TCA Cycle Nature s Oxygen Carbon Cycle Photosynthesis was invented by cyanobacteria and caused the oxygenation of the atmosphere In general photosynthesis drives life on earth The Three Stages of Cellular Respiration The three stages of cellular respiration are acetyl CoA production acetyl CoA oxidation and electron transfer and oxidative phosphorylation Between glycolysis and the citric acid cycle pyruvate is converted to acetyl CoA by the pyruvate dehydrogenase complex releasing CO2 In stage 1 glucose is converted to pyruvate through glycolysis releasing electrons in the process The pyruvate is converted to Acetyl CoA with the use of amino acids and fatty acids by the pyruvate dehydrogenase complex releasing CO2 In stage 2 acetyl CoA enters the citric acid cycle where it is first converted to citrate CO2 is removed twice as well as 4 electrons finally converting the citrate to oxaloacetate The electrons are used to reduce NAD and FAD to NADH and FADH2 which are electron carriers In stage 3 NADH and FADH2 donate their electrons to the respiratory electron transfer chain 2 H and O2 are combined to make water ADP and Pi combine to make ATP The TCA cycle releases 2 CO2 and electrons on reduced electron carriers The respiratory chain occurs in mitochondria in both animals and plants Pathways are connected Metabolic Networks Reactions of the Citric Acid Cycle The citric acid cycle is a catalytic cycle Acetyl CoA is first converted to citrate by citrate synthase This step is a condensation reaction with the addition of water releasing CoA SH Citrate is dehydrated to form cis aconitate by aconitase releasing water Cis aconitate is hydrated to form isocitrate which is catalyzed by aconitase as well Isocitrate undergoes oxidative decarboxylation to form ketoglutarate This reaction is catalyzed by isocitrate dehydrogenase and releases a CO2 Ketoglutarate is converted to succinyl CoA by the ketoglutarate dehydrogenase complex using the CoA SH and released CO2 This step is an oxidative decarboxylation as well Succinyl CoA undergoes substrate level phosphorylation to form GTP or ATP from either GDP or ADP and Pi catalyzed by succinyl CoA synthetase This also releases CoA SH The remaining structure is called succinate Succinate is then dehydrogenated by succinate dehydrogenase releasing FADH2 and forming fumarate Fumarate is hydrated by fumarase to form malate Malate is dehydrogenated to form oxaloacetate by malate dehydrogenase Oxaloacetate goes back through the cycle again The citric acid cycle does not always run in a cyclic fashion There are 8 reactions that start with oxaloacetate which is a 4 carbon compound The oxaloacetate is converted to citrate CO2 does not come from the acetyl CoA end it comes from the other end of the molecules STEP 1 Formation of Citrate Acetyl CoA combines with oxaloacetate to form citrate This is catalyzed by citrate and is a relatively favorable reaction Water is used up and CoA SH is released The substrates are acetyl CoA and oxaloacetate This step is strongly exothermic and acetyl CoA is hydrolyzed Citrate Synthase Citrate synthase undergoes substrate induced fit Oxaloacetate and an acetyl CoA analog bind to the active site inducing a conformational change The thioester linkage in acetyl CoA activates the methyl hydrogens and Asp375 abstracts a proton from the methyl group forming an enolate intermediate The intermediate is stabilized by hydrogen bonding to and or protonation by His274 full protonation is shown Citrate synthase is a dimmer with two domains a stiff domain and flexible domain It binds oxaloacetate first acetyl CoA cannot bind in the empty enzyme This induces a change in the flexible subunit so acetyl CoA can bind Aspartate extracts a proton and histidine provides a proton from to acetyl CoA The second step is a claisen condensation which forms citroyl CoA The third step is the hydrolysis of citroyl CoA to form citrate This causes the reaction to be highly exergonic Induced fit decreases premature cleavage of the thioester bond Claisen Condensation The enol ate rearranges to attack the carbonyl carbon of oxaloacetate with His274 positioned to abstract the proton it had previously donated His320 acts as a general acid The resulting condensation generates citroyl CoA The thioester is subsequently hydrolyzed regenerating CoA SH and producing citrate STEP 1 Formation of Citrate Step 1 is a claisen condensation STEP 2 Formation of Isocitrate via Cis Aconitate A water is removed from citrate by aconitase to form cis aconitate Water is then added in a different way by aconitase to form isocitrate This reaction is not energetically favorable Aconitase is an iron sulfur protein This step eliminates water to form cis aconitase which is bound to the enzyme Water is then added to form isocitrate This step is endergonic but is driven forward because isocitrate is quickly used up Citrate has an Fe S cluster that is good for redox reactions This coordinates the citrate through the enzyme and creates a binding site Iron Sulfur Center in Aconitase There are four irons and four sulfurs in the center of aconitase Citrate is a Prochiral Compound both ends are not equal This affects the positioning of the bonds in order for attack and active site binding CO2 is always released from the fifth carbon There is no chiral carbon but there is a prochiral carbon A prochiral carbon is one step away from being chiral and can be bound in only one way STEP 3 Oxidation of Isocitrate to Ketoglutarate Isocitrate is oxidized by hydride transfer to NAD or NADP depending on the isocitrate dehydrogenase isozyme forming oxalosuccinate Decarboxylation is facilitated by electron withdrawal by bound Mn2 releasing a CO2 Rearrangement of the enol intermediate generates ketoglutarate Two isoforms of isocitrate dehydrogenase exist NADP forms in the cytosol and may serve the production of NADPH Isocitrate is always oxidized a certain way There are 2 isoforms of isocitrate dehydrogenase one takes NAD and is found in the mitochondria The other takes NADPH and is found in the cytosol STEP 4 Oxidation of Ketoglutarate to Succinyl CoA and CO2 Ketoglutarate is converted to succinyl CoA by the ketoglutarate dehydrogenase complex This is an energetically favorable reaction and uses CoA SH and NAD The reaction also forms NADH and releases CO2 The ketoglutarate dehydrogenase complex is very similar to the pyruvate dehydrogenase complex The ketoglutarate dehydrogenase complex works in the same way as