Page 326 - Thermodynamics of Biochemical Reactions

326 Mathematica Solutions to Problems

6.1 Make the stoichiometric number matrix for reactions 6.5-17 to 6.5-19 and use it to print out these reactions.

TableForm t nu 1
-1 0 0
-1 0 -1
1 -1 0
1 0 1
0 1 -1

0 0 1

TableForm[nu,TableHeadings->{names3, {"rx 1311,1mrx 14". "rx 15")}]
rx 13 rx 14 rx 15
Glc -1 0 0

ATP -1 0 -1
G6P 1 -1 0
ADP 1 0 1
F6P 0 1 -1

F16BP 0 0 1
mkeqm[c-List,s-List]:=(*c-List is the list of stoichiometric numbers for a reaction.
s-List is a list of the names of species or reactants. These names have to be put in
I
0
quotation marks. * 1 Map [Max I#, &, -cl . s- >Map [Max [ #, 0 I &, cl . s
nameMatrix[m-List,s-List]:=(*m-List is the transposed stoichiometric number matrix for
the system of reactions. s-List is a list of the names of species or reactants. These
names have to be put in quotation marks.*)Map[mkeqm[#,sl&,ml
mkecp [ { -1, -1,l, 1,0,0 1, names31

ATP + GlC -> ADP + G6P

nameMatrix [Transpose [nu1 ,names3 1
{ATP + GlC -> ADP + G6P, G6P -> F6P, ATP + F6P -> ADP + F16BP)

6.2 Calculate the pathway from glucose to carbon dioxide and water in terms of (1) the net reaction for glycolysis, (2) the net
reaction catalyzed by the pyruvate dehydrogenase complex, (3) the net reaction for the citric acid cycle, and (4) the net
reaction for oxidative phosphorylation.

The stoichiometric number matrix for these four reactions is

TableForm[nu4,TableHeadings->{names,Automatic}l