Protein Permutations

Published: 2014-11-18 10:02 |

Category: Science |

Proteins are some of the most varied, complex, and mind-bending models studied in biology. Built from our genetic code, proteins have multiple levels of organization which can be modeled independently and corporately to learn about their functions based on their structures. Because of this complexity, proteins offer great fodder for the biology classroom and helps tie molecular genetics (DNA, RNA) into the bigger picture of our bodies as a corporate unit.


creative commons licensed ( BY-NC ) flickr photo shared by alumroot

Starting small

Protein is the direct result of your genetic sequence. The building blocks (amino acids) are coded in the strand and your body uses that template to build everything. A common activity is to have student decode the template and come up with a simple amino acid sequence – this is the primary structure. The sequence of acids themselves will determine the rest of the protein’s properties.

After the acids are sequenced, they form either an alpha-helix (spiral) or a beta-sheet (flat). The structure of the helices and sheets begins to give the protein its shape in space. As they are formed, hydrogen bonds and attractions or repulsions are realized and the macrostructure begins to fold into it’s functional shape. These are the secondary and tertiary structures of the protein, and this is where students often get confused. Each time a fold is made, considerations have to be taken for adjacent functional groups and their influence on every other part of the model.

Finally, a protein’s quaternary structure comes from its interaction with other protein subcomponents. Because these molecules are so large and complex, they often form in constituent pieces which then fit together into the functional macromolecule. Your blood, for example, is a protein called hemoglobin, and it’s actually four protein subunits working in conjunction with one another.

Working with Students

A great way to have students think through the folding and conjoining aspects of protein formation is to use something like this origami-based activity where students fold a subunit in part one, and then join those units together to form a working structure in part two. They have to think through how the structure of one subunit contributes to the function of the macrostructure once it is completed. They also quickly learn that if proteins are not shaped properly, they will not function correctly.

Pedagogical Implications

Modeling in science is incredibly important. It’s hard to remember that everything we “know” about tiny structures like atoms and proteins comes from many, many years of environmental observation. We can’t actually see how a protein is folded, but we can make models based on how they interact with the environment. Students don’t realize this, and it’s important to point that out.

Everything in science is based on observation, yet we expect students to learn about structures and their functions, yet they can’t be seen. We have to teach them that first, observation is more than seeing something, and second, that models can help us make those observations. Show a student a physical model of a protein or a bone and ask them to describe what they see and feel and let the science happen. Giving them the experience of trying to fold a protein will help internalize the complexity of our bodies and what a marvel they are.

Too often, biology is complicated pictures, graphs, and data sets. It isn’t made real for students, and building models of blood cells from paper is one way to do that. Making the abstract concrete through modeling and analyzing the building blocks helps students see biology as something to be experienced rather than memorized is a big task, but it’s an important one.


Root-Bernstein, R. & M. (1999). Sparks of genius: The 13 thinking tools of the world’s most creative people. New York: Houghton Mifflin Company.

Turnbough, M.; Martos, M. (2012, August 16). Venom!. ASU – Ask A Biologist. Retrieved November 18, 2014 from

Comments are always open. You can get in touch by sending me an email at