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Essential Cell Biology: An Introduction to

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essential cell biology
second edition

Bruce Alberts • Dennis Bray

Karen Hopkin • Alexander Johnson
Julian Lewis • Martin Raff
Keith Roberts • Peter Walter

Garland Science
Taylor & Francis Group
Contents and Special Features

Chapter 1 Introduction to Cells 1

Panel 1-1 Light and electron microscopy 8
Panel 1-2 Cells: the principal features of animal, plant, and bacterial cells 25
How We Know Life's common mechanisms 30

Chapter 2 Chemical Components of Cells 39

How We Know What are macromolecules? 60
Panel 2-1 Chemical bonds and groups 66
Panel 2-2 The chemical properties of water 68
Panel 2-3 An outline of some of the types of sugars 70
Panel 2-4 Fatty acids and other lipids 72
Panel 2-5 The 20 amino acids found in proteins 74
Panel 2-6 A survey of the nucleotides 76
Panel 2-7 The principal types of weak noncovalent bonds 78

Chapter 3 Energy, Catalysis, and Biosynthesis 83

Panel 3-1 Free energy and biological reactions 96
How We Know Using kinetics to model and manipulate metabolic pathways 103
Chapter 4 Protein Structure and Function 119
Panel4-1 A few examples of some general protein functions 120
How We Know Probing protein structure 129
Panel 4-2 Four different ways of depicting a small protein 132
Panel 4-3 ; Cell breakage and initial fractionation of cell extracts 160
Panel 4-4 Protein separation by chromatography 162
Panel 4-5 Protein separation by electrophoresis 163
Panel 4-6 Making and using antibodies 164

Chapter 5 DNA and Chromosomes 169

How We Know Genes are made of DNA 172

Chapter 6 DNA Replication, Repair, and Recombination 195

How We Know Finding replication origins 198
Chapter 7 From DNA to Protein: How Cells Read the Genome 229
How We Know Cracking the genetic code 246

Chapter 8 Control of Gene Expression 267

How We Know Gene regulation—the story of eve 282

Chapter 9 How Genes and Genomes Evolve 293

How We Know Counting genes 314

ix
Chapter 10 Manipulating Genes and Cells 323
How We Know Sequencing the human genome 334

Chapter 11 Membrane Structure 365

How We Know Measuring membrane flow 384

Chapter 12 Membrane Transport 389

How We Know Squid reveal secrets of membrane excitability 414

Chapter 13 How Cells Obtain Energy from Food 427

Panel 13-1 Details of the 10 steps of glycolysis 432
How We Know Unraveling the citric acid cycle 442
Panel 13-2 The complete citric acid cycle 450

Chapter 14 Energy Generation in Mitochondria and Chloroplasts 453

How We Know How chemiosmotic coupling drives ATP synthesis 460
Panel 14-1 Redox potentials 471

Chapter 15 Intracellular Compartments and Transport 497

How We Know Tracking protein and vesicle transport 520

Chapter-16 Cell Communication 533

How We Know Untangling cell signaling pathways 561

Chapter 17 Cytoskeleton 573

How We Know Pursuing motor proteins 586

Chapter 18 Cell-Cycle Control and Cell Death 611

How We Know Discovery of cyclins and Cdks 618
Chapter 19 Cell Division 637
Panel 19-1 The principal ^stages of M phase in an animal cell 642
How We Know Building the mitotic spindle 646

Chapter 20 Genetics, Meiosis, and the Molecular Basis of Heredity 659

How We Know Reading genetic linkage maps 682
Panel 20-1 Some essentials of classical genetics 685

Chapter 21 Tissues and Cancer 697

Panel 21-1 The cell types and tissues from which higher plants are constructed 700
How We Know Making sense of the genes that are critical for cancer 734

Answers to Questions
Glossary
Index 1:1

Contents and Special Features

 Detailed Contents

Chapter 1 Introduction to Cells

Unity and Diversity of Cells 1 Mitochondria Generate Energy from Food
Cells Vary Enormously in Appearance and to Power the Cell 17
Function 2 Chloroplasts Capture Energy from Sunlight 18
Living Cells All Have a Similar Basic Chemistry 3 Internal Membranes Create Intracellular
All Present-Day Cells Have Apparently Evolved Compartments with Different Functions ,' 19
from the Same Ancestor 4 The Cytosol Is a Concentrated Aqueous Gel
Genes Provide the Instructions for Cellular Form, of Large and Small Molecules 22
Function, and Complex Behavior 5 The Cytoskeleton Is Responsible for Directed
Cell Movements 22
Cells Under the Microscope 5 The Cytoplasm Is Far from Static 23
The Invention of the Light Microscope Led to Eucaryotic Cells May Have Originated as
the Discovery of Cells 6 Predators 24
Cells, Organelles, and Even Molecules Can Be
Seen Under the Microscope 7 M o d e l Organisms 27
Molecular Biologists Have Focused on E. co// 28
The Procaryotic Cell 11 Brewer's Yeast Is a Simple Eucaryotic Cell 28
Procaryotes Are the Most Diverse of Cells 14 Arabidopsis Has Been Chosen Out of 300,000
The World of Procaryotes Is Divided into Two Species as a Model Plant 28
Domains: Eubacteria and Archaea 15 The World of Animals Is Represented by a Fly,
p

The Eucaryotic Cell 16 a Worm, a Mouse, and Homo sapiens 29

Comparing Genome Sequences Reveals
The Nucleus Is the Information Store of the Cell 16
Life's Common Heritage 33

I Chapter 2 Chemical Components of Cells 39

Chemical Bonds 39 Cells Contain Four Major Families of Small
Cells Are Made of Relatively Few Types of Atoms 40 Organic Molecules 51
The Outermost Electrons Determine How Atoms Sugars Are Energy Sources for Cells and Subunits
Interact . 41 of Polysaccharides 52
Ionic Bonds Form by the Gain and Loss Fatty Acids Are Components of Cell Membranes 53
of Electrons 43 Amino Acids Are the Subunits of Proteins 55
Covalent Bonds Form by the Sharing of Electrons 45 Nucleotides Are the Subunits of DNA and RNA 56
Covalent Bonds Vary in Strength 46 Macromolecules in Cells 58
There Are Different Types of Covalent Bonds 47 Macromolecules Contain a Specific Sequence
Water Is Held Together by Hydrogen Bonds 48 of Subunits 59
Some Polar Molecules Form Acids and Bases Noncovalent Bonds Specify the Precise Shape
in Water 49 of a Macromolecule 62
Molecules in Cells 50 Noncovalent Bonds Allow a Macromolecule
A Cell Is Formed from Carbon Compounds 50 to Bind Other Selected Molecules 63

Detailed Contents
Chapter 3 Energy, Catalysis, and Biosynthesis 83
Catalysis and the Use of Energy Rapid Diffusion Allows Enzymes to Find Their
by Cells 84 Substrates 100
Biological Order Is Made Possible by the and KM Measure Enzyme Performance 101
Release of Heat Energy from Cells 85 Activated Carrier Molecules and
Photosynthetic Organisms Use Sunlight to Biosynthesis 106
Synthesize Organic Molecules 88
The Formation of an Activated Carrier Is
Cells Obtain Energy by the Oxidation of Coupled to an Energetically Favorable
Organic Molecules 89 Reaction 106
Oxidation and Reduction Involve Electron ATP Is the Most Widely Used Activated Carrier
Transfers 90 Molecule 107
Enzymes Lower the Barriers That Block Chemical Energy Stored in ATP Is Often Harnessed to
Reactions 91 Join two Molecules Together 108
The Free-Energy Change for a Reaction NADH and NADPH Are Important Electron
Determines Whether It Can Occur 93 109
Carriers
The Concentration of Reactants Influences the There Are Many Other Activated Carrier
Free-Energy Change and a Reaction's 111
Molecules in Cells
Direction 94
The Synthesis of Biological Polymers Requires
The Equilibrium Constant Indicates the an Energy Input 112
Strength of Molecular Interactions 95
For Sequential Reactions, the Changes in
Free Energy Are Additive 98

Chapter 4 Protein Structure and Function 119

The Shape and Structurenof Proteins 119 How Proteins Work 143
The Shape of a Protein Is Specified by Its All Proteins Bind to Other Molecules 143
Amino Acid Sequence 121 The Binding Sites of Antibodies Are Especially
Proteins Fold into a Conformation of Lowest Versatile 144
Energy ( , 124 Enzymes Are Powerful and Highly Specific
Proteins Come in a Wide Variety of Complicated Catalysts 145
Shapes 125 Lysozyme Illustrates How an Enzyme Works 146
The a Helix and the p Sheet Are Common Tightly Bound Small Molecules Add Extra
Folding Patterns 126 Functions to Proteins 149
Helices Form Readily in Biological Structures 134
How Proteins Are Controlled 150
P Sheets Form Rigid Structures at the Core
of Many Proteins 135 The Catalytic Activities of Enzymes Are Often
Regulated by Other Molecules 151
Proteins Have Several Levels of Organization 136
Allosteric Enzymes Have Two Binding Sites That
Few of the Many Possible Polypeptide Chains
Influence One Another 151
Will Be Useful 137 Phosphorylation Can Control Protein Activity
Proteins Can Be Classified into Families 138 by Triggering a Conformational Change 153
Large Protein Molecules Often Contain More GTP-Binding Proteins Are Also Regulated by the
Than One Polypeptide Chain 139 154
Cyclic Gain and Loss of a Phosphate Group
Proteins Can Assemble into Filaments, Sheets,
Nucleotide Hydrolysis Allows Motor Proteins to
or Spheres 140
Produce Large Movements in Cells 155
Some Types of Proteins Have Elongated
Fibrous Shapes 141 Proteins Often Form Large Complexes That
Function as Protein Machines 156
Extracellular Proteins Are Often Stabilized by
Large-Scale Studies of Protein Structure and
Covalent Cross-Linkages 142
Function Are Increasing the Pace of Discovery 157
Chapter 5 DNA and Chromosomes 169
The Structure and Function of DNA 170 Interphase Chromosomes Are Organized
A DNA Molecule Consists of Two Complementary Within the Nucleus 183
Chains of Nucleotides 171 The DNA in Chromosomes Is Highly Condensed, 183
The Structure of DNA Provides a Mechanism for Nucleosomes Are the Basic Units of Chromatin
Heredity 176 Structure 184
Chromosomes Have Several Levels of
The Structure, of Eucaryotic Chromosomes 177 DNA Packing 186
Eucarydtic DNA Is Packaged into Chromosomes 178 Interphase Chromosomes Contain Both
Chromosomes Contain Long Strings of Genes 179 Condensed and More Extended Forms of
Chromosomes Exist in Different States Chromatin 187
Throughout the Life of a Cell 181 Changes in Nucleosome Structure Allow
Access to DNA 189

Chapter 6 DNA Replication, Repair, and Recombination 195

DNA Replication 196 DNA Is Continually Suffering Damage in Cells 212
Base-Pairing Enables DNA Replication 196 The Stability of Genes Depends on DNA Repair 213
DNA Synthesis Begins at Replication Origins 197 The High Fidelity of DNA Maintenance Allows
Closely Related Species to Have Proteins
New DNA Synthesis Occurs at Replication Forks 201
with Very Similar Sequences 214
The Replication Fork Is Asymmetrical 202
DNA Polymerase Is Self-correcting 203 DNA Recombination 215
Short Lengths of RNA Act as Primers for Homologous Recombination Results in
DNA Synthesis 204 an Exact Exchange of Genetic Information 215
Proteins a t a Replication Fork Cooperate to Recombination Can Also Occur Between
Form a Replication Machine 206 Nonhomologous DNA Sequences 216
Telomerase Replicates the Ends of Eucaryotic Mobile Genetic Elements Encode the
Chromosomes 207 Components They Need for Movement 217
DNA Replication Is Relatively Well Understood 208 A Large Fraction of the Human Genome Is
Composed of Two Families of Transposable
DNA Repair 209
Sequences 218
Mutations Can Have Severe Consequences
Viruses Are Fully Mobile Genetic Elements
for an Organism 209
That Can Escape from Cells 219
A DNA Mismatch Repair System Removes
Retroviruses Reverse the Normal Flow of
Replication Errors That Escape the Replication
Genetic Information 221
Machine 210

Detailed Contents XIII

Chapter 7 From DNA to Protein: How Cells Read the Genome 229
From DNA to RNA 230 tRNA Molecules Match Amino Acids to Codons
Portions of DNA Sequence Are Transcribed in mRNA 245
into RNA 230 Specific Enzymes Couple tRNAs to the
Transcription Produces RNA Complementary Correct Amino Acid 248
to One Strand of DNA 231 The RNA Message Is Decoded on Ribosomes 248
Several Types of RNA Are Produced in Cells 233 The Ribosome Is a Ribozyme 251
Signals in DNA Tell RNA Polymerase Where Codons in mRNA Signal Where to Start and
to Start and Finish 234 to Stop Protein Synthesis 253
Eucaryotic RNAs Are Transcribed and Processed Proteins Are Made on Polyribosomes 254
Simultaneously in the Nucleus - 236 Inhibitors of Procaryotic Protein Synthesis
Eucaryotic Genes Are Interrupted by Noncoding Are Used as Antibiotics 255
Sequences 237 Carefully Controlled Protein Breakdown Helps
Introns Are Removed by RNA Splicing 238 Regulate the Amount of Each Protein in
Mature Eucaryotic mRNAs Are Selectively a Cell 256
Exported from the Nucleus 241 There Are Many Steps Between DNA and
mRNA Molecules Are Eventually Degraded Protein 257
by the Cell 242 RNA a n d the Origins of Life 258
The Earliest Cells May Have Had Introns in
Life Requires Autocatalysis 259
Their Genes 242
RNA Can Both Store Information and Catalyze
From RNA to Protein 243 Chemical Reactions 259
An mRNA Sequence Is Decoded in Sets of RNA Is Thought to Predate DNA in Evolution 261
Three Nucleotides 244

Chapter 8 Control of Gene Expression 267

An Overview of Gene Expression 268/ Eucaryotic RNA Polymerase Requires General
The Different Cell Types of a Multicellular Transcription Factors 276
Organism Contain the Same DNA 268 Eucaryotic Gene Regulatory Proteins Control
Different Cell Types Produce Different Sets Gene Expression from a Distance 278
of Proteins 268 Packing of Promoter DNA into Nucleosomes
A Cell Can Change the Expression of Its Genes Can Affect Initiation of Transcription 279
in Response to External Signals 270 The Molecular Mechanisms that Create
Gene Expression Can Be Regulated at Many
Specialized Cell Types 280
of the Steps in the Pathway from DNA to RNA
Eucaryotic Genes Are Regulated by
to Protein 270
Combinations of Proteins 281
How Transcriptional Switches Work 271 The Expression of Different Genes Can Be
Transcription Is Controlled by Proteins Binding Coordinated by a Single Protein 281
to Regulatory DNA Sequences 271 Combinatorial Control Can Create Different
Repressors Turn Genes Off, Activators Turn Cell Types 285
Them On 273 Stable Patterns of Gene Expression Can Be
An Activator and a Repressor Control the Transmitted to Daughter Cells 286
lac Operon 275 The Formation of an Entire Organ Can Be
Initiation of Eucaryotic Gene Transcription Is a Triggered by a Single Gene Regulatory
Complex Process 275 Protein 288
Chapter 9: How Genes and Genomes Evolve
Generating Genetic Variation 293
Five Main Types of Genetic Change Contribute
to Evolution 295
Genome Alterations Are Caused by Failures
of the Normal Mechanisms for Copying and
Maintaining DNA 296
DNA Duplications Give Rise to Families of
Related Genes Within a Single Cell 297
The Evolution of the Globin Gene Family
Shows How DNA Duplicatiops Contribute
to the Evolution of Organisms 298
Gene Duplication and Divergence Provide
a Critical Source of Genetic Novelty for
Evolving Organisms . 299
New Genes Can Be Generated by Repeating
the Same Exon 300
Novel Genes Can Also Be Created by
Exon Shuffling 300
The Evolution of Genomes Has Been
Accelerated by the Movement of
Transposable Elements 301
Genes Can Be Exchanged Between Organisms
by Horizontal Gene Transfer 302
293
Reconstructing Life's Family Tree 304
Genetic Changes That Offer an Organism
a Selective Advantage Are the Most Likely
to Be Preserved 304
The Genome Sequences of Two Species Differ
in Proportion to the Length of Time That
They Have Evolved Separately 305
Humans and Chimpanzee Genomes Are Similar in
Organization as Well as Detailed Sequence 306
Functionally Important Sequences Show Up as
Islands of DNA Sequence Conservation 307
Genome Comparisons Suggest That "Junk DNA"
is Dispensable 308
Sequence Conservation Allows Us to Trace Even
the Most Distant Evolutionary Relationships 309
Examining the Human G e n o m e 311
The Nucleotide Sequence of the Human Genome
Shows How Our Genes Are Arranged 311
Genetic Variation Within the Human Genome
Contributes to Our Individuality 313
Comparing Our DNA with That of Related
Organisms Helps Us to Interpret the Human
Genome 316
The Human Genome Contains Copious
Information Yet to Be Deciphered 317

Chapter 10 Manipulating Genes and Cells 323

Isolating Cells and Growing Them DNA Cloning 341
in Culture 324 DNA Ligase Joins DNA Fragments Together to
A Uniform Population of Cells Can Be Obtained Produce a Recombinant DNA Molecule 341
from a Tissue - 325 Recombinant DNA Can Be Copied Inside
Cells Can Be Grown in a Culture Dish 325 Bacterial Cells 341
Maintaining Eucaryotic Cells in Culture Poses Specialized Plasmid Vectors Are Used to
Special Challenges 326 Clone DNA 342
Human Genes Are Isolated by DNA Cloning 343
How DNA Molecules Are Analyzed 327
Restriction Nucleases Cut DNA Molecules cDNA Libraries Represent the mRNA Produced
by a Particular Tissue 346
at Specific Sites 328
Gel Electrophoresis Separates DNA Fragments The Polymerase Chain Reaction Amplifies
Selected DNA Sequences 347
of Different Sizes 329
The Nucleotide Sequence of DNA Fragments DNA Engineering 352
Can Be Determined 331 Completely Novel DNA Molecules Can Be
Genome Sequences Are Searched to Constructed 352
Identify Genes 333 Rare Cellular Proteins Can Be Made in Large
Amounts Using Cloned DNA 352
Nucleic A c i d Hybridization 336
Engineered Genes Can Reveal When and
DNA Hybridization Facilitates the Diagnosis Where a Gene Is Expressed 353
of Genetic Diseases 336 Mutant Organisms Best Reveal the Function
Hybridization on DNA Microarrays Monitors the of a Gene 355
Expression of Thdusands of Genes at Once 338 Animals Can Be Genetically Altered 356
In Situ Hybridization Locates Nucleic Acid Transgenic Plants Are Important for Both
Sequences in Cells or on Chromosomes 340 Cell Biology and Agriculture 359
Chapter 11 Membrane Structure 365
The Lipid Bilayer 366 A Polypeptide Chain Usually Crosses the
Membrane Lipids Form Bilayers in Water 367 Bilayer as an a Helix 376
The Lipid Bilayer Is a Two-dimensional Fluid 370 Membrane Proteins Can Be Solubilized
in Detergents and Purified 377
The Fluidity of a Lipid Bilayer Depends on
The Complete Structure Is Known for a Few
Its Composition 371
Membrane Proteins 378
The Lipid Bilayer Is Asymmetrical 373
The Plasma Membrane Is Reinforced
Lipid Asymmetry Is Generated Inside the Cell 373
by the Cell Cortex 380
M e m b r a n e Proteins 374 The Cell Surface Is Coated with Carbohydrate 381
Membrane Proteins Associate with the Lipid Cells Can Restrict the Movement of
Bilayer in Various Ways 375 Membrane Proteins 383

Chapter 12 Membrane Transport 389

Principles of Membrane Transport 389 Ion Channels and the Membrane
The Ion Concentrations Inside a Cell Are Very Potential 403
Different from Those Outside 390 Ion Channels Are Ion-Selective and Gated
Lipid Bilayers Are Impermeable to Solutes 403
Ion Channels Randomly Snap Between Open
and Ions 391 and Closed States
Membrane Transport Proteins Fall into Two 405
Different Types of Stimuli Influence the Opening
Classes: Carriers and Channels 391 and Closing of Ion Channels
Solutes Cross Membranes by Passive or Active 407
Voltage-gated Ion Channels Respond to the
Transport 392 Membrane Potential 407
Membrane Potential Is Governed by Membrane
Carrier Proteins a n d Their Functions 393
Permeability to Specific Ions 408
Concentration Gradients and Electrical
Forces Drive Passive Transport 393 Ion Channels a n d Signaling in
Active Transport Moves Solutes Against Their Nerve Cells 411
Electrochemical Gradients 395 Action Potentials Provide for Rapid Long-Distance
Animal Cells Use the Energy of ATP Hydrolysis Communication 411
to Pump Out Na + 396 Action Potentials Are Usually Mediated by
The Na + -K + Pump Is Driven by the Transient Voltage-gated Na + Channels 412
Addition of a Phosphate Group 397 Voltage-gated C a 2 + Channels Convert
Animal Cells Use the Na + Gradient to Take Up Electrical Signals into Chemical Signals at
Nutrients Actively 397 Nerve Terminals 417
The Na + -K + Pump Helps Maintain the Osmotic Transmitter-gated Channels in Target Cells Convert
Balance of Animal Cells 399
Chemical Signals Back into Electrical Signals 417
Intracellular C a 2 + Concentrations Are Kept Neurons Receive Both Excitatory and Inhibitory
Low by C a 2 + Pumps 401
Inputs 419
H + Gradients Are Used to Drive Membrane Transmitter-gated Ion Channels Are Major
Transport in Plants, Fungi, and Bacteria 402 Targets for Psychoactive Drugs 419
Synoptic Connections Enable You to Think,
Act, and Remember 420
Chapter 13 How Cells Obtain Energy from Food 427
The Breakdown of Sugars and Fats 428 Electron Transport Drives the Synthesis of
Food Molecules Are Broken Down in Three the Majority of the ATP in Most Cells 441
Stages 428 Storing and Utilizing Food 444
Glycolysis Is a Central ATP-producing Pathway 430
Organisms Store Food Molecules in Special
Fermentations Allow ATP to Be Produced in the Reservoirs 444
Absence of Oxygen 431
Chloroplasts and Mitochondria Collaborate
Glycolysis illustrates How Enzymes Couple in Plant Cells 446
Oxidation to Energy Storage 434
Many Biosynthetic Pathways Begin with
Sugars and Fats Are Both Degraded to
Glycolysis or the Citric Acid Cycle 447
Acetyl CoA in Mitochondria 435
Metabolism Is Organized and Regulated 448
The Citric Acid Cycle Generates NADH by
Oxidizing Acetyl Groups to CO2 439

Chapter 14 Energy Generation in Mitochondria and Chloroplasts 453

Cells Obtain Most of Their Energy by a Electron Transfers Release Large Amounts
Membrane-based Mechanism 453 of Energy 470
Mitochondria a n d Oxidative Metals Tightly Bound to Proteins Form Versatile
Phosphoryiation 455 Electron Carriers 472
Cytochrome Oxidase Catalyzes Oxygen
A Mitochondrion Contains an Outer
Reduction 474
Membrane, an Inner Membrane, and
The Mechanism of H+ Pumping Will Soon Be
Two Internal Compartments 455
Understood in Atomic Detail 475
High-Energy Electrons Are Generated via
Respiration Is Amazingly Efficient 476
the Citric Acid Cycle 457
A Chemiosmotic Process Converts Chloroplasts a n d Photosynthesis 478
Oxidation Energy into ATP 458 Chloroplasts Resemble Mitochondria but
Electrons Are Transferred Along a Chain of Have an Extra Compartment 478
Proteins in the Inner Mitochondrial Membrane 459 Chloroplasts Capture Energy from Sunlight
Electron Transport Generates a Proton and Use It to Fix Carbon 480
Gradient Across the Membrane 462 Excited Chlorophyll Molecules Funnel Energy
The Proton Gradient Drives ATP Synthesis 464 into a Reaction Center 481
Coupled Transport Across the Inner Light Energy Drives the Synthesis of ATP
Mitochondrial Membrane Is Driven by the and NADPH 482
Electrochemical Proton Gradient 466 Carbon Fixation Is Catalyzed by Ribulose
Proton Gradients Produce Most of the Bisphosphate Carboxylase 485
Cell's ATP 466 Carbon Fixation in Chloroplasts Generates
The Rapid Conversion of ADP to ATP in Sucrose and Starch 486
Mitochondria Maintains a High ATP/ADP Ratio
The Origins of Chloroplasts a n d
in Cells 468
Mitochondria 487
Electron-Transport Chains a n d Proton Oxidative Phosphoryiation Gave Ancient
Pumping 468 Bacteria an Evolutionary Advantage 488
Protons Are Readily Moved by the Transfer of Photosynthetic Bacteria Made Even Fewer
Electrons 468 Demands on Their Environment 489
The Redox Potential Is a Measure of Electron The Lifestyle of Methanococcus Suggests That
Affinities 469 Chemiosmotic Coupling Is an Ancient Process 490
Chapter 15 Intracellular Compartments and Transport 497
Membrane-enclosed Organelles 498 Vesicle Budding Is Driven by the Assembly
Eucaryotic Cells Contain a Basic Set of of a Protein Coat 513
Membrane-enclosed Organelles 498 The Specificity of Vesicle Docking Depends
on SNAREs 515
Membrane-enclosed Organelles Evolved
in Different Ways 500 Secretory Pathways 516
Protein Sorting 502 Most Proteins Are Covalently Modified in the ER 516
Proteins Are Imported into Organelles by Three Exit from the ER Is Controlled to Ensure Protein
Mechanisms 502 Quality . 517
Signal Sequences Direct Proteins to the Correct Proteins Are Further Modified and Sorted
Compartment 503 in the Golgi Apparatus 518
Proteins Enter the Nucleus Through Nuclear Secretory Proteins Are Released from the Cell
Pores 504 by Exocytosis 519
Proteins Unfold to Enter Mitochondria and Endocytic Pathways 523
Chloroplasts 506
Specialized Phagocytic Cells Ingest Large
Proteins Enter the Endoplasmic Reticulum ^
Particles 523
While Being Synthesized 507
Fluid and Macromolecules Are Taken Up by
Soluble Proteins Are Released into the
Pinocytosis 525
ER Lumen 509
Receptor-mediated Endocytosis Provides
Start and Stop Signals Determine the
a Specific Route into Animal Cells 525
Arrangement of a Transmembrane Protein
Endocytosed Macromolecules Are Sorted
in the Lipid Bilayer 510
in Endosomes 526
Vesicular Transport 512 Lysosomes Are the Principal Sites of Intracellular
Transport Vesicles Carry Soluble Proteins and Digestion 527
Membrane Between Compartments 512

Chapter 16 Cell Communication 533

General Principles of Cell Signaling 533 The Cyclic AMP Pathway Can Activate Enzymes
Signals Can Act over Long or Short Range 534 and Turn On Genes 550
Each Cell Responds to a Limited Set of Signals 536 The Inositol Phospholipid Pathway Triggers
a Rise in Intracellular C a 2 + 552
Receptors Relay Signals via Intracellular
Signaling Pathways 538 A C a 2 + Signal Triggers Many Biological
Processes 554
Nitric Oxide Crosses the Plasma Membrane and
Activates Intracellular Enzymes Directly 540 Intracellular Signaling Cascades Can Achieve
Astonishing Speed, Sensitivity, and Adaptability:
Some Hormones Cross the Plasma, Membrane
A Look at Photoreceptors in the Eye 555
and Bind to Intracellular Receptors 541
Cell-Surface Receptors Fall into Three Main Enzyme-linked Receptors 557
Classes 542 Activated Receptor Tyrosine Kinases Assemble a
lon-channel-linked Receptors Convert Chemical Complex of Intracellular Signaling Proteins 557
Signals into Electrical Ones 544
Receptor Tyrosine Kinases Activate the
Many Intracellular Signaling Proteins Act as GTP-binding Protein Ras 559
Molecular Switches 545 Some Enzyme-linked Receptors Activate
G-protein-linked Receptors 546 a Fast Track to the Nucleus 560
Protein Kinase Networks Integrate Information
Stimulation of G-protein-linked Receptors
to Control Complex Cell Behaviors 565
Activates G-Protein Subunits 546
Multicellularity and Cell Communication Evolved
Some G Proteins Regulate Ion Channels 548
Independently in Plants and Animals 566
Some G Proteins Activate Membrane-bound
Enzymes 549
Chapter 17 Cytoskeleton 573
Intermediate Filaments 574 Actin and Tubulin Polymerize by Similar
Intermediate Filaments Are Strong and Ropelike 575 Mechanisms 593
Intermediate Filaments Strengthen Cells Against Many Proteins Bind to Actin and Modify
Mechanical Stress 576 Its Properties , . 594
The Nuclear Envelope Is Supported by a An Actin-rich Cortex Underlies the Plasma
Meshwork of Intermediate Filaments 578 Membrane of Most Eucaryotic Cells 594
Cell Crawling Depends on Actin 595
Microtubules 579 Actin Associates with Myosin to Form
Microtubules Are Hollow Tubes with Structurally Contractile Structures 598
Distinct Ends . 579 Extracellular Signals Control the Arrangement
The Centrosome Is the Major Microtubule- of Actin Filaments 599
organizing Center in Animal Cells 580
Muscle Contraction 600
Growing Microtubules Show Dynamic Instability 581
Muscle Contraction Depends on Bundles
Microtubules Are Maintained by a Balance of
of Actin and Myosin 600
Assembly and Disassembly 582
During Muscle Contraction Actin Filaments
Microtubules Organize the Interior of the Cell 583 Slide Against Myosin Filaments 601
Motor Proteins Drive Intracellular Transport 584 Muscle Contraction Is Triggered by a Sudden
Organelles Move Along Microtubules 585 Rise in C a 2 + 603
Cilia and Flagella Contain Stable Microtubules Muscle Cells Perform Highly Specialized
Moved by Dynein 590 Functions in the Body 605
Actin Filaments 592
Actin Filaments Are Thin and Flexible 593

Chapter 18 Cell-Cycle Control and Cell Death 611

Overview of the Cell Cycle 612 Cells Can Dismantle Their Control System and
The Eucaryotic Cell Cycle Is Divided into Withdraw from the Cell Cycle 624
Four Phases .613 Programmed Cell Death (Apoptosis) 625
A Central Control System Triggers the Major
Apoptosis Is Mediated by an Intracellular
Processes of the Cell Cycle 614
Proteolytic Cascade 626
The Cell-Cycle Control System 615 The Death Program Is Regulated by the
The Cell-Cycle Control System Depends on Bcl-2 Family of Intracellular Proteins 627
Cyclically Activated Protein Kinases 616 Extracellular Control of Cell Numbers
Cyclin-dependent Protein Kinases Are a n d Cell Size 628
Regulated by the Accumulation and
Animal Cells Require Extracellular Signals
Destruction of Cyclins 617
to Divide, Grow, and Survive 629
The Activity of Cdks Is Also Regulated by
Phosphoryiation and Dephosphorylation 617 Mitogens Stimulate Cell Division 629
Different Cyclin-Cdk Complexes Trigger Extracellular Growth Factors Stimulate
Cells to Grow 631
Different Steps in the Cell Cycle 620
Animal Cells Require Survival Factors to Avoid
S-Cdk Initiates DNA Replication and Helps
Apoptosis 631
Block Rereplication 621
Some Extracellular Signal Proteins Inhibit
Cdks Are Inactive Through Most of Gi 622
Cell Growth, Division, or Survival 632
The Cell-Cycle Control System Can Arrest
the Cycle at Specific Checkpoints 622
Chapter 19 Cell Division 637
An Overview of M Phase 638 Chromosomes Line Up at the Spindle Equator
In Preparation for M Phase, DNA-binding at Metaphase 648
Proteins Configure Replicated Chromosomes Daughter Chromosomes Segregate
x
for Segregation 638 atAnaphase 649
The Cytoskeleton Carries Out Both Mitosis and The Nuclear Envelope Re-forms at Telophase 651
Cytokinesis 639 Some Organelles Fragment at Mitosis 651
Centrosomes Duplicate To Help Form the
Cytokinesis 652
Two Poles of the Mitotic Spindle 640
M Phase Is Conventionally Divided into The Mitotic Spindle Determines the Plane of
Cytoplasmic Cleavage V652
Six Stages 640
The Contractile Ring of Animal Cells Is Made
Mitosis ' 641 of Actin and Myosin 653
Microtubule Instability Facilitates the Formation Cytokinesis in Plant Cells Involves New
of the Mitotic Spindle 641 Cell-Wall Formation 654
The Mitotic Spindle Starts to Assemble in Gametes Are Formed by a Specialized Kind
Prophase 644 of Cell Division 655
Chromosomes Attach to the Mitotic Spindle
at Prometaphase 645

Chapter 20 Genetics, Meiosis, and the Molecular Basis of Heredity 659

The Benefits of Sex 660 Each Gamete Carries a Single Allele for Each
Sexual Reproduction Involves Both Diploid and Character 675
Haploid Cells 661 Mendel's Law of Segregation Applies to All
Sexual Reproduction Gives Organisms Sexually Reproducing Organisms 676
a Competitive Advantage 662 Alleles for Different Traits Segregate
Independently 677
Meiosis 663 The Behavior of Chromosomes During Meiosis
Haploid Cells Are Produced From Diploid Cells Underlies Mendel's Laws of Inheritance 678
Through Meiosis 664 The Frequency of Recombination Can Be
Meiosis Involves a Special Process of Used to Order Genes on Chromosomes 680
Chromosome Pairing , 664 The Phenotype of the Heterozygote Reveals
Extensive Recombination Occurs Between Whether an Allele is Dominant or Recessive 681
Maternal and Paternal Chromosomes 665 Mutant Alleles Sometimes Confer a Selective
Chromosome Pairing and Recombination Advantage 684
Ensure the Proper Segregation of Homologs 667
Genetics as a n Experimental Tool 686
The Second Meiotic Division Produces Haploid
Daughter Cells 667 The Classical Approach Begins with Random
The Haploid Cells Contain Extensively Mutagenesis 686
Reassorted Genetic Information 668 Genetic Screens Identify Mutants Deficient
Meiosis Is Not Flawless 670 in Cellular Processes 687
Fertilization Reconstitutes a Complete Genome 671 A Complementation Test Reveals Whether Two
Mutations Are in the Same Gene 688
Mendel a n d the Laws of Inheritance 672 Human Genes Are Inherited in Haplotype Blocks,
Mendel Chose to Study Traits That Are Inherited Which Can Aid in the Search for Mutations
in a Discrete Fashion 673 That Cause Disease 689
Mendel Could Disprove the Alternative Theories Complex Traits Are Influenced by Multiple
of Inheritance ' 674 Genes 691
Mendel's Experiments Were the First to Reveal Is Our Fate Encoded in Our DNA? 692
the Discrete feature of Heredity 674
Chapter 21 Tissues and Cancer 697
Extracellular Matrix a n d Connective Different Tissues Are Renewed at Different
Tissues 698 Rates 720
Plant Cells Have Tough External Walls 698 Stem Cells Generate a Continuous Supply of
Cellulose Fibers Give the Plant Cell Wall Terminally Differentiated Cells 721
Its Tensile Strength 702 Stem Cells Can Be Used to Repair Damaged
Animal Connective Tissues Consist Largely of Tissues 722
Extracellular Matrix 703 Nuclear Transplantation Provides a Way to
Collagen Provides Tensile Strength in Animal Generate Personalized ES Cells: the Strategy
of Therapeutic Cloning 725
Connective Tissues " 704
Cells Organize the Collagen That They Secrete 705 Cancer 726
Integrins Couple the Matrix Outside a Cell Cancer Cells Proliferate, Invade, and
to the Cytoskeleton Inside It 706 Metastasize . 726
Gels of Polysaccharide and Protein Fill Spaces Epidemiology Identifies Preventable Causes
and Resist Compression 706 of Cancer 727
Epithelial Sheets a n d Cell-Cell Junctions 709 Cancers Develop by an Accumulation of
Mutations 728
Epithelial Sheets Are Polarized and Rest on
a Basal Lamina 709 Cancers Evolve Properties That Give Them a
Competitive Advantage 729
Tight Junctions Make an Epithelium Leak-proof
and Separate Its Apical and Basal Surfaces 711 Many Diverse Types of Genes Are Critical
for Cancer 731
Cytoskeleton-linked Junctions Bind Epithelial
Cells Robustly to One Another and to the Colorectal Cancer Illustrates How Loss of a Gene
Basal Lamina s
712 Can Lead to Growth of a Tumor 732
Gap Junctions Allow Ions and Small Molecules An Understanding of Cancer Cell Biology
to Pass from Cell to Cell 715 Opens the Way to New Treatments 736

Tissue M a i n t e n a n c e a n d Renewal 717

Tissues Are Organized Mixtures of Many Cell
Types 718

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