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BIOC 302 Part 2 > Nucleic Acid Chemistry and Nucleotide Metabolism > Flashcards

Nucleic Acid Chemistry and Nucleotide Metabolism Flashcards

1
Q

nucleotides

A
  • molecules composed of 5-membered sugar, phosphate(s), and a nitrogenous base
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2
Q

5-membered sugar

  • name
  • where it is synthesized
  • types (2)
A
  • aldopentose β-furanose
  • synthesized in pentose phosphate pathway
  • ribose or deoxyribose
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3
Q

ribose (2)

A

5-membered sugar with OH group at 2’ carbon

- found in RNA

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4
Q

deoxyribose (2)

A

5-membered sugar with H group at 2’ carbon

- found in DNA

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5
Q

nitrogenous bases

  • attached to
  • function
  • types (2)
A
  • attached to 1’-carbon of sugar
  • stores information
  • can be purine or pyrimidine
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6
Q

purine

  • structure
  • nitrogens
A
  • 6-membered ring fused with 5-membered ring

- contains 4 nitrogens in common ring structure

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7
Q

purine types

A
  • adenine, both DNA and RNA

- guanine, both DNA and RNA

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8
Q

pyrimidine

  • structure
  • nitrogens
A
  • 6-membered ring

- 3 nitrogens in common ring structure

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9
Q

pyrimidine types

A
  • cytosine, both DNA and RNA
  • thymine, DNA with exceptions
  • uracil, RNA with exceptions
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10
Q

nucleotide phosphate

  • attached to
  • role
  • naming
A
  • attached to 5’-carbon on sugar
  • gives nucleotide negative charge at physiological pH
  • can be monophosphate, diphosphate, or triphosphate
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11
Q

nucleoside

A
  • base + sugar
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12
Q

purine nucleoside nomenclature

A
  • change ending to “-osine”
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13
Q

nomenclature: adenine + ribose

A
  • adenosine
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14
Q

nomenclature: guanine + deoxyribose

A
  • deoxyguanosine
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15
Q

nucleotide nomenclature (1st method)

  • rule
  • nomenclature: cytosine + ribose + phosphate
A
  • change ending to “-ylate”

- citidylate: cytosine + ribose + phosphate

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16
Q

nucleotide nomenclature (2nd method)

A
  • name of nucleoside + number of phosphates
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17
Q

nomenclature: cytosine + ribose

A
  • cytidine
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18
Q

nomenclature: cytosine + ribose + 1 phosphate

A
  • cytidine monophosphate (CMP)
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19
Q

nomenclature: guanine + deoxyribose + 2 phosphates

A
  • deoxyguanosine diphosphate (GDP)
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20
Q

nomenclature: adenine + ribose + 3 phosphate

A
  • adenosine triphosphate (ATP)
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21
Q

nomenclature of modified bases

A
  • indicate position of modification with number (if attached to C) or with N^# if attached to N
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22
Q

nucleotide polymers

A
  • DNA or RNA
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23
Q

phosphodiester linkage

A
  • 5’ phosphate of one nucleotide bonds with 3’ OH of another nucleotide
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24
Q

alkaline hydrolysis of RNA (2)

A
  • 2’ OH attacks phosphoester in alkaline conditions (where it is depotonated) leading to hydrolysis of linkage between nucleotides
  • occurs event at pH = 7 at room temperature
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25
Q

what is the first step of IMP synthesis?

A
  • PRPP synthesis
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26
Q

how much ATP is involved in IMP synthesis

A
  • 6 ATP, but 7 ATP equivalents
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27
Q

sources of nitrogen in purine (3)

A
  • glutamine, aspartate, glycine
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28
Q

sources of carbon in purine (3)

A
  • formate/N^10-formyl-tetrahydrofolate, CO2/bicarbonate, and glycine
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29
Q

what energy form is used to convert IMP to AMP

A
  • GTP
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30
Q

what energy form is used to convert IMP to GMP

A
  • ATP (2 equivalents used)
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31
Q

what are 2 ways that pyrimidine synthesis is different from purine synthesis? (2)

A
  • synthesis of one ring: less ATP needed and more simple

- first base is made and then it is attached to scaffold

32
Q

sources of carbon in pyrimidine (2)

A
  • aspartate

- bicarbonate

33
Q

sources of nitrogen in pyrimidine (2)

A
  • aspartate

- glutamine (amide nitrogen)

34
Q

what is the overview of steps in pyrimidine synthesis? (3)

A
  • UMP is synthesized first
  • UMP is converted to UTP
  • CTP and dTTP are made from UTP
35
Q

committed step of pyrimidine synthesis (2)

A

carbamoyl phosphate + aspartate -> carbamoyl aspartate

- catalyzed by aspartate transcarbamoylase

36
Q

committed step of purine synthesis (2)

A
  • pyrophosphate is replaced by amide amino group of glutamine to form 5-phospho-beta-D-ribosylamine
  • catalyzed by glutamine-PRPP-amidotransferase
37
Q

how many enzymes are used for UMP synthesis in bacteria?

A
  • 6 separate enzymes
38
Q

how many enzymes are used for UMP synthesis in eukaryotes? (2)

A
  • 3 enzymes (rxn 1-3, rxn 4, rxn 5-6)

- metabolone: process of using one enzyme for many steps

39
Q

what enzyme is used for rxn 1-3 of UMP synthesis in eukaryotes?

A
  • CAD enzyme
40
Q

what enzyme is used for rxn 5-6 of UMP synthesis in eukaryotes?

A
  • UMP synthase
41
Q

how much ATP is needed for UMP synthesis and what are their roles? (2)

A
  • 2 ATPs needed and are both used in the first step

- one transfers phosphate, the other is hydrolyzed to ADP and Pi

42
Q

are there any condensation reactions involved in UMP synthesis? (2)

A
  • 2 condensation reactions

- formation of carbamoyl aspartate and dihydroorotate

43
Q

what are the details of the attachment of the base to the ribose ring in UMP synthesis? (3)

  • enzyme used
  • what is needed and what provides it
  • reversible or irreversible, why?
A
  • catalyzed by OPRT (orotate phosphoribosyltransferase)
  • PRPP provides ribose-5-P
  • irreversible, PPi splits off PRPP
44
Q

whats results from a mutation in the UMP synthase enzyme?

A
  • results in orotic aciduria
45
Q

orotic aciduria (3)

  • cause
  • effects (2)
A
  • results from deficiency in UMP synthetase caused by genetic mutation
  • pyrimidine synthesis is decreased and excess orotic acid is excreted in the urine
  • affects nucleotide synthesis: cells that proliferate a lot will be affected (RBC, epithelial)
46
Q

treatment for orotic aciduria (2)

A
  • UMP supplementation

- some nucleotides in diet, but not enough so extra supplementation is needed

47
Q

interconversion of nucleotides: NMP -> NDP (2)

  • enzyme used
  • energetic cost
A
  • nucleoside monophosphate kinases (NMP kinase)

- uses an ATP

48
Q

interconversion of nucleotides: NDP -> NTP (2)

  • enzyme used
  • energetic cost
A
  • nucleoside diphosphate kinases (NDP kinase)

- uses an ATP

49
Q

details of interconversion of nucleotides (3)

A
  • specific for bases, but can convert both deoxy and ribo
  • useful for maintaining balanced pools of nucleotides
  • reversible reactions
50
Q

synthesis of deoxyribonucleotides (4)

  • enzyme and function
  • key molecule
  • restrictions, why?
  • reaction
A
  • catalyzed by ribonucleotide reductase: reduces OH to H
  • complex mechanism involving free radical formation
  • only works with NDP (not NMP or NTP) to reduce interference with other processes
  • NDP -> dNDP
51
Q

what enzymes are regulated in purine synthesis? (4)

A
  1. glutamine-PRPP amidotransferase (committed step enzyme)
  2. PRPP synthetase
  3. adenylsuccinate synthetase
  4. IMP dehydrogenase
52
Q

how is glutamine-PRPP amidotransferase inhibited in purine synthesis? (2)

A
  • it is inhibited by AMP, GMP and IMP allosterically

- negative feedback

53
Q

how is PRPP synthetase inhibited in purine synthesis?

A
  • inhibited by AMP, GMP and IMP
54
Q

how is adenylsuccinate synthetase inhibited in purine synthesis? (2)

A
  • inhibited by AMP, lowering production of AMP

- balances pools of AMP and GMP

55
Q

how is IMP dehydrogenase inhibited in purine synthesis? (2)

A
  • inhibited by GMP, lowering production of GMP

- balances pools of AMP and GMP

56
Q

what enzymes are regulated in pyrimidine synthesis? (2)

A
  1. aspartate transcarbamoylase (committed step enzyme)

2. CPS-2

57
Q

how is aspartate transcarbamoylase inhibited in pyrimidine synthesis? (2)

A
  • inhibited by CTP allosterically, lowering the production of carbamoyl aspartate
  • main regulatory step and affects committed step
58
Q

how is CPS-2 inhibited in pyrimidine synthesis?

A
  • inhibited by UMP
59
Q

how is ribonucleotide reductase regulated? (2)

A

by two allosteric sites:

  • primary site
  • substrate specificity site
60
Q

how is the primary allosteric site of ribonucleotide reductase regulated? (2)

  • role
  • inhibition and activation
A
  • primary site: controls overall activity

- activated by ATP and inhibited by dADP and dATP

61
Q

how is the substrate specificity allosteric site of ribonucleotide reductase regulated? (2)

A
  • substate specificity site: has CUGA order of preference

- enzyme switches specificity depending on concentration of products

62
Q

how are nucleic acids broken down? (2)

A
  • broken down to nucleotides by nucleases

- RNase for RNA and DNase for DNA

63
Q

how are nucleotides broken down?

A
  • broken down into nucleosides and phosphates by nucleotidase
64
Q

how are nucleosides broken down?

A
  • broken down into bases and sugars by nucleosidase
65
Q

what is the end product of degradation of purines in primates?

A
  • uric acid
66
Q

what is the end product of degradation of purines in non-primate mammals?

A
  • allantoin, a molecule with higher solubility than uric acid
67
Q

what is the result of the build up of uric acid in the blood?

A
  • gout
68
Q

gout (2)

A
  • caused by elevated levels of uric acid in blood due to defect in an enzyme of purine metabolism or by reduced secretion of uric acid into the urinary tract
  • due to low solubility of uric acid, uric acid crystals precipitate out in joints
69
Q

gout treatment (2)

A
  • allopurinol supplementation

- acts as a competitive inhibitor of xanthine oxidase to lower the production of uric acid

70
Q

what are the final products of the degradation of pyrimidines and where do they go? (2)

A
  • skeleton of pyrimidine is converted to acetyl-CoA and succinyl-CoA; goes to the TCA cycle
  • nitrogen (as ammonia, NH4+) is released from pyrimidine base and converted to urea through the urea cycle
71
Q

what enzyme participates in the recycling of bases by salvage pathways?

A
  • purine/pyrimidine phosphoribosyltransferases (PRTs)
72
Q

phosphoribosyltransferase (PRT) role

A
  • catalyzes transfer of ribose-5-phosphate from PRPP to a base (purine or pyrimidine) to yield a nucleotide
73
Q

what results from a deficiency in HGPRT?

A
  • Lesch-Nyhan Syndrome
74
Q

Lesch-Nyhan Syndrome (2)

A
  • occurs if there is a deficiency in the HGPRT enzyme that results in no salvation of hypoxanthine and guanine
  • causes a build-up of uric acid and gout
75
Q

Lesch-Nyhan Syndrome treatment

A
  • allopurinol supplementation

BIOC 302 Part 2 (7 decks)

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