BIOCHEM 3.4 - N UCLEOTIDES AND ATP

• Nucleosides consist of a base and a sugar.
• Nucleotides consist of a base, a sugar, and a phosphate group.

Purine and Pyrimidine Sources

• De novo synthesis involves creating purines and pyrimidines from scratch.
• Salvage pathways recycle existing purines and pyrimidines.
• Diet provides a source of purines and pyrimidines

Overview of Metabolic Processes Involving Purines and Pyrimidines

• De novo Synthesis utilizes basic metabolites.
• Salvage pathways serve to restore availability.
• Catabolic pathways are for excretion to reduce toxicity.
• Conversion of ribonucleotides into deoxyribonucleotides (precursors of DNA).

Purine and Pyrimidine Biosynthesis

• Biosynthesis is highly regulated due to its high energy cost.
• Synthesis levels vary greatly depending on the need, with high levels occurring during the S-phase, in growing tissues, stem cells, actively proliferating cells, and during wound healing.
• It provides the building blocks of genetic material and serves as key players in bioenergetics.
• They serve as components of coenzymes including NAD+/NADH and NADP+/NADPH.
• They serve as precursors to nucleotides.
• Synthesis can be from metabolic intermediates, therefore they are not required in diet.

Pyrimidine Synthesis

• Pyrimidine base is made first and then the sugar is added.
• Synthesis starts with bicarbonate, glutamine, and aspartate.
• Carbamoyl phosphate synthetase II (CPS II) is the enzyme responsible for catalyzing the first committed step in pyrimidine biosynthesis.
• CPS II converts carbamoyl phosphate from bicarbonate and glutamine.
• Aspartate transcarbamoylase then adds aspartic acid to carbamoyl phosphate, forming carbamoyl aspartate.
• Multifunctional CAD protein catalyzes early steps.
• Dihydroorotase is then used.
• The mitochondrial enzyme dihydroorotate dehydrogenase converts dihydroorotate to orotate.
• Orotate phosphoribosyltransferase then adds a ribose.
• UMP synthase is needed.
• The drug leflunomide inhibits dihydroorotate dehydrogenase

Regulation of Pyrimidine Synthesis

• CTP Synthetase is the rate-limiting enzyme in CTP synthesis.
• TK1, TYMS and DTYMK are rate-limiting enzymes for de novo dTTP synthesis.
• TK1 converts thymidine into TMP using ATP.
• Deoxyuridine is converted into dUMP by TK1.

Purine Synthesis

• Most carbons and all nitrogens are derived from amino acids.
• Synthesis begins with a sugar base.
• Amidophosphoribosyltransferase (ATase) is the rate-limiting enzyme in de novo synthesis.
• Synthesis starts with ribose-5-phosphate.
• Aminophosphoribosyltransferase is then used
• GAR synthetase is needed.

Purine Synthesis: IMP into AMP and GMP

• IMP does not accumulate significantly within cells.
• It is rapidly converted into GMP and AMP.
• AMP serves as the foundation for ATP synthesis.
• Salvage pathways further contribute to the generation of these critical molecules.
• IMP dehydrogenase is rate limiting in GMP synthesis.
• Adenylosuccinate synthetase is rate-limiting in AMP synthesis.

ATP

• ATP serves as an energy reserve in the form of high- energy bonds.
• High-energy bonds can be found between two phosphates, such as in the conversion of ATP to ADP, and then ADP to AMP.
• The term "high-energy bonds" refers to the change in free energy associated with the phosphate bonds.
• Fuel oxidation serves as a major source of ATP, and most metabolic energy is generated through Oxidation-Reduction reactions.
• ATP is utilized in the synthesis of other high-energy compounds like UTP, CTP, and GTP.
• Adenylate kinase is capable of forming ATP from 2ADP molecules.
• Nearly all synthesis pathways in organisms are thermodynamically unfavorable

Coupling Reaction to Hydrolysis of ATP

• Energy requiring (endergonic) reactions are coupled to ATP hydrolysis to make the net reaction thermodynamically favorable (exergonic)
• The net delta G is negative
• Coupling to ATP hydrolysis drives the reaction forward
• Hydrolysis of high-energy compounds is needed.
• The utilization of ATP can trigger increased ATP generation.
• Exercise increases the oxidative capacity of skeletal muscle leads to increased cellular AMP concentrations
• Increased intra-cellular increases triggers other changes to increase ATP production.

Case Study 5: Lesch-Nyhan Syndrome

• Lesch-Nyhan Syndrome is an X-linked recessive, rare inborn error of purine metabolism.
• It is caused by a loss of function mutation in the hypoxanthine-guanine phosphoribosyltransferase (HPRT1) gene.
• It results in the accumulation of hypoxanthine and guanine due to their inability to be incorporated into nucleotides.
• This leads to high levels of uric acid.
• Sodium urate crystals may progressively accumulate in joints and kidneys (GOUT).
• Symptoms and severity expected varies with age.
• Neurological alterations have been observed with a spectrum developmental consequences (~85% exhibit self-injurious behaviors including biting, head-banging, and face scratching).

Case Study 6: Hereditary Orotic Aciduria

• It is characterized by megaloblastic anemia, orotic crystalluria and nephropathy, immunodeficiency with recurrent infections, cardiac malformations, strabismus, and failure to thrive.
• Elevated levels of orotate are detectable in urine.
• It is caused by errors in the uridine monophosphate synthase enzyme.
• Orotic acid accumulates, coupled with a corresponding loss of UMP.
• Treatment involves oral uridine supplementation to replace the missing UMP.