Biology Reference
In-Depth Information
Table 3
Mapping between the numbers in Fig. 8 and the metabolites in reactions
Index
Enzyme/Reaction
Index
Enzyme/Reaction
1
hexokinase
2
phosphoglucose isomerase
3
phosphofructokinase
4
aldolase
5
triosephosphate isomerase
6
glyceraldehyde-3-phosphate dehydrogenase
7
phosphoglycerate kinase
8
phosphoglycerate mutase
9
enolase
10
pyruvate kinase
11
lactate dehydrogenase
Fig. 6. HDN and HFPN representations of the reaction composing monomers to a tetramer. The speed of
v
1
is four times as
fast as the speed of
v
2
.
v
01
is the firing speed of the transition
T
01
.[
I
1
]([
I
2
]) represents the content of the place
I
1
(
I
2
). HPN
can not model this type of reaction, since, any reaction speed should be realized by assigning a function of values of the places
to the continuous transition.
of glucose, the catabolite activator protein (CAP) is bound to the CAP site. Since the CAP helps RNA
polymerase to bind to the promoter, the transcription of the
lac
operon can begin. This regulation
mechanism can be expressed by the HFPN of Fig. 3, consisting of only discrete elements. The place
“promoter” (
m
1) represents the status of the transcription of the
lac
operon. If this place contains
token(s), the
lac
operon is being transcribed, whereas if this place contains no tokens, transcription of
the operon does not begin. The rates of releasing CAP and repressor from the DNA are assigned to the
transitions
T
42
and
T
43
as the delay times, respectively. The production rates of CAP and repressor
are assigned to the transitions
T
63
and
T
64
, respectively, as the delay times. Each time the transition
T
65
fires, the place “promoter” receives one token. This transition fires when both of the following
conditions hold: (1) The place “CAP site” (
m
2) contains tokens (this is the case in which the protein
CAP is bound to the CAP site). (2) The place “operator” (
m
3) has no token (this is the case in which the
repressor is not bound to the operator).
