Topic: Kinetic Proofreading - how the cell uses free energy to increase fidelity of translation. We'll study a sample mechanism describing the exchange of free energy for information.
Reading: Uri Alon, An Introduction to Systems Biology, Chapter 9
Meeting Summary
As planned, we followed Uri Alon's discussion of kinetic proofreading. In brief, Alon shows how the presence of an irreversible process can increase fidelity of translation well beyond what is expected from equilibrium binding-affinity arguments. Alon correctly points out that an "irreversible" process requires energy input (though in reality no molecular process is truly irreversible - it's just that reverse events are highly unlikely). In other words, the cell expends free energy to gain fidelity or information. Personally, I think it's incredible to get some insight into this at the molecular/mechanistic level.
Because Alon's discussion is vague on the molecular players and the means of energy input, we augmented our discussion with the discussion of translation in big Alberts (Ch 6, Section on "From RNA to Protein"). The following sketches give insight into what we learned and fill out some details omitted from Alon's schemes:
