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I thought the translation for What do you do when you get up? would be:

Was machst du, wenn du stehst auf?

But I've read it is:

Was machst du, wenn du aufstehst?

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Wieso sollte es? –  user unknown Aug 11 '13 at 14:25
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Ist schon naheliegend, weil der entsprechende Hauptsatz Du stehst auf lautet. –  chirlu Aug 11 '13 at 19:08
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2 Answers

up vote 10 down vote accepted

I think it makes more sense to look at it the other way round:

The Verb actually is "aufstehen".

The separation of the prefix in certain contexts happens because it's a "trennbares Verb" (separable verb).
When used in a main clause, the prefix moves to the end of the clause. In a dependent clause it doesn't. Since what you have in your example is a dependent clause, the thing stays together.

Also related:

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very nice answer ! –  Emanuel Aug 12 '13 at 10:50
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The verb always comes at the end in a relative clause (Nebensatz).
Wenn, weil, während, als etc. usually signify the relative clause of a sentence.

Was machst du, wenn du stehst auf?

is wrong as the verb aufstehen will be combined in a relative clause when conjugated form of stehen goes at the end.

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The gist of the explanation is right, but note that inversion occurs in all subordinate clauses, not just relative clauses. In fact, none of your examples is a relative clause or a connector introducing a relative clause. –  chirlu Aug 11 '13 at 19:06
    
I'm sorry, I meant subordinate clause, wrong words. –  thandasoru Aug 13 '13 at 4:32
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