The covalent bonds stay the same (which is why it's still the same molecule), apart for sometimes localized modification (e.g. protonation). The 3D structure (

The covalent bonds stay the same (which is why it's still the same molecule), apart for sometimes localized modification (e.g. protonation). The 3D structure (= shape) however, is mostly dependent on the hydrogen bonds (among other things like bisulfide bonds) between the amino acids that make up a protein. So the deprotonated variant of a amino acid side chain might not be able to interact in the same way as its protonated form, which will cause a different 3D structure for the whole protein, which in turn influences how it interacts with other molecules.