Slide 1Slide 2Slide 3Slide 4Slide 5Slide 6Slide 7Slide 8Slide 9Slide 10Slide 11Slide 12Slide 13Slide 14Slide 15Slide 16Slide 17Slide 18Slide 19Slide 20Slide 21Slide 22Slide 23Slide 24Slide 25Slide 26Slide 27Slide 28Slide 29Slide 30Slide 31Slide 32Slide 33Slide 34Slide 35Slide 36Slide 37Slide 38Slide 39Slide 40Slide 41Slide 42Slide 43Slide 44Slide 45Slide 46Krebs cycle8A8BLine up templates 8A and 8B on your desk top.The Krebs cycle is also known as the “citric acid” cycle because it begins with synthesis of citric acid (citrate).Place the citrate card and the blue enzyme card for “citrate synthase” at the lower left.The pathway ends with oxaloacetate. We learned the structure of this compound in gluconeogenesis. There it was produced by adding a COOH group to pyruvate in Bypass I Step A.This compound has 4 C’s.Add it to the lower right of the pathway.In the Krebs CYCLE, this final product cycles back to the beginning of the pathway to make a new citric acid molecule.oxaloacetate OAA4C’sInitially, oxaloacetate (4C) joins the acetyl group (2C) from acetyl-CoA to make citrate (6C). The energy needed for the synthesis is built into Ac-CoA (a high energy thioester). A syn-thase (2 syllables) reaction has 2 chemical reactants. For synthases, a product word is used in the enzyme name instead of a substrate word.2C4C6CPRODUCT wordENERGIZEDRemove the citrate and oxalacetate cards from the template and combine them with the structure cards for other intermediates. Arrange them into groups according to the number of carbon atoms in the structure.There are two structures with 6 C’s, and one structure with 5 C’s.6C’s5C’sThere are five compounds with 4 C’s (not counting the CoA group).The two 6C molecules come 1st. Then a CO2 is released so 5C’s remain.Another CO2 is released so 4 C’s remain. That compound is rearranged into oxaloacetate (OAA), which is recycled to join to 2C’s of Ac-CoA.6 6 5 4 4 4 4 44+2 =incomingacetyl groupOAACO2CO2outgoing CO2’sCitrate is the 6C molecule which is symmetric (no chiral C’s) .Isocitrate is an isomer of citrate. It has two chiral carbons ( ).Both have 3 COOH ( ) , so they are tricarboxylic acids (TCA). The Krebs cycle sometimes is called the TCA cycle for this reason.citrateisocitrate = iso citrate = iso mer of citratetwo identical groupsRemembering that citrate is the SYMMETRIC molecule with 6C’s, set up the citrate synthase reaction at the beginning of the pathway.citrate = 6C’s, symmetricthiol ester cleavedJoining two molecules together is an unfavorable decrease in entropy.This is paid for by cleavage of a CO-S thiol ester (the CO-O product has an extended pi cloud).Add energy factor cards to your flowchart .joining (synthesis)unfavfavWhen a symmetric molecule binds to an asymmetric enzyme, the complex is asymmetric. The enzyme can distinguish between the two identical groups, react with one of them, and make a chiral product.Figure 13-3, pg 461.BiochemistryVoet & Voet (3rd Edit)Wiley (2004)In this way, the 2nd enzyme converts citrate into isocitrate. The two -CH2-COOH groups in citrate are not identical in the enzyme-substrate complex. A specific one of them reacts with the enzyme surface.citrate isocitrateThis end reacts.Conversion of citrate to isocitrate involves formation of an intermediate called aconitic acid, a third molecule with 6 carbons. This intermediate does not escape the active site. It remains bound inside the enzyme.citrate - - > aconitic acid - - > isocitrateThe enzyme first removes the atoms of water (an OH and H). Two electrons left behind form the double bond (C=C) in aconitate. Then the OH and H are pasted back onto the C=C in the opposite direction.The net result looks like sliding an OH from the center C to its neighbor.1st : dehydratase2nd : hydrataseEnzyme 2 is named for the 2nd step, adding water back to the intermediate aconitate .“aconitase”oraconitate hydrataseIn step 3 , the COOH in the middle of 6C isocitrate is released as CO2. In addition, the CH-OH group is oxidized to C=O (by removing 2 H). Thus the enzyme is both a dehydrogenase which oxidizes isocitrate, and a decarboxylase. It is called an oxidative decarboxylase. 6C’s 5C’s2 H’s remain behind2 H’s are removedisocitrateSince isocitrate is being oxidized, something else needs to be reduced.NAD+ is reduced to high energy NADH.Synthesis of high energy NADH is paidfor by release of CO2.CO2 releasedandoxidation(alcohol -> ketone)NADH madeAdd energy factor cards to your flowchart .unfavfavCO2 releasedandoxidation(alcohol -> ketone)Historically, enzyme 3 has been named for its dehydrogenase activity instead of for its decarboxylase activity. The substrate word is isocitrate.isocitrateYou should get out card set #3 and learn the names of these four compounds : linear alkanes with two COOH groups (one at each end).Oxalic acid forms the root word for the oxalogroup. This group is found in oxalo-acetate .We will study malonic acid in fatty acid synthesis.Succinate appears in the Krebs cycle, and glutaric acid forms the root word for another Krebs cycle intermediate.HOOC - C - CH2 - COOH Ooxalic acidmalonic acidsuccinic acidglutaric acidH2NWhen an amino group is added to the alpha position ( ) of the 5C species glutaric acid you get the amino acid called glutamic acid .The sidechain of the amino acid (red box) is attached to the alpha carbon.When a keto group is added to the alpha position of glutaric acid , you get the Krebs cycle intermediate called alpha-ketoglutaric acid glutaric acidglutamic acidalpha-ketoglutaric acid6C’s 5C’sThe only 5C intermediate in the Krebs cycle is alpha-ketoglutarate.Alpha-ketoglutarate and pyruvate both are alpha-keto acids, because there is a keto group at the alpha ( ) position (adjacent to a carboxyl group). PDH catalyzes : pyruvate + CoA -> acetyl-CoA + CO2 + NADH 5C alpha-ketoglutarate4C succinyl-CoA3C pyruvate 2C acetyl-CoAEnzyme 4, which is genetically related to PDH, catalyzes : alpha-ketoglutarate + CoA -> succinyl-CoA + CO2 + NADHenz # 4Enzyme 4 is called the alpha-ketoglutarate dehydrogenase multi-enzyme complex. It contains many copies of 3 kinds of subunits (E1, E2, and E3).Two high energy products are made.They are paid for by release of CO2.NADH