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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
southern blots are for
DNA
26
the pucker is controlled by the underlying
potential energy surface
27
the potential energy surface has
two distinct maxima and is connected by a broad low trough
28
the sugar pucker, base pairing, and base stacking are all in tension with the
phosphate-phosphate repulsions
29
what does salt do to the phosphate-phosphate repulsions
lowers the repulsion exponentially
30
DNA is polymorphic meaning
there is more than one structure
31
DNA structure depends on what external variables
salt concentration humidity temperature etc.
32
three major polymorphs of DNA
A form B form Z form
33
what form of DNA is right handed
A form and B form
34
what form of DNA is left handed
Z form
35
what form of DNA has the largest diameter
A form
36
what form of DNA has the smallest diameter
Z form
37
what form of DNA has the fewest base pairs per turn
B form with 10.5
38
what form of DNA has the largest number of base pairs per turn
Z form with 12
39
What form of DNA has the highest degree of base tilt
A form with 20 degrees
40
what form of DNA has the highest helix rise per base pair
A form DNA
41
Sugar pucker conformation for A form DNA
C-3' endo
42
sugar pucker conformation for B form DNA
C-2' endo
43
sugar pucker conformation for Z form DNA
C-2' endo for pyrimidines C-3' endo for purines
44
glycosyl bond conformation for A form DNA
Anti
45
glycosyl bond conformation for B form DNA
anti
46
glycosyl bond conformation for Z form DNA
anti for pyrimidines syn for purines
47
what form of DNA has less deep grooves and the bases are strongly inclined on the vertical helix axis
A form DNA
48
what form of DNA is chromosomal DNA
A form DNA
49
A form DNA is found under what conditions
high salt low humidity
50
double stranded RNA is close to what form of DNA
A form DNA
51
what form of NDA is more open and stretched out exposing the bases in the grooves
B form DNA
52
what form of DNA is most useful for proteins to read and process
B form DNA
53
under what conditions id B form DNA found
lower salt concentration high humidity
54
DNA changes shape with respect to
salt concentration
55
what happens to DNA with zero salt
DNA does not form a dimer
56
given the same number of base pairs, what form of DNA is the longest and which is the shortest
longest is Z form shortest is A form
57
what happens when A form DNA and B form DNA attach
a kink or bend is made in the DNA due to proteins present
58
what plays a major role in nucleic acid stabilization
base pi-stacking
59
the stacking geometry usually ... the rings to avoid both sterics and to allow for ... to be in proximity to each other
staggers unlike charges
60
how the bases stack depends strongly on the ... orientation as well as...
3'-5' Pu-Py vs Py-Pu vs Py-Py vs Pu-Pu stacking
61
forming duplexes is often called
hybridization
62
true hybridization requires
using two dissociated (melted) samples and mixing them.
63
replication involves
unwinding, duplication and rehybridization (renaturing).
64
there are many base pairing possibilities due to
the number of hydrogen bonding groups
65
triple helices
major groove binding base triplet specific high salt requirement
66
quadruplex
usually G-quartet loops of 3-4 bases binds ions specifically in the core
67
triplets of bases are reasonably
stable
68
regions of triplex DNA can occur in natural settings as in what structure
H-helix
69
G-quartets are very
stable
70
G-quartets are the basis for the
crystal packing of pure guanine and telomers
71
the center of a G-quartet is full of
oxygens so it us very electron rich with lone pairs
72
G-tetrads can form in
any G-rich sequence one strand or multiple stands
73
what does it take to dissociate a G-tetrad
12M LiCl and boiling
74
in regards to G-tetrads, what is the topology like
the bases can be syn or anti and the stands can either be parallel or antiparallel.
75
the loops between the G-tetrad are usually
T's

GSBS Biochem (13 decks)

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