Education Corner

Using Mini-toobers and pushpins to model the primary structure of a protein

The helical secondary structure is then constructed.

The tertiary structure of a protein.

The understanding that protein structure is related to its function is a challenging concept for high school students.  As freshmen in high school, students are taught how the primary structure is constructed during protein synthesis and that the sequence of amino acids is determined by the codes on the DNA. Visualization of how this protein folds to form a 3D structure that has a particular function is more difficult to teach. To help with this visualization, teachers often use a modeling activity with beads on pipe cleaners. In our school, we have been using foam mini-toobers for hands-on modeling of this concept. These kits have been purchased from “3D molecular designs” at the MSOE Center for Biomolecular Modeling. These kits are better than the pipe cleaners because they are longer, and therefore are easier to manipulate and fold.  As an extension, the students also model the tertiary structure of the zinc finger protein. 

We, Cindy Jaworsky (Chemistry) and Meenakshi Bhattacharya (Biology) attended an RCSB PDB workshop at Rutgers and decided that our Advanced Placement (AP) Chemistry and AP Biology students’ participation in the HIV Video Challenge would be a great extension to their learning.  Additionally, this project would hold them to a high standard after the completion of the AP exams.  The video challenge has an obvious link to the AP Biology and high school biology curricula.

To reinforce biological concepts and relate protein folding and the video challenge to AP Chemistry, Jaworsky focused on intermolecular forces and covalent bonding, important concepts in AP Chemistry. The class studied how intermolecular forces and covalent bonding create the active site on a protein that holds a drug. After the Synthesis of Aspirin Lab (Randall, 2007) Cindy Jaworsky uses the Molecule of the Month on Cyclooxoygenase to explain how aspirin is held by a protein, which leads to aspirin’s desired efficacy and possible side effects.  

In order to produce an educational video for the challenge, the students worked together for three weeks in groups of three or four. The third place winner was a team from our school, who described how HIV has been used to fight cancer. The students showed how modified HIV (that is unable to cause infection) is used to modify the T cells which then target and kill cancer cells. These students used UCSF Chimera to show how the related proteins work in the host cells, some groups used UCSF Chimera and free-hand drawings to show how the HIV attacks and enters the T-cells of the host, while others used the 3D animation to show how the HIV RNA uses the host cell machinery to make DNA and then insert itself into the host DNA. In all, 51 students took part in this competition and each group produced a video that explained a unique concept of HIV infection and/or control of infection. Their videos can be viewed at http://education.rcsb.org/videochallenge/index.php.

One of the students said: “The PDB video challenge was an interesting project because it led my group to think about HIV at a smaller and structure-based scale. Using Chimera was difficult at first but we figured it out using YouTube videos and online tutorials (from rcsb.org). It took a lot of time to master the software.”

Another group’s presentation was about how the drug Ritonavir interacts with HIV-1 protease, and they used UCSF Chimera to clarify “our explanation of certain structure and location of mutation sites; we made changes in the protein by highlighting the two Asp-Thr-Gly sequences on the protease. Additionally because Protease is a homodimer, we had to split the protein into its component subunits and spin it to show the detailed structure. Also, when discussing the challenges of drug resistance, we highlighted the codons 82, 46, 50 and 84 for the protease where mutations related to Ritonavir often occur.”
 
A majority of the students said that through this project they learned more about the structure and function relationships of proteins. 

This HIV video challenge was very useful in that it allowed us to assess if the students really understood the structure function relationships of biological molecules. It also allowed the students to take their understanding to a new level and create a product that would be useful in educating others. In addition to the science, they also learned how to use UCSF Chimera and Blender in the process of making the videos. For many this was a novel experience and to their credit, they owned the project, became self-directed learners as they navigated through the intricacies of reading through scientific articles and worked as a team to make the final product. 

For the past few years, I have had the great good fortune to work with the RCSB PDB and Dr. Shuchismita Dutta in professional development opportunities. Workshops, especially free ones, help keep me current with resources in science education. I knew I would learn more about new ideas and resources I could bring to my classroom, but what I did not realize is that would translate into inspiring some of my students to do more. For the past two years, I have had students who have won competitions sponsored by the RCSB PDB. In 2013, students utilized resources from rcsb.org to write a research paper and visualize a protein in a novel way. In 2014, students won the Video Challenge in which they recorded a public service announcement explaining the HIV cycle, The Lifecycle of HIV.

Among the classes I teach, I have the opportunity to teach AP Biology to students who are typically ambitious and motivated high-achievers. What I have discovered that while these students want to learn and bring an energy to class that makes teaching fun, it also means that I have to be able to give them new opportunities, allowing them to use resources in new ways and use their creative skills. Students need more than information and the tried and true labs; they need chances to show what they learn and they need authentic opportunities to showcase their abilities.

With all of the resources that are open and accessible to everyone, it is my experience that students want to use the resources that are used by scientists for research. They are excited when I tell them about the classes I attend and then they get to use these same resources in meaningful ways. Some of the activities we use in school are contrived and artificial; they may serve important purposes, furthering the understanding of different concepts, but they lack the authenticity that fuels curiosity and motivation. Real resources, real questions and real problems bring out the best in students. Presenting to a real audience also brings out the students’ best work; knowing that experts, outside of school, are judging their work is more meaningful than having the teacher assess their work. Some of the difficulties with these real resources lie in the skill set needed to use them effectively.  

Nonetheless, bringing these opportunities into the classroom excites and interests students to do more. Finding or developing these challenges can be difficult.  So when I find them, I use them in a way that makes them worthwhile and gives students time to use their skills in ways that play to their strengths. I show them that they are both learning about real problems and presenting information in a way that is worthwhile.

So what happens in my classroom?  Before I present them with the challenges, I give the students experience with the resources and I make certain that they have the chance to use them at a more basic level and see how and why they are used.  With the RCSB PDB, students started with an exploration around the website where they see some of the proteins we discuss in class and begin to see how they are visualized and what is known and understood about their structure and function.  Ninth graders are exposed to PDB structures in a simple investigation of an enzyme we talk about in class.  They can see the 3D structure, get a sense of the research and begin to understand that you can see how the structure and function are related.  Later as students in AP Biology, they, again, take a tour of molecular structures, but in more depth.  The RCSB PDB is a resource the class accesses periodically through the year as different proteins come into the forefront of the topics discussed such as enzyme action; the role of transport proteins, especially aquaporins; and G-coupled proteins in signal transduction.  In 2013, I required all students to research a protein.  They were allowed to work with a partner, a common practice that is useful in that it allows students the chance to have someone to bounce ideas, while sharing the responsibility and workload.  

In 2014, the challenge centered around HIV/AIDS.  This is a topic that has always been a part of the curriculum I teach because of the relevance of the disease to the lives of the students.  Incorporating the challenge became a natural fit.  Since December 1st is World AIDS Day, I find a way to bring the biology of the disease and an understanding of the virus to class, regardless of the level.  

As the Video Challenge is different from the paper in the original competition, I use it differently in class.  In this case, the challenge is assigned in the spring after the AP Biology test, which for this school year will be May 11, 2015.  Students will have the freedom and the time to explore different ways to work on their presentations while adhering to the topic of the Video Challenge, Detecting and Combating HIV in 3D. Last year, I did not require submission to the contest and I did provide them alternative projects to match the different strengths of the students. For example, they could do an alternate visual presentation such as a power point.  Since the students are accustomed to following rubrics, I wrote my own set of rubrics, modeled after the guidelines that were posted for the project. As a result of these procedures, I had fewer submissions for the competition, but the students that chose to work on the video were excited and showed expertise in the topic.  I will follow these same procedures this year, so students will work on the topic in a medium of their own choice. Regardless of the medium, all presentations will be viewed in class.

The challenges posed by the RCSB PDB provide students an authentic opportunity to learn, a chance to demonstrate what they have learned and an authentic audience to evaluate their presentations.  Using this in the classroom by incorporating prior activities that lead up to these challenges and emphasizing the authenticity of the challenges can result in a rich experience for the students as well as the teacher.