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GSBS Biochem > DNA 3 > Flashcards

DNA 3 Flashcards

1
Q

single bonds are very

A

flexible

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2
Q

nucleic acids have many… per monomer

A

torsions

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3
Q

regarding the backbone and sugar, which torsion angle is the same

A

delta and V3

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4
Q

torsion angles in the backbone

A

alpha
beta
gamma
delta
epsilon
zeta

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5
Q

glycosidic torsion angle

A

X

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6
Q

sugar torsion angles

A

V0
V1
V2
V3
V4

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7
Q

which torsion angle differs between the pyrimidines and the purines

A

the glycosidic torsion angle X

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8
Q

sugars pucker because of

A

tetrahedral carbons

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9
Q

endo and exo are defined with respect to

A

the orientation of the base at C1

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10
Q

the central dihedral defines the

A

torsion angle

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11
Q

cis and syn are

A

interchangeable

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12
Q

anti and trans are

A

interchangeable

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13
Q

between -30 and +30 degrees, it is considered

A

cis or syn

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14
Q

between 30 and 90 degrees, it is considered

A

+syn
+gauche

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15
Q

between -30 and -90 degrees it is considered

A

-syn
-gauche

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16
Q

between 150 and -150 (210) degrees it is considered

A

trans or anti

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17
Q

idealized envelopes and twist forms have a precise

A

nomenclature

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18
Q

E^3 means

A

Endo
the 3’ carbon is pulled up

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19
Q

E^2 means

A

Endo
the 2’ carbon is pulled up

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20
Q

^3↓2T means

A

Twist
the 3’ carbon is pulled up and the 2’carbon is pulled down
o on top

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21
Q

^3T↓2

A

Twist
the 3’ carbon is pulled up and the 2’carbon is pulled down
o on bottom

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22
Q

North puckers inducate

A

A-form DNA
RNA/DNA

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23
Q

South puckers indicate

A

B-Form DNA
DNA not RNA

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24
Q

northern blots are for

A

RNA

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25
Q

southern blots are for

A

DNA

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26
Q

the pucker is controlled by the underlying

A

potential energy surface

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27
Q

the potential energy surface has

A

two distinct maxima and is connected by a broad low trough

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28
Q

the sugar pucker, base pairing, and base stacking are all in tension with the

A

phosphate-phosphate repulsions

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29
Q

what does salt do to the phosphate-phosphate repulsions

A

lowers the repulsion exponentially

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30
Q

DNA is polymorphic meaning

A

there is more than one structure

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31
Q

DNA structure depends on what external variables

A

salt concentration
humidity
temperature
etc.

32
Q

three major polymorphs of DNA

A

A form
B form
Z form

33
Q

what form of DNA is right handed

A

A form and B form

34
Q

what form of DNA is left handed

A

Z form

35
Q

what form of DNA has the largest diameter

A

A form

36
Q

what form of DNA has the smallest diameter

A

Z form

37
Q

what form of DNA has the fewest base pairs per turn

A

B form with 10.5

38
Q

what form of DNA has the largest number of base pairs per turn

A

Z form with 12

39
Q

What form of DNA has the highest degree of base tilt

A

A form with 20 degrees

40
Q

what form of DNA has the highest helix rise per base pair

A

A form DNA

41
Q

Sugar pucker conformation for A form DNA

A

C-3’ endo

42
Q

sugar pucker conformation for B form DNA

A

C-2’ endo

43
Q

sugar pucker conformation for Z form DNA

A

C-2’ endo for pyrimidines
C-3’ endo for purines

44
Q

glycosyl bond conformation for A form DNA

A

Anti

45
Q

glycosyl bond conformation for B form DNA

A

anti

46
Q

glycosyl bond conformation for Z form DNA

A

anti for pyrimidines
syn for purines

47
Q

what form of DNA has less deep grooves and the bases are strongly inclined on the vertical helix axis

A

A form DNA

48
Q

what form of DNA is chromosomal DNA

A

A form DNA

49
Q

A form DNA is found under what conditions

A

high salt
low humidity

50
Q

double stranded RNA is close to what form of DNA

A

A form DNA

51
Q

what form of NDA is more open and stretched out exposing the bases in the grooves

A

B form DNA

52
Q

what form of DNA is most useful for proteins to read and process

A

B form DNA

53
Q

under what conditions id B form DNA found

A

lower salt concentration
high humidity

54
Q

DNA changes shape with respect to

A

salt concentration

55
Q

what happens to DNA with zero salt

A

DNA does not form a dimer

56
Q

given the same number of base pairs, what form of DNA is the longest and which is the shortest

A

longest is Z form
shortest is A form

57
Q

what happens when A form DNA and B form DNA attach

A

a kink or bend is made in the DNA due to proteins present

58
Q

what plays a major role in nucleic acid stabilization

A

base pi-stacking

59
Q

the stacking geometry usually … the rings to avoid both sterics and to allow for … to be in proximity to each other

A

staggers
unlike charges

60
Q

how the bases stack depends strongly on the … orientation as well as…

A

3’-5’
Pu-Py vs Py-Pu vs Py-Py vs Pu-Pu stacking

61
Q

forming duplexes is often called

A

hybridization

62
Q

true hybridization requires

A

using two dissociated (melted) samples and mixing them.

63
Q

replication involves

A

unwinding, duplication and rehybridization (renaturing).

64
Q

there are many base pairing possibilities due to

A

the number of hydrogen bonding groups

65
Q

triple helices

A

major groove binding
base triplet specific
high salt requirement

66
Q

quadruplex

A

usually G-quartet
loops of 3-4 bases
binds ions specifically in the core

67
Q

triplets of bases are reasonably

A

stable

68
Q

regions of triplex DNA can occur in natural settings as in what structure

A

H-helix

69
Q

G-quartets are very

A

stable

70
Q

G-quartets are the basis for the

A

crystal packing of pure guanine and telomers

71
Q

the center of a G-quartet is full of

A

oxygens so it us very electron rich with lone pairs

72
Q

G-tetrads can form in

A

any G-rich sequence
one strand or multiple stands

73
Q

what does it take to dissociate a G-tetrad

A

12M LiCl and boiling

74
Q

in regards to G-tetrads, what is the topology like

A

the bases can be syn or anti and the stands can either be parallel or antiparallel.

75
Q

the loops between the G-tetrad are usually

A

T’s

GSBS Biochem (10 decks)

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