Metabolic Pathways Analysis: A Linear Algebraic Approach - Mathematical Concepts and Methods in Modern Biology - page 260

Table 8.2
r1 I − 1A 1B 1C

Exercise 8.29. Revisit Exercise 8.27 , this time using the extreme paths given by
the software to determine the proper inputs (if any) necessary for the creation of one
molecule of J by the system.

Exercise 8.30. Something interesting happens if you “turn off” an exchange flux
at I .Use ExPA to find out what happens and then explain in laymen's terms what's
going on.

Exercise 8.31. Allow I to be a system output again and use ExPA to explore what
happens if we also allow G to be a system output. Explain in simple terms what's
happening. How do changes in the exchange flux status of G relate to production of
J as a system output?

Now that we've had a chance to play aroundwith some “simple” abstract processes,
let's take a look at an actual biochemical process.
Exercise 8.32. The file rbc.expa , which comes with ExPA , is a sample file con-
taining some of the biochemistry of a red blood cell. Use ExPA to find the extreme
paths. Summarize your findings by creating a table showing only those pieces of
the extreme paths relating to exchange fluxes for the system. Afterwards, com-
pare with the graphical representations in [5], and note further discussion there of
applications.

Exercise 8.33. The following reaction represents the production ofATP formetabolic
energy and NADH for methemoglobin reduction:

2 H + + GLC + 2 Pi + 2 ADP + 2 NAD −→ 2 Pyr + 2 AT P + 2 NADH + 2 H 2 0 .

Is this something the red blood cell can do, according to the extreme paths that
you found?

Acknowledgments
The author gratefully acknowledges the support of the National Science Foundation
under DUE award #0737467. Thanks go to many linear algebra students who exper-
imented with both prototypes and other extended versions of a module, built for that
award, from which parts of it became this chapter and the supplementary materials.
Many thanks also go Robert J. Kipka for his role in preparing the final section/project,
and other contributions as a TEXpert reviewer.