Difference between revisions of "PhET/C3/Gene-Machine-The-Lac-Operon/English"
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||Drag '''lacI promoter'''>> place it on the '''operon'''. | ||Drag '''lacI promoter'''>> place it on the '''operon'''. | ||
| − | Drag '''lacI | + | Drag '''lacI gene''' >>place it on the '''operon'''. |
| − | ||Drag '''lacI | + | ||Drag '''lacI promoter''' and place it on the '''operon'''. |
Similarly drag '''lacI gene''' and place it on the '''operon'''. | Similarly drag '''lacI gene''' and place it on the '''operon'''. | ||
| Line 193: | Line 193: | ||
It binds to the '''Lac operator''' region of the '''Operon'''. | It binds to the '''Lac operator''' region of the '''Operon'''. | ||
| − | |||
|- | |- | ||
|| Point to '''Lactose injector'''. | || Point to '''Lactose injector'''. | ||
| Line 227: | Line 226: | ||
|- | |- | ||
|| Point to '''LacI'''. | || Point to '''LacI'''. | ||
| − | || | + | || In the absence of lactose, |
| − | + | LacI binds to the operator region and prevents RNA polymerase from transcribing the operon. | |
Hence no '''LacZ''' enzyme is produced. | Hence no '''LacZ''' enzyme is produced. | ||
| Line 273: | Line 272: | ||
|| Lactose molecules bind to '''LacZ''' protein. | || Lactose molecules bind to '''LacZ''' protein. | ||
| − | '''LacZ''' protein | + | '''LacZ''' protein cleaves lactose molecules as shown on the screen. |
Observe the Interior Lactose Level meter, lactose level decreases. | Observe the Interior Lactose Level meter, lactose level decreases. | ||
| Line 312: | Line 311: | ||
|- | |- | ||
|| Point to '''LacY''' protein. | || Point to '''LacY''' protein. | ||
| − | || Observe that '''LacY''' protein | + | || Observe that '''LacY''' protein is inserted into the '''Cell Membrane'''. |
|- | |- | ||
|| Point to '''LacY''' protein. | || Point to '''LacY''' protein. | ||
| Line 318: | Line 317: | ||
|- | |- | ||
|| Cursor on the screen. | || Cursor on the screen. | ||
| − | || Inside the cell, lactose molecules are metabolized by '''LacZ''' enzyme as shown on the screen. | + | || Inside the cell, |
| + | |||
| + | lactose molecules are metabolized by '''LacZ''' enzyme as shown on the screen. | ||
|- | |- | ||
|| '''Slide Number 13''' | || '''Slide Number 13''' | ||
| Line 327: | Line 328: | ||
The '''lac''' repressor acts as a lactose sensor. | The '''lac''' repressor acts as a lactose sensor. | ||
| − | It blocks transcription of the '''Lac operon''' when there is no lactose present in the cell. | + | It blocks transcription of the '''Lac operon''', |
| + | |||
| + | when there is no lactose present in the cell. | ||
|- | |- | ||
|| '''Slide Number 14''' | || '''Slide Number 14''' | ||
| Line 334: | Line 337: | ||
|| When lactose is present, the ''lac'' repressor loses its ability to bind DNA. | || When lactose is present, the ''lac'' repressor loses its ability to bind DNA. | ||
| − | It floats off the '''operator''', clearing the way for '''RNA polymerase''' to transcribe the '''operon'''. | + | It floats off the '''operator''', |
| + | |||
| + | clearing the way for '''RNA polymerase''' to transcribe the '''operon'''. | ||
|- | |- | ||
|| '''Slide Number 15''' | || '''Slide Number 15''' | ||
Latest revision as of 16:48, 1 July 2019
| Visual Cue | Narration |
| Slide Number 1
Title Slide |
Welcome to this tutorial on Gene Machine - The Lac Operon simulation. |
| Slide Number 2
Learning Objectives |
In this tutorial we will,
Demonstrate Gene Machine - The Lac Operon PhET simulation. |
| Slide Number 3
Pre-requisites |
To follow this tutorial,
Learner should be familiar with topics in high school Biology. |
| Slide Number 4
System Requirement |
Here I am using,
Ubuntu Linux OS version 14.04 Java version 1.7.0. Firefox Web Browser version 53.02.2 |
| Slide Number 5
Learning Goals |
Using this simulation, students will learn about,
Lactose regulation. Genes involved in Lactose regulation. Factors affecting LacZ gene regulation. |
| Slide Number 6
About Lac Operon |
The lac operon is a set of genes responsible for regulating lactose metabolism in E.coli bacteria. |
| Slide Number 7
Components of Lac Operon |
An operon is made up of 3 basic DNA components: Promoter, Operator and Structural gene.
Promoter: Initiates transcription. Operator: Segment of DNA where repressor binds. Structural gene: A gene which codes for protein. |
| Slide Number 8
Structural gene |
The three structural genes in lac Operon are: lacZ, lacY, and lacA.
These genes are transcribed as a single mRNA, under control of one promoter. Genes in the lac operon specify proteins that help the cell utilize lactose. |
| Slide Number 8
Structural gene |
Genes of the Lac Operon can be expressed and their proteins translated.
The gene product of lacZ is β-galactosidase which cleaves lactose. lacY encodes Beta-galactoside permease, It will enable transport of lactose into the cell. lacA encodes for β-galactoside transacetylase. |
| Slide Number 9
Link for PhET simulation. |
Use the given link to download the simulation. |
| Point to the file in Downloads folder. | I have already downloaded Gene Machine-The Lac Operon simulation to my Downloads folder. |
| Press ctrl, Alt and T keys.
At the prompt type, cd Downloads >>press enter. |
To run the simulation, open the terminal.
At the prompt type, cd Downloads and press enter. |
| Then type, java -jar gene-machine-lac-operon_en.jar >>press enter.
Point to the simulation. |
Then type, java -jar gene-machine-lac-operon_en.jar and press enter.
Gene-Machine-The Lac Operon Simulation opens. |
| Show 2 tabs.
Point the cursor on each tab. |
The simulation screen shows 2 tabs at the top,
Lactose Regulation and Lactose Transport |
| Point to RNA polymerase molecules. | On the Lactose Regulation screen,
You will see two floating RNA polymerase in blue colour. |
| Point to the operon.
Cursor on parts of gene. |
Observe an incomplete operon which needs to be assembled.
Here, you need to match each part given at the bottom, to it's specific place on the gene. |
| Click on the check-box for Show Legend option.
Cursor on Legend Panel. Point to each molecules in Legend panel. |
Click on the Show Legend check box at the bottom-right corner.
This will turn-on the Legend panel on the right-side of the screen. The Legend panel helps you to identify the molecules present on the screen. |
| Point to all the buttons. | At the bottom of the screen we have,
A slider to set the speed of the animation, Play/Pause, step button and Reset All button. |
| Click on LacI promoter .
Point to Yellow highlighted portion. |
Let us now start assembling the gene.
Click on lacI promoter. The specific portions on the gene are highlighted in yellow color. |
| Drag lacI promoter>> place it on the operon.
Drag lacI gene >>place it on the operon. |
Drag lacI promoter and place it on the operon.
Similarly drag lacI gene and place it on the operon. |
| Point to the RNA Polymerase molecule.
Point to mRNA. Point to LacI protein. |
The floating RNA Polymerase molecule binds briefly to the lacI promoter.
This will activate the lacI gene to produce mRNA. This mRNA is translated to LacI protein which is seen floating on the screen. |
| Slide Number 10
LacI Protein |
LacI is a lac repressor protein.
It binds to the Lac operator region of the Operon. |
| Point to Lactose injector. | Notice that as soon as LacI protein is produced,
Lactose injector appears on the top-left corner of the screen. |
| Click on the Show Lactose Meter check-box.
Point to Show Lactose Meter. |
Click on the Show Lactose Meter check-box at the bottom-left corner.
Meter will give an idea about interior lactose level. |
| Drag and place,Lac promoter,Lac Operator on operon. | Next assemble the LacZ gene.
Drag and place, Lac promoter, Lac operator as prompted by the highlighted yellow portions on the operon. |
| Point towards the LacI protein. | LacI protein floating around will now bind to the operator region of operon. |
| Drag and place LacZ gene at its designated place on the gene. | Now place the LacZ gene on operon. |
| Point to LacI. | In the absence of lactose,
LacI binds to the operator region and prevents RNA polymerase from transcribing the operon. Hence no LacZ enzyme is produced. |
| Point to Manual and Auto options.
Click on Manual radio button on Lactose injector. |
Pump a few molecules of lactose on to the screen using Lactose injector.
There are 2 options for pumping, Manual and Auto. Select Manual option. |
| Press the red button on the injector.
Point to lactose meter. |
Press the red button on the injector.
Observe the Lactose level in lactose meter. |
| Point to the LacI with Lactose. | LacI bound to the operator, acts like Lactose sensor.
Lactose molecule bind to the LacI and leaves the Operator region. |
| Point to mRNA and LacZ protein. | The RNA Polymerase will now be able to transcribe the gene.
This mRNA is in turn translated to LacZ protein. |
| Slide Number 11
LacZ Protein |
LacZ is Beta-galactosidase enzyme.
It cleaves lactose into glucose and galactose. |
| Point to LacZ protein.
Point to meter. |
Lactose molecules bind to LacZ protein.
LacZ protein cleaves lactose molecules as shown on the screen. Observe the Interior Lactose Level meter, lactose level decreases. |
| Click on Lactose Transport screen. | Click on Lactose Transport screen. |
| Point to Cell Membrane and LacY gene. | In addition to all the features of the Lactose regulation screen,
Lactose Transport screen has Cell Membrane and LacY gene. |
| Drag and place, lacI promoter, lacI gene, lacZ gene, lac promoter and lac Operator on gene.
Click on Show Legend and Show Lactose Meter check box. |
As demonstrated previously, assemble the Operon.
Drag and place all the components of the Operon in their respective places. Click on Show Legend and Show Lactose Meter check box. |
| Click on Auto radio button on the Lactose injector. | Pump-in few molecules of Lactose using Lactose injector.
Click on Auto radio button on the Lactose injector. |
| Point to LacI, LacZ and LacY proteins. | LacI, LacZ and LacY proteins are produced. |
| Slide Number 12
LacY Protein |
LacY is Beta-galactoside permease enzyme.
It enables transport of lactose into the cell. |
| Point to LacY protein. | Observe that LacY protein is inserted into the Cell Membrane. |
| Point to LacY protein. | Now lactose molecules permeate into cell with the help of LacY protein. |
| Cursor on the screen. | Inside the cell,
lactose molecules are metabolized by LacZ enzyme as shown on the screen. |
| Slide Number 13
Factors affecting LacZ gene regulation |
Factors affecting LacZ gene regulation-
The lac repressor acts as a lactose sensor. It blocks transcription of the Lac operon, when there is no lactose present in the cell. |
| Slide Number 14
Factors affecting LacZ gene regulation |
When lactose is present, the lac repressor loses its ability to bind DNA.
It floats off the operator, clearing the way for RNA polymerase to transcribe the operon. |
| Slide Number 15
Summary |
Let us summarize,
In this tutorial we have demonstrated How to use Gene Machine-The Lac Operon, PhET simulation. |
| Slide Number 16
Summary |
We have also learnt about,
Lactose regulation. Genes involved in Lactose regulation. Factors affecting LacZ gene regulation. |
| Slide Number 17
Assignment |
An an assignment,
Remove some of the components of the Operon (Operator, Promoter and Genes). Run the simulation. Observe the results and give explanation. |
| Slide Number 18
About Spoken Tutorial project |
The video at the following link summarizes the Spoken Tutorial project.
Please download and watch it. |
| Slide Number 19
Spoken Tutorial workshops |
The Spoken Tutorial Project team:
conducts workshops using spoken tutorials and gives certificates on passing online tests. For more details, please write to us. |
| Slide Number 20
Forum for specific questions: Do you have questions in THIS Spoken Tutorial? Please visit this site. Choose the minute and second where you have the question. Explain your question briefly. Someone from our team will answer them. |
Please post your timed queries on this forum. |
| Slide Number 21
Acknowledgements |
This project is partially funded by Pandit Madan Mohan Malaviya National Mission on Teachers and Teaching. |
| Slide Number 22
Acknowledgement |
Spoken Tutorial Project is funded by NMEICT, MHRD, Government of India.
More information on this mission is available at this link. |
| This tutorial is contributed by Snehalatha Kaliappan and Meenal Ghoderao from IIT Bombay.
Thanks for joining. |
