Step 1: Understanding the Concept
Proteins have primary (amino acid sequence), secondary (helix or sheet), tertiary (3D fold) and quaternary (subunit assembly) structure.
Step 2: Detailed Explanation
Denaturation by heat, acids or alkalis disrupts hydrogen bonds, ionic interactions and other weak forces. So secondary, tertiary and quaternary structures change or are lost.
Covalent peptide bonds are not broken, so the primary structure remains intact.
Final Answer:
The primary structure remains unchanged, option (A).
\[ \boxed{\text{Primary}} \]