Are you a pupil? или is you are pupil?

Are you a pupil? - Ты ученик?

Are and is are the present forms of the auxiliary verb to be. We use is with the third person singular. We use are with all the persons plural. You is used both in singular and plural. That's why we use are with you. We can't use both is and are with you.

Are you pupils? (plural). - Вы ученики?

I am a pupil. We are pupils.

You are a pupil. You are pupils.

He is a pupil. They are pupils.

Interrogative.

Am I a pupil? Are we pupils?

Are you a pupil? Are you pupils?

Is he a pupil? Are they pupils?