BCH5413 - EXAM 1 | QUESTIONS AND ANSWERS
ALREADY GRADED A+
1. DNA structure
Answer: - nucleic acid bases (purine (A,G) and pyrimidine (C,U,T))
- sugars (ribose, deoxyribose)
- sugars linked by phosphate groups (sugar-phosphate backbone)
*form antiparallel strands
2. In mammilian DNA, which base has various forms
Answer: cytosine
3. Chargaff's rule
Answer: A=T and C=G
4. Is DNA conservative or semi-conservative?
Answer: semi-conservative
,- parental sequence and daughter strand bind together
5. Alternative Double stranded DNA conformation
- A and Z DNA
Answer: A DNA
- dehydrated form
- right handed helix
- 11 bp per helical
- bp tilted 19 degrees
- major groove narrow and deep
- found with dsRNA and RNA-DNA duplex
z-DNA
- >1% of cellular DNA
- favored by G-C repeats and alternating purines-pyrimidines
- left handed helix
- 12 bp per turn
- bp tilted 9 degrees
- major groove flattened, nearly gone
,- bound by poxvirus E3L virulence factor and down regulates apoptosis genes
6. Non-duplex DNA structures
- cruciform DNA
Answer: - inverted repeat sequence
- favored by excessive negative supercoiling
- AT-rich cruciforms associated with 'fragile' DNA
7. Alternative modes of base pairing
Answer: Watson Crick A--T and C---G
- adenine is at anti-conformation
Hoogsteen
- adenine or guanine can be flipped to sin-conformation (ditterent H-bonding)
8. Hoogsteen base pairing
- when can it occur
Answer: - in triplex and quadruplex DNA structures
9. Triplex DNA
Answer: - pyrimidine rich strand
- negative supercoiling
, 10. Chair DNA
Answer: - two G-rich strands
- down regulation of c-myc transcription
11. Intrinsic Bends in DNA
Answer: - distortion of the ideal B-DNA conformation resulting from base stacking in the nucleotide
sequence
Eg. Adenine-tract DNA results in 20 degree bends
- also can be found in duplex-oligonucleotide model DNA
- causes 23 degree bend and mis-stacking of one GC
- DNA is not a uniform structure
12. Does B-DNA have a perfect structure?
Answer: No
- sequence specific local variation in twist between paired bases, sugat conformation, tilt of base pairs, rise distance,
etc.
13. Supercoiled DNA
- negative v. positive
Answer: - left handed under-twisted DNA is in a negative supercoil
ALREADY GRADED A+
1. DNA structure
Answer: - nucleic acid bases (purine (A,G) and pyrimidine (C,U,T))
- sugars (ribose, deoxyribose)
- sugars linked by phosphate groups (sugar-phosphate backbone)
*form antiparallel strands
2. In mammilian DNA, which base has various forms
Answer: cytosine
3. Chargaff's rule
Answer: A=T and C=G
4. Is DNA conservative or semi-conservative?
Answer: semi-conservative
,- parental sequence and daughter strand bind together
5. Alternative Double stranded DNA conformation
- A and Z DNA
Answer: A DNA
- dehydrated form
- right handed helix
- 11 bp per helical
- bp tilted 19 degrees
- major groove narrow and deep
- found with dsRNA and RNA-DNA duplex
z-DNA
- >1% of cellular DNA
- favored by G-C repeats and alternating purines-pyrimidines
- left handed helix
- 12 bp per turn
- bp tilted 9 degrees
- major groove flattened, nearly gone
,- bound by poxvirus E3L virulence factor and down regulates apoptosis genes
6. Non-duplex DNA structures
- cruciform DNA
Answer: - inverted repeat sequence
- favored by excessive negative supercoiling
- AT-rich cruciforms associated with 'fragile' DNA
7. Alternative modes of base pairing
Answer: Watson Crick A--T and C---G
- adenine is at anti-conformation
Hoogsteen
- adenine or guanine can be flipped to sin-conformation (ditterent H-bonding)
8. Hoogsteen base pairing
- when can it occur
Answer: - in triplex and quadruplex DNA structures
9. Triplex DNA
Answer: - pyrimidine rich strand
- negative supercoiling
, 10. Chair DNA
Answer: - two G-rich strands
- down regulation of c-myc transcription
11. Intrinsic Bends in DNA
Answer: - distortion of the ideal B-DNA conformation resulting from base stacking in the nucleotide
sequence
Eg. Adenine-tract DNA results in 20 degree bends
- also can be found in duplex-oligonucleotide model DNA
- causes 23 degree bend and mis-stacking of one GC
- DNA is not a uniform structure
12. Does B-DNA have a perfect structure?
Answer: No
- sequence specific local variation in twist between paired bases, sugat conformation, tilt of base pairs, rise distance,
etc.
13. Supercoiled DNA
- negative v. positive
Answer: - left handed under-twisted DNA is in a negative supercoil
