Stories from the Scientists
About Biotech Ads on AE WYW Index

Activity 3: Determining the Structure of a Molecule


Students will determine whether they can recreate a molecular structure based on an illustration.

Background Information

Determining the structures of large molecules, such as DNA and proteins, can be difficult because each is made up of an unique combination and arrangement of thousands of atoms. X-ray crystallography can provide scientists with some information on the overall shape of these large molecules. First the molecule is crystallized, then an X-ray beam is directed through the crystal. The orderly arrangement of atoms in the crystal diffract (deflect) the X-rays into a pattern of spots on photographic film. Using complex mathematical equations, a scientist can translate the locations and intensities of the spots into information about the positions of the atoms in three dimensional space. Thus, James Watson and Francis Crick could calculate that DNA had a helical shape based on the X-ray diffraction patterns that Rosalind Franklin provided.


For each group

  • stick and ball molecule kit or clay in several different colors, straws, and scissors or colored marshmallows and toothpicks
  • paper
  • pencil


You may want to prepare several samples of stick and ball molecules for the students.


  1. Divide each group into two teams. Have each team create a simple molecular model using the molecule kit or balls of clay attached to straws.
    Different colors of clay should be used to represent different types of atoms. If you wish, you may have students create models of real molecules, or they can create their own designs. They should not show their completed molecule to the other team.
  2. After each team has made its molecule, have the students place the model so it sits on a flat surface. Then ask them to draw a representation of the model as it is seen from the top. Encourage students to use different sized dots to represent the different types of atoms. They may want to use different patterns or shadings to represent different depths from top to bottom.
  3. Have teams exchange their illustrations. Then ask each team to try to reconstruct the molecule based on the illustration they have received.
  4. Allow students to compare their reconstructions with the original models.

Discussion Questions

  1. Was the reconstruction easy or difficult? Why? (Answers will vary.)
  2. What other information would have made the reconstruction easier? How could you have obtained that information? (Answers will vary.)
  3. Did similar molecular structures produce similar patterns in the illustrations? Why or why not? (Answers will vary.)
  4. How is this procedure similar to using X-ray diffraction patterns? How is it different? (Students should recognize that they are mapping the actual loction of "atoms" in this activity, rather than the deflection of light of the atoms, as is done in X-ray crystallography.)


Resource Book Index: Stories from the Scientists

Winding Your Way Through DNA Resource Book Index

Winding Your Way Through DNA Lectures Index

About Biotech Index

Custom Search on the AE Site