Assignment #3 - Gene Expression Simulation BIO1140 W2021 PDF

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Dr. Pettit

BIO1140

Winter 2021

Assignment #3 – Gene Expression Simulation General Instructions –  Following the instructions found in the worksheet below, explore the PhET Gene Expression Essentials simulation and answer the questions found throughout the worksheet.  Once you have completed the worksheet, open the "Assignment #3 – Gene Expression Simulation” quiz found in the Brightspace block 3 assignment section and input your answers by Apr 7th 5pm. o You are welcome to work collaboratively to explore the simulation, but each student must submit their own quiz for grading.

Academic Integrity – By submitting your quiz on Brightspace, you are attesting to the fact that you have reviewed the entirety of your submitted work and that this assessment meets all of the rules in uOttawa’s Academic Regulations about Academic Integrity. You confirm that you did not act in any way that would constitute cheating, misrepresentation, or unfairness, including but not limited to, using unauthorized aids and assistance, impersonating another person, or providing unauthorized assistance to someone else.

Worksheet – In this computer simulation you will explore how gene expression is regulated at the levels of transcription and translation. To access the simulation either click on this link, type the link below into your favorite web browser, or google “PHET Gene Expression Essentials”. You can then either choose to: 1) use the simulation in your web browser by clicking the ‘play’ symbol or 2) download and run the simulation offline. https://phet.colorado.edu/sims/html/gene-expression-essentials/latest/gene-expressionessentials_en.html

Part 1 – Expression Starting from the home screen, click on the box that says “Expression.” You are presented with a gene that contains a regulatory region and a transcribed region. Your goal is to produce 5 proteins from each of three genes. The proteins are indicated by the shapes in the box at the top right. Using your existing knowledge of the processes involved, drag and drop the required elements from the biomolecule toolbox (top left hand corner) to successfully transcribe each gene, and then translate the message from the gene into a protein. Questions – 1. What two components are required to initiate transcription of the gene 1?  Positive transcription factor  RNA polymerase 2. To which region of the gene do the components required to initiate transcription of the gene bind?

Dr. Pettit

BIO1140

Winter 2021

Regulatory region 3. What is the product of successful transcription of gene 1? A square 4. What component from your biomolecule toolbox is necessary to produce a protein from the transcript? A ribosome 5. Suppose gene 1 produces a protein involved in the development of the eye. What two components in the biomolecular toolbox could the cell use to prevent production of gene 1’s protein in other parts of the body? At what points in the progression from gene to protein do these methods act (i.e. what processes do they prevent)? mRNA destroyer and negative transcription factor, mRNA destroyer destroys the mRNA strand after being released, and negative transcription factors prevents the initiation process. 6. How does initiation of transcription differ in gene 2 and gene 3 as compared to gene 1? They use 2 positive transcription factors instead of 1 in gene 1. 7. Does the same DNA strand serve as the template strand for all 3 genes depicted in this simulation? How did you arrive at this conclusion? Yes, it is all derived from the same genetic material, it just depends on how the gene is expressed when RNA polymerase makes RNA which then becomes a protein when a ribosome is attached to it.

Part 2 – mRNA Click on the box that says “mRNA” (you can find this along the bottom of the simulation screen or by returning to the home screen first). You are presented with a gene that contains a regulatory region and a transcribed region. Your goal is to maximize the rate of transcription of the gene into mRNA. 8. What does the term “affinity mean”? Attraction between 2 molecules 9. What three factors maximize the rate of transcription from the gene?  High concentration of positive transcription factors  High affinity between positive transcription factor and DNA strand  High affinity between RNA polymerase and DNA strand connected and positive transcription factor 10. Keeping the setting from question 9 that lead to a maximal transcription rate, click on the check box on the bottom right to introduce the negative transcription factor into the simulation. Increase the

Dr. Pettit

BIO1140

Winter 2021

concentration and affinity of negative transcription factors to high. What effect does this have on the rate of transcription? circle the correct answer Increase – decrease – no change

11. Reset your simulation by clicking on the circular refresh arrow. Click on the check box on the bottom right to introduce the negative transcription factor into the simulation and increase the concentration and affinity of negative transcription factors to high. Then increase the concentration and affinity of positive transcription factors to high. What effect does this have on the rate of transcription? circle the correct answer Increase – decrease – no change

12. In both of the preceding scenarios (Q10 and Q11) the overall concentration and affinity of the positive and negative transcription factors is equal. Explain why the rate of transcription is the same or different in these circumstances. Because the concentration for negative transcription factor was increased before the positive transcription factor concentration was increased.

Part 3 – Multiple Cells Click on the box that says “Multiple Cells” (you can find this along the bottom of the screen or by returning to the home screen first). You are initially presented with a single E. coli cell that has had the gene for green fluorescent protein (GFP) inserted into its genome. This protein, when present in the cell, causes the bacterial cell to glow green under UV light. 13. Move the slider on the bottom from “one” to “many” cells. Are all of the cells showing equal expression of the GFP? Yes

14. Click on the + signs in each box on the right. Your goal is to make the cells as green as possible by maximizing production of GFP. How should you adjust each slider for each of the following parameters to maximize expression of the GFP gene? a. Positive Transcription Factor Concentration: make it high b. mRNA Destroyer Concentration: make it low c. Positive Transcription Factor Affinity for the Gene Regulatory Sequence: high d. RNA Polymerase Affinity for the Gene Regulatory Sequence: high e. Protein Degradation: slow

Dr. Pettit

BIO1140

Winter 2021

Finished exploring the simulation and answering the associated questions? Don’t forget to submit your answers via the Assignment #3 – Gene Expression Simulation Quiz in Brightspace!...