Biochemistry Nucleic Acid Metabolism

Module: Biochemistry Nucleic Acid Metabolism

• The module focuses on the metabolism of nucleic acids, specifically purines and pyrimidines.
• Learning objectives include comparing and contrasting dietary nucleic acids and de novo biosynthesis in purine and pyrimidine production.
• The sequence of reactions converting IMP to AMP and GMP, and subsequent nucleoside triphosphates, is outlined.
• Degradation of nucleotides is also discussed.

Biomedical Importance

• Humans synthesize nucleic acids (ATP, NAD+, etc.) from amphibolic intermediates.
• Dietary purines and pyrimidines are not directly incorporated, but injected analogues might be.
• Biosynthesis of purine and pyrimidine ribonucleotide triphosphates (NTPs) and dNTPs are carefully controlled.
• Production occurs at appropriate quantities and times matching physiological demands (e.g., cell division).

Nucleic Acid Structure

• Nucleotides are fundamental to all cells.
• They act as carriers of activated intermediates in carbohydrates, lipids, and proteins.
• Nucleotides consist of a five-carbon sugar (ribose or deoxyribose), a nitrogenous base (purine or pyrimidine), and a phosphate group.
• Nucleosides lack the phosphate group.
• DNA and RNA share adenine (A) and guanine (G).
• Both contain cytosine (C) but differ in their second pyrimidine base. DNA has thymine (T) and RNA has uracil (U).

Purines and Pyrimidines

• Purines and pyrimidines in human tissue are synthesized from amphibolic intermediates to meet physiological demand. Ingested nucleic acids are thus not essential.
• Following intestinal degradation, resulting mononucleotides can be absorbed or converted to purine or pyrimidine bases.
• Purine bases are oxidized to uric acid, which is excreted in urine.
• Injected [3H]thymidine incorporation in DNA, measures DNA synthesis rate.

Purine Nucleotide Biosynthesis

• Purine nucleotide biosynthesis involves three main processes; synthesis de novo, phosphoribosylation of purines, and phosphorylation of purine nucleosides.
• Carbon and nitrogen atoms of the purine ring come from glycine, glutamate, and other sources.
• The initial parent nucleotide synthesized is IMP (inosine monophosphate), a nucleotide composed of hypoxanthine, ribose, and phosphate.
• Ribose-5-phosphate, a product of the hexose monophosphate shunt, is the starting material for purine nucleotide synthesis. It reacts with ATP to form phosphoribosyl pyrophosphate (PRPP).
• Specific enzymes (e.g., PRPP synthetase) are involved in this initial step in the biosynthesis.
• Glutamine amidotransferase transfers nitrogen to PRPP to form 5-phosphoribosylamine. This reaction is controlled by feedback inhibition.
• Subsequent reactions involve glycine, N₅,N₁₀-formyltetrahydrofolate and glutamine, leading to the production of formylglycinamide ribonucleotide.
• Further enzymatic steps lead to the closure of the imidazole ring and the synthesis of aminoimidazole carboxylate ribonucleotide.
• Incorporation of CO₂ forms aminoimidazole carboxylate ribonucleotide.
• Aspartate then adds to the chain.
• Adenosuccinase reaction produces aminoimidazole carboxamide ribonucleotide.
• Lastly, N10-formyltetrahydrofolate and other enzymatic reactions finalize the formation of inosine monophosphate (IMP).
• The synthesis of AMP and GMP from IMP involves specific reaction sequences using nucleotides like GTP, including steps involving adenylosuccinate and xanthosine monophosphate/ GMP.

Regulation of Purine Nucleotide Synthesis

• Synthesis is regulated to meet cellular demand.
• Intracellular concentration of PRPP regulates synthesis, depending on ribose 5-phosphate availability and PRPP synthetase activity.
• Further control (feedback inhibition) happens at the amidotransferase reaction if AMP or GMP are present in sufficient quantity.
• AMP influences adenylosuccinate synthetase and GMP affects IMP dehydrogenase.

Nucleoside Di- and Triphosphates

• Nucleotide monophosphates are converted to di- and triphosphates using ATP and kinases.

Conversion of Ribonucleotides to Deoxynucleotides

• Deoxyribonucleotides are formed from ribonucleotides via the enzyme ribonucleotide reductase (which provides reducing equivalents), a reaction requiring thioredoxin and NADPH-dependent thioredoxin reductase.

Degradation of Purine Nucleotides

• The end product of purine metabolism is uric acid.
• Nucleotide monophosphates are converted to nucleosides; amino groups are removed from AMP or adenosine to produce IMP or inosine.
• These intermediates further degrade to xanthine or uric acid, via the action of specific enzymes such as xanthine oxidase.

Disorders of Purine Metabolism

• Hyperuricemia refers to elevated serum uric acid and can be associated with increased excretion (uricosuria).
• Gout is a metabolic disorder characterized by overproduction of uric acid and can lead to build-up of sodium urate crystals in tissues like joints in severe cases.

Salvage Pathway for Purines

• Free purines (adenine, guanine, hypoxanthine) are formed during nucleic acid turnover or from diet.
• These purines can be converted to nucleotides; this process in known as ''salvage pathway''.
• Adenine phosphoribosyl transferase forms AMP from adenine.
• Hypoxanthine-guanine phosphoribosyl transferase forms GMP and IMP from guanine or hypoxanthine respectively, with PRPP as the ribose donor.

Inhibitors of Purine Synthesis

• Sulfonamides are structural analogs of para-aminobenzoic acid (PABA).
• PABA inhibits the synthesis of folic acid by microorganisms, so sulfa drugs indirectly diminish purine and nucleic acid, DNA and RNA, synthesis. This doesn't affect humans since we obtain folic acid from our diet.
• Structural analogs to folic acid, such as methotrexate, block purine synthesis and nucleic acid production, which can control cancer proliferation but also usually impact normal cell growth as well.