July, 2005

by Chris Masterjohn

What is a Molecular Formula?

A molecular forumla is a series of letters and numbers that indicate which atoms, and how many of them, are in a molecule.

The letters are the symbol of an element, and indicate which atom(s) are in the molecule. The numbers are shown in subscript, and represent how many of that atom are in the molecule.

What Is an Atomic Symbol?

A symbol is an abbreviation for an element (you could think of the word "element" as meaning a specific type of atom). Symbols are one or two letters, and always have the first letter capitalized, and the second letter, if present, lower-case.

Some common atomic symbols are C for carbon, H for hydrogen, O for oxygen, and N for nitrogen. Two examples of symbols that are more than one letter are Na for sodium and Cl for chlorine.

The Molecular Formula of Water

An example of a molecular formula would be the one for water, which is H₂O. The "2" that is subscripted immediately after the H indicates that there are two hydrogens. The fact that no number is subscriped after the O indicates that there is only one oxygen.

Note that the number indicating how many of an atom are in a molecule must always be subscripted. A number that is not subscripted indicates the number of molecules. For example, 3H₂O would mean three molecules of water, each having two hydrogens and one oxygen.

The Molecular Formula of Cholesterol

Sometimes certain functional groups — a small group of atoms within the molecule that gives the molecule a certain function or classification — are shown separately in larger molecules to give more information about the molecule's structure.

For example, the molecular formula of cholesterol could be written as C₂₇H₄₅OH, which gives us more information than writing it as C₂₇H₄₆O.

In both cases, there are 46 hydrogens, but the first way of writing the formula shows us that there is an OH, or "hydroxyl" group, which makes cholesterol an alcohol. The OH group also has other important properties that are discussed in later lessons.

August, 2005
by Chris Masterjohn

Cholesterol is a molecule. All molecules are made of atoms. From the structure of an atom to the covalent bonds of a water molecule, if it's all Greek to you, keep reading! Sit tight... you are about to quickly master the basic concepts of chemistry...

The Atom

Atoms are considered to be the most basic and fundamental particle of matter. They are made of positive, negative, and neutral charges. The positive charges are called protons. The negative charges are called electrons. Finally, the neutral charges are called neutrons.

One of the basic tendencies of nature is the tendency toward electric neutrality. That's a fancy way of saying that nature prevents the building up of positive and negative charges in one spot by balancing them out. In order for this balancing to occur, there are two laws:

• like charges repel each other.
• opposite charges attract.

The result? Atoms! Atoms contain equal numbers of positive and negative charges. So the number of protons in an atom is equal to the number of electrons. Since neutrons are not charged, the number of neutrons can vary.

The picture below is a model of oxygen, which shows how these particles are arranged in the structure of an atom.

In the figure shown above, the protons and neutrons are clustered together in the center of the atom, the nucleus. The electrons are shown orbiting around the nucleus. Electrons behave more like a cloud surrounding the atom, but the picture shows individual particles to make the concepts easier to understand.

Oxygen has eight protons and eight electrons. Electric neutrality! Its number of neutrons doesn't affect the charge, so it will vary.

Remember that one oxygen in the cholesterol molecule? Keep it in mind as we move along...

Notice that the electrons are arranged in different shells. The inner shell contains two, and the outer shell contains six. Most shells are considered to be full when they contain eight electrons, but the first shell always fills up with only two.

So, an atom like sodium that has 11 electrons will have a third shell. The first would contain two, the second eight, and the third one. An atom like hydrogen, which contains only 1 electron, would have only the first shell.

Regardless of how many shells there are, the outer shell of each atom is called the valence shell. Keep this in mind when we discuss covalent bonds!

Nature Always Fills the Valence Shell

Do you remember what the first tendency of nature was that we discussed?

Right... a tendency toward electric neutrality.

Let's add one more: the tendency toward a full valence shell. Some atoms naturally have a full valence shell. Most atoms do not. For those atoms that do not have a full valence shell (which usually would contain eight electrons, except for hydrogen and helium, where it would contain two), something has to change.

So nature's tendency toward a full valence shell will lead to one of two things:

• The gain or loss of electrons
• Covalent bonding

We'll discuss covalent bonds first.

Covalent Bonds Make Molecules

The cholesterol molecule is made of covalent bonds. All molecules are made of covalent bonds. Since the cholesterol molecule is so large and complicated, we'll use the water molecule as our example.

Do you recognize any terms you just learned within the word "covalent"?

Covalent = Co - valent

A covalent bond is a bond where two atoms share part of their valence shell. This is one of nature's ways of satisfying the tendency toward a full valence shell.

Consider the picture below, which shows an oxygen and two hydrogens, which are the atoms that make up the water molecule.

Notice that none of the three atoms above have full valence shells. How many electrons does the oxygen need to make its outer shell full? Each hydrogen?

The oxygen needs eight electrons total in its outer shell, and it has six, so it needs:

8-6= 2 electrons.

The hydrogen needs two total in its outer (only) shell, and it has one, so it needs:

2-1= 1 electron.

Say you and a friend both wanted to start a similar type of business, but neither could raise the startup cash on your own. What would you do? Pool your resources together! Your friend gets to go in business despite only having part of the money she needed to start, and you do as well.

This is exactly what the two hydrogens and the oxygen do. If the first hydrogen shares one of its electrons with the oxygen, in exchange for the oxygen sharing one of its electrons with the same hydrogen, the hydrogen's valence shell will be full (with two), and the oxygen's will be one step closer to being full (with seven.)

A second hydrogen sharing in the same way will fill its own valence shell (with two), and will complete oxygen's (with eight.) Thus, a water molecule is born!

The picture of a water molecule below hits this lesson home:

In the figure above, the hydrogen on the left and oxygen share two electrons together. One came from the hydrogen, one from the oxygen. The hydrogen on the right does the same. The other six electrons on the oxygen belong to the oxygen alone.

Since water is made of covalent bonds, it is a molecule. Not all chemical bonds make molecules though. Keep on reading to find out why...

But first, let's quickly recap:

There are two tendencies in nature:

• the tendency toward electric neutrality
• the tendency toward a full valence shell

The tendency toward electric neutrality results in atoms, which contain an equal balance of positive and negative charges.

The tendency toward a full valence shell results in covalent bonds, in which two atoms pool their electrons together and share part of their valence shells so they both end up with full outer electron shells.

But there is one other way that atoms can achieve a full valence shell...

Ionic Bonding

When two atoms pool their electrons together in a covalent bond, they both wind up with more electrons in their valence shell. But take a look at the structure of the sodium atom below.

Sodium has 11 electrons: two in its inner shell, eight in its second shell, and one in its valence shell. Unlike the oxygen, which was able to fill its valence shell with only two electrons, sodium would have to gain seven! That's a lot of work!

Take a closer look. Do you see an easier way to gain a full valence shell? Remember, any of the shells can be the valence shell, as long as it is the outmost shell.

It would be much easier to just lose one electron than to gain seven. So the easiest way is to just get rid of the one electron on the outside, and the already-full shell underneath it becomes the valence shell!

But where would the electron go?

...Simple. It would have to find an atom that wanted to gain one electron. The picture below shows the structure of the sodium and chlorine atoms, and the transfer of the lone electron. This is a special type of reaction called an oxidation-reduction reaction.

Oxidation is the loss of an electron. Reduction is the gain of an electron. The picture above shows the sodium atom becoming oxidized and the chlorine atom becoming reduced. Another way to say this is that sodium reduces chlorine and chlorine oxidizes sodium.

Uh-oh.

Now that we've satisfied nature's tendency toward a full valence shell, do you see what's happened? Now sodium and chlorine both have different numbers of electrons and protons! We've disturbed nature's first rule:

• the tendency toward electric neutrality

Remember, the atoms were made in the first place to balance the positive and negative charges. Now that sodium has lost an electron, it has a positive charge. Now that chlorine has gained an electron, it has a negative charge. Neither are neutral any more.

Something must change. /p>

An atom with a different number of protons and electrons is called an ion. If the atom has more electrons than protons, it is a negative ion,. If it has more protons than electrons, it is a positive ion.

Ions disturb nature's tendency toward electric neutrality. In response, nature forms the ionic bond.

Remember that opposite charges attract? Since the sodium is now positive, and the chloride (the name for ionic chlorine) is now negative, they become attracted to each other. They stick together tightly, but each has its own electrons. There is no valence sharing.

Sodium and chlorine now become sodium chloride... table salt!

SSince there is no valence sharing, there is no covalent bond. Since there is no covalent bond, there is no molecule. There is no such thing as a "molecule of salt"! Instead, ionic bonds like those within salt form crystals...

What Makes a Molecule a Molecule

The picture of water molecules below shows how the molecules would be arranged in, say, a glass of water.

The solid black lines above indicate a covalent bond. The dotted lines show weak bonds between the hydrogen (red) of one water molecule and the oxygen (blue) of another. These bonds are very different from covalent bonds and are fleeting. They are constantly being broken by the movement of water molecules. For a further explanation, see the lesson on the

hydroxyl group.

Notice that every single water molecule has the exact same number of hydrogens, and the exact same number of oxygens. Each molecule has one oxygen and two hydrogens. We designate this "molecular formula" as H_2/sub>O.

While the water molecules are attracted to each other, the attraction is an entirely different kind of bond from the bonds within the water molecule. Each molecule is a distinct entity.

Now look at the next picture, which shows the structure of a salt crystal. Notice that the bonds between all of the atoms are the same kind.

In the salt crystal, sodium chloride, or NaCl, has one atom of sodium (Na+) for every atom of chlorine (Cl-). But as long as this ratio stays constant, you can have as many or as little atoms as you like, and you still have sodium chloride — you still have table salt.

This is why we don't call ionic compounds "molecules." There is no distinct unit. A crystal can be big or small.

A molecule is defined by the precise number of each atom within it. H₄O₂ is not water. The bonds within a molecule never occur between molecules.

An ionic compound is defined by the ratio of atoms within it. The precise number doesn't matter. NaCl is sodium chloride and Na₁₀₀Cl₁₀₀ is sodium chloride. A whole crystal has the same type of bond between every atom, so the type of bond can't distinguish any sub-unit as a "molecule."

Cholesterol is a Molecule

Cholesterol is a molecule. Each atom within it is covalently bound to another. It does not contain ionic bonds. Cholesterol does, however, contain a special type of covalent bond called a polar covalent bond. So does water.

Of the seventy-four atoms in the cholesterol molecule, only two of them form the hydroxyl group. But the hydroxyl group is not only important because it makes cholesterol an alcohol, but becuase it is the only polar part of the molecule. This small polar region is water-soluble. The rest is fat-soluble.

But what does all this mean...?

The Hydroxyl Group is Polar

The hydroxyl group consists of an oxygen atom bound to a hydrogen atom. The picture below shows an oxygen and hydrogen atom that have not formed a bond.

Each of the above atoms is neutral. This means it has neither a positive nor a negative charge. Both atoms each have an equal number of protons (positive charges) and electrons (negative charges) that balance each other out.

Although we can count the number of protons and electrons, the pictures are shown simplistically to cut to the chase, so don't show the individual particles.

Also, electrons whir about the nucleus as if they are a cloud around it, so it is shown that way above with the yellow cloud representing the electrons and the circle representing the nucleus (where the protons are.)

But when the two atoms form a bond, and a hydroxyl group is formed, something changes. Between the two, there are still an equal number of electrons and protons, so the group is neutral. However, the electrons tend to hang out more on one side than the other, so their negativity concentrates a little more on that side. Naturally, the other side becomes a little more positive.

You can see in the above picture that the electron cloud surrounds the whole hydroxyl group, but it is much more drawn towards the oxygen. Since the group as a whole is still neutral, but just has an uneven distribution of charges, we call these partial charges.

The oxygen in a hydroxyl group is called partially negative, and the hydrogen is called partially positive. Since there is a concentration of opposite types of charge on each end of the group, it is called polar, having positive and negative poles. (Like a magnet or the earth has opposing "north" and "south" poles.)

Water as an Example of a Polar Molecule

Notice that the hydroxyl group found in cholesterol is also found — twice — in... water!

You can see in the above diagram that since water is composed of two polar bonds, it also has concentrations of charge. The oxygen is partially negative and both hydrogens are partially positive.

I'm sure you've heard the saying "opposites attract." Right? Sometimes that works with people, but it always works with magnets (north and south attract)... and electric charges (positive and negative attract).

Polar Molecules Mix with Water

If you have a glass of water, even when it looks like it's not moving, two things that you can't see are always going on. First, weak bonds are forming between the partially positive hydrogens of one molecule and the partially negative electrons of another molecule. Second, they are constantly being ripped apart because the molecules are always moving around.

Have you ever mixed oil and water together only to find that most of the oil sits on top, and what little cracks the surface of the water is in large droplets that float back up? Yet if you mix, say, sugar, it dissolves and seems to disappear.

The reason is that the sugar contains hydroxyl groups.

The partially positive hydrogens on the sugar are attracted enough to the partially negative oxygens of water, and vice versa, that each sugar molecule has the strength to break through the weak bonds between individual water molecules. The oil has no partial charges (it is non-polar), so it has no attraction to the water's partial charges.

Cholesterol is Amphipathic

Cholesterol has a small, water-soluble polar region that dissolves in water, but nearly the entire cholesterol molecule is non-polar, which will NOT dissolve in water — like oil. This makes cholesterol an example of an amphipathic molecule — part water-soluble, part water-insoluble.

The picture below demonstrates this property.

In the picture above, the water molecules form a "cage" around the polar hydroxyl group. When you dissolve sugar in water, each sugar molecule is bound up in a similar "cage", surrounded by a cluster of water molecules.

BBut most of the cholesterol molecule has no attraction to the water. If you tried dissolving pure cholesterol in water, like the oil, it would sit at the top. Yet one interesting thing would happen at a microscopic level: all the cholesterol molecules would arrange themselves so that the tiny polar hydroxyl groups were pointing into the water!

As you peruse through the information on this site, you will see that this interesting property is very important to how cholesterol works in your body.

Cholesterol contains a region with four hydrocarbon rings. A hydrocarbon ring is a ring of carbon atoms which are each connected to each other. There are usually six carbons but there can be many different numbers of carbons. Two hydrogens extend off each carbon, and thus hang off the edge of the ring.

For simplicity, rings are usually drawn without showing the carbons and hydrogens. It is assumed that at each corner in the ring there is a carbon, and the presence of the hydrogens is also assumed.

For example, the picture below shows two ways of showing cyclohexane, which is a hydrocarbon ring with six carbons:

In the above picture, the example on the left is how ring structures are typically shown, and is how the ring structures are shown in the picture of cholesterol on the main page of Cholesterol Chemistry 101.

The example on the right is identical to the one on the left, but shows the carbons and hydrogens in detail. Each corner of the ring represents a carbon, and each carbon may be assumed to hold two hydrogens.

Notice that each carbon is bound to four other atoms: two other carbons, and two hydrogens. Each hydrogen is only bound to one atom: a carbon. Carbon always binds to four other atoms, and hydrogen always binds to one atom. So, if another structure is shown protruding off a ring structure, then the carbon it is connected to must be bound to one less hydrogen.

Always assume the number of hydrogens connected to a carbon to be four, minus the number of other atoms it is shown binding to.

Double Bonds in Hydrocarbon Ring Structures

Another way the number of hydrogens bound to a carbon can decrease is if there is a double bond between two carbons. When this occurs in a ring structure, a second line is drawn between the two corners, representing the second bond, as shown on the left below:

The molecule above is benzene, which is the same as cyclohexane but with alternating double bonds instead of single bonds.

The molecule shown on the right is equivalent to the one shown on the left. Because each carbon is involved in a double-bond, there are three, instead of two, bonds for each carbon without involving the hydrogens. Therefore, each carbon can only bind to one hydrogen instead of two.

Cholesterol Contains Hydrocarbon Rings

In the case of cholesterol, there are four hydrocarbon rings. Three of them are six-carbon rings, and one of them is a five-carbon ring. There is a hydroxyl group protruding off one ring, a double bond in one, two protruding CH₃ groups in the middle, and a hydrocarbon tail protruding off the end. Each of these structures reduces the number of hydrogens bound to the carbons to which they are attached.

Because hydrocarbon rings involve a bond between carbon and hydrogen, which is non-polar, the hydrocarbon ring portion of cholesterol is fat-soluble and is not soluble in water.