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3382 > Nucleic Acid Structure > Flashcards

Nucleic Acid Structure Flashcards

1
Q

What are the forces that influence nucleic acid structure?

A

base stacking, base pairing, ionic interactions

applies to DNA and RNA

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2
Q

Which force influences DNA stability the most?

A

base stacking

base pairing HB is important for structure but less in stability

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3
Q

base stacking depends on…

A

sequence-dependent

order matters: AT vs TA on top

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4
Q

What is base stacking?

A

induced dipole and partial charge interactions between rings of bases (nitrogen atoms)

PI BOND STACKING

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5
Q

∆G of stacking is

A

the stability of base stacking; equilibrium of free energy btwn ss vs ds

more -ve = more stable

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6
Q

Which bases affect ∆G of stacking more?

A

G’s and C’s make more -ve = more stable
-> when G is on top of C

GC*GC -> -2.17

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7
Q

why is base stacking sequence dependent?

A

different charge and hydrophobic interactions result

hydrophobic groups together and opposite partial charges together

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8
Q

ss nucleic acid has higher ∆G because

A

no base stacking bc no base pairing
-> HB present with water

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9
Q

What is the advantage of ds to ss in HB?

A

ds = HB between bases
ss = HB between base and H2O

ds advantage = cooperativity

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10
Q

What are ionic interactions?

A

cations shield repulsion between negative phosphates

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11
Q

what are cation-DNA interactions mediated by?

A

H2O

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12
Q

What are the better cation shielding agents?

A

divalent (Mg2+) over monovalent (Na+, K+)

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13
Q

What does a DNA melting curve show?

A

increase in absorbance as temperature increases

higher GC content -> higher melting temperature

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14
Q

What are the 5 factors that influence DNA stability?

A
  1. length and sequence of DNA strands
  2. degree of complementarity
  3. nature of solvent
  4. [] and types of ions present
  5. pH
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15
Q

equation for melting temperature?

A

Tm = 2(A+T) + 4(G+C)

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16
Q

what is the effect of complementarity on DNA stability?

A

mismatches have steric effects -> pur-pur = lose helix and base stacking

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17
Q

What is intra-base pair coordinates?

A

movement of bases; degree of freedom between HB bases

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18
Q

What are the types of intra-base pair coordinates?

A
  1. shear
  2. buckle
  3. stretch
  4. propeller
  5. stagger
  6. opening
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19
Q

what are inter-base pair (step) coordinates?

A

base stacking that gives DNA flexibility to interact w/ other proteins

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20
Q

what are the types of inter-base pair (step) coordinates?

A
  1. shift
  2. tilt
  3. slide
  4. roll
  5. rise
  6. twist
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21
Q

Why does DNA form a double helix?

A
  • hydrophobic structures are driven together so that they aren’t exposed to water
  • phosphate sugar backbone can’t form structures where bases are directly ontop of each other
22
Q

What are the dimensions of a base pair?

A

18Å - base pair to base pair
3.4Å = 0.32nm - height of base pair
2.6Å - space between base pairs on top
6.0Å - middle of bp to middle of next bp

23
Q

Why is the space between base pairs on top of each other 2.6Å?

A

space is large enough for water to fit through

24
Q

bases are pushed together because…

A

water forms ordered networks around the hydrophobic regions -> unfavourable entropy

minimize water - hydrophobic interaction

25
Q

Why must there be a space between base pairs on top of each other?

A

steric hinderence of phosphate backbones due to inflexibility

26
Q

why can’t we have stair-like structure of DNA?

side by side or front and back

A

a lot of exposed hydrophobic bases area

this is why we need a TWIST -> helix

27
Q

what is the pitch length?

A

length of 1 complete turn of B-DNA
3.4 nm

28
Q

average or ideal B-DNA double helix is

A

10 bp/turn
right-handed

lowest energy conformation

29
Q

what is the width of B-DNA? what does it include?

A

2.4 nm
from phosphate to phosphate

30
Q

if you look down a helix…

A

it is a perfect cylinder

31
Q

what is base tilt?

what is it in B-DNA?

A

upward tilt of base from plane

in B-DNA = -1.2º

32
Q

what is propeller twist?

what is it in B-DNA?

A

angle between the base pair and sugar

16º

33
Q

What is A-DNA? where is usually found?

A

rare form of double helix seen when less hydrated and in RNA

34
Q

how is A-DNA different from B-DNA in structure?

A

major groove is much larger than minor groove

35
Q

characterstics of A-DNA?

A

right-handed
11 bp/turn

36
Q

what is the base tilt and propeller twist of A-DNA?

A

base tilt: 19º
propeller twist: 18º

37
Q

what is the width of A-DNA?

A

2.6 nm

38
Q

what is the pitch length and base-pair spacing? A-dna

A

pitch length - 2.5 nm
base-pair spacing - 0.23 nm

39
Q

How is Z-DNA different?

A

left-handed helix
has alternating Pu-Py on one side
Pu x-angles are syn

very rare and requires external forces acting on it

less extreme major groove/minor groove compared to A DNA

40
Q

What causes DNA to flex and utilize its degrees of freedom?

A

protein interactions, chromatin

41
Q

where are the degrees of freedom in DNA?

A

flexibility of the base, base stacking, backbone, transcription, replication

rotation around bonds

deviate from B-DNA

42
Q

dinucleotides vary in…

A

structural flexibility based on sequence

43
Q

What are the 10 differences between DNA and RNA?

A
  • ds vs ss
  • no OH vs 2’OH
  • thymine vs uracil
  • degraded less vs more labile
  • permanent vs moew transient
  • one function vs varied function
  • one major structure vs more varied structure
  • longer vs shorter
  • chromatin vs no chromatin
  • inside nucleus vs inside or outside nucleus
44
Q

What are the six structural elements of RNA?

what has the sixth type?

A
  1. duplexes
  2. single stranded regions
  3. hairpins
  4. bulges
  5. internal loops
  6. junctions

tRNA have junctions

45
Q

most RNA base pairs are

A

GC or AU but other combinations of non-watson crick are common

46
Q

RNA base pairs non-Watson-Crick when…

does RNA form similar to B-DNA structure?

A

ss are across from each other
forced to bp due to proximity form HB (acceptor/donor HBs align)

not standard ds of B-DNA which allow for flexibility

47
Q

melting/unzipping of base pairs occurs easier

A

non-Watson Crick base pairing in experimental conditions

48
Q

what are pseudoknots? when do they occur?

A

hairpin loop within another hairpin loop

often used by viruses for protection/disguse against host and switches structural conformation when needed

49
Q

what does pseudoknot structural switching by viruses result in?

A

different functional properties for the RNA, often involved in ribosome interactions

give RNA unique propoerties: translation (frameshifts, regulation of expression, control of initiation) and general gene expression (especially in viruses)

50
Q

DNA melting temperature depends on

A

strand length, sequence and environmental factors

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