A .mda file is a deployment package which you can use for uploading and deploying your model in the Mendix platform. The .mpr file is your local project file/modeler project, which you indeed use to open/acces and change your local project. However when sending your project to someone else you should use the mpk extension. In contrary to the former, the .mpk file represents a project package. These can include a resource for a project, such as a specific widget or microflow, which you can import in in your moduler, but these can also include a whole project (including a snapshot of the database).
Thanks. My question: what one file has that the other doesnot. Double clicking mpr seems to extract all themes and java files folders same as mpk