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Essential Cell Biology: An Introduction to the Molecular Biology of the
Cell
Article · January 1998
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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
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
30
39
60
66
68
70
72
74
76
78
83
96
103
119
120
129
132
160
162
163
164
169
172
195
198
229
246
267
282
293
314
ix
Chapter 10
How We Know
Chapter 11
How We Know
Chapter 12
How We Know
Chapter 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 Know
Chapter 17
How We Know
Chapter 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 signalingpathways
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
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334
365
384
389
414
427
432
442
450
453
460
471
497
520
533
561
573
586
611
618
637
642
646
659
682
685
697
700
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
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 Microscope 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
Model 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
Macromolecules 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
Detailed Contents
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
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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 Control led
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
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143
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146
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150
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151
153
154
155
156
157
Chapter 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 at 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 Proteinswith 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
Detailed Contents XIII
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 and 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
271How 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
Protein 288
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 Genome 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 Acid 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
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323
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343
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352
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355
356
359
Chapter 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
Membrane 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 and Their Functions
Concentration Gradients and Electrical
Forces Drive Passive Transport
Active Transport Moves Solutes AgainstTheir
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 Ca2 + Concentrations Are Kept
Low by Ca 2 + 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
407
Ion 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 Ca 2 + 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
417
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 and 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
Chemiosmotic Coupling Is an Ancient Process 490
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
502Protein 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-l inked 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 Ca2 + 552
A Ca2 + 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
Independently in Plants and Animals 566
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 ShowDynamic 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 Contract ion 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 Ca 2 + 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
Cell Growth, Division, or Survival 632
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
660The 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
Mendel and 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 an 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 Connect ive
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 Maintenance 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
726Cancer
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
Opens the Way to New Treatments 736
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