. 2007 Apr 20;6:14. doi: 10.1186/1475-925X-6-14

Table 7.

1. Glucose Utilization	GLU + ATP → G6P + ADP
$φ_{GLU \to G6P} = V_{GLU \to G6P} (\frac{\frac{C_{ATP}}{C_{ADP}}}{K_{\frac{ATP}{ADP}} + \frac{C_{ATP}}{C_{ADP}}}) (\frac{\frac{C_{GLU}}{K_{GLU}}}{1 + \frac{C_{GLU}}{K_{GLU}} + \frac{C_{G6P}}{K_{G6P}}})$
2. Glycogen Synthesis	G6P + ATP → GLY + ADP + 2 Pi
$φ_{G6P \to GLY} = V_{G6P \to GLY} (\frac{\frac{C_{ATP}}{C_{ADP}}}{K_{\frac{ATP}{ADP}} + \frac{C_{ATP}}{C_{ADP}}}) (\frac{\frac{C_{G6P}}{K_{G6P}}}{1 + \frac{C_{G6P}}{K_{G6P}} + \frac{C_{GLY}}{K_{GLY}} + \frac{C_{Pi}}{K_{Pi}} + \frac{C_{GLY}}{K_{GLY}} \cdot \frac{C_{Pi}}{K_{Pi}}})$
This is lumping of 4 reactions G6P ↔ G1P, G1P + UTP → UDP-GLC + 2 Pi, UDP-GLC + GLY_n→ UDP + GLY_n+1, and UDP + ATP → UTP + ADP.
3. Glycogen Utilization	GLY + Pi + G6P
$φ_{GLY \to G6P} = V_{GLY \to G6P} (\frac{\frac{C_{AMP}}{C_{ATP}}}{K_{\frac{AMP}{ATP}} + \frac{C_{AMP}}{C_{ATP}}}) (\frac{\frac{C_{GLY}}{K_{GLY}} \cdot \frac{C_{Pi}}{K_{Pi}}}{1 + \frac{C_{GLY}}{K_{GLY}} + \frac{C_{Pi}}{K_{Pi}} + \frac{C_{GLY}}{K_{GLY}} \cdot \frac{C_{Pi}}{K_{Pi}} + \frac{C_{G6P}}{K_{G6P}}})$
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 C_AMP/C_ATPconcentration ratio.
4. Glucose 6-Phosphate Breakdown	G6P + ATP → 2 GA3P + ADP
$φ_{G6P \to GA3P} = V_{G6P \to GA3P} (\frac{\frac{C_{AMP}}{C_{ATP}}}{K_{\frac{AMP}{ATP}} + \frac{C_{AMP}}{C_{ATP}}}) (\frac{\frac{C_{G6P}}{K_{G6P}}}{1 + \frac{C_{G6P}}{K_{G6P}} + \frac{C_{GA3P}}{K_{GA3P}}})$
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 C_AMP/C_ATP.
5. Glyceraldehyde 3-Phosphate Breakdown	GA3P + Pi + NAD⁺→ BPG + NADH
$φ_{GA3P \to BPG} = V_{GA3P \to BPG} (\frac{\frac{C_{{NAD}^{+}}}{C_{NADH}}}{K_{\frac{{NAD}^{+}}{NADH}} + \frac{C_{{NAD}^{+}}}{C_{NADH}}}) (\frac{\frac{C_{GA3P}}{K_{GA3P}} \cdot \frac{C_{Pi}}{K_{Pi}}}{1 + \frac{C_{GA3P}}{K_{GA3P}} + \frac{C_{Pi}}{K_{Pi}} + \frac{C_{GA3P}}{K_{GA3P}} \cdot \frac{C_{Pi}}{K_{Pi}} + \frac{C_{BPG}}{K_{BPG}}})$
6. Pyruvate Production	BPG + 2 ADP → PYR + 2 ATP
$φ_{BPG \to PYR} = V_{BPG \to PYR} (\frac{\frac{C_{ADP}}{C_{ATP}}}{K_{\frac{ADP}{ATP}} + \frac{C_{ADP}}{C_{ATP}}}) (\frac{\frac{C_{BPG}}{K_{BPG}}}{1 + \frac{C_{BPG}}{K_{BPG}} + \frac{C_{PYR}}{K_{PYR}}})$
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⁺
$φ_{PYR \to LAC} = V_{PYR \to LAC} (\frac{\frac{C_{NADH}}{C_{{NAD}^{+}}}}{K_{\frac{NADH}{{NAD}^{+}}} + \frac{C_{NADH}}{C_{{NAD}^{+}}}}) (\frac{\frac{C_{PYR}}{K_{PYR}}}{1 + \frac{C_{PYR}}{K_{PYR}} + \frac{C_{LAC}}{K_{LAC}}})$
8. Lactate Oxidation	LAC + NAD⁺+ PYR + NADH
$φ_{LAC \to PYR} = V_{LAC \to PYR} (\frac{\frac{C_{{NAD}^{+}}}{C_{NADH}}}{K_{\frac{{NAD}^{+}}{NADH}} + \frac{C_{{NAD}^{+}}}{C_{NADH}}}) (\frac{\frac{C_{LAC}}{K_{LAC}}}{1 + \frac{C_{LAC}}{K_{LAC}} + \frac{C_{PYR}}{K_{PYR}}})$
9. Alanine Production	PYR → ALA
$φ_{PYR \to ALA} = V_{PYR \to ALA} (\frac{\frac{C_{PYR}}{K_{PYR}}}{1 + \frac{C_{PYR}}{K_{PYR}} + \frac{C_{ALA}}{K_{ALA}}})$
10. Pyruvate Oxidation	PYR + CoA + NAD⁺→ ACoA + NADH + CO₂
$φ_{PYR \to ACoA} = V_{PYR \to ACoA} (\frac{\frac{C_{{NAD}^{+}}}{C_{NADH}}}{K_{\frac{{NAD}^{+}}{NADH}} + \frac{C_{{NAD}^{+}}}{C_{NADH}}}) (\frac{\frac{C_{PYR}}{K_{PYR}} \cdot \frac{C_{CoA}}{K_{CoA}}}{1 + \frac{C_{PYR}}{K_{PYR}} + \frac{C_{CoA}}{K_{CoA}} + \frac{C_{PYR}}{K_{PYR}} \cdot \frac{C_{CoA}}{K_{CoA}} + \frac{C_{ACoA}}{K_{ACoA}} + \frac{C_{CO2}}{K_{CO2}} + \frac{C_{ACoA}}{K_{ACoA}} \cdot \frac{C_{CO2}}{K_{CO2}}})$
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
$φ_{TGL \to GLC} = V_{TGL \to GLC} (\frac{\frac{C_{TGL}}{K_{TGL}}}{1 + \frac{C_{TGL}}{K_{TGL}} + \frac{C_{FFA}}{K_{FFA}} + \frac{C_{GLC}}{K_{GLC}} + \frac{C_{FFA}}{K_{FFA}} \cdot \frac{C_{GLC}}{K_{GLC}}})$
12. Triglyceride Synthesis	GLC + 3 FFA + 7 ATP → TGL + 7 ADP + 7 Pi
$φ_{GLC \to TGL} = V_{GLC \to TGL} (\frac{\frac{C_{ATP}}{C_{ADP}}}{K_{\frac{ATP}{ADP}} + \frac{C_{ATP}}{C_{ADP}}}) (\frac{\frac{C_{FFA}}{K_{FFA}} \cdot \frac{C_{GLC}}{K_{GLC}}}{1 + \frac{C_{FFA}}{K_{FFA}} + \frac{C_{GLC}}{K_{GLC}} + \frac{C_{FFA}}{K_{FFA}} \cdot \frac{C_{GLC}}{K_{GLC}} + \frac{C_{TGL}}{K_{TGL}} + \frac{C_{Pi}}{K_{Pi}} + \frac{C_{TGL}}{K_{TGL}} \cdot \frac{C_{Pi}}{K_{Pi}}})$
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
$φ_{FFA \to FAC} = V_{FFA \to FAC} (\frac{\frac{C_{ATP}}{C_{ADP}}}{K_{\frac{ATP}{ADP}} + \frac{C_{ATP}}{C_{ADP}}}) (\frac{\frac{C_{FFA}}{K_{FFA}} \cdot \frac{C_{CoA}}{K_{CoA}}}{1 + \frac{C_{FFA}}{K_{FFA}} + \frac{C_{CoA}}{K_{CoA}} + \frac{C_{FFA}}{K_{FFA}} \cdot \frac{C_{CoA}}{K_{CoA}} + \frac{C_{FAC}}{K_{FAC}} + \frac{C_{Pi}}{K_{Pi}} + \frac{C_{FAC}}{K_{FAC}} \cdot \frac{C_{Pi}}{K_{Pi}}})$
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
$φ_{FAC \to ACoA} = V_{FAC \to ACoA} (\frac{\frac{C_{{NAD}^{+}}}{C_{NADH}}}{K_{\frac{{NAD}^{+}}{NADH}} + \frac{C_{{NAD}^{+}}}{C_{NADH}}}) (\frac{\frac{C_{FAC}}{K_{FAC}} \cdot \frac{C_{CoA}}{K_{CoA}}}{1 + \frac{C_{FAC}}{K_{FAC}} + \frac{C_{CoA}}{K_{CoA}} + \frac{C_{FAC}}{K_{FAC}} \cdot \frac{C_{CoA}}{K_{CoA}} + \frac{C_{ACoA}}{K_{ACoA}}})$
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 FADH₂are 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
$φ_{ACoA \to CIT} = V_{ACoA \to CIT} (\frac{\frac{C_{ACoA}}{K_{ACoA}} \cdot \frac{C_{OXA}}{K_{OXA}}}{1 + \frac{C_{ACoA}}{K_{ACoA}} + \frac{C_{OXA}}{K_{OXA}} + \frac{C_{ACoA}}{K_{ACoA}} \cdot \frac{C_{OXA}}{K_{OXA}} + \frac{C_{CIT}}{K_{CIT}} + \frac{C_{CoA}}{K_{CoA}} + \frac{C_{CIT}}{K_{CIT}} \cdot \frac{C_{CoA}}{K_{CoA}}})$
16. α-Ketoglutarate Production	CIT + NAD⁺→ AKG + NADH + CO₂
$φ_{CIT \to AKG} = V_{CIT \to AKG} (\frac{\frac{C_{{NAD}^{+}}}{C_{NADH}}}{K_{\frac{{NAD}^{+}}{NADH}} + \frac{C_{{NAD}^{+}}}{C_{NADH}}}) (\frac{\frac{C_{CIT}}{K_{CIT}}}{1 + \frac{C_{CIT}}{K_{CIT}} + \frac{C_{AKG}}{K_{AKG}} + \frac{C_{CO2}}{K_{CO2}} + \frac{C_{AKG}}{K_{AKG}} \cdot \frac{C_{CO2}}{K_{CO2}}})$
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
$φ_{AKG \to SCoA} = V_{AKG \to SCoA} (\frac{\frac{C_{{NAD}^{+}}}{C_{NADH}}}{K_{\frac{{NAD}^{+}}{NADH}} + \frac{C_{{NAD}^{+}}}{C_{NADH}}}) (\frac{\frac{C_{AKG}}{K_{AKG}} \cdot \frac{C_{CoA}}{K_{CoA}}}{1 + \frac{C_{AKG}}{K_{AKG}} + \frac{C_{CoA}}{K_{CoA}} + \frac{C_{AKG}}{K_{AKG}} \cdot \frac{C_{CoA}}{K_{CoA}} + \frac{C_{SCoA}}{K_{SCoA}} + \frac{C_{CO2}}{K_{CO2}} + \frac{C_{SCoA}}{K_{SCoA}} \cdot \frac{C_{CO2}}{K_{CO2}}})$
18. Succinate Production	SCoA + ADP + Pi → SUC + CoA + ATP
$φ_{SCoA \to SUC} = V_{SCoA \to SUC} (\frac{\frac{C_{ADP}}{C_{ATP}}}{K_{\frac{ADP}{ATP}} + \frac{C_{ADP}}{C_{ATP}}}) (\frac{\frac{C_{SCoA}}{K_{SCoA}} \cdot \frac{C_{Pi}}{K_{Pi}}}{1 + \frac{C_{SCoA}}{K_{SCoA}} + \frac{C_{Pi}}{K_{Pi}} + \frac{C_{SCoA}}{K_{SCoA}} \cdot \frac{C_{Pi}}{K_{Pi}} + \frac{C_{SUC}}{K_{SUC}} + \frac{C_{CoA}}{K_{CoA}} + \frac{C_{SUC}}{K_{SUC}} \cdot \frac{C_{CoA}}{K_{CoA}}})$
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
$φ_{SUC \to MAL} = V_{SUC \to MAL} (\frac{\frac{C_{{NAD}^{+}}}{C_{NADH}}}{K_{\frac{{NAD}^{+}}{NADH}} + \frac{C_{{NAD}^{+}}}{C_{NADH}}}) (\frac{\frac{C_{SUC}}{K_{SUC}}}{1 + \frac{C_{SUC}}{K_{SUC}} + \frac{C_{MAL}}{K_{MAL}}})$
This is lumping of 2 reactions SUC + FAD → FUM + FADH₂and FUM ↔ MAL. FAD and FADH₂are considered equivalent to 2/3 NAD⁺and 2/3 NADH.
20. Oxaloacetate Production	MAL + NAD⁺→ OXA + NADH
$φ_{MAL \to OXA} = V_{MAL \to OXA} (\frac{\frac{C_{{NAD}^{+}}}{C_{NADH}}}{K_{\frac{{NAD}^{+}}{NADH}} + \frac{C_{{NAD}^{+}}}{C_{NADH}}}) (\frac{\frac{C_{MAL}}{K_{MAL}}}{1 + \frac{C_{MAL}}{K_{MAL}} + \frac{C_{OXA}}{K_{OXA}}})$
21. Oxygen Utilization	O₂+ 5.64 ADP + 5.64 Pi + 1.88 NADH → 2 H₂O + 5.64 ATP + 1.88 NAD⁺
$φ_{O2 \to H2O} = V_{O2 \to H2O} (\frac{\frac{C_{ADP}}{C_{ATP}}}{K_{\frac{ADP}{ATP}} + \frac{C_{ADP}}{C_{ATP}}}) (\frac{\frac{C_{O2}}{K_{O2}} \cdot \frac{C_{Pi}}{K_{Pi}} \cdot \frac{C_{NADH}}{K_{NADH}}}{1 + \frac{C_{O2}}{K_{O2}} + \frac{C_{Pi}}{K_{Pi}} + \frac{C_{NADH}}{K_{NADH}} + \frac{C_{O2}}{K_{O2}} \cdot \frac{C_{Pi}}{K_{Pi}} \cdot \frac{C_{NADH}}{K_{NADH}} + \frac{C_{{NAD}^{+}}}{K_{{NAD}^{+}}}})$
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 FADH₂are 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
$φ_{PCR \to CR} = V_{PCR \to CR} (\frac{\frac{C_{ADP}}{C_{ATP}}}{K_{\frac{ADP}{ATP}} + \frac{C_{ADP}}{C_{ATP}}}) (\frac{\frac{C_{PCR}}{K_{PCR}}}{1 + \frac{C_{PCR}}{K_{PCR}} + \frac{C_{CR}}{K_{CR}}})$
23. Phosphocreatine Synthesis	CR + ATP → PCR + ADP
$φ_{CR \to P CR} = V_{CR \to P CR} (\frac{\frac{C_{ATP}}{C_{ADP}}}{K_{\frac{ATP}{ADP}} + \frac{C_{ATP}}{C_{ADP}}}) (\frac{\frac{C_{CR}}{K_{CR}}}{1 + \frac{C_{CR}}{K_{CR}} + \frac{C_{PCR}}{K_{PCR}}})$
24. ATP Hydrolysis	ATP → ADP + Pi
$φ_{ATP \to ADP} = V_{ATP \to ADP} (\frac{\frac{C_{ATP}}{K_{ATP}}}{1 + \frac{C_{ATP}}{K_{ATP}}})$
25. AMP Utilization	AMP + ATP → 2 ADP
$φ_{AMP \to ADP} = V_{AMP \to ADP} (\frac{\frac{C_{AMP}}{K_{AMP}} \cdot \frac{C_{ATP}}{K_{ATP}}}{1 + \frac{C_{AMP}}{K_{AMP}} + \frac{C_{ATP}}{K_{ATP}} + \frac{C_{AMP}}{K_{AMP}} \cdot \frac{C_{ATP}}{K_{ATP}} + \frac{C_{ADP}}{K_{ADP}}})$
26. AMP Production	2 ADP → AMP + ATP
$φ_{ADP \to AMP} = V_{ADP \to AMP} (\frac{\frac{C_{ADP}}{K_{ADP}}}{1 + \frac{C_{ADP}}{K_{ADP}} + \frac{C_{AMP}}{K_{AMP}} + \frac{C_{ATP}}{K_{ATP}} + \frac{C_{AMP}}{K_{AMP}} \cdot \frac{C_{ATP}}{K_{ATP}}})$