Simulating Protein Synthesis (Day 1 of 2)

1.  Remind students of the previous day's lesson introducing the three steps of protein synthesis listed on the board: transcription, RNA processing, translation.  Tell them that today they will be participating in a lab simulation so that they can get further into the details of protein synthesis.

2.  Pass out the lab activity document.  Ask students to read the directions to themselves.  If your student group needs additional reading support, you can choose to read them out loud together.

• Note:  Your only advance preparation will be to cut out the amino acids, snurps, and DNA template strands found in the teacher materials prep document.

3.  Tell students to choose their roles within their lab groups:  RNA polymerase, spliceosome/sNURP, ribosome/rRNA, tRNA

4.  Indicate the various areas of the cell located within the classroom:  cytoplasm with amino acids (side counter), nucleus for both DNA template strands (teacher front demo desk), and RNA processing activites work using snurps, ribosome (lab desks).

• Note:  I prefer to have the nucleus up in the front teacher area so that I can monitor these teams as they work through the intial steps of transcription and processing.  If this nucleus work goes wrong, the rest of the activity will be off course as well.  My immediate presence and support helps to set up a successful lab experience for every team.

5.  Announce that students should meet together as a lab group at their lab tables before beginning the assignment.  Tell students that they should do all of their work in pairs:  RNA polymerase with spliceosome/sNURP, ribosome/rRNA with tRNA.  While two members are away from the lab table doing their job, the other two remaining members can review their roles to come or begin working on the lab document questions.  

• Note:  I ask students to work in pairs because it relieves performance pressure.  In the past, I have seen the RNA polymerase partner feel dejected when they made an error during transcription and their group became frustrated with them later on in the process when they had to start over.  This way, each person has a person with them who can confirm and check their work, guide and encourage them.  The pairing process may not be true to the initial simulation set up, but I have found it helps my younger students navigate a challenging topic with confidence.

1.  Allow student groups to meet briefly at their lab tables before pairs begin moving toward the nucleus for transcription and then processing.  If five minutes go by and student groups don't appear to be moving up to the front, offer additional support as needed. 

2.  As students work on transcription, observe and offer redirection when necessary.  For example, if you see a student transcribing the DNA strand into RNA using thymines instead of uracil, you can prompt them to rethink that by asking, 'What four bases are present in DNA vs. RNA and are they the same?'  At that point, one of the two members will typically figure out the error.  If not, you can suggest that they check their class notes and/or lab group back at the lab table before continuing on with their steps.

Note:  Other issues I see during the lab that require some input from me for some groups include the following:

• When students are processing their RNA, it can be helpful to suggest that they use a pencil to mark each intron on their transcript before cutting and to splice together (tape) each exon as they go, not at the end.  When they wait, they often wind up with random sections of RNA that they may or may not put in the correct order needed for the next step.
• Students will often forget where to find the amino acids.  Having clear signage is helpful and observing lost looking students can allow you to prompt them without them needing to ask. Because their job is later on in the process and other group members who have finished their specific jobs within the simulation are looking relaxed and confidence, students can sometimes feel like they should know where everything is and are relieved I intervened without them having to ask for help they are sure they should need.
• Students may ask you about the start codon.  They should be noticing that each of their polypeptide chains begin with methionine, the amino acid associated with the start codon and at times this makes them uncertain if they have done things correctly.  I always applaud them on their observation and reassure them with a brief reminder of why this is correct. 
• To give you an idea of what this lab looks like in the classroom, see the following photos of each step as my students worked through the process together in their teams:

students at the nucleus for transcription and processing

students at the nucleus again for transcription and processing

students using the codon key to determine which amino acids to bring back to the ribosome

students creating their amino acid chains

students working together to answer the lab analysis questions

1.  As you see student groups finishing up their lab simulation, remind them to return to their lab tables and begin to discuss and respond to the lab document questions. Although their lab documents will not be ready for turn in today, they should have their amino acide sequences listed out on the first side of the document and have begun to answer the lab analysis questions. 

 2.  Tell students that there will be additional time tomorrow to finish up any uncompleted steps or to redo steps they feel they need to revisit.  

And now on to Day 2!