Introduction to Proteins and Amino Acids
Proteins are among the most versatile and important molecules in living organisms. They are built from smaller units called amino acids, which are linked together in long chains called polypeptides.
Amino acid: An amino acid is the monomer unit of proteins. Each amino acid shares a common backbone structure but differs in its variable side chain, called the R-group.
The common backbone of every amino acid consists of:
- A central alpha carbon (Cα)
- An amine group (–NH₂)
- A carboxyl group (–COOH)
- A hydrogen atom (H)
- A variable R-group (side chain)
A generalised amino acid can be represented as:
where the central carbon also bears an H atom and an R-group.
There are 20 standard amino acids encoded by the genetic code, each with a unique R-group that gives it distinct chemical properties:
| R-group category | Properties | Role in protein structure |
|---|---|---|
| Non-polar | Hydrophobic, repel water | Cluster in protein interior; hydrophobic interactions |
| Polar | Hydrophilic, interact with water | Form hydrogen bonds |
| Acidic (e.g., –COOH) | Negatively charged at physiological pH | Form ionic bonds with basic R-groups |
| Basic (e.g., –NH₂) | Positively charged at physiological pH | Form ionic bonds with acidic R-groups |
These chemical differences are the foundation of protein diversity and function , the R-group chemistry directly determines what kinds of bonds and interactions a protein can form as it folds into its three-dimensional shape.
Peptide Bond Formation
Amino acids are joined together by peptide bonds to form polypeptide chains. This is a core reaction in protein synthesis.
Peptide bond: A covalent bond formed between the carboxyl group (–COOH) of one amino acid and the amine group (–NH₂) of the next, with the release of a water molecule. This is a condensation reaction.
The condensation reaction:
Key features of peptide bonds:
- One molecule of water is released for each peptide bond formed
- The resulting –CO–NH– linkage is the peptide bond
- This reaction is carried out by ribosomes during translation
- The reverse reaction , hydrolysis , breaks peptide bonds by adding water (this occurs during digestion)
Polypeptide directionality:
When amino acids are linked, the chain has two distinct ends:
- The N-terminus (free amine group, –NH₂) at one end
- The C-terminus (free carboxyl group, –COOH) at the other end
Polypeptide chains are always synthesised and read in the N-terminus → C-terminus direction. This directionality is important for understanding how the primary structure is encoded and expressed from DNA.
A dipeptide is formed from 2 amino acids with 1 peptide bond and 1 water released. A tripeptide requires 2 peptide bonds and releases 2 water molecules. For amino acids, peptide bonds are formed and water molecules are released.
Worked example: Glycine (H₂N–CH₂–COOH) and alanine react in a condensation reaction. The carboxyl group of glycine reacts with the amine group of alanine, releasing water and forming the dipeptide glycyl-alanine (Gly-Ala). The peptide bond formed is the –CO–NH– linkage between the two residues. The product has a free N-terminus (from glycine) and a free C-terminus (from alanine).
