Denatured proteins lose

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Denaturation breaks the weak forces that hold the folded protein together, so the higher-order shapes unravel while the amino acid sequence remains intact. The secondary structure (like alpha helices and beta sheets) is stabilized mainly by hydrogen bonds along the backbone, and denaturing conditions disrupt those bonds. The tertiary structure arises from a mix of hydrophobic interactions, ionic bonds, hydrogen bonds, and sometimes disulfide bridges between side chains; these interactions are also disrupted, leading to loss of the overall 3D fold. The primary structure, the actual sequence of amino acids connected by covalent peptide bonds, stays unchanged under typical denaturing conditions. So proteins lose their secondary and tertiary structures, which is why their folded function is impaired, even though the sequence itself is preserved.