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CHEM 372 Week 3 Notes

by: Joshua Torres

CHEM 372 Week 3 Notes CHEM 372

Joshua Torres
Cal Poly

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Glycolysis reactions 7-10 and Pyruvate Dehydrogenase
Dr. Jones
Class Notes
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This 9 page Class Notes was uploaded by Joshua Torres on Thursday April 14, 2016. The Class Notes belongs to CHEM 372 at California Polytechnic State University San Luis Obispo taught by Dr. Jones in Fall 2016. Since its upload, it has received 8 views. For similar materials see Metabolism in Chemistry at California Polytechnic State University San Luis Obispo.


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Date Created: 04/14/16
CHEM 372 Week 3 Notes  4/12/16 Reaction 7  1,3-BPG to 3PG using PGK as the enzyme  Slightly exergonic but is the breaking even point of Glycolysis  Close to equilibrium  Uses protein dynamics to drive reaction. Push Pull reaction mech.  Forces phosphates together till they touch and react. Swap phosphates.  Similar to hexokinase mechanism  Active site of enzyme has Lysine that points towards BPG phosphate o Pulls electron density away from phosphate group on BPG o Oxygen on ADP phosphate attacks electrophilic phosphate on BPG o Transition state is the most energetically rich molecule o Lysine on enzyme stabilizes TS to speed up reaction o Substrate level phosphorylation: phosphate group is transferred from metabolite directly onto ADP o Oxidative phosphorylation: ADP + P -i---ATP Reaction 8 o 3PG ---- 2PG, enzyme is PGM o At the active site, phosphohistidine. Absolutely required for activity o Phosphohistidine attacked by deprotonated 2’-OH o Histidine attacks 3’-PO and 3’-O deprotonates and + 3 acid (B-H ) nd o 2 step is the rate-limiting step o Intermediate (2,3-BPG) just hangs out in active site for a while, sometimes it dissociates from the enzyme o Cannot synthesize phosphohistidine complex o Red Blood Cells harness 2,3-BPG to lower the affinity for O2 – regulator of hemoglobin (allosteric inhibitor) – binding favors the T state Reaction 9 o 2PG ---> PEP using Enolase o Elimination reaction – dehydration o Enolase Active Site:  2 Mg+ ion – grab onto carboxyl group of 2PG  2 Lys – one acts as a base, the other stabilizes negative charge in TS  1 His – forms a H bond with phosphate group  1 Protonated Glu-COOH – acts as a Lewis acid o 2 Step reaction  Eliminate proton 2’-H +  Intermediate is only possible through 2Mg  Eliminate –OH from intermediate  3’-OH bond grabs H from protonated Glu  1 step is rate-limiting  Dr. Jones’ favorite enzyme mech. 2 o PEP is highly reactive and unstable Reaction 10 o PEP ---> pyruvate by pyruvate kinase enzyme o ∆G’ = -31.7 kJ/mol o PEP is very energetic and free energy can be released by tautomerization o Substrate level phosphorylation o Tightly regulated reaction o Tetramer or Dimer o Allosterically regulated by AMP and fructose-1,6- BP activate this enzyme, but ATP, Acetyl-CoA, Alanine inhibit enzyme o Inhibition  Product/feedback inhibition and regulation by Energy Charge  Acetyl-CoA is an intermediate in the production of ATP and a build-up means you don’t need more energy o Activation  AMP (allosteric regulator) is related to the EC – if AMP levels are high, so ATP levels are low and this reaction wants to proceed  F-1,6-BP earlier intermediate of Glycolysis. You want to make sure this gets used up. This is the product of the committed step in Glycolysis  Feed-forward activation  Feed-forwards inhibition o Reactant inhibits its own metabolism o Not in any biological inhibition 3  Feedback activation – doesn’t really happen o ATP accelerates Glycolysis o Product of the pathway cannot accelerate the metabolism – explosion  Pathway regulation – understand the rational behind regulation o Involves certain common features o Negative feedback o Feedback inhibition o Feed-forward activation (F-1,3-BP) o Regulating branch points  Enzyme regulation o What specific substance might activate/inhibit this enzyme  Glycolysis regulation – allosteric regulation (90%) o Activation  AMP of PFK and Pyruvate Kinase  F-1,3-BP of Pyruvate Kinase o Inhibit  G6P of Glucose  Acetyl-CoA of Pyruvate Kinase  Citrate of PFK  ATP of PFK and Pyruvate Kinase  Some enzymes are phosphorylated  Enzymes ONLY influence reaction rates, this happens in parallel with shifts in equilibrium (∆G)  If free energy is close to 0, reaction may not go 4 Mannose o Metabolized just like glucose o Mannose (by hexokinase) converted to M6P (by PMI) converted to F6P o ATP to ADP Galactose o Galactose converted to G6P o ATP to ADP (ATP hydrolyzed) Fructose o Path 1: Most tissues  Fructose (by hexokinase) converted to F6P  ATP to ADP o Path 2: Liver cells ONLY  Fructose (by Fructokinase) converted to F1P (by F1P Aldolase) converted into DHAP and Glyceraldehyde (by Triose Kinase) converted to 2 GAP molecules  ATP to ADP in every step o It bypasses F6P and PFK, so it bypasses major regulation/control point o Weakness of Glycolysis pathway  No difference in ATP content (same in vs. out)  Mannose, Galactose, Fructose are all energetically equivalent  Glucose ------> 2Pyruvate, 2ATP, 2NADH o NADH back to NAD , ATP made and O ---> 2 O 2 5 + o NADH and NAD are scarce and thus limiting reagents 3 Catabolic Pathways/Uses for Pyruvate o Lactic Acid Fermentation  Pyruvate reduced (by Lactate dehydrogenase) to L-Lactate  Reversible reaction  Work out too hard and too fast, just not enough O2 +  NADH to NAD o Ethanol fermentation  Pyruvate converted (by pyruvate decarboxylase) to acetaldehyde converted (by alcohol dehydrogenase) to ethanol  1 reaction is irreversible, 2nd is reversible and uses NADH o Pyruvate Dehydrogenase  Bridge step and irreversible because of CO 2 production in 1 step, next steps are reversible  In the matrix of the mitochondria  Single enzyme complex with 3 reactions  Most CO p2oduced through this pathway  Major product is Acetyl CoA  Acetyl CoA can be used for just about anything  Pyruvate + NAD + CoASH à Acetyl CoA + + NADH + CO + 2 6  Enzyme complex if 50 nm wide (E1 + E2 + E3)  Compartmentalize intermediates that don’t happen anywhere else in cell  SLIDE 10 week 3 st  E1 – 1 reaction and enzyme complex – irreversible  Pyruvate + TPP à CO + H2TPP  TPP is the nucleophile  And has a great leaving group  Ketone on pyruvate attacks acidic proton  Forms intermediate (very short-lived)  CO l2aves spontaneously to form negatively charged Carbonanion – irreversible  Resonance stabilized intermediate (longer- lived)  Ketone carbon becomes a hydroxyl – used for next reaction -  First of all, 2e from C1 and get other two C’s in reactive form (acetyl groups)  E2 – 2 ndreaction and enzyme – all steps reversible  HETPP + lipoic acid à TPP + acetyl dihydrolipoate  Lipoic acid – Cofactor linked to Lys -  HETPP – Reduced with 2e when going to Dihydrolipoate o Deprotonated form is active 7 o Carbanion attacks sulfur in lipoic acid and the other sulfur deprotonates base – forms intermediate o HETPP becomes re-oxidized and TPP leaves; base1 grabs proton from hydroxyl to form ketone base2 picks up a proton o TPP recycled back into E1 rxn  C-OH is oxidized and lipoic acid is reduced  Product is a thiolester  Very favorable to hydrolyze thiolester (oxidized carbon)  E3 – 3 reaction  Acetyl dihydrolipoate + CoASH + NAD à + acetyl CoA + lipoic acid + NADH  Lone pair of electrons on thiol attack carbonyl  Proton removed – sulfur steals away the proton from CoASH  Oxidatio+ of Dihydrolipoate and reduction of NAD  Reversible step with FAD as the cofactor  Transesterification of ADHL  ADHL becomes oxidized o Flow of e in pyruvate dehydrogenase complex:  Pyruvate à HETPP à Acetyl Dihydrolipoate à Dihydrolipoate à NADH o Pyruvate Dehydrogenase Reasons: 8  Harvest 2e-  Put other two carbons into a thioester which makes them easy to oxidized in later steps (Acetyl CoA) o Pyruvate Dehydrogenase Regulation:  1. E1 is activated by AMP (allosteric)  Energy Charge strikes again  Need more ATP  2. E3 is inhibited by its products (product inhibition)  Inhibited by NADH and Acetyl CoA  3. Whole complex is phosphorylated by Pyruvate Dehydrogenase Kinase (PDK); yet PDK allosterically activated by NADH and Acetyl CoA  Phosphorylation provides long-term inactivation   9


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