This paper will examine the molecular functioning of the genes and proteins that control and regulate the circadian rhythm that is so fundamental a part of every organism on this planet. It will consider the role that proteins such as PER and TIM play, not to mention photoreceptors like CRY. The paper will not only consider the facts that are known about circadian rhythms on the molecular level, but also what is not known including whether or not circadian controls are centralized or localized in the case of mammals.