Sunday, August 19, 2012

Generality and Contingency.

There's an interesting post over at In the Pipeline regarding the nature of how enzymes work, and it has inspired excellent comments (as is par for the course at ItP).  One notion comes up that if so-called generalized mechanisms can't be devised, it's a failure of sorts for chemists.

My question - the photosynthetic reaction center is an enzyme (oxidoreductase).  Dinky soluble proteins that do isomerizations are enzymes.  Metalloproteins that rip apart chemical bonds are enzymes.  Some proteins float around in the cytoplasm.  Others are embedded are in a membrane of some sort or another.  Others exist at a membrane/solution interface.  Others are extruded from the cell to go do their thing in the cell's environment.  So, how general can a mechanism be for an enzyme? 

One of the things that is often brought up is that there's an element of historical contingency to consider when examining the history of life on this planet.   While we obviously can't just throw up our hands in defeat to try and understand the mechanistic details of biological chemistry, neither can we truck along without acknowledging that context and history are important aspects of the grander scheme.

If that is still not comforting, perhaps one can find some solace in Kornberg's reminder to trust in the universality of biochemistry.  Consider it a tradeoff - while your one enzyme might not shed light on all enzymes, it can shed light on the same enzyme (or similar ones) across many organisms, from the modestly-scaled unicellular beasties to the gargantuan eukaryotes that now populate the Earth.  Read more!