What is a Molecule? - Structure & Models

Instructor: Beth Skwarecki
Water is a molecule. Caffeine is a molecule. DNA is a (really big) molecule. Learn how molecules are constructed and modeled and explore the different types of models.


Have you ever called water 'H2O'? That's a molecule. When two atoms of hydrogen (H) and one atom of oxygen (O) are bonded to each other, they make one molecule of water.

With just three atoms, it's one of the smallest molecules you'll hear about in biology. Others, like DNA, are made of many, many, many atoms. But more about those in a minute.

Putting Molecules Together

Ball-and-stick model of caffeine
ball-and-stick model of caffeine

The way molecules are sometimes drawn (like the caffeine molecule above), it looks like they were built out of toothpicks and gumdrops. That's not too far from the truth; students and scientists often build molecules from kits to help them understand the shape of a molecule.

Think of each gumdrop as an atom. The gumdrops come in different flavors, and the 'flavors' of atoms are called elements, as in the Periodic Table of the Elements. You probably recognize some element names, like gold, helium, and arsenic.

In biology, we study molecules that are mostly made of the elements carbon, hydrogen, oxygen, and nitrogen. When a molecule contains carbon, we say that molecule is organic. The field of organic chemistry includes these biological molecules, plus others like petroleum (think oil and gasoline) that are mostly carbon and hydrogen.


Atoms connect to other atoms by making bonds to them. In our gumdrop example, the toothpicks represent bonds. Carbon can make four bonds, while hydrogen can only make one, oxygen can make two, and nitrogen can make three or sometimes four. (Why? Because of the number of electrons that 'belong' to each atom. Check out our chemistry classes to learn more.)

All of the bonds we're thinking of here are covalent bonds. This means the atoms are truly stuck together - you won't see hydrogens floating off of a water molecule.

There is another type called ionic bonding, which occurs when atoms with positive and negative charge are attracted to each other - think salt, aka sodium chloride. The sodium (positive) hangs around with chloride (negative) in the crystals in your salt shaker. But because there is no covalent bond holding the sodium and chloride together, they can float apart, or dissolve, in water.

Drawing molecules

There are different ways to depict a molecule, depending on what properties you want to show.

Ball-and-Stick Model

A ball-and-stick model looks like the gumdrops and toothpicks we've been talking about. Typically carbon atoms are shown as black balls, nitrogen in blue, oxygen red, and hydrogen white. You'll see these models when you want to study the exact shape of the molecule and how the atoms connect to each other.

Space-Filling Model

Space-filling model of H2O
space-filling model of H2O (water)

A space-filling model looks like blobs stuck together and represents (more or less) the amount of space the atoms and their electron clouds take up. Above is a space-filling model of our friend H2O. You may see this kind of model when learning about how molecules interact with each other and how they fit together.

Line-Angle Drawing

Line-angle drawing of a caffeine molecule
Line-angle drawing of caffeine molecule

When you're reading about small molecules, especially drugs, you may see line-angle drawings. These show the structure of a molecule, minus the details. Carbons are understood to exist anywhere a line bends or ends. Hydrogens aren't drawn. Once you get used to seeing these drawings, they are an easy way to understand the shape of a molecule such as a drug. (The line-angle drawing above is the same molecule, caffeine, as our earlier picture.)

Blob or Ribbon Models

DNA depicted in a ribbon model
dna depicted as ribbons

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