Nucleic Acid Structure Flashcards

1
Q

nucloside

A

base+ ribose

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2
Q

nucleotide

A

base + ribose + phosphATE

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3
Q

Draw ribose

A

picture

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4
Q

draw deoxyribose

A

picture

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5
Q

bond between sugar and backbone

A

N-glycosidic

strong, but less so than C-N

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6
Q

DRAW adenine

A

picture

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7
Q

DRAW thymine

A

picture

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8
Q

DRAW cytosiine

A

picture

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9
Q

DRAW guanine

A

picture

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10
Q

DRAW uracine

A

picture

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11
Q

symbol for: nucleoside, nucleobase, nucleotide

A

N
ACTG
pN or Np

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12
Q

how many rotatable bonds in nucleotide?

which notable?

A

7
chi angle - between base and sugar- either anti or syn
base away from sugar or on top of

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13
Q

sugar pucker

so what?

A

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

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14
Q

3 reading frames per strand bc

A

codons in triplets

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15
Q

charge per nucleotide

A

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

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16
Q

RNA vs DNA

chemical stability

A

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

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17
Q

code for purine, pyrimidine

A

R, Y

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18
Q

isomer of bases: it makes a ___

A

base tautomer: o=c-nh to HO-c=n

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19
Q

ionization of adenine

A

PICTURE

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20
Q

ionizaon of guanine

A

PICTURE

responsible of depurination

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21
Q

depuination mechanism

A

PICTURE

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22
Q

most common DNA modification

A

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

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23
Q

alkylation of ___

sites PICTURE

A

less base pairing/stearic -> doesn’t work well

24
Q

deamination: what?
cytosine
5 methyl C

A

spontaneous loss of amino groups
cytosine-> uracil PICTURE
5meC->thymine PICTURE

but also deaminase enzymes that do this

25
Q

oxidation of DNA to PICTURE

A

guanine! unstable - breaks into odd compounds

26
Q

DRAW base pairings

A

picture

27
Q

base pairing space

A

always 1/100 of angstrom unless mismatch present

28
Q

ridges:

A

from phosphate backbone: 2 grooves that lend access to edges of bp

29
Q

F that holds DNA strands together?

helix?

A

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

30
Q

helical parameters

A

twists: bp per turn (10.5)
rise: angstrom per bp
pitch: angstrom per turn

31
Q

base steps parameters

A

base step: going from bse 1 to 2: CpA is what?

32
Q

base steps parameters: helical twist vs propeller twist

A

PICTURE

propeller twise: better if tilted a little

33
Q

base steps parameters: ROLL VS TWIST

A

PICTURE

34
Q

base steps parameters: rise, slide

A

picture

35
Q

2 right handed helices: which most common?

A

A B-B!

36
Q

BDNA: twist, rise

grooves can fit:

A

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

37
Q

A DNA:

A

RNA form or R/DNA hybrids

larger twist, smaller rise -twisting packs in
stiffer, wider, hollow in middle

38
Q

grooves!

A

minor larger than major in A DNA
PICTURE
what defines major and minor is where protrusions are pointing

39
Q

Z DNA - left handed

A
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

40
Q

ZDNA in normal condition: test?

A

antibodies to z DNA ? no, binding to antibodies and induce

find naturally occuring protein binders

41
Q

hairpins

A

iff some bp complimentary: hold on self and make a non-bp loop: loop face inward for max stacking

less favorable-toxic

42
Q

bulges:

A

noncomplimentary sequence: stuffed in so interrupt backbone

43
Q

flaps and D loops: draw 5’ and 3’ flap

A

PICTURE
d-LOOPS have perfect helices still
both products of DNA repair

44
Q

junctions

orientations

A
where stems meet
PICTURE
H=holliday = 4 intersect
Y= 3 intersect
unstacked open: bp in middle are open
coaxially:
45
Q

structuralist holliday junction

how to choose which cross over?

A

PICTURE

46
Q

branch migration

A

pull on opposite ends PICTURE

by motor protein in bacteria (RUVAB)

47
Q

y junctions

A

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

48
Q

holliday juction

A

2 pairs of same sequences -> holliday junction
a subset of 4 way junctions
non-hollliday junctions can’t branch migrate

49
Q
What kinds of sequences form
 Stem Loops
 4-way Junctions
 Holliday Junctions (can migrate)
 Y-junctions
 Y-junctions that interconvert with
Holliday junctions?
A

ok

50
Q

non-WatsonCrick basepairs

A

from DNAPOL replication errors, damage, tertiary structures RNA,

51
Q

hoogstein

A

wtf

52
Q

telomere

A

rna dependent -primer for elongation; resistant to nuclease; regulate cell death

probably FORM QUADRAPLEX

53
Q

rna SECONDARY structure consists of

A

g base-pairing, mismatch, bulge and loop (4-
5 bp are most favored) energies to predict

structure element

54
Q

rules for predicting RNA secondary structure

A

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

55
Q

tRNA

A

picture

picture

56
Q

how to make tertary interactions

A
  1. make modified bp
  2. GNRA tetraloop tetraloop receptor: intra/intermolecualr
    4/5 bp perfect, others infav, 3 impossible
  3. pseoudoknots-
57
Q

RNA folding is more significant than sequence

A

preach it to me, brotha

so evolutionary, folding structure is more conserved than sequence: rnase example