Molecular Models


ball and stick molecules

Ball and Stick Molecule Building Kit

Covalent bonds are formed when electrons are shared between atoms. Hydrogen, for example, can share one pair of electrons with another atom, so we say that it forms one bond. Similarly, oxygen forms two, nitrogen usually forms three, and carbon forms four. (Remember the "HONC" rule...H=1, O=2, N=3, C=4, but note that unstable molecules can form, creating exceptions.) The ratios of atoms in various molecules are expressed by their chemical formulas. For example, "H2O" represents water, and "C6H12O6" represents glucose. However, this is only part of the story. In biology, the shape of a molcule is often just as important as its chemical formula. Enzymes, for example, need a precise 3-dimensional fit to their substrates, just like a baseball and a well-worn outfielder's glove. In this investigation we will attempt to construct molecular models of some common substances from biology. In several cases, unusual properties will emerge that couldn't have been predicted from the flat projections that are usually drawn on paper.

common groups
Common Groups

Hints: an ether is formed when an oxygen has a carbon on both sides. An aldehyde is formed when a carbon is attached to a hydrogen and double bonded to an oxygen. A ketone is formed when the C=O is in the middle of a chain of carbons. A carboxylic acid is formed when a carbon is double bonded to one oxygen and attached to a second oxygen by an -O-H group. The -O-H group on its own makes an alcohol.

The prefixes meth- eth- prop- but- pent- hex- hept- oct- non- dec- represent increasing numbers of carbons, from 1 to 10.


If you do this lesson in person, use a molecule building kit.

We will work with wooden balls to represent atoms. Hydrogens (white or yellow) have one hole, oxygens (red) have two holes, nitrogens (blue) have three holes, and carbons (grey) have four holes. Use wooden dowels for single bonds, and flexible plastic tubing for double bonds. Each hole must be filled, each "bond" must be capped. For some of the larger examples, it may be necessary to share pieces with other groups.

Experiment with each of the following examples until you are satisfied that you have the one correct solution.

On a separate piece of paper, draw each of these examples as a 3-D shape, not just as a stick figure. Color-code each sketch as needed.

If you do this lesson online, use the Build a Molecule app to construct the molecules listed below. You will be moving from simpler to more complex structures. Use the Larger Molecules tab, and click the yellow arrows to move between atom kits to find one that has all the materials you'll need for each structure. Just drag and drop atoms near each other and a bond will form. Click between atoms to break a bond. Throw unneeded pieces back in the tray and they will sort themselves out. Click Refill Kit to clear the entire screen. The teachers' guide has more instructions on using the tool, but it's fairly intuitive and you can probably figure it out after a few minutes of exploring.

Build a Molecule

Click on the image or this link to start building molecules.

Build the following

(First, try to build them using just the hints below. Then, check your work by clicking the link.)

  1. Hydrogen gas is the simplest and smallest possible molecule.
  2. Oxygen gas requires a double bond.
  3. Ozone has a chemical formula of O3
  4. Carbon dioxide requires two double bonds. (Hint: di- means 2).
  5. You are familiar with water (H2O), but hydrogen peroxide, used for bleaching hair and disinfecting cuts, has one more oxygen.
  6. Add a single carbon to water and you get formaldehyde, a carcinogen and preservative.
  7. Ammonia is the simplest possible molecule made with nitrogen and hydrogen.
  8. Methane is the simplest possible molecule made of carbon and hydrogen.
  9. Methanol is like methane, but it also has one oxygen atom as well. Also called wood alcohol, it is toxic to drink.
  10. Ethanol has a formula of C2H6O. (Hint: it requires one O-H bond!). Ethanol is the alcohol found in beer, wine, and spirits.
  11. Dimethyl ether is an isomer of ethanol; that is, it has the same chemical formula but a different structure. (Hint: it has no O-H bond!)
  12. Carbonic acid has a formula of H2CO3, and is a critical pH buffer in your blood. (Hint: it requires one double bond, and no 3-atom rings!)
  13. Acetic acid, when mixed with water, forms vinegar, and has the formula C2H4O2
  14. Urea has a formula of CH4N2O. This is how your body voids excess nitrogen from proteins that you eat. (Hint: the left and right sides are symmetrical!)
  15. Alanine is one of the simpler amino acids, from which proteins are made. Attached to its central carbon are: a hydrogen atom, an amino group (NH2), a methyl group (CH3), and a carboxyl group (CO2H). See if you can build a second one which is a mirror-image of the original.


  1. Why was carbon at the core of all the larger examples? Why not some other atom, such as hydrogen or oxygen?
  2. If you found a mirror-image of your alanine model, was there some way you could turn or rotate the two versions to make them identical? Why or why not?
  3. Why could there be right- and left-handed versions of alanine, but not urea or carbonic acid?
  4. How can molecules with the same chemical formula, such as ethanol and dimethyl ether, have distinct physical properties?
  5. When wine or beer is exposed to oxygen, the ethanol changes to acetic acid, and water is produced. Compare these two compounds and write out the conversion equation.
  6. In sci-fi movies, sometimes the idea of silicon based life is proposed as an alternate to carbon. Can you guess why? Hint: It's near Carbon on the periodic table.

Further investigation

Explore the Periodic Table of the elements with your Mac or use this online periodic table. For a more powerful Molecule Builder, try Jmol.

Critical Thinking Exercise: Learn about Di-hydrogen Monoxide, the silent killer.