Pyrimidine metabolism synthesis pathway

We should note at this point that the TCA cycle is more than just a means of producing NADH for oxidative phosphorylation. The pathway also provides a number of useful intermediates for other, often synthetic, pathways. For example, citrate is the starting substance for fat synthesis (Chapter 9) succinyl-CoA is required for haem production and 2-oxoglutarate and oxaloacetate in particular are involved with amino acid and pyrimidine metabolism. Pathways which have dual catabolic/anabolic functions are referred to as amphibolic . 

A number of these enzymes are expressed in other tissues as well but cause a notable deficiency predominantly in red blood cells because of the life span of the erythrocyte after the loss of protein synthesis. Once an enzyme is degraded or otherwise becomes nonfunctional, it cannot be replaced by new or other compensating proteins because of the lack of nucleus, mitochondria, ribosomes, and other cell organelles in mature red cells. Disorders have been described in the EMP, HMP, Rapoport-Luebering cycle, the glutathione pathway (Figure 21-9), purine-pyrimidine metabolism and methemoglobin reduction. 

Purine deoxyribonucleotides are derived primarily from the respective ribonucleotide (Fig. 6.2). Intracellular concentrations of deoxyribonucleotides are very low compared to ribonucleotides usually about 1% that of ribonucleotides. Synthesis of deoxyribonucleotides is by enzymatic reduction of ribonucleotide-diphosphates by ribonucleotide reductase. One enzyme catalyzes the conversion of both purine and pyrimidine ribonucleotides and is subject to a complex control mechanism in which an excess of one deoxyribonucleotide compound inhibits the reduction of other ribonucleotides. Whereas the levels of the other enzymes involved with purine and pyrimidine metabolism remain relatively constant through the cell cycle, ribonucleotide reductase level changes with the cell cycle. The concentration of ribonucleotide reductase is very low in the cell except during S-phase when DNA is synthesized. While enzymatic pathways, such as kinases, exist for the salvage of pre-existing deoxyribosyl compounds, nearly all cells depend on the reduction of ribonucleotides for their deoxyribonucleotide... 

When the carbamoyl phosphate level is low, however, orotate only activates the enzyme at low ornithine concentrations and actually causes inhibition when there is a lot of ornithine available. These interactions seem to be designed to achieve the best use of the carbamoyl phosphate, and to ensure that a certain amount is always available for the pyrimidine synthesis pathway. Regulatory interactions between different metabolic pathways are termed as metabolic interlock [90]. 

Fig. 23.1. Pyrimidine pathways Pathways for the de novo synthesis, interconversion, and breakdown of pyrimidine ribonucleotides, indicating their metabolic importance as the essential precursors of the pyrimidine sugars and, with purines, of DNA and RNA. Note that in contrast to purines salvage takes place at the nucleoside not the base level in human cells and pyrimidine metabolism normally lacks any detectable end-product. The importance of this network is highlighted by the variety of clinical symptoms associated with the possible enzyme defects indicated. 23.10, Uridine monophosphate synthase (UMPS), 23.11a, uridine monophosphate hydrolase 1 (UMPHl), 23.12, thymidine phosphorylase (TP), 23.13, dihydropyrimidine dehydrogenase (DPD), 23.14, dihydropyrimidine amidohydrolase (DHP), 23.15, y -ureidopropionase (UP) (23.11b, UMPH superactivity specific to fibroblasts is not shown). CP, carbamoyl phosphate. The pathological metabolites used as specific markers in differential diagnosis are highlighted...

Our present understanding of the pathways of purine and pyrimidine metabolism has been greatly aided by tracer research, nutritional and genetic studies with intact organisms, and tissue studies in vitro. In most cases, the goal has been the isolation from cells of individual enzymes, each of which effects a well-defined single biochemical event. When these enzymic steps are taken in sequence, the result is a pathway for the synthesis or degradation of the structure in question. Discussion of these pathways will form the body of the chapter. 

Dihydropyrimidine dehydrogenase is the first and the rate-limiting enzyme in the three-step metabolic pathway involved in the degradation of the pyrimidine bases uracil and thymine. In addition, this catabolic pathway is the only route for the synthesis of p-alanine in mammals. 

Tumour cells also require glutamine as a fuel for energy generation and as a precursor for the synthesis of purine and pyrimidine nucleotides for DNA and RNA synthesis. The roles and importance of glutamine in tumour cells and possible competition between the cells for glutamine are discussed in Chapter 21. The pathway for the metabolism of glutamine is similar to that in the immune cells. 

Free purine and pyrimidine bases are constantly released in cells during the metabolic degradation of nucleotides. Free purines are in large part salvaged and reused to make nucleotides, in a pathway much simpler than the de novo synthesis of purine nucleotides described earlier. One of the primary salvage pathways consists of a single reaction catalyzed by adenosine phosphoribosyltransferase, in which free adenine reacts with PRPP to yield the corresponding adenine nucleotide ... 

Treatment involves a low-protein diet (0.5-0.7 g/kg BW/day) with a sufficient supply of calories. Substitution of essential amino acids (in about the same quantity) is required. The administration of benzoate (0.1-0.25 g/kg BW/day), arginine hydrochloride (1 mmol/kg BW/day) or sodium phenylacetate (0.3-0.5 g/ kg BW/day) (phenylbutyrate tends to be more effective) facilitates nitrogen excretion via other metabolic pathways. (168-170) With an enhanced excretion of orotate or other metabolites of pyrimidine synthesis, the administration of allopurinol leads to an increase in the excretion of nitrogen via metabolites from pyrimidine synthesis. Ammonia and urea precursors are eliminated by haemodialysis. In individual cases, liver transplantation is indicated. (I7l)... 

The metabolic interrelationship between mitochondrial carbamoyl phosphate synthesis to urea formation and to cytosolic carbamoyl phosphate channeled into pyrimidine biosynthesis. In ornithine transcarbamoyiase (OTC) deficiency, mitochondrial carbamoyl phosphate diffuses into the cytosol and stimulates pyrimidine biosynthesis, leading to orotidinuria. Administration of allopurinol augments orotidinuria by increasing the flux in the pyrimidine biosynthetic pathway. CPS = Carbamoyl phosphate synthase, AT = aspartate transcarbamoyiase, D = dihydroorotase, DH = dihydroorotate dehydrogenase, OPRT = orotate phosphoribosyltransferase, XO = xanthine oxida.se,... 

Nucleotides are synthesized by two types of metabolic pathways de novo synthesis and salvage pathways. The former refers to synthesis of purines and pyrimidines from precursor molecules the latter refers to the conversion of preformed purines and pyrimidines—derived from dietary sources, the surrounding medium, or nucleotide catabolism—to nucleotides, usually by addition of ribose-5-phosphate to the base. De novo synthesis of purines is based on the metabolism of one-carbon compounds. 

It is unknown when and how cooperation with amino acids, peptides, and proteins started to evolve into an RNA-protein world. However, there is an upper size limit of RNAs, which is due to a threshold error of RNA replication. The heart of the core necessary to launch the process of chemical evolution towards the RNA world must have consisted of a number of pathways for the synthesis of organic molecules from CO2, N2, and H2. Additional pathways for the synthesis of amino acids, ribose, purines, pyrimidines, coenzymes, and lipids likely combined into this core. Overall, the number of pathways required to generate nucleotides is relatively small. Pyruvate, ammonia, carbon dioxide, ATP, and glyoxalate suffice to synthesize virtually the compounds required for metabolic cycles. It seems likely that once the RNA world existed that thereafter an RNA-Peptide world developed. Details are on the following website http //www.sciencedirect.com - Cell, Volumel36, Issue 4, page 599, and a description follow below. 

Chloroplasts perform many metabolic reactions in green leaves. In addition to CO2 fixation, the synthesis of almost all amino acids, all fatty acids and carotenes, all pyrimidines, and probably all purines occurs in chloroplasts. However, the synthesis of sugars from CO2 is the most extensively studied biosynthetic pathway in plant cells. We first consider the unique pathway, known as the Calvin cycle (after discoverer Melvin Calvin), that fixes CO2 into three-carbon compounds, powered by energy released during ATP hydrolysis and oxidation of NADPH. 

Fluorouracil is a pyrimidine antimetabolite. The metabolism of fluorouracil in the anabolic pathway blocks the methylation reaction of deoxyuridylic acid to chymidylic acid. In this manner, fluorouracil interferes with the synthesis of DNA and to a lesser extent inhibits the formation of RNA. It is indicated in colon, rectum, breast, gastric, and pancreatic carcinoma (injection) multiple actinic or solar keratoses, and superficial basal-cell carcinoma (topical). 

See also Pathways in Nucleotide Metabolism, Nucleotide Salvage Synthesis, Purine Degradation, Pyrimidine Catabolism... 

CMP is a pyrimidine nucleotide that is an intermediate in several metabolic pathways. It arises from synthesis of phosphatidic acid-containing compounds. In addition to being an intermediate in de novo pyrimidine biosynthesis, it participates in the reactions that follow ... 

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