Pyruvate Decarboxylation & Dehydrogenase Complex

Pyruvate Decarboxylation

• Pyruvate forms from glycolysis, travels to the mitochondrion, and undergoes pyruvate decarboxylation.
• For pyruvate to enter the mitochondrial matrix, it must bring an H+ and enter via a symport mechanism because it is very polar and requires H+.
• The membrane is permeable, but it is difficult for pyruvate to actually enter the matrix.
• The entire process is catalyzed by the protein complex pyruvate dehydrogenase complex.

Pyruvate Dehydrogenase Complex

• Composed of 60 subunits, 3 functional enzymes, and utilizes 5 different cofactors
• E1 (pyruvate dehydrogenase) catalyzes the first two steps, which are decarboxylation and oxidation-reduction.
• E2 (dihydrolipoyl transacetylase) transfers the acetyl group formed in steps 1 and 2 onto CoA.
• E3 (dihydrolipoyl dehydrogenase) restores the oxidized form of lipoamide.

Coenzymes utilized

• Thiamine pyrophosphate (TPP) is a prosthetic group attached to E1.
• Lipoic acid is utilized.
• CoA is used to carry the acetyl group, which is a 2-carbon component removed from pyruvate.
• FAD picks up 2 electrons and reduces NAD+ into NADH + H+.
• NAD+ gets reduced by FAD.

Key Steps

• Step 1: Decarboxylation is heavily exergonic, powering the following steps.
• Step 2: Oxidation-reduction is catalyzed by pyruvate dehydrogenase, transferring the acetyl group to lipoamide, reducing it, and oxidizing TPP.
• Step 3: The acetyl group is transferred from acetyllipoamide to CoA via dihydrolipoyl transferase (E2)
• Step 4: Regeneration of lipoamide occurs via dihydrolipoyl dehydrogenase (E3), passing electrons to FAD.

Regulation of Pyruvate Decarboxylation

• Feedback regulation is facilitated by covalent modification (Pi).
• Acetyl-CoA and NADH + H+ regulate E2 and E3, respectively, by phosphorylating a protein kinase, which phosphorylates E1 and E2, making them inactive.
• Ca2+ and Mg2+ promote pyruvate decarboxylation by inactivating protein kinase and activating phosphatases, which remove phosphate from the pyruvate dehydrogenase complex, allowing it to proceed.
• High energy charge of the cell (high ATP, low ADP) inhibits pyruvate decarboxylation by phosphorylating the complex.
• A low energy charge of the cell (low ATP; high ADP) will dephosphorylate the complex.
• If citrate is high, the TCA cycle functions and the system does not need to be overwhelmed with incoming Acetyl CoA.
• If NADH is high, it either means that ATP production isn't necessary, or the ETC is backed up by O2 malfunction or deficiency (oxygen deprivation).

The Citric Acid Cycle (TCA)

• It is an amphibolic pathway (catabolic and anabolic, depending on pathway taken)
• cellular respiration cycles yield 2 NADH + 2 ATP in glycolysis, 2 NADH in transition, 6 NADH, 2 FADH, and 2 GTP in the Kreb's cycle
• In total, it contains 38 ATP (40% effective).

Side Pathways Include

• Phosphoenolpyruvate carboxykinase
• Pyruvate Carboxylase
• Fatty Acids

Malate Dehydrogenase

• Reversible reaction, oxidizes Malate into oxaloacetate.

Fumerase

• Preforms a hydration reaction with a Carbanion intermediate and is a reversible reaction.

Citrate Synthase

• Condenses oxaloacetate and Acetyl-CoA.
• Irreversible enzyme.
• Not regulated by anything other than concentration.
• High citrate inhibits PFK1 of glycolysis because it indicates an adequate glycolysis process.

Aconitase

• Facilitates dehydration/rehydration steps by utilizing [4Fe-4S] cluster and forms Cis Intermediate.
• Cytoplasmic aconitase regulate iron production, and can reversibly form Iron-sulfur clusters states.

Isocitrate Dehydrogenase

• Oxidizes Isocitrate

Succinate Dehydrogenase

• Catalyzes dehydration utilizing FAD as a cofactor.
• The reduction potential of FAD favors C-C to C=C bond formation

Succinyl-CoA Synthase

• Also referred to as the misleading name, succinyl-phosphate intermediate forms hydrolyzing thioester bonds off and harvesting enough energy to add a phosphate group.
• CoA is released here.
• Enzyme-histidine takes the phosphate group back off, then uses it to perform substrate-level phosphorylation of GDP.

Anapleurotic Reactions

• Can "back fill" Kreb's Cycle at Intermediates
• Fatty acid breakdown can only form Acetyl CoA, so the condensation reaction that allows the cycle to continue requires a 1:1 ratio of Acetyl CoA to oxaloacetate
• Oxaloacetate can produce more glucose, which can create sugars into Fats but cannot make sugars
• Plants are capable of this.
• Seeds store plant energy in an macylglycerides, therefore they generally store a higher percentage of fats rather than sugar for long term storage.

Glycoxylate Modifications

• Glycoxylate cycle will bypass oxidative decarboxylations, thereby retaining 2 carbons that are generally lost as Co2.
• Enables the carbons to recycle efficiently.
• This process allows plants to convert fatty acids into sugars.

Oxidative Phosphorylation and the Electron Transport Chain

• The membranes selectivity drives the electron transport chain.

Malate-Aspartate Shuttle

• Birds can bypass this shuttle and lose some energy in the process or roughly 2 ATP.
• Overview of oxidoreductase reactions and electrochemistry of the electron transport chain
• Oxidation occurs at the Anode, Reduction occurs at the cathode
• If Standard EMF valve is positive, it likes to be reduced and vise versa.
• NADH has Ecell equaling -0.32 v, meaning it likes to get oxidized, but Oxygen has E°cell of + 0.82v meaning it likes to get reduced.
• Standard Free Energy is −220 kJ/mol
• 02 -> H20 is the ideal "reduction-potential" to yield electrons

Electrons Transportation Details

• Complex II Succinate Dehydrogenase FAD
• Succinare to Fumerate results in 2 ATP's instead of
• Cyanide Poisioning inhibits Complex II, killing cells.
• Fmn can exist in reduced, oxidized or semiquinone format, however Because NADH is the ideal election donor, it only fluctuates in mammals.
• Coenzyme Q can exist as CoQ (oxidized), QH (semiquinone/radicalized) or QH2 (Fully reduced).
• Cytochrome C can only accept 1 electron at a time
• Cytochrome C an major initiator of apoptosis
• Contains iron-sulfer cluster called "Rieske Center"

Q-Cycle

• NADH OR FAD will lose all electrons at the eventual reduction into QHz form
• the 2 required QHz will get regenerated and also reduced.
• QH₂ binds to the Qo site, le is passed to the iron-sulfer cluster (pumps 2 H+ out)
• the radicalized QH then pass the election to heme b₂, leaving an oxidized CoA and allowing the NADH cycle to continue.

Class Practice Problems

• Deficiency of Pyruvate dehydrogenase and a severe E3 Subunit mutation would result in Pyruvate increase, leading to severe lactic acid build up (lactic acidosis).
• In effort to treat a patient with E1 of PDH, increase Vitamin B, thiamine, intake.

Jogging Effects

• When starting to jog and becoming short of breath the Following can be observed.
  • NADH increases because Oz not readily available in ETC.
  • ATP decreases blc Its being used for muscle contraction.
  • α-ketogluterate decreases due to Innibition by increased amounts of NADH
• key substrates of the kreb's cycle inhibited by NADH are lsocitrate dehydrogenase and α-ketogluterate dehydrogenase.
• 1 NADH theoretically should be able to yield 7 ATP.
• the enzyme of krebs cycle that produces nucleoside triphosphate is Succinyl CoA Synthase.
• pyruvate decarboxylation reaction occurs in mitochondrial Intermembrane Space
• Once Pyruvate forms from glycolysis, It travels to the mitochondrion.
• Pyruvate must bring a H+ and enter via a symport mechanism because it is polar and requires H+.
• The membrane is permeable, but difficult to enter the matrix.
• The entire process is catalyzed by a protein complex.
• Pyruvate dehydrogenase complex is made up of 60 subunits, 3 function enzymes, and utlizies 5 cofactors.
• Pyruvate dehydrogenase catalyzes the first two states (decarbox;oxidation-reduction)
• Dihydrolipoyl transacetylase transfers acetal gorup fomed onto CoA
• Dihydrolipoyl dehydrogenase restores oxidized form of lipoamide
• Coenzymes utilized include, Thiamine Pyrophosphate (Tpp) with a prosthetic group attached to El, Lipoic Acid ,COA which is used to cartt the acetyl group, Fad picks yo 2 electrons, Nad gets reduced by Fat

Steps To Creating Energy

• 1 Decarboxylation is heavily exergonoic for powering steps
• 2 Oxidation- reduction
• 3.Acetly group transeferred from acetyllipoamide to CoA
• 4 lipoamide Regenerated

Regulation of Pyruvate Decarboxylation

• Feedback regulation is facilitated by covalent modification
• Acetyl-coA and NAHD determine enzymes
• Magnesium and calcium both promote pyruvate decarboxylation.
• High energy inhibits decarboxylation and vice versa.

Citric Acid Cycle

• Amplipathic pathway depending on path taken
• Side pathways include several enzymes
• Malate Dehydrogenase oxidizes material
• Fumerase prefroms a Hydration reaction
• Citrate synthase combines elements
• Acotinase facilitates dehydration

Succinate Details

• Succinate dehydration favors C-C bonds
• Succinyl- COA uses a histadine to promote function
• Can backfill at intermediates
• Glycolosate cycles work to improve glucose yields

Electron Chains and Transport

• Membrane selectivity drives this
• Bypass option for birds yields less atp
• Electrohemistry is red cat ox system
• Electon potentials are 1/1 on reduction and oxidation forms
• 02-120 is large harvesting product
• Cyanide inhibits cycle
• 7theoretical atp for each nadh
• Cytocrome has heme grps and cytocrome C initiates apoptosis
• Nad and ofad are recued into different forms
• Coh2 binds, allows 2H to go on cycle

Explore pyruvate decarboxylation, its journey to the mitochondrion, and the role of the pyruvate dehydrogenase complex. Catalyzed by a protein complex, this process involves enzymes and cofactors. Learn about the enzymes and coenzymes utilized in this reaction.