L22 - Purines

Difference between Purine and Pyrimidine biosynthesis

Purine: Sugar and phosphate group is attached first, and the base is built on that. Very energy expensive, which is why the salvage pathway is critical.

Pyrimidine: Base is built first and phosphate/sugar is attached after

How are purine rings built

Via various different Amino acids and other metabolites

Different to pyrimidines which is built using aspartate and glutamine

Step 1-2 of purine biosynthesis

Commitment step

Gln + PRPP → Glu + PP_i + 5-Phospho-β-_D-ribosylamine via glutamine-PRPP amidotransferase

In the second step, three atoms are added from glycine (Needs ATP)

5-Phospho-β-_D-ribosylamine → Glycinamide ribonucleotide (GAR)

Steps 3-11 of purine biosynthesis

Know that this pathway is very energy expensive; Requires many AAs and an N-Formyl Tetrahydrofolate (Type of THF) (Formyl transfer happens in Step 10)

Step 5 forms the first ring; Step 11 forms the first purine ring set

Inosinate (IMP) is made in step 11 via IMP synthase and is the first nucleotide in this pathway

Know IMP structure

Conversion of IMP to AMP and GMP

IMP to AMP:

1. IMP + D + GTP → Adenylosuccinate + GDP + P_i via Adenylosuccinate synthetase

2. Adenylosuccinate → Adenylate (AMP) + Fumarate via Adenylosuccinate lyase

IMP to GMP:

1. IMP + H₂O + NAD⁺ → Xanthylate (XMP) + NADH + H⁺ via IMP dehydrogenase

2. XMP + H₂O + N + ATP → Guanylate (GMP) + E + AMP + PP_i via XMP-glutamine amidotransferase (GMP synthetase)

Mono and Di-Phosphate Kinases

“housekeeping” kinases that catalyzes the formation of both di and triphosphate

Nucleoside monophosphate kinases use ATP to turn Mono to Di

Nucleoside diphosphate kinases use NTP to turn Di to Tri

Regulation of purine biosynthesis via feedback inhibition

Focus on regulation up to IMP:

Ribose 5-phosphate → PRPP (PRPP synthetase) is inhibited by energy level (ADP)

PRPP → 5-phosphoribosylamine (Glutamine-PRPP amidotransferase) (Step 1) is inhibited by all end products (IMP, GMP, and AMP)

Post IMP (“Fork-in-the-road”):

IMP → AMP is feedback-inhibited by AMP

Same for IMP → GMP feedback-inhibited by GMP

Basically a balancing act so that AMP and GMP levels will stay at the correct level

Purine Salvage Pathway

We want to do this because nuc base biosynthesis is very expensive (Especially for purines)

Free purines can be salvaged into new nucleotides: Begins with a free nitrogenous base

• Hypoxanthine-guanine phosphoribosyltransferase (HGPRT): Catalyzes salvage of guanine and hypoxanthine (deamination product of adenine via adenine deaminase) to from GMP or IMP

• Adenosine phosphoribosyltransferase (APRT): Catalyzes reaction of adenine + PRPP to yield adenine nucleotide (Ex. Adenine + PRPP → AMP + PP_i)

Deoxyribonucleotides

Main Idea: Ribonucleotide reductase enzymes convert ribose to deoxyribose

Thioredoxin: Intermediate H-carrying protein

Glutaredoxin: Transfers reducing power from glutathione (GHS) to ribonucleotide reductase

Thioredoxin reductase: Catalyzes reduction of oxidized form of thioredoxin by NADPH

Purine Degradation Pathway

Purine degradation produces Urea

GMP

• 5’-Nucleotidase removes P_i group

• Nucleosidase removes ribose from guanosine; Guanine deaminase removes an amino group and turns guanine to xanthine

AMP

• Nucleotidase removes P_i group

• Adenosine deaminase removes amino group (Makes inosine); 5’-Nucleosidase removes ribose

• Hypoxanthine is oxidized via xanthine oxidase to make xanthine

Organism organization for what form of Uric acid they can get rid of

Certain species can directly excrete uric acid (Humans); Others must process it down further

Important Cofactors in Purine biosynthesis

One-C transfers typically involve 1 of 3:

Biotin (Transfers CO₂)

THF (Transfers intermediate oxidation states)

SAM (Transfers methyl group)

Metabolism summary

Based on tissue type