by Andre on 2 February 2006
Ribosomes are the organelles inside all of your cells that translate the genetic code (sent from the nucleus as messenger RNA) into proteins – they take the information coded in your genome and turn it into molecular parts that do the work of life. When I first learned about ribosomes I was taught how they read along a strand of messenger RNA and take in complementary free floating transfer RNAs with amino acids attached to them. If the sequence on the transfer RNA matches the current sequence of the messenger RNA then it is accepted and the transfer RNA’s amino acid is added to a growing chain of protein. When I say that the transfer RNA is complementary to the messenger RNA I mean that the sequence of bases that they each present line up with A’s and U’s together and C’s and G’s together. This is the Watson-Crick type pairing that all students of molecular biology are familiar with. It’s a beautiful system and it’s illustrated quite nicely in this video with structurally correct ribosomes from the Ramakrishnan group at Cambridge. This story goes a long way towards explaining how nature makes something useful out of the information stored in DNA, but it runs into a problem that should be appreciated by anyone interested in how biology works: small is different.
The macro world we’re used to and the micro (dare I say nano?!) world of molecular biology are fundamentally different. Studying molecular biophysics is like watching a chaotic thermal ballet. All the players are constantly dancing and you need to be strong to avoid being randomized. How strong? Strong compared to thermal fluctuations whose characteristic energy scale is Boltzmann’s constant times temperature. This condition is so important that biophysicists report energies in units of k*T. If a bond has an energy around k*T is won’t last long. If, on the other hand, a bond has an energy of around 150 k*T like a single covalent bond, it will persist for a long time and its formation will be basically irreversible. And this brings us back to the ribosome.
If a ribosome is to accurately make proteins (it must, and it does: a few mistakes in 10 000 amino acid additions) the reasoning in the last paragraph suggests that the energy difference between a correct base pairing and an incorrect base pairing must be significantly larger than k*T, otherwise random thermal fluctuations could kick out a correct transfer RNA and force in an incorrect one resulting in a modified and probably less functional protein. Unfortunately for our simple view, the critical energy is only a few k*T.
There are two mechanisms that take place during the translation process that complicate our picture, but provide a possible resolution to our dilemma. The first, proposed by J. J. Hopfield in 1974, is called kinetic proofreading. It works because the unbinding of an incorrect transfer RNA is faster than the correct one and if this ‘proofreading’ is done twice (two steps are separated by a common biochemical energy source: irreversible phosphate hydrolysis) it can greatly increase translation specificity. The other mechanism is called induced fit in which the ribosome actively selects the correct transfer RNA based on its shape. Both of these processes have been confirmed by elegant fluorescence and biochemical experiments whose details will have to wait for another post.
While details are interesting (did you know that many common antibiotics work by binding to bacterial ribosomes and so are intimately connected to the details of translation?) they are not today’s take home message. The point I would really like to get across is that a little physical insight can go a long way: without necessarily knowing the solution, it is not too hard to reason that complementary base pairing is not the be-all and end-all of translation – something else has to be going on. These kinds of estimates are indispensable tools in evaluating arguments especially in the world of the cell where everyday intuition can break down.