The words protean, protein sound the same but have different meanings and spellings. Why do protean, protein sound the same even though they are completely different words?
The answer is simple: protean, protein are homophones of the English language.
Readily taking on varied shapes, forms, or meanings.
Exhibiting considerable variety or diversity: "He loved to show off his protean talent” ( William A. Henry III).
Any of a group of complex organic macromolecules that contain carbon, hydrogen, oxygen, nitrogen, and usually sulfur and are composed of one or more chains of amino acids. Proteins are fundamental components of all living cells and include many substances, such as enzymes, hormones, and antibodies, that are necessary for the proper functioning of an organism. They are essential in the diet of animals for the growth and repair of tissue and can be obtained from foods such as meat, fish, eggs, milk, and legumes.
Definitions from The American Heritage® Dictionary of the English Language, 4th Edition and Wordnik.
Homophones (literally "same sound") are usually defined as words that share the same pronunciation, regardless of how they are spelled.
If they are spelled the same then they are also homographs (and homonyms); if they are spelled differently then they are also heterographs (literally "different writing").