Tricarboxylic Acid Cycle

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1 Tricarboxylic Acid Cycle Overview (Also called KREBS CYCLE, or CITRIC ACID CYCLE ) Occur totally in mitochondria. TCA cycle is an aerobic pathway, bcz O 2 is required as the final electron accepter. Supplies intermediates for a number of important synthetic reactions, and provides building blocks for synthesis of some amino acids and heme. Reactions of TCA cycle 1. condensation of oxaloacetate and acetyl coa to form citrate. -catalyzed by citrate synthase. -citrate composed of 6 carbons, with 3 carboxyl groups, and a hydroxyl group on the middle carbon, so it is a symmetrical molecule. -in the following steps we'll need to decarboxylise the middle carbon (removing CO 2 ), but we cannot do so while there is a hydroxyl group on the same carbon, so that we have to transfer the hydroxyl group to the adjacent carbon by forming "isocitrate". 2. isomerization of citrate -citrate is isomarized to isocitrate by aconitase. -this enzyme catalyzes the dehydration-rehydration reaction (removing and adding H2O) to form isocitrate. -there's an intermediate in this reaction called aconitase so that we named the enzyme so. -isocitrate is not symmetrical, so that decarboxylation can occur now. P a g e 1

2 3. oxidation and decarboxylation of isocitrate -this reaction occurs by two steps : a) oxidation of the hydroxyl group to ketone group since there is a ketone group on the middle carbon, then CO 2 is ready now to be removed. b)decarboxylation of isocitrate to α-katoglutarate. -catalyzed by isocitrate dehydrogenase (according to the type of the reaction and the name of the substrate) -the enzyme was not named " decarboxylase" bcz it's an oxidation reduction reaction, it did not decarboxylated simply. -irreversible step. -produces the first NADH and the first CO 2 in the cycle. α-katoglutarate resembles an amino acid called Glutamate, the difference between them is that there is a ketone group on α- carbon of α-katoglutarate, replaced by an amino group in Glutamate, also called (α-aminoglutarate). α-katoglutarate has 5 carbons, when we remove CH 2 we'll get oxaloacetate. 4. oxidative decarboxylation of α-katoglutarate -The conversion of α-katoglutarate to succinyl CoA is catalyzed by the α-katoglutarate dehydrogenase complex (an aggregation of three enzymes), which works in a similar way to "Pyruvate dehydrogenase complex" that was used for the conversion of pyruvate to acetyl coa, but here it's not regulated by phospholyration dephosphorylation reactions. P a g e 2

3 -this complex catalyzes the reaction by three steps: decaboxylation : removal of CO 2. Oxidation of the aldehyde group to carboxyl group, which causes the reduction of NAD + to NADH. Transfer of the resultant acetyl group to coa. This reaction requires 5 cofactors : flavin, riboflavin,niacin, lipoic acid, coa 4 vitamins are needed: thiamine, riboflavin,niacin, coa (synthesized from pantothenic acid (vitamin B5) and cysteine (alfa amino acid )) -The coenzymes required are: thiamine pyrophosphate (TPP), lipoic acid, FAD, NAD +, and coa. 5. cleavage of succinyl coa -catalyzed by succinate thiokinase. -succinyl coa contain a high energy bond (thioester bond), so that we can utilize the energy that is produced from the cleavage of that bond to form GTP from GDP+Pi -GTP and ATP are energetically interconvertible by the nucleside diphosphate kinase reaction: GTP + ADP GDP + ATP -the generation of GTP by succinate thiokinase is an example of substrate-level phosphorylation. -the reaction releases the second CO 2 and produces the second NADH of the cycle. P a g e 3

4 6. oxidation of succinate -Succinate is oxidized to Fumarate by succinate dehydrogenase, as two hydrogens transferred from two adjacent carbons to FAD FADH 2. - Usually when we transfer 2H from an adjacent carbons, the accepter will be FAD not NAD. while NAD accept them from hydroxyl groups. - succinate dehydrogenase is part of electron transport chain "complex II". 7. hydration of fumarate Adding of water to fumarate produces malate in a freely reversible reaction, catalyzed by fumarase. 8. oxidation of malate - Malate is oxidized to oxaloacetate by malate dehydrogenase, which produces the third NADH. -this reaction is highly favorable in the opposite direction, but what pushes it in the forward direction is that oxaloacetate is used in the following reaction which makes the cycle go on and on. -oxaloacetate and malate "maarga 3leina b-ge99et elshuttel" Aspartate-malate shuttle : for transferring NADH from cytoplasm to mitochondria. A SIMPLE WAY TO REMEMBER THE INTERMEDIATES OF THE CYCLE CIA Sends Soldiers From My Office P a g e 4

5 NET REACTION Acetyl-CoA + 3 NAD+ + FAD + GDP + Pi + 2 H 2 O CoA-SH + 3 NADH + 3 H+ + FADH 2 + GTP + 2 CO 2 In short : 2 carbon atoms enter the cycle. Two molecules of CO 2 are released. Substrate level phosphorylation (succinyl coa Succinate) Four reduced coenzyme molecules per acetyl coa oxidized to CO 2. ENERGY PRODUCED BY THE TCA CYCLE TCA cycle is a source of biosynthetic precursors, many of its intermediates used in different pathways : Citrate fatty acids, sterols. α-katoglutarate +ammonia Glutamate other amino acids (Glutamine) purins (Adenine, Guanine). succinyl coa pophyrins, heme, chlorophyll oxaloacetate Asparate, other amino acids, purins, pyrimidines. In case of using the intermediates in pathways other than TCA cycle, the rate of the cycle will decrease. (the cycle will go on but at a very much slower rate). P a g e 5

6 In that case, to retain the normal rate we have to supply the cycle with any intermediate (other than acetyl coa ). -A way by which we can replenish the intermediates is by converting pyruvate to oxaloacetate. (carboxylation of pyruvate, catalyzed by pyruvate carboxylase). -pyruvate (3 carbons), oxaloacetate (4 carbons), CO 2 can be added in the form of bicarbonate (CO 2 + H 2 O H 2 CO 3 ). -this reaction needs energy, since it is a carboxylation reaction. -converting 0xaloacetate to pyruvate is a decarboxylation reaction, so that it did not require ATP. -carbozylation reactions need a vitamin called BIOTIN, a vitamin from the B vitamin groups, it is a carrier for the activated carboxyl group (CO2 is a gas, so it require a carrier so as to be added to pyruvate). Anaplerotic reactions "fill up rxns" : replenishing the cycle with different intermediates. REGULATION OF THE TCA CYCLE It is the final common pathway for the aerobic oxidation of fuel molecules It is an important source of building blocks for a number of biomolecules. Entry into the cycle and the rate of the cycle itself are controlled at several stages. P a g e 6

7 حمض الحصرم = acid pyruvate= pyruvic -Bacteria can convert Acetyl coa back to pyruvate. Regulation should be stated on the level of irreversible steps which is here "pyruvate dehydrogenase complex", which is a large complex composed of about 60 subunits, two of them are "pyruvate dehydrogenase kinase" and "pyruvate dehydrogenase phospatase" which carry on the regulation process by phosphorylation\dephosphorylation rxns. -The dephosphorylated form of the complex is the active form. -Phsphatase works to remove the phosphate group from the complex, hence, transforming it to the active form (glucose will be converted to pyruvate). -kinase works to phosphorylate the complex, converting it to the inactive form (the rxn will be switched off). -those regulatory proteins (phosphatase, kinase) are part of the complex, which increases the efficiency of the regulation process. High concentrations of reaction products inhibit the complex. NADH, Acetyl coa inhibit the dehosphorylated form (the active form). P a g e 7

8 Increasing the NADH/NAD +, acetyl coa/coa, or ATP/ADP ratio promots phosphorylation. Promot the kinase activity phsphorylation will occur the complex is switched off the reaction will be stopped. Pyruvate, coa, NAD + inhibit the kinase enzyme. Pyruvate as well as ADP activate the dehydrogenase by inhibiting the kinase. The rise in mitochondrial Ca 2+ activates the pyruvate dehydrogenase complex by stimulating the phosphatase. This is particularly important in skeletal muscle, where release of Ca 2+ during contraction stimulates the PDH complex, and thereby energy production. Insulin also accelerates the conversion of pyruvate into acetyl coa by stimulating the phosphatase. P a g e 8

9 Phosphatase Deficiency (i.e. pyruvate dehydrogenase phosphatase deficiency) Pyruvate dehydrogenase is always phosphorylated and thus inactive. Glucose is processed to lactic acid lactic acidosis Malfunctioning of many tissues, especially the central nervous system (that's goes for 2 reasons) : - Glucose is a source of energy - Acetyl coa + choline Ach (neurotransmitter in the CNS) In this case, acetyl coa will not be found in proper amounts, hence, no production of Ach, this will affect the function of the CNS. REGULATION OF CYCLE ITSELF Here, the regulation should be done at the level where CO 2 are released, (the release of CO 2 indicates that the reaction is almost irreversible), decarboxylation reactions is irreversible, so they must be regulated. Regulation at the level of isocitrate dehydrogenase (IDH) - Activated by : ADP, Ca+ - Inhibited by : ATP, NADH *high concentrations of NADH indicates energy level in the cell is high. that the *in case of inhibiting the activity of isocitrate dehdrogenase, the accumulated citrate will be converted to fat. P a g e 9

10 *ATP inhibitor, ADP activator when we have high concentrations of ATP, the concentration of ADP will be decreased. ATP+ADP+AMP = constant Regulation at the level of α-katoglutarate dehydrogenase *As we said, it resembles to a high extent the pyruvate dehydrogenase complex, the only difference between them is that the later cannot be phosphorylated. - Activated by : Ca+ - Inhibited by : NADH, succinyl coa (its products), ATP. Regulation at the level of citrate synthase - Regulated only in bacteria not in humans. - Regulates the process of condensation of Acetyl CoA with Oxaloacitate to form Citrate. P a g e 11

11 Dietary deficiency of thiamine (vitamin B1) Causes a disease called " Beriberi " A serious health problem in communities where rice is the major food, "the processed rice is very poor in vitamins, one of which is thimine". -causes difficulty in walking. The patient may also suffer from complications affecting the cardiovascular, nervous, muscular, and gastrointestinal systems. In alcoholics who are severely malnourished Characterized by neurologic and cardiac symptoms Thiamine pyrophosphate is cofactor of : pyruvate dehydrogenase, α-ketoglutarate dehydrogenase, and transketolase. pyruvate and α-ketoglutarate in the blood. The vitamin is missing the enzyme is not functioning the concentrations of the substrates (pyruvate and α- ketoglutarate) will increase in the blood. transketolase activity of red cells, easily measured, is reliable diagnostic indicator of the disease. Mercury or Arsenite (AsO33-) Poisoning الزرنيخ = Arsenite Both elements have a high affinity for neighboring sulfhydryls, (dihydrolipoyl groups) The binding of mercury or arsenite to the dihydrolipoyl groups inhibits the complex energy production central nervous system pathologies Treatment for these poisons is by administration of sulfhydryl reagents with adjacent sulfhydryl groups P a g e 11

12 (2,3-Dimercaptopropanol PDH (antidote) has high affinity to bind Arsenite, the produced complex will be secreted in urine) "Dedicated to all those with the willpower to stay awake in Bacteriology, and all those who were kicked out of Virology for being 2 minutes late" Special thanks to : Mokhlisa AL-Remawi <3 & Khalid Al-Jawhari Done by : me P a g e 12

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