Learn Spanish (Latin America): ¿Tú bebes leche en el desayuno?

The verb is beber (to drink), which is a regular -er verb. Because the subject of the sentence is tú (you), you drop the -er at the end of the word and replace it with -es.

Where is the word for "do" in this Spanish question?

Spanish does not use extra helper words like "do" or "does" to ask questions. You just take the normal statement (Tú bebes leche meaning "You drink milk"), add question marks, and raise your pitch at the end of the sentence.

Do I always have to say tú at the beginning?

No, you can safely drop it and just say ¿Bebes leche en el desayuno?. The -es ending on bebes already makes it perfectly clear that you are talking to "you". Adding tú just makes it sound a bit more emphasized.

Why does it say en el desayuno instead of just translating "at breakfast" word-for-word?

In English, we say "at breakfast", but in Spanish, the natural way to say this is literally "in the breakfast" (en el desayuno). When talking about meals in Spanish, you almost always need to include the word for "the" (el or la).