How do organic molecules know where to go?
  • rkandreasen August 2012
    When I am teaching the central dogma of biology: DNA-RNA-protein-trait, it strikes me that non-living molecules inside cells seem to be acting with purpose.  We speak of RNA polymerase unwinding and unzippling DNA, mRNA is formed, introns are cut out, exons are put back together, cap and tail get added, the finished mRNA goes to a ribosome where all of the appropriate tRNAs bring in the right amino acids as anti-codons match codons.  The amino acid chain gets folded into shape and goes to do whatever job it is supposed to do. 

    How do all of these molecules know to do this?  It seems like they are all acting with purpose.  Is there a deeper biochemistry that I am not aware of?  My degree was marine biology, not molecular biology, so is there really a lot more chaos than what is taught in your high school biology book? 

    Respectfully submitted,
  • SimonSimon August 2012
    Although I fear where this discussion might lead, I think one has to remember that the forces at a small (nm level) scale are quite different from those we are used to experiencing as (metre scale) organisms. Our lives are pretty much ruled by gravity whereas molecules are more influenced by hydrophobicity, surface tension, van der waals, charge-charge interactions etc. As such although videos like Harvard's "Inner Life of a Cell" represent fun ways to visualise molecular activity, the molecular dynamics they represent are probably not ever so accurate. The other thing to remember (especially if you are thinking about transcription/translation) is that there are an awful lot of mRNA trasnscripts that never get out of the nucleus let alone as far as the ribosome, so you have to try and think of these processes in terms of mass action rather than individual molecules just happening to find their way to the right place.
  • Crypto December 2012
    I think it would be incorrect to say that enzymes act according to a purpose. They are just following the laws of chemical kinetics. In other words, the different intracellular compartments are full of substrate molecules that are transformed into product molecules according to models such as Michaelis-Menten: