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2. Glycogen Synthesis | G6P + ATP → GLY + ADP + 2 Pi |
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This is lumping of 4 reactions G6P ↔ G1P, G1P + UTP → UDP-GLC + 2 Pi, UDP-GLC + GLYn → UDP + GLYn+1, and UDP + ATP → UTP + ADP. |
3. Glycogen Utilization | GLY + Pi + G6P |
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This is lumping of 2 reactions GLY + Pi → G1P and G1P ↔ G6P. The activity of the enzyme glycogen phosphorylase is regulated by AMP and ATP [51]; AMP acts as a positive effector (activator) and ATP acts a negative effector (inhibitor) by competing with AMP. So the reaction is controlled by CAMP/CATP concentration ratio. |
4. Glucose 6-Phosphate Breakdown | G6P + ATP → 2 GA3P + ADP |
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This is lumping of 4 reactions G6P ↔ F6P, F6P + ATP → F16BP + ADP, F16BP ↔ DHAP + GA3P, and DHAP ↔ GA3P. The activity of the enzyme phosphofructo kinase in this reaction is assumed to be regulated by the energy metabolite concentration ratio CAMP/CATP. |
5. Glyceraldehyde 3-Phosphate Breakdown | GA3P + Pi + NAD+ → BPG + NADH |
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6. Pyruvate Production | BPG + 2 ADP → PYR + 2 ATP |
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This is lumping of 4 reactions 13BPG + ADP ↔ 3PG + ATP, 3PG ↔ 2PG, 2PG ↔ PEP, and PEP+ADP → PYR + ATP. |
7. Pyruvate Reduction | PYR + NADH → LAC + NAD+
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8. Lactate Oxidation | LAC + NAD+ + PYR + NADH |
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9. Alanine Production | PYR → ALA |
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10. Pyruvate Oxidation | PYR + CoA + NAD+ → ACoA + NADH + CO2
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This reaction links between glycolysis and TCA cycle inside the mitochondrial matrix and contributes to ACoA formation from the carbohydrates. |
11. Lipolysis | TGL → GLC + 3 FFA |
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12. Triglyceride Synthesis | GLC + 3 FFA + 7 ATP → TGL + 7 ADP + 7 Pi |
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This is lumping of 3 reactions GLC + ATP → G3P + ADP, G3P + 3FAC → TGL + 3CoA + Pi, 3FFA + 3CoA + 6ATP → 3FAC + 6ATP + 6Pi. For simplicity, TGL synthesis from DHAP or GA3P (glycolysis) and FAC has been ignored. |
13. Free Fatty Acid Activation | FFA + CoA + 2 ATP → FAC + 2 ADP + 2 Pi |
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This is lumping of 2 reactions FFA + CoA + ATP → FAC + AMP + 2Pi and AMP + ATP ↔ 2 ADP. |
14. Fatty Acyl-CoA Oxidation | FAC + 7 CoA + (35/3) NAD+ → 8 ACoA + (35/3) NADH |
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This reaction producing ACoA from the activated fatty acid inside the mitochondrial matrix is highly complex. It is the result of combining 7 cycles of reactions in which each cycle consists of 4 enzymatic reactions. For simplicity, FAD and FADH2 are considered equivalent to 2/3 NAD+ and 2/3 NADH in terms of the amount of ATP production (though they consume equal amount of O2). |
15. Citrate Production | ACoA + OXA → CIT + CoA |
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16. α-Ketoglutarate Production | CIT + NAD+ → AKG + NADH + CO2
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This is lumping of 2 enzymatic reactions CIT ↔ ICIT and ICIT + NAD+ → AKG + CO2 + NADH. |
17. Succinyl-CoA Production | AKG + CoA + NAD+ → SCoA + NADH + CO2
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18. Succinate Production | SCoA + ADP + Pi → SUC + CoA + ATP |
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Because the reaction GTP + ADP ↔ GDP + ATP is in fast equilibrium, we assume the GTP/GDP ratio proportional to the ATP/ADP ratio. |
19. Malate Production | SUC + (2/3) NAD+ → MAL + (2/3) NADH |
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This is lumping of 2 reactions SUC + FAD → FUM + FADH2 and FUM ↔ MAL. FAD and FADH2 are considered equivalent to 2/3 NAD+ and 2/3 NADH. |
20. Oxaloacetate Production | MAL + NAD+ → OXA + NADH |
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21. Oxygen Utilization | O2 + 5.64 ADP + 5.64 Pi + 1.88 NADH → 2 H2O + 5.64 ATP + 1.88 NAD+
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This is a sum of several enzymatic reactions at complex I – V that constitute the electron transport chain and oxidative phosphorylation in the mitochondrial matrix. FAD and FADH2 are considered equivalent to 2/3 NAD+ and 2/3 NADH. Unlike other reactions, here NADH and NAD+ are treated as substrates rather than controllers. Furthermore, 1 NADH is assumed to produce 3 ATP (i.e., P/O ratio = 3 for substrate NADH). To account for the proton leak, the stoichiometries for NADH and NAD+ are adjusted to 1.88 and that for ATP, ADP and Pi are accordingly adjusted to 3*1.88 = 5.64. |
22. Phosphocreatine Breakdown | PCR + ADP → CR + ATP |
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23. Phosphocreatine Synthesis | CR + ATP → PCR + ADP |
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24. ATP Hydrolysis | ATP → ADP + Pi |
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25. AMP Utilization | AMP + ATP → 2 ADP |
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26. AMP Production | 2 ADP → AMP + ATP |
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