Bicarbonate biosynthesis

Rittenberg and Bloch showed in the late 1940s that acetate units are the building blocks of fatty acids. Their work, together with the discovery by Salih Wakil that bicarbonate is required for fatty acid biosynthesis, eventually made clear that this pathway involves synthesis of malonyl-CoA. The carboxylation of acetyl-CoA to form malonyl-CoA is essentially irreversible and is the committed step in the synthesis of fatty acids (Figure 25.2). The reaction is catalyzed by acetyl-CoA carboxylase, which contains a biotin prosthetic group. This carboxylase is the only enzyme of fatty acid synthesis in animals that is not part of the multienzyme complex called fatty acid synthase. 

Step 1 of Figure 29.13 Carboxylation Gluconeogenesis begins with the carboxyl-afion of pyruvate to yield oxaloacetate. The reaction is catalyzed by pyruvate carboxylase and requires ATP, bicarbonate ion, and the coenzyme biotin, which acts as a carrier to transport CO2 to the enzyme active site. The mechanism is analogous to that of step 3 in fatty-acid biosynthesis (Figure 29.6), in which acetyl CoA is carboxylated to yield malonyl CoA. 

Figure 29-9. Reactions and intermediates of urea biosynthesis. The nitrogen-containing groups that contribute to the formation of urea are shaded. Reactions and occur in the matrix of iiver mitochondria and reactions , , and in iiver cytosoi. COj (as bicarbonate), ammonium ion, ornithine, and cit-ruiiine enter the mitochondriai matrix via specific carriers (see heavy dots) present in the inner membrane of iiver mitochondria.

Shaw and co-workers during studies into the de novo biosynthesis of purine nucleotides demonstrated that 4(5)-aminoimidazole (25 R = H) on treatment with a saturated aqueous solution of potassium bicarbonate at 70°C for 15 min gave 4-aminoimidazole-5-carboxylic acid (38) in an estimated yield of 40% [71JCS(C)1501]. This and related reactions are discussed in more detail in Section V,B,4. 

The antipyretic and analgesic actions of aspirin are believed to occur in a certain area of the brain. It is also thought by some that the salicylates exert their analgesia by their effect on water balance. Aspirin is anti-inflammatory because it inhibits the biosynthesis of chemicals called prostaglandins. The irritation of the stomach lining caused by aspirin can be alleviated with the use of mild bases such as sodium bicarbonate, aluminum glycinate, sodium citrate, aluminum hydroxide, or magnesium trisilicate (a common trademark for this type of aspirin is Bufferin ). 

In this cycle, one molecule of acetyl-CoA is formed from two molecules of bicarbonate (Figure 3.5). The key carboxylating enzyme is the bifunctional biotin-dependent acetyl-CoA/propionyl-CoA carboxylase. In Bacteria and Eukarya, acetyl-CoA carboxylase catalyzes the first step of fatty acid biosynthesis. However, Archaea do not contain fatty acids in their lipids, and acetyl-CoA carboxylase cannot serve as the key enzyme of fatty acid synthesis rather, it is responsible for autotrophy. 

Among activated forms of amino acids, mixed anhydrides with inorganic phosphate or phosphate esters require a special discussion because they are universally involved in peptide biosynthesis through the ribosomal and non-ribosomal pathways. These mixed anhydrides have stimulated studies in prebiotic chemistry very early in the history of this field. Amino acyl adenylates 18c have been shown to polymerize in solution [159,160] and in the presence of clays [139]. However, their participation as major activated amino acid species to the prebiotic formation of peptides from amino acids is unlikely for at least two reasons. Firstly, amino acid adenylates that have a significant lifetime in aqueous solution become very unstable as soon as either CO2 or bicarbonate is present at millimolar concentration [137]. Lacey and coworkers [161] were therefore conduced to consider that CO2 was absent in the primitive atmosphere for aminoacyl adenylate to have a sufficient lifetime and then to allow for the emergence of the modern process of amino acid activation and of the translation apparatus. But this proposition is unlikely, as shown by the analysis of geological records in favor of CO2 contents in the atmosphere higher than present levels [128]. It is also in contradiction with most studies of the evolution of the atmosphere of telluric planets [30,32], Secondly, there is no prebiotic pathway available for adenylate formation and ATP proved to be inefficient in this reaction [162]. 

CPSase catalyzes the formation of carbamyl phosphate from glutamine, bicarbonate, and two equivalents of ATP. The biosynthesis involves four partial reactions. GLNase catalyzes the formation of ammonia from glutamine. The remaining three partial reactions are catalyzed by SYNase. Bicarbonate is activated by ATP to form carboxyphosphate, which reacts with ammonia to form carbamate. The ATP-dependent phosphorylation of carbamate results in the production of carbamyl phosphate. 

The first step in de novo pyrimidine biosynthesis is the synthesis of carbamoyl phosphate from bicarbonate and ammonia in a multistep process, requiring the cleavage of two molecules of ATP. This reaction is catalyzed by carbamoyl phosphate synthetase (CPS) (Section 23.4.1). Analysis of the structure of CPS reveals two homologous domains, each of which catalyzes an ATP-dependent step (Figure 25.3). 

FIGURE 9.7 Pyrimidine biosynthetic pathway. The pathway of pyrimidine biosynthesis involves sbc steps and results in the production of uridine 58-monophosphate. Folate is not used in this pathway The pathway commences with the transfer of the amide nitrogen of glutamine to bicarbonate to produce caibamy I phosphate. This molecule then reacts with aspartate to form the beginnings of the siK-membered pyrimidine ring. 

We already mentioned that the enzymes involved in the P-oxidation of fatty acids are located in the mitochondria. The source of two-carbon fragments for the biosynthesis of both fatty acids and isoprenoids like cholesterol is acetyl CoA, which is generated by oxidative metabolism in the mitochondria. Acetyl CoA cannot escape from the mitochondria, but it can be exported to the cyosol as citrate, where it is reconverted to oxaloacete and acetyl CoA. Fatty acid (and cholesterol) biosynthesis takes place in the cyosol, and requires bicarbonate, which is incorporated into acetyl CoA to form malonyl CoA by acetyl CoA carboxylase. The biosynthesis of fatty acids, mostly the Cie palmitate (Chapter 4), requires one molecule of acetyl CoA and seven molecules of malonyl CoA. In animals, the seven enzymatic reactions which are required for fatty acid synthesis are present in a single multifunctional protein complex, known as fatty acid synthase. The synthase also contains an acyl-carrier protein... 

Phosphonomycin,—Yet another synthesis of phosphonomycin (22) has appeared (Scheme 6). The phosphonoaldehyde (23) was treated with pentan-3-one and cyclohexylamine to give (24), which was then converted into its oxime. Tosylation of this oxime followed by treatment with bicarbonate caused the molecule to fragment, liberating the dimethyl ester of (22). Disodium phosphonoacetic acid when administered orally or topically to mice infected with Herpes simplex virus will reduce significantly the mortality of mice caused by this virus. JV-Phosphonomethyl-glycine is a promising herbicide. Recent work has shown that it exerts its effect by inhibiting the biosynthesis of aromatic amino-acids. ... 

Bicarbonate ion added to rat ileal epithelial cells induces a rapid decrease in the proportion of HMG-CoA reductase in the active, dephosphorylated form which is reflected in a corresponding decrease in the rate of cholesterol biosynthesis [189]. 

Acetyl-CoA carboxylase (ACC) catalyzes the first committed step in long-chain fatty acid biosynthesis (see Chapter 7.11). The overall reaction is catalyzed in two sequential reactions (Scheme 3). First, the biotin carboxylase domain catalyzes the ATP-dependent carboxylation of biotin (which is attached to a carrier protein) using bicarbonate as a CO2 donor. In the second reaction, the carboxyl group is transferred from biotin to acetyl-CoA to form malonyl-CoA. In mammals, both reactions are catalyzed by a single protein, but in Escherichia coli and other bacteria, the activity is catalyzed by two separate proteins, a biotin carboxylase and a carboxytransferase. Due to its role in fatty acid synthesis, inhibitors of the overall ACC reaction are proposed to be useful as antiobesity drugs in mammals as well as novel antibiotics against bacteria. 

Evidence for pyrimidine de novo biosynthesis has also been found in other trematodes. Its enzymes are present in Fasciola gigantica (81), Paragonimus ohirai (112) and Clonorchis sinensis (112). De novo biosynthesis was verified by demonstrating the incorporation of [ C]bicarbonate into the C-2 position of uracil in P. ohirai (112). The pyrimidine salvage enzymes, uridine kinase and thymidine kinase, are found in P. ohirai and C. sinensis extracts (112). Aspartate transcarbamoylase is found in Fasciola hepatica and Paramphistomum cervi extracts (113). 

In the first step of the urea cycle, NH4, bicarbonate, and ATP react to form carbamoyl phosphate (see Fig. 38.12). The cleavage of 2 ATPs is required to form the high-energy phosphate bond of carbamoyl phosphate. Carbamoyl phosphate synthetase I (CPSI), the enzyme that catalyzes this first step of the urea cycle, is found mainly in mitochondria of the liver and intestine. The Roman numeral suggests that another carbamoyl phosphate synthetase exists, and indeed, CPSll, located in the cytosol, produces carbamoyl phosphate for pyrimidine biosynthesis, using nitrogen from glutamine (see Chapter 41). 

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