Biology Reference
In-Depth Information
T-Mode 1 is adopted when more R5P than NADPH is required, for example in rapidly dividing cells
needing R5P for the synthesis of nucleotide precursors of DNA. Most of G6P is converted into F6P and
GAP by the
GP
(
l
2,
l
3,
l
4). Transaldolase (
r
4
) and transketolase (
r
3
) then convert 2 F6P- and 1 GAP-
into 3 R5P-molecules. The reaction reads
5 G6P
+
AT P
→
6 R5P
+
ADP.
First, we recognize that we have to return to the model
P
rev
which contains all
rev
erse reactions
needed. Secondly, we observe that the process (reaction path) does not transform Gluc into Lac, hence,
does not represent a full T-vector. As a consequence, the chosen token colors are no longer appropriate.
Bearing this in mind, we construct the T-vector
[(
l
2, [ (5, ( )) ]), (l3, [ (1, ( ) ]), (
l
4, [ (1, ( ) ]), (
l
5, [ (1, ( ) ]), (
r
1, [ (4, ( ) ]),
(
r
5
, [ (2, ( ) ]), (
r
4
, [ (2, ( ) ]), (
r
3
, [ (2, ( ) ]), (
r
2
, [ (4, ( )])]
and compute its effect, yielding
ADP: D, ATP: - D, F6P: 5 'C - 2 'H - 3'x, G6P: - 5 'C,
GAP: 2 'D - 2 'H, R5P: 6 'G, Ru5P: - 4 'G + 4 'H.
Identifying all token colors with D, i.e., the effects for F6P, GAP, and Ru5P disappear, leads to the
desired overall effect
ADP: D, ATP: - D, G6P: - 5 'D, R5P: 6 'D
which exactly reflects the reaction formula above.
T-mode 2 is adopted when the needs for NADPH and R5P are balanced. Then the oxidative branch of
the
PPP
is executed, converting G6P into NADPH and R5P via
m
1 and
r
1. The reaction formula is
G6P + 2 NADP
+
+H
2
O
→
R5P + 2 NADPH + CO
2
.
For the T-vector
[(
m
1, [ (1, (
x
←
G)) ]), (
r
1, [ (1, ( ) ])]
we verify the corresponding effect
CO
2
: D, G6P: -G, H
2
O: -D, NADPH: 2'D, NADP
+
: -2'D, R5P: G.
T-modes 3 and 4 are adopted when much more NADPH than R5P is required.
T-mode 3 reads
G6P + 12 NADP
+
+7H
2
O
→
6CO
2
+12NADPH+P
i
.
It includes, apart from
l
4
and
l
2
, a reaction
l
3*: FBP
→
F6P, catalyzed by fructose-1,6-biphosphatase,
which is part of the gluconeogenesis and hence outside the scope of the
GP
/
PPP
system covered by the
models of this paper.
Note that both
l
3* and
l
3: F6P
→
FBP are irreversible.
T-mode 4, according to Stryer, 2006, is characterized by the reaction formula
3 G6P + 6 NADP
+
+5NAD
+
+5P
i
+ 8 ADP
→
5 Pyr + 3 CO
2
+6NADPH+5NADH+8ATP+2H
2
O.
If this process is expanded to start with Gluc (instead of G6P) and to end with Lac (instead of Pyr),
the result corresponds precisely to the T-invariant
τ
P
derived in the previous subsection “Effects and
T-invariants”.
