BCH5413 Exam Study Guide Questions
and Answers Verified Solutions Latest
Update 2026/2027
Question:
In mammilian DNA, which base has various forms.
Answer:
cytosine
Question:
Chargaff's rule.
Answer:
A=T and C=G
Question:
Is DNA conservative or semi-conservative?.
Answer:
semi- conservative
- parental sequence and daughter strand bind together
Question:
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
Question:
Non-duplex DNA structures
- cruciform DNA.
Answer:
- inverted repeat sequence
- favored by excessive negative supercoiling
- AT-rich cruciforms associated with 'fragile' DNA
Question:
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 (different H-
bonding)
Question:
Hoogsteen base pairing
- when can it occur.
,Answer:
- in triplex and quadruplex DNA
structures
Question:
Triplex DNA.
Answer:
- pyrimidine rich strand
- negative supercoiling
Question:
Chair DNA.
Answer:
- two G-rich strands
- down regulation of c-myc transcription
Question:
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
Question:
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.
Question:
Supercoiled DNA
- negative v. positive.
Answer:
- left handed under-twisted DNA is in
a negative supercoil
- right handed over-twisted DNA is in a positive supercoil
*most is negatively supercoiled (topoisomerase releaves supercoiling)
Question:
Denaturation/Melting of DNA.
Answer:
- separation of DNA
strands
- can happen due to temp, salt concentration, G---C content, and
length of DNA (Hyperchromicity effect)
- as temp increases, absorption of light increases due to bases
becoming less shielded when they melt apart
Question:
The (greater/lower) the G+C content and the (higher/lower) the salt, the more stable the DNA
duplex.
Answer:
greater G+C and higher salt
Question:
What are higher stringency conditions.
Answer:
high heat and low salt
and Answers Verified Solutions Latest
Update 2026/2027
Question:
In mammilian DNA, which base has various forms.
Answer:
cytosine
Question:
Chargaff's rule.
Answer:
A=T and C=G
Question:
Is DNA conservative or semi-conservative?.
Answer:
semi- conservative
- parental sequence and daughter strand bind together
Question:
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
Question:
Non-duplex DNA structures
- cruciform DNA.
Answer:
- inverted repeat sequence
- favored by excessive negative supercoiling
- AT-rich cruciforms associated with 'fragile' DNA
Question:
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 (different H-
bonding)
Question:
Hoogsteen base pairing
- when can it occur.
,Answer:
- in triplex and quadruplex DNA
structures
Question:
Triplex DNA.
Answer:
- pyrimidine rich strand
- negative supercoiling
Question:
Chair DNA.
Answer:
- two G-rich strands
- down regulation of c-myc transcription
Question:
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
Question:
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.
Question:
Supercoiled DNA
- negative v. positive.
Answer:
- left handed under-twisted DNA is in
a negative supercoil
- right handed over-twisted DNA is in a positive supercoil
*most is negatively supercoiled (topoisomerase releaves supercoiling)
Question:
Denaturation/Melting of DNA.
Answer:
- separation of DNA
strands
- can happen due to temp, salt concentration, G---C content, and
length of DNA (Hyperchromicity effect)
- as temp increases, absorption of light increases due to bases
becoming less shielded when they melt apart
Question:
The (greater/lower) the G+C content and the (higher/lower) the salt, the more stable the DNA
duplex.
Answer:
greater G+C and higher salt
Question:
What are higher stringency conditions.
Answer:
high heat and low salt
