Common Amino Acids
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Common Amino Acids

Proteins are polymers. They are made of long chains of monomers hooked together end to end. The monomers that make up proteins are amino acids.

The general structure of an amino acid is shown here (and in Example 1 of your workbook). Not surprisingly, an amino acid is a molecule that contains both a carboxylic acid group and an amine group. The amino acids that make up proteins all have a carboxylic acid on one end of the main carbon chain and an amine group on the very next carbon atom in the chain.

General structure for an amino acid. [68001.jpg]
This is the number 2 carbon atom in the IUPAC numbering system.

General structure for an amino acid with carbon atoms labeled using numbers. [68002.jpg]
According to an older system of naming organic compounds, this second carbon atom is referred to as the alpha (a) carbon atom, so the amino acids found in proteins are all alpha amino acids.

General structure for an amino acid with carbon atoms labeled using Greek letters. [68003.jpg]

 

The rest of the main carbon chain, represented by an R here, is different on different amino acids. Notice that unless the R is a hydrogen atom or an amino group or a carboxylic group, the alpha carbon is bonded to four different groups. That means that the a-carbon is a stereogenic or asymmetric carbon atom and that the amino acids are therefore optically active.

The general structure for the a -amino acids shown here (and in Example 2 in your workbook) is drawn in a Fisher projection formula. That is the same kind that we used for the open chain form of monosaccharides such as glucose.

Since the amino group on the stereogenic carbon is to the left, this structure has an L-configuration. All of the optically active a-amino acids occur in this form, so that all proteins are made of chains of a-L-amino acids, bonded together end to end.

General structure and model for an amino acid. [68022.jpg]

 

You need not memorize the names and structures of the amino acids studied in this lesson. However, if you are given the structure of the side chain, you should be able to draw the complete structure of the corresponding amino acid. You should also be sufficiently familiar with the names that you can recognize them as being the names of amino acids. (Perhaps I should say that you do need to memorize the names of the amino acids but not which structure goes with each name.) Beside each name is a three letter abbreviation that is commonly used for the amino acid. We will use these abbreviations throughout the lesson, but again, you need not memorize them.

The amino acids can be classified by group according to the chemical properties of their R-groups (or side chains, as they are often called). Example 2 in your workbook lists the twenty common amino acids grouped in this way, and you should refer to that while working through that page of this section. 

For your reference, there is also a page with an alphabetical listing. The structures shown on that page have a different orientation than what you have seen so far. As with many organic molecules, there are a variety of ways (orientations) in which these structures can be drawn.

After you become familiar with the 20 amino acids discussed in this section, we will look at how they bond together in long chains to make the proteins that exist in every living thing.

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