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Lecture Notes

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Lecture Notes BCH 403LEC

GPA 3.9
Biochemical Principles
Willsky, G R; Ponticelli, A S; Liu, T

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Biochemical Principles
Willsky, G R; Ponticelli, A S; Liu, T
Class Notes
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This 15 page Class Notes was uploaded by UBnotetaker on Monday October 19, 2015. The Class Notes belongs to BCH 403LEC at University at Buffalo taught by Willsky, G R; Ponticelli, A S; Liu, T in Fall 2015. Since its upload, it has received 24 views. For similar materials see Biochemical Principles in Biochemistry at University at Buffalo.


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Date Created: 10/19/15
Metabolism I Unit 3 Lecture 5 Slide 8 In cytoplasm we have to get these things into the mitochondria Inner membrane is the one that s impermeable things in cytoplasm not available for things in matrix TCA cycle and oxidative phosphorylation going on in MATRIX OF MITOCIIONDRIA PYRUVATE DEIIYDROGENASE ALSO going on in here So pyruvate created by glycolysis in cytosol has to get through the inner membrane of the mitochondria via transporters so it can be converted to AcetylCoA Slide 9 Need to understand that this enzyme converts pyruvate to AcetylCoA Going from 3 C pyruvate to 2C AcetylCoA so a decarboxylation reaction Also effects electronic consideration in which NADI I is involved and called oxidative decarboxylation In TCA cycle have two oxidative decarboxylation one that uses similar method to PDII and another completely different Know who are the cofactors and structures If see a reaction that has these cofactors and it s a decarboxylation then its an oxidative decarboxylation Regulation occurs in E1 where you have pyruvate decarboxylase MAJOR CONTROL POINT IN METABOLISM Really important to keep this 3C to go on for other metabolic reactions because once go 2 C you will have no net synthesis So if going to want to inhibit this entire enzyme complex you would want to inhibit it at the E1 Slide 10 KNOW STRUCTURES OF COFACTORS Slide 11 Active portion where you put the protons on for both of the FMN and FAD is the same Slide 13 Control is interesting The PDII is inactivated by phosphorylation SO you have two different forms of the enzyme If inactive one is phosphorylated the active one is not phosphorylated If involved in metabolism you have to convert from one to the other So have a phosphatase involved to take off phosphate and kinase involved to put on phosphate Have this regulation all throughout metabolism What s interesting is that the regulation is one step back Not directly controlling the enzyme itself you re controlling the kinase which is controlled by covalent modification So you will inactivate the phosphorylation by a kinase if you have ATP present because if ATP is present there is no reason to continue through the respiratory cycle to generate more ATP Instead you might go through biosynthesis to store energy so makes sense not to do the PDII Inactivation is stimulated by ATP inhibited by NAD and AMP Activation occurs by hydrolysis by phosphatase that removes the phosphate group Regulation of the amount of AcetylCoA which is the result of PDII controls the activity of the TCA cycle Slide 14 In TCA cycle there are TWO oxidative decarboxylations Coming in as AcetylCoA If doing this clearly cant have any NET GROWTH because putting in two carbons and taking two out The two carbons that come in with the AcetylCoA were NOT the ones where C02 come from off The citrate may look like a symmetric molecule to a chemist but NOT to an enzyme Have different things on either side of the carbon at citrate but once you get to the succinate you have just proton on either sides of that carbon So the enzyme cant differentiate between the two COZ groups so the enzyme can be on both portions in different outcomes Slide 15 Citrate is Prochiral and reacts asymmetrically Have represented in blue the enzyme and see which bonds are attacked in the enzyme since its not symmetrical Can radio label to see Slide 16 An asymmetric enzyme can distinguish these two groups Slide 17 If rotate the molecule and it s the same by coincidence its symmetrical IF not in the case of citrate the enzyme will recognize which end is up and will only act at one end of the molecule but for symmetrical it would go to either one since there is a plane of symmetry So the enzyme can treat it as asymmetrical from citrate to succinate but from succinate on its treated as a symmetrical molecule Slide 18 Coenzyme A has the SH Pantothenic acid is something we cant synthesize so it s a Vitamin Have ADP on the other side If don t have supply of pantothenic acid cant make CoA KNOW THE STRUCTURE Slide 19 Although don t have a heavily controlled step in the TCA cycle can think of this as the first committed step in the TCA or krebs cycle Because before this you have AcetylCoA which can be used to make fatty acids or oxaloacetate which can be used to make glucose But once you make the citrate by using citrate synthase you re committed to the TCA cycle Slide 20 Now once you have the citrate you re trying to oxidize it so you have an isomerization Isomerizations tell you that you are needing to rearrange things to enable to change the strain to change the amount of energy Not that favorable going from citrate to isocitrate through cisaconitate Just need to know that Aconitase the enzyme that does this has an ironsulfur protein and doesn t perform any electron transport Moving things around to essentially form an alphaketo acid down the road So need to hydrate and then dehydrate Slide 21 First decarboxylation occurs by isocitrate dehydrogenase Converts NAD to NADII which means it s a oxidative decarboxylation since changing electronic status Very favorable Reducing NAD to NADI I Trying to do complete oxidation of glucose to C02 and Water What doing at the end of the TCA cycle is releasing C02 so got that part but still missing water So what we re doing here now is COLLECTING reduced nucleotides NADII for example which are sitting around in the mitochondrial matrix and they have energy in them and will release it when you get to oxidative phosphorylation When we finally do that the electrons will go to water and finally finished oxidation First decarboxylation here is different than PDI I because it DOESN T have a co factor PDI I had TPP Slide 22 Second decarboxylation you have the co factors which uses same mechanism by PDI I Put in a lot of control in E1 so that was more involved than just the catalytic activity because the regulation was important Know that the complex you see for PDII is that what it has in common with the a keto Glutarate Dehydrogenase Complex is just involved in the active site which is taking away the regulation All the extra stuff in PDII has to do with how it regulates phosphorylation and dephosphorylation All regulatory systems don t exists here but from chemical point of view in the active site its changing the substrate similarly Slide 23 Do have ONE substrate level phosphorylation Now have succinyl coA and it stays on this for a while and then finally have things in form where you can take Pi and GDP to form GTP This is the only place you get the energy molecule from TCA cycle Can convert and no energy change SO THE SAME AS ATP Slide 24 Now want to get more NADII or FADI IZ out of it Need to get back to oxaloacetate so we can be a cycle So in this dehydrogenation converting it to a double bond but will make a FADIIZ FADI IZ doesn t have as much energy as NADII but still a way to store energy that we can use later Slide 25 Have hydration fumarase which forms malate Slide 26 Malate can go back to oxaloacetate to regenerate the cycle Highly unfavorable reaction but other reactions DRIVE it Slide 27 2C are in 2C are out so NO NET SYNTHESIS THERE CAN BE NO NET SYNTHESIS OF GLUCOSE WHEN USING THE TCA CYCLE CATALYTICALLY 2C IN 9 2C OUT Question Under those conditions can a carbon from acetyl group entering the cycle be found in a molecule of glucose IT CAN Concept that explains this is metabolic flux which means these are all enzymes and they all can go backwards if control is perfect Especially since the acetate carbons were NOT released in the TCA cycle as C02 So Yes you can find a molecule from the acetate that you re giving to PDH in glucose BUT THERE WILL BE NO NET SYNTHESIS OF GLUCOSE WHEN USING TCA CYCLE QUESTION Slide 28 You can drive a pathway when you have a series of things with delta G s because if you add them up the reaction of the TCA cycle is negative So the cycle as it RUNS is spontaneous under conditions that you find in the cell All the enzymes are loose and all are NOT physically together In 2nd part for fattyacid biosynthesis do have enzymes that are linked together one polypeptide chain TCA CYCLE IS A CYCLE THAT OCCURS WITHIN MITOCHONDRIAL MATRIX AND THE ENZYMES ARE FAIRLY LOOSE NOT LINKED JUST REACTING ON THE SUBSTRATE OF THE PRODUCT OF ONE MOVING ON TO BECOME THE SUBSTRATE OF ANOTHER ENZYMES NOT BOUND TO EACH OTHER Slide 29 Had glycolysis Had PDH complex Had TCA cycle where you ve gotten GTP converting to ATP So net got glucose and the reduced nucleotides Have the C02 Have all of these reduced nucleotides NADH and FADHZ Oxidative phosphorylation will get the energy out of these energy storage molecules Slide 30 Now will go into what we can use the TCA cycle for As used catalytically 2C s in 2C s out NO NET BIOSYNTHESIS Anaplerotic reactions are for doing intermediates in biosynthesis so in order to do this have to get an increase So when have metabolic fluxes we can replenish the TCA cycle intermediates called Anaplerotic reactions This results in amount of TCA cycle used in anabolism Anabolic pathway important in creating the metabolic flux from going from acetate to glucose build UP from simple to complex So what s going to happen if we re doing a biosynthetic pathway we have succinyl coA that was made and which can come and go into something else Can have citrate now coming into the pathway now pulling out succinyl coA So uses portion of the pathway as an anabolic pathway If really short of energy TCA can be going totally catalytically to make energy But if times are good and you want to do biosynthesis you still need to use energy So 90 of cycle working anaplerotically and some of the rest of the cycle going on catalytically to use energy Slide 31 Have the TCA cycle and one thing we can do is take malate to go to pyruvate and then it can make glucose again Can take these intermediates formed in TCA cycle and make them go backwards biosynthesis to produce glucose anabolic pathway TCA cycle all in the mitochondria But reactions that are making other carbohydrates are in the cytoplasm Slide 32 PEP carboxykinase is an Anaplerotic reaction it can still be seen when glucose can be made Slide 33 Pyruvate Carboxylase Biotin a B enzyme interacts with lysis Know this cofactor Biotin a vitamin Provides oxaloacetate precursors for TCA cycle when exercising and need ATP and the first step when we see gluconeogenesis from pyruvate to phosphoenol pyruvate Slide 34 PEP carbokinase converts PEP to OAA Slide 35 KNOW Pyruvate to Malate Reductive carboxylation of Pyruvate Supplies TCA cycle with Malate and other Anaplerotic reactions to get us to glucose or whatever else we wanna make It s a carboxylation reaction Slide 36 Summary of these Anaplerotic pathways that form oxaloacetate Have phosphoenolpyruvate going to pyruvate It goes to oxaloacetate Malate going to oxaloacetate Pyruvate to oxaloacetate Slide 37 Also have transamination reactions Have like glutamate and aspartate resulting in alpha keto glutarate and oxaloacetate Alpha keto glutarate is a TCA cycle intermediate Oxaloacetate is central to Anaplerotic reactions Transamination reactions go both ways So anything that involves these amino acids can be used in other transaminations to get us the alpha keto glutarate which we eventually want to use First product is keto function second is amine function Without pyridoxal phosphate nothing will happen no transaminase Slide 38 No transporter for oxaloacetate to go outside of the mitochondria to the cytoplasm to contribute to biosynthesis But if we can do a transamination reaction in going from oxaloacetate to aspartate there is a transporter for aspartate and so it can get through the inner mitochondrial membrane and when you get to the other side can have another transamination reaction In which the aspartate produces oxaloacetate So this is how you get it across the INNER mitochondrial membrane WITHOUT having a transporter Slide 39 Metabolism 1 Unit 3 Lecture 6 Slide 39 Glyoxylate shunt is something present in microorganism and shows why we cant make carbohydrate from acetate due to TCA cycle of loss of C02 When break things down use aldol cleavage Pentose phosphate pathway are system of enzymes that allow cell to interconvert different types of carbohydrates depending on what it needs Slide 40 Point A is important Need ribulose 5 phospate for DNA metabolism 5carbon Also need energy stored for anabolism in NADI l nucleotides Made NADII through glycolysis through TCA which we will convert to ATP in catabolism When want to go in other direction take energy in reduced nucleotides and use it in biosynthetics NADPlI is our source for reduced compound of energy store in anabolism Know the enzymes essentially whats going on in Pentose Pathway Slide 41 Activated acetyl moieties AcetylCoA Takes place in an organelle called glyoxysome Called glyoxylate shunt because it uses some of same enzymes and reactions from TCA but BYPASSES the steps of releasing C02 by using glyoxylate Don t see this in mammals TCA cycle is very effective because it helps produce many ATP molecules but Preserves 2 C skeleton of acetylCoA Using acetyl CoA which is a fat and making succinate carb to make glucose carb Slide 42 Make the acetylCoA by getting the fatty acids and acetate Then acetylcoA goes to citrate isocitrate and make glyoxylate by bypassing the decarboxylation Another acetyl CoA can come down and both 2 C s can join to make 4 C malate which goes up to oxaloacetate and then eventually glucose In process of doing this we do make one NADII stores energy to become ATP But in TCA we make much more energy in forms of ATP NADII FADIIZ But if you have these enzymes you can go through the oxaloacetate to make glucose from the acetyl CoA Shows you CAN go from acetate to glucose by bypassing the two decarboxylation Slide 43 DO need to know enzymes involved but not detailed reactions lsocitrate lyase splits isocitrate into glyoxylate which then gives succinate Have a malate synthase which goes from glyoxylate and acetylcoA to form Malate Slide 44 Pathway which oxidizes glucose to 5carbon sugars and NADP Used when we want to do biosynthesis which is anabolic pathway but glucose is still oxidized during process Provides NADPI I which is needed for reductive anabolic biosynthesis Know the points Slide 45 Generates NADPlI by oxidizing glucose 6 phosphate which is made from hexokinase from glycolysis DI I dehydrogenase In nonoxidative phase to the left are the enzymes available to make whatever we need Exchange keto for aldo to use it in the biosynthetic pathway Money makers are transketolase and transaldolase Slide 46 Have oxidative phase when youre taking 3 Glucose6Phosphate going to 3 Ribulose5 Phosphate lose C02 since going from 6 C to 5C but generating NADPI I important Do these when NADPI I is needed to do anabolism If doing nucleotide biosynthesis need the Ribose 5 Phosphate that will go onto nucleotides But if not doing biosynthesis an energy needs are our primary thing we need to remake glucose to go through glycolysis and TCA cycle so we do the non oxidative phase Slide 47 Important slide Shows how we can use the different metabolic needs First column doing nucleotide synthesis so doing oxidative portion and stopping right after Middle one generating NADPI l is most important How can we do this if we want NADPI I We can do the oxidative portion but if we want to do it over and over again we have a ribulose 5phosphate at the end of it Generating it by starting off with glucose 6phosphate and getting ribulose5phosphate this is how we generate NADPI I We need to get more glucose6 phosphate to continue this process for anabolism Rib 5P goes through series of reactions by the 4 enzymes of non oxidative portion and it then generates gluc 6P which we can reuse to make more NADPI I If we really want to get energy we have to do similar things because we have rib 5P wnon oxidative portion and then can convert it to glucose OR we can convert it to pyruvate and then go to Acetyl CoA TCA cycle and oxidative phosphorylation to get energy You can use Pentose Phosphate Pathway to get three metabolic needs Anabolism Nucleic Acid Biosynthesis or Energy Slide 48 Have the oxidative portion which uses 3 enzymes Go from Glu6P to Rib5P and in 2 of them we generate NADPI I So for each Glu6P that goes through this pathway we generate 2 NADPI I and lose C02 Know structures for glu 6p and rib 5p Slide 49 Just know the enzymes that can do this and by adding these reactions together you can get an overall flux 6C is glucose 3 C is pyruvate example of what is made Net response would be taking 3 5 C s and converting them to 2 6C and 1 3 C Slide 50 No co factors here Slide 51 No co factors Know the ribulose 5PII Slide 52 If she says something like transketolase from the Pentose Phosphate Pathway catalyzes isomerization THAT S NOT TRUE IT TRANSFERS TWO CARBONS OF ONE MOLECULE TO ANOTHER Transfers Slide 53 Transaldolase transfers a 3 carbon unit from a ketose to an aldose Two enzymes that can move things around and break bonds KNOW HOW THE 4 ENZYMES ARE WORKING A QUESTION OF PPP KNOW HOW IT WORKS WHAT ENZYMES INVOLVED WHICH DON39T HAVE COFACTORS AND HOW IT MOVES Question In PPP have the oxidative portion which gives us our ribulose 5P but can we form this in the PPP from 3C intermediates wo forming NADPll Can we do this without running the first part of the pathway Can ribulose 5P be generated using enzymes of the PPP from 3C intermediates lots of Pyruvate wo forming NADPII IT CAN Enzymes in the nonoxidative portion of the pathway are reversible so if look at that slide can use the C3 s and go backwards using the NON OXIDATIVE ENZYMES ONLY In oxidative phase under physiological conditions behave as one way reactions So likely to go from glu 6p to rib5p So only can use the reactions of the nonoxidative portion Clue is that all are reversible reactions and flux is controlled by mass action 0 If we wanted to make our rib 5P from our 3 Cs a lot of 3 Cs would be building up and you d make the rib5P but you d generate it to make nucleic acids in which you d take out the rib 5P Then you d have your 3 C s and the flux would be pushing it back to make more rib 5P and you d take it out to do something else Metabolism 1 Unit 4 Slide 2 ETC electron transport chain Can never have oxidation wo reduction or vice versa Point 4 reason being is because different things are at different energy levels and you can get things out of those that are at higher energy Malate Aspartate Shuttle uses NADNADlI to do electron movement Dihydroxyacetone Phosphate shuttle uses FADHZW AD which has less energy in it so everytime we do this we lose something Slide 3 Whole process of oxidative phosphorylation is called respiration Activate intermediates by making acetyl coA from pyruvate by PDII Stage 2 generates C02 and reduced nucleotide formation Stage 3 cell can transfer protons out and if that s also on a gradient that can make energy too So in oxidative portion we are going to transform the energy we have stored in the moment in reduced nucleotide formation into a proton gradient Nucleotides are more stable and can last for a while proton gradient might dissipate but when we generate it we will have the phosphorylation cycle around to make ATP from it Once we take that proton gradient and collapse it to generate ATP we will also form water in the final step of electron transport chain At end of oxidative process we have generated C02 and H20 but still need phosphorylation part to generate ATP from ADP by F1fo Synthase Finally generated C02 and H20 after all this just like if we burned the glucose in a calorimeter Respiration breathing and using same 02 to do this Slide 4 If just you were to use a calorimeter have explosive release of heat and energy which you can t use for anything Want to do everything in stepwise fashion mainly to save the energy released Here we re moving protons and when we do it in stepwise fashion we can do what s listed In biological oxidation have our oxygen being converted to water but the energy that we have harnessed from our NADPII at 3 different points in the ETC you see we can liberate enough energy to transfer some protons outside and those protons can be used to make water and used for phosphorylation Slide 5 All of this is happening in mitochondria 0xidation and then phosphorylation this part to go from ADP to ATP adding phosphate group Can continue generating NADI I in the TCA which also happens in the mitochondria to keep this cycle going to get NAD ATP is our final storage chemical much more stable than proton gradient Metabolism I Unit 4 Lecture 7 2 QUESTIONS DIRECTLY FROM PROBLEM SETS WANTS US TO KNOW TCA CYCLE A QUESTION WHAT HAPPENS TO THE ENERGY WHEN YOU GO FROM ONE PART OF THE TCA CYCLE TO ANOTHER Slide 8 TCA Cycle and OxidativePhosphorylation are all in the MITOCHONDRIA Mitochondria have the infoldings of cristae Inside the matrix have the citric acid cycle The whole oxidative phosphorylation is done in large complexes Complex 14 involved in electron transport chain ETC Complex 5 is involved with FlFo ATP synthase These complexes are not covalently bound to each other so they re like a sea of lipids fluidmosaic These complexes will PUMP PROTONS and STORING our energy in a proton gradient Since not physically touching each other we need something to shuttle the electrons between each complex Coenzyme Q Ubiquinone does just this moves between complexes 13 Then in order to get from complex 3 to complex 4 we have Cytochrome C a small protein It goes from complex 1 to complex 3 and complex 2 to complex 3 FlFo complex is actually making the ATP in the Phosphorylation part from the proton gradient The way complex 5 communicates with the other complexes is through the formation of the proton gradient Slide 9 Most enzymes are soluble since 98 of us is made up of water Intermediates therefore were diffusible at much faster rates Flux through all pathways are controlled by delta G which is dependent on concentration of substrates and products The complexes we ve seen 1 5 are integral to the membrane made up of many proteins Slide 10 Whats in these complexes of the mitochondria The inner membrane of the mitochondria is very active because gt 70 protein Only can get them out by using detergents not just salt DON T MEMORIZE TOTAL COMPOSITION OF EACH COMPLEX UNDERSTAND WHATS INVOLVED IN THE TRANSPORT HOW THEY FUNCTION AND WHATS APART OF THE CHAIN Want to look at the different things that carry electrons some carry electrons and protons Highest energy we start out with is NADH because made a lot of them in the citric acid cycle Carriers are FLAVIN and an IRON SULFUR CENTER COMPLEX 1 3 amp 4 ARE PROTON PUMPS In complex 1 going through a flavin and iron center and want to pass these electrons to complex 3 and we do it through coenzyme Q We pass it to coenzyme Q and it passes it to complex 3 If you re coming in as a lower energy level in TCA cycle had succinate and go to fumurate you go to an FAD complex which is also an ironsulf center but to get to complex 3 you also use coenzyme Q Diffuses from complex 2 to coenzyme q and from there to complex 3 When get to complex 3 have our first cytochrome also have ironsulfur center Directly we will go through cytochrome C small protein into complex 4 Complex 5 is the ATP SYNTHASE PHOSPHORYLATION PART Slide 11 So flow of electrons in ETC is spontaneous IIave these two levels where NADII is the higher oxidation state more energy Succinate comes into complex 2 where as NADII comes into complex 1 KNOW THE ELCTRON CARRIERS Slide 12 Can inhibit the electron transport chain in three ways Rotenone Amytal can inhibit transport of electrons OUT of complex 1 so once electrons come out add this inhibitor and it stops the transport Also can stop the flow in complex 3 by adding Antimycin A In complex 4 you can shut things off with cyanide azide and carbon monoxide Since it s a branched system meaning NADII comes in at complex 1 and Succinate FADII comes in at complex 2 if you stop it with Rotenone Amytal in complex 1 you can still get electrons from complex 2 due to Succinate and process continues If you stop it AFTER the branch after NADH and succinate come in lets say with cyanide the whole process stops because you ve stopped the transport of electrons from both NADH and FADIIZ you die That s why cyanide azide and carbon monoxide are LETIIAL because they stop this electron transport chain Slide 13 When think concentration of protons if chaining concentrations of proton you re changing pII Protons are positive charges ATPase will USE up these electrical and concentration gradients created by the proton Question Is the proton ejected into the mitochondrial matrix by complex 1 the same one donated by NADII WE DON T KNOW A proton disappears from one side and appears on other side This is what proton pumps does If complex 1 were to favor the dissociation of H2 9 ZII and 2 e outside mito matrix this would be similar to 2 II being pumped out of the matrix DON T KNOW THE ANSWER SO CANT SAY IT PUMPS PROTONS FROM ONE SIDE TO THE OTHER Slide 14 You SHOULD KNOW TIIESE STRUCTURES NADII FADI IZ and Ubiquinone which also has 2 hydrogens and can get rid of one hydrogen at a time FADIIZ gets rid of both of the hydrogens at the SAME time when and then you form the oxidized form Slide 15 Know the active site of where proton adds to NAD Its important to have nicotinic acid vitamin B3 because the hydrogen adds to the niacin derivative side of the NAD which is a cofactor that we get from vitamin b3 The niacin side is the active site where H adds Slide 16 Accepts it mostly in pairs Need vitamin b2 riboflavin to make the FMN Cant synthesize riobflavin Slide 17 Active site for FAD is on riboflavin which we cant synthesize so we need to take our vitamin b2 s to get riboflavin Slide 18 Have a heme structure in center of a cytochrome and the IRON is the active site should know these structures Might have a ubiquinone iron sulfur center a heme group and ask to identify Know where sites are important in NADHNADPI I which one is important anabolism one in catabolism and where is that extra phosphate in the NADPI I Slide 19 Know what the heme and iron centers look like and know that they ONLY carry electrons Slide 20 Cytochromes contain HEME By looking at the absorbance spectra we can tell whether cytochromes are oxidized or reduced Characterized a b c based on their absorption pattern They carry one electron at a time either on iron or copper Heme reaction is usually iron getting reduced But complex 4 the cytochrome has a copper iron which carries the electron Question Electrons are always transferred through iron in cytochrome systems is FALSE Slide 21 Showing the cytochrome part of a large complex and showing the active site on the right where we have our direct transfer Question We have these electron transfers enzymes that are in these complexes and pump protons effectively We can inhibit these complexes so if you have an inhibitor of the ETC protein pump does it help with acid reflux Does reducing the activity of a proton pump help acid reflux Inhibitors of proton pumps are very specific Using COZ can kill you so even though you got rid of the acid reflux you ve inhibited the e transfer which killed you These proton pumps are essentially in the mitochondria of your cells and the proton pumps you want to inhibit are the ones on your plasma membrane because those are the ones that are releasing the protons into your GI tract Slide 22 Cytochromes only carry electrons Slide 23 Coenzyme Q called Ubiquinone Diffuses across inner mitochondrial membrane faster than cytochrome because it has a hydrophobic part to it Slide 24 Only active if in membrane of mitochondria Transfer of exlectrons between complex 3 and 4 CANT BIND OXYGEN Slide 25 A and B react in an oxidation reduction reaction Slide 26 Have hydrogen going to 2 protons and 2 electrons oxidation Slide 28 For a reaction to occur it has to have a negative delta G for it to occur spontaneously so NEED DELTA E TO BE POSTIVIE KNOW Slide 29 We are not in standard conditions so we need to consider the non standard potentials We need pH 7 and want 25 degrees Gives us our electrochemical potential which is in volts Slide 30 NADII after having collected the electrons from the metabolic pathways unloads them into the mitochondrial ETC and they will go down a natural gradient and that s the energy this negative delta G from that positive delta E that we use to pump the protons BECAUSE THIS PROTON PUMPING TIITS GOING ON IS IIAPPENING AGAINST THE CONCENTRATION GRADIENT Slide 31 Reaction would be spontaneous if donate from NADII to FMN because FMN is the more positive 03 is more positive than 032 Electrons cancel each other out Slide 32 If delta E comes out to be positive it will be spontaneous There are questions to decide whether something is spontaneous or not Will give the electro potentials to use Just need to know how to deal with it You can simply think about the more positive the e the more spontaneous and you can solve the question Slide 33 At the points in between the complexes we liberate enough energy to help pump the proton AGAINST its concentration gradient Because we re things against the gradient across the membrane this whole system will fall apart if there are holes in the membrane The membrane is a very tight energetically controlled process by putting protons OUT against their concentration gradient A whole in the membrane protons will freely diffuse no gradient no oxidative phosphorylation bad for life Slide 34 NADII cannot get into the mitochondria there is NO CARRIER FOR IT So we use two shuttles glycerol phosphate and malateaspartate shuttle The malateaspartate shuttle on both sides of the barrier uses NADII NAD so no energy consequence of using that one In brain which uses FADII2 to regenerate NADII NAD the FADIIZ starts off at a lower energy and less efficient Slide 35 Have our NADH which we want to go back to NAD So we take DHAP and convert it to glycerol 3 Phosphate in the cytosol by giving the hydrogen to g3p In the inner mitochondrial membrane there is glycerol 3 phosphate dehydrogenase which takes off a hydrogen and oxidizes it which allows FAD to go to FADHZ to form DHAP This cycle continues and we can keep regenerating our NAD but at the expense of using FAD The FADHZ goes into the CoQ Slide 36 Gets more complex with this shuttle Have NADH going to NAD OAA to malate in cytosol Malate can get thrugh the inner mito membrane In matrix of mito can conver the malate to OAA but the OAA cant go back out because there s no transporter for it compartmentalization Instead take OAA and glutamine and have a transaminase to get alpha keto glutarate and aspartate and there is a transport system for this Separate enzymes for both transaminase NOT THE SAME THERE IS NO ENERGY LOSS IN THIS SHUTTLE


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