Sunday, February 14, 2016

Amino acid with alkaline side chains

This class of amino acids includes those amino acids who have in their side chain an alkaline functional group. This means that these amino acids tend to have positive charge on their side chain as the alkali groups tend to pick up H+. As a result, they usually establish ionic bonds (or salt bridges) with amino acids with negatively charged side chains There are 3 amino acids belonging to this class:
Lysine - This amino acid has in its side chain a primary amine, that means, an amine group which is bonded to only one carbon, while the remaining nitrogen substituents are hydrogen atoms. The amine group is the main alkaline group in biochemistry (more information on this post). Lysine is the primary site of glycosylation of proteins, and in this case, the established connections are N-glycosidic bonds.

Arginine - This amino acid has in its side chain a more complex alkali functional group, called guanidine. This is a functional group comprising 3 nitrogen atoms, which displays electronic resonance, and they can be protonated.

Histidine - This amino acid has a cyclic structure in its side chain, more specifically an imidazole ring. It is a heterocycle composed of nitrogen and carbon atoms, in which one of the nitrogens can be protonated. Histidine has a particularly important feature in biochemistry: it is the only amino acid that has substantial buffering capacity at physiological pH (between 6.5 and 7.5), since its pKa is about 6. In this regard, it should be noted, firstly, that the pKa of histidine changes, as this amino acid is inserted into different polypeptide chains, but usually it is not much different from the original value (isolated histidine). Also, the fact that it is important to have a pKa close to physiological pH, relates to the ability of histidine to exist in medium in its acid and alkaline forms at the physiological pH, functioning as an acid-base pair conjugate.

Tuesday, February 2, 2016

Amino acids with uncharged polar side chains

This class of amino acids includes those that do not have ionizable functional groups on its side chain. In fact, despite the definition of this class is given in this way, it is not 100% correct, because according to it, the aromatic amino acids should be included. Therefore, to be a completely correct definition, it must contain the word aliphatic, ie, amino acids that have an aliphatic side chain containing only non-ionizable functional groups. These amino acids can therefore establish non-covalent forces between their polar side chains. In particular, most of them can establish hydrogen bonds, a very important factor for the stability of the conformation of most proteins.
Several amino acids belong to this category:
Serine - This amino acid side has a small side chain with a hydroxyl group, which confers polarity. Under normal conditions the hydroxyl group is not ionized, although in some contexts (particularly on tyrosine, which is an aromatic amino acid such as highlighted in this post), it may function as a weak acid. All amino acids which have hydroxyl groups in the side chain are potential phosphorylation sites, which means, when a protein is phosphorylated, the phosphate groups are usually added to the hydroxyl groups of side chains.

Threonine - This amino acid, such as serine, has a hydroxyl group in its side chain, but in this case this chain is longer than that of serine.

Cysteine ​​- This amino acid deserves special attention because it is the only one of the 20 standard amino acids that has a sulphydryl or thiol group (more information about this functional group here). In addition to providing polarity, this functional group allows the establishment of disulfide bridges, which are the main type of covalent inter- and intramolecular bonds that contribute to the stability of the 3D structure of a protein. In a future post I will talk about the structure of proteins and the interactions that contribute to its stability.

 Proline - Other "special" amino acid! It is the only one of the 20 standard amino acids wherein the R group is covalently linked to the a-amino group, thus, the side chain forms a cyclic structure with the amino acid skeleton itself. The inclusion of this amino acid in the group of amino acids with uncharged polar aliphatic side chains is debatable, as there are those who put it in the group of amino acids with nonpolar aliphatic side chains. If we look closely, the side chain of proline is formed only by carbon and hydrogen, i.e., it is non-polar. However, as it is covalently bound to the nitrogen of the a-amino group, this will impart polarity to that structure. So, in my opinion, any one of the classifications may be used, it depends on the perspective. J Returning to proline cyclic structure, since it comprises the amino acid skeleton, it makes this amino acid more rigid than the remaining amino acids, as its side chain cannot freely rotate. Furthermore, the cyclic structure distorts the amino acid structure. As I always say in my classes, proline "is a wry amino acid", and this has significant implications for the effect of proline in the 3D structure of proteins.
Asparagine - This amino acid has in its side chain an amide group. In fact, in terms of composition, it is very similar to the aspartate amino acid, changing only the terminal functional group. By the way... a call to attention! The amide group is not an ionizable group, i.e., it does not confer basic (not acid!) properties to biomolecules. The basic functional group is the amino group.

Glutamine - As asparagine, glutamine also has an amide group in the side chain. In this case, there are obvious similarities with glutamate, although there is still a notorious difference, which is the amide group.