Biological Chemistry: Protein Structure 2

Vocabulary flashcards covering protein structure concepts from a lecture.

Secondary Structure

Local spatial rearrangement of the backbone of a protein segment, without considering the position/interactions of R groups. Formation is dictated by conformational constraints and mainly directed by hydrogen bonds within backbone atoms.

α-helix

Coil-like structure stabilized by H-bonds where the CO of each amino acid is H-bonded to the NH of the amino acid four residues further toward the C-terminus (n+4). Backbone atoms are on the inside, R groups face the outside.

β-sheet

Formed by the arrangement of multiple β-strands side by side, held together by H-bonds (backbone) between adjacent strands. Can be parallel or antiparallel.

Loops (Turns)

Points where a polypeptide chain reverses direction, often connecting ends of antiparallel β-sheets. Stabilized by H-bonds and often involve proline or glycine.

Ramachandran Plot

Visual representation of allowed Φ and Ψ angles for each residue in a protein, showing restricted, characteristic ranges of values for different secondary structures.

Tertiary Structure

Overall 3-D arrangement of ALL atoms in a polypeptide chain, including secondary structure elements, amino acid side chains and additional chemical components (cofactors).

Hydrophobic Effect

The predominant weak interaction that stabilises tertiary structure where hydrophobic amino acid side chains cluster in the protein’s interior to form a compact hydrophobic core.

Protein Folding

Process by which a polypeptide chain assumes its biologically functional 3-D structure (“native conformation”), driven by thermodynamic stability and achievement of the lowest free-energy state.

Quaternary Structure

3-D arrangement of multiple separate polypeptide chains (folded in tertiary structures) into complexes.

Oligomers/Multimers

Complexes of multiple polypeptide chains (subunits). Dimers (2 subunits), trimers (3 subunits), tetramers (4 subunits).

Conjugated Proteins

Proteins that contain additional chemical components, known as cofactors.

Cofactor

Additional chemical components in a protein. These can be prosthetic groups (tightly bound) or cosubstrates (loosely bound).

Isoelectric Point (pI)

The pH at which a protein is overall uncharged.

Protein Data Bank (PDB)

Archive (https://www.rcsb.org/) where the 3-D structural data determined for all biomacromolecules are deposited.