Don't you wonder what builds up such a long chain of polypeptides? How peptide bonds are formed? What is the basis of the classification of amino acids? Proteins are the polymer of amino acids and these amino acids are the building blocks or hypothetically we can say they are the architecture of proteins. The two neighboring amino acids are joined together covalently. After the removal of water (hydrolysis) peptide bond is formed. Do you know that asparagine was the first amino acid discovered and is extracted from Asparagus, Glutamate is isolated from wheat gluten, tyrosine was first obtained from cheese, and glycine was named so because of its sweet taste.
All 20 amino acids share common structural features. The structure comprises an alpha carbon, Carboxyl group(acid group), amino group(basic group), and R-group which could be any hydrocarbon. The solubility of amino acids is influenced by the R- group due to the difference in structure, size, and electric charge they carry. Being bound to four different groups the alpha carbon is being designated as a chiral carbon. Based on the properties of the R-group the amino acids can be grouped into five categories:
- Nonpolar, aliphatic R group
- Aromatic R group
- Polar, uncharged R group
- Positively charged R group
- Negatively charged R group
Nonpolar, Aliphatic R group
The R group of this class is nonpolar and hydrophobic in nature. Glycine, Alanine, Valine, Leucine, and Isoleucine are some amino acids following under this category. Glycine has the simplest structure. Although it is formally nonpolar, its small side chain makes no contribution to the hydrophobic interaction. Methionine contains nonpolar thioether in its side chain and proline has a distinctive cyclic structure. The secondary amino group imino held the proline residue in a rigid conformation that reduces the flexibility of the structure.
Aromatic R group
This amino acid R group has aromatic side chains that are nonpolar and hydrophobic. The three amino acids namely phenylalanine, tryptophan, and tyrosine. Unlike Nonpolar, aliphatic R group a/a (can not participate in the hydrophobic interaction with water) aromatic a/a can participate in hydrophobic interaction. For case, Tyrosine's hydroxyl group forms a hydrogen bond. Tyrosine and tryptophan are more polar than phenylalanine because tyrosine contains a hydroxyl group and tryptophan has nitrogen on its indole ring. Phenylalanine, tyrosine, and tryptophan absorb ultraviolet light at a wavelength of 280nm. This property is being used for the characterization of proteins.
Polar R group
The a/a under this category are polar, more soluble in water, and hydrophilic. Due to the presence of a functional group they form hydrogen bonds with water. This class includes serine, threonine, cysteine, asparagine, and glutamine. What determines the polarity of these amino acids? Hydroxyl group in serine and threonine, sulfhydryl in cysteine, and amide group in that of asparagine, as well as glutamine, determine the polarity of amino acids. Cysteine on oxidation forms a covalently linked dimeric amino acid called cystine ( two cysteine molecules are joined by a disulfide bond ).
Positively charged R group
The amino acid with positive or negative charges is most hydrophilic. The R group with a positive charge at pH 7.0 is lysine. arginine has a positive charge guanidino group, and histidine has an imidazole group. Histidine residue acts as donor/acceptor.
Negatively charged Rgroup
Aspartate and Glutamate are the two amino acids with a net negative charge at pH 7.0, which contains the second carboxyl group.
In addition to 20 common amino acids, proteins may contain modified residues incorporated into polypeptides. Some of the derivatives of amino acids are 4-hydroxyproline a derivative of proline and 5-hydroxylysine derivative of lysine. These mentioned derivatives are found as a protein of plant cell wall, collagen, and a fibrous protein of connective tissue. 6-N-Methyllysine is another residue derivative constituent of myosin.
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