You can fairly easily substitute peptides (short proteins) from the outside of the body, but you have to supply them by injection. They don't survive the low pH of the stomach unless you encapsulate them into an acid-resistant matrix. Short peptides are often very local and short acting, present only during specific times of the embryonic development (for example, morphokines). However, assuming that you have a peptide hormone like insulin, you can administer it systemically and it will work. There is however over 350 peptides/short protein that are extracellular and many of them are locally restricted. So, you should not just inject them. The problem with larger proteins is, that they do not cross the cell barrier like these small peptides (which have a receptor for crossing/uptake). Many of the broken genes carriers (patients) of genetic diseases have in their genome, are coding for large intracellular proteins, often even tissue-specifically expressed. You cannot get them easily to the right destination, nor can you get them easily into the cell. You have to use a virus that encodes them and infects the cell. Read some Cell / Molecular Biology textbook if you want to learn more details.