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

Nucleic Acid Chemistry and Nucleotide Metabolism Flashcards

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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
what is the first step of IMP synthesis?
- PRPP synthesis
26
how much ATP is involved in IMP synthesis
- 6 ATP, but 7 ATP equivalents
27
sources of nitrogen in purine (3)
- glutamine, aspartate, glycine
28
sources of carbon in purine (3)
- formate/N^10-formyl-tetrahydrofolate, CO2/bicarbonate, and glycine
29
what energy form is used to convert IMP to AMP
- GTP
30
what energy form is used to convert IMP to GMP
- ATP (2 equivalents used)
31
what are 2 ways that pyrimidine synthesis is different from purine synthesis? (2)
- synthesis of one ring: less ATP needed and more simple | - first base is made and then it is attached to scaffold
32
sources of carbon in pyrimidine (2)
- aspartate | - bicarbonate
33
sources of nitrogen in pyrimidine (2)
- aspartate | - glutamine (amide nitrogen)
34
what is the overview of steps in pyrimidine synthesis? (3)
- UMP is synthesized first - UMP is converted to UTP - CTP and dTTP are made from UTP
35
committed step of pyrimidine synthesis (2)
carbamoyl phosphate + aspartate -> carbamoyl aspartate | - catalyzed by aspartate transcarbamoylase
36
committed step of purine synthesis (2)
- pyrophosphate is replaced by amide amino group of glutamine to form 5-phospho-beta-D-ribosylamine - catalyzed by glutamine-PRPP-amidotransferase
37
how many enzymes are used for UMP synthesis in bacteria?
- 6 separate enzymes
38
how many enzymes are used for UMP synthesis in eukaryotes? (2)
- 3 enzymes (rxn 1-3, rxn 4, rxn 5-6) | - metabolone: process of using one enzyme for many steps
39
what enzyme is used for rxn 1-3 of UMP synthesis in eukaryotes?
- CAD enzyme
40
what enzyme is used for rxn 5-6 of UMP synthesis in eukaryotes?
- UMP synthase
41
how much ATP is needed for UMP synthesis and what are their roles? (2)
- 2 ATPs needed and are both used in the first step | - one transfers phosphate, the other is hydrolyzed to ADP and Pi
42
are there any condensation reactions involved in UMP synthesis? (2)
- 2 condensation reactions | - formation of carbamoyl aspartate and dihydroorotate
43
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?
- catalyzed by OPRT (orotate phosphoribosyltransferase) - PRPP provides ribose-5-P - irreversible, PPi splits off PRPP
44
whats results from a mutation in the UMP synthase enzyme?
- results in orotic aciduria
45
orotic aciduria (3) - cause - effects (2)
- 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
treatment for orotic aciduria (2)
- UMP supplementation | - some nucleotides in diet, but not enough so extra supplementation is needed
47
interconversion of nucleotides: NMP -> NDP (2) - enzyme used - energetic cost
- nucleoside monophosphate kinases (NMP kinase) | - uses an ATP
48
interconversion of nucleotides: NDP -> NTP (2) - enzyme used - energetic cost
- nucleoside diphosphate kinases (NDP kinase) | - uses an ATP
49
details of interconversion of nucleotides (3)
- specific for bases, but can convert both deoxy and ribo - useful for maintaining balanced pools of nucleotides - reversible reactions
50
synthesis of deoxyribonucleotides (4) - enzyme and function - key molecule - restrictions, why? - reaction
- 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
what enzymes are regulated in purine synthesis? (4)
1. glutamine-PRPP amidotransferase (committed step enzyme) 2. PRPP synthetase 3. adenylsuccinate synthetase 4. IMP dehydrogenase
52
how is glutamine-PRPP amidotransferase inhibited in purine synthesis? (2)
- it is inhibited by AMP, GMP and IMP allosterically | - negative feedback
53
how is PRPP synthetase inhibited in purine synthesis?
- inhibited by AMP, GMP and IMP
54
how is adenylsuccinate synthetase inhibited in purine synthesis? (2)
- inhibited by AMP, lowering production of AMP | - balances pools of AMP and GMP
55
how is IMP dehydrogenase inhibited in purine synthesis? (2)
- inhibited by GMP, lowering production of GMP | - balances pools of AMP and GMP
56
what enzymes are regulated in pyrimidine synthesis? (2)
1. aspartate transcarbamoylase (committed step enzyme) | 2. CPS-2
57
how is aspartate transcarbamoylase inhibited in pyrimidine synthesis? (2)
- inhibited by CTP allosterically, lowering the production of carbamoyl aspartate - main regulatory step and affects committed step
58
how is CPS-2 inhibited in pyrimidine synthesis?
- inhibited by UMP
59
how is ribonucleotide reductase regulated? (2)
by two allosteric sites: - primary site - substrate specificity site
60
how is the primary allosteric site of ribonucleotide reductase regulated? (2) - role - inhibition and activation
- primary site: controls overall activity | - activated by ATP and inhibited by dADP and dATP
61
how is the substrate specificity allosteric site of ribonucleotide reductase regulated? (2)
- substate specificity site: has CUGA order of preference | - enzyme switches specificity depending on concentration of products
62
how are nucleic acids broken down? (2)
- broken down to nucleotides by nucleases | - RNase for RNA and DNase for DNA
63
how are nucleotides broken down?
- broken down into nucleosides and phosphates by nucleotidase
64
how are nucleosides broken down?
- broken down into bases and sugars by nucleosidase
65
what is the end product of degradation of purines in primates?
- uric acid
66
what is the end product of degradation of purines in non-primate mammals?
- allantoin, a molecule with higher solubility than uric acid
67
what is the result of the build up of uric acid in the blood?
- gout
68
gout (2)
- 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
gout treatment (2)
- allopurinol supplementation | - acts as a competitive inhibitor of xanthine oxidase to lower the production of uric acid
70
what are the final products of the degradation of pyrimidines and where do they go? (2)
- 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
what enzyme participates in the recycling of bases by salvage pathways?
- purine/pyrimidine phosphoribosyltransferases (PRTs)
72
phosphoribosyltransferase (PRT) role
- catalyzes transfer of ribose-5-phosphate from PRPP to a base (purine or pyrimidine) to yield a nucleotide
73
what results from a deficiency in HGPRT?
- Lesch-Nyhan Syndrome
74
Lesch-Nyhan Syndrome (2)
- 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
Lesch-Nyhan Syndrome treatment
- allopurinol supplementation

BIOC 302 Part 2 (7 decks)

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