Saturday, March 31, 2012

Portrait of an Enzyme

Enzymes "herd" molecules and accelerate reactions. They affect change, but do not themselves change. They exist in minuscule amounts, doing their work on more abundant molecules called substrates, building up new molecules or demolishing old ones, leaving behind smaller molecular fragments for further digestion. Enzymes cannot make the impossible happen--they just make the possible happen faster.

Enzymes bring together pieces and stabilize any awkwardness of the encounter.

Let me unpack that sentence. "Bring together pieces" means that enzymes gather pieces using available molecular forces--usually just simple repulsion and attraction--to orient molecules in space.

"Repulsion" usually means hydrophobia, but may also be simple blocking effects. "Steric" is a term of art relating to the latter effect. "Steric hindrance" means that my standing somewhere blocks you from standing in the same place--it's a repulsive effect. Enzymes use repulsive effects to restrict degrees of freedom to reduce the randomness of molecular encounters.

"Attraction" is more familiar. Enzymes deploy acids and bases within their active sites to spatially arrange substrates--they may use a base (negative) to attract and hold an acid (positive) on a substrate. Hydrogen bonding works similarly and is like a shared common interest.

"Stabilizing any awkwardness of the encounter" is the real key to understanding enzymes. This was Linus Pauling's idea. Enzymes don't just bring together and stabilize substrates--if they did just that their insides would soon clog up with unreacted substrates. They have to stabilize the awkward encounter--not just a roomful of substrates looking at each other.

Here's a visual of what I'm trying to say, taken from organic chemistry. Imagine that the enzyme's role is to surround and stabilize each of the following chemical species, but especially the one circled in red:


Stabilizing whatever's in the red circle brings down the height of the blue hump. That's acceleration.

Enzymes lure substrates together, polarizing and fostering attack. Polarize, attack, depolarize
‡ See for example, link


  1. I am afraid that this statement is not correct "Enzymes cannot make the impossible happen--they just make the possible happen faster.".

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  2. Naw, see, its not impossible you'd get your dog back without a chip--the microchip just makes it happend faster.