Genetic lab exam 2

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  1. What add deoxyribonucleotide to RNA-primer during DNA replication and what direction?
    DNA pol 3, from 3'-5'
  2. What does DNA pol I do?
    Replaces DNA pol III at the end of synthesis, removes RNA primer, and replaces with DNA.
  3. What forms the phosphodiester bond b/w the 3'OH and the 5' phosphate after replacement of RNA primer with DNA on the lagging strand?
    DNA ligase
  4. What is the difference b/w the synthesis of DNA for the leading stand and lagging strand during DNA replication?
    • Leading strand synthesizes continuously
    • Lagging strand synthesizes discontinuously
  5. List the events of DNAs synthesis for the lagging strand during DNA replication.
    RNA pol synthesizes primer>DNA pol III adds deoxyribonucleotides to 3'OH of primers>DNA pol I replaces DNA pol III and replaces RNA primer with DNA.
  6. What is the initial step of DNA replication?
    Helicase unwinds a segment of DNA and breaks the hydrogen bond b/w the two strands.
  7. What held the two DNA complementary strands together?
    Hydrogen bond
  8. What is special about the leading strand replication?
    Continuous synthesis from 5'-3'
  9. What is special about the Lagging strand replication?
    Can only be synthesized from a free 3'OH
  10. What direction is DNA pol add nucleotides?
    Only from free 3' end of a growing chain
  11. What is the role of RNA-primase?
    Synthesize a short RNA-primer.
  12. What add deoxyribonucleotides to RNA-primer?
    DNA Pol III
  13. How many RNA-primer is required for synthesis of leading strand? for the lagging strand?
    1 for leading strand, multiple for lagging strand.
  14. What enzymes are required for the synthesis of lagging strand DNA during DNA replication?
    RNA primase, DNA pol III, DNA pol I, and DNA ligase.
  15. What is the requirement for DNA Pol III to add nucleotide?
    a free 3'OH
  16. What is a transposon?
    a jumping gene that move from one location on the genome to another.
  17. Who discovered transposable element?
    Barbara McClintock
  18. What fraction of the human genome are composed of TE?
    50% of human genome
  19. How many different types of transposon and what are they?
    • 2 types
    • Retrotransposon and DNA transposon
  20. What enzyme is required for retrotransposon?
    Reverse transcriptase.
  21. What protein is required for DNA transposon?
  22. What is the role of transposase in DNA transposon?
    for insertion and excision in to DNA
  23. What does DNA transposon gene code for?
  24. True/False DNA transposon requires RNA intermediate.
    False, only retrotransposon require RNA intermediate.
  25. What does DNA transposon contains?
    terminal repeats on both end
  26. What does DNA transposase recognize in the DNA segment?
    terminal repeats
  27. True/False Terminal repeats are inverted complement on both ends.
  28. What are flanking repeats?
    foot prints after TE is excited that can alter gene expression
  29. True/False Flanking direct repeats are a part of TE?
    False. they are a part of both TE classes.
  30. True/False Less than 2% of human genome is type II DNA TE.
  31. What type of TE is majority in human?
  32. What is the Direction flow of Retrotransposon?
  33. What are the two classes of retrotransposase?
    LTR-TE and Non-LTR-TE.
  34. What are some of Non-LTR-TE?
    LINE, L1, Alu (SINE)
  35. Which Non-LTR-TE is common in human genome?
    Alu (Sine)
  36. True/False LTR are ancient relic & it is not capable of  jumping.
  37. True/False Only class one TE is autonomous and class two TE in non-autonomous.
    False. both classes can be autonomous or non-autonomous.
  38. What does autonomous means?
    can move on its own
  39. How does non-autonomous TE move?
    it lacks transposase and reverse transposase, so, it borrows from another TE to move.
  40. What happens when TE inserted into a gene?
    Result in mutation
  41. True/False Most TEs are active
    False, most TEs are silent
  42. What prevent some TEs from being active?
    mutation prevent their function, and inactivation due to epigenetic: methylation, chromatin remodeling, and miRNAs
  43. What is the purpose of PCR and cloning?
    to produce more DNA
  44. What is required for cloning?
    Reverse transcriptase
  45. from which organism does cloning mechanism copy from?
  46. What is special about PCR?
    it uses DNA pol to maker multiple copies of specific fragments
  47. Which method is more efficient PCR or cloning?
  48. If you only have mRNA template, which DNA amplifying method should be used? Cloning or PCR?
    Cloning. PCR is for DNA
  49. What is a cDNA?
    DNA that is complement to mRNA, which is copied using reverse transcriptase.
  50. How does reverse transcriptase work?
    Oligo(dt) binds to poly(A) tails and provides Free 3'Oh> reverse transciptase synthesizes DNA.>RNase partly digest RNA strand> polymerase uses RNA fragment as primers and synthesize DNA> ligase seals nicks
  51. True/False Both eukaryotes and prokaryotes have poly(A) tail.
    False, only eukaryotes have poly(A) tail
  52. What was the problem with the original cloning method?
     5'end of mRNA is not presence in cDNA
  53. What is Biotin Capping?
    Capping 5' end of mRNA with a biotin group and washing the cDNA with an RNA digestion enzyme RNase I. retaining 95% of full cDNA
  54. what does cDNA library use for?
    search matches gene with probes
  55. What are required for PCR?
    DNA polymerase, DNA for template, four deoxynucleotides as substrates, salts and ions, and a pair of primers with exposed 3'OH
  56. What are the 3 stages of PCR? What temperature is corresponded to each stage?
    Denature, heating up to break hydrogen bond of double stands DNA to single stand (94-96). Annealing, allowing for DNA primer to bind to complement region by cooling temp to 48-56C. elongation, Taq polymerase uses template strand and dNTP to extend DNA(64-72C). 
  57. What is the formula for the number DNA strand after certain number of PCR cycle?
    (2^N), N is the number of cycle.
  58. What was the limitation of the original PCR method?
    A new set of DNA polymerase have to be added after every cycle.
  59. What is special about the DNA pol that use for PCR?
    It's a Taq pol, Thermus aquaticus, thermophilic bact pol that can survive up to 950C.
  60. What is real time PCR?
    PCR that uses dyes or fluorescent probes that, eliminate the use of electrophoresis.
Card Set
Genetic lab exam 2
Molecular genetic portion of the lab
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