Download essential cell biology

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
Introduction to Cells
Light and electron microscopy
Cells: the principal features of animal, plant, and bacterial cells
Life's common mechanisms
1
8
25
30
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
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
39
Chapter 3
Energy, Catalysis, and Biosynthesis
Free energy and biological reactions
Using kinetics to model and manipulate metabolic pathways
83
Panel 3-1
How We Know
60
66
68
70
72
74
76
78
96
103
Chapter 4
Panel4-1
How We Know
Panel 4-2
Panel 4-3 ;
Panel 4-4
Panel 4-5
Panel 4-6
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
119
Chapter 5
DNA and Chromosomes
Genes are made of DNA
169
172
Chapter 6
How We Know
DNA Replication, Repair, and Recombination
Finding replication origins
195
198
Chapter 7
How We Know
From DNA to Protein: How Cells Read the Genome
Cracking the genetic code
229
Chapter 8
How We Know
Control of Gene Expression
Gene regulation—the story of eve
267
Chapter 9
How We Know
How Genes and Genomes Evolve
Counting genes
293
314
How We Know
120
129
132
160
162
163
164
246
282
ix
Chapter 10
How We Know
Manipulating Genes and Cells
323
Sequencing the human genome
334
Chapter 11
Membrane Structure
365
Measuring membrane flow
384
Membrane Transport
Squid reveal secrets of membrane excitability
389
414
How Cells Obtain Energy from Food
427
Details of the 10 steps of glycolysis
Unraveling the citric acid cycle
The complete citric acid cycle
432
442
450
Energy Generation in Mitochondria and Chloroplasts
How chemiosmotic coupling drives ATP synthesis
Redox potentials
453
Intracellular Compartments and Transport
497
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
460
471
Chapter 15
How We Know
Tracking protein and vesicle transport
Chapter-16
Cell Communication
533
Untangling cell signaling pathways
561
Cytoskeleton
Pursuing motor proteins
573
Chapter 18
How We Know
Cell-Cycle Control and Cell Death
611
618
Chapter 19
Cell Division
The principal ^stages of M phase in an animal cell
Building the mitotic spindle
637
Chapter 20
How We Know
Panel 20-1
Genetics, Meiosis, and the Molecular Basis of Heredity
659
Reading genetic linkage maps
Some essentials of classical genetics
682
685
Chapter 21
Panel 21-1
How We Know
Tissues and Cancer
The cell types and tissues from which higher plants are constructed
Making sense of the genes that are critical for cancer
697
How We Know
Chapter 17
How We Know
Panel 19-1
How We Know
Discovery of cyclins and Cdks
520
586
642
646
700
734
Answers to Questions
Glossary
Index
Contents and Special Features
1:1
Detailed Contents
Chapter 1
Introduction to Cells
Unity and Diversity of Cells
Cells Vary Enormously in Appearance and
Function
Living Cells All Have a Similar Basic Chemistry
All Present-Day Cells Have Apparently Evolved
from the Same Ancestor
Genes Provide the Instructions for Cellular Form,
Function, and Complex Behavior
Cells Under the Microscope
The Invention of the Light Microscope Led to
the Discovery of Cells
Cells, Organelles, and Even Molecules Can Be
Seen Under the Microscope
The Procaryotic Cell
Procaryotes Are the Most Diverse of Cells
The World of Procaryotes Is Divided into Two
Domains: Eubacteria and Archaea
1
2
3
4
5
5
6
7
11
14
15
p
The Eucaryotic Cell
The Nucleus Is the Information Store of the Cell
I
Chapter 2
16
16
Mitochondria Generate Energy from Food
to Power the Cell
Chloroplasts Capture Energy from Sunlight
Internal Membranes Create Intracellular
Compartments with Different Functions
,'
The Cytosol Is a Concentrated Aqueous Gel
of Large and Small Molecules
The Cytoskeleton Is Responsible for Directed
Cell Movements
The Cytoplasm Is Far from Static
Eucaryotic Cells May Have Originated as
Predators
M o d e l Organisms
Molecular Biologists Have Focused on E. co//
Brewer's Yeast Is a Simple Eucaryotic Cell
Arabidopsis Has Been Chosen Out of 300,000
Species as a Model Plant
The World of Animals Is Represented by a Fly,
a Worm, a Mouse, and Homo sapiens
Comparing Genome Sequences Reveals
Life's Common Heritage
39
Cells Are Made of Relatively Few Types of Atoms
The Outermost Electrons Determine How Atoms
Interact
.
Ionic Bonds Form by the Gain and Loss
of Electrons
Covalent Bonds Form by the Sharing of Electrons
Covalent Bonds Vary in Strength
There Are Different Types of Covalent Bonds
Water Is Held Together by Hydrogen Bonds
Some Polar Molecules Form Acids and Bases
in Water
40
Molecules in Cells
A Cell Is Formed from Carbon Compounds
41
43
45
46
47
48
49
50
50
19
22
22
23
24
27
28
28
28
29
33
39
Chemical Components of Cells
Chemical Bonds
17
18
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
Macromolecules Contain a Specific Sequence
of Subunits
Noncovalent Bonds Specify the Precise Shape
of a Macromolecule
Noncovalent Bonds Allow a Macromolecule
to Bind Other Selected Molecules
Detailed Contents
58
59
62
63
Chapter 3
Energy, Catalysis, and Biosynthesis
Catalysis and the Use of Energy
by Cells
Biological Order Is Made Possible by the
Release of Heat Energy from Cells
Photosynthetic Organisms Use Sunlight to
Synthesize Organic Molecules
Cells Obtain Energy by the Oxidation of
Organic Molecules
Oxidation and Reduction Involve Electron
Transfers
Enzymes Lower the Barriers That Block Chemical
Reactions
The Free-Energy Change for a Reaction
Determines Whether It Can Occur
The Concentration of Reactants Influences the
Free-Energy Change and a Reaction's
Direction
The Equilibrium Constant Indicates the
Strength of Molecular Interactions
For Sequential Reactions, the Changes in
Free Energy Are Additive
Chapter 4
84
85
88
89
90
91
93
94
95
Rapid Diffusion Allows Enzymes to Find Their
Substrates
and KM Measure Enzyme Performance
100
101
Activated Carrier Molecules and
Biosynthesis
106
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
The Shape of a Protein Is Specified by Its
Amino Acid Sequence
Proteins Fold into a Conformation of Lowest
Energy
,
(
Proteins Come in a Wide Variety of Complicated
Shapes
The a Helix and the p Sheet Are Common
Folding Patterns
Helices Form Readily in Biological Structures
P Sheets Form Rigid Structures at the Core
of Many Proteins
Proteins Have Several Levels of Organization
Few of the Many Possible Polypeptide Chains
Will Be Useful
Proteins Can Be Classified into Families
Large Protein Molecules Often Contain More
Than One Polypeptide Chain
Proteins Can Assemble into Filaments, Sheets,
or Spheres
Some Types of Proteins Have Elongated
Fibrous Shapes
Extracellular Proteins Are Often Stabilized by
Covalent Cross-Linkages
106
107
108
109
111
112
98
Protein Structure and Function
The Shape and Structurenof Proteins
83
119
121
124
125
126
134
135
136
137
138
139
140
141
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
119
143
143
144
145
146
149
How Proteins Are Controlled
150
The Catalytic Activities of Enzymes Are Often
151
Regulated by Other Molecules
Allosteric Enzymes Have Two Binding Sites That
151
Influence One Another
Phosphorylation Can Control Protein Activity
153
by Triggering a Conformational Change
GTP-Binding Proteins Are Also Regulated by the
154
Cyclic Gain and Loss of a Phosphate Group
Nucleotide Hydrolysis Allows Motor Proteins to
155
Produce Large Movements in Cells
Proteins Often Form Large Complexes That
156
Function as Protein Machines
Large-Scale Studies of Protein Structure and
Function Are Increasing the Pace of Discovery 157
Chapter 5
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
Eucarydtic DNA Is Packaged into Chromosomes
Chromosomes Contain Long Strings of Genes
Chromosomes Exist in Different States
Throughout the Life of a Cell
Chapter 6
169
DNA and Chromosomes
177
178
179
181
Interphase Chromosomes Are Organized
Within the Nucleus
The DNA in Chromosomes Is Highly Condensed,
Nucleosomes Are the Basic Units of Chromatin
Structure
Chromosomes Have Several Levels of
DNA Packing
Interphase Chromosomes Contain Both
Condensed and More Extended Forms of
Chromatin
Changes in Nucleosome Structure Allow
Access to DNA
DNA Replication, Repair, and Recombination
DNA Replication
196
Base-Pairing Enables DNA Replication
DNA Synthesis Begins at Replication Origins
New DNA Synthesis Occurs at Replication Forks
The Replication Fork Is Asymmetrical
DNA Polymerase Is Self-correcting
Short Lengths of RNA Act as Primers for
DNA Synthesis
Proteins a t a Replication Fork Cooperate to
Form a Replication Machine
Telomerase Replicates the Ends of Eucaryotic
Chromosomes
DNA Replication Is Relatively Well Understood
196
197
201
202
203
DNA Repair
Mutations Can Have Severe Consequences
for an Organism
A DNA Mismatch Repair System Removes
Replication Errors That Escape the Replication
Machine
209
204
206
207
208
209
210
183
183
184
186
187
189
195
DNA Is Continually Suffering Damage in Cells
The Stability of Genes Depends on DNA Repair
The High Fidelity of DNA Maintenance Allows
Closely Related Species to Have Proteins
with Very Similar Sequences
212
213
DNA Recombination
Homologous Recombination Results in
an Exact Exchange of Genetic Information
Recombination Can Also Occur Between
Nonhomologous DNA Sequences
Mobile Genetic Elements Encode the
Components They Need for Movement
A Large Fraction of the Human Genome Is
Composed of Two Families of Transposable
Sequences
Viruses Are Fully Mobile Genetic Elements
That Can Escape from Cells
Retroviruses Reverse the Normal Flow of
Genetic Information
215
Detailed Contents
214
215
216
217
218
219
221
XIII
Chapter 7
From DNA to Protein: How Cells Read the Genome
From DNA to RNA
230
Portions of DNA Sequence Are Transcribed
into RNA
Transcription Produces RNA Complementary
to One Strand of DNA
Several Types of RNA Are Produced in Cells
Signals in DNA Tell RNA Polymerase Where
to Start and Finish
Eucaryotic RNAs Are Transcribed and Processed
Simultaneously in the Nucleus Eucaryotic Genes Are Interrupted by Noncoding
Sequences
Introns Are Removed by RNA Splicing
Mature Eucaryotic mRNAs Are Selectively
Exported from the Nucleus
mRNA Molecules Are Eventually Degraded
by the Cell
The Earliest Cells May Have Had Introns in
Their Genes
230
231
233
234
236
237
238
241
242
242
From RNA to Protein
243
An mRNA Sequence Is Decoded in Sets of
Three Nucleotides
244
Chapter 8
tRNA Molecules Match Amino Acids to Codons
in mRNA
Specific Enzymes Couple tRNAs to the
Correct Amino Acid
The RNA Message Is Decoded on Ribosomes
The Ribosome Is a Ribozyme
Codons in mRNA Signal Where to Start and
to Stop Protein Synthesis
Proteins Are Made on Polyribosomes
Inhibitors of Procaryotic Protein Synthesis
Are Used as Antibiotics
Carefully Controlled Protein Breakdown Helps
Regulate the Amount of Each Protein in
a Cell
There Are Many Steps Between DNA and
Protein
RNA a n d the Origins of Life
Life Requires Autocatalysis
RNA Can Both Store Information and Catalyze
Chemical Reactions
RNA Is Thought to Predate DNA in Evolution
Control of Gene Expression
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
How Transcriptional Switches Work
Transcription Is Controlled by Proteins Binding
to Regulatory DNA Sequences
Repressors Turn Genes Off, Activators Turn
Them On
An Activator and a Repressor Control the
lac Operon
Initiation of Eucaryotic Gene Transcription Is a
Complex Process
268/
268
268
270
270
271
271
273
275
275
Eucaryotic RNA Polymerase Requires General
Transcription Factors
Eucaryotic Gene Regulatory Proteins Control
Gene Expression from a Distance
Packing of Promoter DNA into Nucleosomes
Can Affect Initiation of Transcription
The Molecular Mechanisms that Create
Specialized Cell Types
Eucaryotic Genes Are Regulated by
Combinations of Proteins
The Expression of Different Genes Can Be
Coordinated by a Single Protein
Combinatorial Control Can Create Different
Cell Types
Stable Patterns of Gene Expression Can Be
Transmitted to Daughter Cells
The Formation of an Entire Organ Can Be
Triggered by a Single Gene Regulatory
Protein
229
245
248
248
251
253
254
255
256
257
258
259
259
261
267
276
278
279
280
281
281
285
286
288
Chapter 9:
How Genes and Genomes Evolve
Generating Genetic Variation
Five Main Types of Genetic Change Contribute
to Evolution
Genome Alterations Are Caused by Failures
of the Normal Mechanisms for Copying and
Maintaining DNA
DNA Duplications Give Rise to Families of
Related Genes Within a Single Cell
The Evolution of the Globin Gene Family
Shows How DNA Duplicatiops Contribute
to the Evolution of Organisms
Gene Duplication and Divergence Provide
a Critical Source of Genetic Novelty for
Evolving Organisms
.
New Genes Can Be Generated by Repeating
the Same Exon
Novel Genes Can Also Be Created by
Exon Shuffling
The Evolution of Genomes Has Been
Accelerated by the Movement of
Transposable Elements
Genes Can Be Exchanged Between Organisms
by Horizontal Gene Transfer
293
295
296
297
298
299
300
300
301
302
Reconstructing Life's Family Tree
Genetic Changes That Offer an Organism
a Selective Advantage Are the Most Likely
to Be Preserved
The Genome Sequences of Two Species Differ
in Proportion to the Length of Time That
They Have Evolved Separately
Humans and Chimpanzee Genomes Are Similar
Organization as Well as Detailed Sequence
Functionally Important Sequences Show Up as
Islands of DNA Sequence Conservation
Genome Comparisons Suggest That "Junk DNA"
is Dispensable
Sequence Conservation Allows Us to Trace Even
the Most Distant Evolutionary Relationships
Manipulating Genes and Cells
Isolating Cells and Growing Them
in Culture
A Uniform Population of Cells Can Be Obtained
from a Tissue
Cells Can Be Grown in a Culture Dish
Maintaining Eucaryotic Cells in Culture Poses
Special Challenges
DNA Cloning
324
325
325
326
How DNA Molecules Are Analyzed
Restriction Nucleases Cut DNA Molecules
at Specific Sites
Gel Electrophoresis Separates DNA Fragments
of Different Sizes
The Nucleotide Sequence of DNA Fragments
Can Be Determined
Genome Sequences Are Searched to
Identify Genes
327
Nucleic A c i d Hybridization
DNA Hybridization Facilitates the Diagnosis
of Genetic Diseases
Hybridization on DNA Microarrays Monitors the
Expression of Thdusands of Genes at Once
In Situ Hybridization Locates Nucleic Acid
Sequences in Cells or on Chromosomes
336
328
329
331
333
336
338
340
304
304
305
in
306
307
308
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
313
Contributes to Our Individuality
Comparing Our DNA with That of Related
Organisms Helps Us to Interpret the Human
316
Genome
The Human Genome Contains Copious
Information Yet to Be Deciphered
Chapter 10
293
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
317
323
341
341
341
342
343
346
347
352
352
352
353
355
356
359
Chapter 11
The Lipid Bilayer
366
Membrane Lipids Form Bilayers in Water
The Lipid Bilayer Is a Two-dimensional Fluid
The Fluidity of a Lipid Bilayer Depends on
Its Composition
The Lipid Bilayer Is Asymmetrical
Lipid Asymmetry Is Generated Inside the Cell
367
370
371
373
373
M e m b r a n e Proteins
374
Membrane Proteins Associate with the Lipid
Bilayer in Various Ways
375
Chapter 12
365
Membrane Structure
A Polypeptide Chain Usually Crosses the
Bilayer as an a Helix
Membrane Proteins Can Be Solubilized
in Detergents and Purified
The Complete Structure Is Known for a Few
Membrane Proteins
The Plasma Membrane Is Reinforced
by the Cell Cortex
The Cell Surface Is Coated with Carbohydrate
Cells Can Restrict the Movement of
Membrane Proteins
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 a 2 + Concentrations Are Kept
Low by C a 2 + Pumps
H + Gradients Are Used to Drive Membrane
Transport in Plants, Fungi, and Bacteria
389
390
391
391
392
393
377
378
380
381
383
389
Membrane Transport
Principles of Membrane Transport
376
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
Membrane Potential Is Governed by Membrane
Permeability to Specific Ions
403
403
405
407
407
408
393
Ion Channels a n d Signaling in
Nerve Cells
395
Action Potentials Provide for Rapid Long-Distance
Communication
411
Action Potentials Are Usually Mediated by
412
Voltage-gated Na + Channels
Voltage-gated C a 2 + Channels Convert
Electrical Signals into Chemical Signals at
417
Nerve Terminals
396
397
397
399
401
402
411
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
Chapter 13
How Cells Obtain Energy from Food
The Breakdown of Sugars and Fats
Food Molecules Are Broken Down in Three
Stages
Glycolysis Is a Central ATP-producing Pathway
Fermentations Allow ATP to Be Produced in the
Absence of Oxygen
Glycolysis illustrates How Enzymes Couple
Oxidation to Energy Storage
Sugars and Fats Are Both Degraded to
Acetyl CoA in Mitochondria
The Citric Acid Cycle Generates NADH by
Oxidizing Acetyl Groups to CO2
Chapter 14
428
428
430
431
434
435
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
Chloroplasts and Mitochondria Collaborate
in Plant Cells
Many Biosynthetic Pathways Begin with
Glycolysis or the Citric Acid Cycle
Metabolism Is Organized and Regulated
Cells Obtain Most of Their Energy by a
Membrane-based Mechanism
453
Mitochondria a n d Oxidative
Phosphoryiation
455
Electron-Transport Chains a n d Proton
Pumping
Protons Are Readily Moved by the Transfer of
Electrons
The Redox Potential Is a Measure of Electron
Affinities
444
446
447
448
439
Energy Generation in Mitochondria and Chloroplasts
A Mitochondrion Contains an Outer
Membrane, an Inner Membrane, and
Two Internal Compartments
High-Energy Electrons Are Generated via
the Citric Acid Cycle
A Chemiosmotic Process Converts
Oxidation Energy into ATP
Electrons Are Transferred Along a Chain of
Proteins in the Inner Mitochondrial Membrane
Electron Transport Generates a Proton
Gradient Across the Membrane
The Proton Gradient Drives ATP Synthesis
Coupled Transport Across the Inner
Mitochondrial Membrane Is Driven by the
Electrochemical Proton Gradient
Proton Gradients Produce Most of the
Cell's ATP
The Rapid Conversion of ADP to ATP in
Mitochondria Maintains a High ATP/ADP Ratio
in Cells
427
455
457
458
459
462
464
466
466
468
468
468
469
Electron Transfers Release Large Amounts
of Energy
Metals Tightly Bound to Proteins Form Versatile
Electron Carriers
Cytochrome Oxidase Catalyzes Oxygen
Reduction
The Mechanism of H+ Pumping Will Soon Be
Understood in Atomic Detail
Respiration Is Amazingly Efficient
Chloroplasts a n d Photosynthesis
Chloroplasts Resemble Mitochondria but
Have an Extra Compartment
Chloroplasts Capture Energy from Sunlight
and Use It to Fix Carbon
Excited Chlorophyll Molecules Funnel Energy
into a Reaction Center
Light Energy Drives the Synthesis of ATP
and NADPH
Carbon Fixation Is Catalyzed by Ribulose
Bisphosphate Carboxylase
Carbon Fixation in Chloroplasts Generates
Sucrose and Starch
453
470
472
474
475
476
478
478
480
481
482
485
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
Membrane-enclosed Organelles
Eucaryotic Cells Contain a Basic Set of
Membrane-enclosed Organelles
Membrane-enclosed Organelles Evolved
in Different Ways
Protein Sorting
Proteins Are Imported into Organelles by Three
Mechanisms
Signal Sequences Direct Proteins to the Correct
Compartment
Proteins Enter the Nucleus Through Nuclear
Pores
Proteins Unfold to Enter Mitochondria and
Chloroplasts
Proteins Enter the Endoplasmic Reticulum
While Being Synthesized
Soluble Proteins Are Released into the
ER Lumen
Start and Stop Signals Determine the
Arrangement of a Transmembrane Protein
in the Lipid Bilayer
Vesicular Transport
Transport Vesicles Carry Soluble Proteins and
Membrane Between Compartments
Chapter 16
497
Vesicle Budding Is Driven by the Assembly
of a Protein Coat
The Specificity of Vesicle Docking Depends
on SNAREs
498
498
513
515
500
Secretory Pathways
516
502
Most Proteins Are Covalently Modified in the ER
Exit from the ER Is Controlled to Ensure Protein
Quality
.
Proteins Are Further Modified and Sorted
in the Golgi Apparatus
Secretory Proteins Are Released from the Cell
by Exocytosis
516
502
503
504
506
^
507
509
510
512
517
518
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
512
Cell Communication
General Principles of Cell Signaling
533
Signals Can Act over Long or Short Range
Each Cell Responds to a Limited Set of Signals
Receptors Relay Signals via Intracellular
Signaling Pathways
Nitric Oxide Crosses the Plasma Membrane and
Activates Intracellular Enzymes Directly
Some Hormones Cross the Plasma, Membrane
and Bind to Intracellular Receptors
Cell-Surface Receptors Fall into Three Main
Classes
lon-channel-linked Receptors Convert Chemical
Signals into Electrical Ones
Many Intracellular Signaling Proteins Act as
Molecular Switches
534
536
G-protein-linked Receptors
Stimulation of G-protein-linked Receptors
Activates G-Protein Subunits
Some G Proteins Regulate Ion Channels
Some G Proteins Activate Membrane-bound
Enzymes
546
538
540
541
542
544
545
546
548
549
533
The Cyclic AMP Pathway Can Activate Enzymes
and Turn On Genes
The Inositol Phospholipid Pathway Triggers
a Rise in Intracellular C a 2 +
A C a 2 + Signal Triggers Many Biological
Processes
Intracellular Signaling Cascades Can Achieve
Astonishing Speed, Sensitivity, and Adaptability:
A Look at Photoreceptors in the Eye
550
552
554
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
Intermediate Filaments
573
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
Microtubules Are Hollow Tubes with Structurally
Distinct Ends .
The Centrosome Is the Major Microtubuleorganizing Center in Animal Cells
Growing Microtubules Show Dynamic Instability
Microtubules Are Maintained by a Balance of
Assembly and Disassembly
Microtubules Organize the Interior of the Cell
Motor Proteins Drive Intracellular Transport
Organelles Move Along Microtubules
Cilia and Flagella Contain Stable Microtubules
Moved by Dynein
579
Actin Filaments
Actin Filaments Are Thin and Flexible
592
593
Chapter 18
579
580
581
582
583
584
585
590
Actin and Tubulin Polymerize by Similar
Mechanisms
Many Proteins Bind to Actin and Modify
Its Properties
,
.
An Actin-rich Cortex Underlies the Plasma
Membrane of Most Eucaryotic Cells
Cell Crawling Depends on Actin
Actin Associates with Myosin to Form
Contractile Structures
Extracellular Signals Control the Arrangement
of Actin Filaments
Muscle Contraction
Muscle Contraction Depends on Bundles
of Actin and Myosin
During Muscle Contraction Actin Filaments
Slide Against Myosin Filaments
Muscle Contraction Is Triggered by a Sudden
Rise in C a 2 +
Muscle Cells Perform Highly Specialized
Functions in the Body
Cell-Cycle Control and Cell Death
Overview of the Cell Cycle
The Eucaryotic Cell Cycle Is Divided into
Four Phases
A Central Control System Triggers the Major
Processes of the Cell Cycle
The Cell-Cycle Control System
The Cell-Cycle Control System Depends on
Cyclically Activated Protein Kinases
Cyclin-dependent Protein Kinases Are
Regulated by the Accumulation and
Destruction of Cyclins
The Activity of Cdks Is Also Regulated by
Phosphoryiation and Dephosphorylation
Different Cyclin-Cdk Complexes Trigger
Different Steps in the Cell Cycle
S-Cdk Initiates DNA Replication and Helps
Block Rereplication
Cdks Are Inactive Through Most of Gi
The Cell-Cycle Control System Can Arrest
the Cycle at Specific Checkpoints
612
.613
614
615
616
617
617
620
621
622
622
593
594
594
595
598
599
600
600
601
603
605
611
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
The Death Program Is Regulated by the
Bcl-2 Family of Intracellular Proteins
Extracellular Control of Cell Numbers
a n d Cell Size
Animal Cells Require Extracellular Signals
to Divide, Grow, and Survive
Mitogens Stimulate Cell Division
Extracellular Growth Factors Stimulate
Cells to Grow
Animal Cells Require Survival Factors to Avoid
Apoptosis
Some Extracellular Signal Proteins Inhibit
Cell Growth, Division, or Survival
626
627
628
629
629
631
631
632
Chapter 19
Cell Division
An Overview of M Phase
In Preparation for M Phase, DNA-binding
Proteins Configure Replicated Chromosomes
for Segregation
The Cytoskeleton Carries Out Both Mitosis and
Cytokinesis
Centrosomes Duplicate To Help Form the
Two Poles of the Mitotic Spindle
M Phase Is Conventionally Divided into
Six Stages
Mitosis
'
Microtubule Instability Facilitates the Formation
of the Mitotic Spindle
The Mitotic Spindle Starts to Assemble in
Prophase
Chromosomes Attach to the Mitotic Spindle
at Prometaphase
Chapter 20
637
638
638
639
640
640
641
641
644
Chromosomes Line Up at the Spindle Equator
at Metaphase
Daughter Chromosomes Segregate
x
atAnaphase
The Nuclear Envelope Re-forms at Telophase
Some Organelles Fragment at Mitosis
Cytokinesis
The Mitotic Spindle Determines the Plane of
Cytoplasmic Cleavage
The Contractile Ring of Animal Cells Is Made
of Actin and Myosin
Cytokinesis in Plant Cells Involves New
Cell-Wall Formation
Gametes Are Formed by a Specialized Kind
of Cell Division
Sexual Reproduction Involves Both Diploid and
Haploid Cells
Sexual Reproduction Gives Organisms
a Competitive Advantage
Meiosis
Haploid Cells Are Produced From Diploid Cells
Through Meiosis
Meiosis Involves a Special Process of
Chromosome Pairing
,
Extensive Recombination Occurs Between
Maternal and Paternal Chromosomes
Chromosome Pairing and Recombination
Ensure the Proper Segregation of Homologs
The Second Meiotic Division Produces Haploid
Daughter Cells
The Haploid Cells Contain Extensively
Reassorted Genetic Information
Meiosis Is Not Flawless
Fertilization Reconstitutes a Complete Genome
649
651
651
652
V652
653
654
655
645
Genetics, Meiosis, and the Molecular Basis of Heredity
The Benefits of Sex
648
660
661
662
663
664
664
665
667
667
668
670
671
Mendel 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
659
Each Gamete Carries a Single Allele for Each
Character
Mendel's Law of Segregation Applies to All
Sexually Reproducing Organisms
Alleles for Different Traits Segregate
Independently
The Behavior of Chromosomes During Meiosis
Underlies Mendel's Laws of Inheritance
The Frequency of Recombination Can Be
Used to Order Genes on Chromosomes
The Phenotype of the Heterozygote Reveals
Whether an Allele is Dominant or Recessive
Mutant Alleles Sometimes Confer a Selective
Advantage
Genetics as a n Experimental Tool
The Classical Approach Begins with Random
Mutagenesis
Genetic Screens Identify Mutants Deficient
in Cellular Processes
A Complementation Test Reveals Whether Two
Mutations Are in the Same Gene
Human Genes Are Inherited in Haplotype Blocks,
Which Can Aid in the Search for Mutations
That Cause Disease
Complex Traits Are Influenced by Multiple
Genes
Is Our Fate Encoded in Our DNA?
675
676
677
678
680
681
684
686
686
687
688
689
691
692
Chapter 21
Tissues and Cancer
Extracellular Matrix a n d Connective
Tissues
Plant Cells Have Tough External Walls
Cellulose Fibers Give the Plant Cell Wall
Its Tensile Strength
Animal Connective Tissues Consist Largely of
Extracellular Matrix
Collagen Provides Tensile Strength in Animal
Connective Tissues
"
Cells Organize the Collagen That They Secrete
Integrins Couple the Matrix Outside a Cell
to the Cytoskeleton Inside It
Gels of Polysaccharide and Protein Fill Spaces
and Resist Compression
Epithelial Sheets a n d Cell-Cell Junctions
Epithelial Sheets Are Polarized and Rest on
a Basal Lamina
Tight Junctions Make an Epithelium Leak-proof
and Separate Its Apical and Basal Surfaces
Cytoskeleton-linked Junctions Bind Epithelial
Cells Robustly to One Another and to the
s
Basal Lamina
Gap Junctions Allow Ions and Small Molecules
to Pass from Cell to Cell
Tissue M a i n t e n a n c e a n d Renewal
Tissues Are Organized Mixtures of Many Cell
Types
698
698
702
703
704
705
706
706
709
709
711
712
715
717
718
697
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
Cancer
Cancer Cells Proliferate, Invade, and
Metastasize
.
Epidemiology Identifies Preventable Causes
of Cancer
Cancers Develop by an Accumulation of
Mutations
Cancers Evolve Properties That Give Them a
Competitive Advantage
Many Diverse Types of Genes Are Critical
for Cancer
Colorectal Cancer Illustrates How Loss of a Gene
Can Lead to Growth of a Tumor
An Understanding of Cancer Cell Biology
Opens the Way to New Treatments
720
721
722
725
726
726
727
728
729
731
732
736