Learn French: Je me demande ce qui provoque la réaction du gène. - I wonder what causes the reaction of the gene.

In indirect questions, you use ce qui when 'what' is the subject of the action—meaning it is the thing doing the verb. Here, 'what' is the thing doing the causing (provoque). If 'what' were the object of the action (for example, 'I wonder what he causes'), you would use ce que.

Why does je me demande mean 'I wonder'? Doesn't demander mean 'to ask'?

Yes, demander means 'to ask'. But when you make it reflexive by adding the pronoun me (se demander), it literally translates to 'to ask oneself'. In English, we naturally say 'to wonder', so je me demande is how you express 'I wonder'.

Why is it du gène instead of de le gène for 'of the gene'?

In French, the preposition de (of/from) and the masculine singular article le (the) must always combine into the single word du. Since gène is a masculine noun, 'of the gene' becomes du gène.

Does provoque always mean 'provokes' in a negative way?

Not always! While provoquer can mean 'to provoke' (like starting an argument), it is also the standard verb for 'to cause', 'to trigger', or 'to bring about', especially in medical, technical, or scientific contexts like this one.