Interesting question. These are questions which are only used to get someone to repeat what they have said, whether because you haven't heard, or you don't believe what you heard. The convention is that you repeat as much as the sentence as you can, replacing the bit you didn't hear/understand with a question word.
Bill: I'm going to Leeds for my summer holidays.
Jack: You're going where for your summer holidays??
If Jack just said "where are you going for your summer holidays?" Bill might think Jack wasn't bothering to listen to him. By echoing Bill's sentence structure, Jack shows that he was listening, but there was just one word he didn't get (or believe).
I have to say, tone of voice does a lot of the work here.