What is the difference between them all
A Schema (or schemata) is a cognitive system which helps us organize and make sense of information. For example, you may have a conceptual framework or developed a schema that all homeless people are rude. Because of this schema, you organize your actions around it and more readily look for information that supports this view while discarding information that disagrees with this perspective.
A prototype is the BEST example or cognitive representation of something within a certain category. For example, if I ask you to imagine a dog, what do you imagine? You may consider a German Shepard your prototype for a dog by which you compare all other dogs. So if you see another dog, you could say that other dog is small (compared to your prototype), heavy, ugly, beautiful, etc.