PhET/C3/Gene-Machine-The-Lac-Operon/English - Revision history

Snehalathak at 11:18, 1 July 2019

2019-07-01T11:18:11Z

Meenalghoderao at 11:21, 14 March 2018

2018-03-14T11:21:16Z

Meenalghoderao at 11:20, 14 March 2018

2018-03-14T11:20:08Z

Meenalghoderao at 11:12, 14 March 2018

2018-03-14T11:12:24Z

Meenalghoderao at 11:11, 14 March 2018

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Meenalghoderao at 11:06, 14 March 2018

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Meenalghoderao at 07:33, 14 March 2018

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Meenalghoderao at 05:18, 7 March 2018

2018-03-07T05:18:06Z

Meenalghoderao: Created page with " {|border=1 ||'''Visual Cue''' ||'''Narration''' |- || '''Slide Number 1''' '''Title Slide''' || Welcome to this tutorial on '''Gene Machine - The Lac Operon''' simulation..."

2018-03-06T12:45:04Z

Created page with " {|border=1 ||'''Visual Cue''' ||'''Narration''' |- || '''Slide Number 1''' '''Title Slide''' || Welcome to this tutorial on '''Gene Machine - The Lac Operon''' simulation..."

New page

{|border=1
||'''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.

[http://phet.colorado.edu/ http://phet.colorado.edu]
|-
|| 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 promoter''' >>place it on the '''operon'''.
||Drag '''lacI gene''' 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'''.

In the absence of '''lactose''', it will block the '''RNA polymerase''' to transcribe the '''LacZ gene'''.
|-
|| 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'''

as prompted by the highlighted yellow portions on the '''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'''.
|| Since the '''LacI''' is bound to the '''LacZ''' Operator region,

it blocks the '''RNA polymerase''' to produce '''mRNA'''.

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 dissociates 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, binds to 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.

|}

@@ Line 338: / Line 338: @@
 || 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''',
 |-
 || '''Slide Number 15'''

@@ Line 170: / Line 170: @@
 ||Drag '''lacI promoter'''>> place it on the '''operon'''.
-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'''.

@@ Line 193: / Line 193: @@
 It binds to the '''Lac operator''' region of the '''Operon'''.
 |-
 || Point to '''Lactose injector'''.
@@ Line 227: / Line 226: @@
 |-
 || Point to '''LacI'''.
-|| Since the '''LacI''' is bound to the '''LacZ''' Operator region,
+|| In the absence of lactose,
-it blocks the '''RNA polymerase''' to produce '''mRNA'''.
+LacI binds to the operator region and prevents RNA polymerase from transcribing the operon.
 Hence no '''LacZ''' enzyme is produced.
@@ Line 273: / Line 272: @@
 || Lactose molecules bind to '''LacZ''' protein.
-'''LacZ''' protein dissociates lactose molecules as shown on the screen.
+'''LacZ''' protein cleaves lactose molecules as shown on the screen.
 Observe the Interior Lactose Level meter, lactose level decreases.
@@ Line 312: / Line 311: @@
 |-
 || Point to '''LacY''' protein.
-|| Observe that '''LacY''' protein, binds to the '''Cell Membrane'''.
+|| Observe that '''LacY''' protein is inserted into the '''Cell Membrane'''.
 |-
 || Point to '''LacY''' protein.

@@ Line 318: / Line 318: @@
 |-
 || Cursor on the screen.
-|| Inside the cell, lactose molecules are metabolized by '''LacZ''' enzyme as shown on the screen.
+|| Inside the cell,
 |-
 || '''Slide Number 13'''
@@ Line 327: / Line 329: @@
 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''',
 |-
 || '''Slide Number 14'''

@@ Line 171: / Line 171: @@
 Drag '''lacI promoter''' >>place it on the '''operon'''.
-||Drag '''lacI gene''' and place it on the '''operon'''.
+||Drag '''lacI promoter''' and place it on the '''operon'''.
 Similarly drag '''lacI gene''' and place it on the '''operon'''.

@@ Line 133: / Line 133: @@
 ||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.
+Here, you need to match each part given at the bottom,
 |-
 || Click on the check-box for '''Show Legend''' option.

@@ Line 81: / Line 81: @@
 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.
+'''lacY''' encodes '''Beta-galactoside permease''', It will enable transport of lactose into the cell.
-'''lacA'''encodes for '''β-galactoside transacetylase'''.
+'''lacA''' encodes for '''β-galactoside transacetylase'''.
 |-
 || '''Slide Number 9'''

@@ Line 151: / Line 151: @@
 A slider to set the speed of the animation,
-'''Play'''/'''Pause''', '''step''' button and
+'''Play'''/'''Pause''',
 '''Reset All''' button.
@@ Line 204: / Line 206: @@
 Meter will give an idea about interior lactose level.
 |-
-|| Drag and place,
+|| Drag and place,'''Lac promoter''','''Lac Operator''' on '''operon'''.
 || Next assemble the '''LacZ''' gene.
@@ Line 310: / Line 307: @@
 || '''LacY''' is '''Beta-galactoside permease''' enzyme.
-It enables transport of lactose into the cell
+It enables transport of lactose into the cell.
 |-
 || Point to '''LacY''' protein.
@@ Line 328: / Line 325: @@
 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'''
@@ Line 335: / Line 332: @@
 || 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'''
@@ Line 365: / Line 362: @@
 || An an assignment,
-Remove some of the components of the Operon (Operator, Promoter and Genes).
+Remove some of the components of the '''Operon''' (Operator, Promoter and Genes).
 Run the simulation.