Not sure about this: but as Google can read the content inside .pdf files, I guess Google can also see the links in it. And if these are dofollow links, then most probably, they will pass PR.
When you are publishing a PDF version in website, it will get a web enabled version which you can term as URL or you can treat it as a pdf file. Though I am not sure whether Google treat them as general URL or a pdf file while conferring PR of a website.