Protein Structure – Vocabulary Review

15 vocabulary flashcards covering key terms and definitions related to protein structure, folding, and classification.

Primary structure

The linear sequence of amino acids in a polypeptide chain, linked by covalent peptide bonds

Secondary structure

α-helices, β-sheets and turns, random coils; stabilized by backbone hydrogen bonds.

Tertiary structure

3-D shape that lowers free energy (G); native conformations held by noncovalent interactions, H-bonds, hydrophobic effect, and ionic interactions

Quaternary structure

2+ polypeptide units held by same interactions as 3*

Peptide bond

The planar, partially double-bonded C–N linkage between amino acids that restricts rotation

Φ (phi) angle

The torsion (dihedral) angle around the N–Cα bond

Ψ (psi) angle

The torsion (dihedral) angle around the Cα–C bond

α-Helix

A right-handed helix held by H bonds, with R groups protruding from backbone

β-Sheet

β-strands aligned side-by-side in parallel or antiparallel orientation, held by inter-strand hydrogen bonds

β-Turn

180° turn with hydrogen bonds connecting two antiparallel β-strand segments at residue 1 and 4; involves four residues, often with Gly at position 2 and Pro at position 3.

Ramachandran plot

A 2-D graph that maps allowed φ and ψ angle combinations

Fibrous protein

Long, insoluble strands or sheets that give strength or flexibility (e.g., keratin, collagen).

Intrinsically disordered protein

A protein or region lacking a stable tertiary structure, enriched in charged (Lys, Arg, Glu) and Pro residues, enabling interaction with multiple partners.

Collagen

Secondary: L-handed tripeptide unit of Gly-Pro-Hyp (Hyp introduces stabilizing H-bonds); 3*/4*: R-handed twisted triple helix

Molecular chaperone

Assist in folding

Proline and Glycine don’t form alpha-helixes because…

Proline’s rigid structure and ring; glycine is too flexible for adequate stability

a-keratin

R-handed a-helix; two strands twist to create L-handed supercoil with disulfide bonds

Motif

recognizable folding pattern with 2+ elements of 2* structure and their connections (i.e. b-barrel, b-a-b loop)

Aggregates

misfolded proteins; often form aggregates