WhatsApp is the application or the app that you use on the phone.
What's up? That is a question that you ask someone. It could signify many things - such as Hey! which is an acknowledgement or greeting. It could also mean 'how are things' or 'what's happening with you'.
Incidentally, the WhatsApp got its name from what's up. It is like checking on your friends - Hey, what's up man?
"A love affair with knowledge will never end in heartbreak." -Michael Garrett Marino