Nucleotide Metabolism Flashcards

1
Q

examples of purines

A
  • adenine
  • guanine
  • xanthine
  • hypoxanthine
  • uric acid
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2
Q

hypoxanthine is the base for

A
  • inosine
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3
Q

examples of pyrimidines

A
  • cytosine
  • thymine
  • uracil
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4
Q

nucleoside composed of

A
  • base + sugar
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5
Q

nucleotide composed of

A
  • base + sugar + phosphate
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6
Q

ribose

A
  • OH at 2’ sugar

- less stable

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7
Q

deoxyribose

A

-H at 2- sugar

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8
Q

sources of nucleotides

A
  • dietary
  • de novo synthesis
  • salvage pathway
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9
Q

contribution of dietary

why

A
  • relatively small

- most RNA and DNA in diet are degraded and excreted

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10
Q

primary producer of de novo synthesis

A
  • liver
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11
Q

what do you end up with as the common precursor to purine nucleotides and the branch point for the synthesis of different purines

A
  • IMP
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12
Q
  • first step of purine synthesis

synthesis of PRPP starting with

A
  • ribose-5-phosphate from PPP

- with ATP

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13
Q

synthesis of PRPP enzyme

A
  • PRPP synthetase
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14
Q

importance of PRPP

A
  • pentose molecule

- synthesis and salvage of purines and pyrimidines

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15
Q

what controls the rate of formation of PRPP

A
  • amount of ribose-5-phosphate
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16
Q

activation of synthesis of PRPP

A
  • Pi

- indicates low nucleotide levels

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17
Q

end product inhibition of synthesis of PRPP

A
  • purine nucleotides

- ADP, GDP

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18
Q

Arts syndrome caused by

A
  • genetic disorder in PRPP synthase

- generally decreased PRPP synthetase

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19
Q

genetics of Arts syndrome

A
  • X-linked
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20
Q

reduction of PRPP synthetase causes

A
  • reduced purine levels

- absence of hypoxanthine from urine and uric acid in serum

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21
Q

increases in PRPP synthetase causes

A
  • increased levels of purines

- gout

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22
Q

body system impacted to Arts syndrome

A
  • severe nervous system abnormalities
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23
Q

second step of purine synthesis

with help from

A
  • PRPP -> 5-phosphoribosyl-1-amine

- with help of glutamine - contributes nitrogen

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24
Q

importance of second step of purine synthesis

A
  • committed step
  • irreversible
  • major regulated step
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25
Q

enzyme in second step of purine synthesis

A
  • glutamine phosphoribosyl amidotransferase
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26
Q

inhibition of second step of purine synthesis

A
  • AMP, GMP, IMP, XMP

- pathway products

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27
Q

activation of second step of purine synthesis

A
  • PRPP
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28
Q

which form of glutamine phosphoribosyl amidotransferase is the active form?

A
  • the monomer
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29
Q

which form of glutamine phosphoribosyl amidotransferase is the inactive form?

A
  • dimer
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30
Q

high levels of AMP, GMP, IMP on glutamine phosphoribosyl amidotransferase

A
  • forms a less active dimer
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31
Q

high levels of PRPP on glutamine phosphoribosyl amidotransferase

A
  • form active monomeric form
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32
Q

what levels play a major role in regulating purine synthesis

A
  • PRPP
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33
Q

glutamine effect on kinetics of glutamine phosphoribosyl amidotransferase

A
  • near Km

- does not influence rate significantly

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34
Q

PRPP effect on kinetics of glutamine phosphoribosyl amidotransferase

A
  • PRPP levels way below Km
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35
Q

importance of inhibition of glutamine phosphoribosyl amidotransferase by AMP PLUS GMP or IMP

A
  • 2 distinct binding sites

- regulation in additive way

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36
Q

importance of THF in purine metabolism

A
  • carbon donor at 2 steps
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37
Q

what inhibits bacterial folic acid synthesis

A
  • sulfa drugs
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38
Q

why don’t sulfa drugs interference with human purine synthesis and DNA replication

A
  • humans only acquire folic acid by diet
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39
Q

precursors of making THF

A
  • folate
  • dihydrofolate
  • tetrahydrolate
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40
Q

enzyme that helps make THF

also required

A
  • DHFR

- NADPH

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41
Q

purine synthesis requires what form of THF

A

N10-formyl-THF

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42
Q

methotrexate often used for

MOA

A
  • antitumor drug

- inhibits DHFR reducing synthesis of THF

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43
Q

good effects of methotrexate

A
  • reduces purine synthesis
  • slows down DNA replication
  • slows tumor growth
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44
Q

bad effects of methotrexate

A
  • affects normally dividing cells
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45
Q

IMP precursor for

A
  • AMP

- GMP

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46
Q

base of IMP

A
  • hypoxanthine
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47
Q

AMP requires what for energy

A
  • GTP
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48
Q

other molecule AMP requires for energy

A
  • aspartate

- releases fumerate

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49
Q

GMP requires what for energy

A
  • ATP
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50
Q

other molecules GMP requires for energy

A
  • NAD+

- glutamine

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51
Q

enzyme for formation of GMP from IMP

A
  • GMP synthase
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52
Q

effect of high ATP on GMP/GTP synthesis

A
  • increased
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53
Q

enzyme for formation of AMP from IMP

A
  • adenylosuccinate synthetase
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54
Q

effect of high GTP on AMP/ATP synthesis

A
  • increased
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55
Q

what inhibits IMP dehydrogenase

A
  • GMP
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56
Q

what inhibits adenylosucinate synthetase

A
  • AMP
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57
Q

purpose of mycophenolic acid

A
  • immunosuppressant
  • reduce lymphocyte proliferation
  • prevent graft rejection
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58
Q

MOA of mycophenolic acid

A
  • inhibits IMP dehydrogenase and GMP formation
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59
Q

purpose of ribavirin

A
  • anti-viral

- anti-tumor agent

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60
Q

MOA of ribavirin

A
  • inhibits IMP dehydrogenase
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61
Q

enzyme that converts AMP to ADP

what else is required

A
  • adenylate kinase

- ATP

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62
Q

enzyme that converts GMP to GDP

what else is required

A
  • guanylate kinase

- ATP

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63
Q

what converts ADP, GDP, and NDPs to triphosphates

what else is required

A
  • nucleoside diphosphate kinase

- ATP

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64
Q

purpose of degradation of DNA and RNA

A
  • body to reutilize nucleosides and free bases via salvage pathways
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65
Q

how do we get degraded nucleic acids

A
  • cell death
  • RNA or DNA turnover
  • diet
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66
Q

nucleic aid is digested where?

by what enzyme?

A
  • stomach

- pepsin

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67
Q

RNAse and DNase secreted by what

A
  • pancreas
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68
Q

what do RNAse and DNase do

A
  • digest RNA and DNA into oligonucleotides
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69
Q

role of phosphodiesterases

A
  • degrade oligonucleotides

- to NMPs and dNMPs

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70
Q

role of nucleotidases or phosphatases

A
  • remove phosphate groups

- convert to nucleosides

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71
Q

role of nucleosidases

A
  • degrade nucleosides

- form free bases plus ribose and deoxyribose

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72
Q

degradation products of pyrimidine nucleotides

A
  • all soluble
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73
Q

degradation products of purine nucleotides

A
  • produce uric acid

- lead to hyperuricemia

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74
Q

hyperuricemia can result in

A
  • gout
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75
Q

degradation occurs mostly where

A
  • liver
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76
Q

degradation of AMP to xanthine process

A
  • AMP -> IMP -> inosine
  • AMP -> adenosine -> inosine
  • inosine -> hypoxanthine
  • hypoxanthine -> xanthine
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77
Q

degradation of GMP to xanthine process

A
  • GMP -> guanosine
  • guanosine -> guanine
  • guanine -> xanthine
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78
Q

xanthine degraded to

by what enzyme

A
  • uric acid

- xanthine oxidase

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79
Q

uric acid generated in

transported to

A
  • liver

- kidney for excretion in urine

80
Q

MOA of allopurinol

A
  • inhibits xanthine oxidase

- reduces uric acid levels

81
Q

allopurinol used to treat

A
  • gout
82
Q

enzyme from AMP -> IMP

A
  • AMP deaminase
83
Q

enzyme from IMP -> inosine

A
  • 5’-nucleotidase
84
Q

enzyme from AMP -> adenosine

A
  • 5’-nucleotidase
85
Q

enzyme from adenosine -> inosine

A
  • adenosine deaminase
86
Q

what condition results from blocking of adenosine deaminase

A
  • SCID
87
Q

what other reaction does adenosine deaminase (ADA) catalyze

A
  • deoxyadenosine -> deoxyinosine
88
Q

genetic deficiency of ADA results in

A
  • accumulation of dATP
89
Q

importance of high levels of dATP

A
  • inhibit ribonucleotide reductase
90
Q

importance of inhibition of ribonucleotide reductase

A
  • reduction in DNA synthesis
91
Q

importance of high deoxyadenosine levels

A
  • toxic in lymphocytes

- unable to combat infection leading to SCID

92
Q

AMP deaminase functions in

A
  • skeletal muscle
93
Q

AMP deaminase deficiency symptoms

A
  • skeletal muscle myopathy
  • exercise induced fatigue and cramps
  • often asymptomatic
94
Q

AMP deaminase selective form

A
  • AMP only
95
Q

part of the body where savage is done

A
  • the liver
96
Q

salvage pathway

A
  • building nucleotides from bases and nucleosides
97
Q

benefit of salvage pathway

A
  • energetically advantageous

- less costly than de novo

98
Q

adenine to AMP in purine to NMP salvage pathway uses which enzyme

also requires

A
  • APRT

- PRPP

99
Q

hypoxanthine to IMP in purine to NMP salvage pathway uses which enzyme

  • also requires
A
  • HGPRT

PRPP

100
Q

guanine to GMP in purine to NMP salvage pathway uses which enzyme

also requires

A
  • HGPRT

- PRPP

101
Q

purine to NMP salvage pathway reactions (reversible/irreversible)

A
  • irreversible

- due to generation of pyrophosphate

102
Q

inosine to which base

what also forms

A
  • hypoxanthine

- ribose-1-phosphate

103
Q

inosine -> hypoxanthine by which enzyme

A
  • purine nucleoside phosphorylase
104
Q

guanosine to which base

what also forms

A
  • guanine

- ribose-1-phosphate

105
Q

guanosine -> guanine by which enzyme

A
  • purine nucleoside phosphorylase
106
Q

deficiency of purine nucleoside phosphorylase leads to

A
  • accumulation of nucleosides
  • T-cell immunodeficiency
107
Q

enzyme to make PRPP-> nucleotide

also requires

A
  • APRT and HGRT

- a base

108
Q

hyperuricemia due to

A
  • under excretion of uric acid
109
Q

factors that increase PRPP synthetase lead to

A
  • increased levels of PRPP
  • increased activity of glutamine phosphoribosyl amidotransferase
  • increases production of 5-phosphoribosyl 1-amine and nucleotides
110
Q

von Gierke disease due to

A
  • glucose-6-phosphatase deficiency
111
Q

reduced glucose-6-phosphatase results in

A
  • g-6-p shunted into PPP pathway
112
Q

more G-6-P into PPP results in

A
  • more glutamine phosphoribosyl amidotransferase activity

- increased nucleotide synthesis

113
Q

genetics of Lesch-Nyhan syndrome

A
  • X-linked

- recessive

114
Q

cause of Lesch-Nyhan syndrome

A
  • deficiency of HGPRT
115
Q

symptoms of Lesch-Nyhan syndrome

A
  • neurological and behavioral abnormalities

- gout

116
Q

result of Lesch-Nyhan syndrome

A
  • cannot salvage hypoxanthine or guanine
117
Q

what happens when you can’t salvage hypoxanthine or guanine

A
  • bases degraded to uric acid
118
Q

Lesch-Nyhan syndrome on PRPP levels

A
  • increases
119
Q

Lesch-Nyhan syndrome on AMP and GMP levels

A
  • reduced
120
Q

Lesch-Nyhan syndrome stimulates production of

A
  • 5-phosphoribosyl-1-amine by glutamine phosphoribosyl amidotransferase
121
Q

importance of more PRPP levels in Lesch-Nyhan syndrome

A
  • normally stimulates purine synthesis anyway
122
Q

importance of less AMP and GMP levels in Lesch-Nyhan syndrome

A
  • normally inhibits purine synthesis

- less of them makes purine synthesis go even further

123
Q

colchicine

A
  • treats symptoms only
124
Q

MOA of allopurinol and febuxostate

A
  • inhibit xanthine oxidase
125
Q

result of allopurinol and febuxostat

A
  • lowers purine and uric acid levels
126
Q

MOA of pegloticase and rasburicase

A
  • converts uric acid to more soluble allantoin
127
Q

MOA of probenecid and lesinurad

A
  • promotes renal excretion of uric acid
128
Q

allopurinol structural analog of

A
  • hypoxanthine
129
Q

allopurinol converts to

A
  • oxypurinol
130
Q

significance of oxypurinol

A
  • irreversible inhibitor of xanthine oxidase
131
Q

what happens when inhibition of xanthine oxidase

A
  • accumulates xanthine and hypoxanthine

- more soluble than uric acid

132
Q

salvaging of hypoxanthine result

A
  • reduces PRPP

- reduces de novo purine synthesis

133
Q

cancer patients with large tumors that are undergoing treatment have what

A
  • high levels or uric acid
134
Q

how do we reduce uric acid levels in patients undergoing cancer therapy

A
  • allopurinol

- rasburicase

135
Q

pyrimidine synthesis requires which 2 amino acids

which other compound

A
  • Gln
  • Asp
  • CO2
136
Q

how do we start pyrmidine synthesis

A
  • Glutamine + CO2 -> Carbamoyl phosphate
137
Q

enzyme to convert - Glutamine + CO2 -> Carbamoyl phosphate

A
  • CPS-II

- committed step

138
Q

CPS-II inhibited by

A
  • UTP
139
Q

CPS0II activated by

A
  • PRPP
140
Q

formation of orotic acid

A
  • aspartate -> carbamoyl aspartate -> orotic acid
141
Q

how to form carbamoyl aspartate from aspartate

A
  • aspartate + carbamoyl phosphate
142
Q

first 3 activities of pyrimidine synthesis pathway resides on

A
  • CAD
143
Q

enzyme from aspartate to carbamoyl aspartate

A
  • aspartate transcarbamoylase
144
Q

enzyme from carbamoyl phosphate to orotic acid

A
  • dihydroorotase

- dihydroortate dehydrogenase

145
Q

formation of UMP from orotic acid

A
  • orotic acid -> OMP

- OMP -> UMP

146
Q

orotic acid -> OMP donor

A
  • PRPP
147
Q

orotic acid -> OMP donor reversibility of reaction

A
  • irreversible
148
Q

orotic acid -> OMP donor enzyme

A
  • orotate phosphoribosyl transferase
149
Q

OMP-UMP enzyme

A
  • orotidine 5’-P decarboxylase
150
Q

orotate phosphoribosyl transferase and orotidine 5’-P decarboxylase part of which enzyme

A
  • UMP synthase
151
Q

hereditary orotic aciduria caused by

A
  • mutations in UMP synthase
152
Q

symptoms of orotic aciduria

A
  • poor growth
  • anemia
  • high levels of orotic acid in urine
153
Q

how to treat orotic aciduria

A
  • uridine
154
Q

uridine pathway

A
  • uridine -> UTP

- UTP-CTP

155
Q

what does UTP inhibit

results?

A
  • CSPII

- reduces de novo synthesis of orotic acid to normal levels

156
Q

UMP -> UDP which enzyme

requires

A
  • UMP kinase

ATP

157
Q

UDP -> UTP which enzyme

requires

A
  • NDP kinase

ATP

158
Q

enzyme to produce CTP from UTP

also required

A
  • CTP synthetase

- glutamine

159
Q

negative regulation of synthesis of CTP from UTP

A
  • CTP is negative regulator
160
Q

key regulated step of pyrimidine synthesis

A
  • CSP II
161
Q

CSP activated by

A
  • PRPP
162
Q

what is required for the first step of pyrimidine synthesis

why is this important?

A
  • ATP

- helps balance purine/pyrimidine ratio

163
Q

inhibitors of CPS II

A
  • UTP and UDP
164
Q

inhibitor of OMP decarboxylase

A
  • UMP
165
Q

cytosine degradation pathway

A
  • cytosine
  • uracil
  • beta alanine
166
Q

thymine degradation pathway

A
  • thymine

- beta aminoisobutyrate

167
Q

end result of B-alanine and B-aminoisobutyrate

A
  • excreted in urine
  • converted to malonyl-CoA and used in fatty acid biosynthesis
  • HIGHLY SOLUBLE
168
Q

salvage of pyrimidine bases

A
  • salvaged to nucleosides -> nucleotides
169
Q

uracil/thymine to uridine/thymidine via

also included

A
  • nucleoside phosphorylase
  • ribose-1-phosphate (U)
  • deoxyribose-1-phosphate (T)
170
Q

uridine to UMP via

also included

A
  • nucleoside kinase

- ATP

171
Q

dNDPs are derived from

A
  • NDPs
172
Q

enzyme to reduce NDPs to dNDPs

A
  • ribonucleotide reductase
173
Q

cofactor required by ribonucleotide reductase

for what reason

A
  • thioredoxin

- supply H

174
Q

purpose of NADPH in synthesis of dNDPs

A
  • provides H to replenish thioredoxin
175
Q

hydroxyurea MOA

A
  • inhibits ribonucleotide reductase
  • reduces dNTPs and dNDPs
  • reduces DNA synthesis
176
Q

enzyme for UDP to dUDP

A
  • ribonucleotide reductase
177
Q

why is dUTP quickly hydrolyzed to dUMP

A
  • we don’t use dUTP for DNA synthesis
178
Q

alternative path to produce dUMP

A
  • dCMP -> dUMP
179
Q

dCMP -> dUMP enzyme

A
  • dCMP deaminase
180
Q

dCMP deaminase activated by

A
  • dCTP
181
Q

dCMP deaminase inhibited by

A
  • dTTP
182
Q

dUMP - dTTP by enzyme

also needs

A
  • thymidylase synthase

- N5,N10-methylene tetrahydrofolate

183
Q

N5,N10-methylene tetrahydrofolate derived from

A
  • dihydrofolate
184
Q

what do we need for continued DNA replication

A
  • regeneration of DHF by NADPH
185
Q

activation of ribonucleotide reductase

A
  • ATP
186
Q

inhibition of ribonucleotide reductase

A
  • dATP
187
Q

cross regulation by dNTPs helps with

A
  • balancing correct amounts of each dNTP
188
Q

2 allosteric sites of ribonucleotide reductase

A
  • controls activity

- substrate specificity

189
Q

5-fluorouracil MOA

A
  • converted to 5-fluorodeoxyuridine monophosphate
190
Q

5-fluorodeoxyuridine monophosphate purpose

A
  • permanently binds thymidylate synthetase
191
Q

5-fluorouracil result

A
  • reduces conversion of dUMP to dTMP
192
Q

methotrexate MOA

A
  • competitive inhibitor of DHFR
193
Q

methotrexate result

A
  • reduces levels of THF and N5,N10-methylene

- reduces conversion of dUMP to dTMP

194
Q

6-mercaptopurine MOA

A
  • negatively regulated PRPP amidotransferase

- reduces nucleotides

195
Q

6-mercaptopurine inhibits which pathways

A
  • IMP-> AMP

- IMP -> GMP

196
Q

leflunomide MOA

A
  • inhibits dihydroorotate dehydrogenase
197
Q

importance of inhibiting dihydroorotate dehydrogenase

A
  • blocks orotate and pyrimidine production