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biochemistry Jonklaas > test 3: nucleic acid > Flashcards

test 3: nucleic acid Flashcards

1
Q

what are the nitrogenous bases

A

cytosine, thymine, uracil , adenine and guanine

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2
Q

what are the pyramidine bases

A

cytosine, thymine, uracil

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3
Q

what are the purine bases

A

adenine, guanine

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4
Q

what absorbance do all of the bases have

A

260 nm

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5
Q

what is a common tautomeric form

A

lactam(keto)

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6
Q

what is a rare tautomeric form

A

lacti (enol)

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7
Q

what is a nucleoside

A

base+ sugar

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8
Q

what is sugar

A

D ribose or 2-deoxy-D ribose

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9
Q

what connects nucleosides to the base

A

B-N-glycosidic bond

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10
Q

how is a nucleoside numbered

A

1st number goes to where the base is attatched to the sugar and then 5 is HOCH2

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11
Q

what is a nucleotide

A

nucleoside + phosphate
- phosphoric acid is extrified with an -OH of the monosacc either the 3’ or the 5’OH

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12
Q

what does esterified mean

A

an acid reactions with an alcohol to make an ester

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13
Q

what is 3-5 cyclic adenosine monosphosphate (cyclic adenosinde monophosphate, cAMP)

A
  • derived from ATP
  • used in intracellular signal transduction( signalingn) as a second messenger
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14
Q

wht does the 2nd messenger do in signal transduction

A

amplifies the signal

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15
Q

wht are the bases for DNA and RNA

A

dna: ATGC
RNA; AUGC

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16
Q

what are the nucleoside names based off of the base

A
  1. adenine= adenosine
  2. guanine= guanosine
  3. cytosine= cytidine
  4. Uracil = uridine
  5. thymine = deoxythymidine
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17
Q

what is an example of a nucleoside/ tide in medicine

A
  • antivirals
  • zidovudine = nucleoside analog reverse transcriptase inhibitor
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18
Q

what does NRTI do

A

used to treat HIv

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19
Q

zidovudine is what analog

A

uracil

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20
Q

what is emtricitabine

A
  • used for the treatment of HIV in adults
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21
Q

what analog is emtricitabine

A

cytosine analaog

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22
Q

what contains minor bases in RNA

A

tRNA

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23
Q

what does a methylated form of a major base mean in DNA

A
  • role of regulating and protecting genetic info
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24
Q

what are the names of the xanthines

A

hypoxanthine, inosine, xanthine

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25
Q

where is inosine found

A

in tRNA for wobble base pairs

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26
Q

what structure is this

A

hypoxanthine

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27
Q

what structure is this

A

inosine
insoine = Hypoxanthine + ribose

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28
Q

what structue is this

A

xanthine

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29
Q

what are polynucleotides

A
  • nucleic acids
  • joined by phosphodiester linkage
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30
Q

what is the primary structure of dna and rna

A
  • sequence read from 5’ to 3’ end
  • RNA: 5’-AUCG-3’ or AUGC
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31
Q

what bond is this showing

A

phosphodiester bond

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32
Q

what structure is this

A

phosphoester

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33
Q

what is RNA’s problem

A

stability

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34
Q

what is RNA susecptible to

A

base catalyzed hydrolysis

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35
Q

what makes RNA unstable

A
  • 2 OH group
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36
Q

who examined base rations from bacteria and plants and founded chargaffs rules

A

erwin chargaff

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37
Q

what was chargaffs rules

A

A = T
G= C

38
Q

who discovered complementary base paiting

A

watson and crick

39
Q

who did X ray fiber diffraction

A

rosalind franklin

40
Q

who knew it was a helix

A

francis crick

41
Q

what is the central dogma of biology by francis crick

A

framework that dscribes the flow of genetic information
- dna to rna = trancription
-rna to protein = protein translation

42
Q

what are some characteristics of B DNA structure

A
  • right hand helix
  • bases perpen to the helix axis
  • wide and deep major; narrow and deep minor
  • phosphate backbones on outside
  • pitch = 10 bases per turn = 34 angstroms
  • helix rise per basepair = 3.4
43
Q

what grooves does B DNA have

A
  • wide and deep major, narrow and deep minor
44
Q

what is the pitch of B DNA

A
  • 10 bases per turn = 34 angstroms
45
Q

what is the helix rise for B DNA

A
  • 3.4 angstroms
46
Q

is B DNA antiparallel

A

yes

47
Q

what is anti conformation in base

A

the base is rotated away from the sugar

48
Q

what is syn conformaiton

A

the base is rotated towards the sugar

49
Q

which one is syn which one is anti

A

syn is on the left and anti is on the righ

50
Q

what structure is this

A

a dna

51
Q

what dna is this

A

b dna

52
Q

What type of groove does Z have

A

major flat
minor: narrow and deep

53
Q

what tyeo of groove does A have

A

major groove: narrow and deep
minor: wide and shallow

54
Q

what structure is the one on the far left

A

Z dna

55
Q

what structure does RNA-RNA/ RNA DNA hybrids assume

A

A dna like structure

56
Q

which occurs in alternating purine -

A

z dna

pyramidine tracts and is favored in high salt conc

57
Q

what are telomeres

A

the end of chromosomes

58
Q

what tyoe of dna does the telomers have

A

tetraplex or quadruplex dna

59
Q

what does tetraplex or quadruplex dna have a role in

A
  • transcription, telomere maintenence, dna recom
60
Q

what is the structure of rna

A
  • single stranded
  • double helical regions that assume tupe A helix
61
Q

what structure is this

A

rna

62
Q

describe the tertiary structure of tRNA

A
  • cloverleaf secondary structure’- L or banana tertiary structure
63
Q

dna supercoling topology: what are the different super coiling

A

positive and negative

64
Q

what is positive supercoiling

A
  • dna DH is twisted in the same direction as the natural right handed helical twist
  • makes it tightly wound
65
Q

what is negative supercoiling

A
  • dna is twisted in the opposite direction
  • easier to seprate strands for transcription and replication
66
Q

what supercpil do most natrual dna in cells use

A

negative supercoil

67
Q

how does supercoiling occur in linear dna

A

both strands are anchored

68
Q

what are the enzymes that affect dna superstructures

A
  • topoisomerases
    -type 1 and type 2
69
Q

what does topoisomerase do

A
  • relax or make supercoils in dna by causing a transient nick that is resealed
70
Q

what does type 1 do

A

relax supercoils by breaking 1 strand( ssDNA) break

71
Q

what does type 2 do

A

relax or make supercoil by breaking two strands

72
Q

where are topoisomerase inhibitors uesed

A

in anticancer and antibacterial agents like quinolones

73
Q

what is the size of a human dna molecule

A

3,200,000 Kb

74
Q

describe the dna in prok

A
  • supercoiled circular dna that is bound to basic proteins = bacterial chromosomes in the nucleoid
75
Q

what is a separate small circular molecules that carries genes for their own replicaton adnd code for benefical enzymes like antibiotic degredation

A

bacterial plasmids

76
Q

euk. package dna as what

A

chromatin at normal stage of cell cycle; chromosomes when cells are ready to divide

77
Q

what is dna coiled around

A

histone octamer called a nucleosome

78
Q

what are the types of histones

A

H2A, H2B, H3, and H4 (2x)

79
Q

how many turns of dna arouund the nucleosome

A

1.8

80
Q

what amino acids are histones rich in

A

lysine and argine whose sides chains have a +Ve charge

81
Q

what charge is dna

A

negative (-ve)

82
Q

what is the last histone

A

H1

83
Q

what is the role of H1 histone

A
  • linker histone
  • stabilizes the chromatin fiber
  • regulation of genes and chromatin
84
Q

which structure does not have jistones

A

mitochondrial (mtDNA) and chloroplast DNA(ct DNA)

85
Q

what is mito and chloroplast dna used for

A

forensic analysis when nuclear dna is too degraded

86
Q

what can damage dna

A

UV irridation
thymine dimers(cyclobutyl dimers)
alkylation
HNO2

87
Q

what is alkylation

A

causes dna mismatch mutations that can lad to cancer

88
Q

what are some alkylating agents

A
  • mustard gas
    nitrogen mustard
89
Q

what does HNO2 do

A

causes dna mismatch mutations
- food cured with NaNO2

90
Q
A

biochemistry Jonklaas (17 decks)

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