Download Detailed Contents

xi
Detailed Contents
Chapter 1 Introduction to Cells
1
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
2
2
3
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
6
5
5
6
7
The Procaryotic Cell
Procaryotes Are the Most Diverse of Cells
The World of Procaryotes Is Divided into Two
Domains: Bacteria and Archaea
11
14
The Eucaryotic Cell
The Nucleus Is the Information Store of the Cell
Mitochondria Generate Usable 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
16
16
Model Organisms
Molecular Biologists Have Focused on E. coli
Brewer’s Yeast Is a Simple Eucaryotic Cell
26
27
28
15
17
18
19
21
22
23
23
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 Fish, a Mouse, and the Human Species 29
Comparing Genome Sequences Reveals Life’s
Common Heritage
33
Essential Concepts
End-of-Chapter Questions
Chapter 2 Chemical Components
of Cells
35
36
39
Chemical Bonds
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
Electrostatic Attractions Help Bring Molecules
Together in Cells
Water Is Held Together by Hydrogen Bonds
Some Polar Molecules Form Acids and Bases
in Water
40
40
Molecules in Cells
A Cell Is Formed from Carbon Compounds
Cells Contain Four Major Families of Small
Organic Molecules
Sugars Are Energy Sources for Cells and Subunits
of Polysaccharides
Fatty Acids Are Components of Cell Membranes
Amino Acids Are the Subunits of Proteins
Nucleotides Are the Subunits of DNA and RNA
50
50
41
44
45
46
47
47
48
49
51
52
54
55
56
xii
Detailed Contents
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
58
Essential Concepts
End-of-Chapter Questions
78
79
Chapter 3 Energy, Catalysis, and
Biosynthesis
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
59
59
63
81
82
82
84
86
87
Free Energy and Catalysis
88
Enzymes Lower the Energy Barriers That Prevent
Chemical Reactions from Occurring
89
The Free-Energy Change for a Reaction Determines
Whether It Can Occur
91
The Concentration of Reactants Influences the
Free-Energy Change and a Reaction’s Direction 92
The Standard Free-Energy Change Makes it
Possible to Compare the Energetics of
Different Reactions
92
Cells Exist in a State of Chemical Disequilibrium 92
The Equilibrium Constant is Directly Proportional
to DG°
93
In Complex Reactions, the Equilibrium Constant
Depends on the Concentrations of All
Reactants and Products
96
The Equilibrium Constant Indicates the Strength
of Molecular Interactions
96
For Sequential Reactions, the Changes in Free
Energy are Additive
97
Rapid Diffusion Allows Enzymes to Find Their
Substrates
98
99
Vmax and KM Measure Enzyme Performance
Activated Carrier Molecules and
Biosynthesis
104
The Formation of an Activated Carrier Is Coupled
to an Energetically Favorable Reaction 104
ATP is the Most Widely Used Activated Carrier
Molecule
105
Energy Stored in ATP is Often Harnessed to
Join Two Molecules Together
106
NADH and NADPH Are Important Electron
Carriers
Cells Make Use of Many Other Activated
Carrier Molecules The Synthesis of Biological Polymers Requires
an Energy Input
Essential Concepts
End-of-Chapter Questions
Chapter 4 Protein Structure and
Function
107
109
110
114
115
119
The Shape and Structure of Proteins
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 b Sheet Are Common
Folding Patterns
Helices Form Readily in Biological Structures b 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
121
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
Most Drugs Inhibit Enzymes
Tightly Bound Small Molecules Add Extra
Functions to Proteins
140
140
121
124
125
127
131
132
133
134
135
135
136
138
138
142
143
143
148
148
How Proteins Are Controlled
149
The Catalytic Activities of Enzymes Are Often
Regulated by Other Molecules
150
Allosteric Enzymes Have Binding Sites That
Influence One Another
150
Phosphorylation Can Control Protein Activity by
Triggering a Conformational Change
152
Detailed Contents
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
Covalent Modification Controls the Location and
Assembly of Protein Machines
153
154
155
156
How Proteins Are Studied
Cells Can Be Grown in a Culture Dish Purification Techniques Allow Homogeneous
Protein Preparations to Be Obtained from
Cell Homogenates
Large Amounts of Almost Any Protein Can be
Produced by Genetic Engineering Techniques
Automated Studies of Protein Structure and
Function Are Increasing the Pace of Discovery
157
157
Essential Concepts
End-of-Chapter Questions
168
169
Chapter 5 DNA and Chromosomes
161
163
163
171
The Structure and Function of DNA
172
A DNA Molecule Consists of Two Complementary
Chains of Nucleotides
173
The Structure of DNA Provides a Mechanism for
Heredity
178
The Structure of Eucaryotic
Chromosomes Eucaryotic DNA Is Packaged into Multiple
Chromosomes
Chromosomes Contain Long Strings of Genes
Chromosomes Exist in Different States
Throughout the Life of a Cell
Interphase Chromosomes Are Organized Within
the Nucleus
The DNA in Chromosomes Is Highly Condensed
Nucleosomes Are the Basic Units of Eucaryotic
Chromosome Structure
Chromosome Packing Occurs on Multiple Levels
179
179
181
182
184
184
185
187
The Regulation of Chromosome
Structure
188
Changes in Nucleosome Structure Allow Access
to DNA 188
Interphase Chromosomes Contain Both
Condensed and More Extended Forms
of Chromatin
190
Changes in Chromatin Structure Can Be
Inherited
191
Essential Concepts
End-of-Chapter Questions
192
193
Chapter 6 DNA Replication, Repair,
and Recombination
xiii
197
DNA Replication
198
Base-Pairing Enables DNA Replication
198
DNA Synthesis Begins at Replication Origins
199
New DNA Synthesis Occurs at Replication Forks 203
The Replication Fork Is Asymmetrical
204
DNA Polymerase Is Self-correcting
205
Short Lengths of RNA Act as Primers for DNA
Synthesis
206
Proteins at a Replication Fork Cooperate to Form
a Replication Machine
208
Telomerase Replicates the Ends of Eucaryotic
Chromosomes
210
DNA Repair
Mutations Can Have Severe Consequences for
a Cell or Organism A DNA Mismatch Repair System Removes
Replication Errors That Escape the Replication
Machine
DNA Is Continually Suffering Damage in Cells
The Stability of Genes Depends on DNA Repair
Double-Strand Breaks Can be Repaired Rapidly
But Imperfectly
A Record of the Fidelity of DNA Replication and
Repair Is Preserved in Genome Sequences
211
Homologous Recombination
Homologous Recombination Requires Extensive
Regions of Sequence Similarity
Homologous Recombination Can Flawlessly
Repair DNA Double-strand Breaks Homologous Recombination Exchanges Genetic
Information During Meiosis
218
Mobile Genetic Elements and Viruses Mobile Genetic Elements Encode the
Components They Need for Movement The Human Genome Contains Two Major
Families of Transposable Sequences
Viruses Are Fully Mobile Genetic Elements
That Can Escape from Cells
Retroviruses Reverse the Normal Flow of
Genetic Information
221
Essential Concepts
End-of-Chapter Questions
227
228
Chapter 7 From DNA to Protein:
How Cells Read the Genome
From DNA to RNA
Portions of DNA Sequence Are Transcribed
into RNA
Transcription Produces RNA Complementary
to One Strand of DNA
211
212
213
215
216
217
218
218
220
222
222
223
225
231
232
233
234
xiv
Detailed Contents
Several Types of RNA Are Produced in Cells
Signals in DNA Tell RNA Polymerase Where
to Start and Finish
Initiation of Eucaryotic Gene Transcription Is a
Complex Process
Eucaryotic RNA Polymerase Requires General
Transcription Factors
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
235
From RNA to Protein
An mRNA Sequence Is Decoded in Sets of Three
Nucleotides
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
246
RNA and the Origins of Life
Life Requires Autocatalysis RNA Can Both Store Information and Catalyze
Chemical Reactions
RNA Is Thought to Predate DNA in Evolution
261
261
Essential Concepts
End-of-Chapter Questions
264
266
236
238
239
240
241
242
243
244
245
246
247
251
251
253
254
257
257
258
259
261
263
Chapter 8 Control of Gene Expression 269
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
270
270
270
272
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
Transcription Switches Allow Cells to Respond
to Changes in the Environment Repressors Turn Genes Off, Activators Turn
Them On
An Activator and a Repressor Control the
Lac Operon
Eucaryotic Transcription Regulators Control
Gene Expression from a Distance
Packing of Promoter DNA into Nucleosomes
Affects Initiation of Transcription
272
273
273
275
276
277
278
279
The Molecular Mechanisms That
Create Specialized Cell Types
280
Eucaryotic Genes Are Regulated by Combinations
of Proteins
280
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 287
The Formation of an Entire Organ Can Be
Triggered by a Single Transcription Regulator 288
Post-Transcriptional Controls
289
Riboswitches Provide An Economical Solution
to Gene Regulation
289
The Untranslated Regions of mRNAs Can Control
Their Translation
290
Small Regulatory RNAs Control the Expression of
Thousands of Animal and Plant Genes
290
RNA Interference Destroys Double-Stranded
Foreign RNAs 291
Scientists Can Use RNA Interference to Turn Off
Genes 292
Essential Concepts
End-of-Chapter Questions
Chapter 9 How Genes and Genomes
Evolve
Generating Genetic Variation
In Sexually Reproducing Organisms, Only
Changes to the Germ Line Are Passed Along
To Progeny
Point Mutations Are Caused by Failures of the
Normal Mechanisms for Copying and
Maintaining DNA
Point Mutations Can Change the Regulation
of a Gene
293
294
297
298
299
300
301
xv
Detailed Contents
DNA Duplications Give Rise to Families of
Related Genes
The Evolution of the Globin Gene Family Shows
How Gene Duplication and Divergence Can
Give Rise to Proteins Tailored to an Organism
and Its Development Whole Genome Duplications Have Shaped the
Evolutionary History of Many Species 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 Mobile Genetic Elements
Genes Can Be Exchanged Between Organisms
by Horizontal Gene Transfer
Reconstructing Life’s Family Tree
Genetic Changes That Provide a Selective
Advantage Are Likely to Be Preserved
Human and Chimpanzee Genomes Are Similar in
Organization As Well As in Detailed Sequence Functionally Important Regions Show Up As
Islands of Conserved DNA Sequence Genome Comparisons Show That Vertebrate
Genomes Gain and Lose DNA Rapidly
Sequence Conservation Allows Us to Trace Even
the Most Distant Evolutionary Relationships
302
304
305
306
306
307
308
309
309
310
310
312
313
Examining the Human Genome
315
The Nucleotide Sequence of the Human Genome
Shows How Our Genes Are Arranged
316
Accelerated Changes in Conserved Genome
Sequences Help Reveal What Makes Us
Human
320
Genetic Variation Within the Human Genome
Contributes to Our Individuality
320
The Human Genome Contains Copious
Information Yet to Be Deciphered
321
Essential Concepts
End-of-Chapter Questions
Chapter 10 Analyzing Genes and
Genomes
Manipulating and Analyzing DNA
Molecules Restriction Nucleases Cut DNA Molecules
at Specific Sites
Gel Electrophoresis Separates DNA Fragments
of Different Sizes
Hybridization Provides a Sensitive Way to
Detect Specific Nucleotide Sequences
Hybridization Is Carried Out Using DNA Probes
Designed to Recognize a Desired Nucleotide
Sequence 323
324
327
329
329
330
332
332
DNA Cloning
333
DNA Ligase Joins DNA Fragments Together to
Produce a Recombinant DNA Molecule
334
Recombinant DNA Can Be Copied Inside Bacterial
Cells
334
Specialized Plasmid Vectors Are Used to Clone
DNA
335
Genes Can Be Isolated from a DNA Library 336
cDNA Libraries Represent the mRNA Produced
by a Particular Tissue
338
The Polymerase Chain Reaction Amplifies Selected
DNA Sequences
340
Deciphering and Exploiting Genetic
Information
DNA Can Be Rapidly Sequenced
Completely Novel DNA Molecules Can Be
Constructed
Rare Proteins Can Be Made in Large Amounts
Using Cloned DNA
Reporter Genes and In Situ Hybridization Can
Reveal When and Where a Gene Is Expressed Hybridization on DNA Microarrays Monitors the
Expression of Thousands of Genes at Once
Genetic Approaches Can Reveal the Function
of a Gene
Animals Can be Genetically Altered
RNA Interference Provides a Simple Way to Test
Gene Function
Transgenic Plants Are Important for Both Cell
Biology and Agriculture
Essential Concepts
End-of-Chapter Questions
Chapter 11 Membrane Structure
The Lipid Bilayer
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 Preserved During Membrane
Transport 343
345
347
347
350
352
354
354
356
357
358
360
363
364
365
368
369
370
371
Membrane Proteins
372
Membrane Proteins Associate with the Lipid
Bilayer in Various Ways
373
A Polypeptide Chain Usually Crosses the Bilayer
as an a Helix
374
Membrane Proteins Can Be Solubilized in
Detergents and Purified
375
The Complete Structure Is Known for Relatively
Few Membrane Proteins
376
The Plasma Membrane Is Reinforced by the Cell
Cortex
377
xvi
Detailed Contents
Cells Can Restrict the Movement of Membrane
Proteins
The Cell Surface Is Coated with Carbohydrate
379
380
Essential Concepts
End-of-Chapter Questions
384
385
Chapter 12 Membrane Transport
387
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: Transporters and Channels
Solutes Cross Membranes by Passive or Active
Transport
388
Transporters and 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
The Na+-K+ Pump Helps Maintain the Osmotic
Balance of Animal Cells
Intracellular Ca2+ Concentrations Are Kept Low
by Ca2+ Pumps
Coupled Transporters Exploit Gradients to Take
Up Nutrients Actively
H+ Gradients Are Used to Drive Membrane
Transport in Plants, Fungi, and Bacteria
391
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
388
389
389
390
392
393
394
394
396
397
398
400
400
401
403
405
Transmitter-gated Channels in Target Cells Convert
Chemical Signals Back into Electrical Signals
415
Neurons Receive Both Excitatory and Inhibitory
Inputs
417
Transmitter-gated Ion Channels Are Major
Targets for Psychoactive Drugs
418
Synaptic Connections Enable You to Think, Act,
and Remember
419
Essential Concepts
End-of-Chapter Questions
Chapter 13 How Cells Obtain Energy
from Food
425
The Breakdown and Utilization of
Sugars and Fats
426
Food Molecules Are Broken Down in Three
Stages
426
Glycolysis Is a Central ATP-producing Pathway
427
Fermentations Allow ATP to Be Produced in the
Absence of Oxygen
432
Glycolysis Illustrates How Enzymes Couple
Oxidation to Energy Storage
433
Sugars and Fats Are Both Degraded to Acetyl
CoA in Mitochondria
436
The Citric Acid Cycle Generates NADH by
436
Oxidizing Acetyl Groups to CO2
Many Biosynthetic Pathways Begin with Glycolysis
or the Citric Acid Cycle
439
Electron Transport Drives the Synthesis of the
Majority of the ATP in Most Cells
444
Regulation of Metabolism
Catabolic and Anabolic Reactions Are Organized
and Regulated
Feedback Regulation Allows Cells to Switch from
Glucose Degradation to Glucose Biosynthesis
Cells Store Food Molecules in Special Reservoirs
to Prepare for Periods of Need
445
Essential Concepts
End-of-Chapter Questions
450
451
405
Chapter 14 Energy Generation in
Mitochondria and Chloroplasts
407
Cells Obtain Most of Their Energy by a
Membrane-based Mechanism
Ion Channels and Signaling in
Nerve Cells
409
Action Potentials Provide for Rapid Long-Distance
Communication
409
Action Potentials Are Usually Mediated by
410
Voltage-gated Na+ Channels
2+
Voltage-gated Ca Channels Convert Electrical
Signals into Chemical Signals at Nerve
Terminals 415
420
421
445
447
448
453
454
Mitochondria and Oxidative
Phosphorylation
456
A Mitochondrion Contains an Outer Membrane,
an Inner Membrane, and Two Internal
Compartments
456
The Citric Acid Cycle Generates High-Energy
Electrons 458
A Chemiosmotic Process Converts the Energy
From Activated Carrier Molecules into ATP
458
Detailed Contents
The Electron-Transport Chain Pumps Protons
Across the Inner Mitochondrial Membrane
460
Proton Pumping Creates a Steep Electrochemical
Proton Gradient Across the Inner Mitochondrial
Membrane
460
The Electrochemical Proton Gradient Drives
ATP Synthesis 461
Coupled Transport Across the Inner Mitochondrial
Membrane Is Also Driven by the Electrochemical
Proton Gradient
463
Oxidative Phosphorylation Produces Most of the
Cell’s ATP
464
The Rapid Conversion of ADP to ATP in
Mitochondria Maintains a High ATP/ADP Ratio
in Cells
465
Molecular Mechanisms of Electron
Transport and Proton Pumping
Protons Are Readily Moved by the Transfer of
Electrons
The Redox Potential Is a Measure of Electron
Affinities
Electron Transfers Release Large Amounts of
Energy
Metals Tightly Bound to Proteins Form Versatile
Electron Carriers
Cytochrome Oxidase Catalyzes the Reduction of
Molecular Oxygen
The Mechanism of H+ Pumping Can Be Studied
in Atomic Detail Respiration Is Amazingly Efficient
466
466
467
470
470
473
474
475
Chloroplasts and Photosynthesis
476
Chloroplasts Resemble Mitochondria but Have
an Extra Compartment
477
Chloroplasts Capture Energy from Sunlight and
Use It to Fix Carbon 478
Sunlight is Absorbed by Chlorophyll Molecules 479
Excited Chlorophyll Molecules Funnel Energy
into a Reaction Center
480
Light Energy Drives the Synthesis of Both ATP
and NADPH
481
Chloroplasts Can Adjust their ATP Production
483
Carbon Fixation Uses ATP and NADPH to Convert
484
CO2 into Sugars
Sugars Generated by Carbon Fixation Can Be
Stored As Starch or Consumed to Produce ATP 486
The Origins of Chloroplasts and
Mitochondria Oxidative Phosphorylation Might Have Given
Ancient Bacteria an Evolutionary Advantage
Photosynthetic Bacteria Made Even Fewer
Demands on Their Environment
The Lifestyle of Methanococcus Suggests That
Chemiosmotic Coupling Is an Ancient Process
Essential Concepts
End-of-Chapter Questions
486
487
488
490
491
492
xvii
Chapter 15 Intracellular Compartments
and Transport
495
Membrane-enclosed Organelles
Eucaryotic Cells Contain a Basic Set of
Membrane-enclosed Organelles
Membrane-enclosed Organelles Evolved in
Different Ways
496
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
500
Vesicular Transport
Transport Vesicles Carry Soluble Proteins and
Membrane Between Compartments
Vesicle Budding Is Driven by the Assembly of
a Protein Coat
Vesicle Docking Depends on Tethers and
SNAREs
510
Secretory Pathways
Most Proteins Are Covalently Modified in the ER
Exit from the ER Is Controlled to Ensure Protein
Quality
The Size of the ER Is Controlled by the Amount
of Protein that Flows Through It
Proteins Are Further Modified and Sorted in
the Golgi Apparatus
Secretory Proteins Are Released from the Cell
by Exocytosis
514
514
Endocytic Pathways
Specialized Phagocytic Cells Ingest Large
Particles
Fluid and Macromolecules Are Taken Up by
Pinocytosis
Receptor-mediated Endocytosis Provides a
Specific Route into Animal Cells
Endocytosed Macromolecules Are Sorted in
Endosomes
Lysosomes Are the Principal Sites of Intracellular
Digestion
Essential Concepts
End-of-Chapter Questions
522
496
498
500
501
502
505
505
507
508
510
511
512
516
516
517
518
522
523
524
525
526
527
529
xviii
Detailed Contents
Chapter 16 Cell Communication
531
General Principles of Cell Signaling
532
Signals Can Act over a Long or Short Range
532
Each Cell Responds to a Limited Set of Signals,
Depending on Its History and Its Current
State 534
A Cell’s Response to a Signal Can Be Fast or
Slow
536
Some Hormones Cross the Plasma Membrane
and Bind to Intracellular Receptors
537
Some Dissolved Gases Cross the Plasma Membrane
and Activate Intracellular Enzymes Directly
538
Cell-Surface Receptors Relay Extracellular Signals
via Intracellular Signaling Pathways
539
Some Intracellular Signaling Proteins Act as
Molecular Switches
541
Cell-Surface Receptors Fall into Three Main
Classes
542
Ion-channel–coupled Receptors Convert Chemical
Signals into Electrical Ones
544
G-protein–coupled Receptors
544
Stimulation of GPCRs Activates G-Protein
Subunits
545
Some G Proteins Directly Regulate Ion Channels 547
Some G Proteins Activate Membrane-bound
Enzymes
547
The Cyclic AMP Pathway Can Activate Enzymes
and Turn On Genes
548
The Inositol Phospholipid Pathway Triggers a Rise
551
in Intracellular Ca2+
A Ca2+ Signal Triggers Many Biological Processes 552
Intracellular Signaling Cascades Can Achieve
Astonishing Speed, Sensitivity, and
Adaptability 554
Enzyme-coupled Receptors
Activated RTKs Recruit a Complex of Intracellular
Signaling Proteins
Most RTKs Activate the Monomeric GTPase Ras
RTKs Activate PI 3-Kinase to Produce Lipid
Docking Sites in the Plasma Membrane
Some Receptors Activate a Fast Track to the
Nucleus
Multicellularity and Cell Communication Evolved
Independently in Plants and Animals
Protein Kinase Networks Integrate Information
to Control Complex Cell Behaviors
Essential Concepts
End-of-Chapter Questions
Chapter 17 Cytoskeleton
555
555
556
558
559
564
564
567
569
571
Intermediate Filaments
572
Intermediate Filaments Are Strong and Ropelike 574
Intermediate Filaments Strengthen Cells Against
Mechanical Stress
575
The Nuclear Envelope Is Supported by a
Meshwork of Intermediate Filaments
576
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
577
Actin Filaments
Actin Filaments Are Thin and Flexible
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
590
591
578
579
580
581
582
583
584
585
591
592
594
594
597
597
Muscle Contraction 599
Muscle Contraction Depends on Bundles of
Actin and Myosin
599
During Muscle Contraction Actin Filaments Slide
Against Myosin Filaments
600
Muscle Contraction Is Triggered by a Sudden
602
Rise in Ca2+
Muscle Cells Perform Highly Specialized Functions
in the Body
604
Essential Concepts
605
End-of-Chapter Questions
606
Chapter 18 The Cell Division Cycle
Overview of the Cell Cycle
The Eucaryotic Cell Cycle Is Divided into Four
Phases
A Cell-Cycle Control System Triggers the Major
Processes of the Cell Cycle
Cell-Cycle Control is Similar in All Eucaryotes
609
610
611
612
613
The Cell-Cycle Control System
613
The Cell-Cycle Control System Depends on
Cyclically Activated Protein Kinases called Cdks614
Detailed Contents
The Activity of Cdks Is Also Regulated by
Phosphorylation and Dephosphorylation
614
Different Cyclin–Cdk Complexes Trigger Different
Steps in the Cell Cycle 617
The Cell-Cycle Control System Also Depends on
Cyclical Proteolysis 618
Proteins that Inhibit Cdks Can Arrest the Cell
Cycle at Specific Checkpoints
618
S Phase
S-Cdk Initiates DNA Replication and Helps
Block Re-Replication
Cohesins Help Hold the Sister Chromatids of
Each Replicated Chromosome Together
DNA Damage Checkpoints Help Prevent the
Replication of Damaged DNA 620
M Phase
M-Cdk Drives Entry Into M Phase and Mitosis Condensins Help Configure Duplicated
Chromosomes for Separation
The Cytoskeleton Carries Out Both Mitosis and
Cytokinesis
M Phase Is Conventionally Divided into Six
Stages
622
622
620
621
621
623
624
624
Mitosis
625
Centrosomes Duplicate To Help Form the Two
Poles of the Mitotic Spindle
625
The Mitotic Spindle Starts to Assemble in
Prophase
628
Chromosomes Attach to the Mitotic Spindle at
Prometaphase
628
Chromosomes Aid in the Assembly of the Mitotic
Spindle 630
Chromosomes Line Up at the Spindle Equator
at Metaphase
630
Proteolysis Triggers Sister-Chromatid Separation
and the Completion of Mitosis
631
Chromosomes Segregate During Anaphase
631
Unattached Chromosomes Block Sister-Chromatid
Separation
633
The Nuclear Envelope Re-forms at Telophase
634
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 the Formation
of a New Cell Wall Membrane-Enclosed Organelles Must Be
Distributed to Daughter Cells When a Cell
Divides
634
634
635
636
638
Control of Cell Number and Cell Size 638
Apoptosis Helps Regulate Animal Cell Numbers 638
Apoptosis Is Mediated by an Intracellular
Proteolytic Cascade
The Death Program Is Regulated by the Bcl2
Family of Intracellular Proteins
Animal Cells Require Extracellular Signals to
Survive, Grow, and Divide Animal Cells Require Survival Factors to Avoid
Apoptosis
Mitogens Stimulate Cell Division Growth Factors Stimulate Cells to Grow
Some Extracellular Signal Proteins Inhibit Cell
Survival, Division, or Growth
Essential Concepts
End-of-Chapter Questions
Chapter 19 Sex and Genetics
xix
639
641
642
643
644
645
645
647
649
651
The Benefits of Sex
Sexual Reproduction Involves Both Diploid and
Haploid Cells
Sexual Reproduction Gives Organisms a
Competitive Advantage
652
Meiosis and Fertilization
Haploid Germ Cells Are Produced From Diploid
Cells Through Meiosis
Meiosis Involves a Special Process of
Chromosome Pairing
Crossing-Over Can Occur Between Maternal
and Paternal Chromosomes
Chromosome Pairing and Recombination Ensure
the Proper Segregation of Homologs
The Second Meiotic Division Produces Haploid
Daughter Cells
Haploid Cells Contain Reassorted Genetic
Information
Meiosis Is Not Flawless
Fertilization Reconstitutes a Complete Diploid
Genome
655
Mendel and the Laws of Inheritance
Mendel Chose to Study Traits That Are Inherited
in a Discrete Fashion Mendel Could Disprove the Alternative Theories
of Inheritance
Mendel’s Experiments Were the First to Reveal
the Discrete Nature of Heredity 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
664
652
654
655
656
657
658
659
661
662
663
665
665
666
667
668
669
671
xx
Detailed Contents
Chromosome Crossovers Can Be Used to
Determine the Order of Genes
671
Mutations in Genes Can Cause a Loss of Function
Or a Gain of Function
673
Each of Us Carries Many Potentially Harmful
Recessive Mutant Alleles
673
Specific Signals Maintain the Stem-Cell
Populations
Stem Cells Can Be Used to Repair Damaged
Tissues
Therapeutic Cloning Could Provide a Way to
Generate Personalized ES Cells
Genetics as an Experimental Tool
675
The Classical Approach Begins with Random
Mutagenesis
675
Genetic Screens Identify Mutants Deficient in
Specific Cellular Processes
676
A Complementation Test Reveals Whether Two
Mutations Are in the Same Gene
677
Single-Nucleotide Polymorphisms (SNPs) Serve as
Landmarks for Genetic Mapping
678
Linked Groups of SNPs Define Haplotype Blocks 682
Haplotype Blocks Give Clues to our Evolutionary
History
683
Essential Concepts
684
End-of-Chapter Questions
685
Cancer
Cancer Cells Proliferate, Invade, and
Metastasize
Epidemiology Identifies Preventable Causes of
Cancer
Cancers Develop by an Accumulation of
Mutations
Cancer Cells 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
Essential Concepts
End-of-Chapter Questions
Chapter 20 Cellular Communities:
Tissues, Stem Cells, and Cancer
Extracellular Matrix and Connective
Tissues
Plant Cells Have Tough External Walls
Cellulose Microfibrils 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
689
690
691
692
693
694
696
696
698
Epithelial Sheets and Cell Junctions
700
Epithelial Sheets Are Polarized and Rest on a
Basal Lamina
700
Tight Junctions Make an Epithelium Leak-proof
and Separate Its Apical and Basal Surfaces
701
Cytoskeleton-linked Junctions Bind Epithelial Cells
Robustly to One Another and to the Basal
Lamina
703
Gap Junctions Allow Ions and Small Molecules
to Pass from Cell to Cell
705
Tissue Maintenance and Renewal
707
Tissues Are Organized Mixtures of Many Cell
Types
709
Different Tissues Are Renewed at Different Rates 710
Stem Cells Generate a Continuous Supply of
Terminally Differentiated Cells
711
713
714
715
717
718
718
719
721
722
723
727
729
731