Biology

Lesson 4 - Enzymes

Lesson Plan

State Standards:

1. The Chemistry of Life
1.3 Explain the role of enzymes as catalysts that lower the activation energy of biochemical reactions. Identify factors, such as pH and temperature, that have an effect on enzymes.

Essential Question:

How are enzymes affected by the cellular environment?

Lesson Question:

What is the activity rate of enzymes when you vary the pH, temperature and substrate concentrations of the cellular environment? fulllength_hammerhead_ribozyme_by_wygscot

Introduction:

Life would not exist without the presence of enzymes. Many important biochemical reactions inside of cells require the assistance of enzymes. Enzymes work by lowering the activation energy of a reaction making the reaction more favorable to occur. This ability of enzymes is what classifies them as being catalysts.

We have had a recent experience with enzymes in class. As you recall from our demonstration, the reaction was almost instantaneous when hydrogen peroxide was poured into the test tube of liver. Our demonstration wouldn't have been so volatile without the presence of catalase. Catalase is an enzyme present in liver cells that catalyzes the reaction of hydrogen peroxide breaking apart into water and oxygen.

In today's lesson, you will use a simulation program to investigate how enzymes are affected from the changes you make to their environment. You will run simulations to study what effect does increasing the concentration of enzymes have on the rate of a reaction. You will also run simulations to study how the rate of a reaction changes over time. Most importantly, you will run simulations to determine what effect does changing the temperature or pH have on the activity rate of an enzyme.

Task:

Imagine yourself as a scientist who will be running virtual experiments on enzymes. Your virtual experiments will take place inside of a cell where you will have control of setting the conditions of the cytoplasm. When running your experiments, you will change one condition (or variable) at a time and observe what effect takes place. You will follow a set of instructions in the Process section and record your data and observations on an excel spreadsheet. Upon completing the simulations, you will share your results with the classroom and write a conclusion summarizing your results.

Lesson Experiences:

Introduction to an Enzyme Simulation

  1. Find a lab partner to pair up with.
  2. You and your lab partner choose one computer and sign in.
  3. Open a web browser and visit the web site: http://www.kscience.co.uk/animations/model.swf
  4. Familiarize yourself with the controls and buttons:
    • Controls to adjust cytoplasm conditions are located on the top right.
    • The Legend for enzymes, substrates, and products is located on the bottom right.
    • Setup button is located below the controls.
    • Start and stop buttons are located on the bottom left.
  5. kscience_model_screenshot
  6. Familiarize yourself with the virtual cell:
    • Click on the “setup” button.
    • The yellow screen that appears is the cytoplasm of your virtual cell.
    • The green glob is an enzyme and the blue dots are substrates.
    • Click on the “start” button.
    • Note: The red dots forming are products.
  7. Open the “Virtual Enzyme Lab”excel file by clicking on this link:
  8.   jvittoria_Virtual_Enzyme_Lab.xls

Click “File” and select “Save As,” rename the file with your name and your lab partner's name and save the file on your desktop.

Enzyme Concentration Simulation

  1. Leave conditions set at the default values:
  2. Enzymes = 1
  3. Substrates = 20
  4. Inhibitors = 0
  5. Temperature = 25
  6. Container = 400
  7. pH = 7

    Click on the “start” button.
  8. Start the timer.
  9. Observe the simulation.
  10. Click on the “stop” button when the timer reaches 1 minute.
  11. Count the total number of products.
  12. Note: Products are the red dots.
  13. Record the rate of the reaction in Table 1 of the “Virtual Enzyme Lab” spreadsheet.
  14. Note: Record the rate of reaction as #products/minute
  15. Repeat steps 1 to 7 for “Enzymes” set at 5, 10 and 20.
  16. Record what you observed as you increased the number (concentration) of enzymes in Table 5 of the “Virtual Enzyme Lab” spreadsheet.

Rate of a Reaction Simulation


1. Reset “Enzymes” to 1 and set “Substrates” to 50.
Note: All other conditions should be set at default values.
2. Click on the “setup” button.
3. Click on the “start” button and start the timer.
4. Observe the simulation.
5. Click on the “stop” button when the timer reaches 1 minute.
6. Count the total number of products.
7. Record the total number of products in Table 2 of the “Virtual Enzyme Lab” spreadsheet.
8. Continue the simulation by clicking on the “start” button again and restart the timer.
9. Click on stop when the timer reaches 2 minutes.
10. Click on the “start” button and start the timer again.
11. Count the total number of products.
12. Record the total number of products in Table 2 of the “Virtual Enzyme Lab” spreadsheet.
13. Repeat steps 8 to 12 for the time intervals of 3, 4, and 5 minutes.
14. Record what you observed as time progressed in Table 5 of the “Virtual Enzyme Lab” spreadsheet.

catalase_structure_by_vossman

Temperature Change Simulation
1. Reset “Substrates” to 20, and set “Temperature” to 0.
Note: All other conditions should be set at default values.
2. Click on the button labeled “setup.”
3. Click on the “start” button and start the timer.
4. Observe the simulation.
5. Click on the “stop” button when the timer reaches 1 minute.
6. Count the total number of products.
7. Record the rate of the reaction in Table 3 of the “Virtual Enzyme Lab” spreadsheet.
Note: Record the rate of reaction as #products/minute
8. Repeat steps 1 to 7 for “Temperature” set at 15, 25, 45, 55 and 65.
9. Record what you observed at cold temperatures (< 25 C) and at hot temperatures (>25 C) in Table 5 of the “Virtual Enzyme Lab” spreadsheet.

Change of pH Simulation
1. Reset “Temperature” to 25 and set pH to 1.
Note: All other conditions should be set at default values.
2. Click on the button labeled “setup.”
3. Click on “start” button and start the timer.
4. Observe the simulation.
5. Click on the “stop” button when the timer reaches 1 minute.
6. Count the total number of products.
7. Record the rate of the reaction in Table 4 of the “Virtual Enzyme Lab” spreadsheet.
Note: Record the rate of reaction as #products formed/minute
8. Repeat steps 1 to 7 for “pH” set as 3, 7, 8, 10, and 14
9. Write a blog on what you have observed as you increased the pH from 1 to 14.

Your simulation graphs should appear like these graphs:

Figure 1: This graph was generated from data obtained from the "Enzyme Concentration Simulation."

Graph of Simulation 1

Figure 2: This graph was generated from data obtained from the "Rate of a Reaction Simulation."

Graph of Simulation 2
Figure 3: This graph was generated from data obtained from the "Temperature Change Simulation."


Graph of Simulation 3
Figure 4: This graph was generated from data obtained from the "Change of pH Simulation."


Graph of Simulation 4
During our classroom discussion, you will be introduced to new vocabulary (listed below) that will help you describe what happened in your simulations. Definitions to the vocabulary should be written in your notebook.

Enzyme Vocabulary

  1. active site
  2. catalyst
  3. concentration
  4. denaturation
  5. enzyme
  6. optimal pH
  7. optimal temperature
  8. products
  9. reaction rate
  10. substrates

Upon completion of your simulations, both you and your lab partner should have a pretty good understanding of how enzymes are affected by their cellular environment. Print out two copies of the “Virtual Enzyme Lab” spreadsheet; one for each lab partner. Don't forget to print out Table 5 which is on a separate worksheet from Tables 1-4. Review with your lab partner the data, graphs and recorded observations for each simulation. Be prepared to share with the classroom results from your simulations.

catalase_pdb_7cat_ebi

As a homework assignment, you will write a conclusion that describes the results obtained from each simulation. A significant portion of your grade will be based on using the graphs to describe your results. The target audience of your conclusion is a scientific community. Your essay should include all of the new vocabulary words (listed above). Please refer to the “Enzyme Simulations Essay Rubric" when writing your essay.

When you finish writing your conclusion, grade yourself on the rubric by filling out your scores under the “Student” column. Make sure to include your printout of the “Virtual Enzyme Lab” spreadsheet and your self-scored rubric when you hand in your conclusion.

Evaluation/Assessment

Your teacher will be using the "Enzyme Simulations Essay Rubric" to assess conclusions. You will grade your own conclusions by writing your scores under the "Student's Score" column. The teacher (ME) scores the students' conclusions under the "Teacher's Score" column.

The final grade is based on the Teacher's Score but the Student's Scores are considered.

The actual excel file for the rubric is at this link below: jvittoria_enzymesimulationsessayrubric.xls

After grading the conclusions and handing them back to you, your teacher will review the group's conclusion in class.

Then take an online “Enzyme Quiz” at this link: Enzyme Quiz.

Conclusion:

Now that you have looked at the factors that can influence enzyme reactions, think about what other factors can influence the cellular environment in which the enzymes act. What influences the chemistry of life?

Assessments:

The "Enzyme Simulations Essay Rubric" table is below:

Criteria

Exceeds Expectation

Meets Expectation

Approaches Expectation

Warning

Student's
Score

Teacher's
Score

Locates, organizes and processes information or data

Worth 10 points:
The student locates, organizes and processes information/data from a variety
of written or observed sources to support understanding and consequences.
*Uses the graphs to explain the results.

Worth 8 points:
The student locates, organizes and processes sufficient information/data from a variety of written and observed sources.
*Uses the graphs to explain the results

Worth 5 points:
The student locates, organizes and processes some information/data from some written or observed sources.
*Uses the graphs to explain the results.

Worth 3 points:
The student is unable to locate organize or process information/data from written or observed sources.
*Did NOT use the graphs to explain the results.

Applies reasoning skills

Worth 10 points:
The student consistently applies appropriate and relevant reasoning skills to information/data gathered.
*Explains how the enzymes contributed to the reaction rates observed.

Worth 8 points:
The student frequently applies reasoning skills and strategies at an age appropriate level to information/data gathered.
*Eplains how the enzymes contribute to the reaction rates observed.

Worth 5 points:
The student applies reasoning skills, with moderate success, at an age appropriate level to information/data gathered. *Explains how the enzymes contribute to the reaction rates

Worth 3 points:
The student is unable to apply relevant reasoning skills to information/data gathered.
*Did NOT explain how the enzymes contribute to the reaction rates observed.

Considers, tests, and justifies solutions(s) and conclusion(s)

Worth 10 points:
The student consistently and thoroughly considers tests and gathered information/data to justify solutions and conclusions.
*Concludes the results from all 4 simulations with no errors.

Worth 8 points:
The student frequently considers tests and gathered information/data to justify solutions and conclusions.
*Concludes the results from 3 simulations with no errors.

Worth 5 points:
The student has difficulty considering tests and gathered information/data to justify solutions and conclusions.
*Concludes the results from 2 simulations with no errors.

Worth 3 points:
The student is unable to consider tests and gathered information/data to justify solutions and conclusions.
*Concludes the results from 1 simulation with no errors.

Tools of language

Worth 10 points:
The writer shows a superior command of the tools of language relative to focus, organization, elaboration, support, style, grammar, usage and mechanics.
*Uses paragraph formatting.

Worth 8 points:
The writer shows an adequate command of the tools of language relative to factors such as focus, organization, elaboration, support, style, grammar, usage, and mechanics.
*Uses paragraph formatting.

Worth 5 points:
The writer shows a less than adequate command of the tools of language relative to factors such as focus, organization, elaboration, support, style, grammar, usage, and mechanics.
* Lacks paragraph formatting.

Worth 3 points:
The writer shows a pattern of weakness in command of the tools of language relative to factors such as focus, organization, elaboration, support, style, grammar, usage, and mechanics. *Lacks paragraph formatting.

Use of New Vocabulary

Worth 10 points:
The writer uses all 10 words.

Worth 7 points:
The writer uses at least 7 words.

Worth 5 points:
The writer uses at least 5 words.

Worth 3 points:
The writers uses 3 or less words.

Communicates information

Worth 5 points:
The writer consistently communicates original thoughts and learned information.

Worth 4 points:
The writer frequently communicates original thoughts and learned information.

Worth 3 points:
The writer occasionally communicates original thoughts and learned information.

Worth 1 point:
The writer rarely communicates original thoughts and learned information.

Audience

Worth 5 points:
The writer consistently uses a manner appropriate to the specified audience. * Audience is a scientific community.

Worth 4 points:
The writer frequently uses a manner appropriate to the specified audience. *Audience is a scientific community.

Worth 3 points:
The writer occasionally uses a manner appropriate to the specified audience. *Audience is a scientific community.

Worth 1 point:
The writer rarely uses a manner appropriate to the specified audience. *Audience is a scientific community.

Paper Length

Worth 10 points:
The conclusion is 1 or more pages long.

Worth 8 points:
The conclusion is 3/4 page long.

Worth 5 points:
The conclusion is a 1/2 page long.

Worth 3 points:
The conclusion is under a 1/2 page!

* A score of 70 points in considered a 100% and will be graded as an A+.

Total Score =

Resources:

Teacher Notes:
This lesson can be implemented by one teacher, however, it would be better to have one or two more teachers present when students are running their simulations. Parents can take the place of the teachers as long as they have some experience with using the simulation so they can help students when they get stuck or take a wrong path.

 

Image Credits:

Full length Hammerhead Ribozyme by Wygscot from Wikimedia Commons

Catalase Structure by Vossman from Wikimedia Commonts

"Catalase pdb 7cat ebi" from Wikimedia Commons