Chemistry in Context 7th Edition Chapter 4 Answers

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Cover of Molecular Biology of the Cell

Molecular Biology of the Cell, 4th edition

Bruce Alberts, Alexander Johnson, Julian Lewis, Martin Raff, Keith Roberts, and Peter Walter.

New York: Garland Science; 2002.

ISBN-10: 0-8153-3218-1 ISBN-10: 0-8153-4072-9

Copyright © 2002, Bruce Alberts, Alexander Johnson, Julian Lewis, Martin Raff, Keith Roberts, and Peter Walter; Copyright © 1983, 1989, 1994, Bruce Alberts, Dennis Bray, Julian Lewis, Martin Raff, Keith Roberts, and James D. Watson.

Excerpt

Molecular Biology of the Cell is the classic in-depth text reference in cell biology. By extracting fundamental concepts and meaning from this enormous and ever-growing field, the authors tell the story of cell biology, and create a coherent framework through which non-expert readers may approach the subject. Written in clear and concise language, and illustrated with original drawings, the book is enjoyable to read, and provides a sense of the excitement of modern biology. Molecular Biology of the Cell not only sets forth the current understanding of cell biology (updated as of Fall 2001), but also explores the intriguing implications and possibilities of that which remains unknown.

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Acknowledgments
Preface
A Note to the Reader
Part I. Introduction to the Cell
- Chapter 1. Cells and Genomes
  - The Universal Features of Cells on Earth
    - All Cells Store Their Hereditary Information in the Same Linear Chemical Code (DNA)
    - All Cells Replicate Their Hereditary Information by Templated Polymerization
    - All Cells Transcribe Portions of Their Hereditary Information into the Same Intermediary Form (RNA)
    - All Cells Use Proteins as Catalysts
    - All Cells Translate RNA into Protein in the Same Way
    - The Fragment of Genetic Information Corresponding to One Protein Is One Gene
    - Life Requires Free Energy
    - All Cells Function as Biochemical Factories Dealing with the Same Basic Molecular Building Blocks
    - All Cells Are Enclosed in a Plasma Membrane Across Which Nutrients and Waste Materials Must Pass
    - A Living Cell Can Exist with Fewer Than 500 Genes
    - Summary
  - The Diversity of Genomes and the Tree of Life
    - Cells Can Be Powered by a Variety of Free Energy Sources
    - Some Cells Fix Nitrogen and Carbon Dioxide for Others
    - The Greatest Biochemical Diversity Is Seen Among Procaryotic Cells
    - The Tree of Life Has Three Primary Branches: Bacteria, Archaea, and Eucaryotes
    - Some Genes Evolve Rapidly; Others Are Highly Conserved
    - Most Bacteria and Archaea Have 1000–4000 Genes
    - New Genes Are Generated from Preexisting Genes
    - Gene Duplications Give Rise to Families of Related Genes Within a Single Cell
    - Genes Can Be Transferred Between Organisms, Both in the Laboratory and in Nature
    - Horizontal Exchanges of Genetic Information Within a Species Are Brought About by Sex
    - The Function of a Gene Can Often Be Deduced from Its Sequence
    - More Than 200 Gene Families Are Common to All Three Primary Branches of the Tree of Life
    - Mutations Reveal the Functions of Genes
    - Molecular Biologists Have Focused a Spotlight on E. coli
    - Summary
  - Genetic Information in Eucaryotes
    - Eucaryotic Cells May Have Originated as Predators
    - Eucaryotic Cells Evolved from a Symbiosis
    - Eucaryotes Have Hybrid Genomes
    - Eucaryotic Genomes Are Big
    - Eucaryotic Genomes Are Rich in Regulatory DNA
    - The Genome Defines the Program of Multicellular Development
    - Many Eucaryotes Live as Solitary Cells: the Protists
    - A Yeast Serves as a Minimal Model Eucaryote
    - The Expression Levels of All The Genes of An Organism Can Be Monitored Simultaneously
    - Arabidopsis Has Been Chosen Out of 300,000 Species As a Model Plant
    - The World of Animal Cells Is Represented By a Worm, a Fly, a Mouse, and a Human
    - Studies in Drosophila Provide a Key to Vertebrate Development
    - The Vertebrate Genome Is a Product of Repeated Duplication
    - Genetic Redundancy Is a Problem for Geneticists, But It Creates Opportunities for Evolving Organisms
    - The Mouse Serves as a Model for Mammals
    - Humans Report on Their Own Peculiarities
    - We Are All Different in Detail
    - Summary
  - References
    - General
    - The Universal Features of Cells on Earth
    - The Diversity of Genomes and the Tree of Life
    - Genetic Information in Eucaryotes
- Chapter 2. Cell Chemistry and Biosynthesis
  - The Chemical Components of a Cell
    - Cells Are Made From a 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
    - There Are Different Types of Covalent Bonds
    - An Atom Often Behaves as if It Has a Fixed Radius
    - Water Is the Most Abundant Substance in Cells
    - Some Polar Molecules Form Acids and Bases in Water
    - Four Types of Noncovalent Interactions Help Bring Molecules Together in Cells
    - A Cell Is Formed from Carbon Compounds
    - Cells Contain Four Major Families of Small Organic Molecules
    - Sugars Provide an Energy Source for Cells and Are the 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
    - The Chemistry of Cells is Dominated by Macromolecules with Remarkable Properties
    - Noncovalent Bonds Specify Both the Precise Shape of a Macromolecule and its Binding to Other Molecules
    - Summary
  - Catalysis and the Use of Energy by Cells
    - Cell Metabolism Is Organized by Enzymes
    - 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
    - How Enzymes Find Their Substrates: The Importance of Rapid Diffusion
    - The Free-Energy Change for a Reaction Determines Whether It Can Occur
    - The Concentration of Reactants Influences ΔG
    - For Sequential Reactions, ΔG° Values Are Additive
    - Activated Carrier Molecules are Essential for 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
    - Summary
  - How Cells Obtain Energy from Food
    - Food Molecules Are Broken Down in Three Stages to Produce ATP
    - 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
    - Electron Transport Drives the Synthesis of the Majority of the ATP in Most Cells
    - Organisms Store Food Molecules in Special Reservoirs
    - Amino Acids and Nucleotides Are Part of the Nitrogen Cycle
    - Many Biosynthetic Pathways Begin with Glycolysis or the Citric Acid Cycle
    - Metabolism Is Organized and Regulated
    - Summary
  - References
    - General
    - The Chemical Components of a Cell
    - Catalysis and the Use of Energy by Cells
    - How Cells Obtain Energy from Food
- Chapter 3. Proteins
  - 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
    - The α Helix and the β Sheet Are Common Folding Patterns
    - The Protein Domain Is a Fundamental Unit of Organization
    - Few of the Many Possible Polypeptide Chains Will Be Useful
    - Proteins Can Be Classified into Many Families
    - Proteins Can Adopt a Limited Number of Different Protein Folds
    - Sequence Homology Searches Can Identify Close Relatives
    - Computational Methods Allow Amino Acid Sequences to Be Threaded into Known Protein Folds
    - Some Protein Domains, Called Modules, Form Parts of Many Different Proteins
    - The Human Genome Encodes a Complex Set of Proteins, Revealing Much That Remains Unknown
    - Larger Protein Molecules Often Contain More Than One Polypeptide Chain
    - Some Proteins Form Long Helical Filaments
    - A Protein Molecule Can Have an Elongated, Fibrous Shape
    - Extracellular Proteins Are Often Stabilized by Covalent Cross-Linkages
    - Protein Molecules Often Serve as Subunits for the Assembly of Large Structures
    - Many Structures in Cells Are Capable of Self-Assembly
    - The Formation of Complex Biological Structures Is Often Aided by Assembly Factors
    - Summary
  - Protein Function
    - All Proteins Bind to Other Molecules
    - The Details of a Protein's Conformation Determine Its Chemistry
    - Sequence Comparisons Between Protein Family Members Highlight Crucial Ligand Binding Sites
    - Proteins Bind to Other Proteins Through Several Types of Interfaces
    - The Binding Sites of Antibodies Are Especially Versatile
    - Binding Strength Is Measured by the Equilibrium Constant
    - Enzymes Are Powerful and Highly Specific Catalysts
    - Substrate Binding Is the First Step in Enzyme Catalysis
    - Enzymes Speed Reactions by Selectively Stabilizing Transition States
    - Enzymes Can Use Simultaneous Acid and Base Catalysis
    - Lysozyme Illustrates How an Enzyme Works
    - Tightly Bound Small Molecules Add Extra Functions to Proteins
    - Multienzyme Complexes Help to Increase the Rate of Cell Metabolism
    - The Catalytic Activities of Enzymes Are Regulated
    - Allosteric Enzymes Have Two or More Binding Sites That Interact
    - Two Ligands Whose Binding Sites Are Coupled Must Reciprocally Affect Each Other's Binding
    - Symmetric Protein Assemblies Produce Cooperative Allosteric Transitions
    - The Allosteric Transition in Aspartate Transcarbamoylase Is Understood in Atomic Detail
    - Many Changes in Proteins Are Driven by Phosphorylation
    - A Eucaryotic Cell Contains a Large Collection of Protein Kinases and Protein Phosphatases
    - The Regulation of Cdk and Src Protein Kinases Shows How a Protein Can Function as a Microchip
    - Proteins That Bind and Hydrolyze GTP Are Ubiquitous Cellular Regulators
    - Regulatory Proteins Control the Activity of GTP-Binding Proteins by Determining Whether GTP or GDP Is Bound
    - Large Protein Movements Can Be Generated From Small Ones
    - Motor Proteins Produce Large Movements in Cells
    - Membrane-bound Transporters Harness Energy to Pump Molecules Through Membranes
    - Proteins Often Form Large Complexes That Function as Protein Machines
    - A Complex Network of Protein Interactions Underlies Cell Function
    - Summary
  - References
    - General
    - The Shape and Structure of Proteins
    - Protein Function
Part II. Basic Genetic Mechanisms
- Chapter 4. DNA and Chromosomes
  - The Structure and Function of DNA
    - A DNA Molecule Consists of Two Complementary Chains of Nucleotides
    - The Structure of DNA Provides a Mechanism for Heredity
    - In Eucaryotes, DNA Is Enclosed in a Cell Nucleus
    - Summary
  - Chromosomal DNA and Its Packaging in the Chromatin Fiber
    - Eucaryotic DNA Is Packaged into a Set of Chromosomes
    - Chromosomes Contain Long Strings of Genes
    - The Nucleotide Sequence of the Human Genome Shows How Genes Are Arranged in Humans
    - Comparisons Between the DNAs of Related Organisms Distinguish Conserved and Nonconserved Regions of DNA Sequence
    - Chromosomes Exist in Different States Throughout the Life of a Cell
    - Each DNA Molecule That Forms a Linear Chromosome Must Contain a Centromere, Two Telomeres, and Replication Origins
    - DNA Molecules Are Highly Condensed in Chromosomes
    - Nucleosomes Are the Basic Unit of Eucaryotic Chromosome Structure
    - The Structure of the Nucleosome Core Particle Reveals How DNA Is Packaged
    - The Positioning of Nucleosomes on DNA Is Determined by Both DNA Flexibility and Other DNA-bound Proteins
    - Nucleosomes Are Usually Packed Together into a Compact Chromatin Fiber
    - ATP-driven Chromatin Remodeling Machines Change Nucleosome Structure
    - Covalent Modification of the Histone Tails Can Profoundly Affect Chromatin
    - Summary
  - The Global Structure of Chromosomes
    - Lampbrush Chromosomes Contain Loops of Decondensed Chromatin
    - Drosophila Polytene Chromosomes Are Arranged in Alternating Bands and Interbands
    - Both Bands and Interbands in Polytene Chromosomes Contain Genes
    - Individual Polytene Chromosome Bands Can Unfold and Refold as a Unit
    - Heterochromatin Is Highly Organized and Usually Resistant to Gene Expression
    - The Ends of Chromosomes Have a Special Form of Heterochromatin
    - Centromeres Are Also Packaged into Heterochromatin
    - Heterochromatin May Provide a Defense Mechanism Against Mobile DNA Elements
    - Mitotic Chromosomes Are Formed from Chromatin in Its Most Condensed State
    - Each Mitotic Chromosome Contains a Characteristic Pattern of Very Large Domains
    - Individual Chromosomes Occupy Discrete Territories in an Interphase Nucleus
    - Summary
  - References
    - General
- Chapter 5. DNA Replication, Repair, and Recombination
  - The Maintenance of DNA Sequences
    - Mutation Rates Are Extremely Low
    - Many Mutations in Proteins Are Deleterious and Are Eliminated by Natural Selection
    - Low Mutation Rates Are Necessary for Life as We Know It
    - Summary
  - DNA Replication Mechanisms
    - Base-Pairing Underlies DNA Replication and DNA Repair
    - The DNA Replication Fork Is Asymmetrical
    - The High Fidelity of DNA Replication Requires Several Proofreading Mechanisms
    - Only DNA Replication in the 5′-to-3′ Direction Allows Efficient Error Correction
    - A Special Nucleotide-Polymerizing Enzyme Synthesizes Short RNA Primer Molecules on the Lagging Strand
    - Special Proteins Help to Open Up the DNA Double Helix in Front of the Replication Fork
    - A Moving DNA Polymerase Molecule Stays Connected to the DNA by a Sliding Ring
    - The Proteins at a Replication Fork Cooperate to Form a Replication Machine
    - A Strand-directed Mismatch Repair System Removes Replication Errors That Escape from the Replication Machine
    - DNA Topoisomerases Prevent DNA Tangling During Replication
    - DNA Replication Is Similar in Eucaryotes and Bacteria
    - Summary
  - The Initiation and Completion of DNA Replication in Chromosomes
    - DNA Synthesis Begins at Replication Origins
    - Bacterial Chromosomes Have a Single Origin of DNA Replication
    - Eucaryotic Chromosomes Contain Multiple Origins of Replication
    - In Eucaryotes DNA Replication Takes Place During Only One Part of the Cell Cycle
    - Different Regions on the Same Chromosome Replicate at Distinct Times in S Phase
    - Highly Condensed Chromatin Replicates Late, While Genes in Less Condensed Chromatin Tend to Replicate Early
    - Well-defined DNA Sequences Serve as Replication Origins in a Simple Eucaryote, the Budding Yeast
    - A Large Multisubunit Complex Binds to Eucaryotic Origins of Replication
    - The Mammalian DNA Sequences That Specify the Initiation of Replication Have Been Difficult to Identify
    - New Nucleosomes Are Assembled Behind the Replication Fork
    - Telomerase Replicates the Ends of Chromosomes
    - Telomere Length Is Regulated by Cells and Organisms
    - Summary
  - DNA Repair
    - Without DNA Repair, Spontaneous DNA Damage Would Rapidly Change DNA Sequences
    - The DNA Double Helix Is Readily Repaired
    - DNA Damage Can Be Removed by More Than One Pathway
    - The Chemistry of the DNA Bases Facilitates Damage Detection
    - Double-Strand Breaks are Efficiently Repaired
    - Cells Can Produce DNA Repair Enzymes in Response to DNA Damage
    - DNA Damage Delays Progression of the Cell Cycle
    - Summary
  - General Recombination
    - General Recombination Is Guided by Base-pairing Interactions Between Two Homologous DNA Molecules
    - Meiotic Recombination Is Initiated by Double-strand DNA Breaks
    - DNA Hybridization Reactions Provide a Simple Model for the Base-pairing Step in General Recombination
    - The RecA Protein and its Homologs Enable a DNA Single Strand to Pair with a Homologous Region of DNA Double Helix
    - There Are Multiple Homologs of the RecA Protein in Eucaryotes, Each Specialized for a Specific Function
    - General Recombination Often Involves a Holliday Junction
    - General Recombination Can Cause Gene Conversion
    - General Recombination Events Have Different Preferred Outcomes in Mitotic and Meiotic Cells
    - Mismatch Proofreading Prevents Promiscuous Recombination Between Two Poorly Matched DNA Sequences
    - Summary
  - Site-Specific Recombination
    - Mobile Genetic Elements Can Move by Either Transpositional or Conservative Mechanisms
    - Transpositional Site-specific Recombination Can Insert Mobile Genetic Elements into Any DNA Sequence
    - DNA-only Transposons Move By DNA Breakage and Joining Mechanisms
    - Some Viruses Use Transpositional Site-specific Recombination to Move Themselves into Host Cell Chromosomes
    - Retroviral-like Retrotransposons Resemble Retroviruses, but Lack a Protein Coat
    - A Large Fraction of the Human Genome Is Composed of Nonretroviral Retrotransposons
    - Different Transposable Elements Predominate in Different Organisms
    - Genome Sequences Reveal the Approximate Times when Transposable Elements Have Moved
    - Conservative Site-specific Recombination Can Reversibly Rearrange DNA
    - Conservative Site-Specific Recombination Can be Used to Turn Genes On or Off
    - Summary
  - References
    - General
    - The Maintenance of DNA Sequences
    - DNA Replication Mechanisms
    - The Initiation and Completion of DNA Replication in Chromosomes
    - DNA Repair
    - General Recombination
    - Site-specific Recombination
- Chapter 6. How Cells Read the Genome: From DNA to Protein
  - From DNA to RNA
    - Portions of DNA Sequence Are Transcribed into RNA
    - Transcription Produces RNA Complementary to One Strand of DNA
    - Cells Produce Several Types of RNA
    - Signals Encoded in DNA Tell RNA Polymerase Where to Start and Stop
    - Transcription Start and Stop Signals Are Heterogeneous in Nucleotide Sequence
    - Transcription Initiation in Eucaryotes Requires Many Proteins
    - RNA Polymerase II Requires General Transcription Factors
    - Polymerase II Also Requires Activator, Mediator, and Chromatin-modifying Proteins
    - Transcription Elongation Produces Superhelical Tension in DNA
    - Transcription Elongation in Eucaryotes Is Tightly Coupled To RNA Processing
    - RNA Capping Is the First Modification of Eucaryotic Pre-mRNAs
    - RNA Splicing Removes Intron Sequences from Newly Transcribed Pre-mRNAs
    - Nucleotide Sequences Signal Where Splicing Occurs
    - RNA Splicing Is Performed by the Spliceosome
    - The Spliceosome Uses ATP Hydrolysis to Produce a Complex Series of RNA-RNA Rearrangements
    - Ordering Influences in the Pre-mRNA Help to Explain How the Proper Splice Sites Are Chosen
    - A Second Set of snRNPs Splice a Small Fraction of Intron Sequences in Animals and Plants
    - RNA Splicing Shows Remarkable Plasticity
    - Spliceosome-catalyzed RNA Splicing Probably Evolved from Self-splicing Mechanisms
    - RNA-Processing Enzymes Generate the 3′ End of Eucaryotic mRNAs
    - Mature Eucaryotic mRNAs Are Selectively Exported from the Nucleus
    - Many Noncoding RNAs Are Also Synthesized and Processed in the Nucleus
    - The Nucleolus Is a Ribosome-Producing Factory
    - The Nucleus Contains a Variety of Subnuclear Structures
    - Summary
  - From RNA to Protein
    - An mRNA Sequence Is Decoded in Sets of Three Nucleotides
    - tRNA Molecules Match Amino Acids to Codons in mRNA
    - tRNAs Are Covalently Modified Before They Exit from the Nucleus
    - Specific Enzymes Couple Each Amino Acid to Its Appropriate tRNA Molecule
    - Editing by RNA Synthetases Ensures Accuracy
    - Amino Acids Are Added to the C-terminal End of a Growing Polypeptide Chain
    - The RNA Message Is Decoded on Ribosomes
    - Elongation Factors Drive Translation Forward
    - The Ribosome Is a Ribozyme
    - Nucleotide Sequences in mRNA Signal Where to Start Protein Synthesis
    - Stop Codons Mark the End of Translation
    - Proteins Are Made on Polyribosomes
    - Quality-Control Mechanisms Operate at Many Stages of Translation
    - There Are Minor Variations in the Standard Genetic Code
    - Many Inhibitors of Procaryotic Protein Synthesis Are Useful as Antibiotics
    - A Protein Begins to Fold While It Is Still Being Synthesized
    - Molecular Chaperones Help Guide the Folding of Many Proteins
    - Exposed Hydrophobic Regions Provide Critical Signals for Protein Quality Control
    - The Proteasome Degrades a Substantial Fraction of the Newly Synthesized Proteins in Cells
    - An Elaborate Ubiquitin-conjugating System Marks Proteins for Destruction
    - Many Proteins Are Controlled by Regulated Destruction
    - Abnormally Folded Proteins Can Aggregate to Cause Destructive Human Diseases
    - There Are Many Steps From DNA to Protein
    - Summary
  - The RNA World and the Origins of Life
    - Life Requires Autocatalysis
    - Polynucleotides Can Both Store Information and Catalyze Chemical Reactions
    - A Pre-RNA World Probably Predates the RNA World
    - Single-stranded RNA Molecules Can Fold into Highly Elaborate Structures
    - Self-Replicating Molecules Undergo Natural Selection
    - How Did Protein Synthesis Evolve?
    - All Present-day Cells Use DNA as Their Hereditary Material
    - Summary
  - References
    - General
    - From DNA to RNA
    - From RNA to Protein
    - The RNA World and the Origins of Life
- Chapter 7. Control of Gene Expression
  - An Overview of Gene Control
    - The Different Cell Types of a Multicellular Organism Contain the Same DNA
    - Different Cell Types Synthesize 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
    - Summary
  - DNA-Binding Motifs in Gene Regulatory Proteins
    - Gene Regulatory Proteins Were Discovered Using Bacterial Genetics
    - The Outside of the DNA Helix Can Be Read by Proteins
    - The Geometry of the DNA Double Helix Depends on the Nucleotide Sequence
    - Short DNA Sequences Are Fundamental Components of Genetic Switches
    - Gene Regulatory Proteins Contain Structural Motifs That Can Read DNA Sequences
    - The Helix-Turn-Helix Motif Is One of the Simplest and Most Common DNA-binding Motifs
    - Homeodomain Proteins Constitute a Special Class of Helix-Turn-Helix Proteins
    - There Are Several Types of DNA-binding Zinc Finger Motifs
    - β sheets Can Also Recognize DNA
    - The Leucine Zipper Motif Mediates Both DNA Binding and Protein Dimerization
    - Heterodimerization Expands the Repertoire of DNA Sequences Recognized by Gene Regulatory Proteins
    - The Helix-Loop-Helix Motif Also Mediates Dimerization and DNA Binding
    - It Is Not Yet Possible to Accurately Predict the DNA Sequences Recognized by All Gene Regulatory Proteins
    - A Gel-Mobility Shift Assay Allows Sequence-specific DNA-binding Proteins to Be Detected Readily
    - DNA Affinity Chromatography Facilitates the Purification of Sequence-specific DNA-binding Proteins
    - The DNA Sequence Recognized by a Gene Regulatory Protein Can Be Determined
    - A Chromatin Immunoprecipitation Technique Identifies DNA Sites Occupied by Gene Regulatory Proteins in Living Cells
    - Summary
  - How Genetic Switches Work
    - The Tryptophan Repressor Is a Simple Switch That Turns Genes On and Off in Bacteria
    - Transcriptional Activators Turn Genes On
    - A Transcriptional Activator and a Transcriptional Repressor Control the lac Operon
    - Regulation of Transcription in Eucaryotic Cells Is Complex
    - Eucaryotic Gene Regulatory Proteins Control Gene Expression from a Distance
    - A Eucaryotic Gene Control Region Consists of a Promoter Plus Regulatory DNA Sequences
    - Eucaryotic Gene Activator Proteins Promote the Assembly of RNA Polymerase and the General Transcription Factors at the Startpoint of Transcription
    - Eucaryotic Gene Activator Proteins Modify Local Chromatin Structure
    - Gene Activator Proteins Work Synergistically
    - Eucaryotic Gene Repressor Proteins Can Inhibit Transcription in Various Ways
    - Eucaryotic Gene Regulatory Proteins Often Assemble into Complexes on DNA
    - Complex Genetic Switches That Regulate Drosophila Development Are Built Up from Smaller Modules
    - The Drosophila eve Gene Is Regulated by Combinatorial Controls
    - Complex Mammalian Gene Control Regions Are Also Constructed from Simple Regulatory Modules
    - Insulators Are DNA Sequences That Prevent Eucaryotic Gene Regulatory Proteins from Influencing Distant Genes
    - Bacteria Use Interchangeable RNA Polymerase Subunits to Help Regulate Gene Transcription
    - Gene Switches Have Gradually Evolved
    - Summary
  - The Molecular Genetic Mechanisms That Create Specialized Cell Types
    - DNA Rearrangements Mediate Phase Variation in Bacteria
    - A Set of Gene Regulatory Proteins Determines Cell Type in a Budding Yeast
    - Two Proteins That Repress Each Other's Synthesis Determine the Heritable State of Bacteriophage Lambda
    - Gene Regulatory Circuits Can Be Used to Make Memory Devices As Well As Oscillators
    - Circadian Clocks Are Based on Feedback Loops in Gene Regulation
    - The Expression of a Set of Genes Can Be Coordinated by a Single Protein
    - Expression of a Critical Gene Regulatory Protein Can Trigger Expression of a Whole Battery of Downstream Genes
    - Combinatorial Gene Control Creates Many Different Cell Types in Eucaryotes
    - The Formation of an Entire Organ Can Be Triggered by a Single Gene Regulatory Protein
    - Stable Patterns of Gene Expression Can Be Transmitted to Daughter Cells
    - Chromosome Wide Alterations in Chromatin Structure Can Be Inherited
    - The Pattern of DNA Methylation Can Be Inherited When Vertebrate Cells Divide
    - Vertebrates Use DNA Methylation to Lock Genes in a Silent State
    - Genomic Imprinting Requires DNA Methylation
    - CG-rich Islands Are Associated with About 20,000 Genes in Mammals
    - Summary
  - Posttranscriptional Controls
    - Transcription Attenuation Causes the Premature Termination of Some RNA Molecules
    - Alternative RNA Splicing Can Produce Different Forms of a Protein from the Same Gene
    - The Definition of a Gene Has Had to Be Modified Since the Discovery of Alternative RNA Splicing
    - Sex Determination in Drosophila Depends on a Regulated Series of RNA Splicing Events
    - A Change in the Site of RNA Transcript Cleavage and Poly-A Addition Can Change the C-terminus of a Protein
    - RNA Editing Can Change the Meaning of the RNA Message
    - RNA Transport from the Nucleus Can Be Regulated
    - Some mRNAs Are Localized to Specific Regions of the Cytoplasm
    - Proteins That Bind to the 5′ and 3′ Untranslated Regions of mRNAs Mediate Negative Translational Control
    - The Phosphorylation of an Initiation Factor Globally Regulates Protein Synthesis
    - Initiation at AUG Codons Upstream of the Translation Start Can Regulate Eucaryotic Translation Initiation
    - Internal Ribosome Entry Sites Provide Opportunities for Translation Control
    - Gene Expression Can Be Controlled By a Change In mRNA Stability
    - Cytoplasmic Poly-A Addition Can Regulate Translation
    - Nonsense-mediated mRNA Decay Is Used as an mRNA Surveillance System in Eucaryotes
    - RNA Interference Is Used by Cells to Silence Gene Expression
    - Summary
  - How Genomes Evolve
    - Genome Alterations are Caused by Failures of the Normal Mechanisms for Copying and Maintaining DNA
    - The Genome Sequences of Two Species Differ in Proportion to the Length of Time That They Have Separately Evolved
    - The Chromosomes of Humans and Chimpanzees Are Very Similar
    - A Comparison of Human and Mouse Chromosomes Shows How The Large-scale Structures of Genomes Diverge
    - It Is Difficult to Reconstruct the Structure of Ancient Genomes
    - Gene Duplication and Divergence Provide a Critical Source of Genetic Novelty During Evolution
    - Duplicated Genes Diverge
    - The Evolution of the Globin Gene Family Shows How DNA Duplications Contribute to the Evolution of Organisms
    - Genes Encoding New Proteins Can Be Created by the Recombination of Exons
    - Genome Sequences Have Left Scientists with Many Mysteries to Be Solved
    - Genetic Variation within a Species Provides a Fine-Scale View of Genome Evolution
    - Summary
  - References
    - General
    - An Overview of Gene Control
    - DNA-binding Motifs in Gene Regulatory Proteins
    - How Genetic Switches Work
    - The Molecular Genetic Mechanisms that Create Specialized Cell Types
    - Posttranscriptional Controls
    - How Genomes Evolve
Part III. Methods
- Chapter 8. Manipulating Proteins, DNA, and RNA
  - Isolating Cells and Growing Them in Culture
    - Cells Can Be Isolated from a Tissue Suspension and Separated into Different Types
    - Cells Can Be Grown in a Culture Dish
    - Serum-free, Chemically Defined Media Permit Identification of Specific Growth Factors
    - Eucaryotic Cell Lines Are a Widely Used Source of Homogeneous Cells
    - Cells Can Be Fused Together to Form Hybrid Cells
    - Hybridoma Cell Lines Provide a Permanent Source of Monoclonal Antibodies
    - Summary
  - Fractionation of Cells
    - Organelles and Macromolecules Can Be Separated by Ultracentrifugation
    - The Molecular Details of Complex Cellular Processes Can Be Deciphered in Cell-Free Systems
    - Proteins Can Be Separated by Chromatography
    - Affinity Chromatography Exploits Specific Binding Sites on Proteins
    - The Size and Subunit Composition of a Protein Can Be Determined by SDS Polyacrylamide-Gel Electrophoresis
    - More Than 1000 Proteins Can Be Resolved on a Single Gel by Two-dimensional Polyacrylamide-Gel Electrophoresis
    - Selective Cleavage of a Protein Generates a Distinctive Set of Peptide Fragments
    - Mass Spectrometry Can Be Used to Sequence Peptide Fragments and Identify Proteins
    - Summary
  - Isolating, Cloning, and Sequencing DNA
    - Large DNA Molecules Are Cut into Fragments by Restriction Nucleases
    - Gel Electrophoresis Separates DNA Molecules of Different Sizes
    - Purified DNA Molecules Can Be Specifically Labeled with Radioisotopes or Chemical Markers in vitro
    - Nucleic Acid Hybridization Reactions Provide a Sensitive Way of Detecting Specific Nucleotide Sequences
    - Northern and Southern Blotting Facilitate Hybridization with Electrophoretically Separated Nucleic Acid Molecules
    - Hybridization Techniques Locate Specific Nucleic Acid Sequences in Cells or on Chromosomes
    - Genes Can Be Cloned from a DNA Library
    - Two Types of DNA Libraries Serve Different Purposes
    - cDNA Clones Contain Uninterrupted Coding Sequences
    - Isolated DNA Fragments Can Be Rapidly Sequenced
    - Nucleotide Sequences Are Used to Predict the Amino Acid Sequences of Proteins
    - The Genomes of Many Organisms Have Been Fully Sequenced
    - Selected DNA Segments Can Be Cloned in a Test Tube by a Polymerase Chain Reaction
    - Cellular Proteins Can Be Made in Large Amounts Through the Use of Expression Vectors
    - Summary
  - Analyzing Protein Structure and Function
    - The Diffraction of X-rays by Protein Crystals Can Reveal a Protein's Exact Structure
    - Molecular Structure Can Also Be Determined Using Nuclear Magnetic Resonance (NMR) Spectroscopy
    - Sequence Similarity Can Provide Clues About Protein Function
    - Fusion Proteins Can Be Used to Analyze Protein Function and to Track Proteins in Living Cells
    - Affinity Chromatography and Immunoprecipitation Allow Identification of Associated Proteins
    - Protein-Protein Interactions Can Be Identified by Use of the Two-Hybrid System
    - Phage Display Methods Also Detect Protein Interactions
    - Protein Interactions Can Be Monitored in Real Time Using Surface Plasmon Resonance
    - DNA Footprinting Reveals the Sites Where Proteins Bind on a DNA Molecule
    - Summary
  - Studying Gene Expression and Function
    - 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 or in Different Genes
    - Genes Can Be Located by Linkage Analysis
    - Searching for Homology Can Help Predict a Gene's Function
    - Reporter Genes Reveal When and Where a Gene Is Expressed
    - Microarrays Monitor the Expression of Thousands of Genes at Once
    - Targeted Mutations Can Reveal Gene Function
    - Cells and Animals Containing Mutated Genes Can Be Made to Order
    - The Normal Gene in a Cell Can Be Directly Replaced by an Engineered Mutant Gene in Bacteria and Some Lower Eucaryotes
    - Engineered Genes Can Be Used to Create Specific Dominant Negative Mutations in Diploid Organisms
    - Gain-of-Function Mutations Provide Clues to the Role Genes Play in a Cell or Organism
    - Genes Can Be Redesigned to Produce Proteins of Any Desired Sequence
    - Engineered Genes Can Be Easily Inserted into the Germ Line of Many Animals
    - Gene Targeting Makes It Possible to Produce Transgenic Mice That Are Missing Specific Genes
    - Transgenic Plants Are Important for Both Cell Biology and Agriculture
    - Large Collections of Tagged Knockouts Provide a Tool for Examining the Function of Every Gene in an Organism
    - Summary
  - References
    - General
    - Isolating Cells and Growing Them in Culture
    - Fractionation of Cells
    - Isolating, Cloning, and Sequencing DNA
    - Analyzing Protein Structure and Function
    - Studying Gene Expression and Function
- Chapter 9. Visualizing Cells
  - Looking at the Structure of Cells in the Microscope
    - The Light Microscope Can Resolve Details 0.2 μm Apart
    - Living Cells Are Seen Clearly in a Phase-Contrast or a Differential-Interference-Contrast Microscope
    - Images Can Be Enhanced and Analyzed by Electronic Techniques
    - Tissues Are Usually Fixed and Sectioned for Microscopy
    - Different Components of the Cell Can Be Selectively Stained
    - Specific Molecules Can Be Located in Cells by Fluorescence Microscopy
    - Antibodies Can Be Used to Detect Specific Molecules
    - Imaging of Complex Three-dimensional Objects Is Possible with the Optical Microscope
    - The Confocal Microscope Produces Optical Sections by Excluding Out-of-Focus Light
    - The Electron Microscope Resolves the Fine Structure of the Cell
    - Biological Specimens Require Special Preparation for the Electron Microscope
    - Specific Macromolecules Can Be Localized by Immunogold Electron Microscopy
    - Images of Surfaces Can Be Obtained by Scanning Electron Microscopy
    - Metal Shadowing Allows Surface Features to Be Examined at High Resolution by Transmission Electron Microscopy
    - Freeze-Fracture and Freeze-Etch Electron Microscopy Provide Views of Surfaces Inside the Cell
    - Negative Staining and Cryoelectron Microscopy Allow Macromolecules to Be Viewed at High Resolution
    - Multiple Images Can Be Combined to Increase Resolution
    - Views from Different Directions Can Be Combined to Give Three-dimensional Reconstructions
    - Summary
  - Visualizing Molecules in Living Cells
    - Rapidly Changing Intracellular Ion Concentrations Can Be Measured with Light-emitting Indicators
    - There Are Several Ways of Introducing Membrane-impermeant Molecules into Cells
    - The Light-induced Activation of "Caged" Precursor Molecules Facilitates Studies of Intracellular Dynamics
    - Green Fluorescent Protein Can Be Used to Tag Individual Proteins in Living Cells and Organisms
    - Light Can Be Used to Manipulate Microscopic Objects as Well as to Image Them
    - Molecules Can Be Labeled with Radioisotopes
    - Radioisotopes Are Used to Trace Molecules in Cells and Organisms
    - Summary
  - References
    - General
    - Looking at the Structure of Cells in the Microscope
    - Visualizing Molecules in Living Cells
Part IV. Internal Organization of the Cell
- Chapter 10. Membrane Structure
  - The Lipid Bilayer
    - Membrane Lipids Are Amphipathic Molecules, Most of which Spontaneously Form Bilayers
    - The Lipid Bilayer Is a Two-dimensional Fluid
    - The Fluidity of a Lipid Bilayer Depends on Its Composition
    - The Plasma Membrane Contains Lipid Rafts That Are Enriched in Sphingolipids, Cholesterol, and Some Membrane Proteins
    - The Asymmetry of the Lipid Bilayer Is Functionally Important
    - Glycolipids Are Found on the Surface of All Plasma Membranes
    - Summary
  - Membrane Proteins
    - Membrane Proteins Can Be Associated with the Lipid Bilayer in Various Ways
    - In Most Transmembrane Proteins the Polypeptide Chain Crosses the Lipid Bilayer in an α-Helical Conformation
    - Some β Barrels Form Large Transmembrane Channels
    - Many Membrane Proteins Are Glycosylated
    - Membrane Proteins Can Be Solubilized and Purified in Detergents
    - The Cytosolic Side of Plasma Membrane Proteins Can Be Studied in Red Blood Cell Ghosts
    - Spectrin Is a Cytoskeletal Protein Noncovalently Associated with the Cytosolic Side of the Red Blood Cell Membrane
    - Glycophorin Extends Through the Red Blood Cell Lipid Bilayer as a Single α Helix
    - Band 3 of the Red Blood Cell Is a Multipass Membrane Protein That Catalyzes the Coupled Transport of Anions
    - Bacteriorhodopsin Is a Proton Pump That Traverses the Lipid Bilayer as Seven α Helices
    - Membrane Proteins Often Function as Large Complexes
    - Many Membrane Proteins Diffuse in the Plane of the Membrane
    - Cells Can Confine Proteins and Lipids to Specific Domains Within a Membrane
    - The Cell Surface Is Coated with Sugar Residues
    - Summary
  - References
    - General
    - The Lipid Bilayer
    - Membrane Proteins
- Chapter 11. Membrane Transport of Small Molecules and the Electrical Properties of Membranes
  - Principles of Membrane Transport
    - Protein-free Lipid Bilayers Are Highly Impermeable to Ions
    - There Are Two Main Classes of Membrane Transport Proteins: Carriers and Channels
    - Active Transport Is Mediated by Carrier Proteins Coupled to an Energy Source
    - Ionophores Can Be Used as Tools to Increase the Permeability of Membranes to Specific Ions
    - Summary
  - Carrier Proteins and Active Membrane Transport
    - Active Transport Can Be Driven by Ion Gradients
    - Na⁺ -driven Carrier Proteins in the Plasma Membrane Regulate Cytosolic pH
    - An Asymmetric Distribution of Carrier Proteins in Epithelial Cells Underlies the Transcellular Transport of Solutes
    - The Plasma Membrane Na⁺ -K⁺ Pump Is an ATPase
    - Some Ca²⁺ and H⁺ Pumps Are Also P-type Transport ATPases
    - The Na⁺ -K⁺Pump Is Required to Maintain Osmotic Balance and Stabilize Cell Volume
    - Membrane-bound Enzymes That Synthesize ATP Are Transport ATPases Working in Reverse
    - ABC Transporters Constitute the Largest Family of Membrane Transport Proteins
    - Summary
  - Ion Channels and the Electrical Properties of Membranes
    - Ion Channels Are Ion-Selective and Fluctuate Between Open and Closed States
    - The Membrane Potential in Animal Cells Depends Mainly on K⁺ Leak Channels and the K⁺ Gradient Across the Plasma Membrane
    - The Resting Potential Decays Only Slowly When the Na⁺ -K⁺ Pump Is Stopped
    - The Three-dimensional Structure of a Bacterial K⁺ Channel Shows How an Ion Channel Can Work
    - The Function of a Nerve Cell Depends on Its Elongated Structure
    - Voltage-gated Cation Channels Generate Action Potentials in Electrically Excitable Cells
    - Myelination Increases the Speed and Efficiency of Action Potential Propagation in Nerve Cells
    - Patch-Clamp Recording Indicates That Individual Gated Channels Open in an All-or-Nothing Fashion
    - Voltage-gated Cation Channels Are Evolutionarily and Structurally Related
    - Transmitter-gated Ion Channels Convert Chemical Signals into Electrical Ones at Chemical Synapses
    - Chemical Synapses Can Be Excitatory or Inhibitory
    - The Acetylcholine Receptors at the Neuromuscular Junction Are Transmitter-gated Cation Channels
    - Transmitter-gated Ion Channels Are Major Targets for Psychoactive Drugs
    - Neuromuscular Transmission Involves the Sequential Activation of Five Different Sets of Ion Channels
    - Single Neurons Are Complex Computation Devices
    - Neuronal Computation Requires a Combination of at Least Three Kinds of K⁺ Channels
    - Long-term Potentiation (LTP) in the Mammalian Hippocampus Depends on Ca²⁺ Entry Through NMDA-Receptor Channels
    - Summary
  - References
    - General
    - Principles of Membrane Transport
    - Carrier Proteins and Active Membrane Transport
    - Ion Channels and the Electrical Properties of Membranes
- Chapter 12. Intracellular Compartments and Protein Sorting
  - The Compartmentalization of Cells
    - All Eucaryotic Cells Have the Same Basic Set of Membrane-enclosed Organelles
    - The Topological Relationships of Membrane-enclosed Organelles Can Be Interpreted in Terms of Their Evolutionary Origins
    - Proteins Can Move Between Compartments in Different Ways
    - Signal Sequences and Signal Patches Direct Proteins to the Correct Cellular Address
    - Most Membrane-enclosed Organelles Cannot Be Constructed From Scratch: They Require Information in the Organelle Itself
    - Summary
  - The Transport of Molecules between the Nucleus and the Cytosol
    - Nuclear Pore Complexes Perforate the Nuclear Envelope
    - Nuclear Localization Signals Direct Nuclear Proteins to the Nucleus
    - Nuclear Import Receptors Bind Nuclear Localization Signals and Nucleoporins
    - Nuclear Export Works Like Nuclear Import, But in Reverse
    - The Ran GTPase Drives Directional Transport Through Nuclear Pore Complexes
    - Transport Between the Nucleus and Cytosol Can Be Regulated by Controlling Access to the Transport Machinery
    - The Nuclear Envelope Is Disassembled During Mitosis
    - Summary
  - The Transport of Proteins into Mitochondria and Chloroplasts
    - Translocation into the Mitochondrial Matrix Depends on a Signal Sequence and Protein Translocators
    - Mitochondrial Precursor Proteins Are Imported as Unfolded Polypeptide Chains
    - Mitochondrial Precursor Proteins Are Imported into the Matrix at Contact Sites That Join the Inner and Outer Membranes
    - ATP Hydrolysis and a H⁺ Gradient are Used to Drive Protein Import into Mitochondria
    - Repeated Cycles of ATP Hydrolysis by Mitochondrial Hsp70 Complete the Import Process
    - Protein Transport into the Inner Mitochondrial Membrane and the Intermembrane Space Requires Two Signal Sequences
    - Two Signal Sequences Are Required to Direct Proteins to the Thylakoid Membrane in Chloroplasts
    - Summary
  - Peroxisomes
    - Peroxisomes Use Molecular Oxygen and Hydrogen Peroxide to Perform Oxidative Reactions
    - A Short Signal Sequence Directs the Import of Proteins into Peroxisomes
    - Summary
  - The Endoplasmic Reticulum
    - Membrane-bound Ribosomes Define the Rough ER
    - Smooth ER Is Abundant in Some Specialized Cells
    - Rough and Smooth Regions of ER Can Be Separated by Centrifugation
    - Signal Sequences Were First Discovered in Proteins Imported into the Rough ER
    - A Signal-Recognition Particle (SRP) Directs ER Signal Sequences to a Specific Receptor in the Rough ER Membrane
    - The Polypeptide Chain Passes Through an Aqueous Pore in the Translocator
    - Translocation Across the ER Membrane Does Not Always Require Ongoing Polypeptide Chain Elongation
    - The ER Signal Sequence Is Removed from Most Soluble Proteins After Translocation
    - In Single-Pass Transmembrane Proteins, a Single Internal ER Signal Sequence Remains in the Lipid Bilayer as a Membrane-spanning α Helix
    - Combinations of Start-Transfer and Stop-Transfer Signals Determine the Topology of Multipass Transmembrane Proteins
    - Translocated Polypeptide Chains Fold and Assemble in the Lumen of the Rough ER
    - Most Proteins Synthesized in the Rough ER Are Glycosylated by the Addition of a Common N-linked Oligosaccharide
    - Oligosaccharides Are Used as Tags to Mark the State of Protein Folding
    - Improperly Folded Proteins Are Exported from the ER and Degraded in the Cytosol
    - Misfolded Proteins in the ER Activate an Unfolded Protein Response
    - Some Membrane Proteins Acquire a Covalently Attached Glycosylphosphatidylinositol (GPI) Anchor
    - Most Membrane Lipid Bilayers Are Assembled in the ER
    - Phospholipid Exchange Proteins Help to Transport Phospholipids from the ER to Mitochondria and Peroxisomes
    - Summary
  - References
    - General
    - The Compartmentalization of Cells
    - The Transport of Molecules Between the Nucleus and the Cytosol
    - The Transport of Proteins Into Mitochondria and Chloroplasts
    - Peroxisomes
    - The Endoplasmic Reticulum
- Chapter 13. Intracellular Vesicular Traffic
  - The Molecular Mechanisms of Membrane Transport and the Maintenance of Compartmental Diversity
    - There Are Various Types of Coated Vesicles
    - The Assembly of a Clathrin Coat Drives Vesicle Formation
    - Both The Pinching-off and Uncoating of Coated Vesicles Are Regulated Processes
    - Not All Transport Vesicles are Spherical
    - Monomeric GTPases Control Coat Assembly
    - SNARE Proteins and Targeting GTPases Guide Membrane Transport
    - Interacting SNAREs Need To Be Pried Apart Before They Can Function Again
    - Rab Proteins Help Ensure the Specificity of Vesicle Docking
    - SNAREs May Mediate Membrane Fusion
    - Viral Fusion Proteins and SNAREs May Use Similar Strategies
    - Summary
  - Transport from the ER through the Golgi Apparatus
    - Proteins Leave the ER in COPII-coated Transport Vesicles
    - Only Proteins That Are Properly Folded and Assembled Can Leave the ER
    - Transport from the ER to the Golgi Apparatus Is Mediated by Vesicular Tubular Clusters
    - The Retrieval Pathway to the ER Uses Sorting Signals
    - Many Proteins are Selectively Retained in the Compartments in which they Function
    - The Length of the Transmembrane Region of Golgi Enzymes Determines their Location in The Cell
    - The Golgi Apparatus Consists of an Ordered Series of Compartments
    - Oligosaccharide Chains Are Processed in the Golgi Apparatus
    - Proteoglycans Are Assembled in the Golgi Apparatus
    - What Is the Purpose of Glycosylation?
    - The Golgi Cisternae Are Organized as a Series of Processing Compartments
    - Transport Through the Golgi Apparatus May Occur by Vesicular Transport or Cisternal Maturation
    - Matrix Proteins Form a Dynamic Scaffold That Helps Organize the Apparatus
    - Summary
  - Transport from the Trans Golgi Network to Lysosomes
    - Lysosomes Are the Principal Sites of Intracellular Digestion
    - Lysosomes Are Heterogeneous
    - Plant and Fungal Vacuoles Are Remarkably Versatile Lysosomes
    - Multiple Pathways Deliver Materials to Lysosomes
    - A Mannose 6-Phosphate Receptor Recognizes Lysosomal Proteins in the Trans Golgi Network
    - The M6P Receptor Shuttles Between Specific Membranes
    - A Signal Patch in the Hydrolyase Polypeptide Chain Provides the Cue for M6P Addition
    - Defects in the GlcNAc Phosphotransferase Cause a Lysosomal Storage Disease in Humans
    - Some Lysosomes May Undergo Exocytosis
    - Summary
  - Transport into the Cell from the Plasma Membrane: Endocytosis
    - Specialized Phagocytic Cells Can Ingest Large Particles
    - Pinocytic Vesicles Form from Coated Pits in the Plasma Membrane
    - Not All Pinocytic Vesicles Are Clathrin-coated
    - Cells Import Selected Extracellular Macromolecules by Receptor-mediated Endocytosis
    - Endocytosed Materials That Are Not Retrieved From Endosomes End Up in Lysosomes
    - Specific Proteins Are Removed from Early Endosomes and Returned to the Plasma Membrane
    - Multivesicular Bodies Form on the Pathway to Late Endosomes
    - Macromolecules Can Be Transferred Across Epithelial Cell Sheets by Transcytosis
    - Epithelial Cells Have Two Distinct Early Endosomal Compartments But a Common Late Endosomal Compartment
    - Summary
  - Transport from the Trans Golgi Network to the Cell Exterior: Exocytosis
    - Many Proteins and Lipids Seem to Be Carried Automatically from the Golgi Apparatus to the Cell Surface
    - Secretory Vesicles Bud from the Trans Golgi Network
    - Proteins Are Often Proteolytically Processed During the Formation of Secretory Vesicles
    - Secretory Vesicles Wait Near the Plasma Membrane Until Signaled to Release Their Contents
    - Regulated Exocytosis Can Be a Localized Response of the Plasma Membrane and Its Underlying Cytoplasm
    - Secretory Vesicle Membrane Components Are Quickly Removed from the Plasma Membrane
    - Polarized Cells Direct Proteins from the Trans Golgi Network to the Appropriate Domain of the Plasma Membrane
    - Cytoplasmic Sorting Signals Guide Membrane Proteins Selectively to the Basolateral Plasma Membrane
    - Lipid Rafts May Mediate Sorting of Glycosphingolipids and GPI-anchored Proteins to the Apical Plasma Membrane
    - Synaptic Vesicles Can Form Directly from Endocytic Vesicles
    - Summary
  - References
    - General
    - The Molecular Mechanisms of Membrane Transport and the Maintenance of Compartmental Diversity
    - Transport from the ER Through the Golgi Apparatus
    - Transport from the Trans Golgi Network to Lysosomes
    - Transport into the Cell from the Plasma Membrane: Endocytosis
    - Transport from the Trans Golgi Network to the Cell Exterior: Exocytosis
- Chapter 14. Energy Conversion: Mitochondria and Chloroplasts
  - The Mitochondrion
    - The 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 from NADH to Oxygen Through Three Large Respiratory Enzyme Complexes
    - As Electrons Move Along the Respiratory Chain, Energy Is Stored as an Electrochemical Proton Gradient Across the Inner Membrane
    - How the Proton Gradient Drives ATP Synthesis
    - How the Proton Gradient Drives Coupled Transport Across the Inner Membrane
    - Proton Gradients Produce Most of the Cell's ATP
    - Mitochondria Maintain a High ATP:ADP Ratio in Cells
    - A Large Negative Value of ΔG for ATP Hydrolysis Makes ATP Useful to the Cell
    - ATP Synthase Can Also Function in Reverse to Hydrolyze ATP and Pump H⁺
    - Summary
  - Electron-Transport Chains and Their Proton Pumps
    - Protons Are Unusually Easy to Move
    - The Redox Potential Is a Measure of Electron Affinities
    - Electron Transfers Release Large Amounts of Energy
    - Spectroscopic Methods Have Been Used to Identify Many Electron Carriers in the Respiratory Chain
    - The Respiratory Chain Includes Three Large Enzyme Complexes Embedded in the Inner Membrane
    - An Iron-Copper Center in Cytochrome Oxidase Catalyzes Efficient O₂ Reduction
    - Electron Transfers Are Mediated by Random Collisions in the Inner Mitochondrial Membrane
    - A Large Drop in Redox Potential Across Each of the Three Respiratory Enzyme Complexes Provides the Energy for H⁺ Pumping
    - The Mechanism of H⁺ Pumping Will Soon Be Understood in Atomic Detail
    - H⁺ Ionophores Uncouple Electron Transport from ATP Synthesis
    - Respiratory Control Normally Restrains Electron Flow Through the Chain
    - Natural Uncouplers Convert the Mitochondria in Brown Fat into Heat-generating Machines
    - Bacteria Also Exploit Chemiosmotic Mechanisms to Harness Energy
    - Summary
  - Chloroplasts and Photosynthesis
    - The Chloroplast Is One Member of the Plastid Family of Organelles
    - Chloroplasts Resemble Mitochondria But Have an Extra Compartment
    - Chloroplasts Capture Energy from Sunlight and Use It to Fix Carbon
    - Carbon Fixation Is Catalyzed by Ribulose Bisphosphate Carboxylase
    - Three Molecules of ATP and Two Molecules of NADPH Are Consumed for Each CO₂ Molecule That Is Fixed
    - Carbon Fixation in Some Plants Is Compartmentalized to Facilitate Growth at Low CO₂ Concentrations
    - Photosynthesis Depends on the Photochemistry of Chlorophyll Molecules
    - A Photosystem Consists of a Reaction Center Plus an Antenna Complex
    - In a Reaction Center, Light Energy Captured by Chlorophyll Creates a Strong Electron Donor from a Weak One
    - Noncyclic Photophosphorylation Produces Both NADPH and ATP
    - Chloroplasts Can Make ATP by Cyclic Photophosphorylation Without Making NADPH
    - Photosystems I and II Have Related Structures, and Also Resemble Bacterial Photosystems
    - The Proton-Motive Force Is the Same in Mitochondria and Chloroplasts
    - Carrier Proteins in the Chloroplast Inner Membrane Control Metabolite Exchange with the Cytosol
    - Chloroplasts Also Perform Other Crucial Biosyntheses
    - Summary
  - The Genetic Systems of Mitochondria and Plastids
    - Mitochondria and Chloroplasts Contain Complete Genetic Systems
    - Organelle Growth and Division Determine the Number of Mitochondria and Plastids in a Cell
    - The Genomes of Mitochondria and Chloroplasts Are Diverse
    - Mitochondria and Chloroplasts Probably Both Evolved from Endosymbiotic Bacteria
    - Mitochondrial Genomes Have Several Surprising Features
    - Animal Mitochondria Contain the Simplest Genetic Systems Known
    - Some Organelle Genes Contain Introns
    - The Chloroplast Genome of Higher Plants Contains About 120 Genes
    - Mitochondrial Genes Are Inherited by a Non-Mendelian Mechanism
    - Organelle Genes Are Maternally Inherited in Many Organisms
    - Petite Mutants in Yeasts Demonstrate the Overwhelming Importance of the Cell Nucleus for Mitochondrial Biogenesis
    - Mitochondria and Plastids Contain Tissue-specific Proteins that Are Encoded in the Cell Nucleus
    - Mitochondria Import Most of Their Lipids; Chloroplasts Make Most of Theirs
    - Why Do Mitochondria and Chloroplasts Have Their Own Genetic Systems?
    - Summary
  - The Evolution of Electron-Transport Chains
    - The Earliest Cells Probably Produced ATP by Fermentation
    - Electron-transport Chains Enabled Anaerobic Bacteria to Use Nonfermentable Molecules as Their Major Source of Energy
    - By Providing an Inexhaustible Source of Reducing Power, Photosynthetic Bacteria Overcame a Major Evolutionary Obstacle
    - The Photosynthetic Electron-transport Chains of Cyanobacteria Produced Atmospheric Oxygen and Permitted New Life-Forms
    - Summary
  - References
    - General
    - The Mitochondrion
    - Electron-Transport Chains and Their Proton Pumps
    - Chloroplasts and Photosynthesis
    - The Genetic Systems of Mitochondria and Plastids
    - The Evolution of Electron-Transport Chains
- Chapter 15. Cell Communication
  - General Principles of Cell Communication
    - Extracellular Signal Molecules Bind to Specific Receptors
    - Extracellular Signal Molecules Can Act Over Either Short or Long Distances
    - Autocrine Signaling Can Coordinate Decisions by Groups of Identical Cells
    - Gap Junctions Allow Signaling Information to Be Shared by Neighboring Cells
    - Each Cell Is Programmed to Respond to Specific Combinations of Extracellular Signal Molecules
    - Different Cells Can Respond Differently to the Same Extracellular Signal Molecule
    - The Concentration of a Molecule Can Be Adjusted Quickly Only If the Lifetime of the Molecule Is Short
    - Nitric Oxide Gas Signals by Binding Directly to an Enzyme Inside the Target Cell
    - Nuclear Receptors Are Ligand-activated Gene Regulatory Proteins
    - The Three Largest Classes of Cell-Surface Receptor Proteins Are Ion-Channel-linked, G-Protein-linked, and Enzyme-linked Receptors
    - Most Activated Cell-Surface Receptors Relay Signals Via Small Molecules and a Network of Intracellular Signaling Proteins
    - Some Intracellular Signaling Proteins Act as Molecular Switches
    - Intracellular Signaling Complexes Enhance the Speed, Efficiency, and Specificity of the Response
    - Interactions Between Intracellular Signaling Proteins Are Mediated by Modular Binding Domains
    - Cells Can Respond Abruptly to a Gradually Increasing Concentration of an Extracellular Signal
    - A Cell Can Remember The Effect of Some Signals
    - Cells Can Adjust Their Sensitivity to a Signal
    - Summary
  - Signaling through G-Protein-Linked Cell-Surface Receptors
    - Trimeric G Proteins Disassemble to Relay Signals from G-Protein-linked Receptors
    - Some G Proteins Signal By Regulating the Production of Cyclic AMP
    - Cyclic-AMP-dependent Protein Kinase (PKA) Mediates Most of the Effects of Cyclic AMP
    - Protein Phosphatases Make the Effects of PKA and Other Protein Kinases Transitory
    - Some G Proteins Activate the Inositol Phospholipid Signaling Pathway by Activating Phospholipase C-β
    - Ca²⁺ Functions as a Ubiquitous Intracellular Messenger
    - The Frequency of Ca²⁺ Oscillations Influences a Cell's Response
    - Ca²⁺/Calmodulin-dependent Protein Kinases (CaM-Kinases) Mediate Many of the Actions of Ca²⁺ in Animal Cells
    - Some G Proteins Directly Regulate Ion Channels
    - Smell and Vision Depend on G-Protein-linked Receptors That Regulate Cyclic-Nucleotide-gated Ion Channels
    - Extracellular Signals Are Greatly Amplified by the Use of Small Intracellular Mediators and Enzymatic Cascades
    - G-Protein-linked Receptor Desensitization Depends on Receptor Phosphorylation
    - Summary
  - Signaling through Enzyme-Linked Cell-Surface Receptors
    - Activated Receptor Tyrosine Kinases Phosphorylate Themselves
    - Phosphorylated Tyrosines Serve as Docking Sites For Proteins With SH2 Domains
    - Ras Is Activated by a Guanine Nucleotide Exchange Factor
    - Ras Activates a Downstream Serine/Threonine Phosphorylation Cascade That Includes a MAP-Kinase
    - PI 3-Kinase Produces Inositol Phospholipid Docking Sites in the Plasma Membrane
    - The PI 3-Kinase/Protein Kinase B Signaling Pathway Can Stimulate Cells to Survive and Grow
    - Tyrosine-Kinase-associated Receptors Depend on Cytoplasmic Tyrosine Kinases for Their Activity
    - Cytokine Receptors Activate the Jak-STAT Signaling Pathway, Providing a Fast Track to the Nucleus
    - Some Protein Tyrosine Phosphatases May Act as Cell-Surface Receptors
    - Signal Proteins of the TGF-β Superfamily Act Through Receptor Serine/Threonine Kinases and Smads
    - Receptor Guanylyl Cyclases Generate Cyclic GMP Directly
    - Bacterial Chemotaxis Depends on a Two-Component Signaling Pathway Activated by Histidine-Kinase-associated Receptors
    - Summary
  - Signaling Pathways That Depend on Regulated Proteolysis
    - The Receptor Protein Notch Is Activated by Cleavage
    - Wnt Proteins Bind to Frizzled Receptors and Inhibit the Degradation of β-Catenin
    - Hedgehog Proteins Act Through a Receptor Complex of Patched and Smoothened, Which Oppose Each Other
    - Multiple Stressful and Proinflammatory Stimuli Act Through an NF-κB-Dependent Signaling Pathway
    - Summary
  - Signaling in Plants
    - Multicellularity and Cell Communication Evolved Independently in Plants and Animals
    - Receptor Serine/Threonine Kinases Function as Cell-Surface Receptors in Plants
    - Ethylene Activates a Two-Component Signaling Pathway
    - Phytochromes Detect Red Light, and Cryptochromes Detect Blue Light
    - Summary
  - References
    - General
    - General Principles of Cell Communication
    - Signaling Through G-protein-linked Cell-surface Receptors
    - Signaling Through Enzyme-linked Cell-surface Receptors
    - Signaling Pathways That Depend on Regulated Proteolysis
    - Signaling in Plants
- Chapter 16. The Cytoskeleton
  - The Self-Assembly and Dynamic Structure of Cytoskeletal Filaments
    - Each Type of Cytoskeletal Filament Is Constructed from Smaller Protein Subunits
    - Filaments Formed from Multiple Protofilaments Have Advantageous Properties
    - Nucleation Is the Rate-limiting Step in the Formation of a Cytoskeletal Polymer
    - The Tubulin and Actin Subunits Assemble Head-to-Tail, Creating Filaments that Are Polar
    - The Two Ends of a Microtubule and of an Actin Filament Are Distinct and Grow at Different Rates
    - Filament Treadmilling and Dynamic Instability Are Consequences of Nucleotide Hydrolysis by Tubulin and Actin
    - Treadmilling and Dynamic Instability Require Energy but Are Useful
    - Other Polymeric Proteins Also Use Nucleotide Hydrolysis to Couple a Conformational Change to Cell Movements
    - Tubulin and Actin Have Been Highly Conserved During Eucaryotic Evolution
    - Intermediate Filament Structure Depends on The Lateral Bundling and Twisting of Coiled Coils
    - Intermediate Filaments Impart Mechanical Stability to Animal Cells
    - Filament Polymerization Can Be Altered by Drugs
    - Summary
  - How Cells Regulate Their Cytoskeletal Filaments
    - Microtubules Are Nucleated by a Protein Complex Containing γ-tubulin
    - Microtubules Emanate from the Centrosome in Animal Cells
    - Actin Filaments Are Often Nucleated at the Plasma Membrane
    - Filament Elongation Is Modified by Proteins That Bind to the Free Subunits
    - Proteins That Bind Along the Sides of Filaments Can Either Stabilize or Destabilize Them
    - Proteins That Interact with Filament Ends Can Dramatically Change Filament Dynamics
    - Filaments Are Organized into Higher-order Structures in Cells
    - Intermediate Filaments Are Cross-linked and Bundled Into Strong Arrays
    - Cross-linking Proteins with Distinct Properties Organize Different Assemblies of Actin Filaments
    - Severing Proteins Regulate the Length and Kinetic Behavior of Actin Filaments and Microtubules
    - Cytoskeletal Elements Can Attach to the Plasma Membrane
    - Special Bundles of Cytoskeletal Filaments Form Strong Attachments Across the Plasma Membrane: Focal Contacts, Adhesion Belts, and Desmosomes
    - Extracellular Signals Can Induce Major Cytoskeletal Rearrangements
    - Summary
  - Molecular Motors
    - Actin-based Motor Proteins Are Members of the Myosin Superfamily
    - There Are Two Types of Microtubule Motor Proteins: Kinesins and Dyneins
    - The Structural Similarity of Myosin and Kinesin Indicates a Common Evolutionary Origin
    - Motor Proteins Generate Force by Coupling ATP Hydrolysis to Conformational Changes
    - Motor Protein Kinetics Are Adapted to Cell Functions
    - Motor Proteins Mediate the Intracellular Transport of Membrane-enclosed Organelles
    - Motor Protein Function Can Be Regulated
    - Muscle Contraction Depends on the Sliding of Myosin II and Actin Filaments
    - Muscle Contraction Is Initiated by a Sudden Rise in Cytosolic Ca²⁺ Concentration
    - Heart Muscle Is a Precisely Engineered Machine
    - Cilia and Flagella Are Motile Structures Built from Microtubules and Dyneins
    - Summary
  - The Cytoskeleton and Cell Behavior
    - Mechanisms of Cell Polarization Can Be Readily Analyzed in Yeast Cells
    - Specific RNA Molecules Are Localized by the Cytoskeleton
    - Many Cells Can Crawl Across A Solid Substratum
    - Plasma Membrane Protrusion Is Driven by Actin Polymerization
    - Cell Adhesion and Traction Allow Cells to Pull Themselves Forward
    - External Signals Can Dictate the Direction of Cell Migration
    - The Complex Morphological Specialization of Neurons Depends on The Cytoskeleton
    - Summary
  - References
    - General
    - The Self-Assembly and Dynamic Structure of Cytoskeletal Filaments
    - How Cells Regulate Their Cytoskeletal Filaments
    - Molecular Motors
    - The Cytoskeleton and Cell Behavior
- Chapter 17. The Cell Cycle and Programmed Cell Death
  - An Overview of the Cell Cycle
    - The Cell-Cycle Control System Is Similar in All Eucaryotes
    - The Cell-Cycle Control System Can Be Dissected Genetically in Yeasts
    - The Cell-Cycle Control System Can Be Analyzed Biochemically in Animal Embryos
    - The Cell-Cycle Control System of Mammals Can Be Studied in Culture
    - Cell-Cycle Progression Can Be Studied in Various Ways
    - Summary
  - Components of the Cell-Cycle Control System
    - The Cell-Cycle Control System Triggers the Major Processes of the Cell Cycle
    - The Control System Can Arrest the Cell Cycle at Specific Checkpoints
    - Checkpoints Generally Operate Through Negative Intracellular Signals
    - The Cell-Cycle Control System Is Based on Cyclically Activated Protein Kinases
    - Cdk Activity Can Be Suppressed Both by Inhibitory Phosphorylation and by Inhibitory Proteins
    - The Cell-Cycle Control System Depends on Cyclical Proteolysis
    - Cell-Cycle Control Also Depends on Transcriptional Regulation
    - Summary
  - Intracellular Control of Cell-Cycle Events
    - S-Phase Cyclin-Cdk Complexes (S-Cdks) Initiate DNA Replication Once Per Cycle
    - The Activation of M-Phase Cyclin-Cdk Complexes (M-Cdks) Triggers Entry into Mitosis
    - Entry into Mitosis Is Blocked by Incomplete DNA Replication: The DNA Replication Checkpoint
    - M-Cdk Prepares the Duplicated Chromosomes for Separation
    - Sister Chromatid Separation Is Triggered by Proteolysis
    - Unattached Chromosomes Block Sister-Chromatid Separation: The Spindle-Attachment Checkpoint
    - Exit from Mitosis Requires the Inactivation of M-Cdk
    - The G₁ Phase Is a State of Stable Cdk Inactivity
    - The Rb Protein Acts as a Brake in Mammalian G₁ Cells
    - Cell-Cycle Progression Is Somehow Coordinated With Cell Growth
    - Cell-Cycle Progression is Blocked by DNA Damage and p53: DNA Damage Checkpoints
    - Summary
  - Programmed Cell Death (Apoptosis)
    - Apoptosis Is Mediated by an Intracellular Proteolytic Cascade
    - Procaspases Are Activated by Binding to Adaptor Proteins
    - Bcl-2 Family Proteins and IAP Proteins Are the Main Intracellular Regulators of the Cell Death Program
    - Summary
  - Extracellular Control of Cell Division, Cell Growth, and Apoptosis
    - Mitogens Stimulate Cell Division
    - Cells Can Delay Division by Entering a Specialized Nondividing State
    - Mitogens Stimulate G₁-Cdk and G₁/S-Cdk Activities
    - Abnormal Proliferation Signals Cause Cell-Cycle Arrest or Cell Death
    - Human Cells Have a Built-in Limitation on the Number of Times They Can Divide
    - Extracellular Growth Factors Stimulate Cell Growth
    - Extracellular Survival Factors Suppress Apoptosis
    - Neighboring Cells Compete for Extracellular Signal Proteins
    - Many Types of Normal Animal Cells Need Anchorage to Grow and Proliferate
    - Some Extracellular Signal Proteins Inhibit Cell Growth, Cell Division, and Survival
    - Intricately Regulated Patterns of Cell Division Generate and Maintain Body Form
    - Summary
  - References
    - General
    - An Overview of the Cell Cycle
    - Components of the Cell-Cycle Control System
    - Intracellular Control of Cell-Cycle Events
    - Programmed Cell Death (Apoptosis)
    - Extracellular Control of Cell Division, Cell Growth, and Apoptosis
- Chapter 18. The Mechanics of Cell Division
  - An Overview of M Phase
    - Cohesins and Condensins Help Configure Replicated Chromosomes for Segregation
    - Cytoskeletal Machines Perform Both Mitosis and Cytokinesis
    - Two Mechanisms Help Ensure That Mitosis Always Precedes Cytokinesis
    - M Phase in Animal Cells Depends on Centrosome Duplication in the Preceding Interphase
    - M Phase Is Traditionally Divided into Six Stages
    - Summary
  - Mitosis
    - Microtubule Instability Increases Greatly at M Phase
    - Interactions Between Opposing Motor Proteins and Microtubules of Opposite Polarity Drive Spindle Assembly
    - Kinetochores Attach Chromosomes to the Mitotic Spindle
    - Microtubules Are Highly Dynamic in the Metaphase Spindle
    - Functional Bipolar Spindles Can Assemble Around Chromosomes in Cells Without Centrosomes
    - Anaphase Is Delayed Until All Chromosomes Are Positioned at the Metaphase Plate
    - Sister Chromatids Separate Suddenly at Anaphase
    - Kinetochore Microtubules Disassemble at Both Ends During Anaphase A
    - Both Pushing and Pulling Forces Contribute to Anaphase B
    - At Telophase, the Nuclear Envelope Re-forms Around Individual Chromosomes
    - Summary
  - Cytokinesis
    - The Microtubules of the Mitotic Spindle Determine the Plane of Animal Cell Division
    - Some Cells Reposition Their Spindle to Divide Asymmetrically
    - Actin and Myosin II in the Contractile Ring Generate the Force for Cytokinesis
    - Membrane-enclosed Organelles Must Be Distributed to Daughter Cells During Cytokinesis
    - Mitosis Can Occur Without Cytokinesis
    - The Phragmoplast Guides Cytokinesis in Higher Plants
    - The Elaborate M Phase of Higher Organisms Evolved Gradually from Procaryotic Fission Mechanisms
    - Summary
  - References
    - General
    - An Overview of M Phase
    - Mitosis
    - Cytokinesis
Part V. Cells in Their Social Context
- Chapter 19. Cell Junctions, Cell Adhesion, and the Extracellular Matrix
  - Cell Junctions
    - Occluding Junctions Form a Selective Permeability Barrier Across Epithelial Cell Sheets
    - Anchoring Junctions Connect the Cytoskeleton of a Cell Either to the Cytoskeleton of Its Neighbors or to the Extracellular Matrix
    - Adherens Junctions Connect Bundles of Actin Filaments from Cell to Cell
    - Desmosomes Connect Intermediate Filaments from Cell to Cell
    - Anchoring Junctions Formed by Integrins Bind Cells to the Extracellular Matrix: Focal Adhesions and Hemidesmosomes
    - Gap Junctions Allow Small Molecules to Pass Directly from Cell to Cell
    - A Gap-Junction Connexon Is Made Up of Six Transmembrane Connexin Subunits
    - Gap Junctions Have Diverse Functions
    - The Permeability of Gap Junctions Can Be Regulated
    - In Plants, Plasmodesmata Perform Many of the Same Functions as Gap Junctions
    - Summary
  - Cell-Cell Adhesion
    - Animal Cells Can Assemble into Tissues Either in Place or After They Migrate
    - Dissociated Vertebrate Cells Can Reassemble into Organized Tissues Through Selective Cell-Cell Adhesion
    - Cadherins Mediate Ca²⁺-dependent Cell-Cell Adhesion
    - Cadherins Have Crucial Roles in Development
    - Cadherins Mediate Cell-Cell Adhesion by a Homophilic Mechanism
    - Cadherins Are Linked to the Actin Cytoskeleton by Catenins
    - Selectins Mediate Transient Cell-Cell Adhesions in the Bloodstream
    - Members of the Immunoglobulin Superfamily of Proteins Mediate Ca²⁺-independent Cell-Cell Adhesion
    - Multiple Types of Cell-Surface Molecules Act in Parallel to Mediate Selective Cell-Cell Adhesion
    - Nonjunctional Contacts May Initiate Cell-Cell Adhesions That Junctional Contacts Then Orient and Stabilize
    - Summary
  - The Extracellular Matrix of Animals
    - The Extracellular Matrix Is Made and Oriented by the Cells Within It
    - Glycosaminoglycan (GAG) Chains Occupy Large Amounts of Space and Form Hydrated Gels
    - Hyaluronan Is Thought to Facilitate Cell Migration During Tissue Morphogenesis and Repair
    - Proteoglycans Are Composed of GAG Chains Covalently Linked to a Core Protein
    - Proteoglycans Can Regulate the Activities of Secreted Proteins
    - GAG Chains May Be Highly Organized in the Extracellular Matrix
    - Cell-Surface Proteoglycans Act as Co-receptors
    - Collagens Are the Major Proteins of the Extracellular Matrix
    - Collagens Are Secreted with a Nonhelical Extension at Each End
    - After Secretion, Fibrillar Procollagen Molecules Are Cleaved to Collagen Molecules, Which Assemble into Fibrils
    - Fibril-associated Collagens Help Organize the Fibrils
    - Cells Help Organize the Collagen Fibrils They Secrete by Exerting Tension on the Matrix
    - Elastin Gives Tissues Their Elasticity
    - Fibronectin Is an Extracellular Protein That Helps Cells Attach to the Matrix
    - Fibronectin Exists in Both Soluble and Fibrillar Forms
    - Intracellular Actin Filaments Regulate the Assembly of Extracellular Fibronectin Fibrils
    - Glycoproteins in the Matrix Help Guide Cell Migration
    - Basal Laminae Are Composed Mainly of Type IV Collagen, Laminin, Nidogen, and a Heparan Sulfate Proteoglycan
    - Basal Laminae Perform Diverse Functions
    - The Extracellular Matrix Can Influence Cell Shape, Cell Survival, and Cell Proliferation
    - The Controlled Degradation of Matrix Components Helps Cells Migrate
    - Summary
  - Integrins
    - Integrins Are Transmembrane Heterodimers
    - Integrins Must Interact with the Cytoskeleton to Bind Cells to the Extracellular Matrix
    - Cells Can Regulate the Activity of Their Integrins
    - Integrins Activate Intracellular Signaling Pathways
    - Summary
  - The Plant Cell Wall
    - The Composition of the Cell Wall Depends on the Cell Type
    - The Tensile Strength of the Cell Wall Allows Plant Cells to Develop Turgor Pressure
    - The Primary Cell Wall Is Built from Cellulose Microfibrils Interwoven with a Network of Pectic Polysaccharides
    - Microtubules Orient Cell-Wall Deposition
    - Summary
  - References
    - General
    - Cell Junctions
    - Cell-cell Adhesion
    - The Extracellular Matrix of Animals
    - Integrins
    - The Plant Cell Wall
- Chapter 20. Germ Cells and Fertilization
  - The Benefits of Sex
    - In Multicellular Animals and Most Plants, the Diploid Phase Is Complex and Long, the Haploid Simple and Fleeting
    - Sexual Reproduction Gives a Competitive Advantage to Organisms in an Unpredictably Variable Environment
    - Summary
  - Meiosis
    - Duplicated Homologous Chromosomes Pair During Meiosis
    - Gametes Are Produced by Two Meiotic Cell Divisions
    - Genetic Reassortment Is Enhanced by Crossing-over Between Homologous Nonsister Chromatids
    - Chiasmata Have an Important Role in Chromosome Segregation in Meiosis
    - Pairing of the Sex Chromosomes Ensures That They Also Segregate
    - Meiotic Chromosome Pairing Culminates in the Formation of the Synaptonemal Complex
    - Recombination Nodules Mark the Sites of Genetic Recombination
    - Genetic Maps Reveal Favored Sites for Crossovers
    - Meiosis Ends with Two Successive Cell Divisions Without DNA Replication
    - Summary
  - Primordial Germ Cells and Sex Determination in Mammals
    - Primordial Germ Cells Migrate into the Developing Gonad
    - The Sry Gene on the Y Chromosome Can Redirect a Female Embryo to Become a Male
    - Summary
  - Eggs
    - An Egg Is Highly Specialized for Independent Development, with Large Nutrient Reserves and an Elaborate Coat
    - Eggs Develop in Stages
    - Oocytes Use Special Mechanisms to Grow to Their Large Size
    - Summary
  - Sperm
    - Sperm Are Highly Adapted for Delivering Their DNA to an Egg
    - Sperm Are Produced Continuously in Most Mammals
    - Summary
  - Fertilization
    - Species-Specific Binding to the Zona Pellucida Induces the Sperm to Undergo an Acrosome Reaction
    - The Egg Cortical Reaction Helps to Ensure That Only One Sperm Fertilizes the Egg
    - The Mechanism of Sperm—Egg Fusion Is Still Unknown
    - The Sperm Provides a Centriole for the Zygote
    - Summary
  - References
    - General
    - The Benefits of Sex
    - Meiosis
    - Primordial Germ Cells and Sex Determination in Mammals
    - Eggs
    - Sperm
    - Fertilization
- Chapter 21. Development of Multicellular Organisms
  - Universal Mechanisms of Animal Development
    - Animals Share Some Basic Anatomical Features
    - Multicellular Animals Are Enriched in Proteins Mediating Cell Interactions and Gene Regulation
    - Regulatory DNA Defines the Program of Development
    - Manipulation of the Embryo Reveals the Interactions Between its Cells
    - Studies of Mutant Animals Identify the Genes That Control Developmental Processes
    - A Cell Makes Developmental Decisions Long Before It Shows a Visible Change
    - Cells Have Remembered Positional Values That Reflect Their Location in the Body
    - Sister Cells Can Be Born Different by an Asymmetric Cell Division
    - Inductive Interactions Can Create Orderly Differences Between Initially Identical Cells
    - Morphogens Are Long-Range Inducers That Exert Graded Effects
    - Extracellular Inhibitors of Signal Molecules Shape the Response to the Inducer
    - Programs That Are Intrinsic to a Cell Often Define the Time-Course of its Development
    - Initial Patterns Are Established in Small Fields of Cells and Refined by Sequential Induction as the Embryo Grows
    - Summary
  - Caenorhabditis Elegans: Development from the Perspective of the Individual Cell
    - Caenorhabditis elegans Is Anatomically Simple
    - Cell Fates in the Developing Nematode Are Almost Perfectly Predictable
    - Products of Maternal-Effect Genes Organize the Asymmetric Division of the Egg
    - Progressively More Complex Patterns Are Created by Cell-Cell Interactions
    - Microsurgery and Genetics Reveal the Logic of Developmental Control; Gene Cloning and Sequencing Reveal Its Molecular Mechanisms
    - Cells Change Over Time in Their Responsiveness to Developmental Signals
    - Heterochronic Genes Control the Timing of Development
    - Cells Do Not Count Cell Divisions in Timing Their Internal Programs
    - Selected Cells Die by Apoptosis as Part of the Program of Development
    - Summary
  - Drosophila and the Molecular Genetics of Pattern Formation: Genesis of the Body Plan
    - The Insect Body Is Constructed as a Series of Segmental Units
    - Drosophila Begins Its Development as a Syncytium
    - Genetic Screens Define Groups of Genes Required for Specific Aspects of Early Patterning
    - Interactions of the Oocyte With Its Surroundings Define the Axes of the Embryo: the Role of the Egg-Polarity Genes
    - The Dorsoventral Signaling Genes Create a Gradient of a Nuclear Gene Regulatory Protein
    - Dpp and Sog Set Up a Secondary Morphogen Gradient to Refine the Pattern of the Dorsal Part of the Embryo
    - The Insect Dorsoventral Axis Corresponds to the Vertebrate Ventrodorsal Axis
    - Three Classes of Segmentation Genes Refine the Anterior- Posterior Maternal Pattern and Subdivide the Embryo
    - The Localized Expression of Segmentation Genes Is Regulated by a Hierarchy of Positional Signals
    - The Modular Nature of Regulatory DNA Allows Genes to Have Multiple Independently Controlled Functions
    - Egg-Polarity, Gap, and Pair-Rule Genes Create a Transient Pattern That Is Remembered by Other Genes
    - Summary
  - Homeotic Selector Genes and the Patterning of the Anteroposterior Axis
    - The HOX Code Specifies Anterior-Posterior Differences
    - Homeotic Selector Genes Code for DNA-Binding Proteins That Interact with Other Gene Regulatory Proteins
    - The Homeotic Selector Genes Are Expressed Sequentially According to Their Order in the Hox Complex
    - The Hox Complex Carries a Permanent Record of Positional Information
    - The Anteroposterior Axis Is Controlled by Hox Selector Genes in Vertebrates Also
    - Summary
  - Organogenesis and the Patterning of Appendages
    - Conditional and Induced Somatic Mutations Make it Possible to Analyze Gene Functions Late in Development
    - Body Parts of the Adult Fly Develop From Imaginal Discs
    - Homeotic Selector Genes Are Essential for the Memory of Positional Information in Imaginal Disc Cells
    - Specific Regulatory Genes Define the Cells That Will Form an Appendage
    - The Insect Wing Disc Is Divided into Compartments
    - Four Familiar Signaling Pathways Combine to Pattern the Wing Disc: Wingless, Hedgehog, Dpp, and Notch
    - The Size of Each Compartment Is Regulated by Interactions Among Its Cells
    - Similar Mechanisms Pattern the Limbs of Vertebrates
    - Localized Expression of Specific Classes of Gene Regulatory Proteins Foreshadows Cell Differentiation
    - Lateral Inhibition Singles Out Sensory Mother Cells Within Proneural Clusters
    - Lateral Inhibition Drives the Progeny of the Sensory Mother Cell Toward Different Final Fates
    - Planar Polarity of Asymmetric Divisions is Controlled by Signaling via the Receptor Frizzled
    - Lateral Inhibition and Asymmetric Division Combine to Regulate Genesis of Neurons Throughout the Body
    - Notch Signaling Regulates the Fine-Grained Pattern of Differentiated Cell Types in Many Different Tissues
    - Some Key Regulatory Genes Define a Cell Type; Others Can Activate the Program for Creation of an Entire Organ
    - Summary
  - Cell Movements and the Shaping of the Vertebrate Body
    - The Polarity of the Amphibian Embryo Depends on the Polarity of the Egg
    - Cleavage Produces Many Cells from One
    - Gastrulation Transforms a Hollow Ball of Cells into a Three-Layered Structure with a Primitive Gut
    - The Movements of Gastrulation Are Precisely Predictable
    - Chemical Signals Trigger the Mechanical Processes
    - Active Changes of Cell Packing Provide a Driving Force for Gastrulation
    - Changing Patterns of Cell Adhesion Molecules Force Cells Into New Arrangements
    - The Notochord Elongates, While the Neural Plate Rolls Up to Form the Neural Tube
    - A Gene-Expression Oscillator Controls Segmentation of the Mesoderm Into Somites
    - Embryonic Tissues Are Invaded in a Strictly Controlled Fashion by Migratory Cells
    - The Distribution of Migrant Cells Depends on Survival Factors as Well as Guidance Cues
    - Left-Right Asymmetry of the Vertebrate Body Derives From Molecular Asymmetry in the Early Embryo
    - Summary
  - The Mouse
    - Mammalian Development Begins With a Specialized Preamble
    - The Early Mammalian Embryo Is Highly Regulative
    - Totipotent Embryonic Stem Cells Can Be Obtained From a Mammalian Embryo
    - Interactions Between Epithelium and Mesenchyme Generate Branching Tubular Structures
    - Summary
  - Neural Development
    - Neurons Are Assigned Different Characters According to the Time and Place Where They Are Born
    - The Character Assigned to a Neuron at Its Birth Governs the Connections It Will Form
    - Each Axon or Dendrite Extends by Means of a Growth Cone at Its Tip
    - The Growth Cone Pilots the Developing Neurite Along a Precisely Defined Path in vivo
    - Growth Cones Can Change Their Sensibilities as They Travel
    - Target Tissues Release Neurotrophic Factors That Control Nerve Cell Growth and Survival
    - Neuronal Specificity Guides the Formation of Orderly Neural Maps
    - Axons From Different Regions of the Retina Respond Differently to a Gradient of Repulsive Molecules in the Tectum
    - Diffuse Patterns of Synaptic Connections Are Sharpened by Activity-Dependent Remodeling
    - Experience Molds the Pattern of Synaptic Connections in the Brain
    - Adult Memory and Developmental Synapse Remodeling May Depend on Similar Mechanisms
    - Summary
  - Plant Development
    - Arabidopsis Serves as a Model Organism for Plant Molecular Genetics
    - The Arabidopsis Genome Is Rich in Developmental Control Genes
    - Embryonic Development Starts by Establishing a Root-Shoot Axis and Then Halts Inside the Seed
    - The Parts of a Plant Are Generated Sequentially by Meristems
    - Development of the Seedling Depends on Environmental Signals
    - The Shaping of Each New Structure Depends on Oriented Cell Division and Expansion
    - Each Plant Module Grows From a Microscopic Set of Primordia in a Meristem
    - Cell Signaling Maintains the Meristem
    - Regulatory Mutations Can Transform Plant Topology by Altering Cell Behavior in the Meristem
    - Long-Range Hormonal Signals Coordinate Developmental Events in Separate Parts of the Plant
    - Homeotic Selector Genes Specify the Parts of a Flower
    - Summary
  - References
    - General
    - Universal Mechanisms of Animal Development
    - Caenorhabditis elegans: Development From the Perspective of the Individual Cell
    - Drosophila and the Molecular Genetics of Pattern Formation: Genesis of the Body Plan
    - Homeotic Selector Genes and the Patterning of the Anteroposterior Axis
    - Organogenesis and the Patterning of Appendages
    - Cell Movement and the Shaping of the Vertebrate Body
    - The Mouse
    - Neural Development
    - Plant Development
- Chapter 22. Histology: The Lives and Deaths of Cells in Tissues
  - Epidermis and Its Renewal by Stem Cells
    - Epidermal Cells Form a Multilayered Waterproof Barrier
    - Differentiating Epidermal Cells Synthesize a Sequence of Different Keratins as They Mature
    - Epidermis Is Renewed by Stem Cells Lying in Its Basal Layer
    - The Two Daughters of a Stem Cell Do Not Always Have to Become Different
    - The Basal Layer Contains Both Stem Cells and Transit Amplifying Cells
    - Epidermal Renewal Is Governed by Many Interacting Signals
    - The Mammary Gland Undergoes Cycles of Development and Regression
    - Summary
  - Sensory Epithelia
    - Olfactory Sensory Neurons Are Continually Replaced
    - Auditory Hair Cells Have to Last a Lifetime
    - Most Permanent Cells Renew Their Parts: the Photoreceptor Cells of the Retina
    - Summary
  - The Airways and the Gut
    - Adjacent Cell Types Collaborate in the Alveoli of the Lungs
    - Goblet Cells, Ciliated Cells, and Macrophages Collaborate to Keep the Airways Clean
    - The Lining of the Small Intestine Renews Itself Faster Than Any Other Tissue
    - Components of the Wnt Signaling Pathway Are Required to Maintain the Gut Stem-Cell Population
    - The Liver Functions as an Interface Between the Digestive Tract and the Blood
    - Liver Cell Loss Stimulates Liver Cell Proliferation
    - Summary
  - Blood Vessels and Endothelial Cells
    - Endothelial Cells Line All Blood Vessels
    - New Endothelial Cells Are Generated by Simple Duplication of Existing Endothelial Cells
    - New Capillaries Form by Sprouting
    - Angiogenesis Is Controlled by Factors Released by the Surrounding Tissues
    - Summary
  - Renewal by Multipotent Stem Cells: Blood Cell Formation
    - The Three Main Categories of White Blood Cells: Granulocytes, Monocytes, and Lymphocytes
    - The Production of Each Type of Blood Cell in the Bone Marrow Is Individually Controlled
    - Bone Marrow Contains Hemopoietic Stem Cells
    - A Multipotent Stem Cell Gives Rise to All Classes of Blood Cells
    - Commitment Is a Stepwise Process
    - The Number of Specialized Blood Cells Is Amplified by Divisions of Committed Progenitor Cells
    - Stem Cells Depend on Contact Signals From Stromal Cells
    - Factors That Regulate Hemopoiesis Can Be Analyzed in Culture
    - Erythropoiesis Depends on the Hormone Erythropoietin
    - Multiple CSFs Influence the Production of Neutrophils and Macrophages
    - The Behavior of a Hemopoietic Cell Depends Partly on Chance
    - Regulation of Cell Survival Is as Important as Regulation of Cell Proliferation
    - Summary
  - Genesis, Modulation, and Regeneration of Skeletal Muscle
    - New Skeletal Muscle Fibers Form by the Fusion of Myoblasts
    - Muscle Cells Can Vary Their Properties by Changing the Protein Isoforms They Contain
    - Skeletal Muscle Fibers Secrete Myostatin to Limit Their own Growth
    - Some Myoblasts Persist as Quiescent Stem Cells in the Adult
    - Summary
  - Fibroblasts and Their Transformations: The Connective-Tissue Cell Family
    - Fibroblasts Change Their Character in Response to Chemical Signals
    - The Extracellular Matrix May Influence Connective-Tissue Cell Differentiation by Affecting Cell Shape and Attachment
    - Fat Cells Can Develop From Fibroblasts
    - Leptin Secreted by Fat Cells Provides Negative Feedback to Inhibit Eating
    - Bone Is Continually Remodeled by the Cells Within It
    - Osteoblasts Secrete Bone Matrix, While Osteoclasts Erode It
    - During Development, Cartilage Is Eroded by Osteoclasts to Make Way for Bone
    - Summary
  - Stem-Cell Engineering
    - ES Cells Can Be Used to Make Any Part of the Body
    - Epidermal Stem Cell Populations Can Be Expanded in Culture for Tissue Repair
    - Neural Stem Cells Can Repopulate the Central Nervous System
    - The Stem Cells of Adult Tissues May Be More Versatile Than They Seem
    - Summary
  - References
    - General
    - Epidermis and Its Renewal by Stem Cells
    - Sensory Epithelia
    - The Gut and Its Appendages
    - Blood Vessels and Endothelial Cells
    - Renewal by Pluripotent Stem Cells: Blood Cell Formation
    - Genesis, Modulation, and Regeneration of Skeletal Muscle
    - Fibroblasts and Their Transformations: the Connective-tissue Cell Family
    - Stem-cell Engineering
- Chapter 23. Cancer
  - Cancer as a Microevolutionary Process
    - Cancer Cells Reproduce Without Restraint and Colonize Foreign Tissues
    - Most Cancers Derive From a Single Abnormal Cell
    - Cancers Result From Somatic Mutation
    - A Single Mutation Is Not Enough to Cause Cancer
    - Cancers Develop in Slow Stages From Mildly Aberrant Cells
    - Tumor Progression Involves Successive Rounds of Mutation and Natural Selection
    - Most Human Cancer Cells Are Genetically Unstable
    - Cancerous Growth Often Depends on Defective Control of Cell Death or Cell Differentiation
    - Many Cancer Cells Escape a Built-in Limit to Cell Proliferation
    - To Metastasize, Malignant Cancer Cells Must Survive and Proliferate in an Alien Environment
    - Six Key Properties Make Cells Capable of Cancerous Growth
    - Summary
  - The Preventable Causes of Cancer
    - Many, But Not All, Cancer-Causing Agents Damage DNA
    - The Development of a Cancer Can Be Promoted by Factors That Do Not Alter the Cell's DNA Sequence
    - Viruses and Other Infections Contribute to a Significant Proportion of Human Cancers
    - Identification of Carcinogens Reveals Ways to Avoid Cancer
    - Summary
  - Finding the Cancer-Critical Genes
    - Different Methods Are Used to Identify Gain-of-Function and Loss-of-Function Mutations
    - Oncogenes Are Identified Through Their Dominant Transforming Effects
    - Tumor Suppressor Genes Can Sometimes Be Identified by Study of Rare Hereditary Cancer Syndromes
    - Tumor Suppressor Genes Can Be Identified Even Without Clues from Heritable Cancer Syndromes
    - Genes Mutated in Cancer Can Be Made Overactive or Underactive in Many Ways
    - The Hunt for Cancer-Critical Genes Continues
    - Summary
  - The Molecular Basis of Cancer-Cell Behavior
    - Studies of Developing Embryos and Transgenic Mice Help to Uncover the Function of Cancer-Critical Genes
    - Many Cancer-Critical Genes Regulate Cell Division
    - Mutations in Genes That Regulate Apoptosis Allow Cancer Cells to Escape Suicide
    - Mutations in the p53 Gene Allow Cancer Cells to Survive and Proliferate Despite DNA Damage
    - DNA Tumor Viruses Activate the Cell's Replication Machinery by Blocking the Action of Key Tumor Suppressor Genes
    - Telomere Shortening May Pave the Way to Cancer in Humans
    - In a Population of Telomere-Deficient Cells, Loss of p53 Opens an Easy Gateway to Cancer
    - The Mutations That Lead to Metastasis Are Still a Mystery
    - Colorectal Cancers Evolve Slowly Via a Succession of Visible Changes
    - A Few Key Genetic Lesions Are Common to a Majority of Cases of Colorectal Cancer
    - Defects in DNA Mismatch Repair Provide an Alternative Route to Colorectal Cancer
    - The Steps of Tumor Progression Can Be Correlated with Specific Mutations
    - Each Case of Cancer Is Characterized by Its Own Array of Genetic Lesions
    - Summary
  - Cancer Treatment: Present and Future
    - The Search for Cancer Cures Is Difficult but Not Hopeless
    - Current Therapies Exploit the Loss of Cell-Cycle Control and the Genetic Instability of Cancer Cells
    - Cancers Can Evolve Resistance to Therapies
    - New Therapies May Emerge From Our Knowledge of Cancer Biology
    - Treatments Can Be Designed to Attack Cells That Lack p53
    - Tumor Growth Can Be Choked by Depriving the Cancer Cells of Their Blood Supply
    - Small Molecules Can Be Designed to Target Specific Oncogenic Proteins
    - Understanding of Cancer Biology Leads Toward Rational, Tailored Medical Treatments
    - Summary
  - References
    - General
    - Cancer as a Microevolutionary Process
    - The Preventable Causes of Cancer
    - Finding the Cancer-Critical Genes
    - The Molecular Basis of Cancer Cell Behavior
    - Cancer Treatment: Present and Future
- Chapter 24. The Adaptive Immune System
  - Lymphocytes and the Cellular Basis of Adaptive Immunity
    - Lymphocytes Are Required for Adaptive Immunity
    - The Innate and Adaptive Immune Systems Work Together
    - B Lymphocytes Develop in the Bone Marrow; T Lymphocytes Develop in the Thymus
    - The Adaptive Immune System Works by Clonal Selection
    - Most Antigens Activate Many Different Lymphocyte Clones
    - Immunological Memory Is Due to Both Clonal Expansion and Lymphocyte Differentiation
    - Acquired Immunological Tolerance Ensures That Self Antigens Are Not Attacked
    - Lymphocytes Continuously Circulate Through Peripheral Lymphoid Organs
    - Summary
  - B Cells and Antibodies
    - B Cells Make Antibodies as Both Cell-Surface Receptors and Secreted Molecules
    - A Typical Antibody Has Two Identical Antigen-Binding Sites
    - An Antibody Molecule Is Composed of Heavy and Light Chains
    - There Are Five Classes of Heavy Chains, Each With Different Biological Properties
    - The Strength of an Antibody-Antigen Interaction Depends on Both the Number and the Affinity of the Antigen-Binding Sites
    - Light and Heavy Chains Consist of Constant and Variable Regions
    - The Light and Heavy Chains Are Composed of Repeating Ig Domains
    - An Antigen-Binding Site Is Constructed From Hypervariable Loops
    - Summary
  - The Generation of Antibody Diversity
    - Antibody Genes Are Assembled From Separate Gene Segments During B Cell Development
    - Each Variable Region Is Encoded by More Than One Gene Segment
    - Imprecise Joining of Gene Segments Greatly Increases the Diversity of V Regions
    - Antigen-Driven Somatic Hypermutation Fine-Tunes Antibody Responses
    - The Control of V(D)J Joining Ensures That B Cells Are Monospecific
    - When Activated by Antigen, a B Cell Switches From Making a Membrane-Bound Antibody to Making a Secreted Form of the Same Antibody
    - B Cells Can Switch the Class of Antibody They Make
    - Summary
  - T Cells and MHC Proteins
    - T Cell Receptors Are Antibodylike Heterodimers
    - Antigen-Presenting Cells Activate T Cells
    - Effector Cytotoxic T Cells Induce Infected Target Cells to Kill Themselves
    - Effector Helper T Cells Help Activate Macrophages, B Cells, and Cytotoxic T Cells
    - T Cells Recognize Foreign Peptides Bound to MHC Proteins
    - MHC Proteins Were Identified in Transplantation Reactions Before Their Functions Were Known
    - Class I and Class II MHC Proteins Are Structurally Similar Heterodimers
    - An MHC Protein Binds a Peptide and Interacts with a T Cell Receptor
    - MHC Proteins Help Direct T Cells to Their Appropriate Targets
    - CD4 and CD8 Co-receptors Bind to Nonvariable Parts of MHC Proteins
    - Cytotoxic T Cells Recognize Fragments of Foreign Cytosolic Proteins in Association with Class I MHC Proteins
    - Helper T Cells Recognize Fragments of Endocytosed Foreign Protein Associated with Class II MHC Proteins
    - Potentially Useful T Cells Are Positively Selected in the Thymus
    - Many Developing T Cells That Could Be Activated by Self Peptides Are Eliminated in the Thymus
    - The Function of MHC Proteins Explains Their Polymorphism
    - Summary
  - Helper T Cells and Lymphocyte Activation
    - Costimulatory Proteins on Antigen-Presenting Cells Help Activate T Cells
    - The Subclass of Effector Helper T Cell Determines the Nature of the Adaptive Immune Response
    - T_H1 Cells Help Activate Macrophages at Sites of Infection
    - Antigen Binding Provides Signal 1 to B Cells
    - Helper T Cells Provide Signal 2 to B Cells
    - Immune Recognition Molecules Belong to an Ancient Superfamily
    - Summary
  - References
    - General
    - Lymphocytes and the Cellular Basis of Adaptive Immunity
    - B Cells and Antibodies
    - The Generation of Antibody Diversity
    - T Cells and MHC Proteins
    - Helper T Cells and Lymphocyte Activation
- Chapter 25. Pathogens, Infection, and Innate Immunity
  - Introduction to Pathogens
    - Pathogens Have Evolved Specific Mechanisms for Interacting with Their Hosts
    - The Signs and Symptoms of Infection May Be Caused by the Pathogen or by the Host's Responses
    - Pathogens Are Phylogenetically Diverse
    - Bacterial Pathogens Carry Specialized Virulence Genes
    - Fungal and Protozoan Parasites Have Complex Life Cycles with Multiple Forms
    - Viruses Exploit Host Cell Machinery for All Aspects of Their Multiplication
    - Prions Are Infectious Proteins
    - Summary
  - Cell Biology of Infection
    - Pathogens Cross Protective Barriers to Colonize the Host
    - Pathogens That Colonize Epithelia Must Avoid Clearance by the Host
    - Intracellular Pathogens Have Mechanisms for Both Entering and Leaving Host Cells
    - Viruses Bind to Molecules Displayed on the Host Cell Surface
    - Viruses Enter Host Cells by Membrane Fusion, Pore Formation, or Membrane Disruption
    - Bacteria Enter Host Cells by Phagocytosis
    - Intracellular Parasites Actively Invade Host Cells
    - Many Pathogens Alter Membrane Traffic in the Host Cell
    - Viruses and Bacteria Exploit the Host Cell Cytoskeleton for Intracellular Movement
    - Viruses Take Over the Metabolism of the Host Cell
    - Pathogens Can Alter the Behavior of the Host Organism to Facilitate the Spread of the Pathogen
    - Pathogens Evolve Rapidly
    - Drug Resistant Pathogens Are a Growing Problem
    - Summary
  - Innate Immunity
    - Epithelial Surfaces Help Prevent Infection
    - Human Cells Recognize Conserved Features of Pathogens
    - Complement Activation Targets Pathogens for Phagocytosis or Lysis
    - Toll-like Proteins Are an Ancient Family of Pattern Recognition Receptors
    - Phagocytic Cells Seek, Engulf, and Destroy Pathogens
    - Activated Macrophages Recruit Additional Phagocytic Cells to Sites of Infection
    - Virus-Infected Cells Take Drastic Measures to Prevent Viral Replication
    - Natural Killer Cells Induce Virus-Infected Cells to Kill Themselves
    - Summary
  - References
    - General
    - Introduction to Pathogens
    - Cell Biology of Infection
    - Innate Immunity
Glossary

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Bruce Alberts received his Ph.D. from Harvard University and is President of the National Academy of Sciences and Professor of Biochemistry and Biophysics at the University of California, San Francisco. Alexander Johnson received his Ph.D. from Harvard University and is a Professor of Microbiology and Immunology at the University of California, San Francisco. Julian Lewis received his D.Phil. from the University of Oxford and is a Principal Scientist at the Imperial Cancer Research Fund, London. Martin Raff received his M.D. from McGill University and is at the Medical Research Council Laboratory for Molecular Cell Biology and Cell Biology Unit and in the Biology Department at University College London. Keith Roberts received his Ph.D. from the University of Cambridge and is Associate Research Director at the John Innes Centre, Norwich. Peter Walter received his Ph.D. from The Rockefeller University in New York and is Professor and Chairman of the Department of Biochemistry and Biophysics at the University of California, San Francisco, and an Investigator of the Howard Hughes Medical Institute.

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Bookshelf ID: NBK21054

Chemistry in Context 7th Edition Chapter 4 Answers

Source: https://www.ncbi.nlm.nih.gov/books/NBK21054/

Chemistry in Context 7th Edition Chapter 4 Answers

Molecular Biology of the Cell, 4th edition

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