Review Questions - 3Gene regulationWhat is chemotaxis? Mechanism of chemotaxis. Role of different proteins involved in response.Control of cell cycle Role of DnaA, PBP3, FtsZ Molecular GeneticsMutations, Mutagenesis, Mutagensauxotrophs, prototrophs, wild type, resistant strain* Spontaneous mutations and their causes: transitions, transversions, frameshifts, additions, deletions, apurinic, apyrimidinic site*Induced mutations and mutagens: base analogs, specific mispairing, intercalation, bypass of replication*Expression of mutations: forward mutation, reversion mutation, back mutation, suppressor mutation: intragenic and intergenic* Point mutation: silent, missense, nonsense, frameshift*mutants: lethal, conditional, selection of mutantsDetection and isolation of mutants: replica plating, direct selection. Penicillin enrichment of mutantsCarcinogenicity test: Ames test. Properties of “Salmonella” mutant that make it useful for the Ames test. DNA Repair:Proofreading. Excision repair, removal of lesions, photoreactivation, postreplication repair, recombination repair, SOS repair.Which one of these mechanisms is error proof?Since SOS is so highly error prone, why does a cell use this repair process?Recombination:crossing over, general recombination, heteroduplex, site-specific, replicative.Genotype, phenotype, genome, haploid, diploid, partial diploidyexogenote, endogenote, merozygote, host restriction.Plasmids:Plasmids, replicon, curing, episome, conjugative plasmids, F factor, R factors, [Col plasmids, virulence, metabolic : not done this semester].Transposable elements:Transposition, transposons, insertion sequence, transposase, composite transposon,[Tn3 transposition], R plasmids and transposons. What is the difference between conservative and replicative transposition?Conjugation:F+ X F-, Hfr conjugation, F’ conjugation.What are the ways in which F+ X F-, F’ X F- and Hfr X F- conjugation differ?Transformation:competent cells: naturally competent, artificially competent. Is E.coli naturally competent?What does competence mean in reference to a bacterial cell?Transduction:Lysogenic and lytic cycle, lysogeny, prophage, immunity, temperate phage, virulent phage.Generalized and specialized transduction, transducing particle, [abortive transductants].[Low frequency and high frequency transduction lysates. Helper phage.]Plaques, PFUs. Lambda as an example to demonstrate the lysogenic and lytic cycle. Role of cI repressor in maintaining lysogeny. Mapping the genome:Interrupted mating, conjugation, recombination, transduction, Whole-genome shotgun sequencing.Sequencing: Sanger’s technique. Role of ddNTP, primer etc. Reading of gel . How can yo determine the sequence of the original strand that was used for sequencing.SDM, PCR, Some questions from students in the previous semesters.What are the characteristics of the Genetic code? What is Wobble hypothesis?What is the function of Wobble pairing?What do you understand by the following terms:codon, codon degeneracy, start and stop codon, sense and nonsense codons etc?Why is the genetic code considered degenerate and unambiguous?What is a conditional lethal mutant?How is an auxotroph different from a prototroph? What is a wild type strain?How is Ames test performed? What is the purpose of liver extract in Ames test?What is the importance of penicillin in isolating auxotrophic mutants?What is the advantage of SOS repair mechanism?During repair how does the repair mechanism know as to which one is the new DNA? What is hemimethylation?Mention the different ways in which DNA is repaired in the cell.What is recombination? Name some ways in which bacterial recombination takes place.What is the fate of donor DNA once it enters the recipient?Name 3 different types of DNA transfers in bacteria.Explain the three different types of bacterial conjugation.Distinguish between cells that are Hfr, F’, F+, and F-How is conjugation different from transformation, transduction?What are plasmids? How can you cure a cell of its plasmid?** Name the different types of plasmids.**What is the difference between an IS element and a Transposon?**What is a temperate phage? How is it different from a virulent phage?Explain phage lambda’s lysogenic and lytic cycle. What are the factors that promote lysogeny?What is the role of cI and cro proteins in the life cycle of phage lambda?How would you distinguish between a lysogenic bacterium and one that is resistant?(Hint: immunity to superinfection)Compare and contrast between generalized and specialized transduction. Name the different ways of mapping bacterial genomes.Name two major differences between chemical and enzymatic synthesis of DNA. (Other than restating the question that one is enzymatic and the other is chemical)What all is important for carrying out a PCR reaction?Describe Sanger’s method of sequencing. What is the purpose of ddNTP in the reaction?Does the reaction require a primer? Read a sequencing gel.On what basis are DNA fragments separated on gel electrophoresis?**What is the main difference between agarose and polyacrylamide GE?**Write down a 35 base pair long DNA sequence. Transcribe it to show the mRNA.Show at least 5 codons, (make sure you include the start codon). What is the importance of penicillin in isolating auxotrophic mutants?Discussion questions from previous semestersGene regulation Mention the roles of all the different proteins involved in the process of chemotaxis.How would phosphorylation of Che A be affected by the presence of an attractant?E. coli cells growing with a generation time of 60 minutes or longer have a discontinuous synthesis of chromosomal DNA whereas those growing faster have continuous DNA synthesis………..True/false.What is the role of FtsZ in cell division?How do cell mass and cell length regulate DNA replication and cell division?How would phosphorylation of CheA be affected by the presence of an attractant?Mutation / Phenotypes1. What is the difference between selection and screening?2. Name two methods that can be used to isolate an auxotrophic mutant. Which would youprefer to use and why?3. How can auxotrophic mutants be isolated using penicillin enrichment?4. What is Ames test? Explain how it is performed. Also mention one important and significantapplication of this test. 5. What are the important characteristics of the organism that is used for Ames test? [In otherwords: does it have to be a