Will it hurt my application if I don't take chemistry in high school?

Take a chemistry course.

Some schools specify the sciences required, while others only specify a number of credits. Check their websites. Among the three colleges you list, there's a decent chance that UCB might require it, though I'm not sure how UCB treats out of state students' transcripts vs the California a-g requirements.

Consider that chemistry will be on the transcript of virtually (99.999%) every other applicant to those competitive colleges. It is a foundational science course. Also, many high schools include chemistry as a prerequisite for APES.

APES isn't likely to be helpful to your app; it is not known as one of the more rigorous APs. Accordingly, it seems short-sighted to take APES rather than chemistry.

/r/ApplyingToCollege Thread