116 lecture Midterm 1

  1. Homologus recombination step by step.
    • (During S and G2 phases)
    • 1. endonuclease chews ends of DNA to make strand excision. 
    • 2. homology search via strand invasion. 
    • 3. d-loop formation
    • 4. DNA poly fills in DNA using sister chromatid as template. 
    • 5. DNA ligase fixes backbone
  2. NHEJ process step by step
    • (During G1 phase, no homologus template available here)
    • 1. Ku protein binds
    • 2. DNA-pk binds and autophosphorolate brings ends together. 
    • 3. Regions of microhomology are found when DNA-pk phosphorolates Ku, and Ku has helicase activity. 
    • 4. Base pairing occurs
    • 5. Flaps removed by nucleases
    • 6. Gaps filled in. 
    • DNA ligase fixes backbone.
  3. Mismatch repair process step by step
    • (when replication error occurs)
    • 1. GATC (A methylated) recognized by system. 
    • 2. Bases recognized by Mut H, MutL, MutS
    • 3. Helicase helps unwind DNA
    • 4. exonuclase 1 cleaves out daughter strand
    • 5. DNA poly 3 fills in missing gaps. 
    • 6. DNA ligase fixes backbone. 
    • 7. Daughter strand is methylated.
  4. BER process step by step (prokaryote)
    • 1. DNA base extrusion by DNA glycoslase
    • 2. DNA glycosylase removes base
    • 3. AP site
    • 4. AP endonucleases nick/cut backbone DNA
    • 5. DNA phosphodiesterase removes phosphate
    • 6. DNA poly 1 replaces nucleotide. 
    • 7. DNA ligase fixes backbone.
  5. Prokaryotic NER process step by step
    • 1. Excinuclease removes bases around damage
    • 2. DNA poly 1 fills in gap. 
    • 3. DNA ligase fixes backbone.
  6. high salt concentration denatures DNA t/f?
  7. RNA coeficient is 50ug/ml t/f
  8. name of bond that binds two nucleotides
  9. plasmid vectors should have origin of transcription?
    False. Origin of replication.
  10. Investigate effects of gene, want to see how much it is expressed in tissues, which technique do you use?
    Northern blot
  11. when gene is inserted into frame of another gene it makes a what?
    fusion protein
  12. reporter genes are used to see when genes are expressed at any given time, t/f.
  13. which technique would you use to fill in missing pieces of cDNA after making a cDNA library?
  14. sds PAGE seperates proteins based on?
  15. What technique would you use to determine if protein x binds to protein y?
  16. Reverse transcriptase makes a identical copy of DNA from template RNA, t/f?
    F, it makes a complement DNA.
  17. What should colony color be if you interupt lacz gene and plate on x-gal?
  18. eukaryotic NER requires function of a general transcription factor. t/f
  19. what kind of coils does gyrase pump into strand?
  20. BER fights damage done by alkylating agents, t/f?
  21. what label was used to determine bi-directioanlity of replication?
    radiated thymadine
  22. MutH, MutL, MutS are proteins involved in mismatch repair, t/f.
  23. Dna glycosylase is key enzyme in BER, t/f.
  24. how long are okazaki fragments roughly, before they are ligated together?
  25. DNA primers are used during DNA replication, t/f.
  26. translesion synthesis leads to errors in newly replicated strand. t/f
  27. Nucleotide excision repair fixes damage done by 6,4-pp's. T/F.
  28. replication errors are fixed by which mechanism?
  29. APE1 proofreads errors during replication repair, t/f?
  30. Klenow fragment of DNA poly 1 has exonuclease activity, t/f.
  31. when does recombination repair occur?
    during replication when sister chromatids are present. S and G2
Card Set
116 lecture Midterm 1
Questions regarding material for lectures for midterm one.