Polypeptides (polymers of amino acids) are important biological molecules, encoded by a single (or less than a single) gene. Proteins are composed of one or more polypeptide chains. Polypeptides are thus one of the most important molecules for biotechnologists, as they can be used for all sorts of interesting chemistry (in addition to being part of a balanced diet).

Unfortunately, polypeptides are difficult to synthesize. This is because they are very complex structures, and if you don't take care to control what's going on, you wind up with the wrong end of the molecule or wrong part of the molecule reacting, creating a compound which is most likely of no use to you at all.

For this reason, the thing to do is use protecting groups. That is, functional groups which disable that part of the molecule from reacting with whatever else you've got going on. As amino acids all have an amino group and a carboxyl group, simply adding together two amino acids and heating it up will give you a crazy product mixture. You could have them end up the way you want, backwards, each could react with itself, each could react with itself and then the other, and so forth off into infinity. Not terribly useful. So you've got to protect the carboxyl group of one and the amino group of the other to get exactly the chemistry you want to take place to take place.

One way to do this is to use the Merrifield Solid-Phase Peptide Synthesis (named after Professor Robert B. Merrifield, Nobel Prize 1984 in Chemistry). To simplify, you take some polystyrene and do a bit of chemistry to add a chloromethyl group to the polystyrene. This you react with the amino acid you want to start the polypeptide with (starting with the C terminus and moving to the N terminus, the opposite of how it happens in nature).

The way you protect the amino acid you're adding is you buy it with a BOC group attached to the amino end. You can just buy the amino acids this way. BOC stands for t-ButOxy Carbonyl. You just mix in your amino acid with the other one that's hooked on the polystyrene, and now you have a protected dipeptide. You then remove the BOC group by adding some CF3COOH, and add another BOC protected amino acid. You continue the process until the chain is complete, and then remove the BOC group and the poly styrene by again adding CF3COOH and some hydrogen gas with Pd/C catalyst. And there you have it, a polypeptide.

A good book which includes this and much more organic chemistry is Organic Chemistry: Structure and Function by Vollhardt and Schore.

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