[Biology Class Notes] on Physicochemical Properties of Amino Acids Pdf for EXAM

Amino acids can be defined as the monomer of protein. Large numbers of amino acids come together to form protein.  Amino acid residues are joined by a specific type of covalent bond, the term residue refers to the loss of water molecules when one amino acid is joined to another. There are a total of 20 standard amino acids which when polymerized in varying sequences give rise to the enormous diversity of the protein found among living beings. All amino acids share common structural features, they are all alpha-amino acids. When a carboxyl group and an amino group attached to the same carbon atom, the alpha carbon such amino acids are termed alpha-amino acid. Since all amino acids are alpha-amino acids and share a common structural feature they differ in their side chains, or R groups, which differ in structure, size, and electric charge. The physicochemical properties of amino acids are greatly determined by the analogous structural properties of amino acids.

The general structure of an amino acid

Physicochemical Properties of Amino Acids

It refers to the physical and chemical properties of the compound or molecular attributes that defines the intrinsic chemical reactivity of the compound. It includes stereochemistry, electrostatic characteristics, optical characteristics, absorption spectra, titration pattern, and isoelectric properties.  

Structural Features

All standard amino acids are alpha-amino acid (𝝰) with amino group (NH2), carboxyl group (COO–) and functional group (R) are all attached to the alpha carbon. Diversity among amino acids is the result of different functional groups. Functional groups can be aliphatic, aromatic, carboxylic, sulfur-containing, amino, amide, or hydroxyl groups. Only in glycine, the R group is another hydrogen atom. Because of the tetrahedral arrangement of bonding orbitals around the 𝝰-carbon atom, the four different groups can occupy two unique spatial arrangements, and thus amino acids have two possible stereoisomers.

Absolute Configuration

The absolute configuration of the amino acid can be described based on the stereochemistry of the molecule. Since they are non-superimposable mirror images of each other, the two forms represent a class of stereoisomers known as enantiomers.

Absolute configuration of the molecule can be described based on 2 two systems, the DL system, RS system, among these two DL systems are widely used.

DL system- the absolute configuration of amino acids are simple sugar are determined using this system, it is based on the absolute configuration of glyceraldehyde, a three-carbon sugar. In amino acid configuration is determined by an amino group, if the 𝝰-amino group is in left, the amino acid is said to be in L configuration, similarly, the amino group on the right-hand side represents D configuration. All standard amino acids exhibit L- configuration. 

Optical Characteristics

The optical characteristic of an amino acid refers to the optical activity of amino acid, which in turn can be defined as the ability of compounds to rotate plane-polarized light. The asymmetric 𝝰 carbon of an amino acid act as a chiral molecule. amino acid with a chiral molecule is optically active. The only exception is glycine as mentioned earlier, the functional group of glycine is a hydrogen atom, thus 𝝰- carbon is symmetric acting as an achiral molecule. The achiral molecule is optically inactive, that is, it can not rotate a plane-polarized light.

• Plane Polarized Light- it is a wave of light that consists of unidirectional vibrations, that is, vibration in all the waves is in the same plane (direction). In an unpolarized light, the electric vectors of vibration are at random positions about the axis of propagation, while the direction of wave propagation is the same.

• Plane of Polarization- It refers to the direction of polarization of a polarized wave.

Electrostatic Characteristics

Electrostatic characteristics define the electric charge and the properties associated with it such as the position of an amino acid within protein tertiary structure, protein-protein interaction, amino acid-nucleic acid interaction. Electrostatic features of an amino acid are attributed to the side chain. Charge on the side chain determines the net charge of amino acid and its relative stability in proteins. The standard amino acids can be classified based on polarity as polar and non-polar amino acid side chains. Polar side chains can be further classified into uncharged and charged. Further differentiation of side-chain can be done as positively and negatively charged amino acids.

Classification of Side Chain

Classification of Polar Side Chains

Absorption in Amino Acid

Absorption can be defined as the process of gaining energy in the form of radiation generally UV radiation in the case of amino acid. This gain results in the movement of electrons into an excited state. Every biomolecule has a specific wavelength of absorption. When a graph is plotted the maximum absorption corresponding to the wavelength is termed as absorption peak. In amino acids, there are 3 amino acids that show significant UV absorption due to their aromatic side chain. They are phenylalanine, tryptophan, and tyrosine.

Absorbance of Amino Acids

Titration of Amino Acid

The physicochemical properties of the amino acid can be greatly optimized using the titration method. Amino acids have characteristics titration curve, this represents the gradual addition or removal of protons to form a protonated and deprotonated state. Amino acids at neutral pH are in zwitterionic form. As we decrease the pH, increasing H+ concentration amino acid moves towards a fully protonated state, and as we increase the pH, thereby increasing the concentration of OH-, amino acids move toward a fully deprotonated stage. The tendency of a group to donate protons is measured in pKa, pK1 denotes the pK value for the carboxylic group, while pK2  denotes the pK value of the amino group. pKa value depends on the ionic strength, temperature, and microenvironment of the ionizable group. Titration curves are greatly important to determine isoelectric pH. Isoelectric pH (pI) is the pH at which the net charge of amino acid is zero.

pI = pK1+ pK2/ 2