BCH 380 1st EditionExam # 3 Study Guide Lectures: 22 – 29Chapters 19-21, 24-28 Lecture 22 ( March 18) Chapter 19: The Citric Acid Cycle Know the steps in the CAC i.e. substrates/products and reaction types. Know the enzymes and the reactions they are catalyzing. Know points in cycle where electrons are harvested and whereenergy is gained.Citric Acid Cycle (CAC) - Regulatory PointsStep/Reaction Molecules Enzyme Extra Notes- Energy gained and CO2 lost1. Condensation Acetyl CoA + Oxaloacetate to CitrateCitrate Synthase Lose CoA2. Dehydration/hydration IsomerizationCitrate to Isocitrate Acconitase3. 1st Oxidative Decarboxylation Event= capture electronsIsocitrate to alpha-ketogluturateIsocitrate DehydrogenaseNAD+ to NADHLose CO24. 2nd Oxidative Decarboxylation Event= capture electronsAlpha-ketogluturate toSuccinyl CoAAlpha-ketogluturate dehydrogenaseNAD+ to NADHLose CO25. Phosphorylation Succinyl CoA to SuccinateSuccinyl CoA SynthetaseGDP to GTPOr ADP to ATPLose CoA, Gain Pi6. Dehydrogenation,Oxidation, Harvest electronsSuccinate to Fumerate Succinate DehydrogenaseFAD+ to FADH27. Hydration Fumerate to Malate Fumerase8 Malate to oxaloacetate (will add back to acetyl CoA to Mitochondrial (m) malate dehydrogenaseNAD+ to NADHstart cycle again)- Net Gain: 3NADH, 1FADH2, 1ATP or GTP- Net Loss: 2CO2 at the regulatory points- Series of oxidation/reduction reactions in the mitochondria- take 1 acetyl CoA to 2 CO2- Primary Function: to harvest high energy electrons for proton pumping in the electron transport chain- these used to drive ATP formation from oxidative phosphorylation- Want to maximize the capture of increased transfer potential electrons while regenerating oxaloacetate- Considered aerobic because NAD+/FAD+ can only regenerate via electron transfer chain- 2 Basic Parts:1. Oxidize Acetyl CoA that was made from pyruvate to CO2 and capture the electrons2. Regenerate the starting product (oxaloacetate) to continue the cycleRegulation of CAC (where and how).- Pyruvate to acetyl CoA is important, but acetyl coA can be derived from fatty acid metabolism so needs more control- 2 Primary Control Points1. Isocitrate DehydrogenaseLecture 23 (March 23) Chapter 20: Electron Transport Chain What are the steps in the ETC with regard to e- flow for NADH and FADH2?What are the names of membrane proteins, proton pumps, mobile e- carriers and roles in e- flow? List generalities about the chemical structure of e- carriers within proton pumps and mobile carriers.Movement of Electrons and Protons Through the ETC:o Complex I (proton pump): Uses Complex II to carry electrons through complex II to complex III Accepts NADH (NADH to NAD+) electrons Pumps out 4 H+ o Complex II: Intermediate electron carrier protein  Intermediate Protein Complex II: Accepts e- from FADH2 and gives them to Q for transfer to Complex III. We lose the 4H+ pumped in Complex I.o Q: mobile e- carrier; 2e- carrier from Complex II to Complex III.o Complex III (proton pump): Uses cytochrome C to pump electrons from Complex III to Complex IV Pumps from e- from either NADH or FADH2 Pumps out 4 H+o Cytochrome C: moves electrons (one at a time instead of 2 at a time as with Q) from Complex III to Complex IV. o Complex IV (proton pump):  Pumps 2 H+ Reduces ½ O2 to form H2O = O2 is the final electron acceptor Needs 4e- to reduce oxygen to water at this terminal site of the ETC.Overall yield of pumped protons from NADH and FADH2 o 6 FADH2 o 10 NADHWhat are the Parts of the ETC:o Each component of the mitochondrial ETC has prosthetic groups that are involved in shuttling the e-.o Key among these are flavins, Fe complexes of Fe/S and heme as well as copper complexes.o All are used to stabilize e- on their way to reduce oxygen and the energy of the e- movement is used to pump protons.o Sets up concentration gradient for ATP SynthaseLecture 24 (March 25) Chapter 21: Proton-Motive Force/Oxidative PhosphorylationDefine chemiosmosis and how it relates to ATP Synthase:- The proposal that e- transport and ATP synthesis are coupled by a proton gradient acrossthe mitochondrial membrane.Structure and function of ATP synthase (important protein parts; F0 and F1 subunits).- ATP Synthase has two major domains1. Fo subunit: a proton channel domain composed of a hydrophobic subunit that spans the mitochondrial membrane (and through which the protons flow down their concentration gradient back into the matrix). These are called half channels. This subunit is also known as the C-Ring.2. F1 subunit: The place where ATP is synthesized. Has 5 types of polypeptide chains.o a3b3: alternating hexamer arranged around a g subunit and an e subunit that makes up the stalk that extends down into the a3b3 hexamer.o Also a delta subunit that is mostly structural and does not have a role in ATP synthesis.What are the rotor/stator protein parts and protein conformational changes (L,T,O)?o Synthesis of ATP occurs at the Beta subunits. As the asymmetric gamma stalk rotates, the conformation of the beta subunit changes which induces a conformational change of the beta subunit between the L, T, and O conformations.o The O à L conformation (open to loose) binds ADP and Pi. L à T (loose to tight) forms ATP and the T à O releases ATP and is open for binding more ADP and Pi Describe the mechanism for proton induced C-ring movement through half-channels.o An aspartic acid in the dimeric membrane spanning alpha helices can be protonated which induces a conformational change causing rotational movement.o After a full turn the proton from the intermembrane space is dumped back into the matrix.o Number of ATP made is dependent on number of C-ring half channels which differs between species.o We have 10 half channelsWhat is the overall ATP yield from NADH and FADH2; overall from glucose/acetyl CoA/ fatty acids.- 1 NADH pumps 10 protons, A C-Ring with 10 half-channels would make 3 ATP/10 protons. Thus the “old” but wrong number of 3 ATP per NADH that is in many books. Making ATP takes phosphate and this requires use of 1 proton/ATPThus, the best approximation for # of ATP/ NADH is 2.5. For FADH2 the best is~ 1.5In liver where FADH2 made in first stage, 5 ATP (not 3 ATPs) are made= gives total of 32ATP at theend.What happens to cytosolic NADH? Liver versus muscle.- 32 ATP for liver and Heart because of Malate Shuttle used to transport e-. And give to NADH in mitochondriaLecture 25 (April 6) Chapter 24: Glycogen DegradationReview glycogen