Nucleotide Metabolism Flashcards
examples of purines
- adenine
- guanine
- xanthine
- hypoxanthine
- uric acid
hypoxanthine is the base for
- inosine
examples of pyrimidines
- cytosine
- thymine
- uracil
nucleoside composed of
- base + sugar
nucleotide composed of
- base + sugar + phosphate
ribose
- OH at 2’ sugar
- less stable
deoxyribose
-H at 2- sugar
sources of nucleotides
- dietary
- de novo synthesis
- salvage pathway
contribution of dietary
why
- relatively small
- most RNA and DNA in diet are degraded and excreted
primary producer of de novo synthesis
- liver
what do you end up with as the common precursor to purine nucleotides and the branch point for the synthesis of different purines
- IMP
- first step of purine synthesis
synthesis of PRPP starting with
- ribose-5-phosphate from PPP
- with ATP
synthesis of PRPP enzyme
- PRPP synthetase
importance of PRPP
- pentose molecule
- synthesis and salvage of purines and pyrimidines
what controls the rate of formation of PRPP
- amount of ribose-5-phosphate
activation of synthesis of PRPP
- Pi
- indicates low nucleotide levels
end product inhibition of synthesis of PRPP
- purine nucleotides
- ADP, GDP
Arts syndrome caused by
- genetic disorder in PRPP synthase
- generally decreased PRPP synthetase
genetics of Arts syndrome
- X-linked
reduction of PRPP synthetase causes
- reduced purine levels
- absence of hypoxanthine from urine and uric acid in serum
increases in PRPP synthetase causes
- increased levels of purines
- gout
body system impacted to Arts syndrome
- severe nervous system abnormalities
second step of purine synthesis
with help from
- PRPP -> 5-phosphoribosyl-1-amine
- with help of glutamine - contributes nitrogen
importance of second step of purine synthesis
- committed step
- irreversible
- major regulated step
enzyme in second step of purine synthesis
- glutamine phosphoribosyl amidotransferase
inhibition of second step of purine synthesis
- AMP, GMP, IMP, XMP
- pathway products
activation of second step of purine synthesis
- PRPP
which form of glutamine phosphoribosyl amidotransferase is the active form?
- the monomer
which form of glutamine phosphoribosyl amidotransferase is the inactive form?
- dimer
high levels of AMP, GMP, IMP on glutamine phosphoribosyl amidotransferase
- forms a less active dimer
high levels of PRPP on glutamine phosphoribosyl amidotransferase
- form active monomeric form
what levels play a major role in regulating purine synthesis
- PRPP
glutamine effect on kinetics of glutamine phosphoribosyl amidotransferase
- near Km
- does not influence rate significantly
PRPP effect on kinetics of glutamine phosphoribosyl amidotransferase
- PRPP levels way below Km
importance of inhibition of glutamine phosphoribosyl amidotransferase by AMP PLUS GMP or IMP
- 2 distinct binding sites
- regulation in additive way
importance of THF in purine metabolism
- carbon donor at 2 steps
what inhibits bacterial folic acid synthesis
- sulfa drugs
why don’t sulfa drugs interference with human purine synthesis and DNA replication
- humans only acquire folic acid by diet
precursors of making THF
- folate
- dihydrofolate
- tetrahydrolate
enzyme that helps make THF
also required
- DHFR
- NADPH
purine synthesis requires what form of THF
N10-formyl-THF
methotrexate often used for
MOA
- antitumor drug
- inhibits DHFR reducing synthesis of THF
good effects of methotrexate
- reduces purine synthesis
- slows down DNA replication
- slows tumor growth
bad effects of methotrexate
- affects normally dividing cells
IMP precursor for
- AMP
- GMP
base of IMP
- hypoxanthine
AMP requires what for energy
- GTP
other molecule AMP requires for energy
- aspartate
- releases fumerate
GMP requires what for energy
- ATP
other molecules GMP requires for energy
- NAD+
- glutamine
enzyme for formation of GMP from IMP
- GMP synthase
effect of high ATP on GMP/GTP synthesis
- increased
enzyme for formation of AMP from IMP
- adenylosuccinate synthetase
effect of high GTP on AMP/ATP synthesis
- increased
what inhibits IMP dehydrogenase
- GMP
what inhibits adenylosucinate synthetase
- AMP
purpose of mycophenolic acid
- immunosuppressant
- reduce lymphocyte proliferation
- prevent graft rejection
MOA of mycophenolic acid
- inhibits IMP dehydrogenase and GMP formation
purpose of ribavirin
- anti-viral
- anti-tumor agent
MOA of ribavirin
- inhibits IMP dehydrogenase
enzyme that converts AMP to ADP
what else is required
- adenylate kinase
- ATP
enzyme that converts GMP to GDP
what else is required
- guanylate kinase
- ATP
what converts ADP, GDP, and NDPs to triphosphates
what else is required
- nucleoside diphosphate kinase
- ATP
purpose of degradation of DNA and RNA
- body to reutilize nucleosides and free bases via salvage pathways
how do we get degraded nucleic acids
- cell death
- RNA or DNA turnover
- diet
nucleic aid is digested where?
by what enzyme?
- stomach
- pepsin
RNAse and DNase secreted by what
- pancreas
what do RNAse and DNase do
- digest RNA and DNA into oligonucleotides
role of phosphodiesterases
- degrade oligonucleotides
- to NMPs and dNMPs
role of nucleotidases or phosphatases
- remove phosphate groups
- convert to nucleosides
role of nucleosidases
- degrade nucleosides
- form free bases plus ribose and deoxyribose
degradation products of pyrimidine nucleotides
- all soluble
degradation products of purine nucleotides
- produce uric acid
- lead to hyperuricemia
hyperuricemia can result in
- gout
degradation occurs mostly where
- liver
degradation of AMP to xanthine process
- AMP -> IMP -> inosine
- AMP -> adenosine -> inosine
- inosine -> hypoxanthine
- hypoxanthine -> xanthine
degradation of GMP to xanthine process
- GMP -> guanosine
- guanosine -> guanine
- guanine -> xanthine
xanthine degraded to
by what enzyme
- uric acid
- xanthine oxidase
uric acid generated in
transported to
- liver
- kidney for excretion in urine
MOA of allopurinol
- inhibits xanthine oxidase
- reduces uric acid levels
allopurinol used to treat
- gout
enzyme from AMP -> IMP
- AMP deaminase
enzyme from IMP -> inosine
- 5’-nucleotidase
enzyme from AMP -> adenosine
- 5’-nucleotidase
enzyme from adenosine -> inosine
- adenosine deaminase
what condition results from blocking of adenosine deaminase
- SCID
what other reaction does adenosine deaminase (ADA) catalyze
- deoxyadenosine -> deoxyinosine
genetic deficiency of ADA results in
- accumulation of dATP
importance of high levels of dATP
- inhibit ribonucleotide reductase
importance of inhibition of ribonucleotide reductase
- reduction in DNA synthesis
importance of high deoxyadenosine levels
- toxic in lymphocytes
- unable to combat infection leading to SCID
AMP deaminase functions in
- skeletal muscle
AMP deaminase deficiency symptoms
- skeletal muscle myopathy
- exercise induced fatigue and cramps
- often asymptomatic
AMP deaminase selective form
- AMP only
part of the body where savage is done
- the liver
salvage pathway
- building nucleotides from bases and nucleosides
benefit of salvage pathway
- energetically advantageous
- less costly than de novo
adenine to AMP in purine to NMP salvage pathway uses which enzyme
also requires
- APRT
- PRPP
hypoxanthine to IMP in purine to NMP salvage pathway uses which enzyme
- also requires
- HGPRT
PRPP
guanine to GMP in purine to NMP salvage pathway uses which enzyme
also requires
- HGPRT
- PRPP
purine to NMP salvage pathway reactions (reversible/irreversible)
- irreversible
- due to generation of pyrophosphate
inosine to which base
what also forms
- hypoxanthine
- ribose-1-phosphate
inosine -> hypoxanthine by which enzyme
- purine nucleoside phosphorylase
guanosine to which base
what also forms
- guanine
- ribose-1-phosphate
guanosine -> guanine by which enzyme
- purine nucleoside phosphorylase
deficiency of purine nucleoside phosphorylase leads to
- accumulation of nucleosides
- T-cell immunodeficiency
enzyme to make PRPP-> nucleotide
also requires
- APRT and HGRT
- a base
hyperuricemia due to
- under excretion of uric acid
factors that increase PRPP synthetase lead to
- increased levels of PRPP
- increased activity of glutamine phosphoribosyl amidotransferase
- increases production of 5-phosphoribosyl 1-amine and nucleotides
von Gierke disease due to
- glucose-6-phosphatase deficiency
reduced glucose-6-phosphatase results in
- g-6-p shunted into PPP pathway
more G-6-P into PPP results in
- more glutamine phosphoribosyl amidotransferase activity
- increased nucleotide synthesis
genetics of Lesch-Nyhan syndrome
- X-linked
- recessive
cause of Lesch-Nyhan syndrome
- deficiency of HGPRT
symptoms of Lesch-Nyhan syndrome
- neurological and behavioral abnormalities
- gout
result of Lesch-Nyhan syndrome
- cannot salvage hypoxanthine or guanine
what happens when you can’t salvage hypoxanthine or guanine
- bases degraded to uric acid
Lesch-Nyhan syndrome on PRPP levels
- increases
Lesch-Nyhan syndrome on AMP and GMP levels
- reduced
Lesch-Nyhan syndrome stimulates production of
- 5-phosphoribosyl-1-amine by glutamine phosphoribosyl amidotransferase
importance of more PRPP levels in Lesch-Nyhan syndrome
- normally stimulates purine synthesis anyway
importance of less AMP and GMP levels in Lesch-Nyhan syndrome
- normally inhibits purine synthesis
- less of them makes purine synthesis go even further
colchicine
- treats symptoms only
MOA of allopurinol and febuxostate
- inhibit xanthine oxidase
result of allopurinol and febuxostat
- lowers purine and uric acid levels
MOA of pegloticase and rasburicase
- converts uric acid to more soluble allantoin
MOA of probenecid and lesinurad
- promotes renal excretion of uric acid
allopurinol structural analog of
- hypoxanthine
allopurinol converts to
- oxypurinol
significance of oxypurinol
- irreversible inhibitor of xanthine oxidase
what happens when inhibition of xanthine oxidase
- accumulates xanthine and hypoxanthine
- more soluble than uric acid
salvaging of hypoxanthine result
- reduces PRPP
- reduces de novo purine synthesis
cancer patients with large tumors that are undergoing treatment have what
- high levels or uric acid
how do we reduce uric acid levels in patients undergoing cancer therapy
- allopurinol
- rasburicase
pyrimidine synthesis requires which 2 amino acids
which other compound
- Gln
- Asp
- CO2
how do we start pyrmidine synthesis
- Glutamine + CO2 -> Carbamoyl phosphate
enzyme to convert - Glutamine + CO2 -> Carbamoyl phosphate
- CPS-II
- committed step
CPS-II inhibited by
- UTP
CPS0II activated by
- PRPP
formation of orotic acid
- aspartate -> carbamoyl aspartate -> orotic acid
how to form carbamoyl aspartate from aspartate
- aspartate + carbamoyl phosphate
first 3 activities of pyrimidine synthesis pathway resides on
- CAD
enzyme from aspartate to carbamoyl aspartate
- aspartate transcarbamoylase
enzyme from carbamoyl phosphate to orotic acid
- dihydroorotase
- dihydroortate dehydrogenase
formation of UMP from orotic acid
- orotic acid -> OMP
- OMP -> UMP
orotic acid -> OMP donor
- PRPP
orotic acid -> OMP donor reversibility of reaction
- irreversible
orotic acid -> OMP donor enzyme
- orotate phosphoribosyl transferase
OMP-UMP enzyme
- orotidine 5’-P decarboxylase
orotate phosphoribosyl transferase and orotidine 5’-P decarboxylase part of which enzyme
- UMP synthase
hereditary orotic aciduria caused by
- mutations in UMP synthase
symptoms of orotic aciduria
- poor growth
- anemia
- high levels of orotic acid in urine
how to treat orotic aciduria
- uridine
uridine pathway
- uridine -> UTP
- UTP-CTP
what does UTP inhibit
results?
- CSPII
- reduces de novo synthesis of orotic acid to normal levels
UMP -> UDP which enzyme
requires
- UMP kinase
ATP
UDP -> UTP which enzyme
requires
- NDP kinase
ATP
enzyme to produce CTP from UTP
also required
- CTP synthetase
- glutamine
negative regulation of synthesis of CTP from UTP
- CTP is negative regulator
key regulated step of pyrimidine synthesis
- CSP II
CSP activated by
- PRPP
what is required for the first step of pyrimidine synthesis
why is this important?
- ATP
- helps balance purine/pyrimidine ratio
inhibitors of CPS II
- UTP and UDP
inhibitor of OMP decarboxylase
- UMP
cytosine degradation pathway
- cytosine
- uracil
- beta alanine
thymine degradation pathway
- thymine
- beta aminoisobutyrate
end result of B-alanine and B-aminoisobutyrate
- excreted in urine
- converted to malonyl-CoA and used in fatty acid biosynthesis
- HIGHLY SOLUBLE
salvage of pyrimidine bases
- salvaged to nucleosides -> nucleotides
uracil/thymine to uridine/thymidine via
also included
- nucleoside phosphorylase
- ribose-1-phosphate (U)
- deoxyribose-1-phosphate (T)
uridine to UMP via
also included
- nucleoside kinase
- ATP
dNDPs are derived from
- NDPs
enzyme to reduce NDPs to dNDPs
- ribonucleotide reductase
cofactor required by ribonucleotide reductase
for what reason
- thioredoxin
- supply H
purpose of NADPH in synthesis of dNDPs
- provides H to replenish thioredoxin
hydroxyurea MOA
- inhibits ribonucleotide reductase
- reduces dNTPs and dNDPs
- reduces DNA synthesis
enzyme for UDP to dUDP
- ribonucleotide reductase
why is dUTP quickly hydrolyzed to dUMP
- we don’t use dUTP for DNA synthesis
alternative path to produce dUMP
- dCMP -> dUMP
dCMP -> dUMP enzyme
- dCMP deaminase
dCMP deaminase activated by
- dCTP
dCMP deaminase inhibited by
- dTTP
dUMP - dTTP by enzyme
also needs
- thymidylase synthase
- N5,N10-methylene tetrahydrofolate
N5,N10-methylene tetrahydrofolate derived from
- dihydrofolate
what do we need for continued DNA replication
- regeneration of DHF by NADPH
activation of ribonucleotide reductase
- ATP
inhibition of ribonucleotide reductase
- dATP
cross regulation by dNTPs helps with
- balancing correct amounts of each dNTP
2 allosteric sites of ribonucleotide reductase
- controls activity
- substrate specificity
5-fluorouracil MOA
- converted to 5-fluorodeoxyuridine monophosphate
5-fluorodeoxyuridine monophosphate purpose
- permanently binds thymidylate synthetase
5-fluorouracil result
- reduces conversion of dUMP to dTMP
methotrexate MOA
- competitive inhibitor of DHFR
methotrexate result
- reduces levels of THF and N5,N10-methylene
- reduces conversion of dUMP to dTMP
6-mercaptopurine MOA
- negatively regulated PRPP amidotransferase
- reduces nucleotides
6-mercaptopurine inhibits which pathways
- IMP-> AMP
- IMP -> GMP
leflunomide MOA
- inhibits dihydroorotate dehydrogenase
importance of inhibiting dihydroorotate dehydrogenase
- blocks orotate and pyrimidine production
