Nucleotide Synthesis

Nucleotides are the building blocks of amino acids. They can either be synthesized in a process called "de novo" synthesis--which means "beginning again" in Latin--or they can be recycled through salvage pathways after the RNA or DNA harboring them has been degraded (most likely via DNase or RNase). This article will specifically cover de novo synthesis.

All five nucleotides (including the RNA base "uracil") are synthesized through complex metabolic pathways involving several multi-subunit enzymes. The pathways differ for both purines and pyrimidines (uracil falling in the pyrimidine category since it is thymine's counterpart.)

Contrary to common belief, the nucleotides are not synthesized as bases first then attached to a sugar. As seen in the first step of purine synthesis, sugars usually attach themselves to a base very early on in the process if not in the middle (as with pyrimidine synthesis).

Purine Synthesis:

Reaction Mechanism 1: The purine synthesis pathway begins with 5-phosphoribosyl 1-pyrophosphate (synthesized from ribose 5-phosphate). 5-phosphoribosyl 1-pyrophosphate (from henceforth "PRPP") binds to the first enzyme in this pathway, glutamine-PRPP amidotransferase. This changes the conformation of the enzyme to allow for glutamine binding in another active site. Through this enzyme, glutamine is hydrolyzed to glutamate, and the ammonia (readily turned into a weakly nucleophilic ammonium ion in an aqueous environment) that was hydrolyzed off then travels down a hydrophobic channel to attack PRPP's 1' carbon. Since the O-P-P already on the 1' carbon is a good leaving group, PRPP is stable enough to accept the attack and becomes 5-phospho-beta-D-ribosylamine.

Reaction Mechanism 2: 5-phospho-beta-D-ribosylamine attacks a phosphorylated glycine (the phosphate is a good leaving group). GAR synthetase is the enzyme that catalyzes this reaction. Glycinamide ribonucleotide (GAR) is produced.

Reaction Mechanism 3: GAR is formylated on the newly added amine group (the N terminus of the glycine residue) by N10-Formyl H4 folate. GAR transformylase catalyzes this reaction.

Reaction Mechanism 4: The formylated GAR (known as formylglycinamide ribonucleotide or FGAM) is attacked by another ammonia on the first carbon from the glycine residue. The ammonia is again released after hydrolysis of glutamine. Before ammonia can attack, however, ATP activates the oxygen of the carbonyl from the glycine. After phosphorylation, the O-P substituent becomes a good leaving group, and the nucleophile ammonia can perform an SN2 reaction. The reaction is catalyzed by FGAR amidotransferase (similar mechanism to glutamine-PRPP amidotransferase; the FGAR is activated in tandem with glutamine hydrolysis). The intermediate is now a formylglycinamine and is thus known as FGAM.

Reaction Mechanism 5: FGAM is phosphorylated by ATP through FGAM cyclase to form a five-membered ring. The ATP activates the remaining carbonyl group (from formylation in step 3). That carbon is then attacked by the amine from reaction 1, forming a ring with O-P as a leaving group. The molecule that remains is known as 5-aminoimidazole ribonucleotide (AIR).

Reaction Mechanism 6a: AIR can now by processed in different ways (higher eukaryotes like humans use AIR carboxylase to bypass step 7; mechanism will be covered as step 6b). In this mechanism, AIR can attacked an activated bicarbonate ion using the amine group from the second glutamine reaction (step 4). This steps is catalyzed by N5-CAIR synthetase.

Reaction Mechanism 7: The carboxyl group from the bicarbonate is transferred to the central carbon of the glycine residue from reaction 2. N5-CAIR from 6a now becomes CAIR (or carboxyaminoimidazole ribonucleotide). This is very similar to the glycine binding mechanism. This reaction is catalyzed by N5-CAIR mutase.

Reaction Mechanism 6b: This reaction involves bringing in a carbon dioxide to directly bond with the central carbon of the glycine residue. That carbon attacks the carbon dioxide using the help of AIR carboxylase, an enzyme that is homologous to N5-CAIR mutase.

A few more reactions follow. I will finish this later unless someone would like to finish for me.