Nucleotide Metabolism 8.24 Flashcards
differentiate between a free base, nucleoside, and nucleotide
free base - just the purine or pyrimadine base
nucleoside - base and pentose sugar
nucleotide - base, pentose sugar, and phosphate group
describe nitrogenous base numbering
name the positions at which purines differ
name the positions at which pyrimadines
Where is the glycosidic linkage formed in nucleotides
for purines - 9’ Nitrogen
for pyrimadines - 1’ Nitrogen
Describe the naming of purine and pyrimidine nucleotide derivatives
Give the structure of PRPP (phosphoribosylpyrophosphate)
Describe the linear synthesis portion of purine de novo synthesis
Note donation order/sources, energy requirements, points of regulation and how they are regulated
ribose-5-phosphate to inosine-5-phosphate
ribose-5-phosphate -> PRPP via PRPP synthetase
PRPP -> phosphoribosylamine via ATase = committed step and rate limiting step - allostericaly controlled - high [purine nucleotides] closes dimer - high [PRPP] opens dimer
donation order: 9’N glutamine -> 4’C, 5’C, 7’N glycine -> 8’C formyl -> 3’N glutamine -> 6’ CO2 -> 1’N aspartate -> 2’C formyl
10 steps, 5 ATP
Describe the branch point synthesis portion of purine de novo synthesis
Note important points of regulation and how they are regulated
IMP ends up as G-nucleotides or A-nucleotides
A-nucleotide pathway – (IMP->Adenylosuccinate via adenylosuccinate synthetase)(Adenylosuccinate->AMP via adenylosuccinate lyase)(AMP->ADP via adenylate kinase)(ADP->ATP via nucleoside diphosphate kinase) - high [AMP] downregulates adenylosuccinate synthetase
G-nucleotide pathway – (IMP->XMP via IMP dehydrogenase)(XMP->GMP via GMP synthase)(GMP->GDP via guanylate kinase)(GDP->GTP via nucleoside diphosphate kinase) - high [GMP] downregulates IMP dehydrogenase
cross-regulation - high ATP upregulates GMP synthase - high GTP upregulates adenylosuccinate synthetase
monophosphate->diphosphate is base specific
high [purine nucleotides] downregulates both ATase and PRPP synthetase in linear synthesis pathway
diphosphate->triphosphate has broad specificity
describe steady state behavior of adenylate kinase
maintains a specific ratio of A-nucleotides
100X ATP, 10X ADP, 1X AMP
this is important for maintaining the metabolic capability of the body
summary of Purine de novo synthesis
summary of purine degredation and excretion
three steps - dephosphorylation, deamination, phosphorolysis (removal of sugar)
AMP
option 1: (AMP->Adenosine via nucleotidase)(Adenosine->Inosine via adenosine deaminase)(Inosine->Hypoxanthine via purine nucleoside phosphorylase)(hypoxanthine-> xanthine via xanthine oxidase or xanthine dehydrogenase)(xanthine->uric acid via xanthine or xanthine dehydrogenase)
option 2: (AMP->IMP via AMP deaminase)(IMP->Inosine via nucleotidase)(Inosine->Hypoxanthine via purine nucleoside phosphorylase)(hypoxanthine-> xanthine via xanthine oxidase or xanthine dehydrogenase)(xanthine->uric acid via xanthine or xanthine dehydrogenase)
GMP
(GMP->Guanosine via nucleotidase)(Guanosine->Guanine via purine nucleotide phosphorylase)(Guanine->Xanthine via Guanase)(Xanthine-Uric acid via xanthine oxidase or xanthine dehydrogenase)
Xanthine dehydrogenase vs Xanthine Oxidase
Xanthine dehydrogenase is converted to Xanthine oxidase in low oxygen environment
XDH uses NAD+ as electron acceptor
XO uses water as electron acceptor (produces H2O2 in the process) - can be harmful - in heart attack, low O2 in heart muscle can lead to XO buildup. When O2 is restored, free radicals can be produced
Describe the purine salvage pathway for free bases and nucleosides
free base - requires PRPP
Adenine+PRPP = AMP+PPi via adenine phosphoribosyltransferase (APRT)
Guanine+PRPP = GMP+PPi via hypoxanthine-guanine phosphoribosyltransferase (HPRT)
Hypoxanthine+PRPP = IMP+PPi via HPRT
nucleoside - requires ATP
Adenosine+ATP = AMP+ADP via adenosine kinase
guanosine+ATP = GMP+ADP via guanosine kinase
Summary of the purine pathways
function of adensine in the heart
coronary vasodilator
function of IMP in exercise
IMP is converted to ATP after exercise
How is the purine pathway relevant to Lesch-Nyhan Syndrome
HPRT deficiency = deficient salvage system during DNA processing heavy periods of development - lack of allosteric inhibition of PRPP synthase and ATase leads to higher de novo-purine synthesis and purine metabolites
X-linked and thus affects mostly men, characterized by gout (high uric acid) and serious neurological complications
What is xanthinuria
loss of XDH function leading to xanthine buildup
How is severe combined immunodeficiency (SCID) related to purine pathways
deficiency of adenosine deaminase (ADA) and/or purine nucleoside phosphorylase (PNP) lead to T-cell dysfunction
loss of function in these enzymes results in adenosine and guanosine buildup which causes them to be salvaged and turned into dATP and dGTP - this then inhibits ribonucleotide reductase (RR) from producing other deoxy nucleotides
How does gout arise? how is it treated
uric acid is the least soluble purine base - sits near saturation level at normal
gout is due to overproduction or underexcretion of uric acid which results in crystallization
Causes of primary gout (inherited): high [PRPP synthetase], low [HPRT], problem with renal urate transport protein
Causes of secondary gout (acquired): drug intake or diet
Treat by inhibiting XDH (side effect is that ATase function drops, XDH inhibition causes creater salvage of Guanine and thus makes more nucleotides which inhibit ATase)
Describe de novo pyrimidine synthesis
note donors/positions, major enzymes and regulatory steps
Glutamine/HCO2 -> UMP
3’N Glutamine and 2’C CO2 -> 4’C, 5’C, 6’C, 1’N Aspartate
6 steps, 5 ATP
Carbamoyl-phosphate synthetase, Aspartate transcarbamoylase, and dihydro-orotase are located on one protein (CAD) and form the ring (steps 1-3) - rate limiting step - regulated allosterically and through phosphorylation
Dihydro-orotate dehydrogenase (DHODH) step 4
UMP synthase (step 5-6)
describe synthesis of other pyrimidine nucleotides from UMP
must first convert UMP to either UDP or UTP
UMP + ATP = UDP + ADP via pyrimidine monophosphate kinase - high specificity
UDP + ATP = UTP + ADP via nucleoside diphosphate kinase (broad specificity)
UTP -> CTP via CTP synthetase
describe pyrimidine catabolism
similar to purine catabolism (three phases) - dephosphorylation (nucleotidase), deamination (deaminase), phosphorolysis (phosphorylase)
describe catabolism of uracil and thymine
each uses the same three enzymes - end products are amino acids
uracil -> alanine
thymine ->aminoisobutyrate
describe pyrimidine salvage
occurs mainly at the nucleoside level (as opposed to purines where salvage is mostly at the free base level)
enzymes are base specific
what is orotic aciduria? how is it related to the pyrimidine pathway? how is it treated?
UMP synthase deficiency which results in excessive orotic acid excretion (anemia is the main symptom)
not enough UMP being made (and thus deficient in the other pyrimidines
treat with uridine (can be salvaged by uridine kinase to make UMP) - uracil cannot be salvaged and thus isn’t much use here
what is pyrimidine 5-nucleotidase deficiency? effects?
cannot breakdown nucleoside monophosphates (UMP, CMP, dTMP) in erythrocytes - especially high cytidine nucleotides
results in anemia
what is dihydropyrimidine dehydrogenase deficiency? effects?
cannot breakdown pyrimidine nucleosides into amino acids - results in elevated serum uracil and thymine
leads to seizures and microencephaly
what is dihydropyrimidinase deficiency?
cannot breakdown dihydropyrimidines
elevated serum dihydropyrimidines - neurological symptoms
how are purine and pyrimidine ribonucleotides converted to deoxyribonucleotides
regulation?
ribonucleotide reductase (RR) - broad specificity - requires a ribonucleoside diphosphate substrate
uses NADPH as a reducer
RR is allosterically regulated by dNTP and is an important factor in ADA deficiency
how is Thymidine monophosphate made?
dUMP -> dTMP via thymidylate synthase
