"...Later still, she (the teacher) may start asking the question "What is it?" (pointing to a pen).. What is it? so that students get a chance to hear what question sounds like".
What is it? = I am less confident you'll be able to give me an answer
+ What is it? could mean "What's wrong?"
What is this? = I expect you to be able to give me an answer
+ What's THIS ? could mean "What are you doing?" ( about unexpected behaviour, for example )