In protein chemistry, what does the term secondary structure specifically refer to?

Introduction:
Proteins are described at multiple structural levels. This question distinguishes secondary structure from primary, tertiary, and quaternary arrangements by focusing on what is meant by regular local folding patterns such as alpha helices and beta sheets.

Given Data / Assumptions:

• Primary structure: amino acid sequence.
• Secondary structure: repetitive, local backbone conformations stabilized mainly by hydrogen bonds.
• Tertiary structure: overall 3D fold of a single polypeptide chain.
• Quaternary structure: association of multiple polypeptides.

Concept / Approach:
Secondary structure refers to recurring patterns formed by backbone hydrogen bonds: alpha helices (i to i+4 hydrogen bonding) and beta sheets (inter- or intrachain). Turns and loops are also part of secondary structure. Side chains influence stability but the defining feature is backbone geometry and hydrogen bonding.

Step-by-Step Solution:

Verification / Alternative check:
Secondary structure assignments from crystallography and NMR (e.g., DSSP) classify residues as helix, sheet, turn, or coil based on backbone hydrogen bonding and geometry, not on side-chain arrangements alone.

Why Other Options Are Wrong:

• Primary sequence: defines but is not itself secondary structure.
• Tertiary arrangement: describes the overall fold, not local motifs.
• Quaternary assembly and domain modules: involve multiple chains or higher-level organization.

Common Pitfalls:
Assuming side-chain interactions alone define secondary structure or conflating motifs (e.g., helix-turn-helix) with whole-protein tertiary arrangements.

Final Answer:
regular local folding patterns of the polypeptide backbone