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BIOL303 Lecture Notes - Lecture 12: Heteroduplex, Lambda Phage, Transposable Element

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ochreleopard700
9 Jun 2015
School
University of Waterloo
Department
Biology
Course
BIOL303
Professor
Dragana Miskovic

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Document Summary

12. describe the term non-homologous end joining and explain how this process results in the repair of double strand breaks in dna molecule. 14. distinguish between the two dsb repair mechanisms we talked about in class in respect to their accuracy. 16. list and briefly describe the ways genomic dna can be rearranged (there are three of them). 18. explain the relationship between hybrid duplex and heteroduplex. (you can use diagram. ) 19. describe the function of proteins involved in homologous recombination of: coli. 20. describe the role of chi sequences in homologous recombination of e. coli. 26. explain the role of site-specific recombination in infection of e. coli genome by lambda phage. 28. list and briefly describe three mechanisms used by genetic elements to randomly move from one site in the genome to another. 29. draw a fully annotated diagram illustrating the transposition mechanism of a simple is transposon (or retroviral-like retrotransposon, or non-retroviral retrotransposon).

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Related Questions

Please explain, in your own words

Understand the mechanisms that enable organisms to minimizemutations in stem cells. Understand why this is important!

Know the mechanisms that can introduce mistakes into DNA, therepair pathways that deal with the damage, and the consequences ifthey are not repaired:

  • DNA polymerase errors
  • depurination
  • deamination
  • oxidation
  • X-ray radiation
  • UV radiation
  • Alkylation
  • Adduct formation

Understand the DNA damageresponse, and the types of repair, such as

  • Chemical reversal
  • Nucleotide excision repair
  • Base excision repair
  • Mismatch repair
  • Double strand break repair

Understand the G2 checkpoint: what mechanisms establish thecheckpoint, and how do cells get past it?

Know what BRCA-1 protein does, and why its loss contributes tocancer. Understand the impact of Myriad Genetics

What are the advantages of recombination? What are the disadvantages? Under what kinds of ecological conditions (stable environment, high predation rates, exposure to rapidly evolving parasites, etc.) would you expect to favor one, or the other?

Suppose you found a region of a genome in a vertebrate that was quite large (say, 10 million base pairs) that had an extremely low recombination rate. Suggest a reason why it might be advantageous to not recombine the genes in that genomic region.

How do prokaryotes distinguish the newly synthesized strand from the old template strand? Why don’t eukaryotes use the same mechanism?

What is methylation used for in prokaryotes? In eukaryotes?

What happens if mismatch repair occurs shortly after replication? How does it know which mismatched, normal base is incorrect? What happens if mismatch repair occurs long after replication has occurred?

Why does uracil DNA glycosylase have so an easier task to perform than thymine DNA glycosylase?

Describe the steps that occur following uracil DNA glycosylase activity. What needs to happen; what enzymes are involved?

What do x-rays do to DNA? What does UV radiation do? What do microwaves do?

Is there a safe minimum dose of radiation?

Why is telomerase turned off in human somatic cells? Is it turned off in mouse somatic cells? Would you expect it to be turned off in elephants? Would you expect elephants to have high cancer rates compared to mice?

Where is telomerase necessary? Is it on the leading, or lagging strand, or both? Why don’t bacteria need telomerase?

Why is microsatellite instability used by physicians to measure problems with mismatch repair?

Multiply questions here

Q2. What is the consequence of chromosome inversion on meiosis? (work on a zygote with one normal chromosome and one chromosome with an inversion)

Q3. Search the web or read the textbook. Find a disease that is caused by translocation. What kind of translocation causes the disease?

Q4. Briefly explain how down’s syndrome or other trisomy is generated (3 sentences should be enough for you to explain this clearly)

Q5. I mutated a culture of wild type E. coli cells and wanted to isolate mutants that are unable to synthesize uracil (a nitrogen base in RNA). How can I achieve my goal? (try to finish your answer in 2-3 sentences)

Q6. For the ura- mutant isolated in Q5, I want to convert it to URA+ by transformation. Please tell me how I can achive this transformation with 3 SIMPLE sentences

Q7. What is the difference and relationship between an Hfr cell and an F+ cell?

Q8. I want to set up a mating between an Hfr strain and an F- (ade- his- bio-) strain and detect bio+ recombinant. Please design the experiment for me. (What genotype for Hfr do you need to choose? How will you select your recombinant? etc).

Q9. I want to use phage T2 to transducer the wild type ADE2 gene from the wild type E. coli strain to an ade2- E. coli mutant. How can I do this experimentally? (please briefly describe the approach, not experimental details such as incubation for 10 min, etc).

Q10. We talked about recombination in both eukaryotes and prokaryotes. Are there any differences in these two recombination ? (what are they if there are?)

Q11. Whose (or what) experiment proves that DNA is the genetic material?

Q12. What knowledge did Watson and Crick use in constructing the DNA model?

Q13. How does the double helix model support the three major functions of genetic materials?

Q14. What is the major chemical force that holds DNA and histone together? Hydrogen bonds

Q15. If I label E. coli cells in an N15 medium overnight and chase cells in an N14 medium for 2 generations, what fraction of cells still carry the N15 label?

Q16. If a 1000 kilobase fragment of DNA has five evenly spaced replication origins and DNA polymerase moves at 1 kilobase per second, how many seconds will a cell take to produce two daughter molecules?

Q17. DNA polymerases catalyze the polymerization of nucleotides. Use the formula for enzyme catalyzed reaction (see the example) to describe DNA polymerases. Example: Enzyme Substrate A + substrate B -------------------ïƒ product c + product D Q8. During DNA replication, what is the direction of the growing strand?

Q18. For DNA synthesis in cells, why are there a leading strand and a lagging strand?

Q19. The following is the DNA sequence of a template strand. If the primase begins to synthesize primers from the middle ‘g’, what will the primer sequence be? (assuming the primer can be 8 nucleotides long) 5’ GACTCTAgGACTCCT 3’

Q20. Both DNA polymerase I and DNA polymerase III synthesize DNA during DNA replication. Please state the different roles they played during DNA replication.