Tricarboxylic acid cycle biosynthesis

The 4-phosphopantetheine group of CoA is also utilized (for essentially the same purposes) in acyl carrier proteins (ACPs) involved in fatty acid biosynthesis (see Chapter 25). In acyl carrier proteins, the 4-phosphopantetheine is covalently linked to a serine hydroxyl group. Pantothenic acid is an essential factor for the metabolism of fat, protein, and carbohydrates in the tricarboxylic acid cycle and other pathways. In view of its universal importance in metabolism, it is surprising that pantothenic acid deficiencies are not a more serious problem in humans, but this vitamin is abundant in almost all foods, so that deficiencies are rarely observed. 

Plant metabolism can be separated into primary pathways that are found in all cells and deal with manipulating a uniform group of basic compounds, and secondary pathways that occur in specialized cells and produce a wide variety of unique compounds. The primary pathways deal with the metabolism of carbohydrates, lipids, proteins, and nucleic acids and act through the many-step reactions of glycolysis, the tricarboxylic acid cycle, the pentose phosphate shunt, and lipid, protein, and nucleic acid biosynthesis. In contrast, the secondary metabolites (e.g., terpenes, alkaloids, phenylpropanoids, lignin, flavonoids, coumarins, and related compounds) are produced by the shikimic, malonic, and mevalonic acid pathways, and the methylerythritol phosphate pathway (Fig. 3.1). This chapter concentrates on the synthesis and metabolism of phenolic compounds and on how the activities of these pathways and the compounds produced affect product quality. 

T) Pentose phosphate pathway Gluconeogenesis Glycolysis P-Oxidation (5) Fatty acid biosynthesis Tricarboxylic acid cycle (7) Urea cycle... 

The tricarboxylic acid cycle not only takes up acetyl CoA from fatty acid degradation, but also supplies the material for the biosynthesis of fatty acids and isoprenoids. Acetyl CoA, which is formed in the matrix space of mitochondria by pyruvate dehydrogenase (see p. 134), is not capable of passing through the inner mitochondrial membrane. The acetyl residue is therefore condensed with oxaloacetate by mitochondrial citrate synthase to form citrate. This then leaves the mitochondria by antiport with malate (right see p. 212). In the cytoplasm, it is cleaved again by ATP-dependent citrate lyase [4] into acetyl-CoA and oxaloacetate. The oxaloacetate formed is reduced by a cytoplasmic malate dehydrogenase to malate [2], which then returns to the mitochondrion via the antiport already mentioned. Alternatively, the malate can be oxidized by malic enzyme" [5], with decarboxylation, to pyruvate. The NADPH+H formed in this process is also used for fatty acid biosynthesis. 

Several cycles are required for complete degradation of long-chain fatty acids—eight cycles in the case of stearyl-CoA (C18 0), for example. The acetyl CoA formed can then undergo further metabolism in the tricarboxylic acid cycle (see p. 136), or can be used for biosynthesis. When there is an excess of acetyl CoA, the liver can also form ketone bodies (see p. 312). 

The proteinogenic amino acids (see p. 60) can be divided into five families in relation to their biosynthesis. The members of each family are derived from common precursors, which are all produced in the tricarboxylic acid cycle or in catabolic carbohydrate metabolism. An overview of the biosynthetic pathways is shown here further details are given on pp. 412 and 413. 

In eukaryotes, the cytoplasm, representing slightly more than 50% of the cell volume, is the most important cellular compartment. It is the central reaction space of the cell. This is where many important pathways of the intermediary metabolism take place—e.g., glycolysis, the pentose phosphate pathway, the majority of gluconeogenesis, and fatty acid synthesis. Protein biosynthesis (translation see p. 250) also takes place in the cytoplasm. By contrast, fatty acid degradation, the tricarboxylic acid cycle, and oxidative phosphorylation are located in the mitochondria (see p. 210). 

Mitochondria are also described as being the cell s biochemical powerhouse, since—through oxidative phosphorylation (see p. 112)—they produce the majority of cellular ATP. Pyruvate dehydrogenase (PDH), the tricarboxylic acid cycle, p-oxidation of fatty acids, and parts of the urea cycle are located in the matrix. The respiratory chain, ATP synthesis, and enzymes involved in heme biosynthesis (see p. 192) are associated with the inner membrane. 

The availability of citrate has no relationship to the flow of metabolites through the tricarboxylic acid cycle. Increased citrate concentrations result in increased cytoplasmic acetyl-CoA concentrations, which in turn increases fatty acid biosynthesis. 

Acetyl-CoA. Acetyl-coenzyme A, a high-energy ester of acetic acid that is important both in the tricarboxylic acid cycle and in fatty acid biosynthesis. 

R. Bentley, A history of the reaction between oxaloacetate and acetate for citrate biosynthesis an unsung contribution to the tricarboxylic acid cycle , Perspect. Biol. Med., 1994, 37, 362-383. 

Shihunine.—Preliminary results139 indicated that the orchid alkaloid shihunine (153) was derived from (152), an important intermediate in naphthoquinone biosynthesis.140 Further details are now available in a full paper.141 The intact incorporation of (152) is affirmed by the observation that (152), labelled with 13C at C-l, was an efficient and specific precursor for (153). [l-14C]Acetate was examined as a shihunine precursor and was found only to label C-5. This is consistent with the expected formation of (152) from shikimic acid (144) and a-ketoglutarate (151),140 the latter gaining acetate label in its carboxy-groups through the tricarboxylic acid cycle. 

Actively respiring fungal cells possess a distinct mitochondrion, which has been described as the power-house of the cell (Fig. 4.2). The enzymes of the tricarboxylic acid cycle (Kreb s cycle) are located in the matrix of the mitochondrion, while electron transport and oxidative phosphorylation occur in the mitochondrial inner membrane. The outer membrane contains enzymes involved in lipid biosynthesis. The mitochondrion is a semiindependent organelle as it possesses its own DNA and is capable of producing its own proteins on its own ribosomes, which are referred to as mitoribosomes. 

Buchanan, R. L. and Lewis, D. F. 1984. Regulation of aflatoxin biosynthesis Effect of glucose on the activities of various glycolytic enzymes. Appl. Environ. Microbiol. 48, 306-310. Buchanan, R. L., Federowicz, D., and Stahl, H. G. 1985. Activities of tricarboxylic acid cycle... 

Despite the thousands of secondary metabolites made by microorganisms, they are synthesized from only a few key precursors in pathways that comprise a relatively small number of reactions and which branch off from primary metabolism at a limited number of points. Acetyl-CoA and propionyl-CoA are the most important precursors in secondary metabolism, leading to polyketides, terpenes, steroids, and metabolites derived from fatty acids. Other secondary metabolites are derived from intermediates of the shikimic acid pathway, the tricarboxylic acid cycle, and from amino acids. The regulation of the biosynthesis of secondary metabolites is similar to that of the primary processes, involving induction, feedback regulation, and catabolite repression [6]. 

The citric acid cycle, also known as the tricarboxylic acid cycle or the Krebs cycle, is the final oxidative pathway for carbohydrates, lipids, and amino acids. It is also a source of precursors for biosynthesis. The authors begin Chapter 17 with a detailed discussion of the reaction mechanisms of the pyruvate dehydrogenase complex, followed by a description of the reactions of the citric acid cycle. This description includes details of mechanism and stereospecificity of some of the reactions, and homologies of the enzymes to other proteins. In the following sections, they describe the stoichiometry of the pathway including the energy yield (ATP and GTP) and then describe control mechanisms. They conclude the chapter with a summary of the biosynthetic roles of the citric acid cycle and its relationship to the glyoxylate cycle found in bacteria and plants. 

Figure 6.1 Carbon core metabolism of Corynebacterium glutamicum comprising the major catabolic routes of pentose phosphate pathway and Embden-Meyerhof-Parnas pathway, tricarboxylic acid cycle, glyoxylate shunt, and anaplerotic reactions. The relevance of the individual pathways and carbon building blocks for biosynthesis of the broad product...

Figure 8.4 Biosynthetic potentiai of Pseudomonas putida. Extended carbon core metabolism of Pseudomonas putida KT2440 including the major catabolic routes of Entner-Doudoroff pathway, Embden-Meyerhof-Parnas pathway, pentose phosphate pathway, tricarboxylic acid cycle, glyoxylate shunt, anaplerotic reactions, fatty acid de novo biosynthesis, p-oxidation of fatty acids, as well as the convergent -ketoadipate pathway for catabolism of aromatics. Known pathways for respective precursor supply for the broad product spectrum of P. putida KT2440 are indicated by light red arrows. Natural products and substrates are highlighted in black, heterologous products and substrates In red.

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