The phrase "What do art thou" (or sometimes "What art thou") is an archaic way of asking "What are you?" or "Who are you?". It's using older forms of the verb "to be" and the pronoun "thou".
In the Bible, it's often used in situations where someone is:
* Questioning someone's identity: Is this person who they claim to be? Are they a god, a prophet, a king, or something else?
* Challenging someone's authority or role: What gives you the right to do this? Who made you judge, king, or prophet?
Examples in the King James Version (KJV), where you'll most often find it:
* John 1:22: "Then said they unto him, Who art thou? that we may give an answer to them that sent us. What sayest thou of thyself?" (Here, the priests and Levites are questioning John the Baptist's identity.)
* John 1:19: "And this is the record of John, when the Jews sent priests and Levites from Jerusalem to ask him, Who art thou?"
* John 8:25: "Then said they unto him, Who art thou? And Jesus saith unto them, Even the same that I said unto you from the beginning."
Essentially, it's a formal, somewhat elevated way of asking about someone's identity and/or their purpose. It often carries a tone of inquiry or even challenge.
In modern English, you'd simply say "Who are you?" or "What are you?". The use of "art thou" adds a certain gravitas and formality that is characteristic of older translations of the Bible.