Can you send a university a protected PDF of undergraduate transcripts for graduate applications?
Usually, universities have explicit and hard rules about transcripts. Here's an example. See what you can find out from the institution you're applying to. If they accept official transcripts electronically, they probably only do so through some third-party service, and not by you uploading a PDF to their system.

Such a PDF will likely be considered an unofficial copy. It's still useful for considering applicants, but they'll likely need another version to verify its authenticity. Typically, for US grad schools, this can be an official version submitted by your previous institution through a third-party web service, or a signed printed version sent in a sealed envelope.