BCH5413 - Exam 1 QUESTIONS WITH ANSWERS,

BCH5413 - Exam 1 QUESTIONS WITH |\ |\ |\ |\ |\ |\




ANSWERS


DNA structure - CORRECT ANSWERS ✔✔- nucleic acid bases
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(purine (A,G) and pyrimidine (C,U,T))
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- sugars (ribose, deoxyribose)
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- sugars linked by phosphate groups (sugar-phosphate backbone)
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*form antiparallel strands
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In mammilian DNA, which base has various forms - CORRECT
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ANSWERS ✔✔cytosine |\




Chargaff's rule - CORRECT ANSWERS ✔✔A=T and C=G|\ |\ |\ |\ |\ |\ |\




Is DNA conservative or semi-conservative? - CORRECT ANSWERS
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✔✔semi-conservative
- parental sequence and daughter strand bind together
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Alternative Double stranded DNA conformation |\ |\ |\ |\




- A and Z DNA - CORRECT ANSWERS ✔✔A DNA
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- dehydrated form
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- right handed helix
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- 11 bp per helical
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,- bp tilted 19 degrees
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- major groove narrow and deep
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- found with dsRNA and RNA-DNA duplex
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z-DNA
- >1% of cellular DNA
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- favored by G-C repeats and alternating purines-pyrimidines
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- left handed helix
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- 12 bp per turn
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- bp tilted 9 degrees
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- major groove flattened, nearly gone
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- bound by poxvirus E3L virulence factor and down regulates
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apoptosis genes |\




Non-duplex DNA structures |\ |\




- cruciform DNA - CORRECT ANSWERS ✔✔- inverted repeat
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sequence
- favored by excessive negative supercoiling
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- AT-rich cruciforms associated with 'fragile' DNA
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Alternative modes of base pairing - CORRECT ANSWERS
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✔✔Watson Crick: |\




A--T and C---G
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- adenine is at anti-conformation
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,Hoogsteen:
- adenine or guanine can be flipped to sin-conformation (different
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H-bonding)
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Hoogsteen base pairing |\ |\




- when can it occur - CORRECT ANSWERS ✔✔- in triplex and
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quadruplex DNA structures |\ |\




Triplex DNA - CORRECT ANSWERS ✔✔- pyrimidine rich strand
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- negative supercoiling
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Chair DNA - CORRECT ANSWERS ✔✔- two G-rich strands
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- down regulation of c-myc transcription
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Intrinsic Bends in DNA - CORRECT ANSWERS ✔✔- distortion of the
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ideal B-DNA conformation resulting from base stacking in the
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nucleotide sequence |\




Eg. Adenine-tract DNA results in 20 degree bends
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- also can be found in duplex-oligonucleotide model DNA
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- causes 23 degree bend and mis-stacking of one GC
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- DNA is not a uniform structure
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Does B-DNA have a perfect structure? - CORRECT ANSWERS
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✔✔No

, - sequence specific local variation in twist between paired bases,
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sugat conformation, tilt of base pairs, rise distance, etc.
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Supercoiled DNA |\




- negative v. positive - CORRECT ANSWERS ✔✔- left handed
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under-twisted DNA is in a negative supercoil |\ |\ |\ |\ |\ |\




- right handed over-twisted DNA is in a positive supercoil
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*most is negatively supercoiled (topoisomerase releaves
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supercoiling)


Denaturation/Melting of DNA - CORRECT ANSWERS ✔✔- |\ |\ |\ |\ |\ |\ |\


separation of DNA strands |\ |\ |\




- can happen due to temp, salt concentration, G---C content, and
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length of DNA (Hyperchromicity effect)
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- as temp increases, absorption of light increases due to bases
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becoming less shielded when they melt apart |\ |\ |\ |\ |\ |\




The (greater/lower) the G+C content and the (higher/lower) the
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salt, the more stable the DNA duplex - CORRECT ANSWERS
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✔✔greater G+C and higher salt |\ |\ |\ |\




What are higher stringency conditions - CORRECT ANSWERS
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✔✔high heat and low salt |\ |\ |\ |\




What else can melt DNA? - CORRECT ANSWERS ✔✔pH
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