Molecular biology : principles and practice

Molecular Biology: Principles and Practice
About the Authors
Contents in Brief
Contents
Preface
	Students see science as a set of facts rather than an active human endeavor.
	Students often view science as a completed story with an oversimplified script.
	Students get lost in the details.
	Students see evolution as an abstract theory.
	Experimental Techniques
	Media and Supplements
		eBook
		Companion Website: www.whfreeman.com/cox
Acknowledgments
Part I: Foundations
1 Studying the Molecules of Life
	Moment of Discovery
	1.1: The Evolution of Life on Earth
		What Is Life?
		Evolution Underpins Molecular Biology
		Life on Earth Probably Began with RNA
		HIGHLIGHT 1-1: Evolution. Observing Evolution in the Laboratory
		The Last Universal Common Ancestor Is the Root of the Tree of Life
		Evolution by Natural Selection Requires Variation and Competition
	1.2: How Scientists Do Science
		Science Is a Path to Understanding the Natural Universe
		The Scientific Method Underlies Scientific Progress
		The Scientific Method Is a Versatile Instrument of Discovery
		Scientists Work within a Community of Scholars
		Unanswered Questions
	How We Know
		Adenine Could Be Synthesized with Prebiotic Chemistry
		Clay Had a Role in Prebiotic Evolution
		Darwin’s World Helped Him Connect the Dots
	Key Terms
	Additional Reading
2 DNA: The Repository of Biological Information
	Moment of Discovery
	2.1: Mendelian Genetics
		Mendel’s First Law: Allele Pairs Segregate during Gamete Formation
		Mendel’s Second Law: Different Genes Assort Independently during Gamete Formation
		There Are Exceptions to Mendel’s Laws
	2.2: Cytogenetics: Chromosome Movements during Mitosis and Meiosis
		Cells Contain Chromosomes and Other Internal Structures
		Mitosis: Cells Evenly Divide Chromosomes between New Cells
		Meiosis: Chromosome Number Is Halved during Gamete Formation
	2.3: The Chromosome Theory of Inheritance
		Sex-Linked Genes in the Fruit Fly Reveal That Genes Are on Chromosomes
		Linked Genes Do Not Segregate Independently
		Recombination Unlinks Alleles
		Recombination Frequency Can Be Used to Map Genes along Chromosomes
	2.4: Molecular Genetics
		DNA Is the Chemical of Heredity
		Genes Encode Polypeptides and Functional RNAs
		The Central Dogma: Information Flows from DNA to RNA to Protein
		Mutations in DNA Give Rise to Phenotypic Change
	HIGHLIGHT 2-1: Medicine. The Molecular Biology of Sickle-Cell Anemia, a Recessive Genetic Disease of Hemoglobin
	How We Know
		Chromosome Pairs Segregate during Gamete Formation in a Way That Mirrors the Mendelian Behavior of Genes
		Corn Crosses Uncover the Molecular Mechanism of Crossing Over
		Hershey and Chase Settle the Matter: DNA Is the Genetic Material
	Key Terms
	Problems
	Additional Reading
3 Chemical Basis of Information Molecules
	Moment of Discovery
	3.1: Chemical Building Blocks of Nucleic Acids and Proteins
		Nucleic Acids Are Long Chains of Nucleotides
		Proteins Are Long Polymers of Amino Acids
		Chemical Composition Helps Determine Nucleic Acid and Protein Structure
		Chemical Composition Can Be Altered by Postsynthetic Changes
	3.2: Chemical Bonds
		Electrons Are Shared in Covalent Bonds and Transferred in Ionic Bonds
		Chemical Bonds Are Explainable in Quantum Mechanical Terms
		Both the Making and Breaking of Chemical Bonds Involve Energy Transfer
		Electron Distribution between Bonded Atoms Determines Molecular Behavior
	3.3: Weak Chemical Interactions
		Van der Waals Forces Are Nonspecific Contacts between Atoms
		Hydrophobic Interactions Bring Together Nonpolar Molecules
		Hydrogen Bonds Are a Special Kind of Noncovalent Bond
		Combined Effects of Weak Chemical Interactions Stabilize Macromolecular Structures
		Weak Chemical Bonds Also Facilitate Macromolecular Interactions
	3.4: Stereochemistry
		Three-Dimensional Atomic Arrangements Define Molecules
		Biological Molecules and Processes Selectively Use One Stereoisomer
		Proteins and Nucleic Acids Are Chiral
	HIGHLIGHT 3-1: Medicine. The Behavior of a Peptide Made of D-Amino Acids
	3.5: The Role of pH and Ionization
		The Hydrogen Ion Concentration of a SolutionIs Measured by pH
		Buffers Prevent Dramatic Changes in pH
		The Henderson-Hasselbalch Equation Estimates the pH of a Buffered Solution
	3.6: Chemical Reactions in Biology
		The Mechanism and Speed of Chemical Transformation Define Chemical Reactions
		Biological Systems Follow the Laws of Thermodynamics
		Catalysts Increase the Rates of Biological Reactions
		Energy Is Stored and Released by Making and Breaking Phosphodiester Bonds
	HIGHLIGHT 3-2: Evolution. ATP: The Critical Molecule of Energy Exchange in All Cells
	How We Know
		Single Hydrogen Atoms Are Speed Bumps in Enzyme-Catalyzed Reactions
		Peptide Bonds Are (Mostly) Flat
	Key Terms
	Problems
	Additional Reading
4 Protein Structure
	Moment of Discovery
	4.1: Primary Structure
		Amino Acids Are Categorized by Chemical Properties
		Amino Acids Are Connected in a Polypeptide Chain
		HIGHLIGHT 4-1: A Closer Look. Purification of Proteins by Column Chromatography and SDS-PAGE
		Evolutionary Relationships Can Be Determined from Primary Sequence Comparisons
	4.2: Secondary Structure
		The α Helix Is a Common Form of Secondary Protein Structure
		The β Sheet Is Composed of Long, Extended Strands of Amino Acids
		Reverse Turns Allow Secondary Structures to Fold
	4.3: Tertiary and Quaternary Structures
		Tertiary and Quaternary Structures Can BeRepresented in Different Ways
		Domains Are Independent Folding Units within the Protein
		Supersecondary Structure Elements Are Building Blocks of Domains
		Quaternary Structures Range from Simple to Complex
		HIGHLIGHT 4-2: A Closer Look. Protein Structure Databases
		Protein Structures Help Explain Protein Evolution
	4.4: Protein Folding
		Predicting Protein Folding Is a Goal of Computational Biology
		Polypeptides Fold through a Molten Globule Intermediate
		HIGHLIGHT 4-3: Medicine, Prion-Based Misfolding Diseases
		Chaperones and Chaperonins Can Facilitate Protein Folding
		Protein Isomerases Assist in the Folding of Some Proteins
	4.5: Determining the Atomic Structure of Proteins
		Most Protein Structures Are Solved by X-Ray Crystallography
		Smaller Protein Structures Can Be Determined by NMR
	Unanswered Questions
	How We Know
		Sequence Comparisons Yield an Evolutionary Roadmap from Bird Influenza to a Deadly Human Pandemic
		We Can Tell That a Protein Binds ATP by Looking at Its Sequence
		Disulfide Bonds Act as Molecular Cross-Braces to Stabilize a Protein
	Key Terms
	Problems
	Additional Reading
5 Protein Function
	Moment of Discovery
	5.1: Protein-Ligand Interactions
		Many Proteins Bind to Other Molecules Reversibly
		Protein-Ligand Interactions Can Be Quantified
		DNA-Binding Proteins Guide Genome Structure and Function
	5.2: Enzymes: The Reaction Catalysts of Biological Systems
		Enzymes Catalyze Specific Biological Reactions
		Enzymes Increase the Rate of a Reaction by Lowering the Activation Energy
		The Rates of Enzyme-Catalyzed Reactions Can Be Quantified
		DNA Ligase Activity Illustrates Some Principles of Catalysis
		HIGHLIGHT 5-1: A Closer Look. Reversible and Irreversible Inhibition
	5.3: Motor Proteins
		Helicases Abound in DNA and RNA Metabolism
		Helicase Mechanisms Have Characteristic Molecular Parameters
	5.4: The Regulation of Protein Function
		Modulator Binding Causes Conformational Changes in Allosteric Enzymes
		Allosteric Enzymes Have Distinctive Binding and/or Kinetic Properties
		Enzyme Activity Can Be Affected by Autoinhibition
		Some Proteins Are Regulated by Reversible Covalent Modification
		Phosphoryl Groups Affect the Structure and Catalytic Activity of Proteins
		HIGHLIGHT 5-2: Medicine. HIV Protease: Rational Drug Design Using Protein Structure
		Some Proteins Are Regulated by Proteolytic Cleavage
	Unanswered Questions
	How We Know
		The Lactose Repressor Is One of the Great Sagas of Molecular Biology
		The lacI Gene Encodes a Repressor
		The Lactose Repressor Is Found
	Key Terms
	Problems
	Additional Reading
Part II: Nucleic Acid Structure and Methods
6 DNA and RNA Structure
	Moment of Discovery
	6.1: The Structure and Properties of Nucleotides
		Nucleotides Comprise Characteristic Bases, Sugars,and Phosphates
		Phosphodiester Bonds Link the Nucleotide Units in Nucleic Acids
		Nucleotide Bases Affect the Three-Dimensional Structure of Nucleic Acids
		Nucleotides Play Additional Roles in Cells
	6.2: DNA Structure
		DNA Molecules Have Distinctive Base Compositions
		DNA Is Usually a Right-Handed Double Helix
		DNA Adopts Different Helical Forms
		Certain DNA Sequences Adopt Unusual Structures
		HIGHLIGHT 6-1: Technology. DNA Computing
		HIGHLIGHT 6-2: Technology. The Design of a DNA Octahedron
	6.3: RNA Structure
		RNAs Have Helical Secondary Structures
		RNAs Form Various Stable Three-Dimensional Structures
		HIGHLIGHT 6-3: Medicine. RNA Structure Governing HIV Gene Expression
	6.4: Chemical and Thermodynamic Properties of Nucleic Acids
		Double-Helical DNA and RNA Can Be Denatured
		Nucleic Acids from Different Species Can Form Hybrids
		Nucleotides and Nucleic Acids Undergo Uncatalyzed Chemical Transformations
		Base Methylation in DNA Plays an Important Role in Regulating Gene Expression
		RNA Molecules Are Often Site-Specifically Modified In Vivo
		The Chemical Synthesis of DNA and RNA Has Been Automated
	Unanswered Questions
	How We Know
		DNA Is a Double Helix
		DNA Helices Have Unique Geometries That Depend on Their Sequence
		Ribosomal RNA Sequence Comparisons Provided the First Hints of the Structural Richness of RNA
	Key Terms
	Problems
	Data Analysis Problem
	Additional Reading
7 Studying Genes
	Moment of Discovery
	7.1: Isolating Genes for Study (Cloning)
		Genes Are Cloned by Splicing Them into Cloning Vectors
		Cloning Vectors Allow Amplification of Inserted DNA Segments
		DNA Libraries Provide Specialized Catalogs of Genetic Information
	7.2: Working with Genes and Their Products
		Gene Sequences Can Be Amplified with the Polymerase Chain Reaction
		The Sanger Method Identifies Nucleotide Sequences in Cloned Genes
		HIGHLIGHT 7-1: Technology. A Potent Weapon in Forensic Medicine
		Cloned Genes Can Be Expressed to Amplify Protein Production
		HIGHLIGHT 7-2: Technology. DNA Sequencing: Ever Faster and Cheaper
		Many Different Systems Are Used to Express Recombinant Proteins
		Alteration of Cloned Genes Produces Altered Proteins
		Terminal Tags Provide Handles for Affinity Purification
	7.3: Understanding the Functions of Genes and Their Products
		Protein Fusions and Immunofluorescence Can Localize Proteins in Cell
		Proteins Can Be Detected in Cellular Extractswith the Aid of  Western Blots
		Protein-Protein Interactions Can Help Elucidate Protein Function
		DNA Microarrays Reveal Cellular Protein Expression Patterns and Other Information
	Unanswered Questions
	How We Know
		New Enzymes Take Molecular Biologists from Cloning to Genetically Modified Organisms
		A Dreamy Night Ride on a California Byway Gives Rise to the Polymerase Chain Reaction
		Coelenterates Show Biologists the Light
	Key Terms
	Problems
	Data Analysis Problem
	Additional Reading
8 Genomes, Transcriptomes, and Proteomes
	Moment of Discovery
	8.1: Genomes and Genomics
		Many Genomes Have Been Sequenced in Their Entirety
		Annotation Provides a Description of the Genome
		HIGHLIGHT 8-1: Evolution. Getting to Know the Neanderthals
		Genome Databases Provide Information about Every Type of Organism
		HIGHLIGHT 8-2: Technology. Sampling Biodiversity with Metagenomics
		The Human Genome Contains Many Types of Sequences
		Genome Sequencing Informs Us about Our Humanity
		Genome Comparisons Help Locate Genes Involved in Disease
	8.2: Transcriptomes and Proteomes
		Special Cellular Functions Are Revealed in a Cell’s Transcriptome
		High-Throughput DNA Sequencing Is Used in Transcriptome Analysis
		The Proteins Generated by a Cell ConstituteIts Proteome
		Electrophoresis and Mass Spectrometry Support Proteomics Research
		Computational Approaches Help Elucidate Protein Function
		Experimental Approaches Reveal Protein Interaction Networks
	8.3: Our Genetic History
		All Living Things Have a Common Ancestor
		Genome Comparisons Provide Clues to Our Evolutionary Past
		HIGHLIGHT 8-3: Evolution. Phylogenetics Solves a Crime
		The Human Journey Began in Africa
		Human Migrations Are Recorded in Haplotypes
	Unanswered Questions
	How We Know
		Haemophilus influenzae Ushers in the Era of Genome Sequences
	Key Terms
	Problems
	Data Analysis Problem
	Additional Reading
9 Topology: Functional Deformations of DNA
	Moment of Discovery
	9.1: The Problem: Large DNAs in Small Packages
		Chromosome Function Relies on Specialized Genomic Sequences
		Chromosomes Are Longer Than the Cellular or Viral Packages Containing Them
		HIGHLIGHT 9-1: Medicine. The Dark Side of Antibiotics
	9.2: DNA Supercoiling
		Most Cellular DNA Is Underwound
		DNA Underwinding Is Defined by the Topological Linking Number
		DNA Compaction Requires a Special Form of Supercoiling
	9.3: The Enzymes That Promote DNA Compaction
		Topoisomerases Catalyze Changes in the Linking Number of DNA
		The Two Bacterial Type II Topoisomerases Have Distinct Functions
		Eukaryotic Topoisomerases Have Specialized Functions in DNA Metabolism
		SMC Proteins Facilitate the Condensation of Chromatin
		HIGHLIGHT 9-2: Medicine. Curing Disease by Inhibiting Topoisomerases
	Unanswered Questions
	How We Know
		The Discovery of Supercoiled DNA Goes through Twists and Turns
		The First DNA Topoisomerase Unravels Some Mysteries
		DNA Gyrase Passes the Strand Test
	Key Terms
	Problems
	Data Analysis Problem
	Additional Reading
10 Nucleosomes, Chromatin, and Chromosome Structure
	Moment of Discovery
	10.1: Nucleosomes: The Basic Units of DNA Condensation
		Histone Octamers Organize DNA into Repeating Units
		DNA Wraps Nearly Twice around a Single Histone Octamer
		Histone Tails Mediate Internucleosome Connections That Regulate the Accessibility of DNA
	10.2: Higher-Order Chromosome Structure
		Histone H1 Binds the Nucleosome to Form the Chromatosome
		Chromosomes Condense into a Compact Chromatin Filament
		Higher-Order Chromosome Structure Involves Loops and Coils
		Bacterial DNA, Like Eukaryotic DNA, Is Highly Organized
	10.3: The Regulation of Chromosome Structure
		Nucleosomes Are Intrinsically Dynamic
		ATP-Driven Chromatin Remodeling ComplexesCan Reposition Nucleosomes
		Variant Histone Subunits Alter DNA-Binding Affinity
		Nucleosome Assembly Requires Chaperones
		Modifications of Histone Tails Alter DNA Accessibility
		HIGHLIGHT 10-1: A Closer Look. The Use of a Histone Variant in X Chromosome Inactivation
		Histone Modifications and Remodeling Complexes May Read a Histone Code
		Histone Modifying Enzymes Maintain Epigenetic States through Cell Division
		HIGHLIGHT 10-2: Medicine. Defects in Epigenetic Maintenance Proteins Associated with Cancer
	Unanswered Questions
	How We Know
		Kornberg Wrapped His Mind around the Histone Octamer
		A Transcription Factor Can Acetylate Histones
	Key Terms
	Problems
	Data Analysis Problem
	Additional Reading
III: Information Transfer
11 DNA Replication
	Moment of Discovery
	11.1: DNA Transactions during Replication
		DNA Replication Is Semiconservative
		Replication Is Initiated at Origins and Proceeds Bidirectionally
		Replication Is Semidiscontinuous
	11.2: The Chemistry of DNA Polymerases
		DNA Polymerases Elongate DNA in the 5\'→3\' Direction
		Most DNA Polymerases Contain DNA Exonuclease Activity
		Five E. coli DNA Polymerases Function in DNA Replication and Repair
		DNA Polymerase Structure Reveals the Basis for Its Accuracy
		Processivity Increases the Efficiency of DNA Polymerase Activity
	11.3: Mechanics of the DNA Replication Fork
		DNA Polymerase III Is the Replicative Polymerasein E. coli
		A DNA Sliding Clamp Increases the Speed and Processivity of the Chromosomal Replicase
		Many Different Proteins Advance a Replication Fork
		Helicase Activity Is Stimulated by Its Connection to the DNA Polymerase
		DNA Loops Repeatedly Grow and Collapse on the Lagging Strand
		Okazaki Fragments Require Removal of RNA and Ligase-Mediated Joining of DNA
		The Replication Fork Is More Complex in Eukaryotes Than in Bacteria
	11.4: Initiation of DNA Replication
		Assembly of the Replication Fork Follows an Ordered Sequence of Events
		Replication Initiation in E. coli Is Controlled at Multiple Steps
		Eukaryotic Origins “Fire” Only Once per Cell Cycle
	11.5: Termination of DNA Replication
		E. coli Chromosome Replication Terminates Opposite the Origin
		HIGHLIGHT 11-1: Technology. Two-Dimensional Gel Analysis of Replication Origins
		Telomerase Solves the End Replication Problem inEukaryotes
		Proteins Bind Telomeres to Protect the Ends ofChromosomes
		Telomere Length Is Associated with Immortalityand Cancer
	Unanswered Questions
	How We Know
		DNA Polymerase Uses a Template and a Proofreader: Nature’s Spell Check
		Polymerase Processivity Depends on a Circular Protein That Slides along DNA
		Replication Requires an Origin
	Key Terms
	Problems
	Data Analysis Problem
	Additional Reading
12 DNA Mutation and Repair
	Moment of Discovery
	12.1: Types of DNA Mutations
		A Point Mutation Can Alter One Amino Acid
		Small Insertion and Deletion Mutations Change Protein Length
		Some Mutations Are Very Large and Form Abnormal Chromosomes
	12.2: DNA Alterations That Lead to Mutations
		Spontaneous DNA Damage by Water Can Cause Point Mutations
		Oxidative Damage and Alkylating Agents Can Create Point Mutations and Strand Breaks
		The Ames Test Identifies DNA-Damaging Chemicals
		DNA-Damaging Agents Are Used in Cancer Chemotherapy
		Solar Radiation Causes Interbase Cross-Links and Strand Breaks
		Errant Replication and Recombination Lead to DNA Damage
	12.3: Mechanisms of DNA Repair
		Mismatch Repair Fixes Misplaced-Nucleotide Replication Errors
		HIGHLIGHT 12-1: Medicine. Mismatch Repair and Colon Cancer
		Direct Repair Corrects a Damaged Nucleotide Base in One Step
		Base Excision Repairs Subtle Alterations in Nucleotide Bases
		Nucleotide Excision Repair Removes Bulky Damaged Bases
		Recombination Repairs Lesions That Break DNA
		Specialized Translesion DNA Polymerases Extend DNA Past a Lesion
		HIGHLIGHT 12-2: Medicine. Nucleotide Excision Repair and Xeroderma Pigmentosum
	Unanswered Questions
	How We Know
		Mismatch Repair in E. coli Requires DNA Methylation
		UV Lights Up the Pathway to DNA Damage Repair
		Translesion DNA Polymerases Produce DNA Mutations
	Key Terms
	Problems
	Data Analysis Problem
	Additional Reading
13 Recombinational DNA Repair and Homologous Recombination
	Moment of Discovery
	13.1: Recombination as a DNA Repair Process
		Double-Strand Breaks Are Repaired by Recombination
		Collapsed Replication Forks Are Reconstructed byDouble-Strand Break Repair
		A Stalled Replication Fork Requires Fork Regression
		Single-Stranded DNA Regions Are Filled In by Gap Repair
	13.2: Enzymatic Machines in Bacterial Recombinational DNA Repair
		RecBCD and RecFOR Initiate Recombinational Repair
		RecA Is the Bacterial Recombinase
		RecA Protein Is Subject to Regulation
		Multiple Enzymes Process DNA Intermediates Created by RecA
		Repair of the Replication Fork in Bacteria Can Lead to Dimeric Chromosomes
		HIGHLIGHT 13-1: Evolution. A Tough Organism in a Tough Environment: Deinococcus radiodurans
	13.3: Homologous Recombination in Eukaryotes
		Meiotic Recombination Is Initiated at Double-Strand Breaks
		HIGHLIGHT 13-2: Medicine. Why Proper Chromosomal Segregation Matters
		Meiotic Recombination Is Completed by a Classic DSBR Pathway
		Meiotic Recombination Contributes to Genetic Diversity
		Recombination during Mitosis Is Also Initiated at Double-Strand Breaks
		Programmed Gene Conversion Events Can Affect Gene Function and Regulation
		Some Introns Move via Homologous Recombination
	13.4: Nonhomologous End Joining
		Nonhomologous End Joining Repairs Double-Strand Breaks
		Nonhomologous End Joining Is Promoted by a Set of Conserved Enzymes
	Unanswered Questions
	How We Know
		A Motivated Graduate Student Inspires the Discovery of Recombination Genes in Bacteria
		A Biochemical Masterpiece Catches a Recombination Protein in the Act
	Key Terms
	Problems
	Data Analysis Problem
	Additional Reading
14 Site-Specific Recombination and Transposition
	Moment of Discovery
	14.1: Mechanisms of Site-Specific Recombination
		Precise DNA Rearrangements Are Promoted by Site-Specific Recombinases
		Site-Specific Recombination Complements Replication
		Site-Specific Recombination Can Be a Stage in a Viral Infection Cycle
		Gene Expression Can be Regulated by Site-Specific Recombination
		Site-Specific Recombination Reactions Can Be Guided by Auxiliary Proteins
	14.2: Mechanisms of Transposition
		HIGHLIGHT 14-1: Technology. Using Site-Specific Recombination to Trace Neurons
		Transposition Takes Place by Three Major Pathways
		Bacteria Have Three Common Classes of Transposons
		Retrotransposons Are Especially Common in Eukaryotes
		HIGHLIGHT 14-2: Evolution. Awakening Sleeping Beauty
		Retrotransposons and Retroviruses Are Closely Related
		A Retrovirus Causes AIDS
		HIGHLIGHT 14-3: Medicine. Fighting AIDS with HIV Reverse Transcriptase Inhibitors
	14.3: The Evolutionary Interplay of Transposons and Their Hosts
		Viruses, Transposons, and Introns Have an Interwoven Evolutionary History
		A Hybrid Recombination Process Assembles Immunoglobulin Genes
	Unanswered Questions
	How We Know
		Bacteriophage   Provided the First Example of Site-Specific Recombination
		If You Leave Out the Polyvinyl Alcohol, Transposition Gets Stuck
	Key Terms
	Problems
	Data Analysis Problem
	Additional Reading
15 DNA-Dependent Synthesis of RNA
	Moment of Discovery
	15.1: RNA Polymerases and Transcription Basics
		RNA Polymerases Differ in Details but Share Many Features
		HIGHLIGHT 15-1: A Closer Look. The ABCs of RNA: Complexity of the Transcriptome
		Transcription Initiation, Elongation, and Termination Occur in Discrete Steps
		DNA-Dependent RNA Polymerases Can Be Specifically Inhibited
		Transcriptional Regulation Is a Central Mechanism in the Control of Gene Expression
	15.2: Transcription in Bacteria
		Promoter Sequences Alter the Strength and Frequency of Transcription
		Sigma Factors Specify Polymerase Binding to Particular Promoters
		Structural Changes Lead to Formation of the Transcription-Competent Open Complex
		Initiation Is Primer-Independent and Produces Short, Abortive Transcripts
		Transcription Elongation Is Continuous until Termination
		Specific Sequences in the Template Strand Cause Transcription to Stop
	15.3: Transcription in Eukaryotes
		Eukaryotic Polymerases Recognize Characteristic Promoters
		HIGHLIGHT 15-2: Medicine. Using Transcription Factors to Reprogram Cells
		Pol II Transcription Parallels Bacterial RNA Transcription
		Transcription Factors Play Specific Roles in the Transcription Process
		Transcription Initiation In Vivo Requires the Mediator Complex
		Termination Mechanisms Vary among RNA Polymerases
		Transcription Is Coupled to DNA Repair, RNA Processing, and mRNA Transport
	Unanswered Questions
	How We Know
		RNA Polymerase Is Recruited to Promoter Sequences
		RNA Polymerases Are Both Fast and Slow
	Key Terms
	Problems
	Data Analysis Problem
	Additional Reading
16 RNA Processing
	Moment of Discovery
	16.1: Messenger RNA Capping and Polyadenylation
		Eukaryotic mRNAs Are Capped at the 5\' End
		Eukaryotic mRNAs Have a Distinctive 3\'-End Structure
		HIGHLIGHT 16-1: Evolution. Eukaryotic mRNA with Unusual 3\' Tails
		mRNA Capping, Polyadenylation, and Splicing Are Coordinately Regulated during Transcription
	16.2: Pre-mRNA Splicing
		Eukaryotic mRNAs Are Synthesized as Precursors Containing Introns
		A Gene Can Give Rise to Multiple Products by Alternative RNA Splicing
		The Spliceosome Catalyzes Most Pre-mRNA Splicing
		Some Introns Can Self-Splice without Protein or Spliceosome Assistance
		Exons from Different RNA Molecules Can Be Fused by Trans-Splicing
		HIGHLIGHT 16-2: Evolution. The Origin of Introns
	16.3: RNA Editing
		RNA Editing Can Involve the Insertion or Deletion of Bases
		RNA Editing by Substitution Involves Deamination of A or C Residues
	16.4: RNA Transport and Degradation
		Different Kinds of RNA Use Different Nuclear Export Pathways
		mRNA Transport from the Nucleus to the Cytoplasm Is Coupled to Pre-mRNA Splicing
		Some mRNAs Are Localized to Specific Regions of the Cytoplasm
		Cellular mRNAs Are Degraded at Different Rates
		Processing Bodies Are the Sites of mRNA Storage and Degradation in Eukaryotic Cells
	16.5: Processing of Non-Protein-Coding RNAs
		Maturation of tRNAs Involves Site-Specific Cleavage and Chemical Modification
		Maturation of rRNA Involves Site-Specific Cleavage and Chemical Modification
		Small Regulatory RNAs Are Derived from Larger Precursor Transcripts
	16.6: RNA Catalysis and the RNA World Hypothesis
		Ribozyme Diversity Correlates with Function
		HIGHLIGHT 16-3: Evolution. A Viral Ribozyme Derived from the Human Genome?
		Could RNA Have Formed the Basis for Early Life on Earth?
	Unanswered Questions
	How We Know
		Studying Autoimmunity Led to the Discovery of snRNPs
		RNA Molecules Are Fine-Tuned for Stability or Function
		Ribozyme Form Explains Function
	Key Terms
	Problems
	Data Analysis Problem
	Additional Reading
17 The Genetic Code
	Moment of Discovery
	17.1: Deciphering the Genetic Code: tRNA as Adaptor
		All tRNAs Have a Similar Structure
		The Genetic Code Is Degenerate
		Wobble Enables One tRNA to Recognize Two or More Codons
		Translation Is Started and Stopped by Specific Codons
		The Genetic Code Resists Single-Base Substitution Mutations
		Some Mutations Are Suppressed by Specialt RNAs
	17.2: The Rules of the Code
		The Genetic Code Is Nonoverlapping
		There Are No Gaps in the Genetic
		The Genetic Code Is Read in Triplets
		Protein Synthesis Is Linear
	17.3: Cracking the Code
		Random Synthetic RNA Polymers Direct Protein Synthesis in Cell Extracts
		RNA Polymers of Defined Sequence Complete the Code
		The Genetic Code Is Validated in Living Cells
	17.4: Exceptions Proving the Rules
		Evolution of the Translation Machinery Is a Mystery
		Mitochondrial tRNAs Deviate from the Universal Genetic Code
		HIGHLIGHT 17-1: Evolution. The Translation Machinery
		Initiation and Termination Rules Have Exceptions
	Unanswered Questions
	How We Know
		Transfer RNA Connects mRNA and Protein
		Proteins Are Synthesized from the N-Terminus to the C-Terminus
		The Genetic Code In Vivo Matches the Genetic Code In Vitro
	Key Terms
	Problems
	Data Analysis Problem
	Additional Reading
18 Protein Synthesis
	Moment of Discovery
	18.1: The Ribosome
		The Ribosome Is an RNA-Protein Complex Composed of Two Subunits
		Ribosomal Subunits Associate and Dissociate in Each Cycle of Translation
		The Ribosome Is a Ribozyme
		The Ribosome Structure Facilitates Peptide Bond  Formation
		HIGHLIGHT 18-1: Evolution. Mitochondrial Ribosomes: A Window into Ribosome Evolution?
	18.2: Activation of Amino Acids for Protein Synthesis
		Amino Acids Are Activated and Linked to Specifict RNAs
		Aminoacyl-tRNA Synthetases Attach the Correct Amino Acids to Their tRNAs
		The Structure of tRNA Allows Accurate Recognition by tRNA Synthetases
		Proofreading Ensures the Fidelity of Aminoacyl-tRNA Synthetases
	18.3: Initiation of Protein Synthesis
		Base Pairing Recruits the Small Ribosomal Subunit to Bacterial mRNAs
		HIGHLIGHT 18-2: Technology. Genetic Incorporation of Unnatural Amino Acids into Proteins
		Eukaryotic mRNAs Recruit the Small Ribosomal Subunit Indirectly
		A Specific Amino Acid Initiates Protein Synthesis
		Initiation in Bacterial Cells Requires Three Initiation Factors
		Initiation in Eukaryotic Cells Requires Additional Initiation Factors
		Some mRNAs Use 5\' End–Independent Mechanisms of Initiation
	18.4: Elongation of the Polypeptide Chain
		Peptide Bonds Are Formed in the Translation Elongation Stage
		Substrate Positioning and the Incoming tRNA Contribute to Peptide Bond Formation
		The GTPase EF-G Drives Translocation by Displacing the A-Site tRNA
		GTP Binding and Hydrolysis Regulate Successive Elongation Cycles
	18.5: Termination of Protein Synthesis and Recycling of the Synthesis Machinery
		Completion of a Polypeptide Chain Is Signaled by an mRNA Stop Codon
		Ribosome Recycling Factor Prepares Ribosomes for New Rounds of Translation
		Fast and Accurate Protein Synthesis Requires Energy
		Antibiotics and Toxins Frequently Target the Protein Synthesis Cycle
		HIGHLIGHT 18-3: Medicine. Toxins That Target the Ribosome
	18.6: Translation-Coupled Removal of Defective mRNA
		Ribosomes Stalled on Truncated mRNAs Are Rescued by tmRNA
		Eukaryotes Have Other Mechanisms to Detect Defective mRNAs
	18.7: Protein Folding, Covalent Modification, and Targeting
		Some Proteins Fold Spontaneously, and Others Need Help from Molecular Chaperones
		Covalent Modifications Are Common in Newly Synthesized Proteins
		Proteins Are Targeted to Correct Locations during or after Synthesis
		Posttranslational Modification of Many Eukaryotic Proteins Begins in the Endoplasmic Reticulum
		Glycosylation Plays a Key Role in Eukaryotic Protein Targeting
		Signal Sequences for Nuclear Transport Are Not Removed
		Bacteria Also Use Signal Sequences for Protein Targeting
	Unanswered Questions
	How We Know
		The Ribosome Is a Ribozyme
		Ribosomes Check the Accuracy of Codon-Anticodon Pairing, but Not the Identity of the Amino Acid
	Key Terms
	Problems
	Data Analysis Problems
	Additional Reading
Part IV: Regulation
19 Regulating the Flow of Information
	Moment of Discovery
	19.1: Regulation of Transcription Initiation
		Activators and Repressors Control RNA Polymerase Function at a Promoter
		Transcription Factors Can Function by DNA Looping
		Regulators Often Work Together for Signal Integration
		Gene Expression Is Regulated through Feed back Loops
		Related Sets of Genes Are Often Regulated Together
		Eukaryotic Promoters Use More Regulators Than Bacterial Promoters
		Multiple Regulators Provide Combinatorial Control
		Regulation by Nucleosomes Is Specific to Eukaryotes
	19.2: The Structural Basis of Transcriptional Regulation
		Transcription Factors Interact with DNA and Proteins through Structural Motifs
		Transcription Activators Have Separate DNA Binding and Regulatory Domains
	19.3: Posttranscriptional Regulation of Gene Expression
		Some Regulatory Mechanisms Act on the Nascent RNA Transcript
		Small RNAs Sometimes Affect mRNA Stability
		Some Genes Are Regulated at the Level of Translation
		Some Covalent Modifications Regulate Protein Function
		Gene Expression Can Be Regulated by Intracellular Localization
		HIGHLIGHT 19-1: Medicine. Insulin Regulation: Control by Phosphorylation
		Protein Degradation by Ubiquitination Modulates Gene Expression
	Unanswered Questions
	How We Know
		Plasmids Have the Answer to Enhancer Action
	Key Terms
	Problems
	Data Analysis Problem
	Additional Reading
20 The Regulation of Gene Expression in Bacteria
	Moment of Discovery
	20.1: Transcriptional Regulation
		The lac Operon Is Subject to Negative Regulation
		The lac Operon Also Undergoes Positive Regulation
		HIGHLIGHT 20-1: Technology. Classical Techniques in the Analysis of Gene Regulation
		CRP Functions with Activators or Repressors to Control Gene Transcription
		Transcription Attenuation Often Controls Amino Acid Biosynthesis
		The SOS Response Leads to Coordinated Transcription of Many Genes
	20.2: Beyond Transcription: Control of Other Steps in the Gene Expression Pathway
		RNA Sequences or Structures Can Control Gene Expression Levels
		Translation of Ribosomal Proteins Is Coordinated with rRNA Synthesis
		HIGHLIGHT 20-2: A Closer Look. T-Box Riboswitches
	20.3: Control of Gene Expression in Bacteriophages
		Bacteriophage Propagation Can Take One of Two Forms
		Differential Activation of Promoters Regulates Bacteriophage λ Infection
		The λ Repressor Functions as Both an Activator and a Repressor
		More Regulation Levels Are Invoked during the Bacteriophage λ Life Cycle
	Unanswered Questions
	How We Know
		TRAPped RNA Inhibits Expression of Tryptophan Biosynthetic Genes in Bacillus subtilis
		Autoinducer Analysis Reveals Possibilities for Blocking Cholera Infection
	Key Terms
	Problems
	Data Analysis Problem
	Additional Reading
21 The Transcriptional Regulation of Gene Expression in Eukaryotes
	Moment of Discovery
	21.1: Basic Mechanisms of Eukaryotic Transcriptional Activation
		Eukaryotic Transcription Is Regulated by Chromatin Structure
		Positive Regulation of Eukaryotic Promoters Involves Multiple Protein Activators
		HIGHLIGHT 21-1: A Closer Look. The Intertwining of Transcription and mRNA Splicing
		Transcription Activators and Coactivators Help Assemble General Transcription Factors
	21.2: Combinatorial Control of Gene Expression
		Combinatorial Control of the Yeast GAL Genes Involves Positive and Negative Regulation
		HIGHLIGHT 21-2: Technology. Discovering and Analyzing DNA-Binding Proteins
		Yeast Mating-Type Switches Result from Combinatorial Control of Transcription
		Combinatorial Mixtures of Heterodimers Regulate Transcription
		Differentiation Requires Extensive Use of Combinatorial Control
	21.3: Transcriptional Regulation Mechanisms Unique to Eukaryotes
		Insulators Separate Adjacent Genes in a Chromosome
		Some Activators Assemble into Enhanceosomes
		Gene Silencing Can Inactivate Large Regions of Chromosomes
		Imprinting Enables Selective Gene Expression from One Allele Only
		HIGHLIGHT 21-3: A Closer Look. Gene Silencing by Small RNAs
		Dosage Compensation Balances Gene Expression from Sex Chromosomes
		Steroid Hormones Bind Nuclear Receptors That Regulate Gene Expression
		Nonsteroid Hormones Control Gene Expression by Triggering Protein Phosphorylation
	Unanswered Questions
	How We Know
		Transcription Factors Bind Thousands of Sites in the Fruit Fly Genome
		Muscle Tissue Differentiation Reveals Surprising Plasticity in the Basal Transcription Machinery
	Key Terms
	Problems
	Data Analysis Problem
	Additional Reading
22 The Posttranscriptional Regulation of Gene Expression in Eukaryotes
	Moment of Discovery
	22.1: Posttranscriptional Control inside the Nucleus
		Alternative Splicing Controls Sex Determination in Fruit Flies
		Multiple mRNA Cleavage Sites Allow the Production of Multiple Proteins
		Nuclear Transport Regulates Which mRNAs Are Selected for Translation
	22.2: Translational Control in the Cytoplasm
		Initiation Can Be Down-Regulated by Phosphorylation of eIF2
		The 3\'UTR of Some mRNAs Controls Translational Efficiency
		Upstream Open Reading Frames Control the Translation of GCN4 mRNA
		Translational Efficiency Can Be Controlled by mRNA Degradation Rates
	22.3: The Large-Scale Regulation of Groups of Genes
		Some Sets of Genes Are Regulated by Pre-mRNA Splicing in the Nucleus
		5\'UTRs and 3\'UTRs Coordinate the Translation of Multiple mRNAs
		Conserved AU-Rich Elements in 3\'UTRs Control Global mRNA Stability for Some Genes
		HIGHLIGHT 22-1: Evolution. Regulation of Splicing in Response to Stress
	22.4: RNA Interference
		MicroRNAs Encoded in Eukaryotic Genomes Target mRNAs for Gene Silencing
		Short Interfering RNAs Target mRNAs for Degradation
		RNAi Pathways Regulate Viral Gene Expression
		RNAi Provides a Useful Tool for Molecular Biologists
		HIGHLIGHT 22-2: Medicine. Viral Takeover Using a Cell Type–Specific miRNA
	22.5: Putting It All Together: Gene Regulation in Development
		Development Depends on Asymmetric Cell Divisions and Cell-Cell Signaling
		Early Development Is Mediated by Maternal Genes
		Segmentation Genes Specify the Development of Body Segments and Tissues
		Homeotic Genes Control the Development of Organs and Appendages
		Stem Cells Have Developmental Potential That Can Be Controlled
	22.6: Finale: Molecular Biology, Developmental Biology, and Evolution
		The Interface of Evolutionary Biology and Developmental Biology Defines a New Field
		Small Genetic Differences Can Produce Dramatic Phenotypic Changes
	Unanswered Questions
	How We Know
		A Natural Collaboration Reveals a Binding Protein for a 3\'UTR
		Little RNAs Play a Big Role in Controlling Gene Expression
		Everything Old Is New Again: Beauty at the Turn of a Developmental Switch
	Key Terms
	Problems
	Data Analysis Problem
	Additional Reading
Appendix: Model Organisms
	A Few Organisms Are Models for Understanding Common Life Processes
	Three Approaches Are Used to Study Human Disease
	Bacterium, Escherichia coli
		Early Studies of E. coli as a Model Organism
		Life Cycle
		Genetic Techniques
		E. coli as a Model Organism Today
	Budding Yeast, Saccharomyces cerevisiae
		Early Studies of Yeast as a Model Organism
		Life Cycle
		Genetic Techniques
		Yeast as a Model Organism Today
	Bread Mold, Neurospora crassa
		Early Studies of Neurospora as a Model  Organism
		Life Cycle
		Genetic Techniques
		Neurospora as a Model Organism Today
	Nematode, Caenorhabditis elegans
		Early Studies of C. elegans as a Model Organism
		Life Cycle
		Genetic Techniques
		C. elegans as a Model Organism Today
	Mustard Weed, Arabidopsis thaliana
		Early Studies of Arabidopsis as a Model Organism
		Life Cycle
		Genetic Techniques
		Arabidopsis as a Model Organism Today
	Fruit Fly, Drosophila melanogaster
		Early Studies of Drosophila as a Model Organism
		Life Cycle
		Genetic Techniques
		Drosophila as a Model Organism Today
	House Mouse, Mus musculus
		Early Studies of the Mouse as a Model Organism
		Life Cycle
		Genetic Techniques
		The Mouse as a Model Organism Today
Glossary
Appendix: Solutions to Problems
	Chapter 2
	Chapter 3
	Chapter 4
	Chapter 5
	Chapter 6
	Chapter 7
	Chapter 8
	Chapter 9
	Chapter 10
	Chapter 11
	Chapter 12
	Chapter 13
	Chapter 14
	Chapter 15
	Chapter 16
	Chapter 17
	Chapter 18
	Chapter 19
	Chapter 20
	Chapter 21
	Chapter 22
Index