DedicationPreface to second editionAcknowledgementsUNIT 1. Basic Chemical and Biological Principles1. Cells and Organisms1 What Is Life?2 Living Creatures Are Made of Cells3 Eubacteria and Archaea Are Genetically Distinct4 Eukaryotic Cells Are Subdivided into Compartments5 The Diversity of Eukaryotes6 Haploidy, Diploidy, and the Eukaryote Cell Cycle7 Organisms Are Classified8 Some Widely-Studied Organisms Serve as Models9 Basic Characteristics of a Model Organism10 Purifying DNA from Model Organisms11 Viruses Are Not Living Cells12 Bacterial Viruses Infect Bacteria13 Human Viral Diseases Are Common14 A Variety of Subcellular Genetic Entities Exist2. Basic Genetics1 Gregor Mendel, The Father of Classical Genetics2 Genes Determine Each Step in Biochemical Pathways3 Mutants Result from Alterations in Genes4 Phenotypes and Genotypes5 Chromosomes Are Long, Thin Molecules That Carry Genes6 Dominant and Recessive Alleles7 Genes from Both Parents Are Mixed by Sexual Reproduction8 Neighboring Genes Are Linked During Inheritance Unless the DNA Recombines9 Identifying Genes that Cause Human Diseases3. DNA, RNA, and Protein1 History of DNA as the Genetic Material2 Nucleic Acid Molecules Carry Genetic Information3 Chemical Structure of Nucleic Acids4 Double-Stranded DNA Forms a Double Helix5 Constituents of Chromosomes6 The Central Dogma Outlines the Flow of Genetic Information7 Ribosomes Read the Genetic Code8 Various Classes of RNA Have Different Functions9 Proteins Carry Out Many Cell Functions4. Genomes and DNA1 Genome Organization2 Repeated Sequences Are a Feature of Eukaryotic DNA3 Palindromes, Inverted Repeats, and Stem and Loop Structures4 Multiple A-Tracts Cause DNA to Bend5 Supercoiling Is Necessary for Packaging of Bacterial DNA6 Separation of DNA Fragments by Electrophoresis7 Alternative Helical Structures of DNA Occur8 Packaging DNA in Eukaryotic Nuclei5. Manipulation of Nucleic Acids1 Manipulating DNA2 Chemical Synthesis of DNA3 Measuring the Concentration of DNA and RNA with Ultraviolet Light4 Radioactive Labeling of Nucleic Acids5 Fluorescence in the Detection of DNA and RNA6 The Electron Microscope7 Hybridization of DNA and RNAUNIT 2. The Genome6. Polymerase Chain Reaction1 Fundamentals of the Polymerase Chain Reaction2 Inverse PCR3 Randomly Amplified Polymorphic DNA (RAPD)4 Reverse Transcriptase PCR5 Differential Display PCR6 Rapid Amplification of cDNA Ends (RACE)7 PCR in Genetic Engineering8 Directed Mutagenesis9 Engineering Deletions and Insertions by PCR10 Real-Time Fluorescent PCR11 Molecular Beacons and Scorpion Primers12 Use of PCR in Medical Diagnosis13 Environmental Analysis by PCR14 Rescuing DNA from Extinct Life Forms by PCR7. Cloning Genes for Analysis1 Properties of Cloning Vectors2 Detecting Insertions in Vectors3 Moving Genes Between Organisms: Shuttle Vectors4 Bacteriophage Lambda Vectors5 Cosmid Vectors6 Yeast Artificial Chromosomes7 Bacterial and P1 Artificial Chromosomes8 Recombineering Increases the Speed of Gene Cloning9 A DNA Library is a Collection of Genes from One Source10 Cloning Complementary DNA Avoids Introns11 Chromosome Walking12 Cloning by Subtractive Hybridization13 Expression Vectors8. DNA Sequencing1 DNA Sequencing—General Principles for Chain Termination Sequencing2 Primer Walking Along a Strand of DNA3 Automated Sequencing4 Cycle Sequencing5 The Emergence of DNA Chip Technology6 Pyrosequencing7 Second-Generation Sequencing8 Third-Generation Sequencing9 Nanopore Detectors for DNA9. Genomics & Systems Biology1 Large-Scale Mapping with Sequence Tags2 Assembling Small Genomes by Shotgun Sequencing3 Race for the Human Genome4 Survey of the Human Genome5 Pharmacogenomics—Genetically-Individualized Drug Treatment6 Personal Genomics and Comparative Genomics7 Bioinformatics and Computer Analysis8 Systems Biology9 Metagenomics and Community Sampling10 Epigenetics and EpigenomicsUNIT 3. The Central Dogma of Molecular Biology10. Cell Division and DNA Replication1 Cell Division and Reproduction Are Not Always Identical2 DNA Replication Occurs at the Replication Fork3 Properties of DNA Polymerase4 Nucleotides Are the Precursors for DNA Synthesis5 DNA Polymerase Elongates DNA Strands6 The Complete Replication Fork Is Complex7 Discontinuous Synthesis of the Lagging Strand8 Chromosome Replication Initiates at oriC9 Chromosome Replication Terminates at terC10 Cell Division in Bacteria Occurs after Replication of Chromosomes11 The Concept of the Replicon12 Replicating Linear DNA in Eukaryotes13 Cell Division in Higher Organisms11. Transcription of Genes1 Genes Are Expressed by Making RNA2 How Is the Beginning of a Gene Recognized?3 Manufacturing the Message4 RNA Polymerase Knows Where to Stop5 How Does the Cell Know Which Genes to Turn On?6 Transcription in Eukaryotes Is More Complex12. Processing of RNA1 RNA Is Processed in Several Ways2 Coding and Non-Coding RNA3 Processing of Ribosomal and Transfer RNA4 Eukaryotic Messenger RNA Contains a Cap and a Tail5 Introns Are Removed from RNA by Splicing6 Alternative Splicing Produces Multiple Forms of RNA7 Inteins and Protein Splicing8 Base Modification of rRNA Requires Guide RNA9 RNA Editing Alters the Base Sequence10 Transport of RNA out of the Nucleus11 Degradation of mRNA13. Protein Synthesis1 Overview of Protein Synthesis2 Proteins Are Chains of Amino Acids3 Decoding the Genetic Information4 The Ribosome: The Cell’s Decoding Machine5 Three Possible Reading Frames Exist6 The tRNA Occupies Three Sites During Elongation of the Polypeptide7 Bacterial mRNA Can Code for Several Proteins8 Some Ribosomes Become Stalled and Are Rescued9 Differences between Eukaryotic and Prokaryotic Protein Synthesis10 Protein Synthesis Is Halted When Resources Are Scarce11 A Signal Sequence Marks a Protein for Export from the Cell12 Protein Synthesis Occurs in Mitochondria and Chloroplasts13 Mistranslation Usually Results in Mistakes in Protein Synthesis14 Many Antibiotics Work by Inhibiting Protein Synthesis15 Post-Translational Modifications of Proteins16 Selenocysteine and Pyrrolysine: Rare Amino Acids17 Degradation of Proteins14. Protein Structure and Function1 The Structure of Proteins Reflects Four Levels of Organization2 Determining Protein Structures3 Nucleoproteins, Lipoproteins, and Glycoproteins Are Conjugated Proteins4 Proteins Serve Numerous Cellular Functions5 Protein (Nano)-Machines6 Enzymes Catalyze Metabolic Reactions7 Binding of Proteins to DNA Occurs in Several Different Ways8 Denaturation of Proteins15. Proteomics1 The Proteome2 Antibodies Are Essential Proteomics Tools3 Western Blotting of Proteins4 Isolating Proteins with Chromatography5 Mass Spectrometry for Protein Identification6 Protein-Tagging Systems7 Selection by Phage Display8 Protein Interactions: The Yeast Two-Hybrid System9 Protein Interaction by Co-Immunoprecipitation10 Protein Arrays11 MetabolomicsUNIT 4. Regulating Gene Expression16. Regulation of Transcription in Prokaryotes1 Gene Regulation Ensures a Physiological Response2 Regulation at the Level of Transcription Involves Several Steps3 Alternative Sigma Factors in Prokaryotes Recognize Different Sets of Genes4 Activators and Repressors Participate in Positive and Negative Regulation5 Two-Component Regulatory Systems6 Specific versus Global Control7 Accessory Factors and Nucleoid-Binding Proteins8 Anti-Termination as a Control Mechanism17. Regulation of Transcription in Eukaryotes1 Transcriptional Regulation in Eukaryotes Is More Complex Than in Prokaryotes2 Specific Transcription Factors Regulate Protein-Encoding Genes3 Negative Regulation of Transcription Occurs in Eukaryotes4 Heterochromatin Blocks Access to DNA in Eukaryotes5 Methylation of Eukaryotic DNA Controls Gene Expression6 X-Chromosome Inactivation Occurs in Female XX Animals18. Regulation at the RNA Level1 Regulation at the Level of mRNA2 Basic Principles of RNA Interference (RNAi)3 Long Non-coding Regulatory RNA4 CRISPR: Anti-Viral Defense in Bacteria5 Premature Termination Causes Attenuation of RNA Transcription6 Riboswitches—RNA Acting Directly As a Control Mechanism19. Analysis of Gene Expression1 Monitoring Gene Expression2 Reporter Genes for Monitoring Gene Expression3 Deletion Analysis of the Upstream Region4 DNA-Protein Complexes Can Be Isolated by Chromatin Immunoprecipitation5 Location of the Start of Transcription by Primer Extension6 Transcriptome Analysis7 DNA Microarrays for Gene Expression8 TaqMan Quantitative PCR to Assay Gene Expression9 Serial Analysis of Gene Expression (SAGE)UNIT 5. Subcellular Life Forms20. Plasmids1 Plasmids as Replicons2 General Properties of Plasmids3 Plasmid DNA Replicates by Two Alternative Methods4 Many Plasmids Help Their Host Cells5 Plasmids May Provide Aggressive Characters6 Ti Plasmids Are Transferred from Bacteria to Plants7 The 2µ Plasmid of Yeast8 Certain DNA Molecules May Behave as Viruses or Plasmids21. Viruses1 Viruses Are Infectious Packages of Genetic Information2 The Great Diversity of Viruses3 Viruses with RNA Genomes Have Very Few Genes4 Retroviruses Use Both RNA and DNA5 Subviral Infectious Agents22. Mobile DNA1 Subcellular Genetic Elements as Gene Creatures2 Most Mobile DNA Consists of Transposable Elements3 Retroelements Make an RNA Copy4 The Multitude of Transposable Elements5 Junk DNA and Selfish DNAUNIT 6. Changing the DNA Blueprint23. Mutations and Repair1 Mutations Alter the DNA Sequence2 The Major Types of Mutation3 Chemical Mutagens Damage DNA4 Overview of DNA Repair5 Mutations Occur More Frequently at Hotspots6 Reversions Are Genetic Alterations That Change the Phenotype Back to Wild-Type7 Site-Directed Mutagenesis24. Recombination1 Overview of Recombination2 Molecular Basis of Homologous Recombination3 Site-Specific Recombination4 Recombination in Higher Organisms5 Gene Conversion25. Bacterial Genetics1 Reproduction versus Gene Transfer2 Fate of the Incoming DNA after Uptake3 Transformation Is Gene Transfer by Naked DNA4 Gene Transfer by Virus—Transduction5 Transfer of Plasmids between Bacteria6 Gene Transfer among Gram-Positive Bacteria7 Archaeal Genetics8 Whole-Genome Sequencing26. Molecular Evolution1 Getting Started—Formation of the Earth2 Oparin’s Theory of the Origin of Life3 Origin of Informational Macromolecules4 The Autotrophic Theory of the Origin of Metabolism5 Evolution of DNA, RNA, and Protein Sequences6 Different Proteins Evolve at Very Different Rates7 Symbiotic Origin of Eukaryotic Cells8 DNA Sequencing and Biological Classification9 Evolving Sideways: Horizontal Gene TransferGlossaryIndex