Amino Acid Structure and Protein Folding

Amino Acids

Proteins are composed of amino acids joined by peptide bonds. Macromolecules consisting of 20 different amino acids are typically made up of 100 to 300 amino acids.

Amino acids are enantiomers, and all share the same general structure. Proteins exclusively utilize the L-series of amino acids.

Amino acids are linked covalently through a peptide bond. Two amino acids react via their carboxyl and amino groups to form this bond through a condensation reaction.

An amino acid may exist as a Zwitterion, possessing a protonated basic amino group and a deprotonated carboxylic acid group, resulting in a net zero charge.

Properties of the Peptide Bond

The peptide bond exhibits partial double bond character between the C and O atoms, and between the C and N atoms. This partial double bond character prevents free rotation around the C-N axis, which favors a planar structure. The bond is also polar.

Proteins

Primary Structure

The primary structure of proteins consists of the specific sequence of amino acids linked by peptide bonds in the polypeptide chain.

Secondary Structure

Secondary structure refers to regular, repeating structures that the polypeptide chains can adopt.

• The $\alpha$-helix: This structure is stabilized by hydrogen bonds formed between amino groups (as donors) and carboxyl groups (as acceptors).
• Lamin A Basic Unit: The basic unit of Lamin A is the thread A, which consists of a fully extended chain fragment. Each turn covers a specific distance, rotating 180 degrees per unit. This structure is stabilized by hydrogen bonds.
• Antiparallel $\beta$-sheets: Adjacent strands run in opposite directions.
• Folds (Twists): A long strand with a twist, placed side by side.

Upper secondary structures (Motifs): These are discrete aggregates of secondary structures commonly observed in protein-protein interactions.

Tertiary Structure

The tertiary structure is stabilized by noncovalent interactions, including van der Waals forces. It may incorporate various secondary structures.

Quaternary Structure

The quaternary structure involves the noncovalent association of two or more polypeptide chains (subunits).

Protein Domains

Domains fold independently, forming compact units. They are typically formed by 50 to 300 amino acids and are connected by segments lacking regular structure. One type of domain can be found in different proteins and may possess distinct functions.

Disulfide Bonds

Disulfide bonds confer resistance to high temperatures ($t^{\circ}$) and prevent denaturation by urea, but they are cleaved by $\beta$-mercaptoethanol.