updated to OS X 10.9.3 and my mail ad other apps no longer open. The error message says that they are old versions which need to be updated. Seems they need to be moved into the applications folder but I cant do

I have just updated to 10.9.3 and my Iphoto, Mail, Photobooth,System Preferences no longer open. When I click on for example, Mail, the error message says "You cannot use this version of the application with this version of OSX. You have Mail 4.6".

Clearly these apps have missed the updating process (I suspect that is because my son has been dragging the icons around and dropping them in random places). I understand that the apps need to be in the applications folder in order to be included in the update but if I try to drag them in there I get a message saying that the "app cannot be modified or deleted because it is required by OS X". Any suggestions please?