What is a molecule? -- in my notes, I have written down that the bonding of the subunits in hemoglobin is a molecule even though there are no covalent bonds -- so what exactly constitutes a protein molecule?  A molecule in biochemistry is what stays together in the cell and can be isolated such that all the subunits stay together when subjected to mild separation techniques. That is, if the atoms all stay together in the same superimposable way from one structure to another, then that structure is a molecule even though it is held together by non-covalent, weak bonds.