Biology Reference
In-Depth Information
Fig. 8. A part of the glycolytic pathway consisting of glucose (Gluc), glucose 6-phosphate (G6P), fructose 6-phosphate (F6P),
fructose 1,6-diphosphate (FBP), dihydroxyacetone phosphate (DHAP), glyceraldehyde 3-phosphate (GAP), 1,3-diphosphoglyc-
erate (1,3-BPG), 3-phosphoglycerate (3PG), 2-phosphoglycerate (2PG), phosphoenolpyruvate (PEP), and pyruvate (Pry).
Main pathway from glucose to pyruvate acid
m
39
), and
pyruvate (
m
40). Default continuous places are introduced at this step though these places are meant to
represent the concentrations of the corresponding substrates. Then, by following the pathway in Fig. 8,
we put continuous transitions (
T
83
−
First we create continuous places corresponding to glucose (
m
6), intermediates (
m
31
−
T
92
) together with normal arcs between two consecutive places in
the pathway. These transitions and arcs shall represent the reactions, but default transitions and arcs are
initially introduced without any parameter tuning. By considering the natural degradation of substrates,
we put continuous transitions
T
17
for glucose and
T
23
−
T
31
for intermediates with normal arcs. By
taking into account the fact that natural degradation is very slow in glycolysis, the firing speed of these
transitions is given by the formula
mX/
10000
, where
X
=17
,
23
,
24
,...,
31
.
Production of ATP from ADP and NADH from phosphoric acid
Next we consider ADP, ATP, Pi (phosphoric acid) and NADH. In the pathway shown in Fig. 8, two
ADP molecules and two Pi's are invested to produce four ATP molecules and two NADH molecules.
Continuous places “ADP” (
m
12), “ATP” (
m
51), “Pi” (
m
52, initial value
=
200), and “NADH” (
m
53)
