essential cell biology
second edition
Bruce Alberts • Dennis Bray
Karen Hopkin • Alexander Johnson
Julian Lewis • Martin Raff
Keith Roberts • Peter Walter
Garland Science
Contents and Special Features
Chapter 1
Panel 1-1
Panel 1-2
How We Know
Chapter 2
How We Know
Panel 2-1
Panel 2-2
Panel 2-3
Panel 2-4
Panel 2-5
Panel 2-6
Panel 2-7
Chapter 3
Panel 3-1
How We Know
Chapter 4
Panel4-1
How We Know
Panel 4-2
Panel 4-3
;Panel 4-4
Panel 4-5
Panel 4-6
Chapter 5
How We Know
Chapter 6
How We Know
Chapter 7
How We Know
Chapter 8
How We Know
Chapter 9
How We Know
Introduction to Cells
Light and electron microscopy
Cells: the principal features of animal, plant, and bacterial cells
Life's common mechanisms
Chemical Components of Cells
What are macromolecules?
Chemical bonds and groups
The chemical properties of water
An outline of some of the types of sugars
Fatty acids and other lipids
The 20 amino acids found in proteins
A survey of the nucleotides
The principal types of weak noncovalent bonds
Energy, Catalysis, and Biosynthesis
Free energy and biological reactions
Using kinetics to model and manipulate metabolic pathways
Protein Structure and Function
A few examples of some general protein functions
Probing protein structure
Four different ways of depicting a small protein
Cell breakage and initial fractionation of cell extracts
Protein separation by chromatography
Protein separation by electrophoresis
Making and using antibodies
DNA and Chromosomes
Genes are made of DNA
DNA Replication, Repair, and Recombination
Finding replication origins
From DNA to Protein: How Cells Read the Genome
Cracking the genetic code
Control of Gene Expression
Gene regulation—the story of eve
How Genes and Genomes Evolve
Counting genes
1
8 25 3039
60 66 68 70 72 74 76 7883
96
103
119
120 129 132 160 162 163 164169
172
195
198
229
246267
282293
314
ixChapter 10
How We Know
Chapter 11
How We KnowChapter 12
How We KnowChapter 13
Panel 13-1
How We Know
Panel 13-2
Chapter 14
How We Know
Panel 14-1
Chapter 15
How We Know
Chapter-16
How We KnowChapter 17
How We KnowChapter 18
How We Know
Chapter 19
Panel 19-1
How We Know
Chapter 20
How We Know
Panel 20-1
Chapter 21
Panel 21-1
How We Know
Manipulating Genes and Cells
Sequencing the human genome
Membrane Structure
Measuring membrane flow
Membrane Transport
Squid reveal secrets of membrane excitability
How Cells Obtain Energy from Food
Details of the 10 steps of glycolysis
Unraveling the citric acid cycle
The complete citric acid cycle
Energy Generation in Mitochondria and Chloroplasts
How chemiosmotic coupling drives ATP synthesis
Redox potentials
Intracellular Compartments and Transport
Tracking protein and vesicle transport
Cell Communication
Untangling cell signaling pathways
Cytoskeleton
Pursuing motor proteins
Cell-Cycle Control and Cell Death
Discovery of cyclins and Cdks
Cell Division
The principal ^stages of M phase in an animal cell
Building the mitotic spindle
Genetics, Meiosis, and the Molecular Basis of Heredity
Reading genetic linkage maps
Some essentials of classical genetics
Tissues and Cancer
The cell types and tissues from which higher plants are constructed
Making sense of the genes that are critical for cancer
323
334365
384389
414
427
432 442 450453
460
471
497
520533
561
573
586611
618
637
642 646659
682 685697
700 734Answers to Questions
Glossary
Index
1:1
Detailed Contents
Chapter 1
Introduction to Cells
Unity and Diversity of Cells 1
Cells Vary Enormously in Appearance and
Function 2 Living Cells All Have a Similar Basic Chemistry 3 All Present-Day Cells Have Apparently Evolved
from the Same Ancestor 4 Genes Provide the Instructions for Cellular Form,
Function, and Complex Behavior 5 Cells Under the M i c r o s c o p e 5 The Invention of the Light Microscope Led to
the Discovery of Cells 6 Cells, Organelles, and Even Molecules Can Be
Seen Under the Microscope 7 The Procaryotic Cell 11 Procaryotes Are the Most Diverse of Cells 14 The World of Procaryotes Is Divided into Two
Domains: Eubacteria and Archaea 15 p
The Eucaryotic Cell 16 The Nucleus Is the Information Store of the Cell 16
Mitochondria Generate Energy from Food
to Power the Cell 17 Chloroplasts Capture Energy from Sunlight 18 Internal Membranes Create Intracellular
Compartments with Different Functions ,' 19 The Cytosol Is a Concentrated Aqueous Gel
of Large and Small Molecules 22 The Cytoskeleton Is Responsible for Directed
Cell Movements 22 The Cytoplasm Is Far from Static 23 Eucaryotic Cells May Have Originated as
Predators 24 M o d e l Organisms 27 Molecular Biologists Have Focused on E. co// 28 Brewer's Yeast Is a Simple Eucaryotic Cell 28
Arabidopsis Has Been Chosen Out of 300,000
Species as a Model Plant 28 The World of Animals Is Represented by a Fly,
a Worm, a Mouse, and Homo sapiens 29 Comparing Genome Sequences Reveals
Life's Common Heritage 33
I Chapter 2 Chemical Components of Cells
39
Chemical Bonds 39
Cells Are Made of Relatively Few Types of Atoms 40 The Outermost Electrons Determine How Atoms
Interact . 41 Ionic Bonds Form by the Gain and Loss
of Electrons 43 Covalent Bonds Form by the Sharing of Electrons 45 Covalent Bonds Vary in Strength 46 There Are Different Types of Covalent Bonds 47 Water Is Held Together by Hydrogen Bonds 48 Some Polar Molecules Form Acids and Bases
in Water 49 Molecules in Cells 50 A Cell Is Formed from Carbon Compounds 50
Cells Contain Four Major Families of Small
Organic Molecules 51 Sugars Are Energy Sources for Cells and Subunits
of Polysaccharides 52 Fatty Acids Are Components of Cell Membranes 53 Amino Acids Are the Subunits of Proteins 55 Nucleotides Are the Subunits of DNA and RNA 56 M a c r o m o l e c u l e s in Cells 58 Macromolecules Contain a Specific Sequence
of Subunits 59 Noncovalent Bonds Specify the Precise Shape
of a Macromolecule 62 Noncovalent Bonds Allow a Macromolecule
to Bind Other Selected Molecules 63
Chapter 3 Energy, Catalysis, and Biosynthesis
83
Catalysis and the Use of Energy
by Cells 84
Biological Order Is Made Possible by the
Release of Heat Energy from Cells 85 Photosynthetic Organisms Use Sunlight to
Synthesize Organic Molecules 88 Cells Obtain Energy by the Oxidation of
Organic Molecules 89 Oxidation and Reduction Involve Electron
Transfers 90 Enzymes Lower the Barriers That Block Chemical
Reactions 91 The Free-Energy Change for a Reaction
Determines Whether It Can Occur 93 The Concentration of Reactants Influences the
Free-Energy Change and a Reaction's
Direction 94 The Equilibrium Constant Indicates the
Strength of Molecular Interactions 95 For Sequential Reactions, the Changes in
Free Energy Are Additive 98
Rapid Diffusion Allows Enzymes to Find Their Substrates
and KM Measure Enzyme Performance
Activated Carrier Molecules and Biosynthesis
The Formation of an Activated Carrier Is Coupled to an Energetically Favorable Reaction
ATP Is the Most Widely Used Activated Carrier Molecule
Energy Stored in ATP Is Often Harnessed to Join two Molecules Together
NADH and NADPH Are Important Electron Carriers
There Are Many Other Activated Carrier Molecules in Cells
The Synthesis of Biological Polymers Requires an Energy Input 100 101 106 106 107 108 109 111 112
Chapter 4 Protein Structure and Function
The Shape and Structurenof Proteins 119
The Shape of a Protein Is Specified by Its
Amino Acid Sequence 121 Proteins Fold into a Conformation of Lowest
Energy ( , 124
Proteins Come in a Wide Variety of Complicated Shapes 125 The a Helix and the p Sheet Are Common
Folding Patterns 126 Helices Form Readily in Biological Structures 134 P Sheets Form Rigid Structures at the Core
of Many Proteins 135 Proteins Have Several Levels of Organization 136 Few of the Many Possible Polypeptide Chains
Will Be Useful 137 Proteins Can Be Classified into Families 138 Large Protein Molecules Often Contain More
Than One Polypeptide Chain 139 Proteins Can Assemble into Filaments, Sheets,
or Spheres 140 Some Types of Proteins Have Elongated
Fibrous Shapes 141 Extracellular Proteins Are Often Stabilized by
Covalent Cross-Linkages 142
How Proteins Work
All Proteins Bind to Other Molecules
The Binding Sites of Antibodies Are Especially Versatile
Enzymes Are Powerful and Highly Specific Catalysts
Lysozyme Illustrates How an Enzyme Works Tightly Bound Small Molecules Add Extra
Functions to Proteins
How Proteins Are Controlled
The Catalytic Activities of Enzymes Are Often Regulated by Other Molecules
Allosteric Enzymes Have Two Binding Sites That Influence One Another
Phosphorylation Can Control Protein Activity by Triggering a Conformational Change GTP-Binding Proteins Are Also Regulated by the
Cyclic Gain and Loss of a Phosphate Group Nucleotide Hydrolysis Allows Motor Proteins to
Produce Large Movements in Cells Proteins Often Form Large Complexes That
Function as Protein Machines
Large-Scale Studies of Protein Structure and Function Are Increasing the Pace of Discovery
119
143 143 144 145 146 149 150 151 151 153 154 155 156 157Chapter 5
DNA and Chromosomes
169
The Structure and Function of DNA 170
A DNA Molecule Consists of Two Complementary Chains of Nucleotides 171 The Structure of DNA Provides a Mechanism for
Heredity 176 The Structure, of Eucaryotic Chromosomes 177 Eucarydtic DNA Is Packaged into Chromosomes 178 Chromosomes Contain Long Strings of Genes 179 Chromosomes Exist in Different States
Throughout the Life of a Cell 181
Interphase Chromosomes Are Organized
Within the Nucleus 183 The DNA in Chromosomes Is Highly Condensed, 183 Nucleosomes Are the Basic Units of Chromatin
Structure 184 Chromosomes Have Several Levels of
DNA Packing 186 Interphase Chromosomes Contain Both
Condensed and More Extended Forms of
Chromatin 187 Changes in Nucleosome Structure Allow
Access to DNA 189
Chapter 6 DNA Replication, Repair, and Recombination
195
DNA Replication 196
Base-Pairing Enables DNA Replication 196 DNA Synthesis Begins at Replication Origins 197 New DNA Synthesis Occurs at Replication Forks 201 The Replication Fork Is Asymmetrical 202 DNA Polymerase Is Self-correcting 203 Short Lengths of RNA Act as Primers for
DNA Synthesis 204 Proteins a t a Replication Fork Cooperate to
Form a Replication Machine 206 Telomerase Replicates the Ends of Eucaryotic
Chromosomes 207 DNA Replication Is Relatively Well Understood 208 DNA Repair 209 Mutations Can Have Severe Consequences
for an Organism 209 A DNA Mismatch Repair System Removes
Replication Errors That Escape the Replication Machine 210
DNA Is Continually Suffering Damage in Cells 212 The Stability of Genes Depends on DNA Repair 213 The High Fidelity of DNA Maintenance Allows
Closely Related Species to Have Proteins
with Very Similar Sequences 214 DNA Recombination 215 Homologous Recombination Results in
an Exact Exchange of Genetic Information 215 Recombination Can Also Occur Between
Nonhomologous DNA Sequences 216 Mobile Genetic Elements Encode the
Components They Need for Movement 217 A Large Fraction of the Human Genome Is
Composed of Two Families of Transposable
Sequences 218 Viruses Are Fully Mobile Genetic Elements
That Can Escape from Cells 219 Retroviruses Reverse the Normal Flow of
Genetic Information 221
Chapter 7 From DNA to Protein: How Cells Read the Genome
229
From DNA to RNA 230
Portions of DNA Sequence Are Transcribed
into RNA 230 Transcription Produces RNA Complementary
to One Strand of DNA 231 Several Types of RNA Are Produced in Cells 233 Signals in DNA Tell RNA Polymerase Where
to Start and Finish 234 Eucaryotic RNAs Are Transcribed and Processed
Simultaneously in the Nucleus - 236 Eucaryotic Genes Are Interrupted by Noncoding
Sequences 237 Introns Are Removed by RNA Splicing 238 Mature Eucaryotic mRNAs Are Selectively
Exported from the Nucleus 241 mRNA Molecules Are Eventually Degraded
by the Cell 242 The Earliest Cells May Have Had Introns in
Their Genes 242 From RNA to Protein 243 An mRNA Sequence Is Decoded in Sets of
Three Nucleotides 244
tRNA Molecules Match Amino Acids to Codons in mRNA 245 Specific Enzymes Couple tRNAs to the
Correct Amino Acid 248 The RNA Message Is Decoded on Ribosomes 248 The Ribosome Is a Ribozyme 251 Codons in mRNA Signal Where to Start and
to Stop Protein Synthesis 253 Proteins Are Made on Polyribosomes 254 Inhibitors of Procaryotic Protein Synthesis
Are Used as Antibiotics 255 Carefully Controlled Protein Breakdown Helps
Regulate the Amount of Each Protein in
a Cell 256 There Are Many Steps Between DNA and
Protein 257 RNA a n d the Origins of Life 258 Life Requires Autocatalysis 259 RNA Can Both Store Information and Catalyze
Chemical Reactions 259 RNA Is Thought to Predate DNA in Evolution 261
Chapter 8 Control of Gene Expression
267
An Overview of Gene Expression
The Different Cell Types of a Multicellular Organism Contain the Same DNA Different Cell Types Produce Different Sets
of Proteins
A Cell Can Change the Expression of Its Genes in Response to External Signals
Gene Expression Can Be Regulated at Many of the Steps in the Pathway from DNA to RNA to Protein 268/ 268 268 270 270 271 How Transcriptional Switches Work
Transcription Is Controlled by Proteins Binding
to Regulatory DNA Sequences 271 Repressors Turn Genes Off, Activators Turn
Them On 273 An Activator and a Repressor Control the
lac Operon 275
Initiation of Eucaryotic Gene Transcription Is a
Complex Process 275
Eucaryotic RNA Polymerase Requires General
Transcription Factors 276 Eucaryotic Gene Regulatory Proteins Control
Gene Expression from a Distance 278 Packing of Promoter DNA into Nucleosomes
Can Affect Initiation of Transcription 279
The Molecular Mechanisms that Create
Specialized Cell Types 280
Eucaryotic Genes Are Regulated by
Combinations of Proteins 281 The Expression of Different Genes Can Be
Coordinated by a Single Protein 281 Combinatorial Control Can Create Different
Cell Types 285 Stable Patterns of Gene Expression Can Be
Transmitted to Daughter Cells 286 The Formation of an Entire Organ Can Be
Triggered by a Single Gene Regulatory
Chapter 9: How Genes and Genomes Evolve
293
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
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 Genetic Variation Within the Human Genome
Contributes to Our Individuality
Comparing Our DNA with That of Related Organisms Helps Us to Interpret the Human Genome
The Human Genome Contains Copious Information Yet to Be Deciphered
Chapter 10 Manipulating Genes and Cells
Isolating Cells and Growing Them
in Culture 324
A Uniform Population of Cells Can Be Obtained from a Tissue - 325 Cells Can Be Grown in a Culture Dish 325 Maintaining Eucaryotic Cells in Culture Poses
Special Challenges 326 How DNA Molecules Are Analyzed 327 Restriction Nucleases Cut DNA Molecules
at Specific Sites 328 Gel Electrophoresis Separates DNA Fragments
of Different Sizes 329 The Nucleotide Sequence of DNA Fragments
Can Be Determined 331 Genome Sequences Are Searched to
Identify Genes 333 Nucleic A c i d Hybridization 336 DNA Hybridization Facilitates the Diagnosis
of Genetic Diseases 336 Hybridization on DNA Microarrays Monitors the
Expression of Thdusands of Genes at Once 338
In Situ Hybridization Locates Nucleic Acid
Sequences in Cells or on Chromosomes 340
DNA Cloning
DNA Ligase Joins DNA Fragments Together to Produce a Recombinant DNA Molecule Recombinant DNA Can Be Copied Inside
Bacterial Cells
Specialized Plasmid Vectors Are Used to Clone DNA
Human Genes Are Isolated by DNA Cloning cDNA Libraries Represent the mRNA Produced
by a Particular Tissue
The Polymerase Chain Reaction Amplifies Selected DNA Sequences
DNA Engineering
Completely Novel DNA Molecules Can Be Constructed
Rare Cellular Proteins Can Be Made in Large Amounts Using Cloned DNA
Engineered Genes Can Reveal When and Where a Gene Is Expressed
Mutant Organisms Best Reveal the Function of a Gene
Animals Can Be Genetically Altered Transgenic Plants Are Important for Both
Cell Biology and Agriculture
311 313 316 317
323
341 341 341 342 343 346347
352
352 352 353 355 356 359Chapter 11 Membrane Structure
365
The Lipid Bilayer 366
Membrane Lipids Form Bilayers in Water 367 The Lipid Bilayer Is a Two-dimensional Fluid 370 The Fluidity of a Lipid Bilayer Depends on
Its Composition 371 The Lipid Bilayer Is Asymmetrical 373 Lipid Asymmetry Is Generated Inside the Cell 373 M e m b r a n e Proteins 374 Membrane Proteins Associate with the Lipid
Bilayer in Various Ways 375
A Polypeptide Chain Usually Crosses the
Bilayer as an a Helix 376 Membrane Proteins Can Be Solubilized
in Detergents and Purified 377 The Complete Structure Is Known for a Few
Membrane Proteins 378 The Plasma Membrane Is Reinforced
by the Cell Cortex 380 The Cell Surface Is Coated with Carbohydrate 381 Cells Can Restrict the Movement of
Membrane Proteins 383
Chapter 12 Membrane Transport
Principles of Membrane Transport
The Ion Concentrations Inside a Cell Are Very Different from Those Outside
Lipid Bilayers Are Impermeable to Solutes and Ions
Membrane Transport Proteins Fall into Two Classes: Carriers and Channels
Solutes Cross Membranes by Passive or Active Transport
Carrier Proteins a n d Their Functions Concentration Gradients and Electrical
Forces Drive Passive Transport
Active Transport Moves Solutes Against Their Electrochemical Gradients
Animal Cells Use the Energy of ATP Hydrolysis to Pump Out Na+
The Na+-K+ Pump Is Driven by the Transient Addition of a Phosphate Group
Animal Cells Use the Na+ Gradient to Take Up Nutrients Actively
The Na+-K+ Pump Helps Maintain the Osmotic Balance of Animal Cells
Intracellular C a2 + Concentrations Are Kept Low by C a2 + Pumps
H+ Gradients Are Used to Drive Membrane Transport in Plants, Fungi, and Bacteria
389 390 391 391 392 393 393 395 396 397 397 399 401 402
389
403 403 405 407Ion Channels and the Membrane Potential
Ion Channels Are Ion-Selective and Gated Ion Channels Randomly Snap Between Open
and Closed States
Different Types of Stimuli Influence the Opening and Closing of Ion Channels
Voltage-gated Ion Channels Respond to the
Membrane Potential 407 Membrane Potential Is Governed by Membrane
Permeability to Specific Ions 408 Ion Channels a n d Signaling in
Nerve Cells 411 Action Potentials Provide for Rapid Long-Distance
Communication 411 Action Potentials Are Usually Mediated by
Voltage-gated Na+ Channels
Voltage-gated C a2 + Channels Convert Electrical Signals into Chemical Signals at Nerve Terminals
Transmitter-gated Channels in Target Cells Convert Chemical Signals Back into Electrical Signals 417 Neurons Receive Both Excitatory and Inhibitory
Inputs 419 Transmitter-gated Ion Channels Are Major
Targets for Psychoactive Drugs 419 Synoptic Connections Enable You to Think,
Act, and Remember 420 412
Chapter 13 How Cells Obtain Energy from Food
427
The Breakdown of Sugars and Fats 428
Food Molecules Are Broken Down in Three
Stages 428 Glycolysis Is a Central ATP-producing Pathway 430 Fermentations Allow ATP to Be Produced in the
Absence of Oxygen 431 Glycolysis illustrates How Enzymes Couple
Oxidation to Energy Storage 434 Sugars and Fats Are Both Degraded to
Acetyl CoA in Mitochondria 435 The Citric Acid Cycle Generates NADH by
Oxidizing Acetyl Groups to CO2 439
Electron Transport Drives the Synthesis of
the Majority of the ATP in Most Cells 441
Storing and Utilizing Food 444
Organisms Store Food Molecules in Special
Reservoirs 444 Chloroplasts and Mitochondria Collaborate
in Plant Cells 446 Many Biosynthetic Pathways Begin with
Glycolysis or the Citric Acid Cycle 447 Metabolism Is Organized and Regulated 448
Chapter 14 Energy Generation in Mitochondria and Chloroplasts
453
Cells Obtain Most of Their Energy by a
Membrane-based Mechanism 453 Mitochondria a n d Oxidative
Phosphoryiation 455 A Mitochondrion Contains an Outer
Membrane, an Inner Membrane, and
Two Internal Compartments 455 High-Energy Electrons Are Generated via
the Citric Acid Cycle 457 A Chemiosmotic Process Converts
Oxidation Energy into ATP 458 Electrons Are Transferred Along a Chain of
Proteins in the Inner Mitochondrial Membrane 459 Electron Transport Generates a Proton
Gradient Across the Membrane 462 The Proton Gradient Drives ATP Synthesis 464 Coupled Transport Across the Inner
Mitochondrial Membrane Is Driven by the
Electrochemical Proton Gradient 466 Proton Gradients Produce Most of the
Cell's ATP 466 The Rapid Conversion of ADP to ATP in
Mitochondria Maintains a High ATP/ADP Ratio in Cells 468 Electron-Transport Chains a n d Proton
Pumping 468 Protons Are Readily Moved by the Transfer of
Electrons 468 The Redox Potential Is a Measure of Electron
Affinities 469
Electron Transfers Release Large Amounts
of Energy 470 Metals Tightly Bound to Proteins Form Versatile
Electron Carriers 472 Cytochrome Oxidase Catalyzes Oxygen
Reduction 474 The Mechanism of H+ Pumping Will Soon Be
Understood in Atomic Detail 475 Respiration Is Amazingly Efficient 476 Chloroplasts a n d Photosynthesis 478 Chloroplasts Resemble Mitochondria but
Have an Extra Compartment 478 Chloroplasts Capture Energy from Sunlight
and Use It to Fix Carbon 480 Excited Chlorophyll Molecules Funnel Energy
into a Reaction Center 481 Light Energy Drives the Synthesis of ATP
and NADPH 482 Carbon Fixation Is Catalyzed by Ribulose
Bisphosphate Carboxylase 485 Carbon Fixation in Chloroplasts Generates
Sucrose and Starch 486 The Origins of Chloroplasts a n d
Mitochondria 487 Oxidative Phosphoryiation Gave Ancient
Bacteria an Evolutionary Advantage 488 Photosynthetic Bacteria Made Even Fewer
Demands on Their Environment 489 The Lifestyle of Methanococcus Suggests That
Chapter 15 Intracellular Compartments and Transport
497
Membrane-enclosed Organelles
Eucaryotic Cells Contain a Basic Set of Membrane-enclosed Organelles Membrane-enclosed Organelles Evolved
in Different Ways 498 498 500 502 Protein Sorting
Proteins Are Imported into Organelles by Three Mechanisms 502 Signal Sequences Direct Proteins to the Correct
Compartment 503 Proteins Enter the Nucleus Through Nuclear
Pores 504 Proteins Unfold to Enter Mitochondria and
Chloroplasts 506 Proteins Enter the Endoplasmic Reticulum ^
While Being Synthesized 507 Soluble Proteins Are Released into the
ER Lumen 509 Start and Stop Signals Determine the
Arrangement of a Transmembrane Protein
in the Lipid Bilayer 510 Vesicular Transport 512 Transport Vesicles Carry Soluble Proteins and
Membrane Between Compartments 512
Vesicle Budding Is Driven by the Assembly
of a Protein Coat 513 The Specificity of Vesicle Docking Depends
on SNAREs 515
Secretory Pathways 516
Most Proteins Are Covalently Modified in the ER 516 Exit from the ER Is Controlled to Ensure Protein
Quality . 517 Proteins Are Further Modified and Sorted
in the Golgi Apparatus 518 Secretory Proteins Are Released from the Cell
by Exocytosis 519 Endocytic Pathways 523 Specialized Phagocytic Cells Ingest Large
Particles 523 Fluid and Macromolecules Are Taken Up by
Pinocytosis 525 Receptor-mediated Endocytosis Provides
a Specific Route into Animal Cells 525 Endocytosed Macromolecules Are Sorted
in Endosomes 526 Lysosomes Are the Principal Sites of Intracellular
Digestion 527
Chapter 16 Cell Communication
General Principles of Cell Signaling 533
Signals Can Act over Long or Short Range 534 Each Cell Responds to a Limited Set of Signals 536 Receptors Relay Signals via Intracellular
Signaling Pathways 538 Nitric Oxide Crosses the Plasma Membrane and
Activates Intracellular Enzymes Directly 540 Some Hormones Cross the Plasma, Membrane
and Bind to Intracellular Receptors 541 Cell-Surface Receptors Fall into Three Main
Classes 542 lon-channel-linked Receptors Convert Chemical
Signals into Electrical Ones 544 Many Intracellular Signaling Proteins Act as
Molecular Switches 545 G-protein-linked Receptors 546 Stimulation of G-protein-linked Receptors
Activates G-Protein Subunits 546 Some G Proteins Regulate Ion Channels 548 Some G Proteins Activate Membrane-bound
Enzymes 549
533
The Cyclic AMP Pathway Can Activate Enzymes and Turn On Genes 550 The Inositol Phospholipid Pathway Triggers
a Rise in Intracellular C a2 + 552 A C a2 + Signal Triggers Many Biological
Processes 554 Intracellular Signaling Cascades Can Achieve
Astonishing Speed, Sensitivity, and Adaptability: A Look at Photoreceptors in the Eye 555 Enzyme-linked Receptors 557 Activated Receptor Tyrosine Kinases Assemble a
Complex of Intracellular Signaling Proteins 557 Receptor Tyrosine Kinases Activate the
GTP-binding Protein Ras 559 Some Enzyme-linked Receptors Activate
a Fast Track to the Nucleus 560 Protein Kinase Networks Integrate Information
to Control Complex Cell Behaviors 565 Multicellularity and Cell Communication Evolved
Chapter 17 Cytoskeleton
573
Intermediate Filaments 574
Intermediate Filaments Are Strong and Ropelike 575 Intermediate Filaments Strengthen Cells Against
Mechanical Stress 576 The Nuclear Envelope Is Supported by a
Meshwork of Intermediate Filaments 578 Microtubules 579 Microtubules Are Hollow Tubes with Structurally
Distinct Ends . 579 The Centrosome Is the Major
Microtubule-organizing Center in Animal Cells 580 Growing Microtubules Show Dynamic Instability 581 Microtubules Are Maintained by a Balance of
Assembly and Disassembly 582 Microtubules Organize the Interior of the Cell 583 Motor Proteins Drive Intracellular Transport 584 Organelles Move Along Microtubules 585 Cilia and Flagella Contain Stable Microtubules
Moved by Dynein 590 Actin Filaments 592 Actin Filaments Are Thin and Flexible 593
Actin and Tubulin Polymerize by Similar
Mechanisms 593 Many Proteins Bind to Actin and Modify
Its Properties , . 594 An Actin-rich Cortex Underlies the Plasma
Membrane of Most Eucaryotic Cells 594 Cell Crawling Depends on Actin 595 Actin Associates with Myosin to Form
Contractile Structures 598 Extracellular Signals Control the Arrangement
of Actin Filaments 599 Muscle C o n t r a c t i o n 600 Muscle Contraction Depends on Bundles
of Actin and Myosin 600 During Muscle Contraction Actin Filaments
Slide Against Myosin Filaments 601 Muscle Contraction Is Triggered by a Sudden
Rise in C a2 + 603
Muscle Cells Perform Highly Specialized
Functions in the Body 605
Chapter 18 Cell-Cycle Control and Cell Death
611
Overview of the Cell Cycle 612
The Eucaryotic Cell Cycle Is Divided into
Four Phases . 6 1 3 A Central Control System Triggers the Major
Processes of the Cell Cycle 614 The Cell-Cycle Control System 615 The Cell-Cycle Control System Depends on
Cyclically Activated Protein Kinases 616 Cyclin-dependent Protein Kinases Are
Regulated by the Accumulation and
Destruction of Cyclins 617 The Activity of Cdks Is Also Regulated by
Phosphoryiation and Dephosphorylation 617 Different Cyclin-Cdk Complexes Trigger
Different Steps in the Cell Cycle 620 S-Cdk Initiates DNA Replication and Helps
Block Rereplication 621 Cdks Are Inactive Through Most of Gi 622 The Cell-Cycle Control System Can Arrest
the Cycle at Specific Checkpoints 622
Cells Can Dismantle Their Control System and
Withdraw from the Cell Cycle 624 Programmed Cell Death (Apoptosis) 625 Apoptosis Is Mediated by an Intracellular
Proteolytic Cascade 626 The Death Program Is Regulated by the
Bcl-2 Family of Intracellular Proteins 627 Extracellular Control of Cell Numbers
a n d Cell Size 628 Animal Cells Require Extracellular Signals
to Divide, Grow, and Survive 629 Mitogens Stimulate Cell Division 629 Extracellular Growth Factors Stimulate
Cells to Grow 631 Animal Cells Require Survival Factors to Avoid
Apoptosis 631 Some Extracellular Signal Proteins Inhibit
Chapter 19 Cell Division
637
An Overview of M Phase 638
In Preparation for M Phase, DNA-binding Proteins Configure Replicated Chromosomes
for Segregation 638 The Cytoskeleton Carries Out Both Mitosis and
Cytokinesis 639 Centrosomes Duplicate To Help Form the
Two Poles of the Mitotic Spindle 640 M Phase Is Conventionally Divided into
Six Stages 640 Mitosis ' 641 Microtubule Instability Facilitates the Formation
of the Mitotic Spindle 641 The Mitotic Spindle Starts to Assemble in
Prophase 644 Chromosomes Attach to the Mitotic Spindle
at Prometaphase 645
Chromosomes Line Up at the Spindle Equator
at Metaphase 648 Daughter Chromosomes Segregate
atAnaphase x 649 The Nuclear Envelope Re-forms at Telophase 651 Some Organelles Fragment at Mitosis 651 Cytokinesis 652 The Mitotic Spindle Determines the Plane of
Cytoplasmic Cleavage V652 The Contractile Ring of Animal Cells Is Made
of Actin and Myosin 653 Cytokinesis in Plant Cells Involves New
Cell-Wall Formation 654 Gametes Are Formed by a Specialized Kind
of Cell Division 655
Chapter 20 Genetics, Meiosis, and the Molecular Basis of Heredity 659
660 The Benefits of Sex
Sexual Reproduction Involves Both Diploid and Haploid Cells
Sexual Reproduction Gives Organisms
a Competitive Advantage 662 661
Meiosis 663
Haploid Cells Are Produced From Diploid Cells Through Meiosis 664 Meiosis Involves a Special Process of
Chromosome Pairing , 664 Extensive Recombination Occurs Between
Maternal and Paternal Chromosomes 665 Chromosome Pairing and Recombination
Ensure the Proper Segregation of Homologs 667 The Second Meiotic Division Produces Haploid
Daughter Cells 667 The Haploid Cells Contain Extensively
Reassorted Genetic Information 668 Meiosis Is Not Flawless 670 Fertilization Reconstitutes a Complete Genome 671 M e n d e l a n d the Laws of Inheritance 672 Mendel Chose to Study Traits That Are Inherited
in a Discrete Fashion 673 Mendel Could Disprove the Alternative Theories
of Inheritance ' 674 Mendel's Experiments Were the First to Reveal
the Discrete feature of Heredity 674
Each Gamete Carries a Single Allele for Each
Character 675 Mendel's Law of Segregation Applies to All
Sexually Reproducing Organisms 676 Alleles for Different Traits Segregate
Independently 677 The Behavior of Chromosomes During Meiosis
Underlies Mendel's Laws of Inheritance 678 The Frequency of Recombination Can Be
Used to Order Genes on Chromosomes 680 The Phenotype of the Heterozygote Reveals
Whether an Allele is Dominant or Recessive 681 Mutant Alleles Sometimes Confer a Selective
Advantage 684 Genetics as a n Experimental Tool 686 The Classical Approach Begins with Random
Mutagenesis 686 Genetic Screens Identify Mutants Deficient
in Cellular Processes 687 A Complementation Test Reveals Whether Two
Mutations Are in the Same Gene 688 Human Genes Are Inherited in Haplotype Blocks,
Which Can Aid in the Search for Mutations
That Cause Disease 689 Complex Traits Are Influenced by Multiple
Genes 691 Is Our Fate Encoded in Our DNA? 692
Chapter 21 Tissues and Cancer
697
Extracellular Matrix a n d C o n n e c t i v e
Tissues 698 Plant Cells Have Tough External Walls 698 Cellulose Fibers Give the Plant Cell Wall
Its Tensile Strength 702 Animal Connective Tissues Consist Largely of
Extracellular Matrix 703 Collagen Provides Tensile Strength in Animal
Connective Tissues " 704 Cells Organize the Collagen That They Secrete 705 Integrins Couple the Matrix Outside a Cell
to the Cytoskeleton Inside It 706 Gels of Polysaccharide and Protein Fill Spaces
and Resist Compression 706 Epithelial Sheets a n d Cell-Cell Junctions 709 Epithelial Sheets Are Polarized and Rest on
a Basal Lamina 709 Tight Junctions Make an Epithelium Leak-proof
and Separate Its Apical and Basal Surfaces 711 Cytoskeleton-linked Junctions Bind Epithelial
Cells Robustly to One Another and to the
Basal Lamina s 712 Gap Junctions Allow Ions and Small Molecules
to Pass from Cell to Cell 715 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
Different Tissues Are Renewed at Different Rates
Stem Cells Generate a Continuous Supply of Terminally Differentiated Cells
Stem Cells Can Be Used to Repair Damaged Tissues
Nuclear Transplantation Provides a Way to Generate Personalized ES Cells: the Strategy of Therapeutic Cloning 720 721 722 725
726
Cancer
Cancer Cells Proliferate, Invade, and
Metastasize . 726 Epidemiology Identifies Preventable Causes
of Cancer 727 Cancers Develop by an Accumulation of
Mutations 728 Cancers Evolve Properties That Give Them a
Competitive Advantage 729 Many Diverse Types of Genes Are Critical
for Cancer 731 Colorectal Cancer Illustrates How Loss of a Gene
Can Lead to Growth of a Tumor 732 An Understanding of Cancer Cell Biology
