Neurotransmitters and Mood

I think it is safe to say that the most interesting organ in the body is also the most confusing. Even when you understand all the functions of the brain, it is really difficult to comprehend how quickly all these functions occur. One such example is the release of neurotransmitters. I took CIS Anatomy and Physiology in high school, and my class spent a good three weeks discussing the role that these chemicals play in our body, including how they are released, how drugs affect them, etc. However, something that was not covered much was how these affect our moods. I understand that certain neurotransmitters make us feel happy, and that a lack of certain neurotransmitters can have negative emotional effects. Something that baffles me, though, is why we sometimes wake up in a bad mood, and whether neurotransmitters have anything to do with it. I know that hormones have a lot to do with our emotions, but certain disorders like depression are caused by neurotransmitters. So why does this happen? Are we predisposed to these types of things, or do our brains just "do" it?