Unless you need to keep using the original file as a presentation you can use Keynote to export the presentation as a PDF. There are dozens of good to great annotation tools for PDF, some of which are designed specifically for a college student's needs.
I use PDF Expert (good for highlighting, annotating, and PDF page shuffling)
Many prefer iAnnotate
If you do a search for note taking apps for college you should turn up several suggestions, most which will let you take notes on/with a PDF.