Draft:Biochemical cascade (quantitative)

A biochemical cascade, also known as a signaling cascade or signaling pathway, is a series of chemical reactions that occur within a biological cell when initiated by a stimulus.

A common motif found in signaling pathways is the phosphorylation cycle where a protein is phosphorylated in response to a signal and dephosphorylated to return the protein to its original state. Often, such cycles form layers or cascades, where one cycle activates the next. Given the ubiquity of phosphorylation cycles, such cycles can be considered as fundamental processing units in biochemical cascades (ref). As a result a study of their dynamics properties is of importance (ref book James Ferrell).

Many signaling proteins are phosphorylated at more than one site. For example, the proteins MEK and ERK can be doubly phosphorylated. In this case, phosphorylation is processive, meaning that phosphorylation occurs in a strict order, resulting in a two-cycle motif structure.

One of the characteristics of phosphorylation cycles is that over short periods of time that are less than the time scale for protein expression and degradation, the total concentration of protein is a constant. That is for the single cycle, the total A + AP is fixed. Likewise for the double cycle, the total A + AP + APP is fixed. The protein A is called a moiety which is conserved during phosphorylation and dephosphorylation.