This model simulates Nirenberg and Matthaei's work in 1960s--cracking genetic code! Users may input nucleotides to synthesize an 18-bases mRNA and translate it. Users may examine the mRNA sequence, codons, peptide length, and involved amino acids to decipher genetic code.
HOW TO USE
NetLogo version: 6.0.2 or higher
1. Press on "Synthesize mRNA"
2. Input nucleotide(s). Must be capitalized, A, C, G and/or U. Any other letters will lead to an error user message. Click on "OK".
3. Press on "Translate mRNA".
HOW IT WORKS
1. The mRNA is synthesized based on the types and ratios of input nucleotides, not the order. E.g., an input of "UUUUA" will generate a mRNA containing more "U" than an input of "UA".
2. The mRNA is read from 5' to 3' end.
3. No start codon is needed in this simulation.
4. A peptide appears at the bottom of simulation window simultaneously to display the number of amino acids.
5. The simulation only lists the types of involved amino acids, not the linear sequence of the peptide.
6. Translation will be terminated when ribosome encounters a stop codon.
Student In-class Work Example
Students may be asked to think how genetic code might be deciphered and why it is important.Teachers may introduce Nirenberg and Matthaei's work through a short video or relevant reading for students to gain the basic understanding about the process of deciphering genetic code.
Students may conduct a preliminary exploration on the module. They may input various combinations of nucleotides (A,C,G,U), synthesize and translate mRNAs, and examine the involved codons and amino acids. In this phase, students may learn how to use the module and how it works. They may also realize the level of complexity of cracking genetic code.
After students gain a certain familiarity with the module and process of cracking genetic code. Teacher may let students consider how to crack genetic code more strategically. Teacher may guide students to consider the following strategies:
- Start with the codons containing fewer types of nucleotides, e.g. UUU, AAA, CCG, etc
- Work collaboratively
Then teacher may put students in small groups and assign only two nucleotides to each group. Teacher may assign same two nucleotides to two groups to compare results. A big blank genetic code table may be used for whole class sharing and discussion. Deciphering genetic code can be intensive and exhausting. Teacher may let students work for 10 minutes and then have them share their results on the blank genetic code table. It is very important for them to articulate the evidence and how it determines the code. When students come up with different amino acids for a codon, it will be great moment for a discussion. When students learn for each other through class sharing and discussion, let them work for another 10 min.
Teacher may add start codon "AUG" into a mRNA and let students to translate the sequence, or discuss degeneracy of the genetic code based on students' results.
Depending on students' results, teacher may ask students to determine the amino acid for a codon that has not been cracked in class. Ask students to write a paragraph to explain how they determine the amino acid.
CREDITS & REFERENCES
There are several existing paper and pencil activities on genetic code, see related resources below, but this module provides a more effective and engaging learning experience. This module was developed by Dr. Lin Xiang at Weber State University in 2018. If you mention this model in a publication, we ask that you include the citations below.
Xiang, L. (2018). Genetic Code. Zoology Department, Weber State University, Ogden, UT. https://sites.google.com/view/3d-science-ABM/genetics/genetic-code