php mysql and javascript can be used for creating web apps, but all those three has different areas to look for.
javascript is a client side language (it can also be run on the server side)
php is a server side language (it powers facebook)
mysql is a database , that stores the data of the app.
As your question, when you can use javascript for front end and back end then why use php and mysql? i use Meteorjs, which goes with the saying: one language to rule them all. you write the back end and the front end of the app, using javascript. again you would be needing a database to store the data, meteor for default use Mongodb.