What exactly is going on biologically at the molecular level with acne and causes breakouts? Hormonally, there is a lot going on but I'm curious about what is going on chemically.
Acne is caused by blockage of hair follicles by oils (sebum) from your skin and dead skin cells. Hormonal changes in puberty cause your skin glands to produce a lot of oil. Blocked follicles are visible as a small black dot (blackheads).
The recognizable pimples occurring during normal puberty acne form because of bacterial infection (the sebum/skin mix forms a good growth medium for bacteria). The immune system responds with inflammation (the red "base"). The pus (the white "middle") is a dead bacteria, skin and white blood cell mix.
Most treatments for acne focus on either killing the bacteria or removing the dead skin or sebum. Professional medical treatments might also focus on altering hormonal levels (this is also why the COCP usually lessens acne in women). Popular over-the-counter remedies for acne (e.g. Clearasil) usually contain a lot of alcohol which both kills the bacteria and removes the sebum, but also makes the skin dry. This in turn causes the skin to produce more sebum thus making the problem worse.