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Well, to be specific, caffeine (like most psychoactive drugs) exerts its effect on us by altering the activity of some of our neurotransmitters. Neurotransmitters are the nervous system's way of conveying messages between neurons, and also to muscle tissue. Some neurotransmitters that caffeine is known to increase the activity of are norepinephrine, dopamine, and serotonin. The increase in norepinphrine is likely what causes the heart rate to increase, however each of these neurotransmitters has some stimulatory effects. Norepinephrine, however, is a powerfully stimulating neurotransmitter; it is associated with the 'fight or flight' response, which of course includes an increased heart rate. I believe it may effect epinephrine as well, which is similar to nor epinephrine except that it is also a hormone (and a neurotransmitter). This means it has both short and long lasting stimulatory action.

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