Molecular Biology

Cover
Molecular Biology
Copyright
Dedication
Preface to Third Edition
	Changes in the Third Edition
	Online Materials
Acknowledgments
Unit 1: Basic Chemical and Biological Principles
1 Cells and Organisms
	1 What Is Life?
	2 Living Creatures Are Made of Cells
		2.1 Essential Properties of a Living Cell
		2.2 Prokaryotic Cells Lack a Nucleus
	3 Eubacteria and Archaea Are Genetically Distinct
	4 Eukaryotic Cells Are Subdivided Into Compartments
	5 The Diversity of Eukaryotes
	6 Haploidy, Diploidy, and the Eukaryote Cell Cycle
	7 Organisms Are Classified
	8 Some Widely Studied Organisms Serve as Models
		8.1 Bacteria Are Used for Fundamental Studies of Cell Function
		8.2 Escherichia coli Is a Model Bacterium
		8.3 Yeast Is a Widely Studied Single-Celled Eukaryote
		8.4 A Roundworm and a Fly Are Model Multicellular Animals
		8.5 Zebrafish and Xenopus Are Used to Study Vertebrate Development
		8.6 Mouse and Man
		8.7 Arabidopsis Serves as a Model for Plants
	9 Basic Characteristics of a Model Organism
	10 Purifying DNA From Model Organisms
	11 Viruses Are Not Living Cells
	12 Bacterial Viruses Infect Bacteria
	13 Human Viral Diseases Are Common
	14 A Variety of Subcellular Genetic Entities Exist
	Review Questions
	Further Reading
2 Basic Genetics
	1 Gregor Mendel, the Father of Classical Genetics
	2 Genes Determine Each Step in Biochemical Pathways
	3 Mutants Result From Alterations in Genes
	4 Phenotypes and Genotypes
	5 Chromosomes Are Long, Thin Molecules That Carry Genes
		5.1 Different Organisms May Have Different Numbers of Chromosomes
	6 Dominant and Recessive Alleles
		6.1 Partial Dominance, Co-Dominance, Penetrance, and Modifier Genes
	7 Genes From Both Parents Are Mixed by Sexual Reproduction
		7.1 Sex Determination and Sex-Linked Characteristics
	8 Neighboring Genes Are Linked During Inheritance Unless the DNA Recombines
		8.1 Recombination During Meiosis Ensures Genetic Diversity
	9 Identifying Genes That Cause Human Diseases
	Review Questions
	Further Reading
3 Nucleic Acids and Proteins
	1 History of DNA as the Genetic Material
	2 Nucleic Acid Molecules Carry Genetic Information
	3 Chemical Structure of Nucleic Acids
		3.1 DNA and RNA Each Have Four Bases
		3.2 Nucleosides are Bases Plus Sugars; Nucleotides are Nucleosides Plus Phosphate
	4 Double-Stranded DNA Forms a Double Helix
		4.1 Base Pairs are Held Together by Hydrogen Bonds
		4.2 Complementary Strands Reveal the Secret of Heredity
		4.3 Melting Separates DNA Strands; Cooling Anneals Them
	5 Constituents of Chromosomes
	6 The Central Dogma Outlines the Flow of Genetic Information
	7 Ribosomes Read the Genetic Code
		7.1 The Genetic Code Dictates the Amino Acid Sequence of Proteins
	8 Various Classes of RNA Have Different Functions
	9 Proteins Carry Out Many Cell Functions
		9.1 The Structure of Proteins Has Four Levels of Organization
		9.2 Proteins Vary in Their Biological Roles
		9.3 Protein Structure is Elucidated by X-Ray Crystallography
	Review Questions
	Further Reading
4 Genes, Genomes, and DNA
	1 Overview of Genome Organization
		1.1 Genome Organization of Viruses and Prokaryotes
		1.2 Some Bacteria Are Polyploid
		1.3 Genome Organization of Organelles and Symbionts
	2 The Eukaryotic Genome
		2.1 General Structure of Eukaryotic Genomes
		2.2 Repeated Sequences Are a Feature of Eukaryotic DNA
		2.3 Satellite DNA Is Noncoding DNA in the Form of Tandem Repeats
		2.4 Minisatellites and VNTRs
	3 Palindromes, Inverted Repeats, and Stem and Loop Structures
	4 Purine Rich DNA Structures
		4.1 Multiple A-Tracts Cause DNA to Bend
		4.2 The G-Quadruplex
	5 Supercoiling Is Necessary to Package Bacterial DNA
		5.1 Topoisomerases and DNA Gyrase
		5.2 Catenated and Knotted DNA Must Be Corrected
		5.3 Local Supercoiling
		5.4 Supercoiling Affects DNA Structure
	6 Separation of DNA Fragments by Electrophoresis
	7 Alternative Helical Structures of DNA Occur
	8 Packaging DNA in Eukaryotic Nuclei
	Review Questions
	Further Reading
5 Manipulation of Nucleic Acids
	1 Cutting and Rejoining DNA
		1.1 Restriction and Modification of DNA
		1.2 Recognition of DNA by Restriction Endonucleases
		1.3 Naming of Restriction Enzymes
		1.4 Cutting of DNA by Restriction Enzymes
		1.5 DNA Fragments Are Joined by DNA Ligase
		1.6 Making a Restriction Map
		1.7 Restriction Fragment Length Polymorphisms (RFLPs)
	2 Chemical Synthesis of DNA
		2.1 Chemical Synthesis of Complete Genes
		2.2 Peptide Nucleic Acid
		2.3 Other Nucleic Acid Mimics
	3 Measuring DNA and RNA Concentration With Ultraviolet Light
	4 Radioactive Labeling of Nucleic Acids
		4.1 Detection of Radioactively Labeled DNA
	5 Fluorescence in the Detection of DNA and RNA
		5.1 Chemical Tagging With Biotin or Digoxigenin
	6 The Electron Microscope
	7 Hybridization of DNA and RNA
		7.1 Southern, Northern, and Western Blotting
		7.2 Zoo Blotting
		7.3 Fluorescence in Situ Hybridization (FISH)
	Review Questions
	Further Reading
Unit 2: The Genome
6 Polymerase Chain Reaction
	1 Fundamentals of PCR
		1.1 Cycling Through PCR
		1.2 PCR Primers
		1.3 Alternative Polymerases
	2 Preventing Mispriming
	3 Adding Sequences to PCR Amplicons
	4 Degenerate PCR Primers
	5 Inverse PCR
	6 Reverse Transcriptase PCR
	7 PCR in Genetic Engineering
	8 Directed Mutagenesis
	9 Engineering Deletions and Insertions by PCR
	10 Real-Time PCR or Quantitative PCR (qPCR)
	11 Molecular Beacons
	12 Use of PCR in Forensics
	13 PCR in Medical Diagnosis
	14 Environmental DNA (eDNA) Analysis by PCR
	15 Rescuing DNA From Extinct Life Forms by PCR
	Review Questions
	Further Reading
7 Cloning Genes for Synthetic Biology
	1 Properties of Cloning Vectors
		1.1 Plasmid Vectors
			1.1.1 Origin of Replication
			1.1.2 Promoters
			1.1.3 Terminator/PolyA Sequences
	2 Adding Inserts to a Vector
		2.1 Restriction Enzyme Cloning
		2.2 TA Cloning of Polymerase Chain Reaction (PCR) Products
		2.3 Recombineering Increases the Speed of Gene Cloning
		2.4 Isothermal or Gibson DNA Assembly
		2.5 Gateway Cloning
	3 Adding Vectors to Host Organisms With Transformation
	4 Detecting Inserts in Vectors
		4.1 Reporter Genes
		4.2 Blue/White Color Screening
		4.3 CcdB, a Toxin That Kills Bacteria Without an Insert
		4.4 Selection/Counterselection Using GalK
	5 Types of Cloning Vectors
		5.1 Moving Genes Among Organisms: Shuttle Vectors
		5.2 Bacteriophage Lambda Vectors
		5.3 Cosmid Vectors
		5.4 Yeast Artificial Chromosomes
		5.5 Bacterial and P1 Artificial Chromosomes
		5.6 Expression Vectors
		5.7 Mammalian Expression Vectors
	6 Synthetic Biology Standardizes Vector Construction
	7 A DNA Library Is a Collection of Genes
		7.1 Screening DNA Libraries
		7.2 Cloning Complementary DNA Avoids Introns
	Review Questions
	Further Reading
8 DNA Sequencing
	1 DNA Sequencing—Overview of Chain Termination Sequencing
		1.1 Details of the Chain Termination Method for Sequencing DNA
		1.2 DNA Polymerases for Sequencing DNA
	2 Automated Sequencing
	3 Next Generation Sequencing
		3.1 Illumina Sequencing by Synthesis
			3.1.1 Library Preparation
			3.1.2 Partitioning the Library and Cluster Generation
			3.1.3 Sequencing by Synthesis
			3.1.4 Analyzing NGS Data
		3.2 Ion Torrent Sequencing Technology
			3.2.1 Library Preparation and Partitioning of the Library Fragments
			3.2.2 Sequencing by Synthesis on the Ion Torrent Platform
	4 Targeted Sequencing
	5 Third-Generation Sequencing
		5.1 Nanopore Detectors for DNA
		5.2 Long Reads From SMRT Sequencing
	6 DNA Microarrays for Sequence Analysis
	Review Questions
	Further Reading
9 Genomics and Systems Biology
	1 Large-Scale Mapping With Sequence Tags
	2 Assembling Genomes by Shotgun Sequencing
	3 Assembling the Human Genome
	4 Survey of the Human Genome
		4.1 Sequence Polymorphisms: SSLPs and SNPs
		4.2 Gene Identification by Exon Trapping
		4.3 The Evolution of “Junk” DNA
	5 Personal Genomics and Pharmacogenomics
		5.1 Pharmacogenomics
		5.2 Personal Genomics
	6 Bioinformatics and Computer Analysis
		6.1 Systems Biology
	7 Metagenomics and Community Sampling
		7.1 Bacterial Metagenomics
		7.2 The Human Microbiome
	Review Questions
	Further Reading
Unit 3: The Central Dogma of Molecular Biology
10 Cell Division and DNA Replication
	1 Cell Division and Reproduction Are Not Always Identical
	2 DNA Replication Occurs at the Replication Fork
		2.1 Supercoiling Causes Problems for Replication
		2.2 Strand Separation Precedes DNA Synthesis
	3 Properties of DNA Polymerase
	4 Nucleotides Are the Precursors for DNA Synthesis
	5 DNA Polymerase Elongates DNA Strands
	6 The Complete Replication Fork Is Complex
	7 Discontinuous Synthesis of the Lagging Strand
		7.1 Completing the Lagging Strand
	8 Chromosome Replication Initiates at oriC
		8.1 DNA Methylation and Membrane Attachment Control Initiation of Replication
	9 Chromosome Replication Terminates at terC
		9.1 Disentangling the Daughter Chromosomes
	10 Cell Division in Bacteria Occurs After Chromosome Replication
		10.1 How Long Does It Take for Bacteria to Replicate?
	11 The Concept of the Replicon
	12 Replicating Linear DNA in Eukaryotes
		12.1 Eukaryotic Chromosomes Have Multiple Origins
		12.2 Synthesis of Eukaryotic DNA
		12.3 Histones are Remodeled and Replaced During Replication
	13 Cell Division in Higher Organisms
	Review Questions
	Further Reading
11 Transcription of Genes
	1 Genes Are Expressed by Making RNA
		1.1 Short Segments of the Chromosome Are Turned Into Messages
		1.2 Terminology: Cistrons, Coding Sequences, and Open Reading Frames
	2 How Is the Beginning of a Gene Recognized?
	3 Manufacturing the Message
	4 RNA Polymerase Knows Where to Stop
	5 How Does the Cell Know Which Genes to Turn On?
		5.1 What Activates the Activator?
		5.2 Negative Regulation Results From the Action of Repressors
		5.3 Many Regulator Proteins Bind Small Molecules and Change Shape
	6 Transcription in Eukaryotes Is More Complex
		6.1 Transcription of rRNA and tRNA in Eukaryotes
		6.2 Transcription of Protein-Encoding Genes in Eukaryotes
		6.3 Upstream Elements Increase the Efficiency of RNA Polymerase II Binding
		6.4 Enhancers Control Transcription at a Distance
	7 Transcription in Archaea
	Review Questions
	Further Reading
12 Processing of RNA
	1 RNA Is Processed in Several Ways
	2 Coding and Noncoding RNA
	3 Processing of Ribosomal and Transfer RNA
	4 Eukaryotic Messenger RNA Contains a Cap and a Tail
		4.1 Capping Is the First Step in Maturation of Eukaryotic mRNA
		4.2 A Poly(A) Tail Is Added to Eukaryotic mRNA
	5 Introns Are Removed From RNA by Splicing
		5.1 Different Classes of Intron Show Different Splicing Mechanisms
		5.2 R-Loop Analysis Determines Intron and Exon Boundaries
	6 Alternative Splicing Produces Multiple Forms of RNA
		6.1 Alternative Promoter Selection
		6.2 Alternative Tail Site Selection
		6.3 Alternative Splicing by Exon Cassette Selection
		6.4 Trans-Splicing
	7 Inteins and Protein Splicing
	8 Base Modification of rRNA Requires Guide RNA
	9 RNA Editing Alters the Base Sequence
	10 Transport of RNA Out of the Nucleus
	11 Degradation of mRNA
		11.1 Nonsense-Mediated Decay of mRNA
	Review Questions
	Further Reading
13 Protein Synthesis
	1 Overview of Protein Synthesis
	2 Proteins Are Chains of Amino Acids
		2.1 Twenty Amino Acids Form Biological Polypeptides
	3 Decoding the Genetic Information
		3.1 Transfer RNA Forms a Folded “L” Shape With Modified Bases
		3.2 Some tRNA Molecules Read More Than One Codon
		3.3 Charging the tRNA with the Amino Acid
	4 The Ribosome: The Cell’s Decoding Machine
	5 Three Possible Reading Frames Exist
		5.1 The Start Codon Is Chosen
		5.2 The Initiation Complex Assembles
	6 The tRNA Occupies Three Sites During Elongation of the Polypeptide
		6.1 Termination of Translation and Ribosome Recycling
		6.2 Several Ribosomes Usually Read the Same Message at Once
	7 Bacterial mRNA Can Code for Several Proteins
		7.1 Transcription and Translation Are Coupled in Bacteria
	8 Some Ribosomes Become Stalled and Are Rescued
	9 Differences Between Eukaryotic and Prokaryotic Protein Synthesis
		9.1 Initiation, Elongation, and Termination of Protein Synthesis in Eukaryotes
	10 Protein Synthesis Is Halted When Resources Are Scarce
	11 A Signal Sequence Marks a Protein for Export From the Cell
		11.1 Molecular Chaperones Oversee Protein Folding
	12 Protein Synthesis Occurs in Mitochondria and Chloroplasts
		12.1 Proteins Are Imported Into Mitochondria and Chloroplasts by Translocases
	13 Mistranslation Usually Results in Mistakes in Protein Synthesis
	14 Many Antibiotics Work by Inhibiting Protein Synthesis
	15 Post-Translational Modifications of Proteins
	16 Selenocysteine and Pyrrolysine: Rare Amino Acids
	17 Degradation of Proteins
	Review Questions
	Further Reading
14 Protein Structure and Function
	1 The Structure of Proteins Reflects Four Levels of Organization
		1.1 The Secondary Structure of Proteins Relies on Hydrogen Bonds
		1.2 The Tertiary Structure of Proteins
		1.3 A Variety of Forces Maintain the 3D Structure of Proteins
		1.4 Cysteine Forms Disulfide Bonds
		1.5 Multiple Folding Domains in Larger Proteins
		1.6 Quaternary Structure of Proteins
		1.7 Co-factors and Metal Ions are Often Associated with Proteins
	2 Determining Protein Structures
	3 Nucleoproteins, Lipoproteins, and Glycoproteins are Conjugated Proteins
	4 Proteins Serve Numerous Cellular Functions
	5 Protein (Nano)-Machines
	6 Enzymes Catalyze Metabolic Reactions
		6.1 Enzymes Have Varying Specificities
		6.2 Enzymes Act by Lowering the Energy of Activation
		6.3 The Rate of Enzyme Reactions
		6.4 Substrate Analogs and Enzyme Inhibitors Act at the Active Site
		6.5 Enzymes May Be Directly Regulated
		6.6 Allosteric Enzymes are Affected by Signal Molecules
		6.7 Enzymes May Be Controlled by Chemical Modification
	7 Binding of Proteins to DNA Occurs in Several Different Ways
	8 Denaturation of Proteins
	Review Questions
	Further Reading
15 Proteomics: The Global Analysis of Proteins
	1 The Proteome
		1.1 Isolating and Quantifying Proteins
		1.2 Gel Electrophoresis of Proteins
		1.3 2D-PAGE of Proteins
	2 Antibodies Are Essential Proteomics Tools
	3 Western Blotting of Proteins
	4 Isolating Proteins With Chromatography
	5 Mass Spectrometry for Protein Identification
	6 Protein-Tagging Systems
		6.1 Full-Length Proteins Used as Fusion Tags
		6.2 Self-Cleavable Intein Tags
	7 Selection by Phage Display
	8 Protein Interactions
		8.1 The Yeast Two-Hybrid System
		8.2 Modified Two-Hybrid Systems Address the Limitations of the Yeast Two-Hybrid System
		8.3 Protein Fragment Complementation Can Provide Quantitative Data on Protein Interactions
		8.4 Protein Interaction Systems in Non-Yeast Organisms
		8.5 Co-Immunoprecipitation to Identify Mammalian Protein Interactions
	9 Protein Arrays
	10 Metabolomics
	Review Questions
	Further Reading
Unit 4: Regulating Gene Expression
16 Regulation of Transcription in Prokaryotes
	1 Gene Regulation Ensures a Physiological Response
	2 Regulation at the Level of Transcription Involves Several Steps
	3 Alternative Sigma Factors Recognize Different Sets of Genes
		3.1 Heat Shock Sigma Factors Are Regulated by Temperature
		3.2 Cascades of Alternative Sigma Factors Occur in Bacillus Spore Formation
		3.3 Antisigma Factors Inactivate Sigma
		3.4 Small Noncoding 6S RNA Regulates RNA Polymerase
	4 Activators, Repressors and Operons
		4.1 The Operon Model of Gene Regulation
		4.2 Some Proteins May Act As Both Repressors and Activators
		4.3 Nature of the Signal Molecule
		4.4 Activators and Repressors May Be Covalently Modified
	5 Two-Component Regulatory Systems
		5.1 Phosphorelay Systems
	6 Specific Versus Global Control
		6.1 Crp Protein Is an Example of a Global Control Protein
		6.2 Regulatory Nucleotides
		6.3 Quorum Sensing
	7 Accessory Factors and Nucleoid-Binding Proteins
		7.1 Action at a Distance and DNA Looping
	8 Antitermination As a Control Mechanism
	Review Questions
	Further Reading
17 Regulation of Transcription in Eukaryotes
	1 Transcriptional Regulation in Eukaryotes Is More Complex Than in Prokaryotes
	2 Specific Transcription Factors Regulate Protein-Encoding Genes
		2.1 The Mediator Complex Transmits Information to RNA Polymerase
		2.2 Enhancers and Insulator Sequences Segregate DNA Functionally
		2.3 Matrix Attachment Regions Allow DNA Looping
	3 Negative Regulation of Transcription in Eukaryotes
	4 Heterochromatin Blocks Access to DNA in Eukaryotes
		4.1 The Histone Code
	5 Methylation of Eukaryotic DNA Controls Gene Expression
		5.1 Silencing of Genes Is Caused by DNA Methylation
		5.2 Genetic Imprinting in Eukaryotes Is Due to DNA Methylation Patterns
	Review Questions
	Further Reading
18 Regulation of Protein Synthesis
	1 Regulation at the Level of mRNA
	2 Regulation by Cleavage of mRNA
		2.1 Binding of Proteins Controls the Rate of mRNA Degradation
		2.2 Some mRNA Molecules Must Be Cleaved Before Translation
	3 Regulation by mRNA-Binding Proteins
		3.1 Some Regulatory Proteins Cause Translational Repression
		3.2 Some Regulatory Proteins Activate Translation
		3.3 Regulation of Translation by Alterations to the Ribosome
	4 Regulation by Antisense RNA
	5 Regulation by mRNA Upstream and Downstream Regions
		5.1 Role of the 5′-Untranslated Region and Upstream ORFs
		5.2 Effects of the mRNA 3′-Untranslated Region
	6 Premature Termination Causes Attenuation of Transcription
	7 Riboswitches—RNA Acting Directly As a Control Mechanism
	8 Regulation of mRNA by Methylation
	Review Questions
	Further Reading
19 Noncoding RNA
	1 Survey of RNA Classes
	2 Ribozymes and the Enzyme Activity of RNA
	3 RNA in Prokaryotes Versus Eukaryotes
	4 Short Regulatory RNA
	5 tRNA Fragments
	6 Long Noncoding RNA
	7 Circular RNA
	Review Questions
	Further Reading
20 Genome Defense
	1 Introduction to Genome Defense
	2 The Multifaceted Approach to Defending the Genome
	3 Principles of RNA Interference (RNAi)
		3.1 Sources of Double-Stranded RNA That Trigger RNAi
		3.2 MicroRNA Is Short Regulatory RNA
		3.3 Piwi-Interacting RNA (piRNA)
		3.4 Dicer Cuts Double-Stranded RNA Into Small RNAs
		3.5 The Argonaut Family of Proteins Destroys the Target mRNA
		3.6 Amplification and Spread of RNAi
	4 Delivery of siRNA and Applications of RNAi
	5 CRISPR: Antiviral Defense in Bacteria
		5.1 Principle of CRISPR
	6 CRISPR Systems Are Functionally and Structurally Classified
		6.1 Class 1 Systems Use Multiprotein Effector Complexes
		6.2 Class 2 Systems Require Only Single Effector Proteins
	7 Applications Using CRISPR
		7.1 Applications of CRISPR/Cas Systems in Bacteria, Fungi, and Algae Improve Sustainable Energy and Biofuels Research
		7.2 CRISPR Technology Improves Crop Plants
		7.3 CRISPR Technology in Drosophila Identifies Developmental Networks
		7.4 CRISPR Impacts Human Health Through Several Mechanisms
	8 Other Genome Editing Tools
	Review Questions
	Further Reading
21 Analysis of Gene Expression
	1 Monitoring Gene Expression
	2 Reporter Genes for Monitoring Gene Expression
		2.1 Easily Assayable Enzymes as Reporters
		2.2 Light Emission by Luciferase As a Reporter System
		2.3 Green Fluorescent Protein As Reporter
		2.4 Gene Fusions
	3 Deletion Analysis of the Upstream Region
		3.1 Locating Protein-Binding Sites in the Upstream Region
	4 DNA-Protein Complexes Can Be Isolated by Chromatin Immunoprecipitation
	5 Location of the Start of Transcription by Primer Extension
		5.1 Location of the Start of Transcription by S1 Nuclease
	6 Transcriptome Analysis
		6.1 Assessing the Purity of RNA
		6.2 Differential Display PCR Provides Relative Expression Profiles
		6.3 RNA-Seq Simultaneously Quantifies Expression and Maps the Transcriptome
		6.4 Single-Cell RNA-Seq Captures Transcription Profiles of a Single Cell
	7 DNA Microarrays for Gene Expression
	8 TaqMan Quantitative PCR to Assay Gene Expression
	9 Serial Analysis of Gene Expression (SAGE)
	Review Questions
	Further Reading
22 Epigenetics and Epigenomics
	1 Defining Epigenetics and Epigenomics
	2 Epigenetics of Bacteria
	3 Methylation of DNA
	4 Protein and RNA-Based Epigenetic Regulation
		4.1 Protein Based Mechanisms
		4.2 RNA Based Mechanisms
	5 Structural Inheritance
		5.1 Bioelectric Fields
	6 Epigenetics of Humans and Other Mammals
		6.1 X Chromosome Inactivation in Female Mammals
	7 Epigenetics of Insects
	8 Epigenetics of Plants
	9 Epigenetics of Protozoa
	Review Questions
	Further Reading
Unit 5: Subcellular Genetic Elements
23 Plasmids
	1 Plasmids As Replicons
	2 General Properties of Plasmids
		2.1 Plasmid Families and Incompatibility
		2.2 Occasional Plasmids Are Linear or Made of RNA
	3 Plasmid DNA Replicates by Two Alternative Methods
		3.1 Plasmid Partition Systems
		3.2 Control of Copy Number by Antisense RNA
		3.3 Plasmid Addiction and Host-Killing Functions
	4 Many Plasmids Help Their Host Cells
		4.1 Antibiotic Resistance Plasmids
		4.2 Resistance to Beta-Lactam Antibiotics
		4.3 Resistance to Chloramphenicol
		4.4 Resistance to Aminoglycosides
		4.5 Resistance to Tetracycline
		4.6 Resistance to Sulfonamides and Trimethoprim
	5 Plasmids May Provide Aggressive Characters
		5.1 Most Colicins Kill by One of Two Different Mechanisms
		5.2 Bacteria Are Immune to Their Own Colicins
		5.3 Colicin Synthesis and Release
		5.4 Virulence Plasmids
	6 Ti Plasmids Are Transferred From Bacteria to Plants
	7 The 2Micron Plasmid of Yeast
	8 Certain DNA Elements May Behave As Viruses or Plasmids
	Review Questions
	Further Reading
24 Viruses, Viroids, and Prions
	1 Viruses Are Infectious Packages of Genetic Information
		1.1 Lifecycle of a Virus
		1.2 Bacterial Viruses Are Known as Bacteriophage
		1.3 Lysogeny or Latency by Integration
	2 The Classification of Viruses
	3 The Great Diversity of Viruses
		3.1 Small Single-Stranded DNA Viruses of Bacteria
		3.2 Complex Bacterial Viruses With Double-Stranded DNA
		3.3 DNA Viruses of Higher Organisms
	4 Giant Viruses
	5 Viruses With RNA Genomes Have Very Few Genes
		5.1 Bacterial RNA Viruses
		5.2 Double-Stranded RNA Viruses of Animals
		5.3 Positive-Stranded RNA Viruses Make Polyproteins
		5.4 Strategy of Negative-Strand RNA Viruses
		5.5 Plant RNA Viruses
	6 Retroviruses Use Both RNA and DNA
		6.1 Life Cycle of the Retrovirus
		6.2 Genome of the Retrovirus
	7 Subviral Infectious Agents
		7.1 Satellite Viruses
		7.2 Viroids Are Naked Molecules of Infectious RNA
	8 Prions Are Infectious Proteins
		8.1 Mammalian Prions Cause Disease of the Nervous System
		8.2 Yeast Prions Control Environmental Responses
		8.3 Neurological Diseases and Prionoids
	Review Questions
	Further Reading
25 Mobile DNA
	1 Subcellular Genetic Elements As Gene Creatures
	2 Most Mobile DNA Consists of Transposable Elements
		2.1 The Essential Parts of a DNA Transposon
		2.2 Movement by Conservative Transposition
		2.3 Complex Transposons Move by Replicative Transposition
		2.4 Replicative and Conservative Transposition Are Related
		2.5 Insertion Sequences—the Simplest Transposons
		2.6 Composite Transposons
		2.7 Transposition May Rearrange Host DNA
		2.8 Transposons in Higher Life Forms
	3 Retroelements Make an RNA Copy
		3.1 Repetitive DNA of Mammals
		3.2 Retro-Insertion of Host-Derived DNA
		3.3 Retrons Encode Bacterial Reverse Transcriptase
	4 The Multitude of Transposable Elements
	5 Hybrids Combine Properties of Multiple Genetic Elements
		5.1 Mu Is Both a Transposon and a Bacteriophage
		5.2 Conjugative Transposons
	6 Mobile DNA That Is Not Transposable
		6.1 Integrons Collect Genes for Transposons
		6.2 Homing Endonucleases
	7 Junk DNA and Selfish DNA
		7.1 Selfish DNA Evolves Into Junk DNA
		7.2 Putting Junk DNA to Work
	Review Questions
	Further Reading
Unit 6: Changing the DNA Blueprint
26 Mutations and Repair
	1 Mutations Alter the DNA Sequence
	2 The Major Types of Mutation
		2.1 Base Substitution Mutations
		2.2 Missense Mutations May Have Major or Minor Effects
		2.3 Nonsense Mutations Cause Premature Polypeptide Chain Termination
		2.4 Deletion Mutations Result in Shortened or Absent Proteins
		2.5 Insertion Mutations Commonly Disrupt Existing Genes
		2.6 Frameshift Mutations Sometimes Produce Abnormal Proteins
		2.7 DNA Rearrangements Include Inversions, Translocations, and Duplications
		2.8 Mutations Occur More Frequently at Hotspots
	3 Chemical Mutagens Damage DNA
		3.1 Radiation Causes Mutations
		3.2 Spontaneous Mutations Can Be Caused by DNA Polymerase Errors
		3.3 Mutations Can Result From Mispairing and Recombination
		3.4 Spontaneous Mutation May Result From Tautomerization
		3.5 Spontaneous Mutation Can Be Caused by Inherent Chemical Instability
	4 Overview of DNA Repair
		4.1 DNA Mismatch Repair System
		4.2 General Excision Repair System
		4.3 DNA Repair by Excision of Specific Bases
		4.4 Specialized DNA Repair Mechanisms
		4.5 Photoreactivation Cleaves Thymine Dimers
		4.6 Repair by Recombination
		4.7 SOS Error-Prone Repair in Bacteria
		4.8 Transcriptional Coupling of Repair
		4.9 Repair in Eukaryotes
		4.10 Double-Strand Repair in Eukaryotes
	5 Reversions Are Genetic Alterations That Change the Phenotype Back to Wild Type
		5.1 Reversion Can Occur by Compensatory Changes in Other Genes
		5.2 Altered Decoding by tRNA May Cause Suppression
	6 Site-Directed Mutagenesis
	Review Questions
	Further Reading
27 Recombination
	1 Overview of Recombination
	2 Molecular Basis of Homologous Recombination
		2.1 Single-Strand Invasion and Chi Sites
	3 Site-Specific Recombination
	4 Recombination in Higher Organisms
	5 Gene Conversion
	Review Questions
	Further Reading
28 Bacterial Genetics
	1 Reproduction Versus Gene Transfer
	2 Fate of the Incoming DNA After Uptake
	3 Transformation Is Gene Transfer by Naked DNA
		3.1 Transformation As Proof That DNA Is the Genetic Material
		3.2 Transformation in Nature
	4 Gene Transfer by Virus—Transduction
		4.1 Generalized Transduction
		4.2 Specialized Transduction
	5 Transfer of Plasmids Between Bacteria
		5.1 Transfer of Chromosomal Genes Requires Plasmid Integration
	6 Gene Transfer Among Gram-Positive Bacteria
	7 Archaeal Genetics
	8 Whole-Genome Sequencing
		8.1 Bacterial Genome Assembly and Transplantation
	Review Questions
	Further Reading
29 Molecular Evolution
	1 Getting Started—Formation of the Earth
		1.1 The Early Atmosphere
	2 The Chemical Origin of Life
		2.1 The Miller Experiment
		2.2 Organic Molecules in Outer Space
	3 Origin of Informational Macromolecules
		3.1 Polymerization of Monomers to Give Macromolecules
		3.2 Enzyme Activities of Random Proteinoids
		3.3 Primeval RNA Synthesis
	4 Ribozymes and the RNA World
		RNA Shows Enzymatic Activity
		Details of DNA Synthesis Imply It Emerged After RNA
		RNA Components Take Part in Metabolism
		RNA Plays a Major Role in Regulating Gene Expression
		Genomic RNA Encodes Proteins in Some Viruses
		4.1 The First Cells
	5 The Autotrophic Theory of the Origin of Life
	6 Evolution of DNA and Encoded Proteins
		6.1 Creating New Genes by Duplication
		6.2 Paralogous and Orthologous Sequences
		6.3 Creating New Genes by Shuffling
		6.4 Different Proteins Evolve at Very Different Rates
		6.5 Molecular Clocks to Track Evolution
	7 Ribosomal RNA and the Three Domains
		7.1 Ribosomal RNA—A Slowly Ticking Clock
		7.2 The Archaea Versus the Bacteria
		7.3 Two Domains or Three—The Lokiarchaeota
	8 Symbiotic Origin of Eukaryotic Cells
		8.1 The Genomes of Mitochondria and Chloroplasts
		8.2 Primary and Secondary Endosymbiosis
	9 DNA Sequencing and Biological Classification
		9.1 Mitochondrial DNA—A Rapidly Ticking Clock
		9.2 The African Eve Hypothesis
		9.3 Ancient DNA From Extinct Animals
	10 Evolving Sideways: Horizontal Gene Transfer
		10.1 Problems in Estimating Horizontal Gene Transfer
	Review Questions
	Further Reading
Index