Genetics and Molecular Biology - Online Course

 Genetics and Molecular Biology

Genetics and Molecular Biology - -

An Overview of Cell Structure and Function

1. Cell�s Need for Immense Amounts of Information
2. Rudiments of Prokaryotic Cell Structure
3. Rudiments of Eukaryotic Cell Structure
4. Packing DNA into Cells
5. Moving Molecules into or out of Cells
6. Diffusion within the Small Volume of a Cell
7. Exponentially Growing Populations
8. Composition Change in Growing Cells
9. Age Distribution in Populations of Growing Cell

Nucleic Acid and Chromosome Structure

1. The Regular Backbone of DNA
2. Grooves in DNA and Helical Forms of DNA
3. Dissociation and Reassociation of Base-paired Strands
4. Reading Sequence Without Dissociating Strands
5. Electrophoretic Fragment Separation
6. Bent DNA Sequences
7. Measurement of Helical Pitch
8. Topological Considerations in DNA Structure
9. Generating DNA with Superhelical Turns
10. Measuring Superhelical Turns
11. Determining Lk, Tw, and Wr in Hypothetical Structures
12. Altering Linking Number
13. Biological Significance of Superhelical Turns
14. The Linking Number Paradox of Nucleosomes
15. General Chromosome Structure
16. Southern Transfers to Locate Nucleosomes on Genes
17. ARS Elements, Centromeres, and Telomeres

DNA Synthesis

1. DNA Synthesis
2. Proofreading, Okazaki Fragments, and DNA Ligase - Enzymology
3. Detection and Basic Properties of DNA Polymerases - Enzymology
4. In vitro DNA Replication - Enzymology
5. Error and Damage Correction - Enzymology
6. DNA Replication Areas In Chromosomes - Physiological Aspects
7. Bidirectional Replication from E. coli Origins - Physiological Aspects
8. The DNA Elongation Rate - Physiological Aspects
9. Constancy of the E. coli DNA Elongation Rate - Physiological Aspects
10. Regulating Initiations - Physiological Aspects
11. Gel Electrophoresis Assay of Eukaryotic Replication Origins - Physiological Aspects
12. How Fast Could DNA Be Replicated? - Physiological Aspects

RNA Polymerase and RNA Initiation

1. Measuring the Activity of RNA Polymerase
2. Concentration of Free RNA Polymerase in Cells
3. The RNA Polymerase in Escherichia coli
4. Three RNA Polymerases in Eukaryotic Cells
5. Multiple but Related Subunits in Polymerases
6. Multiple Sigma Subunits
7. Structure of Promoters
8. Enhancers
9. Enhancer-Binding Proteins
10. DNA Looping in Regulating Promoter Activities
11. Steps of the Initiation Process
12. Measurement of Binding and Initiation Rates
13. Relating Abortive Initiations to Binding and Initiating
14. Roles of Auxiliary Transcription Factors
15. Melted DNA Under RNA Polymerase

TranscriptionTermination and RNA Processing

1. Polymerase Elongation Rate
2. Transcription Termination at Specific Sites
3. RNA Termination
4. Processing Prokaryotic RNAs After Synthesis
5. S1 Mapping to Locate 5� and 3� Ends of Transcripts
6. Caps, Splices, Edits, and Poly-A Tails on Eukaryotic RNAs
7. The Discovery and Assay of RNA Splicing
8. Involvement of the U1 snRNP Particle in Splicing
9. Splicing Reactions and Complexes
10. The Discovery of Self-Splicing RNAs
11. A Common Mechanism for Splicing Reactions
12. Other RNA Processing Reactions

Protein Structure

1. Protein Structure
2. The Amino Acids - Protein Structure
3. Peptide Bond - Protein Structure
4. Electrostatic Forces that Determine Protein Structure - Protein Structure
5. Hydrogen Bonds and the Chelate Effect - Protein Structure
6. Hydrophobic Forces - Protein Structure
7. Thermodynamic Considerations of Protein Structure
8. Structures within Proteins
9. Alpha Helix, Beta Sheet, and Beta Turn - Protein Structure
10. Calculation of Protein Tertiary Structure
11. Secondary Structure Predictions - Protein Structure
12. Structures of DNA-Binding Proteins
13. Salt Effects on Protein-DNA Interactions
14. Locating Specific Residue-Base Interactions - Protein Structure

Protein Synthesis

1. Activation of Amino Acids During Protein Synthesis
2. Fidelity of Aminoacylation - Protein Synthesis
3. How Synthetases Identify the Correct tRNA Molecule
4. Decoding the Message - Protein Synthesis
5. Base Pairing between Ribosomal RNA and Messenger
6. Experimental Support for the Shine-Dalgarno Hypothesis - Protein Synthesis
7. Eukaryotic Translation and the First AUG - Protein Synthesis
8. Tricking the Translation Machinery into Initiating - Protein Synthesis
9. Protein Elongation - Protein Synthesis
10. Peptide Bond Formation - Protein Synthesis
11. Translocation - Protein Synthesis
12. Termination, Nonsense, and Suppression - Protein Synthesis
13. Chaperones and Catalyzed Protein Folding - Protein Synthesis
14. Resolution of a Paradox - Protein Synthesis
15. Messenger Instability - Protein Synthesis
16. Protein Elongation Rates - Protein Synthesis
17. Directing Proteins to Specific Cellular Sites - Protein Synthesis
18. Verifying the Signal Peptide Model - Protein Synthesis
19. The Signal Recognition Particle and Translocation - Protein Synthesis
20. Expectations for Ribosome Regulation - Protein Synthesis
21. Proportionality of Ribosome Levels and Growth Rates - Protein Synthesis
22. Regulation of Ribosome Synthesis - Protein Synthesis
23. Balancing Synthesis of Ribosomal Components - Protein Synthesis

Genetics

1. Genetics Mutations
2. Point Mutations, Deletions, Insertions, and Damage
3. Classical Genetics of Chromosomes
4. Complementation, Cis, Trans, Dominant, and Recessive
5. Mechanism of a trans Dominant Negative Mutation
6. Genetic Recombination
7. Genetics Mapping by Recombination Frequencies
8. Genetics: Mapping by Deletions
9. Heteroduplexes and Genetic Recombination
10. Genetics: Branch Migration and Isomerization
11. Elements of Recombination in E. coli, RecA, RecBCD, and Chi
12. Genetic Systems
13. Growing Cells for Genetics Experiments
14. Testing Purified Cultures, Scoring
15. Isolating Auxotrophs, Use of Mutagens and Replica Plating
16. Genetic Selections
17. Mapping with Generalized Transducing Phage
18. Principles of Bacterial Sex
19. Elements of Yeast Genetics
20. Elements of Drosophila Genetics
21. Isolating Mutations in Muscle or Nerve in Drosophila
22. Fate Mapping and Study of Tissue-Specific Gene Expression

Genetic Engineering and Recombinant DNA

1. Isolation of DNA
2. Biology of Restriction Enzymes
3. Cutting DNA with Restriction Enzymes
4. Isolation of DNA Fragments
5. Joining DNA Fragments
6. Vectors: Selection and Autonomous DNA Replication
7. Plasmid Vectors
8. A Phage Vector for Bacteria
9. Vectors for Higher Cells
10. Putting DNA Back into Cells
11. Cloning from RNA
12. Plaque and Colony Hybridization for Clone Identification
13. Walking Along a Chromosome to Clone a Gene
14. Arrest of Translation to Assay for DNA of a Gene
15. Chemical DNA Sequencing
16. Enzymatic DNA Sequencing

Advanced Genetic Engineering

1. Finding Clones from a Known Amino Acid Sequence
2. Finding Clones Using Antibodies Against a Protein
3. Southern, Northern, and Western Transfers - Genetic Engineering
4. Polymerase Chain Reaction
5. Isolation of Rare Sequences Utilizing PCR
6. Physical and Genetic Maps of Chromosomes
7. Chromosome Mapping
8. DNA Fingerprinting - Forensics
9. Megabase Sequencing
10. Footprinting, Premodification and Missing Contact Probing
11. Antisense RNA: Selective Gene Inactivation
12. Hypersynthesis of Proteins
13. Altering Cloned DNA by in vitro Mutagenesis
14. Mutagenesis with Chemically Synthesized DNA

Repression and the lac Operon

1. Repression and the lac Operon
2. Role of Inducer Analogs in the Study of the lac Operon
3. Proving lac Repressor is a Protein
4. An Assay for lac Repressor
5. Difficulty of Detecting Wild Type lac Repressor
6. Detection and Purification of lac Repressor
7. Repressor Binds to DNA: The Operator is DNA
8. Migration Retardation Assay and DNA Looping - Repression and the lac Operon
9. Isolation and Structure of Operator - Repression and the lac Operon
10. In vivo Affinity of Repressor for Operator
11. DNA-binding Domain of lac Repressor
12. A Mechanism for Induction - Repression and the lac Operon

Induction Repression and the araBAD Operon

1. Sugar Arabinose and Arabinose Metabolism
2. Genetics of the Arabinose System
3. Detection and Isolation of AraC Protein
4. Repression by AraC
5. Regulating AraC Synthesis
6. Binding Sites of the ara Regulatory Proteins
7. DNA Looping and Repression of araBAD
8. In vivo Footprinting Demonstration of Looping
9. How AraC Protein Loops and Unloops
10. Why Looping is Biologically Sensible
11. Why Positive Regulators are a Good Idea

Attenuation and the trp Operon

1. Attenuation and the trp Operon
2. Rapid Induction Capabilities of the trp Operon
3. Serendipitous Discovery of trp Enzyme Hypersynthesis
4. Early Explorations of the Hypersynthesis
5. trp Multiple Secondary Structures in trp Leader RNA
6. Coupling Translation to Termination
7. RNA Secondary Structure and the Attenuation Mechanism
8. Other Attenuated Systems: Operons, Bacillus subtilis and HIV

Lambda Phage Genes and Regulatory Circuitry

1. Physical Structure of Lambda
2. Genetic Structure of Lambda
3. Lysogeny and Immunity
4. Lambda�s Relatives and Lambda Hybrids
5. Lambda Adsorption to Cells
6. Early Transcription of Genes N and Cro
7. N Protein and Antitermination of Early Gene Transcription
8. Role of Cro Protein
9. Initiating DNA Synthesis with the O and P Proteins
10. Proteins Kil, ?, ?, and Exo
11. Q Protein and Late Protein Synthesis
12. Lysis
13. Chronology of Becoming a Lysogen
14. Site for Cro Repression and CI Activation
15. Cooperativity in Repressor Binding and its Measurement
16. Need for and the Realization of Hair-Trigger Induction
17. Induction from the Lysogenic State
18. Entropy, a Basis for Lambda Repressor Inactivation

Xenopus 5S RNA Synthesis

1. Biology of 5S RNA Synthesis in Xenopus
2. In vitro 5S RNA Synthesis
3. TFIIIA Binding to the Middle of its Gene as Well as to RNA
4. Switching from Oocyte to Somatic 5S Synthesis
5. Structure and Function of TFIIIA

Regulation of Mating Type in Yeast

1. Regulation of Mating Type in Yeast
2. Yeast Cell Cycle
3. Mating Type Conversion in Saccharomyces cerevisiae
4. Cloning the Mating Type Loci in Yeast
5. Transfer of Mating Type Gene Copies to an Expression Site
6. Structure of the Mating Type Loci
7. Expression and Recombination Paradoxes
8. Silencing HML and HMR
9. Isolation of ?2 Protein
10. ?2 and MCM1
11. Sterile Mutants, Membrane Receptors and G Factors
12. DNA Cleavage at the MAT Locus
13. DNA Strand Inheritance and Switching in Fission Yeast

Genes Regulating Development

1. General Considerations on Signaling
2. Outline of Early Drosophila Development
3. Classical Embryology
4. Using Genetics to Begin Study of Developmental Systems
5. Cloning Developmental Genes
6. Enhancer Traps for Detecting and Cloning Developmental Genes
7. Expression Patterns of Developmental Genes
8. Similarities Among Developmental Genes
9. Overall Model of Drosophila Early Development

Lambda Phage Integration and Excision

1. Mapping Integrated Lambda
2. Simultaneous Deletion of Chromosomal and Lambda DNA
3. DNA Heteroduplexes Prove that Lambda Integrates
4. Gene Order Permutation and the Campbell Model
5. Isolation of Integration-Defective Mutants
6. Isolation of Excision-Deficient Mutants
7. Properties of the int and xis Gene Products
8. Incorrect Excision and gal and bio Transducing Phage
9. Transducing Phage Carrying Genes Other than gal and bio
10. Use of Transducing Phage to Study Integration and Excision
11. The Double att Phage, att.squ
12. Demonstrating Xis is Unstable
13. Inhibition By a Downstream Element
14. In vitro Assay of Integration and Excision
15. Host Proteins Involved in Integration and Excision
16. Structure of the att Regions
17. Structure of the Intasome
18. Holliday Structures and Branch Migration in Integration

Transposable Genetic Elements

1. Transposable Genetic Elements
2. IS Elements in Bacteria
3. Structure and Properties of IS Elements
4. Discovery of Tn Elements
5. Structure and Properties of Tn Elements
6. Inverting DNA Segments by Recombination, Flagellin Synthesis
7. Mu Phage As a Giant Transposable Element
8. An Invertible Segment of Mu Phage
9. In vitro Transposition, Threading or Global Topology?
10. Hopping by Tn10
11. Retrotransposons in Higher Cells
12. An RNA Transposition Intermediate
13. P Elements and Transformation
14. P Element Hopping by Chromosome Rescue

Generating Genetic Diversity

1. Generating Genetic Diversity: Antibodies
2. Basic Adaptive Immune Response
3. Telling the Difference Between Foreign and Self
4. Number of Different Antibodies Produced
5. Myelomas and Monoclonal Antibodies
6. Structure of Antibodies
7. Many Copies of V Genes and Only a Few C Genes
8. J Regions - Generating Genetic Diversity: Antibodies
9. D Regions in H Chains
10. Induced Mutations and Antibody Diversity
11. Class Switching of Heavy Chains
12. Enhancers and Expression of Immunoglobulin Genes
13. AIDS Virus
14. Engineering Antibody Synthesis in Bacteria
15. Assaying for Sequence Requirements of Gene Rearrangements
16. Cloning the Recombinase

Biological Assembly Ribosomes and Lambda Phage

1. Biological Assembly, Ribosomes and Lambda Phage
2. RNAse and Ribosomes
3. Global Structure of Ribosomes
4. Assembly of Ribosomes
5. Experiments with in vitro Ribosome Assembly
6. Determining Details of Local Ribosomal Structure
7. Lambda Phage Assembly: General Aspects
8. Geometry of Capsids
9. Structure of the Lambda Particle
10. Head Assembly Sequence and Host Proteins
11. Packaging the DNA and Formation of the cos Ends
12. Formation of the lambda Tail
13. In vitro Packaging

Chemotaxis

1. Chemotaxis
2. Assaying Chemotaxis
3. Fundamental Properties of Chemotaxis
4. Genetics of Motility and Chemotaxis
5. How Cells Swim
6. Mechanism of Chemotaxis
7. Energy for Chemotaxis
8. Adaptation
9. Methylation and Adaptation
10. Phosphorylation and the Rapid Response

Oncogenesis Molecular Aspects

1. Bacterially Induced Tumors in Plants
2. Transformation and Oncogenesis by Damaging the Chromosome
3. Identifying a Nucleotide Change Causing Cancer
4. Retroviruses and Cancer
5. Cellular Counterparts of Retroviral Oncogenes
6. Identification of the src and sis Gene Products
7. DNA Tumor Viruses
8. Recessive Oncogenic Mutations, Tumor Suppressors
9. ras-fos-jun Pathway
10. Directions for Future Research in Molecular Biology