In class today we discussed three mechanisms for how enzymes function. These three mechanisms are:
1. Bringing substrates together in a way that promotes the appropriate interaction.
2. Another way they function is to couple exergonic and endergonic reactions.
3. They also lower the Activation Energy of the reactions they catalyze
Ashley asked a good followup question: how, exactly, do enzymes lower the activation energy in reactions?
I’ve looked around for a good explanation of this without finding much satisfaction. One explanation found on Wiki.answers was that, according to the induced fit model, when substrates bind to enzymes, there is strain put on the molecule that promotes the reaction. But this answer felt unsatisfactory for a couple reasons: First, it was unsupported by any links to primary data and second, it’s really only a partial answer – i.e., does it take energy to get the enzyme into this strained conformation? If so, where does that energy come from (perhaps the particle’s movement?) If it doesn’t require energy, why do the substrates get themselves into this position?
Enzyme placing strain on substrate
A better answer was found from Science magazine back in 2004. The article, Mireia Garcia-Viloca, Jiali Cao, Martin Karplus, Donald G. Truhlar. “How Enzymes Work: Analysis by Modern Rate Theory and Computer Simulations.”Science. 303:186 – 195 (9 January 2004), refers back to a statement by Linus Pauling where he posited that the only actual power enzymes have is in stabilizing a transition state. What does this mean? It means essentially the same thing as was stated above – however it also refers to a kind of ‘in between’ state that substrates enter while bound to the enzymes that makes it easy to convert into the ‘desired’ product.
Apparently, people have observed this lowering of the activation energy, but it’s been difficult for even those who study these things to define. I’ve posted the article on blackboard if any of you are interested in taking a peak at it.
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