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BIOC 311 > Nucleic Acids > Flashcards

Nucleic Acids Flashcards

1
Q

what is the difference between the de novo pathway and the salvage pathway?

A
  • de novo: synthesis of nucleotides from starting material (AAs, ribose, CO2, …) and highly conserved process in eukaryotes
  • salvage: recovery of bases for making new nucleotides and more divergent/varies process
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2
Q

what are the two de novo pathways?

A
  • purine pathway
  • pyrimidine pathway
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3
Q

what molecules/substrates are needed for the purine pathway to make IMP?

A

PRPP, glutamine, aspartate, CO2, glycine, formate

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4
Q

what molecules/substrates are needed for the pyrimidine pathway to make UMP?

A

CO2, glutamine, aspartate, PRPP

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5
Q

what is a base?

A

the aromatic part of a nucleotide

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6
Q

what does a molecules ending with “-side” contain?

A

a base + sugar (like ribose)

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7
Q

what does a molecules ending with “-tide” contain?

A

base + phosphosugar

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8
Q

what is the difference between a purine and pyrimidine?

A
  • purine: two rings
  • pyrimidine: 1 ring
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9
Q

what are the two types of sugar and what differentiates the two?

A
  • ribose (for RNA): has an extra 2’OH
  • deoxyribose (for DNA): doesn’t have 2’OH
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10
Q

nucleotide sugars are __ sugars in ____ conformation

A

D ; furanose

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11
Q

bases are linked to sugars by which type of bond and is that above or below?

A

B glycosidic bond, which is above

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12
Q

where is the sugar linked on a purine?

A

9-N

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13
Q

where is the sugar linked on a pyrimidine?

A

1-N

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14
Q

how are nucleotides numbered? How does it differ for purines and pyrimidines?

A
  • primed numbers are given to the sugar ring (starting where it is linked to base)
  • unprimed numbers given to bases
  • pyrimidines: nitrogen at 1, 3 (not 5)
  • purine: nitrogen at 1, 3, 7, 9 (not 5)
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15
Q

caffeine and theobromine are derivatives of which nucleotide?

A

xanthine

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16
Q

what is the de novo synthesis steps of purines?

A

the purine ring is assembled on the ribose phosphate
- 5-phosphoribose to PRPP
- PRPP to 5-phosphoribosylamine
- then 11 steps to make IMP

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17
Q

how many high energy phosphate bonds are needed for de novo purine synthesis?

A

7

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18
Q

is the pyrophosphate at the alpha or beta position on the ribose?

A

alpha

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19
Q

what is the committing step of de novo purine synthesis? what happens during this step?

A
  • step 2 (conversion of PRPP to 5-phosphoribosylamine)
  • anomeric conversion (forms b anomer)
  • PPi released (so irreversible)
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20
Q

what donates the amine group in the second step of purine de novo synthesis?

A

glutamine

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21
Q

what are the different nitrogen donor and which part specifically is used?

A
  • side chain of glutamine
  • backbone of aspartate
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22
Q

how is the first ring of the purine synthesized (de novo)?

A
  • start from 5-phosphoribosylamine
  • addition of glycine
  • N added from glutamine
  • C from THF
  • cyclization
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23
Q

how is the 2nd ring of the purine synthesized? what is the product?

A
  • addition of HCO3-
  • N from aspartate added in two steps ( N-succinyl adduct and release of fumarate)
  • C from THF
  • ring closed by dehydration (no ATP required)
  • product is IMP
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24
Q

inosine monophosphate (IMP) is the branch point for ___________

A

AMP and GMP synthesis

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25
Q

how is AMP synthesized from IMP?

A

uses aspartate and GTP to add amine

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26
Q

how is GMP synthesized from IMP?

A

via XMP uses glutamine and ATP to add amine

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27
Q

what is the general rule of nucleotide synthesis?

A

amino groups put on/take off via carbonyls

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28
Q

how are diphosphates made?

A

via base specific kinases:
- adenylate kinase: AMP+ATP <=> 2ADP
- uridylate kinase: UMP+UTP <=> 2UDP

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29
Q

how are triphosphates made?

A

via non-specific kinases
- nucleoside diphosphate kinase: NDP + N’TP <=> NTP + N’DP

30
Q

what is the G of the formation of di- and tri-phosphates? what does this mean?

A

~0, meaning the reactions are driven by concentration gradient

31
Q

how do the amount of the following (intracellular concentrations) compare: RNA, NTP, dNTP, NDP, DNA, NMP (not necessarily in this order)

A
  • 7x more RNA than DNA
  • 7x more NTP than dNTP
  • 7x more NTP than NDP
  • 7x more NDP than NMP
32
Q

how is the de novo purine synthesis regulated?

A
  • feedback inhibition by nucleotides
  • feedforward by PRPP
  • inhibition and stimulation for AMP and GMP synthesis
  • regulation at steps 1 and 2
33
Q

how many times in the de novo purine pathway is folate used?

A

2

34
Q

where does THF come from?

A

from folic acid

35
Q

what are the possible different oxidation states and chemical forms of carbon units carried by THF?

A

oxidation:
1. methanol
2. formaldehyde
3. formate

chemical:
- methyl
- methylene
- formyl
- formimino
- methenyl

36
Q

what are the following carbon units carried by THF used in: N6-methyl-THF, N5,N10-methylene-THF, N10-formyl-THF

A
  • N6-methyl-THF: methionine cycle
  • N5,N10-methylene-THF: thymidylate synthesis
  • N10-formyl-THF: purine de novo
37
Q

why is DNA the genetic material?

A
  • removing the 2’OH makes the DNA phosphodiester backbone more stable
  • Thymine allows spontaneous deamination of cytosine to be detected
38
Q

is DNA or RNA more reduced?

A

DNA (1 less OH)

39
Q

the synthesis of deoxyribose is carried out at which level?

A

DNPs (diphosphates)

40
Q

how are NDP reduced to dNDP?

A
  • reducing equivalent originate from NADPH
  • goes through a series of thiols, where cysteine residues are oxidized/reduced:
    1. thioredoxin reductase
    2. thioredoxin
    3. ribonucleotide reductase (RR)
  • then NDP reduced to dNDP
41
Q

what are the two types of subunits of ribonucleotide reductase?

A
  • regulator
  • catalytic
42
Q

what are the two allosteric sites on ribonucleotide reductase? what do they control?

A
  • controls activity: binds ATP (activates) /dATP (inhibits)
  • controls specificity: dATP/dGTP/dTTP
43
Q

why is ribonucleotide reductase an unusually stable enzyme? what can destabilize it?

A
  • due to tyrosine free radicals
  • inhibited by hydroxyurea
44
Q

what makes ribonucleotide reductase a good therapeutic target?

A
  • lots of variation with species
  • so, could specifically inhibit DNA synthesis
45
Q

how is riboreductase regulated?

A

two types of feedback regulation:
- negative feedback (either specific to that nucleotide or can influence other types)
- positive: dNTPs can affect production of other types of dNTPs

46
Q

incorporation of uracil into DNA induces _________

A

DNA repair enzymes

47
Q

how does the body try to prevent incorporation of dUTP in DNA?

A

presence of UTPase hydrolyzes dUTP to dUMP (which is then converted to dTMP by thymidylate synthase) to decrease its concentration and prevent its incorporation

48
Q

how does purine and pyrimidine de novo synthesis differ?

A
  • purine: PRPP made first then ring assembled on it
  • pyrimidine: ring assembled separately then PRPP added
49
Q

explain the de novo UMP synthesis?

A
  • channeling of steps 1,2,3:
    1. make carbamoyl phosphate with CPSII
    2. make carbamoyl aspartate with ATCase (aspartate added to carbamoyl phosphate)
    3. makes dihydroorotase
  1. is at mitochondrial membrane: makes orotate
  • channeling of steps 5,6
    5. make OMP
    6. make UMP (remove COO- group)
50
Q

loss of steps 5 or 6 in pyrimidine synthesis leads to ______

A

orotic aciduria

51
Q

how is pyrimidine de novo synthesis regulated?

A
  • step 1 (CPSII) for animals: compartmentalization
  • step 2 (aspartate transcarboxylase) for bacteria: allosteric regulation – activated by ATP and inhibited by CTP
52
Q

At what level is CTP made?

A

Tri phosphate

53
Q

How is CTP made?

A
  • from UTP
  • N from glutamine
  • energy from ATP
54
Q

How is the pyrimidine de novo pathway regulated?

A
  • inhibition by pyrimidine nucleoside triphosphate
  • activation by ATP and PRPP
  • both either first or second step depending of organism
55
Q

thymidylate synthesis is done at which level?

A

monophosphate

56
Q

what does thymidylate synthase do?

A

synthesis of dTMP from dUMP

57
Q

what is the methyl donor for dTMP synthesis by thymidylate synthase? what is the end-product?

A

Methylene-THF, released as DHF

58
Q

what is the role of tetrahydrofolate? why is it important?

A
  • to reduce DHF to THF
  • cell would run out of THF due to dTMP synthesis
59
Q

what is the thymidylate synthase cycle?

A
  • THF is oxidized to DHF (produces dTMP from dUMP)
  • DHF reduced by DHF reductase
  • methylene group added from serine
60
Q

what is FdUMP?

A

a suicide inhibitor that can be used to target infections or cancer (it covalently modifies thymidylate synthase so it stops synthesis)

61
Q

what are different types of inhibitors of DHF reductase and what do they all do?

A
  • all inhibit DNA synthesis
  • THF analogs, competitive inhibitor, anti-cancer, anto-bacterial
62
Q

what is the principle of the salvage pathway?

A

recovery of bases for making new nucleotides

63
Q

what is Lesch-Nyhan disease?

A
  • genetic loss of HGPRT activity (cannot salvage hypoxanthine and guanine)
  • symptoms: gout and mental retardation
64
Q

what is HGPRT and what is its role?

A
  • hypoxanthine/guanine phosphoribosyl transferase
  • converts either: hypoxanthine + PRPP to inosinate or guanine + PRPP to guanylate
65
Q

how can nucleosides be formed in the salvage pathway? are these specific?

A
  • nucleotide phosphorylase
  • nucleotide transglucosylase (exchange bases)
  • they are specific to avoid making thymine ribonucl.
66
Q

what are the salvage pathway enzymes?

A
  • phosphoribosyl transferase (e.g. making OMP with orotic acid)
  • nucleotide phosphorylase
  • nucleoside kinase
  • nucleotide transglucosylase (exchange bases)
  • deaminases
  • nucleoside monophosphate kinase
  • nucleoside diphosphate kinase
67
Q

how are purines degraded?

A

funnel downwards:
- nucleotides (AMP, IMP, XMP, GMP)
- nucleosides (adenosine, inosine, xanthosine, guanosine)
- bases, xanthine
- uric acid

68
Q

what results in loss of adenosine deaminase?

A

SCID

69
Q

what is a treatment for gout?

A

inhibit xanthine oxidase

70
Q

what is gout? what causes it?

A
  • deposition of uric acid in joints
  • symptomatic of metabolic imbalance (excess de novo purine synthesis like high levels of PRPP)
71
Q

how do birds eliminate nitrogen? why?

A

by making uric acid in order to conserve water since what we do (ammonia) takes a lot of water

72
Q

how are pyrimidines degraded?

A
  • nucleotides (CMP, UMP/dTMP)
  • nucleosides (cytidine, uridine/deoxythymidine)
  • uracil or thymine
  • deaminated to carbonyls and ring reduced

BIOC 311 (7 decks)

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