This one's for those of you like me, who had the "what am I doing here??" sinking feeling as they contemplated Stryer and Lehninger and the Biochem midterms. To further drive you into an abyss of despair (as if the enzyme cascades and arrows going everywhich where, punctuated only by an active site inhibitor or two, and the odd alternate 'cycle'), the June 17 issue of PLoS Biology has an article on the fourth dimension of these pathways, very familiar to physists and phospho-signaling folks, but usually ignored by biologists who study metabolism: time is the key. 

>>Chen-Shan Chin, Victor Chubukov, Hao Li, and colleagues begin to address this problem by using a novel method to track the time course of a cell's response to depletion of the amino acid leucine. They show that the time responses of upstream and downstream segments differ dramatically, and they go on to develop a mathematical model that predicts the response of the pathway to experimental perturbations.<<

For those of you already in the aforementioned depth of despair, fear not, help is at hand, in the form of an excellent synopsis in the same issue. As R. Robinson states, "a static map can't depict the complexity of a subway system in motion, and a wall chart can't capture the four-dimensional dynamism of a cell in action, because neither one captures the crucial dimension of time. It matters not only where a train is going, but when it will get there, and it matters not only whether a pathway can produce a nutrient, but how quickly it responds when the nutrient is depleted".

Robinson R (2008) The Fourth Dimension of Biochemical Pathways. PLoS Biol 6(6): e151 doi:10.1371/journal.pbio.0060151