What are Amino Acids?
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
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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
FAQs on Physicochemical Properties of Amino Acids
1. What are the key physicochemical properties of amino acids?
The main physicochemical properties of amino acids are determined by their structure, which includes a central carbon atom (α-carbon), an amino group (-NH₂), a carboxyl group (-COOH), and a variable side chain (R-group). Key properties include:
- Amphoteric Nature: They can act as both an acid (due to the carboxyl group) and a base (due to the amino group).
- Zwitterionic Form: At physiological pH, they exist as dipolar ions, or zwitterions, with a positive charge on the amino group (NH₃⁺) and a negative charge on the carboxyl group (COO⁻), resulting in a net zero charge.
- Optical Activity: All standard amino acids (except glycine) are optically active because their α-carbon is chiral, meaning it is attached to four different groups. This allows them to rotate plane-polarised light.
- Solubility: Their solubility in water depends on the polarity of their side chains. Polar amino acids are more soluble than non-polar ones.
- UV Absorption: Aromatic amino acids like Tryptophan, Tyrosine, and Phenylalanine can absorb ultraviolet light, a property used to quantify protein concentration.
2. How are amino acids classified based on their side chains (R-groups)?
Amino acids are primarily classified into four groups based on the polarity and charge of their R-group, which dictates their function in proteins:
- Nonpolar, Aliphatic R-Groups: These side chains are hydrophobic and tend to cluster inside proteins. Examples include Glycine, Alanine, Valine, Leucine, and Isoleucine.
- Polar, Uncharged R-Groups: These side chains are hydrophilic and can form hydrogen bonds. Examples include Serine, Threonine, Cysteine, Asparagine, and Glutamine.
- Aromatic R-Groups: These are relatively nonpolar and can absorb UV light. Examples are Phenylalanine, Tyrosine, and Tryptophan.
- Positively Charged (Basic) R-Groups: These side chains are hydrophilic and carry a positive charge at physiological pH. Examples include Lysine, Arginine, and Histidine.
- Negatively Charged (Acidic) R-Groups: These side chains are hydrophilic and have a net negative charge at physiological pH due to an extra carboxyl group. Examples are Aspartate and Glutamate.
3. Why are amino acids considered amphoteric molecules?
Amino acids are considered amphoteric because they possess both acidic and basic functional groups within the same molecule. The carboxyl group (-COOH) can donate a proton, acting as an acid, while the amino group (-NH₂) can accept a proton, acting as a base. This dual nature allows an amino acid to react with both acids and bases, and its net charge changes depending on the pH of the surrounding solution.
4. What is a zwitterion and why do amino acids exist in this form at physiological pH?
A zwitterion is a molecule that has both a positive and a negative electrical charge, yet its net charge is zero. Amino acids exist in this form at physiological pH (around 7.4) because the environment is neither strongly acidic nor strongly basic. In this state, the acidic carboxyl group (-COOH) donates its proton to become a negatively charged carboxylate ion (-COO⁻), and the basic amino group (-NH₂) accepts a proton to become a positively charged ammonium ion (-NH₃⁺). This internal acid-base reaction results in the stable zwitterionic form.
5. How does the structure of an amino acid determine its optical activity?
The optical activity of an amino acid is determined by the presence of a chiral center. For all standard amino acids except glycine, the alpha-carbon (α-carbon) is bonded to four different groups: a hydrogen atom, a carboxyl group, an amino group, and a unique side chain (R-group). This asymmetry makes the α-carbon a chiral center. Molecules with a chiral center are capable of rotating the plane of polarised light, making them optically active. Glycine is the only exception because its R-group is another hydrogen atom, making its α-carbon achiral and thus optically inactive.
6. Which amino acids absorb UV light, and why is this property important in biology?
The aromatic amino acids—Tryptophan (Trp), Tyrosine (Tyr), and Phenylalanine (Phe)—are the ones that significantly absorb ultraviolet (UV) light. This is due to the presence of aromatic rings in their side chains. Tryptophan and Tyrosine have the strongest absorbance, typically around a wavelength of 280 nm. This property is extremely important in biochemistry and molecular biology because it provides a simple, non-destructive method for determining the concentration of proteins in a solution using a technique called spectrophotometry, as most proteins contain these amino acids.
7. What is the isoelectric point (pI) of an amino acid?
The isoelectric point (pI) is the specific pH at which an amino acid has no net electrical charge and exists predominantly in its zwitterionic form. At this pH, the positive charge on the amino group exactly balances the negative charge on the carboxyl group. For simple amino acids with non-ionisable side chains, the pI can be calculated by averaging the pKa values of the carboxyl (pK₁) and amino (pK₂) groups: pI = (pK₁ + pK₂) / 2. The pI is a crucial property because amino acids are least soluble at their isoelectric point, a principle used for their separation and purification.
