Transport Chain Complexes Established the Stoichiometry of Proton Pumping 549
The Proton-Motive Force in Mitochondria Is Due Largely to a Voltage Gradient Across the Inner Membrane 550
12.5 Harnessing the Proton-Motive Force to Synthesize ATP 551
The Mechanism of ATP Synthesis Is Shared Among Bacteria，Mitochondria，and Chloroplasts 552
ATP Synthase Comprises F 0 and F1 Multiprotein Complexes 553
Rotation of the F1 y Subunit，Driven by Proton Movement Through F0，Powers ATP Synthesis 554
Multiple Protons Must Pass Through ATP Synthase to Synthesize One ATP 555
F 0 c Ring Rotation Is Driven by Protons Flowing Through Transmembrane Channels 556
ATP-ADP Exchange Across the Inner Mitochondrial Membrane Is Powered by the Proton-Motive Force 556
The Rate of Mitochondrial Oxidation Normally Depends on ADP Levels 558
Mitochondria in Brown Fat Use the Proton-Motive Force to Generate Heat 558
12.6 Photosynthesis and Light-Absorbing Pigments 560
Thylakoid Membranes in Chloroplasts Are the Sites of Photosynthesis in Plants 560
Chloroplasts Contain Large DNAs Often Encoding More Than a Hundred Proteins 560
Three of the Four Stages in Photosynthesis Occur Only During Illumination 561
Photosystems Comprise a Reaction Center and Associated Light-Harvesting Complexes 563
Photoelectron Transport from Energized Reaction-Center Chlorophyll a Produces a Charge Separation 564
Internal Antennas and Light-Harvesting Complexes Increase the Efficiency of Photosynthesis 566
12.7 Molecular Analysis of Photosystems 567
The Single Photosystem of Purple Bacteria Generates a Proton-Motive Force but No O2 567
Chloroplasts Contain Two Functionally and Spatially Distinct Photosystems 567
Linear Electron Flow Through Both Plant Photosystems Generates a Proton-Motive Force，O2，and NADPH 568
An Oxygen-Evolving Complex Is Located on the Luminal Surface of the PSII Reaction Center 569
Multiple Mechanisms Protect Cells Against Damage from Reactive Oxygen Species During Photoelectron Transport 570
Cyclic Electron Flow Through PSI Generates a Proton-Motive Force but No NADPH or O2 570
Relative Activities of Photosystems Ⅰ and Ⅱ Are Regulated 571
12.8 CO2 Metabolism During Photosynthesis 573
Rubisco Fixes CO2 in the Chloroplast Stroma 573
Synthesis of Sucrose Using Fixed CO2 Is Completed in the Cytosol 573
Light and Rubisco Activase Stimulate CO2 Fixation 574
Photorespiration Competes with Carbon Fixation and Is Reduced in C4 Plants 576
13 Moving Proteins into Membranes and Organelles 583
13.1 Targeting Proteins To and Across the ER Membrane 585
Pulse-Chase Experiments with Purified ER Membranes Demonstrated That Secreted Proteins Cross the ER Membrane 586
A Hydrophobic N-Terminal Signal Sequence Targets Nascent Secretory Proteins to the ER 586
Cotranslational Translocation Is Initiated by Two GTP-Hydrolyzing Proteins 588
Passage of Growing Polypeptides Through the Translocon Is Driven by Translation 589
ATP Hydrolysis Powers Post-translational Translocation of Some Secretory Proteins in Yeast 591
13.2 Insertion of Membrane Proteins into the ER 593
Several Topological Classes of Integral Membrane Proteins Are Synthesized on the ER 593
Internal Stop-Transfer Anchor and Signal-Anchor Sequences Determine Topology of Single-Pass Proteins 594
Multipass Proteins Have Multiple Internal Topogenic Sequences 597
A Phospholipid Anchor Tethers Some Cell-Surface Proteins to the Membrane 598
The Topology of a Membrane Protein Can Often Be Deduced from Its Sequence 599
13.3 Protein Modifications，Folding，and Quality Control in the ER 601
A Preformed N-Linked Oligosaccharide Is Added to Many Proteins in the Rough ER 601
Oligosaccharide Side Chains May Promote Folding and Stability of Glycoproteins 602
Disulfide Bonds Are Formed and Rearranged by Proteins in the ER Lumen 603
Chaperones and Other ER Proteins Facilitate Folding and Assembly of Proteins 604
Improperly Folded Proteins in the ER Induce Expression of Protein-Folding Catalysts 606
Unassembled or Misfolded Proteins in the ER Are Often Transported to the Cytosol for Degradation 607
13.4 Targeting of Proteins to Mitochondria and Chloroplasts 608
Amphipathic N-Terminal Targeting Sequences Direct Proteins to the Mitochondrial Matrix 609
Mitochondrial Protein Import Requires Outer-Membrane Receptors and Translocons in Both Membranes 610
Studies with Chimeric Proteins Demonstrate Important Features of Mitochondrial Protein Import 612
Three Energy Inputs Are Needed to Import Proteins into Mitochondria 613
Multiple Signals and Pathways Target Proteins to Submitochondrial Compartments 613
Import of Chloroplast Stromal Proteins Is Similar to Import of Mitochondrial Matrix Proteins 617
Proteins Are Targeted to Thylakoids by Mechanisms Related to Bacterial Protein Translocation 617
13.5 Targeting of Peroxisomal Proteins 619
A Cytosolic Receptor Targets Proteins with an SKL Sequence at the C-Terminus to the Peroxisomal Matrix 619
Peroxisomal Membrane and Matrix Proteins Are Incorporated by Different Pathways 621
13.6 Transport Into and Out of the Nucleus 622
Large and Small Molecules Enter and Leave the Nucleus via Nuclear Pore Complexes 622
Nuclear Transport Receptors Escort Proteins Containing Nuclear-Localization Signals into the Nucleus 624
A Second Type of Nuclear Transport Receptor Escorts Proteins Containing Nuclear-Export Signals Out of the Nucleus 625
Most mRNAs Are Exported from the Nucleus by a Ran-Independent Mechanism 627
14 Vesicular Traffic，Secretion，and Endocytosis 631
14.1 Techniques for Studying the Secretory Pathway 634
Transport of a Protein Through the Secretory Pathway Can Be Assayed in Live Cells 634
Yeast Mutants Define Major Stages and Many Components in Vesicular Transport 635
Cell-Free Transport Assays Allow Dissection of Individual Steps in Vesicular Transport 637
14.2 Molecular Mechanisms of Vesicle Budding and Fusion 638
Assembly of a Protein Coat Drives Vesicle Formation and Selection of Cargo Molecules 638
A Conserved Set of GTPase Switch Proteins Controls the Assembly of Different Vesicle Coats 639
Targeting Sequences on Cargo Proteins Make Specific Molecular Contacts with Coat Proteins 641
Rab GTPases Control Docking of Vesicles on Target Membranes 641
Paired Sets of SNARE Proteins Mediate Fusion of Vesicles with Target Membranes 642
Dissociation of SNARE Complexes After Membrane Fusion Is Driven by ATP Hydrolysis 644
14.3 Early Stages of the Secretory Pathway 645
COPII Vesicles Mediate Transport from the ER to the Golgi 645
COPI Vesicles Mediate Retrograde Transport Within the Golgi and from the Golgi to the ER 647
Anterograde Transport Through the Golgi Occurs by Cisternal Maturation 648
14.4 Later Stages of the Secretory Pathway 650
Vesicles Coated with Clathrin and Adapter Proteins Mediate Transport from the trans-Golgi 651
Dynamin Is Required for Pinching Off of Clathrin-Coated Vesicles 652
Mannose 6-Phosphate Residues Target Soluble Proteins to Lysosomes 653
Study of Lysosomal Storage Diseases Revealed Key Components of the Lysosomal Sorting Pathway 655
Protein Aggregation in the trans-Golgi May Function in Sorting Proteins to Regulated Secretory Vesicles 655
Some Proteins Undergo Proteolytic Processing After Leaving the trans-Golgi 656
Several Pathways Sort Membrane Proteins to the Apical or Basolateral Region of Polarized Cells 657
14.5 Receptor-Mediated Endocytosis 659
Cells Take Up Lipids from the Blood in the Form of Large，Well-Defined Lipoprotein Complexes 659
Receptors for Macromolecular Ligands Contain Sorting Signals That Target Them for Endocytosis 660
The Acidic pH of Late Endosomes Causes Most Receptor-Ligand Complexes to Dissociate 662
The Endocytic Pathway Delivers Iron to Cells Without Dissociation of the Transferrin-Transferrin Receptor Complex in Endosomes 663
14.6 Directing Membrane Proteins and Cytosolic Materials to the Lysosome 665
Multivesicular Endosomes Segregate Membrane Proteins Destined for the Lysosomal Membrane from Proteins Destined for Lysosomal Degradation 665
Retroviruses Bud from the Plasma Membrane by a Process Similar to Formation of Multivesicular Endosomes 666
The Autophagic Pathway Delivers Cytosolic Proteins or Entire Organelles to Lysosomes 667
15 Signal Transduction and G protein-Coupled Receptors 673
15.1 Signal Transduction：From Extracellular Signal to Cellular Response 675
Signaling Molecules Can Act Locally or at a Distance 675
Receptors Bind Only a Single Type of Hormone or a Group of Closely Related Hormones 676
Protein Kinases and Phosphatases Are Employed in Many Signaling Pathways 676
GTP-Binding Proteins Are Frequently Used in Signal Transduction Pathways as On/Off Switches 677
Intracellular “Second Messengers” Transmit Signals from Many Receptors 678
Signal Transduction Pathways Can Amplify the Effects of Extracellular Signals 679
15.2 Studying Cell-Surface Receptors and Signal Transduction Proteins 681
The Dissociation Constant Is a Measure of the Affinity of a Receptor for Its Ligand 681
Binding Assays Are Used to Detect Receptors and Determine Their Affinity and Specificity for Ligands 681
Near-Maximal Cellular Response to a Signaling Molecule Usually Does Not Require Activation of All Receptors 682
Sensitivity of a Cell to External Signals Is Determined by the Number of Cell-Surface Receptors and Their Affinity for Ligand 683
Hormone Analogs Are Widely Used as Drugs 683
Receptors Can Be Purified by Affinity Chromatography Techniques 683
Immunoprecipitation Assays and Affinity Techniques Can Be Used to Study the Activity of Signal Transduction Proteins 684
15.3 G Protein-Coupled Receptors：Structure and Mechanism 686
All G Protein-Coupled Receptors Share the Same Basic Structure 686
Ligand-Activated G Protein-Coupled Receptors Catalyze Exchange of GTP for GDP on the α Subunit of a Heterotrimeric G Protein 689
Different G Proteins Are Activated by Different GPCRs and In Turn Regulate Different Effector Proteins 691
15.4 G Protein-Coupled Receptors That Regulate Ion Channels 693
Acetylcholine Receptors in the Heart Muscle Activate a G Protein That Opens K+ Channels 693
Light Activates Rhodopsin in Rod Cells of the Eye 694
Activation of Rhodopsin by Light Leads to Closing of cGMP-Gated Cation Channels 695
Signal Amplification Makes the Rhodopsin Signal Transduction Pathway Exquisitely Sensitive 696
Rapid Termination of the Rhodopsin Signal Transduction Pathway Is Essential for the Temporal Resolution of Vision 697
Rod Cells Adapt to Varying Levels of Ambient Light by Intracellular Trafficking of Arrestin and Transducin 698
15.5 G Protein-Coupled Receptors That Activate or Inhibit Adenylyl Cyclase 699
Adenylyl Cyclase Is Stimulated and Inhibited by Different Receptor-Ligand Complexes 699
Structural Studies Established How Gαs·GTP Binds to and Activates Adenylyl Cyclase 701
cAMP Activates Protein Kinase A by Releasing Inhibitory Subunits 701
Glycogen Metabolism Is Regulated by Hormone-Induced Activation of PKA 702
cAMP-Mediated Activation of PKA Produces Diverse Responses in Different Cell Types 703
Signal Amplification Occurs in the cAMP-PKA Pathway 704
CREB Links cAMP and PKA to Activation of Gene Transcription 704
Anchoring Proteins Localize Effects of cAMP to Specific Regions of the Cell 705
Multiple Mechanisms Suppress Signaling from the GPCR/cAMP/PKA Pathway 706
15.6 G Protein-Coupled Receptors That Trigger Elevations in Cytosolic and Mitochondrial Calcium 708
Calcium Concentrations in the Mitochondrial Matrix，ER，and Cytosol Can Be Measured with Targeted Fluorescent Proteins 709
Activated Phospholipase C Generates Two Key Second Messengers Derived from the Membrane Lipid Phosphatidylinositol 4，5-Bisphosphate 709
The Ca 2+-Calmodulin Complex Mediates Many Cellular Responses to External Signals 713
DAG Activates Protein Kinase C 714
Integration of Ca 2+ and cAMP Second Messengers Regulates Glycogenolysis 714
Signal-Induced Relaxation of Vascular Smooth Muscle Is Mediated by a Ca 2+ -Nitric Oxide-cGMP-Activated Protein Kinase G Pathway 714
16 Signaling Pathways That Control Gene Expression 719
16.1 Receptor Serine Kinases That Activate Smads 722
TGF-β Proteins Are Stored in an Inactive Form in the Extracellular Matrix 722
Three Separate TGF-β Receptor Proteins Participate in Binding TGF-β and Activating Signal Transduction 722
Activated TGF-β Receptors Phosphorylate Smad Transcription Factors 724
The Smad3/Smad4 Complex Activates Expression of Different Genes in Different Cell Types 724
Negative Feedback Loops Regulate TGF-β/Smad Signaling 725
16.2 Cytokine Receptors and the JAK/STAT Signaling Pathway 726
Cytokines Influence the Development of Many Cell Types 727
Binding of a Cytokine to Its Receptor Activates One or More Tightly Bound JAK Protein Tyrosine Kinases 728
Phosphotyrosine Residues Are Binding Surfaces for Multiple Proteins with Conserved Domains 730
SH2 Domains in Action：JAK Kinases Activate STAT Transcription Factors 731
Multiple Mechanisms Down-Regulate Signaling from Cytokine Receptors 731
16.3 Receptor Tyrosine Kinases 734
Binding of Ligand Promotes Dimerization of an RTK and Leads to Activation of Its Intrinsic Tyrosine Kinase 734
Homo- and Hetero-oligomers of Epidermal Growth Factor Receptors Bind Members of the Epidermal Growth Factor Family 735
Activation of the EGF Receptor Results in the Formation of an Asymmetric Active Kinase Dimer 736
Multiple Mechanisms Down-Regulate Signaling from RTKs 737
16.4 The Ras/MAP Kinase Pathway 739
Ras，a GTPase Switch Protein，Operates Downstream of Most RTKs and Cytokine Receptors 739
Genetic Studies in Drosophila Identified Key Signal-Transducing Proteins in the Ras/MAP Kinase Pathway 739
Receptor Tyrosine Kinases Are Linked to Ras by Adapter Proteins 741
Binding of Sos to Inactive Ras Causes a Conformational Change That Triggers an Exchange of GTP for GDP 742
Signals Pass from Activated Ras to a Cascade of Protein Kinases Ending with MAP Kinase 742
Phosphorylation of MAP Kinase Results in a Conformational Change That Enhances Its Catalytic Activity and Promotes Its Dimerization 744
MAP Kinase Regulates the Activity of Many Transcription Factors Controlling Early Response Genes 745
G Protein-Coupled Receptors Transmit Signals to MAP Kinase in Yeast Mating Pathways 746
Scaffold Proteins Separate Multiple MAP Kinase Pathways in Eukaryotic Cells 746
16.5 Phosphoinositide Signaling Pathways 748
Phospholipase Cγ Is Activated by Some RTKs and Cytokine Receptors 749
Recruitment of PI-3 Kinase to Activated Receptors Leads to Synthesis of Three Phosphorylated Phosphatidylinositols 749
Accumulation of PI 3-Phosphates in the Plasma Membrane Leads to Activation of Several Kinases 750
Activated Protein Kinase B Induces Many Cellular Responses 750
The PI-3 Kinase Pathway Is Negatively Regulated by PTEN Phosphatase 751
16.6 Signaling Pathways Controlled by Ubiquitinylation and Protein Degradation：Wnt，Hedgehog，and NF-κB 751
Wnt Signaling Triggers Release of a Transcription Factor from a Cytosolic Protein Complex 752
Concentration Gradients of Wnt Protein Are Essential for Many Steps in Development 753
Hedgehog Signaling Relieves Repression of Target Genes 754
Hedgehog Signaling in Vertebrates Requires Primary Cilia 757
Degradation of an Inhibitor Protein Activates the NF-κB Transcription Factor 757
Polyubiquitin Chains Serve as Scaffolds Linking Receptors to Downstream Proteins in the NF-κB Pathway 760
16.7 Signaling Pathways Controlled by Protein Cleavage：Notch/Delta，SREBP，and Alzheimer’s Disease 761
On Binding Delta，the Notch Receptor Is Cleaved，Releasing a Component Transcription Factor 761
Matrix MetaIloproteases Catalyze Cleavage of Many Signaling Proteins from the Cell Surface 763
Inappropriate Cleavage of Amyloid Precursor Protein Can Lead to Alzheimer’s Disease 763
Regulated Intramembrane Proteolysis of SREBPs Releases a Transcription Factor That Acts to Maintain Phospholipid and Cholesterol Levels 763
16.8 Integration of Cellular Responses to Multiple Signaling Pathways：Insulin Action 766
Insulin and Glucagon Work Together to Maintain a Stable Blood Glucose Level 766
A Rise in Blood Glucose Triggers Insulin Secretion from the β Islet Cells 767
In Fat and Muscle Cells，Insulin Triggers Fusion of Intracellular Vesicles Containing the GLUT4 Glucose Transporter to the Plasma Membrane 767
Insulin Inhibits Glucose Synthesis and Enhances Storage of Glucose as Glycogen 769
Multiple Signal Transduction Pathways Interact to Regulate Adipocyte Differentiation Through PPARγ，the Master Transcriptional Regulator 770
Inflammatory Hormones Cause Derangement of Adipose Cell Function in Obesity 770
17 Cell Organization and Movement Ⅰ：Microfilaments 775
17.1 Microfilaments and Actin Structures 778
Actin Is Ancient，Abundant，and Highly Conserved 778
G-Actin Monomers Assemble into Long，Helical F-Actin Polymers 779
F-Actin Has Structural and Functional Polarity 780
17.2 Dynamics of Actin Filaments 781
Actin Polymerization In Vitro Proceeds in Three Steps 781
Actin Filaments Grow Faster at （+） Ends Than at （-） Ends 782
Actin Filament Treadmilling Is Accelerated by Profilin and Cofilin 784
Thymosin-β4 Provides a Reservoir of Actin for Polymerization 785
Capping Proteins Block Assembly and Disassembly at Actin Filament Ends 785
17.3 Mechanisms of Actin Filament Assembly 786
Formins Assemble Unbranched Filaments 786
The Arp2/3 Complex Nucleates Branched Filament Assembly 787
Intracellular Movements Can Be Powered by Actin Polymerization 789
Microfilaments Function in Endocytosis 790
Toxins That Perturb the Pool of Actin Monomers Are Useful for Studying Actin Dynamics 791
17.4 Organization of Actin-Based Cellular Structures 793
Cross-Linking Proteins Organize Actin Filaments into Bundles or Networks 793
Adapter Proteins Link Actin Filaments to Membranes 793
17.5 Myosins：Actin-Based Motor Proteins 796
Myosins Have Head，Neck，and Tail Domains with Distinct Functions 797
Myosins Make Up a Large Family of Mechanochemical Motor Proteins 798
Conformational Changes in the Myosin Head Couple ATP Hydrolysis to Movement 800
Myosin Heads Take Discrete Steps Along Actin Filaments 802
17.6 Myosin-Powered Movements 803
Myosin Thick Filaments and Actin Thin Filaments in Skeletal Muscle Slide Past Each Other During Contraction 803
Skeletal Muscle Is Structured by Stabilizing and Scaffolding Proteins 805
Contraction of Skeletal Muscle Is Regulated by Ca 2+ and Actin-Binding Proteins 805
Actin and Myosin Ⅱ Form Contractile Bundles in Nonmuscle Cells 807
Myosin-Dependent Mechanisms Regulate Contraction in Smooth Muscle and Nonmuscle Cells 808
Myosin V-Bound Vesicles Are Carried Along Actin Filaments 808
17.7 Cell Migration：Mechanism，Signaling，and Chemotaxis 811
Cell Migration Coordinates Force Generation with Cell Adhesion and Membrane Recycling 811
The Small GTP-Binding Proteins Cdc42，Rac，and Rho Control Actin Organization 813
Cell Migration Involves the Coordinate Regulation of Cdc42，Rac，and Rho 815
Migrating Cells Are Steered by Chemotactic Molecules 816
18 Cell Organization and Movement Ⅱ：Microtubules and Intermediate Filaments 821
18.1 Microtubule Structure and Organization 822
Microtubule Walls Are Polarized Structures Built from αβ-Tubulin Dimers 822
Microtubules Are Assembled from MTOCs to Generate Diverse Configurations 824
18.2 Microtubule Dynamics 827
Individual Microtubules Exhibit Dynamic Instability 827
Localized Assembly and “Search and Capture” Help Organize Microtubules 829
Drugs Affecting Tubulin Polymerization Are Useful Experimentally and in Treatment of Diseases 829
18.3 Regulation of Microtubule Structure and Dynamics 830
Microtubules Are Stabilized by Side-Binding Proteins 830
+TIPs Regulate the Properties and Functions of the Microtubule （+） End 831
Other End-Binding Proteins Regulate Microtubule Disassembly 832
18.4 Kinesins and Dyneins：Microtubule-Based Motor Proteins 833
Organelles in Axons Are Transported Along Microtubules in Both Directions 833
Kinesin-1 Powers Anterograde Transport of Vesicles Down Axons Toward the （+） Ends of Microtubules 835
The Kinesins Form a Large Protein Superfamily with Diverse Functions 835
Kinesin-1 Is a Highly Processive Motor 836
Dynein Motors Transport Organelles Toward the （-） Ends of Microtubules 838
Kinesins and Dyneins Cooperate in the Transport of Organelles Throughout the Cell 841
Tubulin Modifications Distinguish Different Classes of Microtubules and Their Accessibility to Motors 842
18.5 Cilia and Flagella：Microtubule-Based Surface Structures 844
Eukaryotic Cilia and Flagella Contain Long Doublet Microtubules Bridged by Dynein Motors 844
Ciliary and Flagellar Beating Are Produced by Controlled Sliding of Outer Doublet Microtubules 844
Intraflagellar Transport Moves Material Up and Down Cilia and Flagella 845
Primary Cilia Are Sensory Organelles on Interphase Cells 847
Defects in Primary Cilia Underlie Many Diseases 848
18.6 Mitosis 849
Centrosomes Duplicate Early in the Cell Cycle in Preparation for Mitosis 849
Mitosis Can Be Divided into Six Stages 850
The Mitotic Spindle Contains Three Classes of Microtubules 851
Microtubule Dynamics Increase Dramatically in Mitosis 852
Mitotic Asters Are Pushed Apart by Kinesin-5 and Oriented by Dynein 853
Chromosomes Are Captured and Oriented During Prometaphase 853
Duplicated Chromosomes Are Aligned by Motors and Microtubule Dynamics 854
The Chromosomal Passenger Complex Regulates Microtubule Attachment at Kinetochores 855
Anaphase A Moves Chromosomes to Poles by Microtubule Shortening 857
Anaphase B Separates Poles by the Combined Action of Kinesins and Dynein 858
Additional Mechanisms Contribute to Spindle Formation 858
Cytokinesis Splits the Duplicated Cell in Two 859
Plant Cells Reorganize Their Microtubules and Build a New Cell Wall in Mitosis 860
18.7 Intermediate Filaments 861
Intermediate Filaments Are Assembled from Subunit Dimers 861
Intermediate Filaments Are Dynamic 861
Cytoplasmic Intermediate Filament Proteins Are Expressed in a Tissue-Specific Manner 862
Lamins Line the Inner Nuclear Envelope To Provide Organization and Rigidity to the Nucleus 865
Lamins Are Reversibly Disassembled by Phosphorylation During Mitosis 866
18.8 Coordination and Cooperation Between Cytoskeletal Elements 867
Intermediate Filament-Associated Proteins Contribute to Cellular Organization 867
Microfilaments and Microtubules Cooperate to Transport Melanosomes 867
Cdc42 Coordinates Microtubules and Microfilaments During Cell Migration 867
Advancement of Neural Growth Cones Is Coordinated by Microfilaments and Microtubules 868
19 The Eukaryotic Cell Cycle 873
19.1 Overview of the Cell Cycle and Its Control 875
The Cell Cycle Is an Ordered Series of Events Leading to Cell Replication 875
Cyclin-Dependent Kinases Control the Eukaryotic Cell Cycle 876
Several Key Principles Govern the Cell Cycle 876
19.2 Model Organisms and Methods of Studying the Cell Cycle 877
Budding and Fission Yeasts Are Powerful Systems for Genetic Analysis of the Cell Cycle 877
Frog Oocytes and Early Embryos Facilitate Biochemical Characterization of the Cell Cycle Machinery 878
Fruit Flies Reveal the Interplay Between Development and the Cell Cycle 879
The Study of Tissue Culture Cells Uncovers Cell Cycle Regulation in Mammals 880
Researchers Use Multiple Tools to Study the Cell Cycle 881
19.3 Regulation of CDK Activity 882
Cyclin-Dependent Kinases Are Small Protein Kinases That Require a Regulatory Cyclin Subunit for Their Activity 883
Cyclins Determine the Activity of CDKs 884
Cyclin Levels Are Primarily Regulated by Protein Degradation 885
CDKs Are Regulated by Activating and Inhibitory Phosphorylation 886
CDK Inhibitors Control Cyclin-CDK Activity 886
Genetically Engineered CDKs Led to the Discovery of CDK Functions 887
19.4 Commitment to the Cell Cycle and DNA Replication 887
Cells Are Irreversibly Committed to Division at a Cell Cycle Point Called START or the Restriction Point 888
The E2F Transcription Factor and Its Regulator Rb Control the G1-S Phase Transition in Metazoans 889
Extracellular Signals Govern Cell Cycle Entry 889
Degradation of an S Phase CDK Inhibitor Triggers DNA Replication 890
Replication at Each Origin Is Initiated Once and Only Once During the Cell Cycle 892
Duplicated DNA Strands Become Linked During Replication 893
19.5 Entry into Mitosis 895
Precipitous Activation of Mitotic CDKs Initiates Mitosis 896
Mitotic CDKs Promote Nuclear Envelope Breakdown 897
Mitotic CDKs Promote Mitotic Spindle Formation 897
Chromosome Condensation Facilitates Chromosome Segregation 899
19.6 Completion of Mitosis：Chromosome Segregation and Exit from Mitosis 901
Separase-Mediated Cleavage of Cohesins Initiates Chromosome Segregation 901
APC/C Activates Separase Through Securin Ubiquitinylation 901
Mitotic CDK Inactivation Triggers Exit from Mitosis 902
Cytokinesis Creates Two Daughter Cells 903
19.7 Surveillance Mechanisms in Cell Cycle Regulation 904
Checkpoint Pathways Establish Dependencies and Prevent Errors in the Cell Cycle 905
The Growth Checkpoint Pathway Ensures That Cells Enter the Cell Cycle Only After Sufficient Macromolecule Biosynthesis 905
The DNA Damage Response System Halts Cell Cycle Progression When DNA Is Compromised 905
The Spindle Assembly Checkpoint Pathway Prevents Chromosome Segregation Until Chromosomes Are Accurately Attached to the Mitotic Spindle 908
The Spindle Position Checkpoint Pathway Ensures That the Nucleus Is Accurately Partitioned Between Two Daughter Cells 909
19.8 Meiosis：A Special Type of Cell Division 911
Extracellular and Intracellular Cues Regulate Germ Cell Formation 912
Several Key Features Distinguish Meiosis from Mitosis 912
Recombination and a Meiosis-Specific Cohesin Subunit Are Necessary for the Specialized Chromosome Segregation in Meiosis Ⅰ 915
Co-orienting Sister Kinetochores Is Critical for Meiosis I Chromosome Segregation 917
DNA Replication Is Inhibited Between the Two Meiotic Divisions 917
Part Ⅳ Cell Growth and Differentiation 921
20 Integrating Cells into Tissues 921