I have to go on a freeway a lot. will my lung be permanently be affected if i drive with my car windows down?

Probably not: The air you breath on the freeway is the same whether windows are up or down, its the way cars are constructed. Heavy smog associated with a long drive(exposure) day after day, can be of concern because of the presence of carbon monoxide, sulfur trioxide and other combustion products, but probably not associated with permanent damage. Consider a different route to work if it is bothersome.

Depends: Probably only if you get stuck in traffic and have to breathe exhaust fumes excessively ...