pallidin said:
When I first awaken, I often feel groggy.
But as time goes on I feel more awake and alert(even without coffee, etc...)
What changes in my body that makes me more alert?
Hope that's not a silly question.
Silly?! That isn't remotely silly. First, you have to remember a few things about sleep, the first of which is pretty basic:
1.) Your heart rate and BP fall, as does your respiration.
2.) Your neurochemistry adapts, with signaling molecules such as melatonin being a single well-known example.
3.) Drugs, including the endogenous variety, have half-lives. You wake up, a little drugged essentially.
Most people feel thoughts "coming back to them", and often people who have undergone a grievous loss or other such find that it takes a minute or two before they remember this. Your brain activity as a diffuse series of interactions is depressed during sleep.
Now, some people feel perky as hell when they wake up, but usually those people have well adjusted circadian rhythms, and slowly wake up. If you wake up to an alarm or some other abrupt external stimuli your body takes some time to adjust. Often people will note their body temperature has dropped as well, in concert with their BP and HR, and this also takes time to recover. Your brain has just jolted from either REM sleep (which includes paralysis), or very even brain-wave patterns. As you know, our brains may be "electric" but the signaling between neurons is chemical. It takes time for the body to change the balances of your basic neurotransmitters from "SNOOORE" to "I'm AWAKE!"
Sleep, is not perfectly understood either, and while much of what occurs is known, there are about 7 critical chemicals which moderate "alert and awake" vs. "drowsy or asleep". Drugs such as Modafinil usually deal with 3 or 5 of these, and even then the effects are a bit unclear. Here is some excellent information on sleep in general: http://www.ninds.nih.gov/disorders/brain_basics/understanding_sleep.htm
Here is one warning: you sound perfectly healthy, but if you wake up with a headache, feeling short of breath, if you find yourself nodding off during the day, if you snore, have a weight problem... this grogginess COULD be the result of sleep apnea. Unlikely given your description of becoming wakeful, but I feel it is worth mentioning.