BCH5413 - Exam 1 with Actual Complete Questions and
Correct Detailed Answer with Rationales Already Graded A+ |
2026/2027 Updated
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 mammalian 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
How do sequence specific DNA binding proteins bind in a sequence specific manner - ANSWER-
the amino acids of sequence specific DNA binding proteins recognize the pattern of chemical
groups in the major/minor groove
- may interact through different bonding to permit sequence specific recognition
Zinc finger binding proteins - ANSWER-- custom designed DNA binding proteins
- two beta sheets attached to an alpha helix coordinate by a zinc molecule
- triple zinc finger can bind in the major groove of DNA
Zinc finger custom design - ANSWER-swapping the alpha helix domain and beta-hairpin
segments allows for different sequence specificity
Correct Detailed Answer with Rationales Already Graded A+ |
2026/2027 Updated
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 mammalian 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
How do sequence specific DNA binding proteins bind in a sequence specific manner - ANSWER-
the amino acids of sequence specific DNA binding proteins recognize the pattern of chemical
groups in the major/minor groove
- may interact through different bonding to permit sequence specific recognition
Zinc finger binding proteins - ANSWER-- custom designed DNA binding proteins
- two beta sheets attached to an alpha helix coordinate by a zinc molecule
- triple zinc finger can bind in the major groove of DNA
Zinc finger custom design - ANSWER-swapping the alpha helix domain and beta-hairpin
segments allows for different sequence specificity
