Proteins

Proteins are polymers made from amino acid monomer units. Each link is an amide link in the general sense of function groups - but in biochemistry speak, those are peptide links and a protein is also known as a polypeptide. The basic set up was shown in the chapter on polymers under Nature's Polymers.

20 Amino Acids

There are 20 naturally occurring amino acids that are used to build all of our proteins. Our body can actually synthesize 11 of these amino acids when functioning normally. That means that there are 9 essential amino acids that we must include in our diet in order to adequately maintain proper health.

As you know, each amino acid is characterized by the side chain or R-group off the carbon between the amino group and the carboxylic acid group. The set of 20 amino acids can be grouped based on the fundamental properties of the side chain. The break downs are based on the following designations.

  • Nonpolar / hydrophobic When the side chain is all (or mostly) C's and H's you have a very nonpolar group - just like all hydrocarbons. There are 9 amino acids in this grouping.
  • Polar / hydrophilic The rest of the amino acids (11 of them) are polar or hydrophilic. Within this group we further categorize into the following 3 categories.
    • Acidic The side chain is a carboxylic acid and therefore acidic.
    • Basic The side chain is an amine or amine-derivative which means it is basic.
    • Neutral The side chain is neither acid nor basic which means it is fairly neutral in aqueous solution.

MEMORIZE the structures of the highlighted amino acids- there are 5 of them.


9 Nonpolar Amino Acids


6 Polar Amino Acids (neutral)


2 Acidic Amino Acids


3 Basic Amino Acids



Zwitterions

You will notice that all the amino acids shown have carboxylate groups (–COO) and ammonium groups (-NH3+). These charged groups are the result of the base (the amine) accepting a proton from the acid (carboxylic acid). This self-neutralization leads to a special chemical species where there is equal + and – charge within a structure such that the overall charge is still neutral. This +/– species is called a zwitterion. The self-neutralization is show below for a generic amino acid. The zwitterion form is the dominate form in neutral conditions like in our bodies.



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