BIOCHEMICAL PATHWAYS AND PROCESSES
Biochemical processes mediate
the interaction of cells with their environment and are responsible for most of
the information processing inside the cell. Networks of interacting proteins
underlie many of these processes. Three major types of biochemical processes
are distinguished:
Metabolic
pathways are sequences of chemical reactions, each catalyzed by an enzymes, where
certain product molecules are formed from other small substrates. Metabolites
are usually small molecules while enzymes are proteins.
Signal
transduction networks are pathways
of molecular interactions that provide communication between the cell membrane
and intracellular end-points, leading to some change in the cell. Signals are transduced by modification of
one protein’s activity or location by another protein.
Gene regulation circuits determine
whether or not a particular gene is expressed at any particular time.
Transcription factors, proteins that promote or repress transcription, either
directly or indirectly bind regulatory DNA elements.
Metabolic, transduction and
regulatory circuits are interleaved and integrated. For example, gene
regulation circuits are fed by external signals transmitted by signal
transduction pathways. The high complexity of these systems makes their proper
understanding difficult. The BioSPI
project is addressing this challenge by developing a novel framework
for the representation, simulation and analysis of biochemical processes in
the pi-calculus and related process
algebras.
More info and resources on biochemical
pathways can be found here.