The university probably offers you the ability to download the PP (or if they don't, ask them, because they should). Once you can download it, there are several Power Point compatible apps on the iPad, and most will export as PDF. Once you have the PDF there are any number of great PDF annotation tools available for the iPad.
My personal picks are Keynote for the Power Point and PDF Expert for PDF annotation. If you search for student and note taking on the forum (using the websites Google Custom Search at the top right) you'll probably find suggestions more attuned to a college student.
Good luck.