Chemistry of Coffee: Science Behind the Black Nectar

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Depending on your affection for coffee, you might call it black nectar, black gold, or life-blood—some of us get more extreme than others. Like anything else in life, there is a chemistry of coffee.

Whatever you call it, it’s coffee, and it has a lot of power backed in every single bean.

Different aspects of coffee impact your health, your stamina, awareness, reaction time, and more. We’ll get into the nitty-gritty of it all right here.

Coffee Cherry Structure

First thing’s first, we need to look at the structure (anatomy) and composition of the coffee fruit. The photo below shows the natural coffee fruit and its anatomy.

coffee cherry structure and anatomy


Source of image maybe or yoddoikafaedoichaange

Coffee contains a vast amount of antioxidants, which are used to help combat issues in your body that slip past your immune system.

Our bodies naturally oxidize, which affects our aging process and how our body handles stress.

But it’s not so simple.

You need to roast coffee in order to get those antioxidant benefits, and you might actually get more benefits from light-roasted coffee as opposed to a dark roast.

That’s because there’s a higher concentration of chlorogenic acid in light roast, which is an antixodant and anti-inflammatory agent.

Chlorogenic acids and caffeine work together to give you the health benefits of coffee. We have created a caffeine and chlorogenic acid calculator so that you know how much of these two compounds you drink each day.

Light roasts also has the highest concentration of other antioxidants as opposed to dark roast coffee.

You can find evidence of antioxidants in coffee from mass marketing campaigns, most notably, Nestle’s “Green Coffee” that claims to contain a higher percentage of polyphenols.

Polyphenols are the term used to describe the profile of antioxidants, which are found in red wine, chocolate, and other foods that you’ve seen described as healthy or cancer-fighting.

Coffee usually gets grouped together with those.

Compounds of Coffee

Biological compounds are the basic building blocks of anything living, especially coffee.

We previously talked about chlorogenic acids, but there are also three other coffee components that you should know about besides chlorogenic acids.


Caffeine is a naturally occurring plant product and a mild stimulant (which we will get into later). It’s the most referenced aspect of coffee.


diterpens in coffee

Diterpenes are happy inside the oils of coffee and are derived from cholesterol. In western coffee making techniques that involve paper filters the diterpenes are absorbed. In European methods such as Turkish coffee and Scandanavian boiled coffee, these molecules are passed on to the finished product.



This is where your coffee gets its color.

If you just dropped beans into water, it’s just going to look dirty, but melanoidins are created during the roasting process as a result of a chemical breakdown and structural change.

As we mentioned earlier, you don’t get all the benefits from coffee until you roast it.

Melanoidins allow those traits and benefits to come through.

Coffee components come into play when you discuss roast type, volume, milligrams of caffeine in a daily dosage, and any health benefits.

Let’s discuss the various ways that coffee affects your body, for better or worse.

Where Coffee Acts in the Body

Effects on Body

We know that anything we eat will affect all of our bodies, in one way or another.

Coffee is no different, but there are positives and negatives to consider.

The primary areas that coffee impacts your body are your stomach, heart, digestive tract, numerous muscles, and your brain.

Due to the high metabolic rate of coffee, it enters our bloodstream very quickly and goes through us equally quickly.

The second that coffee touches the inner walls of your mouth, it’s in your bloodstream. It has its effects everywhere, but now let’s see how it behaves once consumed.

Positive Bodily Effects of Coffee

Coffee Effects and Benefits

Coffee serves a multitude of benefits but has a few drawbacks if you aren’t careful with how much you consume.

The first thing that you might notice after drinking coffee is how it raises your blood pressure and heart rate.

Some people are hypersensitive to the effects of caffeine, which can be related to a matter of genetics.

Coffee has cardiovascular benefits, so long as you aren’t consuming too much caffeine in a single day.

For most healthy adults in their respective BMI ranges, about 400 milligrams of caffeine is acceptable each day, provided you are not substituting coffee for a good night’s sleep.

It’s been speculated, in more instances than one, that a lack of sleep or low quality of sleep may be related to heart disease. Caffeine can keep you awake at night.

As for the cardiovascular benefits, some are still emerging.

With how popular coffee is in the western world, and the introduction of a more coffee-based culture in the eastern world, coffee studies are constantly going on.

Coffee could be helping to move a p27 protein into mitochondria, offering benefits such as restoring heart muscle and tissue.

In short, it could help prevent cardiovascular disease, when consumed in healthy increments.

Coffee can boost your metabolism, which makes it an excellent pre-workout beverage, especially if it’s consumed prior to a cardio-based workout.

Coffee aids in breaking up fats at a faster rate, thanks to the introduction of multiple chemical reactions from the roasting and brewing process.

That benefit actually carries on further down as well.

There are rather comical mentions of coffee when it comes to expediting a bowel movement, and despite the humor surrounding it, there’s also truth to it.

The acids help with movements, but everyone reacts differently.

Lastly, before we continue to the negative impacts, the caffeine in coffee acts as a stimulant (hence why it affects your heart, colon, and stomach, which are all muscles).

Your level of alertness and mental stamina can also be increased, but only temporarily.

You have something in your brain called adenosine, which basically makes you feel sleepy, and caffeine blocks the adenosine receptors for a short amount of time.

Negative Bodily Effects of Coffee

Drawbacks of Coffee

We talked about movements earlier.

For some of us, three cups a day keeps us regular and on time, but others might find diarrhea follows about thirty minutes after consumption.

Everyone is different and the chemistry of coffee may have different effects on each of us.

However, one of the potential beneficial effects of coffee is the breakdown of fats. This may not lead to weight loss because many other factors are involved. But this is a good start.

Coffee may also cause frequent urination, and in turn, dehydration.

Dehydration is also associated with constipation, so in an ironic way, your coffee could have a polar opposite outcome to what we discussed earlier, even though it’s reacting the same way.

While coffee can help you stay alert and focused, those adenosine receptors we talked about earlier come back into play when insomnia is on the table.

Since everyone reacts differently, some find that caffeine blocks those receptors for longer than others, resulting in the symptoms of insomnia.

That being said, caffeine does not cause insomnia, merely the symptoms of it: waking early, waking through the night, restlessness, impaired cognitive function as a result of sleep loss, difficulty falling asleep.

Studies have also shown that increased caffeine consumption (up to four cups per day) has been linked to an early death.

We include this here to notify you of everything, however, there are notable inconsistencies in these studies.

The subjects were more likely to smoke and less likely to work out, which are both factors in early death on their own.

While correlation is not causation, it is still important to give you as much literature from both sides of the argument as possible.

As with anything, too much of a good thing is a bad thing.

Because caffeine affects the brain, it’s not uncommon to develop a dependency on it.

This is known as caffeine withdrawal, and when you deny your body caffeine, you can experience light headaches.

These begin behind the eyes, work into the forehead and temples, and can linger for two to three days.

At this point, the best possible thing you could do is consume a little more than your daily recommended water intake.

Go from eight cups (64 oz) of water a day to ten cups (80 oz), and drink one or two coffees spaced out through the day.

Depriving your brain of caffeine can be unpleasant, so come down slowly with a coffee and water mix.

Where to Draw the Line

For as many positives that you can find about coffee, you will find as many attempted negatives.

The bottom line is this: coffee is good for you, provided that you don’t have a hypersensitivity that can bring on the symptoms of insomnia or other risks.

Slight peaks in blood pressure, spatial awareness and alertness are positive, primarily in a healthy individual.

Consuming an abundance of anything can have negative effects, so limit your consumption to 250-350 milligrams per day for optimal performance, and to prevent dependency.

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