Amino acids

Amino acids are at the heart of bioinformatics. Evolution of life is mainly governed by individual amino acid changes that slowly accumulate over the eons (this is not the whole story, of course, but surely a large part of it). If we want to align two sequences, we align amino acids. And your body's workhorses, the enzymes, consist of mainly amino acids, and if we want to modify a protein using protein engineering techniques, we exchange amino acids.

Therefore, a thorough understanding of the amino acids is needed. At the end of this course you will all know the twenty amino acids as if they are your friends. You will know their names, abbreviations, physico-chemical characteristics, and a whole lot more. At several moments we will relate things to thermodynamics and we will mention the "rule of 10":

The most important characteristic of amino acids is their hydrophobicity, but their size and charge are also important. The hydrophobicity is intimately connected to the role of water:

Figure 1. Many people have tried to make pictures that explain ALL amino acid properties in one shot. Obviously they all failed; just like this picture. Still, I hope that you come back to this picture at the end of this step, and explain how it got this shape. Be aware that this picture, originally designed by Willy Taylor more than 20 years ago, calls cysteine polar only because it can form (a very weak) hydrogen bond, and it doesn't know about intermediate size or intermediate hydrophobicity. I do not know why Histidine is in the hydrophobic circle, it certaily is very hydrophylic.