The mistake that people make is that they expect to be 100% wired the second they get up from bed, while in actuality it takes an hour a two for the (enzyme that wakes you up) to start being produced in your body.

Also: caffeine doesn't make you more alert, it just borrows alertness from the future by blocking the receptors where Adenosine attaches to. The enzymes are still produced, they're not going anywhere.