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.

Merry Christmas!

Video about ethanol metabolism

Thanks for the suggestion Vasco! :)
.

Cartoon - electrons

Thank you for the cartoon Pedro! :)
.

Metabolic map - Apoptosis

Video about DNA repair

Thank you for the suggestion Vasco! :)
.

Amino acids with aromatic side chains

By definition, a molecule is considered aromatic when in its constitution there is at least one derivative of benzene, ie, a cyclic structure with 6 vertices (all carbon atoms!), and 3 double bonds (in fact, as I said in other posts, they are not 3 double bonds, but 6 partially double bonds, with bond order of 1.5). Therefore, when, in a molecule, there is at least one such structure, the molecule is considered aromatic.

Probably some of you may be questioning yourself why to use the concept of "aromatic". In fact, most of the substances we know that have flavour (e.g., cinnamon or clove), have their aroma exactly due to the presence of molecules containing aromatic rings, in this particular case, cinnamaldehyde and eugenol, respectively. It is the delocalized electron cloud of the derivatives of benzene rings that give the fragrance to these (and many other!) molecules, and hence the chemical definition of aromatic is clearly related to the "physiological" setting of aromatic.

Let us return to amino... there are 3 that contain a derivative of the benzene ring on its side chain and are, therefore, referred to as aromatic amino acids:

Phenylalanine - the name itself explains the composition of this amino acid. In a previous post I talked about the nonpolar amino acids with aliphatic side chains, among whom was alanine (this post). Phenylalanine is no more than an alanine with a phenyl group, ie with a benzene ring. Since it only has carbon and hydrogen in its side chain, it is a nonpolar chain.

Tyrosine - this aminoacid is a hydroxylated phenylalanine. In fact, it only differs from phenylalanine because it presents a hydroxyl group on the aromatic ring, more precisely on a diametrically opposed carbon to the alpha carbon position. This hydroxyl group gives it some polarity, with the resulting side chain being therefore amphipathic.

Tryptophan – it is the amino acid with the more complex side chain comprising two cyclic structures: one is a benzene derivative, another is a heterocycle (ring composed of 2 different atoms, carbon and nitrogen in this case). These two fused rings form a functional group called indol group, which is amphipathic, since the nitrogen confers some polarity. Tryptophan is very important from a biological standpoint, because in addition to being used in the production of proteins, it is also the precursor of many important molecules, such as, for example, serotonin.

The tyrosine and tryptophan have an important characteristic, which is that of absorbing ultraviolet radiation. Due to this, the proteins having these amino acids (almost all!) present the ability to absorb UV light. In fact, phenylalanine also absorbs UV radiation, but in much smaller amount than the other aromatic amino acids, because the chemical modifications of the benzene ring (hydroxyl group in the case of tyrosine, and embedding the indole group in the case of tryptophan) significantly increase the UV absorptive capacity of aromatic rings.

Cartoon - Krebs cycle

Thank you for the input Ferraz! :)
.