In the eyes of Google, a PDF is just another web page – a web page that offers a prime opportunity to boost your content ahead of your competitors and vice versa.
The reason I say is that Google ranks PDF files in the SERPs. It is sure that it crawls the PDF files. If PDF content is fresh and relevant, it will increase your website reputation. It always better to protect the PDF files from crawlers if you think they would be destructive.
Use robots.txt to block the files from search engines crawlers
# Block the /pdfs/directory.
# Block pdf files. Non-standard but works for major search engines
Use nofollow on your links to the PDF
<a href="something.pdf" rel="nofollow">Download PDF</a>
You can also use
x-robot-tags to prevent them from indexing
HTTP/1.1 200 OK
Date: Tue, 25 May 2010 21:42:43 GMT
X-Robots-Tag: googlebot: nofollow
X-Robots-Tag: otherbot: noindex, nofollow
If you follow the first two points. The PDF will not effect your SEO, no matter what it contain.