Protein Secondary Structure – MBB 222 (W5-1, p.11-21)

Vocabulary flashcards cover key terms from pages 11-21 of the lecture, emphasizing backbone geometry, dihedral angles, secondary structures, hydrogen-bonding patterns, and special roles of Proline and Glycine.

α-Helix

Right-handed, compactly coiled secondary structure in which every backbone C=O hydrogen bonds to the backbone N–H of the residue four positions downstream (n, n+4), giving a rigid cylindrical core with side chains projecting outward.

β-Sheet

Secondary structure composed of two or more β-strands hydrogen-bonded together; forms a pleated, extended array with side chains alternating above and below the sheet.

β-Strand

Individual, extended zig-zag segment of polypeptide that pairs with others via backbone hydrogen bonds to form a β-sheet; depicted with an arrow showing N→C polarity.

β-Turn

Four-residue tight turn that reverses chain direction; often stabilized by an n, n+3 hydrogen bond and favored by Gly and Pro.

Secondary Structure

Local, repetitive arrangement of the polypeptide backbone (e.g., α-helix, β-strand/sheet) defined mainly by backbone dihedral angles φ and ψ.

Conformation

Rotational position (torsional angle) about a covalent bond; describes how a molecule’s shape changes via bond rotation without breaking covalent bonds.

Configuration

Fixed spatial arrangement of atoms bonded to a chiral center (e.g., L vs. D amino acids); cannot be changed without breaking covalent bonds.

Torsional (Dihedral) Angle

Angle describing rotation about a bond between two planar units; in proteins the key dihedral angles are φ and ψ.

φ (Phi) Angle

Dihedral angle around the N–Cα bond of the peptide backbone, variable for each residue and critical to overall conformation.

ψ (Psi) Angle

Dihedral angle around the Cα–C′ (carbonyl carbon) bond of the peptide backbone, variable for each residue.

Peptide Bond Planarity

Resonance locks the six atoms of the peptide bond in one plane, fixing its dihedral angle at ~180° and limiting backbone freedom to φ and ψ rotations.

Right-Handed Helix

Helical structure that twists clockwise when viewed from the N-terminus toward the C-terminus; the common sense of the protein α-helix.

Extended Conformation

Stretched, zig-zag backbone geometry characteristic of β-strands where φ and ψ are obtuse.

Antiparallel β-Sheet

β-sheet in which adjacent strands run in opposite N→C directions, allowing nearly linear hydrogen bonds and greater stability.

Parallel β-Sheet

β-sheet whose neighboring strands run in the same N→C direction; hydrogen bonds are angled and slightly less stable than in antiparallel sheets.

Pleated Sheet

Zig-zag appearance of β-sheets resulting from alternating Cα positions along the strand; produces a rippled, pleated topology.

Side-Chain Orientation in α-Helix

R-groups radiate outward from the helical axis, minimizing steric clash and enabling interactions with other structural elements.

Side-Chain Orientation in β-Sheet

In each β-strand, side chains alternate up and down relative to the sheet plane, facilitating packing and intermolecular contacts.

n, n+4 Hydrogen Bond

Specific backbone hydrogen bond pattern that stabilizes the α-helix; C=O of residue n accepts an H-bond from N–H of residue n+4.

Proline (Helix-Breaker)

Amino acid whose side-chain forms a ring with the backbone N, fixing φ to an acute angle; disrupts α-helix hydrogen bonding and is incompatible with β-strand geometry.

Glycine

Smallest amino acid; side chain is a single hydrogen atom, reducing steric hindrance and favoring tight turns such as β-turns.

Chiral Carbon (Cα)

The central carbon in amino acids bonded to four different groups, giving rise to stereoisomers (L and D configurations).

N→C Polarity Arrow

Graphic convention in ribbon diagrams showing directionality of β-strands; arrowhead points from N-terminus to C-terminus.

Stereochemistry

Study of spatial arrangement of atoms; in proteins includes configuration (L/D) and conformation (φ, ψ angles).

Periodic Structure

Regular, repeating backbone geometry in α-helices and β-strands where successive residues adopt similar dihedral angles.