Nitrogen metabolism and nucleotide synthesis and metabolism

Tryptophan is the precursor to serotonin, melatonin, and niacin.

Tryptophan ---(tetrahydrobiopterin)--> 5-hydroxytryptophan

5-hydroxytryptophan ---(pyridoxine)-->serotonin

Serotonin ---(SAM)--> melatonin

Serotonin breakdown product: 5-HIAA

Serotonin effects: arteriole vasocontrictor, intestinal peristalsis. Carcinoid syndrome, where serotonin secreting tumor of small intestine metastasizes to liver, has symptoms of cyanotic flushing, low blood pressure (arteriole vasoconstriction), also watery diarrhea (increased peristalsis).

Glutamate --> GABA (decarboxylation)

Histidine --> Histamine (decarboxylation)

Arginine, glycine, and SAM --> creatine.

Creatine --> Creatine phosphate (creatine kinase)

Creatine is a source of high energy phosphate, to regenerate ATP from ADP

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Purines include adenine and guanine (Mnemonic: Pure As Gold)

The pyrimidines are cytosine, thymine, and uracil. Thymine is found only in DNA; uracil, only in RNA.

A nucleotide consists of three components: base, pentose, and phosphate group. A nucleoside is a base and a pentose. Hence, you can call ATP either a nucleotide or a nucleoside triphosphate.

The pentose can be in the deoxy form or the non-deoxy form. The non-deoxy form of the nucleoside DIPHOSPHATE, found in RNA bases, is reduced to the deoxy form by an important enzyme, ribonucleotide reductase. For instance, ADP --> dADP. Reduced thioredoxin is required as a cofactor. In the process, thioredoxin is oxidized. To continue the process, oxidized thioredoxin must be converted to reduced thioredoxin.

Oxidized thioredoxin --> Reduced thioredoxin (NADPH)

Compare: BH2 --> BH4

Ribose 5-phosphate --> PRPP (can now go purine salvage, purine synthesis, pyrimidine synthesis). PRPP synthethase (requires ATP-->AMP) is the rate-limiting enzyme of purine synthesis.

PRPP --> 5-phosphoribosylamine (glutamine --> glutamate) is the committed step of purine synthesis. This is a highly regulated transformation. The end products inhibit: IMP, AMP, GMP. An accumulation of PRPP will enhance.

5-phosphoribosylamine --> IMP in a series of 9 reactions.

IMP is the decision point between AMP and GMP synthesis. Control of relative amounts of each is controlled partly by end-product inhibition (AMP, GMP) respectively as well as cross-regulation (GTP and ATP are required for AMP and GMP synthesis, respectively).

Purine salvage: PRPP conveys ribose 5-phosphate to "salvaged" free bases to form nucleotides.

Nucleoside diphosphates and triphosphates formed from monophosphates by kinase activity utilizing ATP.

Purine ring synthesis happens on the scaffold of the ribose 5-phosphate. On the other hand, synthesis of the pyrimidine ring happens before the ribose 5-phosphate comes in, in the form of PRPP. The defining enzyme of pyrimidine synthesis is carbamoyl phosphate synthetase II (CPS II), which is a cytosolic enzyme (as opposed to the mitochondrial urea cycle enzyme, CPS I; note that CPS II, unlike CPS I, is not activated by N-acetyl glutamate). It catalyzes the formation of carbamoyl phosphate from phosphorylated bicarbonate (CO2, ATP) and an amine group (donated from glutamine --> glutamate). CPS II catalyzes the committed step of pyrimidine synthesis and is inhibited by UTP, activated by ATP.

Addition of aspartate by aspartate transcarbamoylase takes carbamoyl phosphate to carbamoyl aspartate. This step is inhibited by CTP, and activated by ATP. The regulation of the these last two steps represents both end-product inhibition (UTP, CTP) as well as a mechanism to balance synthesis of pyrimidines and purines (ATP activation).

Dihydroorotase takes carbamoyl aspartate to dihydroorotate, which is then oxidized to produce orotic acid, or orotate. Conversion of orotate to UMP requires orotate phosphoribosyl transferase (addition of ribose 5-phosphate from PRPP) and orotidine phosphate decarboxylase. UMP can give rise to dUMP (ribonucleotide reductase) and then dTMP (thymidylate synthase, which uses methylene tetrahydrofolate as the carbon donor to methylate dUMP). UMP goes to UTP (ATP addition x2) before becoming CTP (amine donation from Gln --> Glu).

Methotrexate, fluorouracil, and hydroxyurea are anticancer drugs that work by inhibiting nucleotide synthesis. Methotrexate competitively inhibits dihydrofolate reductase, inhibiting dTMP synthesis and fluorouracil in its activated form (5-fluorodeoxyuridine monophosphate) inhibits thymidylate synthase (irreversible suicide inhibitor) directly, also inhibiting dTMP synthesis.

Purine degradation and salvage. The central pathway is IMP --> Inosine --> Hypoxanthine --> Xanthine --> Uric acid. AMP goes to IMP by AMP deaminase. Adenosine goes to inosine by adenosine deaminase. [*CC] SCID, autosomal recessive. Deficiency of ADA causes this. First effect is accumulation of adenosine, which is toxic to B and T cells. It also leads to accumulation of dAMP, which gets converted to excess dATP, which inhibits ribonucleotide reductase, which reduces conversion of ribonucleotides to deoxyribonucleotides, resulting in decrease in DNA synthesis of B and T cells. SCID leads to recurrent infections with bacteria, viruses, fungi, and protozoa (loss of humoral and cellular immunity). Note that the "A" derivatives dump into the degradation pathway via AMP and adenosine only. The "G" derivatives, on the other hand, dump in with Guanine going to Xanthine. You can have GMP --> Guanosine --> Guanine, with Guanine having the option to not degrade via Xanthine, and instead using HGPRT to reinstate itself as GMP by condensing with PRPP. Similarly AMP can be created by adenine condensing with PRPP via enzyme APRT action. Note however that adenine, unlike guanine, cannot dump into the degradation pathway directly. Hypoxanthine can go to IMP via HGPRT as well. [**CC] If HGPRT is blocked, you get no salvage of hypoxanthine to IMP, or guanine to GMP, and therefore more degradation of hypoxanthine and guanine to xanthine and then uric acid, hence hyperuricemia. Since this is a X-linked recessive condition, you get hyperuricemia during development causing severe mental retardation, self-mutilating behavior, spasticity, gout and urate deposition in the kidney, leading to renal failure, which is what kills you in the first or second decade. Hypoxanthine to xanthine, and xanthine to uric acid, is catalyzed by xanthine oxidase. [**CC] Gout is caused either by overproduction of uric acid (overactivity of PRPP synthetase, or deficiency of HGPRT -- as in Lesch-Nyhan), or undersecretion (renal issue). Acute gout strikes the MP joint of the large toe. Recurrent attacks, hyperuricemia with deposition of monosodium urate crystals in synovial fluid. Tx: Reduce alcohol, red meats, use uricosuric agents like probenecid (blocks OAT, organic anion transporter, hence uptake of uric acid from renal tubules) with undersecreters and allopurinol (xanthine oxidase competitive inhibitor) with overproducers. Colchicine also can be administered; it inhibits urate crystal formation by raising tissue pH (low tissue pH promotes urate crystal formation).

Pyrimidine degradation: beta-amino acids, carbon dioxide, and NH4+. Ultimately the degradation product is urea (from NH4+ degradation).

Note that adenine is salvaged with a separate enzyme (APRT) than hypoxanthine and guanine (HGPRT).