BCH5413 - EXAM 1 | STUDY GUIDE QUESTIONS
AND CORRECT DETAILED ANSWERS
(VERIFIED ANSWERS) | ALREADY GRADED A+ |
LATEST UPDATE 2025-2026
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
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.
Where are chemical groups present in the DNA - ANSWER major and minor
groove
AND CORRECT DETAILED ANSWERS
(VERIFIED ANSWERS) | ALREADY GRADED A+ |
LATEST UPDATE 2025-2026
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
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.
Where are chemical groups present in the DNA - ANSWER major and minor
groove
