BCH5413 TEST 2 PRACTICE EXAM 2026 TEST
PAPER QUESTIONS AND SOLUTIONS
REVISED VERSION GRADED A+
⩥ In mammilian DNA, which base has various forms. Answer: cytosine
⩥ Chargaff's rule. Answer: A=T and C=G
⩥ Is DNA conservative or semi-conservative?. Answer: semi-
conservative
- parental sequence and daughter strand bind together
⩥ 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
⩥ Non-duplex DNA structures
- cruciform DNA. Answer: - inverted repeat sequence
- favored by excessive negative supercoiling
- AT-rich cruciforms associated with 'fragile' DNA
⩥ 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)
,⩥ Hoogsteen base pairing
- when can it occur. Answer: - in triplex and quadruplex DNA structures
⩥ Triplex DNA. Answer: - pyrimidine rich strand
- negative supercoiling
⩥ Chair DNA. Answer: - two G-rich strands
- down regulation of c-myc transcription
⩥ 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
⩥ 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.
⩥ 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)
⩥ 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
⩥ 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
⩥ What are higher stringency conditions. Answer: high heat and low salt
⩥ What else can melt DNA?. Answer: pH
⩥ DNA renaturing and hybridization. Answer: - add complementary
RNA and re-anneal by gradually lowering temp.
PAPER QUESTIONS AND SOLUTIONS
REVISED VERSION GRADED A+
⩥ In mammilian DNA, which base has various forms. Answer: cytosine
⩥ Chargaff's rule. Answer: A=T and C=G
⩥ Is DNA conservative or semi-conservative?. Answer: semi-
conservative
- parental sequence and daughter strand bind together
⩥ 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
⩥ Non-duplex DNA structures
- cruciform DNA. Answer: - inverted repeat sequence
- favored by excessive negative supercoiling
- AT-rich cruciforms associated with 'fragile' DNA
⩥ 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)
,⩥ Hoogsteen base pairing
- when can it occur. Answer: - in triplex and quadruplex DNA structures
⩥ Triplex DNA. Answer: - pyrimidine rich strand
- negative supercoiling
⩥ Chair DNA. Answer: - two G-rich strands
- down regulation of c-myc transcription
⩥ 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
⩥ 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.
⩥ 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)
⩥ 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
⩥ 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
⩥ What are higher stringency conditions. Answer: high heat and low salt
⩥ What else can melt DNA?. Answer: pH
⩥ DNA renaturing and hybridization. Answer: - add complementary
RNA and re-anneal by gradually lowering temp.
