Amino Acids: Structure, Classification, and Properties - SS3 Chemistry Lesson Note

Amino acids are fundamental building blocks of proteins and play essential roles in various biological processes. They are organic compounds that contain both an amino group (-NH2) and a carboxyl group (-COOH) attached to the same carbon atom, known as the alpha carbon (α-carbon). The structure, classification, and properties of amino acids are crucial for understanding their significance in biochemistry and various other fields. Let's explore these aspects in detail:

Structure of Amino Acids:

The general structure of an amino acid can be represented as follows:

H2N-C-COOH

In this structure:

● H2N represents the amino group (NH2) attached to the α-carbon.

● COOH represents the carboxyl group (COOH) attached to the α-carbon.

● R represents the side chain or the variable group attached to the α-carbon. The nature of the R group varies among different amino acids and gives them their unique properties.

Classification of Amino Acids:

Amino acids can be classified into several categories based on the properties of their R groups:

1. Non-Polar (Hydrophobic) Amino Acids:

Amino acids with hydrophobic R groups are typically uncharged and do not form hydrogen bonds with water. They tend to be found buried in the interior of proteins away from the surrounding aqueous environment. Examples include glycine (Gly), alanine (Ala), valine (Val), leucine (Leu), isoleucine (Ile), methionine (Met), proline (Pro), phenylalanine (Phe), and tryptophan (Trp).

2. Polar (Hydrophilic) Amino Acids:

Amino acids with polar R groups are capable of forming hydrogen bonds with water and other polar molecules. They are often found on the surface of proteins, interacting with the surrounding solvent. Polar amino acids can be further divided into two categories:

a. Neutral Polar Amino Acids: Serine (Ser), threonine (Thr), cysteine (Cys), asparagine (Asn), and glutamine (Gln) have uncharged polar side chains.

b. Charged Polar Amino Acids: Aspartic acid (Asp) and glutamic acid (Glu) have negatively charged side chains due to the presence of an additional carboxyl group (-COO-). Lysine (Lys), arginine (Arg), and histidine (His) have positively charged side chains due to the presence of an additional amino group (-NH3+).

3. Special Amino Acids:

● Cysteine (Cys) is unique among amino acids because its side chain contains a thiol (-SH) group, which can form disulfide bonds with other cysteine residues in proteins, stabilising their tertiary and quaternary structures.

● Glycine (Gly) is the smallest amino acid, with a hydrogen atom as its R group. Due to its small size, glycine can fit into tight protein structures and often serves as a flexible linker.

Properties of Amino Acids:

1. Acid-Base Properties: Amino acids are amphoteric, meaning they can act as both acids and bases. The α-carboxyl group can donate a proton (H+) to form a carboxylate ion, while the α-amino group can accept a proton to form an ammonium ion. At physiological pH, amino acids exist in their zwitterionic form, where both the carboxyl group and the amino group are charged.

2. Optical Activity: Except for glycine, all-natural amino acids are chiral and exist in two enantiomeric forms (mirror images) called L-amino acids (left-handed) and D-amino acids (right-handed). In proteins, only L-amino acids are commonly found.

3. Protein Synthesis: Amino acids are the building blocks of proteins. During protein synthesis, amino acids are linked together by peptide bonds to form polypeptide chains, which then fold into functional proteins.

4. Buffering Capacity: Amino acids and their derivatives are involved in maintaining the pH of biological systems through their buffering capacity, helping to stabilise the intracellular and extracellular environments.

In conclusion, amino acids are critical molecules with diverse properties, making them essential for life processes and the foundation of proteins. The variation in their R groups leads to a wide range of chemical behaviours and functional roles, making amino acids central to the field of biochemistry and molecular biology.