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mcb 124 > Nucleic Acid Structure > Flashcards

Nucleic Acid Structure Flashcards

(57 cards)

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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

Study These Flashcards
A

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

24
Q

deamination: what?
cytosine
5 methyl C

Study These Flashcards
A

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

but also deaminase enzymes that do this

25
oxidation of DNA to PICTURE
guanine! unstable - breaks into odd compounds
26
DRAW base pairings
picture
27
base pairing space
always 1/100 of angstrom unless mismatch present
28
ridges:
from phosphate backbone: 2 grooves that lend access to edges of bp
29
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
30
helical parameters
twists: bp per turn (10.5) rise: angstrom per bp pitch: angstrom per turn
31
base steps parameters
base step: going from bse 1 to 2: CpA is what?
32
base steps parameters: helical twist vs propeller twist
PICTURE | propeller twise: better if tilted a little
33
base steps parameters: ROLL VS TWIST
PICTURE
34
base steps parameters: rise, slide
picture
35
2 right handed helices: which most common?
A B-B!
36
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
37
A DNA:
RNA form or R/DNA hybrids larger twist, smaller rise -twisting packs in stiffer, wider, hollow in middle
38
grooves!
minor larger than major in A DNA PICTURE what defines major and minor is where protrusions are pointing
39
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
40
ZDNA in normal condition: test?
antibodies to z DNA ? no, binding to antibodies and induce | find naturally occuring protein binders
41
hairpins
iff some bp complimentary: hold on self and make a non-bp loop: loop face inward for max stacking less favorable-toxic
42
bulges:
noncomplimentary sequence: stuffed in so interrupt backbone
43
flaps and D loops: draw 5' and 3' flap
PICTURE d-LOOPS have perfect helices still both products of DNA repair
44
junctions | orientations
``` where stems meet PICTURE H=holliday = 4 intersect Y= 3 intersect unstacked open: bp in middle are open coaxially: ```
45
structuralist holliday junction | how to choose which cross over?
PICTURE
46
branch migration
pull on opposite ends PICTURE | by motor protein in bacteria (RUVAB)
47
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
48
holliday juction
2 pairs of same sequences -> holliday junction a subset of 4 way junctions non-hollliday junctions can't branch migrate
49
``` What kinds of sequences form  Stem Loops  4-way Junctions  Holliday Junctions (can migrate)  Y-junctions  Y-junctions that interconvert with Holliday junctions? ```
ok
50
non-WatsonCrick basepairs
from DNAPOL replication errors, damage, tertiary structures RNA,
51
hoogstein
wtf
52
telomere
rna dependent -primer for elongation; resistant to nuclease; regulate cell death probably FORM QUADRAPLEX
53
rna SECONDARY structure consists of
g base-pairing, mismatch, bulge and loop (4- 5 bp are most favored) energies to predict 2˚ structure element
54
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
55
tRNA
picture | picture
56
how to make tertary interactions
1. make modified bp 2. GNRA tetraloop tetraloop receptor: intra/intermolecualr 4/5 bp perfect, others infav, 3 impossible 3. pseoudoknots-
57
RNA folding is more significant than sequence
preach it to me, brotha so evolutionary, folding structure is more conserved than sequence: rnase example

mcb 124 (3 decks)

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