Genetics and Molecular Biology

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Genetics and Molecular Biology

An Overview of Cell Structure and Function


=> Cell’s Need for Immense Amounts of Information
=> Rudiments of Prokaryotic Cell Structure
=> Rudiments of Eukaryotic Cell Structure
=> Packing DNA into Cells
=> Moving Molecules into or out of Cells
=> Diffusion within the Small Volume of a Cell
=> Exponentially Growing Populations
=> Composition Change in Growing Cells
=> Age Distribution in Populations of Growing Cell

Nucleic Acid and Chromosome Structure


=> The Regular Backbone of DNA
=> Grooves in DNA and Helical Forms of DNA
=> Dissociation and Reassociation of Base-paired Strands
=> Reading Sequence Without Dissociating Strands
=> Electrophoretic Fragment Separation
=> Bent DNA Sequences
=> Measurement of Helical Pitch
=> Topological Considerations in DNA Structure
=> Generating DNA with Superhelical Turns
=> Measuring Superhelical Turns
=> Determining Lk, Tw, and Wr in Hypothetical Structures
=> Altering Linking Number
=> Biological Significance of Superhelical Turns
=> The Linking Number Paradox of Nucleosomes
=> General Chromosome Structure
=> Southern Transfers to Locate Nucleosomes on Genes
=> ARS Elements, Centromeres, and Telomeres

DNA Synthesis


=> DNA Synthesis
=> Proofreading, Okazaki Fragments, and DNA Ligase - Enzymology
=> Detection and Basic Properties of DNA Polymerases - Enzymology
=> In vitro DNA Replication - Enzymology
=> Error and Damage Correction - Enzymology
=> DNA Replication Areas In Chromosomes - Physiological Aspects
=> Bidirectional Replication from E. coli Origins - Physiological Aspects
=> The DNA Elongation Rate - Physiological Aspects
=> Constancy of the E. coli DNA Elongation Rate - Physiological Aspects
=> Regulating Initiations - Physiological Aspects
=> Gel Electrophoresis Assay of Eukaryotic Replication Origins - Physiological Aspects
=> How Fast Could DNA Be Replicated? - Physiological Aspects

RNA Polymerase and RNA Initiation


=> Measuring the Activity of RNA Polymerase
=> Concentration of Free RNA Polymerase in Cells
=> The RNA Polymerase in Escherichia coli
=> Three RNA Polymerases in Eukaryotic Cells
=> Multiple but Related Subunits in Polymerases
=> Multiple Sigma Subunits
=> Structure of Promoters
=> Enhancers
=> Enhancer-Binding Proteins
=> DNA Looping in Regulating Promoter Activities
=> Steps of the Initiation Process
=> Measurement of Binding and Initiation Rates
=> Relating Abortive Initiations to Binding and Initiating
=> Roles of Auxiliary Transcription Factors
=> Melted DNA Under RNA Polymerase

TranscriptionTermination and RNA Processing


=> Polymerase Elongation Rate
=> Transcription Termination at Specific Sites
=> RNA Termination
=> Processing Prokaryotic RNAs After Synthesis
=> S1 Mapping to Locate 5’ and 3’ Ends of Transcripts
=> Caps, Splices, Edits, and Poly-A Tails on Eukaryotic RNAs
=> The Discovery and Assay of RNA Splicing
=> Involvement of the U1 snRNP Particle in Splicing
=> Splicing Reactions and Complexes
=> The Discovery of Self-Splicing RNAs
=> A Common Mechanism for Splicing Reactions
=> Other RNA Processing Reactions

Protein Structure


=> Protein Structure
=> The Amino Acids - Protein Structure
=> Peptide Bond - Protein Structure
=> Electrostatic Forces that Determine Protein Structure - Protein Structure
=> Hydrogen Bonds and the Chelate Effect - Protein Structure
=> Hydrophobic Forces - Protein Structure
=> Thermodynamic Considerations of Protein Structure
=> Structures within Proteins
=> Alpha Helix, Beta Sheet, and Beta Turn - Protein Structure
=> Calculation of Protein Tertiary Structure
=> Secondary Structure Predictions - Protein Structure
=> Structures of DNA-Binding Proteins
=> Salt Effects on Protein-DNA Interactions
=> Locating Specific Residue-Base Interactions - Protein Structure

Protein Synthesis


=> Activation of Amino Acids During Protein Synthesis
=> Fidelity of Aminoacylation - Protein Synthesis
=> How Synthetases Identify the Correct tRNA Molecule
=> Decoding the Message - Protein Synthesis
=> Base Pairing between Ribosomal RNA and Messenger
=> Experimental Support for the Shine-Dalgarno Hypothesis - Protein Synthesis
=> Eukaryotic Translation and the First AUG - Protein Synthesis
=> Tricking the Translation Machinery into Initiating - Protein Synthesis
=> Protein Elongation - Protein Synthesis
=> Peptide Bond Formation - Protein Synthesis
=> Translocation - Protein Synthesis
=> Termination, Nonsense, and Suppression - Protein Synthesis
=> Chaperones and Catalyzed Protein Folding - Protein Synthesis
=> Resolution of a Paradox - Protein Synthesis
=> Messenger Instability - Protein Synthesis
=> Protein Elongation Rates - Protein Synthesis
=> Directing Proteins to Specific Cellular Sites - Protein Synthesis
=> Verifying the Signal Peptide Model - Protein Synthesis
=> The Signal Recognition Particle and Translocation - Protein Synthesis
=> Expectations for Ribosome Regulation - Protein Synthesis
=> Proportionality of Ribosome Levels and Growth Rates - Protein Synthesis
=> Regulation of Ribosome Synthesis - Protein Synthesis
=> Balancing Synthesis of Ribosomal Components - Protein Synthesis

Genetics


=> Genetics Mutations
=> Point Mutations, Deletions, Insertions, and Damage
=> Classical Genetics of Chromosomes
=> Complementation, Cis, Trans, Dominant, and Recessive
=> Mechanism of a trans Dominant Negative Mutation
=> Genetic Recombination
=> Genetics Mapping by Recombination Frequencies
=> Genetics: Mapping by Deletions
=> Heteroduplexes and Genetic Recombination
=> Genetics: Branch Migration and Isomerization
=> Elements of Recombination in E. coli, RecA, RecBCD, and Chi
=> Genetic Systems
=> Growing Cells for Genetics Experiments
=> Testing Purified Cultures, Scoring
=> Isolating Auxotrophs, Use of Mutagens and Replica Plating
=> Genetic Selections
=> Mapping with Generalized Transducing Phage
=> Principles of Bacterial Sex
=> Elements of Yeast Genetics
=> Elements of Drosophila Genetics
=> Isolating Mutations in Muscle or Nerve in Drosophila
=> Fate Mapping and Study of Tissue-Specific Gene Expression

Genetic Engineering and Recombinant DNA


=> Isolation of DNA
=> Biology of Restriction Enzymes
=> Cutting DNA with Restriction Enzymes
=> Isolation of DNA Fragments
=> Joining DNA Fragments
=> Vectors: Selection and Autonomous DNA Replication
=> Plasmid Vectors
=> A Phage Vector for Bacteria
=> Vectors for Higher Cells
=> Putting DNA Back into Cells
=> Cloning from RNA
=> Plaque and Colony Hybridization for Clone Identification
=> Walking Along a Chromosome to Clone a Gene
=> Arrest of Translation to Assay for DNA of a Gene
=> Chemical DNA Sequencing
=> Enzymatic DNA Sequencing

Advanced Genetic Engineering


=> Finding Clones from a Known Amino Acid Sequence
=> Finding Clones Using Antibodies Against a Protein
=> Southern, Northern, and Western Transfers - Genetic Engineering
=> Polymerase Chain Reaction
=> Isolation of Rare Sequences Utilizing PCR
=> Physical and Genetic Maps of Chromosomes
=> Chromosome Mapping
=> DNA Fingerprinting - Forensics
=> Megabase Sequencing
=> Footprinting, Premodification and Missing Contact Probing
=> Antisense RNA: Selective Gene Inactivation
=> Hypersynthesis of Proteins
=> Altering Cloned DNA by in vitro Mutagenesis
=> Mutagenesis with Chemically Synthesized DNA

Repression and the lac Operon


=> Repression and the lac Operon
=> Role of Inducer Analogs in the Study of the lac Operon
=> Proving lac Repressor is a Protein
=> An Assay for lac Repressor
=> Difficulty of Detecting Wild Type lac Repressor
=> Detection and Purification of lac Repressor
=> Repressor Binds to DNA: The Operator is DNA
=> Migration Retardation Assay and DNA Looping - Repression and the lac Operon
=> Isolation and Structure of Operator - Repression and the lac Operon
=> In vivo Affinity of Repressor for Operator
=> DNA-binding Domain of lac Repressor
=> A Mechanism for Induction - Repression and the lac Operon

Induction Repression and the araBAD Operon


=> Sugar Arabinose and Arabinose Metabolism
=> Genetics of the Arabinose System
=> Detection and Isolation of AraC Protein
=> Repression by AraC
=> Regulating AraC Synthesis
=> Binding Sites of the ara Regulatory Proteins
=> DNA Looping and Repression of araBAD
=> In vivo Footprinting Demonstration of Looping
=> How AraC Protein Loops and Unloops
=> Why Looping is Biologically Sensible
=> Why Positive Regulators are a Good Idea

Attenuation and the trp Operon


=> Attenuation and the trp Operon
=> Rapid Induction Capabilities of the trp Operon
=> Serendipitous Discovery of trp Enzyme Hypersynthesis
=> Early Explorations of the Hypersynthesis
=> trp Multiple Secondary Structures in trp Leader RNA
=> Coupling Translation to Termination
=> RNA Secondary Structure and the Attenuation Mechanism
=> Other Attenuated Systems: Operons, Bacillus subtilis and HIV

Lambda Phage Genes and Regulatory Circuitry


=> Physical Structure of Lambda
=> Genetic Structure of Lambda
=> Lysogeny and Immunity
=> Lambda’s Relatives and Lambda Hybrids
=> Lambda Adsorption to Cells
=> Early Transcription of Genes N and Cro
=> N Protein and Antitermination of Early Gene Transcription
=> Role of Cro Protein
=> Initiating DNA Synthesis with the O and P Proteins
=> Proteins Kil, γ, β, and Exo
=> Q Protein and Late Protein Synthesis
=> Lysis
=> Chronology of Becoming a Lysogen
=> Site for Cro Repression and CI Activation
=> Cooperativity in Repressor Binding and its Measurement
=> Need for and the Realization of Hair-Trigger Induction
=> Induction from the Lysogenic State
=> Entropy, a Basis for Lambda Repressor Inactivation

Xenopus 5S RNA Synthesis


=> Biology of 5S RNA Synthesis in Xenopus
=> In vitro 5S RNA Synthesis
=> TFIIIA Binding to the Middle of its Gene as Well as to RNA
=> Switching from Oocyte to Somatic 5S Synthesis
=> Structure and Function of TFIIIA

Regulation of Mating Type in Yeast


=> Regulation of Mating Type in Yeast
=> Yeast Cell Cycle
=> Mating Type Conversion in Saccharomyces cerevisiae
=> Cloning the Mating Type Loci in Yeast
=> Transfer of Mating Type Gene Copies to an Expression Site
=> Structure of the Mating Type Loci
=> Expression and Recombination Paradoxes
=> Silencing HML and HMR
=> Isolation of α2 Protein
=> α2 and MCM1
=> Sterile Mutants, Membrane Receptors and G Factors
=> DNA Cleavage at the MAT Locus
=> DNA Strand Inheritance and Switching in Fission Yeast

Genes Regulating Development


=> General Considerations on Signaling
=> Outline of Early Drosophila Development
=> Classical Embryology
=> Using Genetics to Begin Study of Developmental Systems
=> Cloning Developmental Genes
=> Enhancer Traps for Detecting and Cloning Developmental Genes
=> Expression Patterns of Developmental Genes
=> Similarities Among Developmental Genes
=> Overall Model of Drosophila Early Development

Lambda Phage Integration and Excision


=> Mapping Integrated Lambda
=> Simultaneous Deletion of Chromosomal and Lambda DNA
=> DNA Heteroduplexes Prove that Lambda Integrates
=> Gene Order Permutation and the Campbell Model
=> Isolation of Integration-Defective Mutants
=> Isolation of Excision-Deficient Mutants
=> Properties of the int and xis Gene Products
=> Incorrect Excision and gal and bio Transducing Phage
=> Transducing Phage Carrying Genes Other than gal and bio
=> Use of Transducing Phage to Study Integration and Excision
=> The Double att Phage, att.squ
=> Demonstrating Xis is Unstable
=> Inhibition By a Downstream Element
=> In vitro Assay of Integration and Excision
=> Host Proteins Involved in Integration and Excision
=> Structure of the att Regions
=> Structure of the Intasome
=> Holliday Structures and Branch Migration in Integration

Transposable Genetic Elements


=> Transposable Genetic Elements
=> IS Elements in Bacteria
=> Structure and Properties of IS Elements
=> Discovery of Tn Elements
=> Structure and Properties of Tn Elements
=> Inverting DNA Segments by Recombination, Flagellin Synthesis
=> Mu Phage As a Giant Transposable Element
=> An Invertible Segment of Mu Phage
=> In vitro Transposition, Threading or Global Topology?
=> Hopping by Tn10
=> Retrotransposons in Higher Cells
=> An RNA Transposition Intermediate
=> P Elements and Transformation
=> P Element Hopping by Chromosome Rescue

Generating Genetic Diversity


=> Generating Genetic Diversity: Antibodies
=> Basic Adaptive Immune Response
=> Telling the Difference Between Foreign and Self
=> Number of Different Antibodies Produced
=> Myelomas and Monoclonal Antibodies
=> Structure of Antibodies
=> Many Copies of V Genes and Only a Few C Genes
=> J Regions - Generating Genetic Diversity: Antibodies
=> D Regions in H Chains
=> Induced Mutations and Antibody Diversity
=> Class Switching of Heavy Chains
=> Enhancers and Expression of Immunoglobulin Genes
=> AIDS Virus
=> Engineering Antibody Synthesis in Bacteria
=> Assaying for Sequence Requirements of Gene Rearrangements
=> Cloning the Recombinase

Biological Assembly Ribosomes and Lambda Phage


=> Biological Assembly, Ribosomes and Lambda Phage
=> RNAse and Ribosomes
=> Global Structure of Ribosomes
=> Assembly of Ribosomes
=> Experiments with in vitro Ribosome Assembly
=> Determining Details of Local Ribosomal Structure
=> Lambda Phage Assembly: General Aspects
=> Geometry of Capsids
=> Structure of the Lambda Particle
=> Head Assembly Sequence and Host Proteins
=> Packaging the DNA and Formation of the cos Ends
=> Formation of the lambda Tail
=> In vitro Packaging

Chemotaxis


=> Chemotaxis
=> Assaying Chemotaxis
=> Fundamental Properties of Chemotaxis
=> Genetics of Motility and Chemotaxis
=> How Cells Swim
=> Mechanism of Chemotaxis
=> Energy for Chemotaxis
=> Adaptation
=> Methylation and Adaptation
=> Phosphorylation and the Rapid Response

Oncogenesis Molecular Aspects


=> Bacterially Induced Tumors in Plants
=> Transformation and Oncogenesis by Damaging the Chromosome
=> Identifying a Nucleotide Change Causing Cancer
=> Retroviruses and Cancer
=> Cellular Counterparts of Retroviral Oncogenes
=> Identification of the src and sis Gene Products
=> DNA Tumor Viruses
=> Recessive Oncogenic Mutations, Tumor Suppressors
=> ras-fos-jun Pathway
=> Directions for Future Research in Molecular Biology



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