Education Corner

AP Biology students at John H. Pitman High School were tasked with creating animations depicting an active site in catalase and the mechanistic breakdown of two hydrogen peroxide molecules. These animations were created using pipe cleaners, clay, toothpicks, and stop-motion cinematography. The data used to generate these animations were from RCSB Protein Data Bank resources, AlphaFold DB, and various scientific publications. This project represents a Science Technology Engineering Art and Math (STEAM) and Project Based Learning (PBL) approach to a common enzyme lab. Below is an anecdote depicting what the project was and meant to one of the students in the class.

During this project, I found it to be a beneficial part of my learning experience for our unit about enzymes. Like the pipe cleaners used to make the catalase model, the project was filled with mental twists and turns that were challenging for both myself and my classmates. Even though challenges can be frustrating sometimes, they help students grow and learn how to persevere through difficult content. After I completed the project, I felt a sense of accomplishment that was rewarding and made me more confident in my understanding of the content; for instance, I got a better idea of how competitive and non-competitive inhibitors were able to alter enzyme activity. I also learned how important hydrogen bonds are in the decomposition of catalase and in biology as a whole.

When the project began, I felt overwhelmed because, even though we were working in groups, the workload felt like too much to handle. I found the construction of the catalase model to be intimidating. The sequence count for the digestive enzyme was in the hundreds, and the number 527 made me scared to even begin the project. I had never worked with online models or done anything to this scale in previous science courses, so the task of crafting an enzyme seemed otherworldly. To handle this stress, I took the project day-by-day and the sequence on the computer quickly became a tangible model. Although, during the building process, it was difficult to keep the model organized because of all of the various pipe cleaners that protruded in all directions. Beta pleated sheets and alpha helices were all over the table, and moving everything around to make the perfect model became tedious at times.

In addition, I also encountered further challenges throughout the project. For instance, I had some trouble interpreting supplemental images and diagrams that were provided to the class to assist in making sense of how catalase functioned and why its structure is significant. (1)

Because I was not used to viewing scientific images that depicted complex ideas, I had difficulty making sense of what the images were showing and how I could put what the image was depicting into my own words. In order to comprehend the images, I researched further written information about catalase and connected the words to the diagrams and images.

Though numerous challenges arose throughout the project, they made the successes from this project worthwhile. The biggest success in my eyes was completing the catalase model and being able to see its structure through something other than a computer screen. It helped highlight the importance of catalase’s structure and the model helped me better understand the key concept of how structure determines function. To continue, the project also helped me gain a better grasp on active sites and how vital they are to enzymes to function properly. One of the key amino acids that is on the catalase active site, as well as the active site of numerous enzymes, is histidine. Being able to label histidine on the model was useful because it helped tie everything I had learned together and it made the idea of active sites tangible. This also highlighted the importance of the beta barrel and the significance of the tertiary structure of catalase, which helped answer questions that I had about why the structure was shaped the way it was.

In order to gain a full understanding of the content, there were additional resources that were beneficial to my comprehension. I felt that taking notes on videos on a regular basis assisted in my comprehension because it allowed me to get the concepts on paper and write them down in a place where I can refer back to them if needed. I make an effort to create notes that are colorful and highlight key ideas with images, and I have found that taking my time with my notes has both improved their quality and the quality of my comprehension. These videos were a part of the flipped-classroom model that was implemented by my instructor. In this model, students take notes as homework and then expand on the ideas in class through lectures, games, and projects. Additionally, the aforementioned supplemental images and diagrams provided by my instructor allowed me to connect depicted concepts to the pipe cleaner model and other parts of the project. Finally, being able to use the project as an example in the future when studying this material will be beneficial because I find I learn better when provided with examples that are connected to complex topics.

Video by Cristian Perez, Vanessa Hulbert, Carmen Barajas, Benjamin Vallier

To conclude, this project has proven to be beneficial to me as I have progressed in this course by improving my critical thinking skills, ability to interpret scientific images and research papers, and the ability to take effective notes. Since the conclusion of this project, many notes have been taken and the task of interpreting images has never ceased. This project that showed how catalase broke down hydrogen peroxide has provided me with many skills that have helped in other topics, such as epigenetics, cell signaling, and cellular respiration. Without this project, I feel I would not have been as successful in this course, and my other courses, as I am now.

1. The Molecular Mechanism of the Catalase Reaction Mercedes Alfonso-Prieto, Xevi Biarnés, Pietro Vidossich, and Carme Rovira
   Journal of the American Chemical Society (2009) 131 (33), 11751-11761
   DOI: 10.1021/ja9018572