Or if money is deposited it remains as a BitCoin?
Some exchanges, Mt. Gox being the largest, operate as market exchanges. So when you transfer via a bank transaction those funds are added to your exchange account. But then you would need to convert those funds to bitcoin. You do not need to remove those bitcoins, and at a later time you can sell those bitcoins and withdraw the proceeds as a bank transaction if you want.
Basically stocks.
So yes, ... an exchanger like Mt. Gox works basically just like an online broker does for stocks.
And just like with stocks, holding bitcoins exposes you to the risk of the value dropping as well.