Computational Thinking in the Process of Translation of a Protein

When my Analytical Biology (Honors Bio) class got to the topics of heredity and molecular genetics I decided to try out an activity found in the January 2018 edition of The American Biology Teacher. The title of the article was, Algorithms, Abstractions, and Iterations: Teaching Computational Thinking Using Protein Synthesis Translation. It's available for free here. The author was talking about how the process of translation mirrored the computational thinking in computer science and programming languages.  This ties in well with the NGSS science practice of computational thinking. 

Students started by working through the free app Light Bot: Code Hour. As they progressed through the levels, they learned about loops, if-then statements, and procedures. My kids (who are 8th and 9th graders) loved this. We dedicated a whole 80 minute block to working through the app. There was great collaboration when students got stuck and cheers of success when the challenge was solved.  

Then students moved onto understanding the process of translation and working on describing the process as if it were programming code.

When we did this in class, we discussed as a group what some of the commands would be and then they diagramed out the process of translation using those commands in loops and if-then statements as well as procedures that repeat multiple times. We printed out the basic commands, students cut them out and used chalk markers to create their "program" on the desks. 

As a bonus, our technology teacher coordinated with me as she had students begin an animation project in Google Slides. Students had to create an animation of transcription or translation.  She helped them with the technical issues of creating their animation and I helped them with the scientific accuracy. They were fabulous!

Transcription and Translation Modeling in Biology

4 different already "Unzipped" DNA strands 

When deciding what we'd do in class to help students understand the process of transcription and translation several blog posts gave me inspiration.  I had just done the transcription translation lab from Kim Foglia in AP Bio and I read these posts on making proteins out of beads on the Science Matters blog. Inspiration struck to combine these two labs into one for my class.

RNA nucleotides ready for transcription

I started the process backwards, by deciding which amino acids would be in the finished proteins. Since the pack of beads I already had at home only had 7 different colors, there were only 7 types of amino acids in our proteins. Two of the designed proteins were identical. I wanted students to be able to see that two strands of mRNA with different orders of nucleotides could produce the same protein because there are multiple codons that code for the same amino acid.  The visual also helps during discussions of silent mutations.

Using DNA as the template for transcription

Next, I wrote the mRNA code for each protein, making sure that I used different codons for the amino acids in the matching proteins. Then I wrote the DNA code that would be transcribed into our mRNA strands.  I felt a little like reverse transcriptase as this point! Now that I had all of the codes I wanted, it was time to prepare the model materials,

I made the beaded proteins and labeled them with a number and set them aside as an answer key for students to check when they were finished. I used a sheet of DNA molecules from Biology Corner, and used the RNA nucleotides from Kim Foglia's lab.  I color coded each DNA nucleotide we would use in the lab, laminated them, and lined them up in the correct order for each of the 4 DNA strands that we would start with in the lab. I taped the line of DNA together with two long strips of packing tape-one on the front and one on the back.  I wanted to make sure it was super sturdy since I wanted it to last for several years (OK, true confession, I want them to last forever). This was time consuming, but hopefully won't need to be repeated any time soon (unless someday I have a class with more than 4 lab groups).

Amino acids ready for translation

Kim Foglia's RNA nucleotides fit perfectly with the DNA from Biology Corner, so I printed each type of nucleotide on a different color paper and laminated them before cutting them all out. These I just put in containers for students to take as they are modeling the process of transcription as they build their mRNA molecule.  Since each RNA nucleotide (A, C, G, and U) is a different color, it's easy for us to hold each lab groups' finished mRNA molecules together to compare them.

After they finish transcribing their mRNA molecules, students move onto translating the mRNA code into a protein. Once the proteins are made, we can compare them. We focus on protein 1 and 4, which match. Then we go back to the mRNA molecules and observe that they are not the same.  At this point we can look at the codon chart, talk about multiple codons for the same amino acid, and what it means to have a silent mutation.

Comparing mRNA from strand 1 and 4 since they built identical proteins 

Here's the link to the student lab. And here's the link to the lists of DNA, mRNA, and protein strands.