Does the university of your undergrad make a difference to your medical school appli?

[merykonil]

Does the university of your undergrad make a difference to your medical school application?
I am in the Nanotechnology Engineering program at the University of Waterloo, which is the best engineering program at the best engineering institution in Canada.

I am planning to take some of my pre-med courses like Biology and Immunology at my University. Would it make a difference if my university is not that well known for undergraduate studies in sciences? Or does my MCAT score compensate for the quality of my university?