Protein (2): Amphoteric Amino Acids, Physical, Chemical Properties

There exist more than 500 amino acids in natural. Majority of them which aren’t involved in protein synthesis. They’re called non-proteinogenic amino acids. Only 22 types coded by DNA are found in proteins. 20 kinds are regulated by standard genetic code and an additional two, selenocysteine and pyrrolysine are inserted into proteins by special translation mechanisms.

Sometimes, the peptide will be modified by enzyme to form uncommon amino acids. Hydroxyproline and hydroxylysine is the classical example that contribute to triple helix of collagen.

Proteinogenic Amino Acid: Structure, Physical, Chemical Properties

They share common structural features. Each amino acid has an amino group (-NH₂), a carboxyl group (-COOH), a hydrogen atom, and a distinctive side chain called R group. They’re all attach to the same central carbon atom. Although the R group can vary widely, there’re only 20 different R groups in protein.

Amino acids are white crystalline solids with melting points of about 200°C. The hydrophilic group makes most of them soluble in water, but aspartic acid, glycine and tyrosine are less hydrophilic. Most amino acids are insoluble in organic solvents except for a few that can be dissolved in polar organic solvents. For instance, leucine and tryptophan are soluble in formic acid. The acetic acid dissolves cysteine. The alanine, proline, and tyrosine can dissolve in ethanol.

Their central chiral carbon rotates plane-polarized light, except for achiral glycine where this atom doesn’t exist. L-amino acids, only involved in proteins, rotate plane of polarization to left, while D-amino acids rotate it to right.

Amphoteric Amino Acid

Amino acids contain an acidic carboxyl group that ionizes into COO⁻ and H⁺ in water. Their basic amino group capture a hydrogen ion to become NH₃⁺, leaving OH⁻ in water. This dual acidic and basic nature makes amino acid an amphiprotic compound with both positive and negative charges. The net surface charge of an amino acid is influenced by solution pH value. Lower pH or acidic solution will make it positively charged (NH₂ and COO- absorb H⁺ to become COOH and NH₃⁺), while raising pH will make amino acid negatively charged (NH₃⁺ and COOH release H⁺ to become COO- and NH₂). When it has zero net charge, it doesn’t move toward anode or cathode during electrophoresis. This specific pH value is the isoelectric point (pI). For amino acids with non-ionizable R groups, the pI is usually around 5 to 6. Carboxyl groups in R group significantly lower pI to render the amino acid solution more acidic, while amino or imino groups in the R group raise pI to make it more basic. Therefore, amino acids are classified as either basic or acidic according to their R groups.

The hydrophobicity or hydrophilicity is determined by its R group. When amino acids form a polypeptide, only the R groups are exposed to water. The peptide folds into conformation with the lowest free energy spontaneously: hydrophilic R groups are located on the exterior to interact with water, while hydrophobic R groups are buried inside away from water. It’s important to note that the hydrophilic parts in R group doesn’t always make amino acid more soluble. If the hydrophobic portion of R group is too large, it can reduce solubility despite the hydrophilic parts. Tyrosine is a prime example due to the dominant hydrophobic structure. A large benzene ring with a methylene counteracts hydrophilic hydroxyl group to results in a solubility of only 0.05 g.

Chemical Reactions of Amino Acids

Its chemical properties are associated with carboxyl, amino and hydroxyl groups. At room temperature, nitrous acid reacts with their hydroxyl groups to produce nitrogen gas. Measuring nitrogen volume will determine the amount of amino acids. The hydrogen atom on amino group can be substituted with alkyl or cycloalkyl groups. It’s similar to organic acids that the carboxyl group undergoes corresponding reactions to produce esters, salts and amides. Their lone pairs of electrons on thiol, amino, hydroxyl and carboxyl groups readily complex with heavy metal ions to form stable compounds. It explains why proteins will be easily denatured by heavy metals. The most significant chemical reaction is formation of peptide bonds. The amino group of one amino acid reacts with the carboxyl group of another, releasing a water molecule and forming a polypeptide.