Soon after you drink a cup of coffee, caffeine, a strong stimulant is absorbed into your intestinal tract and into your blood. Peak absorption occurs in less than an hour, usually within thirty minutes.

Once absorbed, it is rapidly distributed into all of your body's fluids, then processed by your liver and eventually excreted in urine.

Three hours after you drink a cup of coffee, the level of caffeine in your blood will be half of what it was at its peak.  Six hours after drinking coffee, you will have eliminated most of the caffeine from your system.

Once caffeine is distributed throughout the body, it stimulates your nerves and causes adrenalin to be released. Adrenalin is the main neuro-transmitter that changes your levels of energy and alertness.

Effects Of Adrenalin

Adrenalin increases your heart rate, which results in more blood pumped per minute.  This blood carries extra oxygen to your brain, making you feel more alert.  Caffeine also directly stimulates the spinal cord and the cortex of the brain, which enhances these alert feelings.

Many people experience a dip in energy several hours after drinking coffee. Though scientists aren't exactly certain why this happens, a possible explanation may be that, after the effects of caffeine wear off, your brain needs to adjust to working without the stimulus the caffeine provided.

So, though that first cup of coffee might get you going in the morning, it might also leave you feeling fatigued half way through the day.