Biology Reference
In-Depth Information
carried out by a large enzyme complex called RNA polymerase. Preceding cell
division, the DNA is copied, and the original and the copy end up in different
daughter cells.
This set of networks that drive the synthesis of proteins on the basis of
information of nucleic acids and information concerning the status of the cell
and its environment is one that is often summarized as 'DNA makes RNA makes
protein' (see Fig. 1). It is the domain of molecular biology.
Two aspects are of additional importance here: (i) DNA is not converted
into RNA, nor is RNA converted into protein. This is a difference with a
metabolic pathway where material parts ('mass') of the first molecule ends up
in the last molecule. The gene-expression pathways only transfer information.
(ii) Where the scheme suggests a hierarchy, DNA directing RNA, which directs
enzymes, which then catalyse and hence also direct metabolism, this 'hierarchy'
is not dictatorial but 'democratic' (Westerhoff et al., 1990): The rate at which
transcription occurs depends on the binding of other proteins (called transcription
factors) to parts of the DNA close to or relating to the gene. That binding
in turns depends on the concentrations of metabolites that may bind to these,
depending on whether the transcription factors are in the proximity of the DNA
or depending on whether they have been modified chemically.
The chemical modification of transcription factors responds to the status of
intracellular metabolism and to the presence of extracellular signals, such as
light, and the presence of food. This response is achieved by yet another set
of networks. These networks specialize in this signal transduction and again
consist of pathways in which each step is catalysed by proteins. In most of these
pathways however, there is no transfer of mass from the beginning to the end.
Only information about the conditions measured at the beginning of the pathway
is reflected by the state elsewhere in the pathway.
Metabolism, gene-expression and signal-transduction constitute networks in
the dimensions of time, information and chemistry. The living cell also depends
on other networks that address the dimensions of chemistry, structure and space.
The cell itself is a membrane-bounded compartment. In eukaryotes such as mam-
mals, the cell also contains many membrane bounded subcompartments, which
house networks that can be incompatible with networks in other subcompart-
ments. Without catalysis, transport across most of the membranes is impossible,
and the transport of some macromolecules through compartments is also catal-
ysed. The DNA is folded into a complex structure with proteins called chromatin.
These networks of structure and transport through and around structures have
been well characterized. In recent years, more and more of these structures have
been shown to be displaced from equilibrium, being maintained continuously
by regulated active networks. Examples include the DNA structure, certainly in
bacteria (Snoep et al., 2002), the asymmetric lipid distribution in membranes
and the microtubular and actin networks in the cell sap.
