With iTunes U 3.0 and later, students can annotate assignments in PDF format and then turn in the annotated PDF as homework.
If a student uses an iPad (4th generation or later) or an iPad mini 2 or later, the PDF can be annotated and turned in all within iTunes U. But on older devices, the student must send the PDF from iTunes U to a PDF editor. The student can annotate the PDF in the separate app, then return the PDF back to iTunes U on the device and turn it in.
Learn more about iTunes U on the iTunes U support page.