16.2 Reactions of the Citric Acid Cycle

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1 16.2 Reactions of the Citric Acid Cycle The Sequence of Reactions in the Citric Acid Cycle Make Chemical Sense Acetyl CoA, an intermediate of the breakdown of carbohydrates, fats, and proteins, must be completely oxidized to CO 2 in order to extract the maximum amount of potential energy in the fuel. FUEL SOURCE Carbohydrates Fats Proteins Glycolysis converts fuel into pyruvate Pyruvate Pyruvate Dehydrogenase Complex converts pyruvate into acetyl-coa Acetyl-CoA etc..until the fuel is completely oxidized to CO 2

2 The Citric Acid Cycle Has Eight Steps Reactants: 1. Acetyl CoA 2. Oxaloacetate Enzyme: Citrate Synthase Product(s): Citrate By-products (that are released): CoA-SH Type of Reaction: Hydrolysis (that means that H 2 O must be added so that it can break the Citroyl-CoA (intermediate) up. Free CoA and citrate are formed, which are released from the active site. Where do the released products go? The released CoA is recycled back into the oxidative decarboxylation of another pyruvate molecule in the PDH complex. Exergonic (energy is released) because this reaction is the hydrolysis of a high energy thioester (Citroyl-CoA) intermediate. What drives this reaction? The large, negative standard free energy change is the driving force behind this reaction. Oxaloacetate is present at such a low concentration that it cannot be the one driving the reaction to the products side. ❶ Formation of Citrate

3 ❷ Formation of Isocitrate via cis-acontitate Reactant(s): Citrate Enzyme: Aconitase What does aconitase do? 1. Aconitase catalyzes the reversible transformation of citrate to isocitrate. A reaction intermediate, cis-aconitase, forms along the way. 2. Has an iron-sulfur center, which serves two purposes: - It helps the substrate bind to the active site - It helps with the addition and removal of H 2 O. Product(s): (a) Intermediate Product: cis-aconitate (b) Final Product: Isocitrate Type of Reaction: (a) Citrate to cis-aconitase is a dehydration reaction (H 2 O is removed). NOTE: cis-aconitate does not dissociate from the active site usually. (b) cis-aconitase to Isocitrate is a hydration reaction (H 2 O is added). Endergonic. What drives this reaction? The next reaction in the citric acid cycle (Rxn. # 3) consumes isocitrate rapidly, so the stead-state concentration of isocitrate is low. Therefore, the reaction gets pushed to the right, towards isocitrate formation. NOTE: This occurs despite the fact that the equilibrium mixture of citrate and isocitrate at ph 7.4 and T = 25 C is only 10% isocitrate. However, the quick consumption of isocitrate in the following reaction, forces the reaction to the right. ❸ Oxidation of Isocitrate to α-ketoglutarate and Reactant(s): Isocitrate Enzyme: Isocitrate Dehydrogenase There are two forms of isocitrate dehydrogenase: 1. One requiring NAD + as an electron acceptor. 2. One requiring NADP + as an e - acceptor. Product(s): α-ketoglutarate, CO 2, NAD(P)H + H + Type of Reaction: Oxidative Decarboxylation CO 2

4 ❹ Oxidation of α-ketoglutarate to Succinyl-CoA Reactant(s): α-ketoglutarate Enzyme: α-ketoglutarase dehydrogenase complex (very similar reaction mechanism to pyruvate dehydrogenase complex) α-ketoglutarate DEHYDROGENASE COMPLEX VS. PYRUVATE DEHYDROGENASE COMPLEX Similarities Differences and CO 2 Both complexes have 3 enzymes subunits. (The three enzymes share similarities, but are ultimately different structures, except E 3?). E 1 E 2 E 1 of both complexes are structurally similar. e.g. both have enzyme bound TPP Both have covalently bound lipoyl moieties. Their amino acid sequences differ. They have different binding specificities. PDC: E 1 binds pyruvate KGDC: E 1 binds α- Ketoglutarate. E 3 Identical Structures. Product(s): Succinyl-CoA, CO 2 Type of Reaction: Oxidative Decarboxylation NAD + serves as the electron acceptor CoA is the carrier of the succinyl group What drives this reaction forward? A large and negative free energy change.

5 α-ketoglutarate Dehydrogenase Complex ❺ Conversion of Succinyl-CoA to Succinate Reactant: Succinyl CoA Succinyl CoA has a thioester bond (with a very large and negative standard free energy of hydrolysis ΔG = -36 kj/mol). Enzyme: Succinyl-CoA Synthetase This reaction is reversible Product(s): Succinate, GTP, CoA-SH. NOTE: The GTP molecule produced can be considered as an ATP molecule because both are energetically equivalent and are interchangeable as long as the required enzyme is present for the conversion. GTP + ADP GDP + ATP ΔG = 0 kj/mol What drives this reaction: The large, negative ΔG of hydrolysis for Succinyl CoA drives the reaction forward. The energy that is released when Succinyl-CoA s thioester bond breaks drives the synthesis of a phosphoanhydride bond in ATP or GTP, with a net ΔG of only -2.9 kj/mol.

6 ❻ Oxidation of Succinate to Fumarate Reactant: Succinate Enzyme: Succinate Dehydrogenase o Malonate, although usually not present in cells, is a strong competitive inhibitor of succinate dehydrogenase. Its addition to the mitochondria blocks the activity of the citric acid cycle. Product(s): Fumarate, FADH 2 ❼ Hydration of Fumarate to Malate Reversible Hydration of Fumarate to L-Malate. Catalyst: Fumarase.

7 Very stereospecific. ❽ Oxidation of Malate to Oxaloacetate The equilibrium of this reaction lies far to the left under standard thermodynamic conditions; however, the highly exergonic citrate synthase reaction (the next step/step ❶) keep consuming oxaloactetate, lowering the concentration of the products side of reaction 8. Thus, the reaction is pulled to the right, towards the formation of oxaloacetate, such that a state of equilibrium can be maintained.

8 BOX 16-2 SYNTHASES AND SYNTHETASES; LIGASES AND LYASES; KINASES, PHOSPHATASES, AND PHOSPHORYLASES: YES, THE NAMES ARE CONFUSING! Enzyme Type Function Example Synthases Catalyze condensation reactions in which no nucleoside triphosphate (ATP, GTP) is required as an energy source. Citrate Synthase (Citric Acid Cycle, Reaction # 1) Synthetases Catalyze condensations that use ATP or a nucleoside triphosphate as a source of energy for the synthetic reaction. Succinyl-CoA Synthetase (Citric Acid Cycle, Reaction # 6) Ligases...from the Latin word ligare to tie together Catalyze condensations in which 2 atoms are joined using ATP or another energy source. Synthetases are Ligases. DNA ligase closes breaks in DNA molecules. Lyases Catalyze cleavages (or in the reverse direction, additions) in which electronic rearrangements occurs The Pyruvate Dehydrogenase Complex cleaves CO 2 from pyruvate. Kinases Catalyzes a phosphorylation reaction. Transfers a phosphoryl group from a nucleoside Hexokinase Glucokinase

9 triphosphate (e.g. ATP) to an acceptor molecule. Phosphorylases A phosphate attacks a molecule and covalently bonds at the point of bond breakage. Glycogen Phosphorylase phosphorolysis of glycogen, producing glucose 1-phosphate. Phosphatases Dehydrogenase Catalysis of dephosphorylation of a phosphate ester, with water as the attacking species. An enzyme that catalyzes the removal of hydrogen from a substrate and the transfer of the hydrogen to an acceptor in an oxidation-reduction reaction. - Citric Acid Cycle: Isocitrate Dehydrogenase (Rxn. 3) α-ketoglutarate Dehdyrogenase Complex (Rxn. 4) Succinate Dehydrogenase (Rxn. 6) Malate Dehydrogenase (Rxn. 8) TYPES OF REACTIONS THAT OCCUR IN THE CITRIC ACID CYCLE Reaction Description Example Condensation A condensation reaction (i.e. dehydration synthesis) is a chemical reaction in which two molecules or moieties (functional groups) combine to form a larger molecule, together with the loss of a small molecule. [1] Possible small molecules lost are water, hydrogen chloride, methanol, or acetic acid. Dehydration A dehydration reaction is a chemical reaction that involves the loss of a water molecule from the reacting molecule. Hydration A hydration reaction is a reaction where a hydrogen and hydroxyl ion is attached to a carbon in a carbon double bond. Decarboxylation Decarboxylation is a chemical reaction that removes a carboxyl group and releases carbon dioxide (CO 2 ).

10 Oxidation Loss of electrons Always coupled with a reduction reaction gain of electrons Substrate-Level Phosphorylation Substrate-level phosphorylation is a type of metabolic reaction that results in the formation of adenosine triphosphate (ATP) or guanosine triphosphate (GTP) by the direct transfer and donation of a phosphoryl (PO 3 ) group to adenosine diphosphate (ADP) or guanosine diphosphate (GDP) from a phosphorylated reactive intermediate.

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