Gene expression essentials

Gene Expression Lab Simulation worksheet adapted by L. McPheron & Shannon Nixon; Phet Simulation by Elizabeth Hobbs; Mutation worksheet by Eliza Woo

Objectives:

● Identify the roles transcription factors, RNA polymerase, ribosomes, and mRNA destroyers have on transcription and translation.

● Distinguish between the location and function of regulatory regions compared to transcribed regions of DNA.

● Predict the effects of concentration, affinity, and degradation rates of transcription factors and RNA polymerase on gene expression.

● Identify the effects of mutations on gene expression. Background: Transcription​ is the process of making mRNA from DNA. This is a highly regulated process that our cells complete in preparation to make a protein. ​Translation​ is the process of making a protein from a piece of mRNA.

DNA --------------------> mRNA --------------------> protein transcription translation

Not all regions of DNA are used to make mRNA - only the parts of DNA that correspond to genes. Even then, not all gene regions are transcribed all the time. When genes are transcribed into mRNA depends on the needs of the cell. Once mRNA is made from DNA, it is translated into protein. Translation is an energy expensive process (it requires LOTS of ATP) which is one reason the cell only completes the process when the protein product is needed. This week’s “Reading and Lesson” explains many of the details of these highly complicated processes, transcription and translation. Please review the lesson for a deeper understanding of the concepts in this lab activity. Procedure: Click the Play arrow on this ​Gene Expression activity​ to complete the simulations. (The simulations are also embedded in the Canvas lab assignment page.) You will complete 3 simulations: 1) Expression, 2) mRNA, and 3) Multiple Cells.

Part 1: Expression Simulation

Click “Expression” to start that simulation. Notice the molecule that spans across the screen, from left to right. Answer the following 2 questions:

1. What is this molecule that spans across the page that is shown in red and blue?

2. What do you think the different colors (red and blue) of the molecule represent?

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https://phet.colorado.edu/en/simulation/gene-expression-essentials
Now, start the process of transcription.

For transcription, you need these things to happen. First, most genes require 1 or 2 “transcription factors” to bind to the area in front of the gene (called the “regulatory region”). Second, an RNA polymerase (an enzyme that makes mRNA from DNA) needs to be present in order for transcription to occur.

1. Drag one Positive Transcription Factor and one RNA Polymerase from the box called Biomolecule Toolbox to the regulatory region on the DNA molecule. This should start TRANSCRIPTION.

2. Now, drag a ribosome next to the mRNA, in order to do TRANSLATION. 3. The mRNA is eventually broken down by an mRNA destroyer protein. Drag one of these next to the

mRNA when it is done making a protein. 4. Put the protein in Your Protein Collection. 5. Stop the gene from working by dragging the Negative Transcription Factor to the Regulatory Area, and

remove the Positive Transcription Factor by dragging it out of the way.

After you have made 1 protein, answer these 5 questions. HINT: Think about what/where things are at the start, and what/ where things are at the end of the process.

1. What does the “Positive Transcription Factor” do?

2. What does the “RNA Polymerase” do?

3. What does the “Ribosome” do?

4. What does the “mRNA destroyer” do?

5. What does the “negative transcription” factor do?

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Click the yellow “Next Gene” box to begin working on the second gene. Can you remember the steps in order from your first trial? Try to see if you can! (HINT: There is one small difference between the transcription of gene 2 versus gene 1 - the difference is not in the order of steps but in the amount of something!) If not, not to worry, we are still learning… As a reminder, the steps are:

1. Drag Positive Transcription Factors and one RNA Polymerase from the box called Biomolecule Toolbox to the regulatory region on the DNA molecule. This should start TRANSCRIPTION!

2. Now, drag a ribosome next to the mRNA, in order to do TRANSLATION! 3. The mRNA is eventually broken down by an mRNA destroyer protein. Drag one of these next to the

mRNA when it is done making a protein. 4. Put the protein in Your Protein Collection. 5. Stop the gene from working by dragging the Negative Transcription Factor to the Regulatory Area, and

remove the Positive Transcription Factors by dragging them out of the way.

After you have made the second protein, answer these 2 questions.

1. What is one difference you noticed that was required to initiate the transcription of gene 2 versus gene 1?

2. What could be an advantage of multiple positive transcription factors versus only one?

Now, put all of your items back in the Biomolecule Toolbox and begin again, and answer the following 2 questions.

1. What happens if you add 2 RNA Polymerases (one after the first, before transcription is complete), and then 2 ribosomes (one for each mRNA)?

2. What would be the benefit of working this way versus adding RNA Polymerase one at a time?

Click the yellow “Next Gene” box to begin working on the third gene. Can you remember the steps in order from your first trial? Try to see if you can!

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Additional 4 Questions from the Expression Simulation:

1. What is gene expression?

2. What molecules are involved in gene expression? List them all and state the role of each.

3. What is the difference between the “regulatory region” and the “transcribed region”?

4. A student says that “ALL DNA codes for proteins.” Do you agree with her? Why or why not? Give evidence to support your answer.

Part 2: mRNA Simulation

At the bottom of the simulation page, click on the next simulation (it’s greyed out) called mRNA.

You should see a strand of DNA with a bunch of RNA Polymerases floating around. (If the RNA Polymerases are not moving, click the Play button.) Answer the following 7 questions.

1. Is mRNA being made?

2. In the Positive Transcription Factor box, slide the Concentration slider from NONE to just a tad (a couple millimeters or so) away from NONE. What do you notice is happening in the simulation now?

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3. Move the Concentration slider all the way to HIGH. How does this affect what is happening in the simulation?

4. Leave the Concentration slider on HIGH but move the Affinity slider all the way to LOW. What happens? Move the Affinity slider to a midway setting? What happens now? Based on these observations, what do you think ​affinity​ means in this simulation?

5. Place both sliders in the Positive Transcription Factor box on the HIGH setting. ​Predict ​what will happen to the simulation if you were to move the RNA Polymerase affinity slider to the LOW position. Record your prediction.

6. Now, move the RNA Polymerase affinity slider to the LOW position and record your observations. Was your prediction correct?

7. Place all the sliders in the HIGH position. Check the box to add Negative Transcription Factors and place the concentration and affinity sliders on HIGH. How does this change transcription compared to without Negative Transcription Factors?

Continue to play around with the sliders until you can accurately predict how the change will affect transcription each time.

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