1. What is denaturation of a protein?

   Denaturation is the process in which a protein loses its native three-dimensional shape due to heat, pH change, chemicals, etc.

2. Which levels of protein structure are affected?

   Proteins have four levels of structure:

   • Primary structure: linear sequence of amino acids joined by peptide bonds.
   • Secondary structure: $\alpha$-helix, $\beta$-sheet, etc., mainly stabilized by hydrogen bonding.
   • Tertiary structure: overall 3D folding of a single polypeptide chain.
   • Quaternary structure: arrangement of multiple polypeptide subunits.

3. Effect of denaturation

   Denaturation generally disrupts the weaker interactions responsible for:

   • secondary structure,
   • tertiary structure,
   • quaternary structure.

   However, it does not break peptide bonds under ordinary denaturation conditions.

4. Therefore

   Since peptide bonds remain intact, the amino acid sequence remains unchanged.

   So, the structure that remains intact is: $\boxed{\text{Primary structure}}$

5. Option analysis

   • A: Primary — Correct
   • B: Secondary — Destroyed during denaturation
   • C: Tertiary — Destroyed during denaturation
   • D: Quaternary — Destroyed during denaturation

Hence, the correct answer is A.