'하다' is rarely used. It's like 'be' in english. Usually they use 'am', 'are', or 'is'.
Instead of '하다' we use '한다' or '합니다' depending on target audience.
'합니다' is more polite expression.
If we want to use it in question, '하나?', '하나요?', '해요?', or '합니까' should be used.
I think this type of conjugation is one of big barriers in learning Korean.
It must be better that you remember conjugated forms instead of original one for this kind of words.