Genetics and Molecular Biology

Lecture Notes, Study Materials and Important questions answers

Subject : Genetics and Molecular Biology

An Overview of Cell Structure and Function
1. Cell’s Need for Immense Amounts of Information - Answer (click here)
2. Rudiments of Prokaryotic Cell Structure - Answer (click here)
3. Rudiments of Eukaryotic Cell Structure - Answer (click here)
4. Packing DNA into Cells - Answer (click here)
5. Moving Molecules into or out of Cells - Answer (click here)
6. Diffusion within the Small Volume of a Cell - Answer (click here)
7. Exponentially Growing Populations - Answer (click here)
8. Composition Change in Growing Cells - Answer (click here)
9. Age Distribution in Populations of Growing Cell - Answer (click here)

Nucleic Acid and Chromosome Structure

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

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

RNA Polymerase and RNA Initiation

1. Measuring the Activity of RNA Polymerase - Answer (click here)
2. Concentration of Free RNA Polymerase in Cells - Answer (click here)
3. The RNA Polymerase in Escherichia coli - Answer (click here)
4. Three RNA Polymerases in Eukaryotic Cells - Answer (click here)
5. Multiple but Related Subunits in Polymerases - Answer (click here)
6. Multiple Sigma Subunits - Answer (click here)
7. Structure of Promoters - Answer (click here)
8. Enhancers - Answer (click here)
9. Enhancer-Binding Proteins - Answer (click here)
10. DNA Looping in Regulating Promoter Activities - Answer (click here)
11. Steps of the Initiation Process - Answer (click here)
12. Measurement of Binding and Initiation Rates - Answer (click here)
13. Relating Abortive Initiations to Binding and Initiating - Answer (click here)
14. Roles of Auxiliary Transcription Factors - Answer (click here)
15. Melted DNA Under RNA Polymerase - Answer (click here)
TranscriptionTermination and RNA Processing
1. Polymerase Elongation Rate - Answer (click here)
2. Transcription Termination at Specific Sites - Answer (click here)
3. RNA Termination - Answer (click here)
4. Processing Prokaryotic RNAs After Synthesis - Answer (click here)
5. S1 Mapping to Locate 5’ and 3’ Ends of Transcripts - Answer (click here)
6. Caps, Splices, Edits, and Poly-A Tails on Eukaryotic RNAs - Answer
(click here)
7. The Discovery and Assay of RNA Splicing - Answer (click here)
8. Involvement of the U1 snRNP Particle in Splicing - Answer (click here)
9. Splicing Reactions and Complexes - Answer (click here)
10. The Discovery of Self-Splicing RNAs - Answer (click here)
11. A Common Mechanism for Splicing Reactions - Answer (click here)
12. Other RNA Processing Reactions - Answer (click here)

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

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

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

Genetic Engineering and Recombinant DNA

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

Advanced Genetic Engineering

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

Repression and the lac Operon

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

Induction Repression and the araBAD Operon

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

Attenuation and the trp Operon

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

Lambda Phage Genes and Regulatory Circuitry

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

Xenopus 5S RNA Synthesis

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

Regulation of Mating Type in Yeast

1. Regulation of Mating Type in Yeast - Answer (click here)
2. Yeast Cell Cycle - Answer (click here)
3. Mating Type Conversion in Saccharomyces cerevisiae - Answer (click here)
4. Cloning the Mating Type Loci in Yeast - Answer (click here)
5. Transfer of Mating Type Gene Copies to an Expression Site - Answer
(click here)
6. Structure of the Mating Type Loci - Answer (click here)
7. Expression and Recombination Paradoxes - Answer (click here)
8. Silencing HML and HMR - Answer (click here)
9. Isolation of α2 Protein - Answer (click here)
10. α2 and MCM1 - Answer (click here)
11. Sterile Mutants, Membrane Receptors and G Factors - Answer (click here)
12. DNA Cleavage at the MAT Locus - Answer (click here)
13. DNA Strand Inheritance and Switching in Fission Yeast - Answer (click
here)

Genes Regulating Development

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

Lambda Phage Integration and Excision

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

Transposable Genetic Elements

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

Generating Genetic Diversity

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

Biological Assembly Ribosomes and Lambda Phage

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

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

Oncogenesis Molecular Aspects

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