Lecture 7 (4A) - Pyrimidine Biosynthesis Flashcards
Pyrimidines
thymine and cytosine
1 ring
Pyrimidine biosynthesis
2 methods
- de novo - forms uridine monophosphate (before makes T or C)
- salvage pathways
de novo biosynthesis
6 steps (purines 9 steps)
de novo biosynthesis
steps
- carbamoyl phosphate synthesized
- phosphate to aspartate (phosphate displaced by aspartate)
- ring closure
- dihydroorotate oxidation
- sugar added (have ring, then put sugar on)
- decarboxylation
de novo biosynthesis
- carbamoyl phosphate synthesized
- requires 2 ATP, glutamine, whater, HCO3- (bicarbonate)
- glutamine side chain gives up N (ammonia) → glutamate
- 1 ATP for phosphate group
- 1 ATP as energy source
- ATP + H2O → ADP + Pi
- glutamine → glutamate
- forms: carbamoyl phosphate (seen in urea cycle in mito, here it cytosol)
- enzyme - carbamoyl phosphate synthetase
- has 3 active sites
- glutamine hydrolys site ( → ammonia)
- bicarbonate phosphorylation site
- carbamic acid phosphorylation site
- the product of 1 is channelled to become the substrate of the next (nothing escapes except the ultimate products, prevents unwanted byproduct and makes sure you get the product you want)
de novo biosynthesis
- carbamoyl phosphate synthesized
requires
- 2 ATP
- 1 for phosphate group
- 1 for energy source
- ATP + H2O → ADP + Pi
- glutamine
- side chain gives up N (ammonia) → glutamate
- glutamine → glutamate
- water
- HCO3- (bicarbonate)
de novo biosynthesis
- carbamoyl phosphate synthesized
forms
carbamoyl phosphate
(seen in urea cycle in mitochondria, here in cytosol)
de novo biosynthesis
- carbamoyl phosphate synthesized
enzyme
carbamoyl phosphate synthetase
has 3 active sites
- glutamine hydrolysis site ( → ammonia)
- bicarbonate phosphorylation site
- carbamic acid phosphorylation site
- the product of 1 is channelled to become the substrate of the next
- (nothing escapes except the ultimate products)
- prevents unwanted byproduct and makes sure you get what you want
de novo biosynthesis
- phosphate to aspartate
phosphate displaced by aspartate
- requires asparate (removes Pi)
- forms carbamoyl aspartate
- important: flux-generating step
- makes production go faster
- upregulated
- wante N and C from carbamoyl phosphate
- enzyme asparate transcarbamoylase
- similar to ornithine transcarbamoylase
by the end have the whole pyrimidine ring assembled, just need ring closure
de novo biosynthesis
- phosphate to aspartate
requires
aspartate (removes Pi)
de novo biosynthesis
- phosphate to aspartate
forms
carbamoyl aspartate
whole body of pyrimidine assembled, now just need ring closure
de novo biosynthesis
- phosphate to aspartate
important step…
flux-generating step
- makes production go faster
- upregulated
- want N and C from carbamoyl phosphate
de novo biosynthesis
- phosphate to aspartate
enzyme
aspartate transcarbamoylase
(similar to ornithine transcarbamoylase)
de novo biosynthesis
- ring closure
- condensation reaction (removes water)
- forms dihydroorotate (oxidized to orotate)
- enzyme dihydroorotase
de novo biosynthesis
- ring closure
forms
dihydroorotate
(oxidized to orotate)
de novo biosynthesis
- ring closure
enzyme
dihrydoorotase
de novo biosynthesis
- dihydroorotate oxidation
- NAD+ → NADH
- mammals FAD and FADH
- requires a flavin-cotainiing enzyme
- flavin in mitochondrial membrane
- quinone → reduced quinone
- forms orotate
- enzyme - dihydroorotate oxidase
de novo biosynthesis
- dihydroorotate oxidation
requires
a flavin-containing enzyme
(in inner mitochondrial membrane)
de novo biosynthesis
- dihydroorotate oxidation
forms
orotate
de novo biosynthesis
- dihydroorotate oxidation
enzyme
dihydoorotate oxidase
de novo biosynthesis
- sugar added
- have ring then put sugar on
- compare with purines - purines built onto sugar
- requies sugar PRPP
- formed in ourine biosynthesis (primer)
- hydrolyzed → energy
- hydrolysis of PRPP (sugar) drives action
- PPi lost
- forms orotidine monophosphate (OMP) aka oroditylate
- enzyme pyrimidine phosphoribosyl transferase
- inversion of β to α form (nucleophilic attack
- enzyme has 2 functions - named separately (see next step)
de novo biosynthesis
- decarboxylation
- unusual step because requires no cofactors
- enzyme itself has the capacity to carry out reaction
- loses CO2
- forms: uridine monophosphate (UMP) or uridylate
- enzyme: orotidylate decarboxylation
- 2nd half of the reaction step 5 enzyme
de novo biosynthesis
- decarboxylation
unusual step because
requires no cofactors
the enzyme itself has the capacity to carry out the reaction
de novo biosynthesis
- decarboxylation
forms
uridine monophosphate (UMP) or uridylate
(loses CO2)
