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Hi, can anyone please tell me what the main differrence is beween these two sets of questions?

A B

a) Where's my pen? a) Are you listening?
b) What's the time? b) Would you like some more tea?
c) How are you? c) Isn't that my pen?
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Hi chantelzn, welcome to English Forums! I thought I had a good answer, but realized I was wrong.

The questions in group A all begin with one of the famous interrogatives, who, where, what, when, how, and why. (b)'s an interrogative pronoun, the others are adverbs.

Hopefully, someone will come by with a better answer.

Best wishes, - A.
Comments  
The questions on the right all require yes/no answers.  The ones on the left require some sort of statement to be made about circumstances (E.g. the location, the time, or the condition).

This is a particularly important distinction to make when reporting questions. 

The questions on the left will all be reported using the question word.

E.g. He asked what the time was.  (Notice the change in word order.)

The questions on the right will all be reported using if or whether.  

E.g. He asked if I was listening.  (Notice that again the word order changes.)