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Purine Biosynthesis
Purine Biosynthesis
Purine biosynthesis occurs via two key pathways:
De Novo synthesis
- The base, itself, is synthesized from scratch
- from such components as: ATP, key amino acids, N10-formyltetrahydrofolate, CO2).
- Then attached to the activated (phosphorylated) ribose (sugar) to form the desired nucleotide.
Salvage pathway
- The base is reattached to the phosphorylated ribose (ribose phosphate) to form the nucleotide.
Nucleoside vs. Nucleotide
Let's remind ourselves, now, of some key nucleic acid terminology:
- A nucleoside is a BASE + SUGAR
- A nucleotide is a BASE + SUGAR + PHOSPHATE
We divide purine biosynthesis into 3 parts:
- Part 1: Formation of 5-Phosphoribosyl-1-amine from ribose-5-phosphate
- Part 2: Formation of the Purine Ring
- Part 3: Derivation of adenosine monophosphate (AMP) and guanosine monophosphate (GMP) from inosinate (IMP).
Part 1
Formation of 5-Phosphoribosyl-1-amine from ribose-5-phosphate
- Draw out Ribose 5-Phosphate (R5P), which allows us to review what we learned in the Nucleic Acids tutorial.
Ribose
- A pentagon with an oxygen atom inserted at the top.
- Label carbons 1' through 4' going clockwise from the oxygen atom.
- Add carbon 5' as an attachment to carbon 4'.
- Finally, add hydroxyl groups to carbons 1', 2', and 3'.
- Now, add a phosphate to the 5' carbon: hence, Ribose (the sugar), 5-Phosphate).
- We leave the 5' and 3' in different colors, so we can already tell the 5' to 3' orientation of the sugar/phosphate backbone.
PRPP
- R5P but at the 1' hydroxyl add a pyrophosphate.
- This is PRPP: 5-phosphoribosyl-1-pyrophsophate (aka 5'-phosphoribosyl-1'-pyrophosphate) via PRPP synthetase, which catalyzes the addition of 2 phosphate (a pyrophosphate) from ATP, which then converts to AMP.
5-Phosphoribosyl-1-amine
De Novo formation of the purine ring. Draw 5-Phosphoribosyl-1-amine (aka 5'-Phosphoribosyl-1'-amine):
- Redraw PRPP but here show that:
- The pyrophosphate (PPi) leaves.
- In its place add an amine.
- Glutamine hydrolysis produces ammonia, which provides the amine group, which adds the N9 nitrogen of the Purine Ring.
- This is why nucleotide production occurs in the liver, because it is the organ that can best handle nitrogen (ammonia) waste – so it makes sense that if nucleotide synthesis relies on ammonia formation, it ought to occur in a body organ that can best manage ammonia!
- So if we think about why we would want nucleotide biosynthesis to occur in the liver, again, one reason is that it's where the management of ammonia occurs!
Formation of the Purine Ring
- Glycine provides C4, C5, N7.
- N10-Formyltetrahydrofolate (THF) provides C8 (via a formyl group).
- Glutamine hydrolysis adds N3 (via ammonia).
- Thus, although the purine ring is large, it has some key repetitions in its formations, which make its biosynthesis easier to remember.
- CO2 provides C6
- Aspartate provides N1
- N10-Formyltetrahydrofolate (THF) provides C2, adjacent to N3 (in the same way that C8 was added adjacent to N9).
We've built the purine ring, specifically show that we've built:
Derivation of adenosine monophosphate (AMP) and guanosine monophosphate (GMP) from inosinate (IMP).
Inosinate (IMP) from purine ring:
- N9 (from glutamine hydrolysis) (with the ribose-5-phosphate attached).
- C4, C5, N7 (from Glycine)
- C8 (from THF)
- N3 (from glutamine hydrolysis)
- C6 (from CO2)
- N1 (from Aspartate)
- C2 (from THF)
- double bonds between C8 and N7, C4 and C5, and C2 and N3.
- C6 carbon is double-bonded to oxygen.
Adenosine Monophosphate (AMP)
- With the addition of aspartate and the phosphorylation by GTP, IMP forms AMP, by passing through adenylosuccinate.
- GTP is the phosphoryl-group donor (and converts to GDP in the process).
Guanosine Monophosphate (GMP)
- Then, an amine group is added via ammonia produced from glutamine hydrolysis in the process of IMP conversion to GMP.
- However, this actually happens AFTER inosinate is oxidized to xanthylate (XMP) with NAD+ acting as the hydrogen acceptor.
- And this time it is ATP, which serves as the phosphoryl-group donor (which converts to ADP) (rather than GTP).
- Cross-regulation & end-product inhibition maintain a balanced production of these end-products.
- Cross-regulation means that: GMP (the building-block of GTP) is necessary for the formation of AMP & vice-versa: AMP (the building-block of ATP) is necessary for the formation of GMP.
Purine nomenclature
As a final check on our understanding of purine biosynthesis and the full breadth of its impact on molecular biochemistry, let's run through nomenclature of the purines:
- The bases are:
- Adenine and guanine
- The ribonucleosides (meaning the sugars + bases) are:
- Adenosine and guanosine
- The ribonucleotides (meaning the sugars + bases + 5'-monophosphates) are:
- Adenylate (AMP) and guanylate (GMP)
- The diphosphates are:
- Adenosine diphosphate ADP and Guanosine diphosphate GDP
- The triphosphates are:
- Adenosine triphosphate ATP and Guanosine triphosphate GTP
Drug Correlations:
- Dihydrofolate inhibitors
- Methotrexate inhibits dihydrofolate in humans.
- Trimethorpim inhibits dihydrofolate in bacteria.
- Pyrimethamine inhibits dihydrofolate in protozoa.
- De novo purine synthesis inhibitors
- 6-mercaptopurine (and its prodrug, azathioprine).
- Inosine monophosphate dehydrogenase inhibitors
- Mycophenolate and ribavirin.