If you're unfamiliar with the PS2 controller, it's well worth familiarizing yourself with the layout of the right-hand buttons before starting a Chemistry class.
The classes require you to press a random sequence of buttons as they pass through the center of the screen. As the classes progress, the sequences get faster and begin to incorporate the shoulder buttons as well as the four right-side face buttons.
Rewards
Chemistry 1
Passing Chemistry 1 unlocks the chem set in Jimmy's dorm room, and the ability to make your own firecrackers.
Chemistry 2
Passing Chemistry 2 unlocks the ability to make your own stink bombs.
Chemistry 3
Passing Chemistry 3 unlocks the ability to make your own itching powder.
Chemistry 4
Passing Chemistry 4 unlocks the ability to fill your inventory capacity for firecrackers, stink bombs and itching powder.
Chemistry 5
Passing Chemistry 5 unlocks the ability to use your chemistry set more than once per day.