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CHEM 4500

by: ChasePrater

CHEM 4500 Chem 4...

GPA 4.0

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Biochemistry II
Dr. Ooi
Class Notes
biochemistry, biochem, Dr.Ooi
25 ?




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This 6 page Class Notes was uploaded by ChasePrater on Friday March 11, 2016. The Class Notes belongs to Chem 4... at Middle Tennessee State University taught by Dr. Ooi in Spring 2016. Since its upload, it has received 16 views.


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Date Created: 03/11/16
Biochem 2 Review 2 TCA cycle: Acetyl CoA is oxidized to give 3NADH, FADH2, 2CO2, GTP and 3H+ Bridging step: Pyruvate DH - Irreversible oxidative decarboxylation that removes a CO2 from pyruvate to make acetyl-CoA. - 1CO2, 1H+ and 1 NADH are made per pyruvate Pyruvate DH enzyme complex - Needs TPP (E1), Lipoic acid(E2), CoA (E2), FAD (E3), and NADH (E3) - E2 produces the acetyl CoA, and E3 regenerates the oxidized form of lipoamide Reaction 1: Regulatory step. Uses Citrate synthase - condensation of OAA and acetyl-CoA to make citrate - inhibited by citrate, ATP. NADH, and succinyl-CoA - Citrate can be used to make glucose, fatty acids, and cholesterol Reaction 2: Aconitase isomerizes citrate to isocitrate, which has an oxidizable secondary alcohol. - citrate is prochiral; only one isomer is formed. - Iron-sulfur site orients substrate. Reaction 3: Isocitrate DH - decarboxylation of isocitrate to make a-ketogluterate - first CO2 and NADH produced - inhibited by ATP and NADH - activated by Ca+, ADP, and NAD+] - product can be used to form amino acids Reaction 4: a-Ketoglutarate DH complex - decarboxylates it to form succinyl-CoA - 2nd CO2 and NADH are made. - Complex is very similar is pyruvate DH, and needs same coenzymes. - Inhibited by succinyl-CoA and NADH - Activated by Ca+ - Product can form porphyrins, Reaction 5: Succinyl-CoA synthetase - cleaves thioester bond to make succinate and GTP - Substrate level phosphorylation Reaction 6: Succinate DH - stereospecific dehydrogenation of succinate to make fumerate - only membrane bound enzyme - FADH2 is made and directly feeds electrons into the ETC through CoQ Reaction 7: Fumarase - reversible hydration of the double bond to make L-malate - very specific; only works if fumerate is in trans form Reaction 8: Malate DH - oxidation of hydroxyl group to make OAA - 3rd NADH is made Regulation of Bridging Step Pyruvate DH - Allosterically: product inhibition by ATP, NADH, and acetyl- CoA. Activated by AMP, NAD+, and CoA. Fatty acids also inhibit it. - Covalently (E1): inactive when phosphorylated - NADH and acetyl-CoA activate kinase, which adds P - Pyruvate and ADP inhibit kinase, so pyruvate DH is active - Ca+ inhibits kinase and activates phosphatase - Hormonal: Insulin activates phosphatase, favoring active form. Regulation of TCA Steps 1,3, and 4 are regulated by 1. Substrate availability 2. Product inhibition 3. Competitive feedback inhibition Amphibolic: TCA can be anabolic or catabolic because many intermediates can be used in anabolic reactions. Path QUESTIONS 1. How is Pyruvate DH regulated? - product inhibition by NADH, ATP and acetyl-CoA - Allosterically activated by AMP, NAD+ and CoA - covalent modification by phosphorylation of E1. NADH and acetyl-CoA activate kinase, which inactivates the enzyme. - Hormonal: insulin activates phosphatase, which removes the P groups and activates the enzyme. Ca+ does this too, as well as inactivating kinase. 2. How is Citrate synthase inhibited? - Citrate, succinyl-CoA, ATP, and NADH. - Succinyl-CoA competes with acetyl-CoA and citrate competes with OAA. 3. How is isocitrate DH regulated? - Inhibited by ATP and NADH - Activated by Ca+, ADP, and NAD+ 4. How is a-ketoglutarate regulated? - Inhibited by succinyl-CoA and NADH - Activated by Ca+ 5. What pathways use TCA intermediates? - Gluconeogenesis: glucose can be made from OAA - Fatty acid synthesis uses citrate - Amino acid synthesis uses a-ketoglutarate or OAA - Porphyrins and heme can be made from succinyl-CoA 6. What is the main Anaplerotic reaction? - Conversion of pyruvate to OAA by pyruvate carboxylase. - This is done when there are low amounts of TCA intermediates, which causes TCA to slow down. 7. What is the Glyoxylate Pathway? - Only in plants. - Converts 2 acetyl-CoA into OAA 8. Where is the only example of substrate level phosphorylation is the TCA? - Reaction 5. Succinyl-CoA synthetase cleaves thioester bond to form succinate and a GTP 9. What is the only membrane bound enzyme in the TCA? - Succinate DH of reaction 6 How much ATP is generated by Pyruvate DH and the TCA cycle per pyruvate? - 11. How many NADH and FADH2 are made from each glucose? - 10 NADH and 2 FADH 12. What is the most active NADH shuttle and where does it function? - Malate-aspartate shuttle, and it functions in liver, kidney, and heart. 13. Why is Glycerophosphate shuttle not as effective? - It uses an NADH to make FADH, which is only worth 1.5 ATP. 14. What drives Ca+ into the matrix and how does this effect the TCA? - because protons are pumped out of matrix, the negative charge pulls Ca+ in. - during muscle contraction Ca+ levels in the matrix increase, which activates enzymes in the TCA. 15. What is another name for ADP-ATP translocase, and what drives it? - adenine nucleotide translocase - driven by the membrane potential caused by proton gradient. 16.What is another name for Complex 1? - NADH- Coenzyme Q Oxidoreductase 17. What is the Rieske Center and where is it found? - [2Fe-2S] iron sulfur protein in complex 3, which has a Fe coordinated by two His residues instead of Cys. - 18. What cofactors go with each of the enzymes of Pyruvate DH? - TPP goes with E1 - Lipoic acid and CoA go with E2 - FAD and NAD+ go with E3 19. How is arsenic toxic? - binding to sulfhydryl groups of lipoamide, causing inactivation. 20. What enzyme in the TCA cycle uses its iron-sulfur center differently? - Aconitase uses it to orient the substrate properly 21. How is Fumarase stereospecific? - it only catalyzes the hydration of the trans form of fumarate 22. How many NADH, FAD, and GTP are made in the TCA per glucose? - 6NADH, 2FADH, and 2 GTP 23. How many pairs of electrons are carried away during one TCA cycle? - 4 pairs; 3 carried by the 3 NADH and 1 pair carried by FADH 24. What are the three general ways the TCA is regulated? - substrate availability - product inhibition - competitive feedback inhibition 25. When muscles work hard, how does this effect the concentration of OAA, and the rate of the TCA? - muscles work hard, which uses NADH. A decrease in NADH causes in increase in the formation of OAA, which will make TCA speed up. - During muscle contraction Ca+ is released, which enters the matrix and activates TCA enzymes and speeds up the process. 26. Does complex 4 have a bigger or smaller reduction potential than complex 1? - greater 27. What are the inhibitors for each of the complexes in the ETC? - Rotenone= complex 1 - Carboxin= complex 2 - Stigmatellin= comple 3 - Cyanide and carbon monoxide= complex 4 - Oligomycin= ATP synthase 28. How many electron oxidation/reduction reactions can each iron- sulfur center undergo? - one CHAPTER 18 Mitochondria Structure 2 membranes Inner membrane: - Impermeable to large polar or ionic things, but is permeable to uncharged things like water, CO2 and oxygen. - Has folds called cristae, where the proteins involved in electron transport are found. Outer membrane - very permeable - contains porins, which allow diffusion of ions and water soluble things. Matrix (inside inner membrane) - gel like that contains enzymes, substrates, coenzymes, and ions - also contains mitochondrial DNA, RNA and ribosomes. Intermembrane space - due to porins, the area between membranes has same composition of ions and metabolites as cytosol Mito. Transport Systems Rather than transporting cytosolic NADH into matrix, the reducing equivalents are transported. Malate-Aspartate shuttle - When run in reverse; cytosolic OAA is reduced to malate for transport into mito. When malate is re-oxidized in matrix to OAA,where it gives up the reducing equivalents inside. - Once NADH is inside it enters ETC. Glycerophosphate Shuttle - Common in insect flight mucles, and mammalian skeletal muscle and brain. - cytosolic DHAP is reduced to G3P as NADH is oxidized to NAD+ - G3P is oxidized back into DHAP by the membrane bound enzyme G3P DH, which makes FADH. This FADH can then enter ETC. - Not an even trade because it uses an NADH to make FADH. ADP-ATP Translocase ( adenine nucleotide translocase) - pumps ATP out of matrix and ADP in. - driven by the membrane potential because ATP has a -4 charge and ADP has a -3 charge. The ETC NADH Complex 1 - Largest of the complexes - NADH is oxidized and gives a pair of electrons to the FMN prosthetic group to form FMNH2. - FMNH2 donates one electron at a time to an iron sulfur cluster. - Coenzyme Q accepts the electrons from iron sulfur sites. - 4 protons are pumped out of matrix due to conformation change as each pair of electrons moves across complex. - CoQ then moves to complex 3. Complex 2 - accepts electrons from TCA enzyme succinate DH in form of FADH. - Electrons are given to CoQ, bypassing complex 1, therefore pumping 4 protons fewer than when NADH binds to complex 1. Complex 3 ( coenzyme Q-cytochrome c oxidoreductase) - ubiquinol (QH2) transfers electrons to cytochrome c. - contains cytochrome C1, cytochrome B, and Rieske Center. - Q cycle: process of two cycles where electrons are transferred from QH2 to cytochrome C. - Half-cycle 1: When QH2 binds, 2 protons are released and 2 electrons enter complex 3 and one goes to Rieske center to cytochrome C1 to cytochrome C, which then detaches, while the other electron goes to cytochrome B to another Q forming semiquinone. - Half-cycle 2: s second ubiquinol binds and does same things happen. The single electron the goes to cytochrome B then goes to the previously formed semiquinone, which then picks up 2 protons from matrix and re-generates QH2 that re-enters innermembrane and can be used again by complex 3. - QH2 can carry 2 electrons at a time, but cytochrome c can only carry 1 at a time. - In one cycle: 2 cytochrome C’s are reduced, 2 QH2’s are oxidized releasing 4 protons, and 1 QH2 is regenerated. Complex 4 - overall: 2 electrons are transferred from cytochrome C to oxygen - contains two heme groups and 3 copper atoms.


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