Question

Draw a color-coded diagram (to indicate the origin of each atom) for the de novo biosynthetic pathway of purine nucleotides AMP and GMP. You must provide structures and names of all the intermediates, cofactors involved, names of enzymes, and other necessary information for full credit

Answer 1

SYNTHESIS OF PURINE RIBONUCLEOTIDES:

John Buchanan performed experiments in birds by feeding a variety of isotopically labelled compounds to pigeons and to determine chemically the positions of the labelled atoms in their excreted uric acid.  The N1 of purines arise from amine group of aspartate; C2 and C8 origin from the formate; N3 and N9 from the amide group of glutamine,C4,C5 and N7 are derived from glycine and C6 from HCO-3.

Purines are biosynthesized from purine derivative Inosine Monophosphate(IMP) the nucleotide of base hypoxanthine.Purines are initially formed as ribonucleotides rather than as free bases.

Synthesis of Inosine Monophosphate:

It involves 11 steps.

1. Activation of ribose 5 phosphate :

The alpha D ribose 5 phosphate in the presence of ribose phosphate pyrophosphokinase(enzyme) reacts with ATP to form 5 phosphoribosyl alpha pyrophosphate

2. Acquisition of purine atom N9:

The enzyme aminophosphoribosyl transferase catalyzes the displacement of phospho ribosyl pyrophosphate by glutamine amide nitrogen and establishes anomeric form of future nucleotide to form beta 5 phosphoribosylamine.

3. Acquisition of purine atoms C4,C5, N7

Glycine carboxyl group forms an amide with the amino group of phosphoribosylamine to give glycinamide ribotide facilitated by intermediate phosphorylation of glycine carboxyl group

4. Acquisition of Purine atom C8

Glycine amide ribotide free alpha amino group is formylated to yield formylglycinamide ribotide. N10 formyltetrahydrofolate a cofactor that transfers C1 units from serine, glycine, formate to acceptors.

5. Acquistion of purine atom N3:

The amide amino group of a second glutamine is transferred to growing purine ring to form formylglycinamidine ribotide. The reaction is driven by hydrolysis of ATP.

6. Formation of purine ring imidazole ring:

The imidazole ring is closed in an ATP requiring intramolecular condensation to yield 5 amino imidazole ribotide (AIR) . It involves tautomeric shift of reactant from imine to enamine form.

7. Acquisition of C6:

Purine C6 is introduced as HCO-3 in a reaction catalyzed by AIR carboxylase that yields carboxyamino imidazole ribotide (CAIR)

8. Acquisition of N1:

Purine atom N1 is contributed by aspartate in an amide forming condensation reaction yielding 5 aminoimidazole 4 - N- succinylcarboxamide ribotide(SACAIR) driven by ATP hydrolysis.

9. Elimination of fumarate:

SACAIR is cleaved with release of fumarate, yielding 5- aminoimidazole-4- carboxyamide ribotide (AICAR)

10.Acquistion of C2

The final purine ring atom is acquired theough formylation of N10 formyltetrahydrofolate yielding 5- formaminoimidazole - 4- carboxamide ribotide.

11. Cyclization to form IMP

The ring is closed to form IMP occurs through elimination of water.

SYNTHESIS OF ADENINE AND GUANINE RIBONUCLEOTIDES FROM INOSINE MONOPHOSPHATE:

In the first step the aspartate amino group is linked to IMP powered by the hydrolysis of GTP to GDP and Pi to yield adenylosuccinate. The adenylosuccinate lyase eliminates fumarate from adenylosuccinate to form AMP.

GMP is also synthesized from IMP by dehydrogenationvia reduction of NAD+ to form xanthosine monophosphate and to GMp by transfer of glutamine amide nitrogen driven by hydrolysis of ATP.