Information Technology Reference
In-Depth Information
Here we will describe metabolic networks along the perspective of the
comparison between static (anatomical, purely topological) and dynamic
(physiological, kinetic) information, highlighting the particular relations holding
between these two approaches in the biochemical regulation of cells.
a) What is a metabolic network?
Biological systems, by the exploitation of suitable energy sources, achieve
spontaneous self-organization (order) allowing them to reach high levels of
diversity and complexity by means of adaptive processes. From the
thermodynamic point of view, the actual decrease of entropy of the system,
relative to its organization, is balanced by the entropy increase of the surrounding
environment.
The whole level emergent properties of which the most basic of all being the
fact an organism can perform a metabolism sufficient to sustain its life by the
utilization of the energy embedded in the chemical bonds of lipids, carbohydrates
and proteins coming from food, impose the constraints to the molecular
organization, but these constraints can be managed in a relatively flexible way by
the microscopic level atomisms due to their extreme redundancy and richness of
interaction patterns. This allows for the display of a huge repertoire of possible
solutions that appear as equivalent in terms of the perceived result (the organisms
can live in a myriad of different environments by the use of very different energy
sources and passing through many diverse intermediate states).
The presence of multiple solutions to the same problem (and thus the basic
degeneracy of the structure/function problem in biological settings) arises very
early in biological organization: a single protein (an object in the twilight zone
between chemistry and biology) presents a multiplicity of almost equally
energetically available configurations, and this multiplicity of possible states
allows the protein to display a rich dynamics that is necessary for playing its
physiological role, moreover the same basic 'average structure' can be obtained
by completely different sequences or different 'structures' generated on demand
by the same sequence. Moreover, there are many evidences of proteins that
'moonlight', or have more than one role in an organism. The same degeneracy
holds at all the levels of biological organization from genetic regulatory networks
up to ecological communities. This is particularly evident in the case of
metabolism, looking at the myriads of possible chemical reactions transforming a
small organic molecule (metabolites) into another by one or more enzymes that,
drastically lowering the activation barrier between a reactant and a product
molecule makes the reaction kinetically feasible.
