Summer Research Program for Science Teachers

Allison Granberry

Hostos-Lincoln Academy

Bronx, New York

August 2005


Molecular Structure of Proteins


Course:  Living Environment (New York State Curriculum) or Honors Biology


Grade:  9th/10th


Unit:  Cellular Structure and/or Protein Synthesis


Objective:  Students will develop a concept of how a watery environment such as the cell cytoplasm, affects the shape of a protein.  In the first activity, the students will construct and test how certain molecules like water while others hate water.  Then using molecular modeling, the second activity will explore how the concept of water loving and water hating help to form the shape of a protein.


Background Information:  Proteins are long chains of amino acids that are linked together by peptide bonds.  There are 20 different types of essential amino acids each of which has its unique side chain with its unique chemical property.   The shape or three-dimensional folding pattern of a protein is derived from not only the sequence of amino acids but also the type of side chain that the amino acid contains and the interaction of these side chains with their environment. 

The folded structure of a protein is actually thermodynamically less favorable because it reduces the disorder or entropy of the protein.  So, why do proteins fold?  One of the most important factors driving the folding of a protein is the interaction of polar and nonpolar side chains with the environment.  Nonpolar (water hating) side chains tend to push themselves to the inside of a protein while polar (water loving) side chains tend to place themselves to the outside of the molecule.  In addition, other noncovalent interactions including electrostatic and van der Waals will enable the protein once folded to be slightly more stable than not. 

When oil, a nonpolar, hydrophobic molecule, is placed into water there is a reduction in disorder of the water molecules around the oil, that is, water molecules do not interact with the oil but instead have to be structured around the oil. This interaction lowers the entropy. By contrast if you remove the oil molecule from the water there will be an increase in disorder or entropy of the water molecules. Now if you take oil molecule and mechanically disperse it through out the water by stirring, it will eventually reform a globular shape. This globular shape allows for the reduction in the number of nonpolar molecules being exposed to water and actually slightly increases entropy as water molecules are liberated by the burying of nonpolar molecules to the center of the globular structure. 

Since proteins have nonpolar side chains their reaction in a watery environment is similar to that of oil in water.  The nonpolar side chains are pushed to the interior of the protein allowing them to avoid water molecule and giving the protein a globular shape. There is, however, a substantial difference in how the polar side chains react to the water.  The polar side chains place themselves to the outside of the protein molecule which allows for their interact with water molecules by forming hydrogen bonds.  The folding of the protein increases entropy by placing the nonpolar molecules to the inside, which in turn, compensates for the decrease in entropy as hydrogen bonds form with the polar side chains and water molecules.


Overview of Activities:  There are two sets of activities within this lesson. The first activity involves the students forming 3-dimensional models of simple compounds including water, ethyl alcohol, and methyl alcohol.  Upon completing these models students will examine how these 3 polar molecules interact with each other and with non-polar molecules.  Students will be allowed to develop their own idea of how these molecules are related or not related and then test that concept.  This is a 60 to 80 minute activity.  Time for this activity can be reduced by having molecular models prepared for students to observe, and not allowing students to build the molecules.

In the second activity students will construct a model of protein.  Although there are multiple rules about how a protein will fold, this activity will only focus on the side chains that are either water loving (polar) or water hating (nonpolar).  This is a 45 minute activity which should either follow the first activity or a discussion of water loving or water hating molecules.  For an advance class it is strongly suggested that acid/base side chains be included.




Activity One

Activity Two

*Copies of Lab Sheets

*Gum drops (3 colors)


*6 test tubes w/rack (per group)

*10ml graduated cylinder

*Stocks of

        Isopropyl Alcohol

        Ethyl Alcohol

        Vegetable oil (corn)

        Mineral oil

        Olive oil


*Small squares of wax paper

(for use when students mix contents of  test tubes)

*Pre-cut amino acids

         (see template)

*7 white and 8 yellow pipe        

         cleaners—at least 8in

          in length

*Toober (see resources for

        where to purchase)





National Science Education Standards:   Content Standard A:  Ability to do scientific inquiry; Content Standard B:  Structure, Property of Matter; Content Standard C:  Matter, Energy and Organization in Living Systems.

Living Environment*:  Standard 1-Inquiry, Analysis Design:  1.1a;  1.2a, b;  2.3b,c;  3.4a;  Standard 4-Content:  2.1i  (*NY state standards)



Individual Mini-Toobers can be purchased from:

3D Molecular Designs

2223North 72nd Street

Wauwatosa, Wisconsin 53213-1807


To view amino acids using Rasmol:

School of Biomedical Science

Curtin University of Technology

Perth, Western Austrialia


Note activities for part one of this lesson were adapted from:

Cornell Institute for Biology Teachers

Cornell University

Ithaca, New York