A yes/no question is only negated when the speaker has an expectation of the answer. Therefore, it often carries an annoyed or concerned tone.
- Isn’t he happy? (I assumed he was happy.)
- Aren’t we late? (I wanted to get there on time.)
Notice that ‘not’ is contracted to the verb which takes the first position in the sentence.
- Is he not happy? — Isn’t he happy?