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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
Mahendra Varman Mahendra Varman Mahendra Varman Mahendra Varman Mahendra Varman

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