Citric acid cycle

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Overview of the citric acid cycle

The citric acid cycle—also known as the Krebs cycle, Szent–Györgyi–Krebs cycle or the TCA cycle (tricarboxylic acid cycle)

aerobic respiration. In addition, the cycle provides precursors of certain amino acids, as well as the reducing agent NADH, that are used in numerous other reactions. Its central importance to many biochemical pathways suggests that it was one of the earliest components of metabolism.[3][4] Even though it is branded as a "cycle", it is not necessary for metabolites to follow only one specific route; at least three alternative segments of the citric acid cycle have been recognized.[5]

The name of this metabolic pathway is derived from the citric acid (a tricarboxylic acid, often called citrate, as the ionized form predominates at biological pH[6]) that is consumed and then regenerated by this sequence of reactions to complete the cycle. The cycle consumes acetate (in the form of acetyl-CoA) and water, reduces NAD+ to NADH, releasing carbon dioxide. The NADH generated by the citric acid cycle is fed into the oxidative phosphorylation (electron transport) pathway. The net result of these two closely linked pathways is the oxidation of nutrients to produce usable chemical energy in the form of ATP.

In

inner membrane of the mitochondrion
.

For each pyruvate molecule (from glycolysis), the overall yield of energy-containing compounds from the citric acid cycle is three NADH, one FADH2, and one GTP.[7]

Discovery

Several of the components and reactions of the citric acid cycle were established in the 1930s by the research of

Nobel Prize for Physiology or Medicine in 1953, and for whom the cycle is sometimes named the "Krebs cycle".[11]

Overview

acetyl group; the portion in black is coenzyme A
.

The citric acid cycle is a

enzymes that completely oxidize acetate (a two carbon molecule), in the form of acetyl-CoA, into two molecules each of carbon dioxide and water. Through catabolism of sugars, fats, and proteins, the two-carbon organic product acetyl-CoA is produced which enters the citric acid cycle. The reactions of the cycle also convert three equivalents of nicotinamide adenine dinucleotide (NAD+) into three equivalents of reduced NAD+ (NADH), one equivalent of flavin adenine dinucleotide (FAD) into one equivalent of FADH2, and one equivalent each of guanosine diphosphate (GDP) and inorganic phosphate (Pi) into one equivalent of guanosine triphosphate (GTP). The NADH and FADH2 generated by the citric acid cycle are, in turn, used by the oxidative phosphorylation
pathway to generate energy-rich ATP.

One of the primary sources of acetyl-CoA is from the breakdown of sugars by glycolysis which yield pyruvate that in turn is decarboxylated by the pyruvate dehydrogenase complex generating acetyl-CoA according to the following reaction scheme:

CH3C(=O)C(=O)Opyruvate + HSCoA + NAD+CH3C(=O)SCoAacetyl-CoA + NADH + CO2

The product of this reaction, acetyl-CoA, is the starting point for the citric acid cycle. Acetyl-CoA may also be obtained from the oxidation of fatty acids. Below is a schematic outline of the cycle:

Steps

There are ten basic steps in the citric acid cycle, as outlined below. The cycle is continuously supplied with new carbon in the form of acetyl-CoA, entering at step 0 in the table.[14]

Reaction type Substrates Enzyme Products Comment
0 / 10 Aldol condensation
Acetyl CoA
+ H2O
Citrate synthase Citrate + CoA-SH irreversible, extends the 4C oxaloacetate to a 6C molecule
1 Dehydration
Citrate
Aconitase cis-Aconitate + H2O reversible isomerisation
2 Hydration
cis-Aconitate
+ H2O
Isocitrate
3
Oxidation
Isocitrate + NAD
+
Isocitrate dehydrogenase Oxalosuccinate + NADH + H + generates
NADH
(equivalent of 2.5 ATP)
4 Decarboxylation
Oxalosuccinate
α-Ketoglutarate
+ CO2
rate-limiting, irreversible stage, generates a 5C molecule
5 Oxidative
decarboxylation
α-Ketoglutarate
+ NAD+ + CoA-SH
α-Ketoglutarate
dehydrogenase, Thiamine pyrophosphate, Lipoic acid
, Mg++,transsuccinytase
Succinyl-CoA + NADH + H + + CO2 irreversible stage, generates NADH (equivalent of 2.5 ATP), regenerates the 4C chain (CoA excluded)
6 substrate-level
phosphorylation
Pi
Succinyl-CoA synthetase Succinate + CoA-SH + GTP or involve the H2O needed for balanced equation.
7 Oxidation
ubiquinone
(Q)
Succinate dehydrogenase Fumarate + ubiquinol (QH2) uses FAD as a prosthetic group (FAD→FADH2 in the first step of the reaction) in the enzyme.[15]
These two electrons are later transferred to QH2 during Complex II of the ETC, where they generate the equivalent of 1.5 ATP
8 Hydration
Fumarate
+ H2O
Fumarase L-Malate Hydration of C-C double bond
9 Oxidation
L-Malate
+ NAD+
Malate dehydrogenase
Oxaloacetate
+ NADH + H+
reversible (in fact, equilibrium favors malate), generates
NADH
(equivalent of 2.5 ATP)
10 / 0 Aldol condensation
Acetyl CoA
+ H2O
Citrate synthase Citrate + CoA-SH This is the same as step 0 and restarts the cycle. The reaction is irreversible and extends the 4C oxaloacetate to a 6C molecule

Two

coenzyme Q, which is the final electron acceptor of the reaction catalyzed by the succinate:ubiquinone oxidoreductase complex, also acting as an intermediate in the electron transport chain.[15]

Mitochondria in animals, including humans, possess two succinyl-CoA synthetases: one that produces GTP from GDP, and another that produces ATP from ADP.[16] Plants have the type that produces ATP (ADP-forming succinyl-CoA synthetase).[14] Several of the enzymes in the cycle may be loosely associated in a multienzyme protein complex within the mitochondrial matrix.[17]

The GTP that is formed by GDP-forming succinyl-CoA synthetase may be utilized by nucleoside-diphosphate kinase to form ATP (the catalyzed reaction is GTP + ADP → GDP + ATP).[15]

Products

Products of the first turn of the cycle are one GTP (or ATP), three NADH, one FADH2 and two CO2.

Because two acetyl-CoA

molecules are produced from each glucose molecule, two cycles are required per glucose molecule. Therefore, at the end of two cycles, the products are: two GTP, six NADH, two FADH2, and four CO2.[18]

Description Reactants Products
The sum of all reactions in the citric acid cycle is: Acetyl-CoA + 3 NAD+ + FAD + GDP + Pi + 2 H2O → CoA-SH + 3 NADH + FADH2 + 3 H+ + GTP + 2 CO2
Combining the reactions occurring during the pyruvate oxidation with those occurring during the citric acid cycle, the following overall pyruvate oxidation reaction is obtained: Pyruvate ion + 4 NAD+ + FAD + GDP + Pi + 2 H2O → 4 NADH + FADH2 + 4 H+ + GTP + 3 CO2
Combining the above reaction with the ones occurring in the course of glycolysis, the following overall glucose oxidation reaction (excluding reactions in the respiratory chain) is obtained: Glucose + 10 NAD+ + 2 FAD + 2 ADP + 2 GDP + 4 Pi + 2 H2O → 10 NADH + 2 FADH2 + 10 H+ + 2 ATP + 2 GTP + 6 CO2

The above reactions are balanced if Pi represents the H2PO4 ion, ADP and GDP the ADP2− and GDP2− ions, respectively, and ATP and GTP the ATP3− and GTP3− ions, respectively.

The total number of ATP molecules obtained after complete oxidation of one glucose in glycolysis, citric acid cycle, and oxidative phosphorylation is estimated to be between 30 and 38.[19]

Efficiency

The theoretical maximum yield of

malate-aspartate shuttle, transport of two of these equivalents of NADH into the mitochondria effectively consumes two equivalents of ATP, thus reducing the net production of ATP to 36. Furthermore, inefficiencies in oxidative phosphorylation due to leakage of protons across the mitochondrial membrane and slippage of the ATP synthase/proton pump commonly reduces the ATP yield from NADH and FADH2 to less than the theoretical maximum yield.[19] The observed yields are, therefore, closer to ~2.5 ATP per NADH and ~1.5 ATP per FADH2, further reducing the total net production of ATP to approximately 30.[20] An assessment of the total ATP yield with newly revised proton-to-ATP ratios provides an estimate of 29.85 ATP per glucose molecule.[21]

Variation

While the citric acid cycle is in general highly conserved, there is significant variability in the enzymes found in different taxa[22] (note that the diagrams on this page are specific to the mammalian pathway variant).

Some differences exist between eukaryotes and prokaryotes. The conversion of D-threo-isocitrate to 2-oxoglutarate is catalyzed in eukaryotes by the NAD+-dependent EC 1.1.1.41, while prokaryotes employ the NADP+-dependent EC 1.1.1.42.[23] Similarly, the conversion of (S)-malate to oxaloacetate is catalyzed in eukaryotes by the NAD+-dependent EC 1.1.1.37, while most prokaryotes utilize a quinone-dependent enzyme, EC 1.1.5.4.[24]

A step with significant variability is the conversion of succinyl-CoA to succinate. Most organisms utilize EC 6.2.1.5, succinate–CoA ligase (ADP-forming) (despite its name, the enzyme operates in the pathway in the direction of ATP formation). In mammals a GTP-forming enzyme, succinate–CoA ligase (GDP-forming) (EC 6.2.1.4) also operates. The level of utilization of each isoform is tissue dependent.[25] In some acetate-producing bacteria, such as Acetobacter aceti, an entirely different enzyme catalyzes this conversion – EC 2.8.3.18, succinyl-CoA:acetate CoA-transferase. This specialized enzyme links the TCA cycle with acetate metabolism in these organisms.[26] Some bacteria, such as Helicobacter pylori, employ yet another enzyme for this conversion – succinyl-CoA:acetoacetate CoA-transferase (EC 2.8.3.5).[27]

Some variability also exists at the previous step – the conversion of 2-oxoglutarate to succinyl-CoA. While most organisms utilize the ubiquitous NAD+-dependent 2-oxoglutarate dehydrogenase, some bacteria utilize a ferredoxin-dependent 2-oxoglutarate synthase (EC 1.2.7.3).[28] Other organisms, including obligately autotrophic and methanotrophic bacteria and archaea, bypass succinyl-CoA entirely, and convert 2-oxoglutarate to succinate via

succinate semialdehyde, using EC 4.1.1.71, 2-oxoglutarate decarboxylase, and EC 1.2.1.79, succinate-semialdehyde dehydrogenase.[29]

In

ten-eleven translocation (TET) enzymes; ordinarily TETs hydroxylate 5-methylcytosines to prime them for demethylation. However, in the absence of alpha-ketoglutarate this cannot be done and there is hence hypermethylation of the cell's DNA, serving to promote epithelial-mesenchymal transition (EMT) and inhibit cellular differentiation. A similar phenomenon is observed for the Jumonji C family of KDMs which require a hydroxylation to perform demethylation at the epsilon-amino methyl group.[33] Additionally, the inability of prolyl hydroxylases to catalyze reactions results in stabilization of hypoxia-inducible factor alpha, which is necessary to promote degradation of the latter (as under conditions of low oxygen there will not be adequate substrate for hydroxylation). This results in a pseudohypoxic phenotype in the cancer cell that promotes angiogenesis, metabolic reprogramming, cell growth, and migration.[citation needed
]

Regulation

Allosteric regulation by metabolites. The regulation of the citric acid cycle is largely determined by product inhibition and substrate availability. If the cycle were permitted to run unchecked, large amounts of

allosteric mechanism that can account for large changes in reaction rate from an allosteric effector whose concentration changes less than 10%.[6]

Citrate is used for feedback inhibition, as it inhibits phosphofructokinase, an enzyme involved in glycolysis that catalyses formation of fructose 1,6-bisphosphate, a precursor of pyruvate. This prevents a constant high rate of flux when there is an accumulation of citrate and a decrease in substrate for the enzyme.[34]

Regulation by calcium. Calcium is also used as a regulator in the citric acid cycle. Calcium levels in the mitochondrial matrix can reach up to the tens of micromolar levels during cellular activation.

α-ketoglutarate dehydrogenase.[36] This increases the reaction rate of many of the steps in the cycle, and therefore increases flux throughout the pathway.[citation needed
]

Transcriptional regulation. There is a link between intermediates of the citric acid cycle and the regulation of

prolyl 4-hydroxylases. Fumarate and succinate have been identified as potent inhibitors of prolyl hydroxylases, thus leading to the stabilisation of HIF.[37]

Major metabolic pathways converging on the citric acid cycle

Several

catabolic pathways converge on the citric acid cycle. Most of these reactions add intermediates to the citric acid cycle, and are therefore known as anaplerotic reactions, from the Greek meaning to "fill up". These increase the amount of acetyl CoA that the cycle is able to carry, increasing the mitochondrion's capability to carry out respiration if this is otherwise a limiting factor. Processes that remove intermediates from the cycle are termed "cataplerotic" reactions.[38]

In this section and in the next, the citric acid cycle intermediates are indicated in italics to distinguish them from other substrates and end-products.

NADH, as in the normal cycle.[39]

However, it is also possible for pyruvate to be

carboxylated by pyruvate carboxylase to form oxaloacetate. This latter reaction "fills up" the amount of oxaloacetate in the citric acid cycle, and is therefore an anaplerotic reaction, increasing the cycle's capacity to metabolize acetyl-CoA when the tissue's energy needs (e.g. in muscle) are suddenly increased by activity.[40]

In the citric acid cycle all the intermediates (e.g.

alpha-ketoglutarate, succinate, fumarate, malate, and oxaloacetate) are regenerated during each turn of the cycle. Adding more of any of these intermediates to the mitochondrion therefore means that that additional amount is retained within the cycle, increasing all the other intermediates as one is converted into the other. Hence the addition of any one of them to the cycle has an anaplerotic effect, and its removal has a cataplerotic effect. These anaplerotic and cataplerotic reactions will, during the course of the cycle, increase or decrease the amount of oxaloacetate available to combine with acetyl-CoA to form citric acid. This in turn increases or decreases the rate of ATP production by the mitochondrion, and thus the availability of ATP to the cell.[40]

fatty acids, is the only fuel to enter the citric acid cycle. With each turn of the cycle one molecule of acetyl-CoA is consumed for every molecule of oxaloacetate present in the mitochondrial matrix, and is never regenerated. It is the oxidation of the acetate portion of acetyl-CoA that produces CO2 and water, with the energy thus released captured in the form of ATP.[40] The three steps of beta-oxidation resemble the steps that occur in the production of oxaloacetate from succinate in the TCA cycle. Acyl-CoA is oxidized to trans-Enoyl-CoA while FAD is reduced to FADH2, which is similar to the oxidation of succinate to fumarate. Following, trans-Enoyl-CoA is hydrated across the double bond to beta-hydroxyacyl-CoA, just like fumarate is hydrated to malate. Lastly, beta-hydroxyacyl-CoA is oxidized to beta-ketoacyl-CoA while NAD+ is reduced to NADH, which follows the same process as the oxidation of malate to oxaloacetate.[41]

In the liver, the carboxylation of

epinephrine in the blood.[40] Here the addition of oxaloacetate to the mitochondrion does not have a net anaplerotic effect, as another citric acid cycle intermediate (malate) is immediately removed from the mitochondrion to be converted into cytosolic oxaloacetate, which is ultimately converted into glucose, in a process that is almost the reverse of glycolysis.[40]

In

ketone bodies, which too can only be burned in tissues other than the liver where they are formed, or excreted via the urine or breath.[40] These latter amino acids are therefore termed "ketogenic" amino acids, whereas those that enter the citric acid cycle as intermediates can only be cataplerotically removed by entering the gluconeogenic pathway via malate which is transported out of the mitochondrion to be converted into cytosolic oxaloacetate and ultimately into glucose. These are the so-called "glucogenic" amino acids. De-aminated alanine, cysteine, glycine, serine, and threonine are converted to pyruvate and can consequently either enter the citric acid cycle as oxaloacetate (an anaplerotic reaction) or as acetyl-CoA to be disposed of as CO2 and water.[40]

In

glyceraldehyde-3-phosphate by way of gluconeogenesis. In skeletal muscle, glycerol is used in glycolysis by converting glycerol into glycerol-3-phosphate, then into dihydroxyacetone phosphate (DHAP), then into glyceraldehyde-3-phosphate.[42]

In many tissues, especially heart and skeletal

muscle tissue, fatty acids are broken down through a process known as beta oxidation, which results in the production of mitochondrial acetyl-CoA, which can be used in the citric acid cycle. Beta oxidation of fatty acids with an odd number of methylene bridges produces propionyl-CoA, which is then converted into succinyl-CoA and fed into the citric acid cycle as an anaplerotic intermediate.[43]

The total energy gained from the complete breakdown of one (six-carbon) molecule of glucose by glycolysis, the formation of 2 acetyl-CoA molecules, their catabolism in the citric acid cycle, and oxidative phosphorylation equals about 30 ATP molecules, in eukaryotes. The number of ATP molecules derived from the beta oxidation of a 6 carbon segment of a fatty acid chain, and the subsequent oxidation of the resulting 3 molecules of acetyl-CoA is 40.[citation needed]

Citric acid cycle intermediates serve as substrates for biosynthetic processes

In this subheading, as in the previous one, the TCA intermediates are identified by italics.

Several of the citric acid cycle intermediates are used for the synthesis of important compounds, which will have significant cataplerotic effects on the cycle.[40] Acetyl-CoA cannot be transported out of the mitochondrion. To obtain cytosolic acetyl-CoA, citrate is removed from the citric acid cycle and carried across the inner mitochondrial membrane into the cytosol. There it is cleaved by

bile salts, and vitamin D.[39][40]

The carbon skeletons of many

aspartate and asparagine; and alpha-ketoglutarate which forms glutamine, proline, and arginine.[39][40]

Of these amino acids, aspartate and glutamine are used, together with carbon and nitrogen atoms from other sources, to form the

purines that are used as the bases in DNA and RNA, as well as in ATP, AMP, GTP, NAD, FAD and CoA.[40]

The

pyrimidines are partly assembled from aspartate (derived from oxaloacetate). The pyrimidines, thymine, cytosine and uracil, form the complementary bases to the purine bases in DNA and RNA, and are also components of CTP, UMP, UDP and UTP.[40]

The majority of the carbon atoms in the porphyrins come from the citric acid cycle intermediate, succinyl-CoA. These molecules are an important component of the hemoproteins, such as hemoglobin, myoglobin and various cytochromes.[40]

During gluconeogenesis

phosphoenolpyruvate by phosphoenolpyruvate carboxykinase, which is the rate limiting step in the conversion of nearly all the gluconeogenic precursors (such as the glucogenic amino acids and lactate) into glucose by the liver and kidney.[39][40]

Because the citric acid cycle is involved in both

anabolic processes, it is known as an amphibolic
pathway. Evan M.W.Duo Click on genes, proteins and metabolites below to link to respective articles. [§ 1]

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TCACycle_WP78Go to articleGo to articleGo to articleGo to articleGo to HMDBGo to articleGo to articleGo to articleGo to HMDBGo to HMDBGo to articleGo to WikiPathwaysGo to articleGo to articleGo to articleGo to WikiPathwaysGo to articleGo to articleGo to articleGo to articleGo to articleGo to articleGo to articleGo to articleGo to articleGo to articleGo to articleGo to articleGo to articleGo to articleGo to articleGo to articleGo to articleGo to articleGo to articleGo to WikiPathwaysGo to articleGo to articleGo to articleGo to HMDBGo to articleGo to articleGo to articleGo to articleGo to articleGo to WikiPathwaysGo to articleGo to WikiPathwaysGo to HMDBGo to articleGo to WikiPathwaysGo to articleGo to HMDBGo to articleGo to articleGo to articleGo to articleGo to articleGo to articleGo to articleGo to articleGo to articleGo to article
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TCACycle_WP78 edit
  1. ^ The interactive pathway map can be edited at WikiPathways: "TCACycle_WP78".

Glucose feeds the TCA cycle via circulating lactate

The metabolic role of lactate is well recognized as a fuel for tissues, mitochondrial cytopathies such as DPH Cytopathy, and the scientific field of oncology (tumors). In the classical Cori cycle, muscles produce lactate which is then taken up by the liver for gluconeogenesis. New studies suggest that lactate can be used as a source of carbon for the TCA cycle.[45]

Evolution

It is believed that components of the citric acid cycle were derived from

anaerobic bacteria, and that the TCA cycle itself may have evolved more than once.[46] It may even predate biosis: the substrates appear to undergo most of the reactions spontaneously in the presence of persulfate radicals.[47] Theoretically, several alternatives to the TCA cycle exist; however, the TCA cycle appears to be the most efficient. If several TCA alternatives had evolved independently, they all appear to have converged to the TCA cycle.[48][49]

See also

References

  1. .
  2. .
  3. .
  4. .
  5. .
  6. ^ a b c Voet D, Voet JG (2004). Biochemistry (3rd ed.). New York: John Wiley & Sons, Inc. p. 615.
  7. OCLC 769803483
    .
  8. ^ "The Nobel Prize in Physiology or Medicine 1937". The Nobel Foundation. Retrieved 2011-10-26.
  9. ^ Chandramana, Sudeep. (2014). Inclusive Growth And Youth Empowerment: A Development Model For Aspirational India. Journal of Science, Technology and Management. 7. 52–62.
  10. PMID 16746382
    .
  11. ^ "The Nobel Prize in Physiology or Medicine 1953". The Nobel Foundation. Retrieved 2011-10-26.
  12. PMID 2106256
    .
  13. .
  14. ^ .
  15. ^ .
  16. .
  17. .
  18. ^ "The citric acid cycle". Khan Academy. Retrieved 10 August 2021.
  19. ^
    PMID 7654171
    .
  20. .
  21. .
  22. ^ "Citric acid cycle variants at MetaCyc".
  23. S2CID 12950388
    .
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  29. .
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  35. .
  36. .
  37. .
  38. .
  39. ^ .
  40. ^ .
  41. .
  42. .
  43. .
  44. . this process is outlined graphically in page 73
  45. .
  46. .
  47. . 83.
  48. (PDF) from the original on 2017-08-12.
  49. (PDF) from the original on 2003-05-08.

External links