How would your typical day be? List at least 5 things that you would do throughout the day.
Overview
This lesson focuses on how molecular interactions between genes and proteins result in a specific behavior at organismic level.
Students explore a computational model of lac operon in E. coli to investigate molecular mechanisms of genetic regulation.
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. Be a bacterium!
- 2. Let's install NetLogo to start exploring computational models
- 3. Let's get to know the model
- 4. Upload your NetLogo Logging File
Student Directions and Resources
Do you think bacteria can make smart decisions? Let's investigate!
1. Be a bacterium!
Imagine that you are a bacterium.
Question 1.1
Question 1.2
What information about the world and about yourself that you would need to live successfully as a bacterium?
List at least 5 questions.
2. Let's install NetLogo to start exploring computational models
In order to run the computational models that we will use in this course on your computer, you need to install a software called NetLogo.
Use this link to download and install NetLogo: DOWNLOAD NETLOGO
3. Let's get to know the model
Click here to download the model.
We are going to be real scientists to figure out if bacteria can make smart decisions. We are going to use a computational model to perform our research investigations.
Let’s get to know the model first!
Components of the model:
How to run the model:
- Click ‘SETUP’ to set the initial state for the bacterial cell.
This step is to setup the initial positions of the violet and brown proteins inside the cell. If you click ‘SETUP’ again, the positions of the violet and brown proteins change, whereas the position of the DNA stays the same.
- Click ‘Go’ to run the model.
This model is a computational simulation of the external and internal environments of a bacterial cell. When you click ‘Go’, you can see the protein molecules move around inside the cell. They do not go outside of the cell. Some of them interact with DNA. Observe their interactions with the DNA. DNA and proteins are molecular machines. Smart decisions that cells make are because of interactions between genes and proteins.
- Sugar control:
We are going to investigate how bacteria cells smartly make decisions to eat different sugars. In their natural environments, bacteria use different food sources to produce energy. They need energy to survive and reproduce. If they don’t get enough energy they die.
In our experiments, we can control which sugar is available to bacteria by turning ON or OFF the following switches:
Glucose and lactose are two different types of sugars. Using these switches, we can have different combinations of these two sugars available to bacteria.
For example, keeping these two switches ON means both these sugars are available to bacteria.
- Genetic Control:
We have several sliders available to control the genetic properties of the bacterial cell.
We will investigate what each of these sliders do during the course of our investigation.
Use the RESET button to set the values to default.
Molecular biologists and synthetic biologists, which are special types of scientists, make such changes in real cells. We will make these changes to our computational cell!
Question 3.1
Explore the model. Write down observations that you find interesting.
Question 3.2
You can take a screenshot of an interesting observation, which you could later use as an evidence to support your claim. Take a screenshot of an interesting observation. You can even take multiple screenshots. Upload your screenshot/s. The total file size should be less than 2 MB.
Upload files that are less than 5MB in size.
| File | Delete |
|---|---|
Upload files to the space allocated by your teacher.
Question 3.3
Describe your interesting observation/s that you have captured with a screenshot/s.
4. 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 4.1
Upload your log file/s here.
Upload files that are less than 5MB in size.
| File | Delete |
|---|---|
Upload files to the space allocated by your teacher.
