From what I've heard, a 3.5 from Harvard and a 3.5 from a no-name state university is still a 3.5 GPA. Yes, some may say that Harvard is a better school than the no-name university -- but, coming from a non-name state university, I know that you have to work extra hard because the professors don't have a reputation to keep and have no problem failing you if you're not doing well. But, a bachelor's degree from Harvard just has a certain presence (for lack of a better word) and there's no denying that -- however I'm sure that they look at a 3.5 as a 3.5 -- maybe with some prejudice as to your undergrad institution. Just remember that there are many other parts to your application, besides GPA, that will help you show your potential as a doctor (ie: extra currics and letters of recommendation).
Good luck! 🙂