Information Technology Reference
In-Depth Information
In order to understand the organization of a biological system we need both
classical energy constraints and topological (energetically neutral) invariants
emerging as bottom up (not necessarily induced by superimposed energy
minimization principles) organizational principles. Even without advocating a
vitalistic principle that we consider outside the range of science, we must in any
case think of still neglected dimensions of optimisation that could be “energetic”
but outside the reach of what we nowadays call energy balances.
Nevertheless, as we said above, even if we cannot predict which of the
multiple possible routes a given metabolic process will take, we have a very
detailed and reliable picture of 'what can in principle happen' as reported in the
metabolism charts. The situation is analogue to have a map reporting all the roads
but with no indication of the relative traffic on them, we will discover in the
following that this sole information is embedded with many important
information about the whole system behaviour at the biochemical level.
b) How a metabolic network is built?
Notwithstanding the wide spectrum of diversity existing in nature, metabolic
networks of different organism show some very important invariant features.
The presence of some 'universal' molecules like ADP, ATP, CO2, H2O,
NADPH... intervening in the great majority of ongoing reactions and thus
constituting a sort of 'continuous phase' in which the network is embedded. The
ubiquitary character of these molecules implies the impossibility to consider
them as 'nodes' like the other metabolites and obliges the modeller to eliminate
such molecules from the picture in order not to distort the network architecture.
This choice is not new in network modelling: exactly the same happens with
hydrogen atoms in graph modelling of organic molecules.
A metabolic network is composed of four distinct classes of nodes (Fig. 8.2).
The first one is the strongly connected component (SCC), made of nodes each
other linked by direct paths. This is the 'central portion' of the network where the
multiplicity of possible paths giving rise to the same general behaviour in terms
of molecular profile (concentrations of different molecular species) is maximal.
The 'reactant subset' consists of metabolites entering the system as reactants
from the surrounding environment. They are called 'sources' because they can
reach the SCC, but cannot be reached from it. The third class is represented by
the 'product subset', made of metabolites that are accessible from SCC, but don't
have any connections to it. Such metabolites are positioned at the end of a given
pathway and thus exiting the system as products (sinks). The metabolites in the
last class, called 'isolated subset', are inserted in autonomous pathways with
