Exam 3 Nucleic Acid Structure and Function Flashcards
what are the 3 parts to a nucleotide
- phosphate group
- sugar
- nitrogenous base
nucleoTides have _ whereas nucleoSides do not
nucleotides HAVE PHOSPHATES
what is the pKa of (PO4)
around 0-2
what does the pKa of (PO4) help to explain?
explains why DNA and RNA are negatively charged because at nearly all pHs, the pH > pKa and thus deprotonated at our phosphate
ATP is special because it is:
a nucleoside triphosphate and a nucleotide because has at least 1 phosphate present
the sugar in the nucleotide:
1’ is where:
the anomeric carbon where the nitrogenous base attaches
nitrogenous base attach to sugars via a _ bond
glycosidic bond (attaching a sugar to something)
the sugar in the nucleotide:
2’ is where:
can can (OH) = ribose vs having (-H) = deoxyribose
the sugar in the nucleotide:
3’ is where:
phosphodiester bond forms here; can link to next phosphate in the chain
the sugar in the nucleotide:
4’ is where:
O in ring; contributes the oxygen to the ring
the sugar in the nucleotide:
5’ is where:
where (PO4-) attaches in nucleotide structure and other half of phosphodiester bond; C 3’ & 5’ in relation to orientation of dna and rna originate. Which oxygens of which carbons are associate with our phosphate
Carbon 3 and 5 in sugar is important because:
in relation to orientation of DNA and RNA originate; associates with our phosphate
c-3’-endo: which carbon is up?
3’
c-2’=endo: which carbon is up?
2’
purines have _ ring(s)
2
pyrimidines have _ ring(s)
1
in DNA, purines always base-pair with _ to create:
pyrimidines; creates an antiparallel double-helix of consistent width
In nature, nucleic acid strand growth is in the _ to _ direction
growth is always 5’ to 3’
what are the 3 forms of double helix structure
B, A, and Z
the B and A form is _ handed compared to Z
B and A are right handed whereas Z is left handed
B form has _ bp/turn alluding to
10-10.4 alluding to a compact structure
A form has _ bp/turn alluding to
10.7-11 alluding to more spread out structure
RNA will fold back on itself to make _
double stranded regions
B form has _ major groove
wide, deep
B form has _ minor groove
narrow, shallow
B form bp plane vs helix axis is
perfectly perpendicular (0-1 degree)
A and Z form bp plane vs helix axis is
skewed (19 and 9 degree)
B form sugar pucker is _-endo
C2’-endo
A form sugar pucker is _-endo
C3’-endo
constitutional isomers are _
tautomers (follow the (-H)
conformational isomers are _
reversible rotations (eg sugar pucker)
syn conformational isomers result in
Left; base is sitting over top of sugar
anti conformational isomers result in
right; base is away from sugar and less ‘bulky’
B and A form nitrogenous base orientation is:
anti
what form of double helix is physiologically relevant
B form (DNA)
what form of double helix is seen primarily in RNA
A form
_, _, and _ can be artificially induced via changing amount of water and/or salt
A, C, and Z DNA
DNA function is _
storage
RNA function is:
transport, catalysis, and regulation
Pyrimidines in DNA include:
C and T
pyrimidines in RNA include:
C and U
2 hairpins = _
a cruciform
hairpins and cruciforms require
a palindromic sequence (inverted repeat)
T/F: triplexes can use DNA/RNA and may or may not occur in nature
true
triplexes require a - duplex
homopurine-homopyrimidine duplex
triplexes uses _ H bonds
hoogsteen
what groove accommodates 3rd strand
major groove
with H bonding in Hoogsteen, makes attachments to _ only
purines
cysteine is protonated in hoogsteen H bond, this means
protonated at N (amine) thus need pH < pKa ie more stable in acidic pHs
quadruplexes only happens when:
you have 4 guanines only
quadruplexes occur at:
telomeres and some promoters
