Protein Structure

Flashcards covering key vocabulary and concepts from the lecture on protein structure. Focuses on protein folding, stabilizing interactions, primary and secondary structures, and related topics.

Conformation

The spatial arrangement of atoms in a structure generated by rotation about C-C single bonds.

Native protein

Proteins in their functional, folded state.

Protein stability

The tendency of a protein to maintain its folded state.

Folding

The process in which a protein acquires its three-dimensional shape.

Van der Waals interactions, Hydrogen bonds, Ionic bonds (aka “salt bridges”), Hydrophobic interactions, Disulphide bonds

Weak, non-covalent interactions that stabilize proteins.

Water's role in protein folding

A hydrophobic group in water immobilizes an ice-like ‘shell’ of molecules around it, decreasing entropy. Clustering minimizes surface area and immobilizes fewer water molecules, promoting protein folding.

Prions

Misfolded proteins that can cause misfolding in neighboring proteins, leading to infective diseases.

Primary Structure

The sequence of amino acids linked by peptide bonds.

Partial double bond nature

The characteristic of the peptide bond that makes it rigid and planar.

N-Ca and Ca-C bond angles

Angles designated f (phi) and y (psi) which describe the rotation around the N-Ca and Ca-C bonds, respectively.

Ramachandran plots

Plots illustrating the allowed f and y angles due to steric hindrance.

Secondary Structure

Particularly stable local conformations of adjacent amino acids in a polypeptide chain.

α-helix

A common secondary protein structure stabilized by hydrogen bonds between the ith and i+4th amino acid.

β conformation/sheets

A secondary structure where strands of the peptide backbone are fully extended and arranged in sheets.

β Turns

Connect ends of an antiparallel β-sheet.