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The Theme of Chemistry of Enzymes in Acids and Bases

Acids and Bases in Enzymes

Many acids and bases are highly toxic and there's no way they would get along inside the cells of your body. Strong acids and bases could probably explode some cells much like this exploding watermelon. However, relatively weak acids and bases are everywhere in biology and help cells do some amazing chemistry.

On example of weak acids and bases in action is their use by enzymes to catalyze many of the vital biochemical reactions going on all the time within cells. Enzymes are nature's most common nano-machines. They are large molecules consisting of a long string of amino acids that folds up into a precise structure. Scientists can take pictures of enzymes using X-rays (see below) to get an overall map of how the amino acid string is folded up and to find the location where the enzymes interact with the chemicals that need catalyzing. This special location is called the active site. The active site is where all the amazing chemistry happens that is needed to keep reactions going faster than they would otherwise. 


An X-ray crystal structure of an enzyme. (Image from here.)

Enzyme active sites contain an arsenal of amino acid side chains that interact with the reactant molecule(s) undergoing catalysis, better known as the substrate(s) of the enzyme. Amino acid side chains are the parts of the amino acid that do not participate in the bonds that make up the long chain. There are 20 different common amino acids, each with their own side chain. One of the most deadly weapons in the active site arsenal is an amino acid side chain that can transfer or accept protons from the substrate.

Of the 20 common amino acids, several of them have side chain groups that can act as acids or bases. These acidic or basic amino acid side chains are called "general acids" or "general bases" in the context of the enzyme. It turns out that in order to react many substrates need to pick-up or lose a proton in order to get to the products side of the equation. Enzymes make this happen faster by having weak acids and bases in the active site to transfer the needed protons like a super-quick ball boy shuttles tennis balls back and forth during a match. Saved yet again by acids and bases.

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