Modeling Trna S Translator Function

Teaching Notes Modeling tRNA’s Translator Function

Overview: In this activity you will make a paper models of a transfer Ribonucleic acid (tRNA) and model its translator function.

Learning Goals: 1. Make a 3D model of transfer Ribonucleic acid (tRNA) using the template(s) provided. 2. Study the 3D model of tRNA to understand its structure and functions (e.g. codon- anticodon recognition and delivering the correct amino acid). 3. Apply knowledge of the central dogma and genetic code to explore the interactions between mRNA and tRNA and how that relates to protein synthesis

Educational Standards A. Common Core a. Key Ideas and Details a.i. RST.11-12.3 b. Integration of Knowledge and Ideas b.i. RI.11-12.7 B. Next Generation Science Standards a. Practices a.i. 2. Developing and using models b. Crosscutting Concepts b.i. 3. Scale, proportion and quantity b.ii. 4. Systems and system models b.iii. 6. Structure and function c. Disciplinary Core Ideas c.i. LS1.A: Structure and Function c.ii. LS1.D: Information Processing c.iii. PS1.A: Structure and Properties of Matter c.iv. PS2.B: Types of Interactions C. Advanced Placement Biology - Essential Knowledge (EK), Learning Objectives (LO), Science Practices (SP) a. EK 4.A.1 a.i. LO 4.2, SP 1.3 a.ii. LO 4.3, SP 6.1, 6.4 b. EK 4.A.2 b.i. LO 4.4, SP 6.4 b.ii. LO 4.6, SP 1.4

Teaching Notes 1. The activity is designed for a group of six to twelve students. 2. Each student (or a pair of students) will make a different tRNA model using the provided templates. The model assembling instructions remain the same for all tRNA paper models. 3. Students compare their tRNA model with the experimentally determined on include on the tRNA activity page. 4. Students will work with others in the group to compare their models, answer questions and devise a model of Translation based upon their individual models.

Developed as part of the RCSB Collaborative Curriculum Development Program 2015 Teaching Notes 5. Student will present their models and how it works to the teacher and also their peers. 6. The teacher will assess each group based upon their presentation. 7. The teacher should review the concepts with their students: a. The tRNA and mRNA interact via complementary base pairing b. The directionality of reading the RNA strand is 5’ to 3’, while that for proteins/peptides is N- to C. c. The genetic code table can be used to figure out which codon will correspond to which amino acid. The complementary sequence (read in the opposite direction) is the anticodon sequence in that tRNA d. There are no tRNAs that recognize the stop codons – specific proteins called release factors bind to those sites. The binding of release factors is currently still being actively studied. e. The 3D folding of the tRNA exposes and facilitates the functions of its business ends.

Developed as part of the RCSB Collaborative Curriculum Development Program 2015 Teaching Notes Key to Questions asked in activity:

Q. What is the function of tRNA? A. tRNA acts as a translator in the central dogma of biology – it recognizes codons in mRNA and brings in specific and corresponding amino acids to the ribosome for protein synthesis.

Q. How many bases are in anti-codon region of the model A. 3 bases

Q. Name of the amino acid attached to your tRNA model? A. This will depend of the template sheet that the student has received.

Q. What is meant by “Primary structure?” (See provided instructions)? A. This refers to the RNA sequence that forms the tRNA.

Q. What is meant by “Secondary structure?” (See provided instructions)? A. This refers to organization of the tRNA sequence with the formation of local regions of base- pairing. This state is often referred to as the clover-leaf shape with acceptor, TC, D and anticodon arms.

Q. What is meant by “Tertiary structure?” (See provided instructions)? A. This refers to the organization of the 3D shape of tRNA forming the inverted L-shaped structure. In this conformation the two business ends of the molecule are available for their functions.

Q. Can you locate the anticodon region and amino acid attachment sites? What color(s) are they? A. red

Q. What do the other colored regions in the models represent? A. Acceptor, TC, and D arms

Q. What is the anticodon in your tRNA model? Write the sequence here. A. The answers are given with Phe as the example – anticodon sequence is GAA

Q. Write the mRNA codon that matches your anti-codon? A. UUC

Q. Which amino acid is usually at the start of a synthesized peptide/protein? What is its codon? A. Methionine, AUG.

Q. What happens when the stop codon is read by the ribosome? (Hint: Read the Molecule of the Month article on Ribosomes for clues http://pdb101.rcsb.org/motm/121) A. A release factor binds to the stop codon to end the protein synthesis of that chain – there is no tRNA that binds to stop codons.

Q. Create a strand of mRNA that your tRNA’s can decode. Use each tRNA only once. Write down the mRNA sequence and the protein sequence below.

Developed as part of the RCSB Collaborative Curriculum Development Program 2015 Teaching Notes A. Possible mRNA sequence is: AUG-AAG–CCG-CUA-UUC-CGC-UAA Corresponding peptide made is: Met-Lys-Pro-Leu-Phe-Arg

Q. Final Reflection: How does the real tRNA structure (from the model and the webpage) compare to how RNA is explained in textbooks? A. Based in the textbooks you use – assess the student response.

Developed as part of the RCSB Collaborative Curriculum Development Program 2015