Lesson 3. Understanding Genetic Switch Part 2: DNA-Protein Interactions

Sugat Dabholkar
Biology
3 class periods (135 min)
High School
v1

Overview

In this lesson, students explore the DNA-protein interactions in the Genetic Switch Model of the lac operon. We emphasize that knowing the names of the proteins and regions on the DNA is not important. What is really important that students develop understanding of how interactions between genes and proteins allow cells to make 'smart' decisions and respond to environmental changes. 

Standards

Next Generation Science Standards
  • Life Science
    • [HS-LS4] Biological Evolution: Unity and Diversity
  • NGSS Practice
    • Analyzing Data
    • Communicating Information
    • Constructing Explanations, Designing Solutions
    • Asking Questions, Defining Problems
    • Using Models
    • Arguing from Evidence
    • Conducting Investigations
Computational Thinking in STEM
  • Data Practices
    • Analyzing Data
    • Collecting Data
    • Creating Data
    • Manipulating Data
    • Visualizing Data
  • Modeling and Simulation Practices
    • Using Computational Models to Find and Test Solutions
    • Using Computational Models to Understand a Concept
  • Systems Thinking Practices
    • Investigating a Complex System as a Whole
    • Thinking in Levels
    • Understanding the Relationships within a System

Activities

  • 1. DNA and Proteins
  • 2. Let's start the model
  • 3. Functions of different proteins
  • 4. DNA - Protein Interactions
  • 5. Upload your NetLogo logging file

Student Directions and Resources


In this lesson, you will explore the relationship with DNA and proteins in the context of this model.

1. DNA and Proteins


What do you know about DNA and proteins? It's perfectly ok, if you do not know much. We will use this model to understand some of the functions different proteins and different parts of DNA play inside a cell.


Question 1.1

What do you know about DNA?



Question 1.2

What do you know about genes?



Question 1.3

What do you know about proteins?

2. Let's start the model


Let's use the Genetic Switch model to understand the interactions between DNA and proteins.

Follow the instructions below to get started:

Open NetLogo folder and click on NetLogo Logging.

Open the Genetic Switch NetLogo Model that you downloaded earlier.


Question 2.1

In this model, all the molecules that only appear inside the cell are proteins. How many different types of proteins are there in this model?

Hint: Change the sugar settings and see when certain types of proteins appear and disappear.



Question 2.2

Explain your scientific investigation process.

Part 1: What were the changes that you made in the model?



Question 2.3

Part 2: What were your observations?



Question 2.4

Part 3: How did you arrive at your answer using your observations.

3. Functions of different proteins


Proteins perform different functions. Let's explore the model to understand the different functions that the proteins in our model perform. 


Question 3.1

Observe and write down the functions performed by different proteins.



Question 3.2

Explain how you figured out the answers.

Part 1: What were the changes that you made in the model?



Question 3.3

Part 2: What were your observations?



Question 3.4

Part 3: How did you arrive at your answer using your observations.



Question 3.5

Upload the supporting materials (experimental evidence for your answer) here. Make sure that the file size is less than 2 MB.

Upload files that are less than 5MB in size.
File Delete
Upload files to the space allocated by your teacher.


4. DNA - Protein Interactions


Some proteins seem to interact with DNA. Let's figure out these interactions.


Question 4.1

Describe your observations about DNA-Protein interactions.



Question 4.2

Do you think these interactions are important? What might be importance of these interactions?



Question 4.3

Explain how you figured out the answers.

Part 1: What were the changes that you made in the model?



Question 4.4

Part 2: What were your observations?



Question 4.5

Part 3: How did you arrive at your answer using your observations.



Question 4.6

Upload the supporting materials (experimental evidence for your answer) here. Make sure that the file size is less than 2 MB.

Upload files that are less than 5MB in size.
File Delete
Upload files to the space allocated by your teacher.


5. Upload your NetLogo logging file


NetLogo’s logging facility allows researchers to record student actions for later analysis.

Use the following information to find a logging file on your computer.

Logs are stored in the OS-specific temp directory. On most Unix-like systems that is /tmp. On Windows computers the logs can be found in c:\Users\<user>\AppData\Local\Temp, where <user> is the logged in user.

On Mac OS X, the temp directory varies for each user. You can determine your temp directory by opening the Terminal application and typing echo $TMPDIR at the prompt.

After you find the log files (.xml format), check for the file names that correspond to the date today. Upload those files.


Question 5.1

Upload your NetLogo logging file here.

Upload files that are less than 5MB in size.
File Delete
Upload files to the space allocated by your teacher.