Modeling Biological Molecules
Can you develop a model of something as small and complex as an organic molecule? In this Guided Inquiry, you
will make models to see how atoms are arranged and rearranged in biological systems. Because we are investigating a part of
the world that we can’t directly see, using models helps us to actually see and make sense of what happens in a chemical
reaction. The atoms in molecules are held together by chemical bonds. Each atom has the ability to form a specific number of
bonds with other atoms. The bonding abilities of the atoms that are most common in organic molecules are as follows:
Carbon (C) – 4 possible bonds; Oxygen (O) – 2 possible bonds; Hydrogen (H) – 1 possible bond; and Nitrogen (N) – 3 possible bonds.
In this Guided Inquiry, you will make models of some common organic molecules and use these models to understand
how atoms are rearranged in the course of a chemical reaction. You will use toothpicks and colored marshmallows to construct
the models. The marshmallows represent atoms, and the toothpicks represent chemical bonds. Drawings of molecules, like the
ones below are called structural formulas because they represent how atoms are joined together to make molecules.
1. Work in pairs. As a class we will decide what color of marshmallow will represent each kind of atom. For example pink
marshmallows will represent Hydrogen; Yellow will represent Oxygen; Green will represent Carbon; and Orange will
represent Nitrogen.
2. Working with your partner, break the toothpicks in half and use them to join the marshmallows to form the molecules listed
below. Consult the first paragraph of this handout for the number of bonds each atom can form. Sketch each molecule from
the list below and use the appropriate number of bonds.
3. Construct your model molecules using toothpicks and marshmallows. Each toothpick represents a single bond or a shared
pair of electrons, and two toothpicks representing a double bond or two pairs of shared electrons. Each marshmallow
represents a single atom.
Model #
Chemical Formula
Molecules Name
#1
CO2
Carbon dioxide
#2
H2O
Water
#3
O2
Oxygen gas (molecular oxygen)
#4
C2H5OH
Ethyl alcohol
#5
NH2CH2COOH
Glycine (an amino acid)
#6
C6H12O6
Glucose
EC
N2
Nitrogen gas (molecular nitrogen)