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).
I know of some schools in Florida that actually inflate or deflate your GPA based on what school you went to. So it does matter for certain schools. But there's tons of other factors to take into consideration- major, courseload, etc.