Page 328 - Thermodynamics of Biochemical Reactions

328 Mathematica Solutions to Problems

(a) The stoichlometric number matrix for glycolysis

TableForm[nu2,TableHeadings->{n~es2,{1,2,3,4,5,6,7,8,9,lO}}l
1 2 3 4 5 6 7 8 9 10
G1 c - 1 0 0 0 0 0 0 0 0 0
ATP - 1 0 - 1 0 0 0 1 0 0 1
ADP 1 0 1 0 0 0 -1 0 0 -1

NADOX 0 0 0 0 0 - 1 0 0 0 O
NADredO 0 0 0 0 1 0 0 0 0
Pi 0 0 0 0 0 - 1 0 0 0 0
G6P 1 - 1 0 0 0 0 0 0 0 0
F6P 0 1 - 1 0 0 0 0 0 0 0

FBP 0 0 1 - 1 0 0 0 0 0 0
DHAP 0 0 0 1 - 1 0 0 0 0 0
13BPG 0 0 0 0 0 1 -1 0 O 0
3PG 0 0 0 0 0 0 1 - 1 0 0

2 PG 0 0 0 0 0 0 0 1 - 1 0
PEP 0 0 0 0 0 0 0 0 1-1
GAP 0 0 0 1 1 - 1 0 0 0 0
PY r 0 0 0 0 0 0 0 0 0 1

This is Fig. 6.1.
(b) Use mathematica to type out the reactins of glycolysis

mkeqm [c-List , s-List ] : =Map [Max [ #, 01 &, -cl . s->Mag [Max I#, 01 &, Cl . S

nameMatrix [m-Li S t , s-Lis t 1 : =Map [mkeqm [ # , s 1 & ,ml

{ATP + GlC -> ADP + G6P, G6P -> F6P, ATP + F6P -> ADP + FBP, FBP -> DHAP + GAP,
DHAP -> GAP, GAP + NADox + Pi -> 13BPG + NADred, 13BPG + ADP -> 3PG + ATP,
3PG -> 2PG, 2PG -> PEP, ADP + PEP -> ATP + Pyr}

(c) Equation 6.1-3 (v.s = nunet) is given by

nu2.{1,1,1,1,1,2,2,2,2,2}