1. What is the building block of DNA?
  2. How can chemical methods help you "see" DNA?
    Chemicals bind to DNA, can be colors or light indicative.
  3. What is Spectrophotometer?
    An indirect method of seeing DNA (seeing if DNA is present). The spectrophotometer measures the absorbance of nucleic acid solutions at a certain wavelength. Just sort of see how much light is absorbed by the object in the test tube, if not much there is not a lot of DNA, if a lot is absorbed, there is a lot of DNA.
  4. What is electrophoresis?
    a technique used to seperate DNA fragments from one another using electrical pulses in an electrophoretic gel stained with E.B.
  5. What is polymorphism?
    • When there are different types or forms of the same "thing"
    • examples include the same gene with different alleles (coding for variations in traits) or the same DNA locus with different sequences.
  6. What is a point mutation?
    one change in a long DNA sequence (example, A switches to G)
  7. What is an insertion or deletion?
    A more serious form of genetic mutation where a nucleotide is inserted or deleted. Can be devestating depending on where the mutation occurs in the gentic code.
  8. How do you estimate the length of DNA fragments using electrophoresis?
    shorter fragments travel farther than larger fragments
  9. What is a primer?
    A short DNA sequence designed by the researcher as a fish hook. Must have right and left primers for successful PCR amplification. A primer automatically binds to the identical spot in the DNA area and will trigger multiplication.
  10. Why is electrophoresis used for aDNA studies?
    After PCR amplification you use the gel staining to see how much DNA was sucessfully amplified. Do not want to have too long of a sequence, because that would be contamination, but something under 300bp is feasible.
  11. PCR Taq polymerase is?
    the enzyme used to "read" and attach corresponding nucleotides during DNA amplification
  12. Reaction Buffer is?
    The optimal chemical condiition with magnesium ions that allows PCR amplification to suceed.
  13. What are things to keep in mind when designing a primer?
    Can not be too long or too short, and you do not want complementary sequences within a primer or to a part of the opposite primer. Also want to have similar Tm values for your primer and DNA. And avoid more than 3 consecutive Cs or Gs because this may lead to repeating.
  14. What is STR?
    Short Tandem Repeats. Used for DNA fingerprinting. Looks at short repeated sequences of DNA (4 or 5 repeat base pairs), can look at 16 different loci and the chances of any two people have the same 16 different STR's at these locations is almost none.
  15. What is the formula for Tm?
    Tm = (4 x GC) + (2 x AT)
  16. What chemicals are used with electrophorysis?
    • EB: ethidium-bromide: used for staining
    • Agarose gel for molecular seive and electrical medium
    • remember the intensity of gel staining is proportional to the amount of DNA
  17. What is wrong witha primer that is too short?
    besides probably not being sensitive enough, it is also not sticky enough.
  18. What are the temperatures for PCR amplification?
    • Denaturing at 94-95 degrees celsius
    • Annealing at 50-60 degrees celsius
    • Extension at 72 degrees celsius
  19. What is the perfect Tm?
    Between 55-60 degrees celsius
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