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Biochemistry > Exam 3 Nucleic Acid Structure and Function > Flashcards

Exam 3 Nucleic Acid Structure and Function Flashcards

1
Q

what are the 3 parts to a nucleotide

A
  1. phosphate group
  2. sugar
  3. nitrogenous base
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2
Q

nucleoTides have _ whereas nucleoSides do not

A

nucleotides HAVE PHOSPHATES

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3
Q

what is the pKa of (PO4)

A

around 0-2

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4
Q

what does the pKa of (PO4) help to explain?

A

explains why DNA and RNA are negatively charged because at nearly all pHs, the pH > pKa and thus deprotonated at our phosphate

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5
Q

ATP is special because it is:

A

a nucleoside triphosphate and a nucleotide because has at least 1 phosphate present

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6
Q

the sugar in the nucleotide:

1’ is where:

A

the anomeric carbon where the nitrogenous base attaches

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7
Q

nitrogenous base attach to sugars via a _ bond

A

glycosidic bond (attaching a sugar to something)

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8
Q

the sugar in the nucleotide:

2’ is where:

A

can can (OH) = ribose vs having (-H) = deoxyribose

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9
Q

the sugar in the nucleotide:

3’ is where:

A

phosphodiester bond forms here; can link to next phosphate in the chain

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10
Q

the sugar in the nucleotide:

4’ is where:

A

O in ring; contributes the oxygen to the ring

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11
Q

the sugar in the nucleotide:

5’ is where:

A

where (PO4-) attaches in nucleotide structure and other half of phosphodiester bond; C 3’ & 5’ in relation to orientation of dna and rna originate. Which oxygens of which carbons are associate with our phosphate

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12
Q

Carbon 3 and 5 in sugar is important because:

A

in relation to orientation of DNA and RNA originate; associates with our phosphate

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13
Q

c-3’-endo: which carbon is up?

A

3’

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14
Q

c-2’=endo: which carbon is up?

A

2’

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15
Q

purines have _ ring(s)

A

2

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16
Q

pyrimidines have _ ring(s)

A

1

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17
Q

in DNA, purines always base-pair with _ to create:

A

pyrimidines; creates an antiparallel double-helix of consistent width

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18
Q

In nature, nucleic acid strand growth is in the _ to _ direction

A

growth is always 5’ to 3’

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19
Q

what are the 3 forms of double helix structure

A

B, A, and Z

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20
Q

the B and A form is _ handed compared to Z

A

B and A are right handed whereas Z is left handed

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21
Q

B form has _ bp/turn alluding to

A

10-10.4 alluding to a compact structure

22
Q

A form has _ bp/turn alluding to

A

10.7-11 alluding to more spread out structure

23
Q

RNA will fold back on itself to make _

A

double stranded regions

24
Q

B form has _ major groove

A

wide, deep

25
Q

B form has _ minor groove

A

narrow, shallow

26
Q

B form bp plane vs helix axis is

A

perfectly perpendicular (0-1 degree)

27
Q

A and Z form bp plane vs helix axis is

A

skewed (19 and 9 degree)

28
Q

B form sugar pucker is _-endo

A

C2’-endo

29
Q

A form sugar pucker is _-endo

A

C3’-endo

30
Q

constitutional isomers are _

A

tautomers (follow the (-H)

31
Q

conformational isomers are _

A

reversible rotations (eg sugar pucker)

32
Q

syn conformational isomers result in

A

Left; base is sitting over top of sugar

33
Q

anti conformational isomers result in

A

right; base is away from sugar and less ‘bulky’

34
Q

B and A form nitrogenous base orientation is:

A

anti

35
Q

what form of double helix is physiologically relevant

A

B form (DNA)

36
Q

what form of double helix is seen primarily in RNA

A

A form

37
Q

_, _, and _ can be artificially induced via changing amount of water and/or salt

A

A, C, and Z DNA

38
Q

DNA function is _

A

storage

39
Q

RNA function is:

A

transport, catalysis, and regulation

40
Q

Pyrimidines in DNA include:

A

C and T

41
Q

pyrimidines in RNA include:

A

C and U

42
Q

2 hairpins = _

A

a cruciform

43
Q

hairpins and cruciforms require

A

a palindromic sequence (inverted repeat)

44
Q

T/F: triplexes can use DNA/RNA and may or may not occur in nature

A

true

45
Q

triplexes require a - duplex

A

homopurine-homopyrimidine duplex

46
Q

triplexes uses _ H bonds

A

hoogsteen

47
Q

what groove accommodates 3rd strand

A

major groove

48
Q

with H bonding in Hoogsteen, makes attachments to _ only

A

purines

49
Q

cysteine is protonated in hoogsteen H bond, this means

A

protonated at N (amine) thus need pH < pKa ie more stable in acidic pHs

50
Q

quadruplexes only happens when:

A

you have 4 guanines only

51
Q

quadruplexes occur at:

A

telomeres and some promoters

Biochemistry (32 decks)

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