Organic Chemistry
The Basic Ideas Make Everything About Nutrition and Medicine Clearer
Often when I prescribe a medication for a patient, he
or she will ask "what is in it?".

I usually answer by saying something like "Well, it is a
drug, a single chemical called 'drugX'".

To that patients often reply: "Yeah, but WHAT IS in

The purpose of this section is to try to answer that
question in a meaninful way. This means that I have to
talk about the subject of chemistry. But don't let the
word scare you off: the ideas are actually simple.

What is Chemistry?

Chemistry is the study of, you guessed it: chemicals.
But what exactly IS a chemical? Chemicals are
incredibly tiny structures built up of atoms that are
'glued' together in particular ways.

What is ORGANIC Chemistry?
Organic chemistry is the chemistry of carbon containing
molecules. At first this might seem like a slightly odd
chemistry to focus upon, but organic molecules happen
to be the molecules of life and are incredibly complex.

What are Atoms?

Atoms are the smallest particles in matter. They are
the building blocks of all matter--everything that is a
solid, liquid gas or plasma is made of atoms. We are
made of atoms. In the whole universe, there are 90
different kinds of naturally occuring atoms (see the
periodic table to the right). Every single thing that
exists anywhere or ever has existed is therefore made
of no more than 90 basic parts called atoms. Now you
may ask: "how can that be? How can all the incredible
richness and variety of objects and living things in the
world be made up of 90 or fewer parts? The answer to
that question lies largely in chemistry. When atoms are
glued together, the structures that are created have
very unique properties and since the possible
combinations are practically unlimited, chemicals have
have a huge number of different properties. But, and
this is important, the properties of chemicals are
entirely determined by the atoms they are made of
which means that if we understand the properties of
the atoms, we can predict the properties of the
molecules (in theory). This is what makes chemistry so
useful and what allows us to do amazing things like
design drugs to treat illness. Which brings us back to
the question: what is in 'DrugX'?
'DrugX' is a chemical...a molecule (actually a tablet or capsule containing trillions of trillions of the exact same molecule). What is iniside of 'DrugX' are
atoms bound or glued together in a very particular way that gives 'drugX' very particular properties. In order to understand those properties, we have
to have a way of showing how the atoms in the chemical are connected to each other. We have to draw them

The drawing at the top right is of a molecule called palmitic acid. It's not a drug, it's a fat, but it illustrates the point: palmitic acid is molecule that is
made up of sixteen carbon atoms glued together in a chain. One end of the chain has two oxygen atoms glued to an end-carbon. The rest of the
carbons in the chain are glued to each other and to hydrogen atoms. The top-most drawing is very explicit in that it shows every single atom. Most of
the time in organic chemistry, drawings are more abbreviated and look like the second one down. The carbon atoms are not drawn but are defined as
lying at the vertices of the straight lines and only important hydrogen atoms are shown. This sort of drawing is the bread and butter of organic

Therefore, to answer the original question: "What is in 'DrugX'?", one needs to draw the organic chemical. Let's say therefore that "DrugX" is the diet
medication called phentermine. What is 'in' phentermine, or better still, what phentermine IS is a molecule whose atomic structure can be depicted by
the third drawing down. The drawing tells us a lot.

It tells us that phentermine is an organic chemical with a "benzene ring (the six-sided structure) and that bound to one carbon in that ring are four
more carbons and a nitrogen atom. The way that everything is arranged tells us that phentermine is an organic chemical called a "phenyl-ethyl-amine"
and any organic chemist with a basic knowledge of pharmacolgy would know that this means that phentermine is very likely to have effects on human
beings that are very similar to the effects of other phenylethylamines who share the basic backbone structure with phentermine but have slight
structural differences on the side.

To illustrate this point, I have drawn the strucrtures of a bunch of common phenylethylamines on this page.

Why Won't Oil Mix With Water?

Now lets use a little bit of this knowledge to explain some basic properties of matter. We all know that oil won't dissolve in water the way that sugar
does. No matter how much we shake or stir, the oil might break up into little droplets, but it never dissolves. This is a basic property of nearly all fats
as we shall see. The reason why oil and water don't mix is because water is what is called a highly "polar" molecule. Each end of the "H-O-H" molecule
is a hydrogen that acts a bit like a magnet and wants to grab onto other "magnetic" atoms of opposite charge like the oxygen in another water
molecule or the oxygen in a sugar molecule. Fat, on the other hand has lots of "H-C-H" or "hydrocarbon" bonds and these hydrogens don't act like a
magnet which makes hydrocarbons therefore "non-polar" molecules and they like to associate only with each other and not with polar molecules like
water. The key to all this is that the STRUCTURE and COMPOSITION of a molecule determines its properties and as luck would have it, living things like
humans are made of bother polar molecules and fats and the properties of these types of compounds and how they interact is key to understanding
not only digestion, calories, macronutrients and obesity, but life itself.


In order to truly understand what a medication is or what a nutrient is, one needs to understand a little bit about chemistry, specifically, the chemistry
of carbon-containing molecule which is called organic chemistry. A key concept is that the structure of organic molecules determines the properties of
those molecules and generally, organic molecules that contain lots of hydrocarbon bonds (hydrogen-to-carbon) tend to be insoluble in water (olive oil
for example) whereas carbon-containing molecules that have lots of "Oxygen-hydrogen" bonds tend the soluble in water (sugar for example).

Everything in the universe is made of atoms and there are only 90
naturally occuring "types" of atoms (called elements).
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