I’m 16, and planning to transfer to University (from a California Community College) next Fall. My GPA is a 3.8, and I’m planning to apply to UCLA, UC Berkeley and UC Davis. My question is whether my age would affect my application in any way. My dream school is Berkeley, and I’m making all of my decisions based on what will raise my chances of getting in (taking all of the Calculus series, and O-Chem Series, doing an internship with a lab etc.)
Don’t think age matters, as long as you meet requirements 
I have a friend whos studying PhD at CalTech now, hes only 21.
No, your age will not affect your application at all.
It depends on where you plan to live. Check with admissions about living in dorms as a minor. They may require you live in substance-free housing or at home.
Academically it shouldn’t be a problem.