Learn French: Pourquoi est-ce que tu ne comprends pas ?

In French, a very common way to ask an open question is to start with your question word (here, Pourquoi for 'why'), immediately add the fixed phrase est-ce que, and then just plug in a normal statement. Here, the statement is tu ne comprends pas (you don't understand). It is often much easier than having to reverse the subject and verb!

Where exactly do the negative words ne and pas go when using est-ce que?

They always 'hug' the main action verb of the sentence. Even though est is technically a verb inside the est-ce que phrase, that whole phrase just acts as a question marker. The real action is understanding (comprends), so ne and pas go directly around it.

Would que change to qu' if we used a different subject?

Yes! Here we have que tu, which stays as two separate words because tu starts with a consonant. But if your subject pronoun started with a vowel, like il or elle, the 'e' in que would drop. For example, 'Why doesn't he understand?' would be Pourquoi est-ce qu'il ne comprend pas ?

Why does the verb comprends end with an 's'?