we use do to ask someone if he has something or do something ..ex: Do you have pen? Do you go to work? would use to ask someone if he like or need something or help would you like some tea? would you need help?

why was the sky blue?

p.p.:had+V3(two things happened in past but not the same time ) ex:He had talked on the phone before he started cooking. p.p.c:had+been+v+ing(used for an activity which started in the past before some things else in the past) ex: I had been talking to him before I sent that email.

It is the first meal we have got after we get up at morning.

They have same meaning