Biology Reference
In-Depth Information
CHAPTER
8
Metabolic Pathways
Analysis: A Linear Algebraic
Approach
Terrell L. Hodge
Department of Mathematics and College of Arts and Sciences Dean's Office,
Western Michigan University, Kalamazoo, MI 49008, USA
8.1 INTRODUCTION
To quote from a well-known biochemistry textbook [ 1 ], “Metabolism is the over-
all process through which living systems acquire and utilize free energy to carry
out their various functions.” Metabolism is enacted through metabolic pathways:
chains of consecutive enzymatic reactions that produce specific products for use
by an organism. As explored by biologists and biochemists, there are hundreds
of such “chains of reactions” fitting together in many complex (and sometimes
not well-understood) ways. For example, the single bacterium Escherichia coli is
known to have 600-700 metabolic reactions. Standard (bio)chemical diagrams of
such systems of reactions for multiple cellular reactions can easily take up wall-
sized charts across multiple walls. To get a sample of this (with relatively uncom-
plicated diagrams) in the case of E. coli , go to the Kegg reference pathway site
http://www.genome.jp/kegg/pathway/map/map01100.html . Similar
diagrams exist for human and animal cell metabolism, with even more complexity;
a portion is shown below in Figure 8.1 .The metabolites in a metabolic pathway are
usually taken to be the substrates, intermediates, and reactants in a chain of reactions.
So why the interest? Cellular metabolism is the complex set of chemical reac-
tions that enable a cell to extract energy and other necessities for life from nutrients,
and to build the new structures it needs to live and to reproduce. While it may not
provide a metaphysical answer to the question “Why are we alive?” metabolism
certainly provides a physical answer to the question of how our cells, and hence
ourselves, are able to exist, to grow, and, ultimately, what fails and results in death.
The study of cellular metabolism is at the heart of numerous questions and basic
research about health, such as aging, and on the emerging sidelines as a consideration
for others, such as autism. The degree of interconnectedness of our bodies and our
environment, through metabolic interactions in the cells of our gut and numerous
other cells 1 that we host there, has emerged as a hot research topic, via the study of
the microbiome (resp., metabalome), like a biosphere of the gut (resp., a complete
profile at a metabolic level). Such research suggests that a broad spectrum of modern
1 Ten times the number of our own!
 
 
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