Citric Acid Cycle Biochemistry Lecture Notes PDF 2023/2024

Biochemistry Assist.Prof. Dr. Amina Al-Obaidi 2023/ 2024 Lec3- Carbohydrate metabolism The Citric Acid Cycle This cycle also called Kreb's cycle, or the tricarboxylic acid cycle (TCA), its c entral f...

Biochemistry Assist.Prof. Dr. Amina Al-Obaidi 2023/ 2024 Lec3- Carbohydrate metabolism The Citric Acid Cycle This cycle also called Kreb's cycle, or the tricarboxylic acid cycle (TCA), its c entral function is the oxidation of Acetyl-CoA to CO2, and H2O. Acety l-CoA is derived from the metabolism of fuel molecules such as Amino acids , Fatty acids, and Carbohydrates. The cycle occurs totally in the mitochondrial matrix. The cycle oxidizes organic fuel derived from pyruvate, generating 1 ATP, 3 NADH, and 1 FADH2 per turn 1 Biochemistry Assist.Prof. Dr. Amina Al-Obaidi 2023/ 2024 Lec3- Carbohydrate metabolism Citric acid cycle reactions In the CAC, Oxaloacetate is first condensed with acetate, then regenerated as the cycle is completed. However, these Reaction should not be viewed onl y as a closed circle, but rather like a traffic circle with compounds entering and leaving as required. A-Oxidative decarboxylation of pyruvate: - Before the citric acid cycle can begin, pyruvate must be converted to acetyl Coenzyme A (acetyl CoA), which links glycolysis to the citric ac id cycle This step is carried out by a multienzyme complex that catalyses thre e reactions 2 Biochemistry Assist.Prof. Dr. Amina Al-Obaidi 2023/ 2024 Lec3- Carbohydrate metabolism Pyruvate (The end produce of aerobic glycolysis) was converted to acetyl -C oA (a major fuel for CAC) by the reaction catalyzed by Pyruvate Dehydrog enase Complex, this enzyme is: 1. Located in the mitochondrial matrix. 2. Is not a part of citric acid cycle, but is the major source of Acetyl- Co A (2 carbon substrate for the cycle). 3. The reaction is irreversible, Precludes the formation of pyruvate from Acetyl -CoA, and explain why glucose cannot be formed from acetyl - CoA in gluconeogenesis. 4. The enzyme complex is inhibited by acetyl -CoA, which accumulates when it is produce faster than it can be oxidized by the citric acid cycl e. 5. Also, enzyme is inhibited by increased levels of NADH, which occurs when Electron Transport Chain is overloaded with substrate and O2 i s limiting. 3 Biochemistry Assist.Prof. Dr. Amina Al-Obaidi 2023/ 2024 Lec3- Carbohydrate metabolism B- Synthesis of Citrate from Acetyl CoA and Oxalac etate: - Condensation of: Acetyl-CoA + Oxaloacetate + H2O → Citrate + + CoASH + H (Enzyme involved: Citrate Synthase) Citrate Synthase. This enzyme inhibited by ATP, NADH, Succinyl -CoA and Acetyl- CoA derivatives of fatty acid. C- Isomerization of Citrate to Isocitrate: Citrate (cis- Aconitate) + H2O → Isocitrate (Enzyme involved: Aconitase) D- Oxidation and Decarboxylation of Isocitrate: - 1. Irreversible oxidative decarboxylation. 2. The first release of CO2 in the cycle and yielding the first NADH. 3. This step is one is one of the rate limiting steps of the cycle. 4. The enzyme is activated by ⬆ADP Mitochondrial level signal a need for generation of more high energy, and the enzyme is inhibited by ⬆ATP and⬆ NADH when the cell has abundant energy stores. 4 Biochemistry Assist.Prof. Dr. Amina Al-Obaidi 2023/ 2024 Lec3- Carbohydrate metabolism Isocitrate + NAD+ → α-ketoglutarate + CO2 + NADH (Enzyme involved: Isocitrate Dehydrogenase complex) E- Oxidative Decarboxylation of Ketoglutarate: - Alpha-ketoglutarate + NAD+ + CoASH → Succinyl-CoA + CO2 + NADH (Enzyme involved: α-ketoglutarate Dehydrogenase Complex) 1. The reaction releases the second CO2 an NADH. 2. The enzyme is inhibited by ATP, GTP, NAD and Succinyl- CoA. F- Cleavage of Succinyl CoA: - The reaction catalyzed by succinate thiokinase cleaves the high-energy thioester bond of Succinyl -CoA. This reaction is coupled to production GTP from GDP (some energy content as that of ATP, they inter converted to each other). GTP+ADP⇔ATP+GDP Succinyl-CoA + Pi + GDP → Succinate + GTP + CoA SH (Enzyme involved: Succinyl-CoA Synthetase) 5 Biochemistry Assist.Prof. Dr. Amina Al-Obaidi 2023/ 2024 Lec3- Carbohydrate metabolism Also, succinyl-CoA is formed from fatty acid with odd number of carbon atoms, and from propionyl- CoA derived from metabolism of branched _Chain `α, α`` Succinyl -CoA is used in the biosynthesis of Heme. G- Oxidation of Succinate: - Succinate + FAD → Fumarate + FADH2 (Enzyme involved: Succinate Dehydrogenase) FAD rather than NAD+ reduced coenzyme to FADH2, Because the reducing power of succinate is not sufficient to reduce NAD+. H- Hydration of Fumarate: - Fumarate catalyze the hydration of fumarate to Malate (Reversible reaction). Fumarate + H2O → L-Malate (Enzyme involved: Fumarate Hydratase) 6 Biochemistry Assist.Prof. Dr. Amina Al-Obaidi 2023/ 2024 Lec3- Carbohydrate metabolism I- Oxidation of Malate: - Malate oxidized to oxaloacetate; this reaction produces the third NADH of the cycle. L-Malate + NAD+ → Oxaloacetate + NADH + H+ (Enzyme involved: Malate Dehydrogenase) Summary Of Reaction 1. Two Carbon atoms enter the cycle as acetyl -CoA and leave as CO2. 2. The cycle doesn't involve net consumption and production of oxaloacetate and of only other intermediate. 3. Four pairs of electrons are transferred during one turn of the cycle: three Pairs of electrons reducing NAD+ to NADH+H+ and one pair reducing FAD to FADH2. 4. Acetyl-CoA + 3NAD+ + FAD + GDP + Pi + 2H2O → 2CO2 + 3NADH + FADH2 + GTP + 3H+ + CoA. Yieldd Of ATP Oxidation of one NADH by ETC➡ Formation of 3ATP. Oxidation of one FADH2 by ETC➡ Formation of 2ATP. GDP + Pi→ GTP ~ 1ATP 12ATP/Acetyl -CoA oxidized 7 Biochemistry Assist.Prof. Dr. Amina Al-Obaidi 2023/ 2024 Lec3- Carbohydrate metabolism The citric acid cycle can be regulated at several places: 1. The prime control of the citric acid cycle is the availability of NAD+ molecules. The amounts of NAD+ and NADH are controlled by the processes of the electron transport chain and the oxidative phosphorylation. These processes like the citric acid cycle occur in the mitochondria. 2. During the low levels of oxygen, the electron transport process is inhibited which results in the accumulation of NADH. Due to this there is reduction in the amount of NAD+ available for the citric acid cycle. Thus, the more the availability of oxygen, more the process of citric acid cycle takes place. 3. The enzymes that allosterically control the citric acid cycle are the isocitrate dehydrogenase and α- ketoglutarate dehydrogenase. The isocitrate dehydrogenase is activated by ADP, inhibited by NADH, inactivated by phosphorylation. The α- ketoglutarate dehydrogenase is inhibited by succinyl-CoA and NADH. 4. The acetyl-CoA production is also another limitation of the cycle. The acetyl-CoA comes from many sources. Acetyl CoA produced by pyruvate dehydrogenase can be inhibited by acetyl-CoA, NADH and ATP. The pyruvate dehydrogenase can be activated by AMP. 5. The citric acid cycle is also regulated by the availability of substrate that is used by the enzyme citrate synthase. These substrates include acetyl-CoA and oxaloacetate. 6. The cycle is also regulated according the state and energy needs of the cell. The energy state of cells varies with the work performed by the cells and the oxygen available; this affects the electron transport chain and oxidative phosphorylation which in turn affects the citric acid cycle 8 Biochemistry Assist.Prof. Dr. Amina Al-Obaidi 2023/ 2024 Lec3- Carbohydrate metabolism Glycolysis and the citric acid cycle connect to many other metabolic pathways Glycolysis and the citric acid cycle are major intersections to various catabolic and anabolic pathways Catabolic pathways funnel electrons from many kinds of organic molecules into cellular respiration Glycolysis accepts a wide range of carbohydrates Proteins must be digested to amino acids; amino groups can feed glycolysis or the citric acid cycle Fats are digested to glycerol (used in glycolysis) and fatty acids (used in generating acetyl CoA) Fatty acids are broken down by beta oxidation and yield acetyl CoA An oxidized gram of fat produces more than twice as much ATP as an oxidized gram of carbohydrate 9 Biochemistry Assist.Prof. Dr. Amina Al-Obaidi 2023/ 2024 Lec3- Carbohydrate metabolism Regulation of the cycle by the availability of ADP: - 1-_Effects of elevated ADP: -energy consumption due to muscular contraction biosynthetic reaction as other processes results in the hydrolysis of ATP to ADP and Pi → ⬆ADP→ acceleration rate of reaction that use ADP to generate ATP. The most important is oxidative Phosphorylation _Production of ATP increase until it match the rate of ATP consumption by energy requiring reactions. 2-_Effect of low ADP: - If ADP as (Pi) is present in limited concentration ➡↓Formation of ATP by oxidative Phosphorylation. The oxidation of NADH and FADH2 by ETC also stops. (Because the oxidation and Phosphorylation are tightly coupled and must occur simultaneously). As NADH and FADH2 accumulate → their oxidized form depleted → oxidation of Acetyl -CoA by CAC will inhibit owing to lock oxidized coenzymes. 11