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Proteins are the structural scaffolds of our bodies. At the molecular level whatever function is going on, it is being assisted or done by a protein. Proteins have a wide array of structures and functions, but all proteins are similar when it comes to their building blocks. These are the amino acids.
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The amino acids, as the name suggests, consist of an “amino” group and a “carboxyl acid” group. In addition to that, there is an alpha-carbon to which those two functional groups are linked. There is also something called the “R” group that creates a whole lot of difference in different amino acids. There are 20 naturally occurring amino acids that makeup all the proteins that we have ever heard about. These amino acids are of various natures depending on the R-group that they possess.
All 20 amino acids are broadly classified into two distinct types. These are the aromatic and aliphatic amino acids.
The aromatic amino acids are 3 in number. These are Phenylalanine, Tyrosine, and Tryptophan. All these three have an aromatic ring in the R-group residue which gives them some special properties and moreover, makes them a little different from the others.
The aliphatic amino acids do not have an aromatic R group and can be further divided as polar and non-polar. The non-polar R group-containing amino acids are 7 in number. These are Glycine, Alanine, Methionine, Proline, Valine, Isoleucine and Leucine.
The polar amino acids can be further divided into charged R-group and uncharged R-group. In the uncharged R-group, there are 5 amino acids which are Serine, Threonine, Cysteine, Asparagine, and Glutamine. The charged R-group amino acids are of 2 types, the positively charged and the negatively charged. There are three positively charged amino acids namely, Arginine, Histidine, and Lysine. The negatively charged amino acids are Glutamic acid and Aspartic acid.
The basic hierarchy of protein structure
Two amino acids can join together by releasing a water molecule in the process through a bond called the peptide bond. Therefore, many amino acids join together to form a protein. There are a certain structural hierarchy of proteins.
The linear sequence of amino acids forming a long chain is referred to as the primary structure of a protein. This is the simplest form. Now, these peptide bonds can rotate about its axis which gives rise to something called the torsional angles. The Cα-C forms the psi angle and Cα-N forms the phi angle. If a stretch of the polypeptide has the same phi and psi angle repeatedly, that particular stretch would locally fold into a specific structure. This localized folding is referred to as the secondary structure of a protein. Therefore, a single protein can have a lot of secondary structures. Some examples of secondary structures are alpha-helix, beta sheets and beta turns. When the secondary structure containing proteins fold in a 3-dimensional form, it is called the tertiary structure and if a protein contains different tertiary structured chains, it is referred to as the quaternary structure
This tertiary and Quaternary structure of a protein is absolutely essential for its particular function. If these structures are disrupted, the function of the protein disrupts as well.
- David L. Nelson, Michael M. Cox-Lehninger Principles of Biochemistry, 5th Edition-W. H. Freeman (2008)
Amino acids and Proteins