Biology Reference
In-Depth Information
Table 1
Data richness of roots and branches of systems biology.
Kind of data
Pathway
modeling
Biological
cybernetics
Omics
Bottom-up
systems
biology
Top-down
systems
biology
Structural
−
−
+
+
/
−
+
Systems
dynamics
−
/
+
+
−
+
/
−
+
Components
dynamics
+
−
−
+
+
/
−
Note
: For the five different roots and branches of systems biology we discern the typical richness
(allowing for exceptions) in data of a certain kind, '
+
' indicating high richness, '
−
' poverty
of data.
3. THE FIRST ROOT OF SYSTEMS BIOLOGY: MODELS OF
METABOLIC AND SIGNALING PATHWAYS
Enzymes are the biocatalysts that enable the metabolic transformation of organic
molecules under thermodynamical conditions relevant for life on earth. Enzyme
kinetics, including its regulation by all kinds of effectors, is therefore one of
the main fields that help explain metabolism and its regulation. Most anabolic
and catabolic biochemical processes involve several reaction steps that lead, say,
from a molecule that is taken up (or stored) either to one that is incorporated
into a functional structure; or to one with less free energy, allowing part of the
released reaction energy to be used to drive other, energy-consuming reactions;
or from a degraded structure to an excretable molecule. Such multireaction
processes are thus traditionally regarded as metabolic pathways, leading from
one molecule species to another, each enzyme having its specific role within the
pathway.
3.1. Regulatory metabolic and signaling systems
All known metabolic pathways are regulated. Those that are simple enough and
sufficiently separable from the embedding system were often chosen for analysis
through mathematical modeling and simulation. The theoretical background of
such models is to be found in enzyme kinetics, the theory of dynamical systems,
and nonlinear thermodynamics (Westerhoff & Palsson, 2004). Regulation may
involve both negative and positive feedback and feed-forward control within
the pathway, and also regulation by external effectors. As pathways are usually
not completely separated from each other, regulation may also occur by direct
'crosstalk' with other pathways through shared metabolites (see, e.g., Michal,
