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Proteins
2. The a-amino acid building blocks Page 4




2.1 The a-amino acids
Amino acids are the monomer building blocks from which proteins are made. In general an acid is an organic molecule that contains both a carboxylic acid (-COOH) and an amine (-NH2) functional group. The acids that make proteins are all a-amino acids. In these acids both functional groups are attached to the same carbon atom (the a-carbon atom) at one end of the molecule. The simplest way to draw the structure of an a-amino acids is shown on the left.

In this diagram R stands for the rest of the molecule - the side chain group. R is the part of the molecule that makes one a-amino acid different from another. There are some twenty different a-amino acidsthat can make up proteins, so there are twenty different possibilities for the structure of the side chain group (see Figure 3).

2.2 Amino acids in 3D

The structures you have seen so far give us only a limited picture of what a-amino acid molecules may look like; they show the atoms that the molecules contain and how these atoms are linked together. They give no information about the 3-dimensional shape of the molecule - how the atoms are arranged in space. In some cases a pair of molecules that share the same sequence of atoms can have different arrangements in space called configurations. This leads to a type of isomerism called stereoisomerism.

Figure 1
a-amino acids in 3D.
Almost all a-amino acids display a particular type of stereoisomerism that comes from the molecules being chiral . This means that the two arrangements of the molecules are non-identical mirror images, in the same way that your left hand is a non-identical mirror image of your right hand (see Figure 1). Non-identical mirror images are sometimes described as non-superimposable (you can't put a left hand glove on your right hand). The two molecules are called enantiomers.
Figure 2
The conventional way to show the 3D shape of a molecule - in this case an amino acid.
Chirality in an a-amino acid is due to the a-carbon atom in the molecule being joined to four different atoms or groups. The a-carbon is called the chiral centre. We can draw the configurations of two enantiomers using a convention to show three dimensions (see Figure 2). Nearly all a-amino acids in nature share the same configuration, called the L configuration. Its mirror image is called the D configuration.
structures
Questions:
(Refer to Figure 3 - Structures of the a-amino acids - to help you answer these questions.)

1. Glycine is the only a-amino acid that is not chiral . Explain why.

2. Which two a-amino acids have a chiral centre in their side group? Draw out the structures and label these centres.

3. Using 3D diagrams like those in Figure 2, draw out the configurations of L-alanine, D-alanine, L-cysteine and L-proline.



Figure 3. shows you the general shapes of the a-amino acids.
When you cover a molecule with your mouse, its name will appear in the status bar at the bottom.
You can see a bigger diagram of a group of molecules by clicking on that group

Unilever Education Advanced Series: Proteins
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