Protein Structures



            Proteins play an extremely important role in biological systems.  They help you break down your food, they support transportation of materials across cell membranes, and they act as messengers in your body (hormones).  What is the chemical basis of a protein?  Proteins are long chains of amino acids that once made in a living system will fold and form a 3 dimensional shape that will give the protein its specific function.  What causes this folding behavior of a protein?  It is in part dependent upon the water contained with in the environment of the cell the response of water loving and water hating molecules found in the proteins.


Chains of Amino Acids

Proteins are made of chains of amino acids.  Below you will see the general formula for an amino a


          H       H     O

          │       │     ║





If two amino acids were bonded together the structure would look like the following:



           H      H   O            H    O                                      H

           │      │   ║            │    ║                                       │

  HNCC N C C OH            +       HO

                          │                   │        │

                         R           H     R

*Notice that one water molecule was removed in the process of the bonding of the two amino acids.


1. In the space below draw for what you think the structural formula would be if three amino acids were bonded together.













2.  Notice the R in the above diagram.  This represents various side chains each of which can be identified as either water loving or water hating.  Recall that water hating molecules tend to be made of carbons surrounded by hydrogen atoms. Below is a chart of various side chains from different amino acids.  Identify each as either water hating or water loving.





                              H    H─C─H   H

                               │        │       │

                          C    C   CH

                               │        │       │

                               H       H       H


Leucine (Leu)





          H      H       O        H

          │      │       ║        │

     C   C  C    O

          │      │

          H      H



Glutamic Acid (Glu)







                                  C O

                                      │      │

                                      H      H


Serine (Ser)





            H    O    H

            │    ║    │





Aspartic Acid (Asp)





                            H      H

                            │      │

                        C CH

                            │      │

                     HO      H


Threonine (Thr)





                   H        H

                    │       │

                C  C H

                    │       │

            HC H


Valine  (Val)




There are twenty different amino acids and each is identified by its side chain.  Although you have only examined 6 of these twenty, it is because of these 20 side chains (R) that a protein can make the shape that it needs to in order to function in a living system. 





Model of a Protein Structure

*Obtain a baggie of pre-cut amino acid side chains, 15 pipe cleaners (8 yellow and 7 white), a role of tape, and a ruler.  You also need a Toober.  A Toober is a foam-covered wire that will be used to represent a chain of amino acids.


*Select 15 different amino acid side chains from the baggie.  Be sure to select 7 white papers and 8 yellow.  Notice that you do not have all twenty different side chains but instead you have repeats.  Divide your selection into two groups:  Water loving and Water hating.  White paper represents water loving side chains while yellow represents water hating side chains.


*Bend each pipe cleaner in half and twist it such that you have a loop.  Next tape one of the water loving side chains over the loop. Let white pipe cleaners be for water loving side chains.  Be sure that you have selected 7 of these.  Repeat the process with the yellow pipe cleaners but this time taping the water hating side chains onto the loop of the pipe cleaner.  



*Now take your Toober and place one side chain every approximately every 8cm.  You can attach the side chain by simply twisting the two unattached ends of the pipe cleaners around the Toober.


*Protein functions because of their specific shape.  Take your Toober with side chains and fold it so that the water hating molecules are to the inside of the folds and the water loving side chains are to the outside of the folds. 



Protein Structure Questions




1.  How many amino acid molecules were bonded to form your protein?


2.  Look at your neighbors protein molecule.  More than likely, all proteins models in the classroom have a different shape.  Why?  What makes your protein unique?





3.  Record the sequence of your molecule.  Remember to begin at one end and continue to the other when listing the amino acids.






4.  Sketch a diagram of the shape of the Toober in the space below.  Do not try to include the side chains but list them in the chart as to whether water loving or water hating.

Model Protein Diagram

Water Loving

Amino Acids

Water Hating

Amino Acids













5.  If you rearranged your amino acid sequence of your model, would your protein continue to have the same shape? Why or Why not?






6.   Do you think that changing the shape of the protein has an effect on the function of the protein? Why or Why not?  




7.  In your model we assume that the protein in a water based environment such as that of the cytoplasm.  What would happen if you placed your protein into a water hating environment such as a channel protein of a membrane?