Nucleic Acid Structure Flashcards
nucloside
base+ ribose
nucleotide
base + ribose + phosphATE
Draw ribose
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draw deoxyribose
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bond between sugar and backbone
N-glycosidic
strong, but less so than C-N
DRAW adenine
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DRAW thymine
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DRAW cytosiine
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DRAW guanine
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DRAW uracine
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symbol for: nucleoside, nucleobase, nucleotide
N
ACTG
pN or Np
how many rotatable bonds in nucleotide?
which notable?
7
chi angle - between base and sugar- either anti or syn
base away from sugar or on top of
sugar pucker
so what?
sugar base not planar - C2; endo/exp (up/dow) C3’
given base and C5 up
changes “inclination of phosphate of
charactaristic - RNA and DNA tends toward endo
3 reading frames per strand bc
codons in triplets
charge per nucleotide
1 negative: shared between 2 ox in phos - pKALOW
5’ phosphate ends have 2: one with low PKA, other about 7 for enzymes to distinguish from s
RNA vs DNA
chemical stability
low chemical stability(acid/base) because of 2’ OH: perfectly oriented to undergo esterification to 3’ophosphate to break chain; DNA needs enzyme to do so.
+base-> backbone cleavag
+acid -> 3’-2’ migration (not bioactive) or depurination
DNA: good, but still acid labile
code for purine, pyrimidine
R, Y
isomer of bases: it makes a ___
base tautomer: o=c-nh to HO-c=n
ionization of adenine
PICTURE
ionizaon of guanine
PICTURE
responsible of depurination
depuination mechanism
PICTURE
most common DNA modification
methylation - post-transcriptional
6-me adenine in prok; 5-methyl cytosine both
prokaryotes: tag parental strand and self, restriction/modification system(in bateria-cut other dna)
5-methyl cytosine: 1st signal for silence by pack up into bundle
alkylation of ___
sites PICTURE
less base pairing/stearic -> doesn’t work well
deamination: what?
cytosine
5 methyl C
spontaneous loss of amino groups
cytosine-> uracil PICTURE
5meC->thymine PICTURE
but also deaminase enzymes that do this
oxidation of DNA to PICTURE
guanine! unstable - breaks into odd compounds
DRAW base pairings
picture
base pairing space
always 1/100 of angstrom unless mismatch present
ridges:
from phosphate backbone: 2 grooves that lend access to edges of bp
F that holds DNA strands together?
helix?
london dispersion forces from base stacking!
H bonds only are responsible for specificity
even in single stranded, they still try to stack
cations stabilize phosphate
helical parameters
twists: bp per turn (10.5)
rise: angstrom per bp
pitch: angstrom per turn
base steps parameters
base step: going from bse 1 to 2: CpA is what?
base steps parameters: helical twist vs propeller twist
PICTURE
propeller twise: better if tilted a little
base steps parameters: ROLL VS TWIST
PICTURE
base steps parameters: rise, slide
picture
2 right handed helices: which most common?
A B-B!
BDNA: twist, rise
grooves can fit:
DNA form
10.5bp/turn; 3.4 angstrom per bp (thickness of aromatic ring-stearically right on top of each other!)
MAJOR:alpha helix
mino: polypeptide strand
A DNA:
RNA form or R/DNA hybrids
larger twist, smaller rise -twisting packs in
stiffer, wider, hollow in middle
grooves!
minor larger than major in A DNA
PICTURE
what defines major and minor is where protrusions are pointing
Z DNA - left handed
RNa and DNA both zig zaggy backbone less wound than others, larger rise bases not stacked- not stabliz grooves shallow, normal length
*synG/anti C(normal) - so must be poly GC form
from negative supercoiling, hi salt, special protein
ZDNA in normal condition: test?
antibodies to z DNA ? no, binding to antibodies and induce
find naturally occuring protein binders
hairpins
iff some bp complimentary: hold on self and make a non-bp loop: loop face inward for max stacking
less favorable-toxic
bulges:
noncomplimentary sequence: stuffed in so interrupt backbone
flaps and D loops: draw 5’ and 3’ flap
PICTURE
d-LOOPS have perfect helices still
both products of DNA repair
junctions
orientations
where stems meet PICTURE H=holliday = 4 intersect Y= 3 intersect unstacked open: bp in middle are open coaxially:
structuralist holliday junction
how to choose which cross over?
PICTURE
branch migration
pull on opposite ends PICTURE
by motor protein in bacteria (RUVAB)
y junctions
always open
not in nature
natural proteins recognize because similar to holliday
natural y junctions are knicked - can stacked - in replication forks! PICTURE
closed if bulges are there
picture
holliday juction
2 pairs of same sequences -> holliday junction
a subset of 4 way junctions
non-hollliday junctions can’t branch migrate
What kinds of sequences form Stem Loops 4-way Junctions Holliday Junctions (can migrate) Y-junctions Y-junctions that interconvert with Holliday junctions?
ok
non-WatsonCrick basepairs
from DNAPOL replication errors, damage, tertiary structures RNA,
hoogstein
wtf
telomere
rna dependent -primer for elongation; resistant to nuclease; regulate cell death
probably FORM QUADRAPLEX
rna SECONDARY structure consists of
g base-pairing, mismatch, bulge and loop (4-
5 bp are most favored) energies to predict
2˚
structure element
rules for predicting RNA secondary structure
Tinoco Rules
accurate for ordered units of 2 bp (4 bases)-incorporates stacking energy, that helix initiation takes energy, ends (GC better)
not good for prediction tertiary
tRNA
picture
picture
how to make tertary interactions
- make modified bp
- GNRA tetraloop tetraloop receptor: intra/intermolecualr
4/5 bp perfect, others infav, 3 impossible - pseoudoknots-
RNA folding is more significant than sequence
preach it to me, brotha
so evolutionary, folding structure is more conserved than sequence: rnase example
