Steps of the TCA Cycle

Citrate rearranges to isocitrate in a reaction catalyzed by aconitase. 

This is a dual reaction that combines decarboxylation to release CO2 and oxidation, with capture of the electrons in NADH. 

Isocitrate dehydrogenase is the major regulatory enzyme of the TCA cycle. 

Conversion of a-ketoglutarate to succinyl CoA, COj, and NADH is catalyzed by the a-ketoglutarate dehydrogenase complex. 

This reaction again represents a combined oxidation and decarboxylation. 

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The First Five Steps of the TCA Cycle Produce NADH, CO, GTP (ATP), and Succinate... 

FIGURE 20.28 The glyoxylate cycle. The first two steps are identical to TCA cycle reactions. The third step bypasses the C09-evolving steps of the TCA cycle to produce snc-cinate and glyoxylate. The malate synthase reaction forms malate from glyoxylate and another acetyl-CoA. The result is that one torn of the cycle consumes one oxaloacetate and two acetyl-CoA molecnles bnt produces two molecnles of oxaloacetate. The net for this cycle is one oxaloacetate from two acetyl-CoA molecnles. 

Starting with citrate, isocitrate, u-ketoglntarate, and succinate, state which of the individual carbons of the molecule undergo oxidation in the next step of the TCA cycle. Which molecules undergo a net oxidation ... 

B. The rate-limiting step of the TCA cycle is the synthesis of a-ketoglutarate from citrate, catalyzed by isocitrate dehydrogenase (Figure 7—2). 

Isocitrate dehydrogenase catalyzes the irreversible oxidative decar boxylation of isocitrate, yielding the first of three NADH molecules produced by the cycle, and the first release of C02 (see Figure 9.5). This is one of the rate-limiting steps of the TCA cycle. The enzyme is allosterically activated by ADP (a low-energy signal) and Ca, and is inhibited by ATP and NADH, whose levels are elevated when the cell has abundant energy stores. 

The first step of the TCA cycle is the reaction catalyzed by citrate synthase, in which acetyl-CoA enters the cycle and citrate is formed. 

The glyoxylate cycle permits growth on a two-carbon source. The glyoxylate cycle bypasses the two steps of the TCA cycle in which C02 is released. Furthermore, two molecules of acetyl-CoA are taken in per turn of the cycle rather than just one, as in the TCA cycle. The net result is the conversion of two mole-... 

Figure 20-4. Biochemical pathways for gluconeogenesis in the liver. Alanine, a major gluconeogenic substrate, is used to synthesize oxaloacetate. The carbon skeletons of glutamine and other glucogenic amino acids feed into the TCA cycle as a-ketoglutarate, succinyl-CoA, fumarate, or oxaloacetate and thus also provide oxaloacetate. Conversion of oxaloacetate to phosphoenolpyruvate and ultimately to glucose limits the availability of oxaloacetate for citrate synthesis and thus greatly diminishes flux through the initial steps of the TCA cycle (dashed lines). Concurrent P-oxidation of fatty acids provides reducing equivalents (NADH and FADH2) for oxidative phosphorylation but results in accumulation of acetyl-CoA.

In the next step of the TCA cycle, the hydroxyl (alcohol) group of citrate is moved to an adjacent carbon so that it can be oxidized to form a keto group. The isomerization of citrate to isocitrate is catalyzed by the enzyme aconitase, which is named for an intermediate of the reaction. The enzyme isocitrate dehydrogenase catalyzes the oxidation of the alcohol group and the subsequent cleavage of the carboxyl group to release CO2 (an oxidative decarboxylation). 

The next step of the TCA cycle is the oxidative decarboxylation of a-ketoglutarate to succinyl CoA, catalyzed by the a-ketoglutarate dehydrogenase complex (see Fig. 20.3). The dehydrogenase complex contains the coenzymes thiamine pyrophosphate, lipoic acid, and FAD. 

Up to this stage of the TCA cycle, two carbons have been stripped of their available electrons and released as CO2. Two pairs of these electrons have been transferred to 2 NAD, and one GTP has been generated. However, two additional pairs of electrons arising from acetyl CoA still remain in the TCA cycle as part of succinate. The remaining steps of the TCA cycle transfer these two pairs of electrons to FAD and NAD and add H2O, thereby regenerating oxaloacetate. 

The TD-induced inhibition of metabolic flux through PDHC takes place in all cells of the affected organism (Jankowska-Kulawy et al. 2010). It causes primary inhibition of acetyl-CoA synthesis in the mitochondria, yielding a proportional reduction of its metabolic flux through first steps of the TCA cycle and further aggravation of this suppression due to inhibition of KDHC (Jankowska-Kulawy et al. 2010 Shi et al. 2007) (Figure 33.1). As a result, oxidative phosphorylation process slows down, yielding ATP deficits (Jhala and Hazell 2011). 

Citrate synthase is the first step in this metabolic pathway, and as stated the reaction has a large negative AG°. As might be expected, it is a highly regulated enzyme. NADH, a product of the TCA cycle, is an allosteric inhibitor of citrate synthase, as is succinyl-CoA, the product of the fifth step in the cycle (and an acetyl-CoA analog). 

A carrier molecule containing four carbon atoms (the C4 unit) takes up a C2 unit (the activated acetic acid ), which is introduced into the cycle. The product is a six-carbon molecule (the C6 unit), citric acid, or its salt, citrate. CO2 is cleaved off in a cyclic process, so that a C5 unit is left this loses a further molecule of CO2 to give the C4 unit, oxalacetate. In the living cell, this process involves ten steps, which are catalysed by eight enzymes. However, the purpose of the TCA cycle is not the elimination of CO2, but the provision of reduction equivalents, i.e., of electrons, and... 

The transformation of pyruvate to carbon dioxide is achieved by the several steps in a cyclical series of reactions known as the tricarboxylic acid (TCA) cycle. The name of the cycle comes from the first step where acetyl-CoA is condensed with oxaloacetic acid to form citric acid, a tricarboxylic acid. Once citrate is formed the material is converted back to oxaloacetate through a series of 10 reactions, as illustrated in Fig. 5.22, with the net production of 2 molecules of carbon dioxide and reducing equivalents in the form of 4 molecules of NADH + H and 1 molecule of FADH2, together with 1 mole of ATP. The overall stoichiometry of the TCA cycle from pyruvate is ... 

The first oxidative conversion of the TCA cycle is catalyzed by isocitrate dehydrogenase. This conversion takes place in two steps oxidation of the secondary alcohol to a ketone (oxalosuccinate), followed by a j8 decarboxylation to produce a-ketoglutarate (fig. 13.9). 

The next step in the TCA cycle, the oxidation of succinate to fumarate, involves insertion of a double bond into a saturated hydrocarbon chain. 

As outlined in Section 6.1, the next step in building a computational model of the TCA cycle is determining an expression for the biochemical fluxes in the system. Flux expressions used here are adopted from Wu et al. [213], who developed thermodynamically balanced flux expressions for the reactions illustrated in Figure 6.2 and listed in Table 6.2. Here we describe in detail the mechanistic model and the associated rate law for one example enzyme (pyruvate dehydrogenase) from Wu et al. s model. For all other enzymes we simply list the flux expression and refer readers to the supplementary material to [213] for further details. 

Isocitrate dehydrogenase releases the first CO2, and a-ketoglutarate dehydrogenase releases the second CO2. There is no net consumption of oxaloacetate in the TCA cycle— the first step use an oxaloacetate, and the last step produces one. The utilization and regeneration of oxaloacetate is the "cycle" part of the TCA cycle. 

Although alanine is the major gluconeogenic amino acid, other amino acids, such as serine, serve as carbon sources for the synthesis of glucose because they also form pymvate, the substrate for the initial step in the process. Some amino acids form intermediates of the TCA cycle (see Chapter 20), which can enter the gluconeogenic pathway. 

In glycolysis, PEP is converted to pyruvate by pyruvate kinase. In gluconeogenesis, a series of steps are required to accomplish the reversal of this reaction (Fig. 31.5). Pyruvate is carboxylated by pyruvate carboxylase to form oxaloacetate. This enzyme, which requires biotin, is the catalyst of an anaplerotic (refilling) reaction of the TCA cycle (see Chapter 20). In gluconeogenesis, this reaction replenishes the oxaloacetate that is used for the synthesis of glucose (Fig. 31.6). 

Two turns of the TCA cycle, with NADH produced at the pyruvate dehydrogenase, isocitrate dehydrogenase, alpha-ketoglutarate, and malate dehydrogenase steps and FADH2 produced at the succinate dehydrogenase step and GTP (equivalent to ATP) produced at the succinyl-coenzyme A synthetase step. 

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