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BIOCH 200 winter sem 2024 > Nucleic acids > Flashcards

Nucleic acids Flashcards

1
Q

What does each colour represent in a ball and stick model?

A

Red- oxygen
Blue- Nitrogen
Grey/black - Carbon
White- Hydrogen
Yellow- Sulfur

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2
Q

Are these Pyrimidines or Purines? And what base is each?

A

They are pyrimidines, the left is cytosine and the right is thymine

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3
Q

Are these Pyrimidines or Purines? And what base is each?

A

They are Purines, the left is adenine and the right is guanine

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4
Q

What is this the common structure of?

A

A pyrimidine

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5
Q

What is this the common structure of?

A

A purine

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6
Q

What structure is this?

A

Uracil

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7
Q

What structure is this?

A

Deoxyribose

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8
Q

What structure is this?

A

Ribose

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9
Q

What is the numbering order of this base

A
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10
Q

what is the numbering of this base?

A
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11
Q

what did Avery-Macleod-McCarty discover when the mouse was injected with the rough strain?

A

the mouse lived

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11
Q

what did Avery-Macleod-McCarty discover when the mouse was injected with the smooth strain?

A

the mouse died

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12
Q

what did Avery-Macleod-McCarty discover when the mouse was injected with the heat killed smooth strain?

A

the mouse lived

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13
Q

what did Avery-Macleod-McCarty discover when the mouse was injected with the rough strain and heat killed smooth strain?

A

the mouse died

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14
Q

what is T2

A

a virulent virus that infects E.coli
-protein coat high in S and DNA high in P

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15
Q

what experiment proved to scientists that DNA is the genetic material and not protein?

A

Hershey-chase experiment showed that DNA is responsible for genetic transduction

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16
Q

what are nucleotides comprised of?

A

Phosphate, sugar and base

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17
Q

what determines the structure of nucleic acids?

A

the strucuture of nucleotides incorporated into nucleic acids

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18
Q

what is the structural difference between uracil and thymine?

A

thymine has a methyl group at C5

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19
Q

what is a nucleoside?

A

a base and a sugar (no phosphate group)

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20
Q

what N of the base is the 5C sugar linked to in pyrimidines vs purines?

A

N1 in pyrimidines
N9 in Purines

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21
Q

what is the suffix when naming purine nucleosides? what is adenine and guanine called when attatched to a ribose? and deoxyribose?

A

“osine”

adenosine and guanosine
deoxyadenosine and deoxyguanosine
-depends on the sugar attached

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22
Q

what is the suffix when naming pyrimidine nucleosides? what are cytosine, thymine and uracil called when attatched to a ribose? and deoxyribose?

A

“idine”

cytidine, thymidine, uridine

deoxycytidine, deoxythymidine, deoxyuridine

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23
Q

what is the difference between a phospho ester and a phosphodiester?

A

phospho diester is attatched to 2 R groups while a phospho ester is only attatched to one

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24
Q

what bond links a carbon group to a phosphate group?

A

phosphoesters

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25
Q

what bond links TWO different CARBONS to one phosphate group?

A

phosphodiester

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26
Q

what bond links TWO PHOSPHATES to each other?

A

phosphoanhydride

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27
Q

what is the conventional nucleotide structure sequence?

A

5’ to 3’

28
Q

is DNA or RNA more readily hydrolyzed?

A

RNA is more readily hydrolyzed due to the prescence of a 2’ OH

29
Q

is DNA or RNA more stable under basic conditions?

A

DNA is more stable due to abscence of 2’ OH

30
Q

how can uracil be formed from cytosine?

A

-spontaneous uncatalyzed reactions that convert C to U
-Uncorrected DNA mutation

31
Q

what products can form fromhydrolysis of phosphodiester bonds?

A

https://youtu.be/HO0B3j7HBuA?si=JO8xxZ_dj7DEJBYu

32
Q

are the bases polar or non-polar?

A

they are poorly soluble in water as they are largly hydrophobic

33
Q

is the sugar phosphate backbone polar or non-polar?

A

it is polar

34
Q

are pyrimidines numbered clockwise or counterclockwise?

A

clockwise

35
Q

are purines numbered clockwise or counterclockwise?

A

counterclockwise

36
Q

what kind of light do bases absorb? why?

A

they absorb UV light due to their electron delocalization of the ring

37
Q

what can UV absorption of DNA be used to determine?

A

purity
-1.95 is pure

38
Q

what wavelength is protein maximally absorbed at?

A

280nm

39
Q

will impure DNA have a higher or lower A260/A280 ratio?

A

lower

40
Q

what is A260nm used to measure?

A

the [nucleic acids] in a solution

41
Q

what carbons are joined together in phosphodiester bonds that link adjacent nucleotides?

A

carbon 3’ to the adjacent 5’ nucleotide carbon

42
Q

what is the prominent form of DNA in the body?

A

B form
-right handed twist

43
Q

what is the primary stabilising force in DNA?

A

base stacking forces
-van der waals (primary)
-hydrophobic

44
Q

why are bases in DNA largely excluded from H2O?

A

to stabalize H-bonds

45
Q

what part of DNA is exposed to H2O?

A

ribose / deoxyribose and phosphates due to their higher polarity

46
Q

how many base pair are there per turn of DNA?

A

~10 bp per turn

47
Q

what is found in the core of DNA?

A

the hydrophobic bases

48
Q

why is DNA more stable in high [salt]?

A

salt reduces electrostatic repulsion among phosphodiester groups
-low [salt] will destabalize H-bonds

49
Q

will absorption increase or decreases after denaturation?

A

increase in absorption will be seen at 260nm as strands separate

50
Q

what is Tm?

A

the midpoint of melting and is characteristic of the base composition

51
Q

does single stranded DNA or double stranded DNA have higher absorbance?

A

single stranded

52
Q

what is hyperchromicity?

A

high absorbance
-SS DNA

53
Q

what is hypochromicity?

A

low absorbance
-DS DNA

54
Q

what is the difference between nucleation and zippering?

A

they are both renaturation (reformation of DS DNA) to regain native conformation
-nucleation is slow
-zippering is fast

55
Q

why is Tm lower for AT in comparison to GC?

A

there are stronger base stacking interactions in GC than in AT

56
Q

what does Tm depend on?

A

primary structure, solvent environment and base pairing

57
Q

how can you tell this spot is AT rich?

A

there is more denaturation indicating high [AT]; Tm is lower so it requires less energy to unwind

58
Q

how does pH affect Tm?

A

it affects protonation state of DNA

59
Q

what does changing [salt] do to Tm?

A

decreased [salt] decreases Tm; destabilizes the double helix
-ions shield negative charges on phosphate backbone

60
Q

does increased hybridization following renaturation show an increase or decrease in Tm?

A

high Tm
-used to identify similar sequences in different species

61
Q

what kind of base pairing does DNA have?

A

interstrand

62
Q

what forces stabalize RNA?

A

same as DNA
-hydrogen bonds (base pairs)
-base stacking

63
Q

why can RNA form complex structures better than SS DNA?

A

the abscence of OH in DNA limits it from forming structures as complex as RNA

64
Q

can DNA and complimetary RNA forma a DS helix?

A

yes this is common in trancription

65
Q

what is the absorption 260nm/280nm ratio for pure RNA?

A

~2.1

66
Q

can RNA for DS helices?

A

yes, even though it is SS, it will still form some SS or DS helical structures in which G may pair with U

67
Q

why does the absorption melting curve for RNA begin higher than DNA?

A

due to the mixture of DS and SS strutcures

BIOCH 200 winter sem 2024 (13 decks)

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