Pyrimidine Synthesis and Degradation

Unlike the synthesis of the purine ring, which is constructed on a preexisting ribose 5-phosphate donated by PRPP, the pyrimidine ring is synthesized first and the sources of the atoms are glutamine, CO2, and aspartic acid

A. Synthesis of carbamoyl phosphate This is the first (regulated) step of this pathway. Carbamoyl phosphate is synthesized from glutamine and CO2, catalyzed by carbamoyl phosphate synthetase (CPS) II. CPS II is inhibited by UTP (the end product of this pathway) and is activated by ATP and PRPP.

B. Synthesis of orotic acid The second step in pyrimidine synthesis is the formation of carbamoylaspartate, catalyzed by [aspartate transcarbamoylase]. The pyrimidine ring is then closed hydrolytically by dihydroorotase. The resulting dihydroorotate is oxidized to produce orotic acid (orotate) by enzyme called [dihydroorotate dehydrogenase].

Note: All enzymes that participate in pyrimidine biosynthesis are cytoplasmic, except dihydroorotate dehydrogenase which is attached to the inner mitochondrial membrane.

C. Formation of a pyrimidine nucleotide Following the completion of closure of pyrimidine ring (orotate), the ring will be converted to a pyrimidine nucleotide by an enzyme called [orotate phosphoribosyl transferase] utilizing PRPP again as a source of ribose 5′-phosphate with liberation of phosphate.

The resulting nucleotide is called OMP (Orotidine 5′- monophosphate) which is the parent pyrimidine nucleotide. OMP will finally be decarboxylated by [OMP decarboxylase] to UMP (uridine monophosphate). UMP is phosphorylated to UTP.

The last 2 enzymes i.e. Orotate phosphoribosyltransferase and orotidylate decarboxylase are catalytic domains of a single polypeptide chain called UMP Synthase.

Orotic aciduria— a rare genetic defect—is caused by a deficiency of this bifunctional enzyme, resulting in orotic acid to appear in the urine in association to growth impairment and megaloblastic anaemia. Treatment is by administration of uridine leading to inhibition of the 1st step reaction (i.e CSP II) and reduction of orotate production.

D. Synthesis of cytidine triphosphate (CTP)

E. Synthesis of thymidine monophosphate (TMP) from dUMP dUMP is converted to dTMP by [thymidylate synthase], which uses N5,N10-methylene tetrahydrofolate as the source of the methyl group. Inhibitors of thymidylate synthase include thymine analogs such as 5-fluorouracil, which serve as successful antitumor agents.

Salvage of pyrimidines Few pyrimidine bases are salvaged in human cells. However, the pyrimidine nucleosides can be salvaged by nucleoside kinases that utilize ATP in the phosphorylation of the nucleosides to nucleotides. [Note: The salvage of pyrimidine nucleotides is the basis for using uridine in the treatment of hereditary orotic aciduria.]

Degradation of pyrimidine nucleotides Unlike the purine bases that are not in cleaved human cells, the pyrimidine ring is opened and degraded to highly soluble products, β-alanine and β-aminoisobutyrate, with the production of NH3 and CO2.

Naturally Occurring free nucleotides that are not part of nucleic acids but have important biological functions: Some nucleotides are not part of nucleic acids but they freely present in the cell cytosole and they have important functions like the following:

1. ATP (Adenosine triphosphate):

It is the primary source of energy in too many energy requiring biological processes. It is used and converted to ADP+ Pi in the cytoplasm, however, the inner mitochondrial membrane requires specialized carriers to transport ADP and Pi from cytoplasm to mitochondria where it is synthesized again by an enzyme called ATP- synthetase. This enzyme complex synthesizes ATP using the energy of one proton gradient generated by [Electron Transport Chain]. ATP is important in oxidative phosphorylation reactions.

2. Cyclic Adenosine monophosphate (cAMP) A membrane bound enzyme called (adenylate cyclase) converts ATP to 3′,5′-adenosine monophosphate (also called cyclic AMP or cAMP). It is considered as a second messenger for chemical signals like hormones or neurotransmitters, each of which binds to a unique type of membrane receptor and considered as 1st messenger.

cAMP is rapidly hydrolyzed to 5′- AMP by an enzyme called [c AMP Phosphodiesterase] which cleaves the cyclic 3′,5 phosphodiester bond. 5′- AMP is not an intracellular signaling molecule, thus the effects of neurotransmitters or hormone- mediated increases of c AMP are rapidly terminated if the extracellular signal (1st messenger) is removed.

3- UDP- GLUCOSE, UDP-GALACTOSE, UDP-N- ACETYLGLUCOSAMINE AND UDP- N- ACETYLGALACTOSAMINE These are nucleotide sugars that are considered as the precursors of the carbohydrate components of glycoproteins. In addition, GDP-mannose, GDP-L-fucose (which is synthesized from GDP-mannose), and CMP-N-acetylneuraminic acid may donate sugars to the growing glycoprotein chain.

4. UDP- glucoronic acid It is produced by the oxidation of UDP- glucose. It is the active form of glucoronic acid that donates the sugar in glycosaminoglycans synthesis and other glucuronylation reactions. In addition, UDP- glucoronic acid is involved in the conjugation to less polar compounds like steroids, some drugs, and bilirubin. Thus it is an important detoxifying intermediate.

5- Flavine Adenine Dinucleotide (FAD) and Nicotinamide Adenine Dinucleotide (NAD): These are important co-enzymes that play important roles in certain metabolic processes like citric acid cycle and electron transport system