The levels of structure which are broken when a protein is denatured are the secondary, tertiary, and quaternary structure.
Secondary structure: This level of structure describes the local folding pattern of the polypeptide backbone and is stabilized by hydrogen bonds between N-H and C=O groups.
Tetiary structure describes how regions of secondary structure fold together – that is, the 3D arrangement of a polypeptide chain, including a helices, b sheets, and any other loops and folds. Tertiary structure results from interactions between side chains, or between side chains and the polypeptide backbone, which are often distant in sequence.
Quaternary structure: Some proteins are composed of more than one polypeptide chain. In such proteins, quaternary structure refers to the number and arrangement of the individual polypeptide chains.
