Understanding Amino Acid Properties and Protein Structure
Amphoteric Character
Amino acids possess an amphoteric character due to the presence of both carboxyl and amino groups. The carboxyl group can lose a proton, acting as an acid, while the amino group can accept a proton, acting as a base. This dual behavior allows amino acids to act as both acids and bases depending on the pH of the environment. The side chain may also contain ionizable groups, further influencing the amino acid’s charge.
Isoelectric Point
The isoelectric point (pI) is the pH at which the net charge of an amino acid is zero. Each amino acid has a unique pI.
Peptide Bond
Amino acids are linked together by peptide bonds, formed between the carboxyl group of one amino acid and the amino group of another. This bond releases a water molecule. Two amino acids joined form a dipeptide, three a tripeptide, and many amino acids linked together form a polypeptide. The peptide bond has partial double bond character due to resonance, meaning the C, O, and N atoms are in the same plane. This restricts rotation around the peptide bond, but rotation is possible around other bonds in the polypeptide.
Protein Structure
Protein function is determined by its three-dimensional structure. The polypeptide chain folds in specific ways to create a structure suitable for its biological activity.
Primary Structure
The primary structure of a protein is the linear sequence of amino acids in the polypeptide chain. Different proteins have unique sequences, determined by the genetic code. Each polypeptide chain has a free amino group at one end (N-terminus) and a free carboxyl group at the other end (C-terminus).
Secondary Structure
The secondary structure refers to local folded structures within the polypeptide chain, stabilized by hydrogen bonds. Common secondary structures include:
Alpha Helix
The alpha helix is a right-handed coil stabilized by hydrogen bonds between the NH group of one amino acid and the C=O group of another amino acid four residues away. Side chains extend outward from the helix.
Beta Sheet (or Pleated Sheet)
The beta sheet consists of polypeptide chains arranged side-by-side, forming a pleated structure. Hydrogen bonds between the NH and C=O groups of adjacent strands stabilize the sheet. Side chains extend above and below the sheet.
Certain combinations of alpha helices and beta sheets form stable structural domains, which can be found in different proteins with diverse functions.
Tertiary Structure
The tertiary structure is the overall three-dimensional arrangement of the polypeptide chain. In an aqueous environment, nonpolar amino acids tend to be buried within the protein core, while polar amino acids are exposed on the surface. The tertiary structure is stabilized by various interactions between amino acid side chains, including:
- Electrostatic interactions
- Hydrogen bonds
- Hydrophobic interactions
- Van der Waals forces
- Disulfide bonds (between cysteine residues)
Quaternary Structure
Quaternary structure refers to the spatial arrangement of multiple polypeptide chains (subunits) in a protein complex. This level of structure is relevant for proteins composed of two or more subunits. The same types of interactions that stabilize tertiary structure also contribute to quaternary structure.
Denaturation
Denaturation is the loss of a protein’s native structure and function due to changes in environmental conditions, such as pH, temperature, or exposure to certain chemicals. Denaturation disrupts the interactions that maintain secondary, tertiary, and quaternary structures, but not the peptide bonds of the primary structure. If the changes are mild or short-lived, denaturation can be reversible (renaturation). However, intense or prolonged changes can lead to irreversible denaturation.