Activity 3: Determining the Structure of a Molecule
Students will determine whether they can recreate a molecular structure
based on an illustration.
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
You may want to prepare several samples of stick and ball molecules for
- 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.
- 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
- Have teams exchange their illustrations. Then ask each team to try
to reconstruct the molecule based on the illustration they have received.
- Allow students to compare their reconstructions with the original models.
- Was the reconstruction easy or difficult? Why? (Answers will vary.)
- What other information would have made the reconstruction easier? How
could you have obtained that information? (Answers will vary.)
- Did similar molecular structures produce similar patterns in the illustrations?
Why or why not? (Answers will vary.)
- 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.)