PhET/C3/Gene-Expression-The-Basics/English - Revision history

Snehalathak at 11:07, 1 July 2019

2019-07-01T11:07:47Z

Snehalathak at 11:05, 1 July 2019

2019-07-01T11:05:33Z

Meenalghoderao at 12:38, 1 February 2018

2018-02-01T12:38:48Z

Meenalghoderao at 09:55, 1 February 2018

2018-02-01T09:55:51Z

Meenalghoderao at 09:48, 1 February 2018

2018-02-01T09:48:33Z

Meenalghoderao at 12:15, 25 January 2018

2018-01-25T12:15:34Z

Show changes

Meenalghoderao at 09:41, 25 January 2018

2018-01-25T09:41:26Z

Show changes

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

2018-01-25T07:29:11Z

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

New page

{|border=1
||'''Visual Cue'''
||'''Narration'''

|-
|| '''Slide Number 1'''

'''Title Slide'''
|| Welcome to this tutorial on '''Gene-Expression-The Basics simulation'''.
|-
|| '''Slide Number 2'''

'''Learning Objectives'''
|| In this tutorial we will,

Demonstrate '''Gene Expression-The Basics''', '''PhET Simulation'''.
|-
|| '''Slide Number 3'''

'''Pre-requisites'''
|| To follow this tutorial,

Learners 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 we will learn,

About steps involved in Protein Synthesis.

Factors affecting Protein Synthesis and

To observe the average level of Green Fluorescent Protein produced in cells.
|-
|| '''Slide Number 6'''

'''Central Dogma of Genetics'''

|| Let us recall about '''Central Dogma of Genetics'''.

It was proposed by '''Francis Crick'''.

It states that the genetic information flows from '''DNA''' to '''mRNA''' to Protein.
|-
|| '''Slide Number 7'''

'''Steps involved in Protein Synthesis'''.

|| Protein Synthesis involves two steps.

'''Transcription''': is a process of making, '''mRNA'''.

'''Translation''': is a process by which '''mRNA''' directs protein synthesis.
|-
||
|| Let us begin the demonstration.
|-
|| '''Slide Number 8'''

'''Link for PhET simulation'''

[http://phet.colorado.edu/ ]
|| 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 Expression-The Basics''' simulation to my '''Downloads''' folder.

|-
|| Press '''ctrl''', '''Alt''' and '''T''' keys simultaneously.

At the prompt type,

'''cd Downloads''' and press enter.

Then type, '''java -jar gene-expression-basics_en.jar''' and press enter.

Point to the simulation.
|| To run the simulation, open the terminal.

At the prompt type, '''cd Downloads''' and press enter.

Then type, '''java -jar gene-expression-basics_en.jar''' and press enter.

'''Gene Expression-The Basics''' Simulation opens.
|-
|| Cursor on simulation.

Point the cursor on each tab.
|| The simulation screen shows 3 tabs at the top-

'''Cell Gene Expression'''

'''Messenger RNA Production''' and

'''Multiple Cells'''.
|-
|| Point to '''Cell Gene Expression''' screen.
|| By default '''Cell Gene Expression''' screen opens.

|-
|| Cursor on the '''Biomolecule Toolbox'''.
|| Left side of the screen has a '''Biomolecule Toolbox'''.

It contains '''transcription''' and '''translation''' regulatory elements.
|-
|| Cursor on the '''DNA''' strand.

Point to '''Gene 1'''.
|| At the bottom of the screen a DNA strand is shown.

It represents '''Gene 1'''.
|-
|| Point to '''Regulatory region''' and a '''Transcribed region'''.
|| '''Gene 1''' has a '''Regulatory region''' and a '''Transcribed region'''.

|-
|| Point to '''Regulatory region'''.
|| '''Regulatory Region''' is acted upon by,

'''Positive''' and '''Negative Transcription Factors'''.
|-
|| Point to '''Transcribed region'''.

|| '''Transcribed Region''' is located after the '''Regulatory Region''' in the DNA strand.

It is used to create '''mRNA'''.

Information that '''mRNA''' strand contains, is found in the '''Transcribed Region'''.
|-
|| Point to '''Your Protein Collection''' box.
|| On the right side, we have a box showing '''Protein Collection'''.

It shows the type of protein which we make.
|-
|| Point to '''Positive Transcription Factor''' from '''Biomolecule Toolbox'''.
|| Now let us select '''Positive Transcription Factor''' from the '''Biomolecule Toolbox'''.
|-
|| Click on '''Positive Transcription Factor'''.
|| Click on the '''Positive Transcription Factor'''.
|-
|| Point to '''Regulatory Region''' on '''Gene1'''.

Point to highlighted '''Positive Transcription Factor'''.
|| Observe the '''Regulatory Region''' on '''Gene1'''.

Shape of '''Positive Transcription Factor''' is highlighted.
|-
|| Drag and place it on the highlighted '''Regulatory Region'''.
|| Drag and place it on the highlighted '''Regulatory Region'''.
|-
|| Click on '''RNA Polymerase'''.

Point to '''Gene1''' and highlighted '''RNA polymerase'''.
|| Now click on '''RNA Polymerase''' from '''Biomolecule Toolbox'''.

Observe '''Gene1''', shape of '''RNA polymerase''' is highlighted.
|-
|| Drag and place '''RNA Polymerase''' on the highlighted area.

Cursor on the simulation.
|| Drag and place it on the highlighted area of '''RNA Polymerase'''.

RNA Polymerase initiates the transcription process.

|-
|| Point to '''mRNA''' on screen.
|| We can see '''mRNA''' is produced as the '''Transcription''' process is initiated.
|-
|| '''Slide Number 9 +10'''

'''Positive Transcription Factor'''

|| Now let's see the roles of transcription elements.

'''Positive Transcription Factor''' is also known as an activator.

It positions itself on the '''Regulatory Region'''.

It encourages the binding of '''RNA polymerase''' to the '''Regulatory Region'''.

It allows '''RNA polymerase''' to produce '''mRNA'''.
|-
|| '''Slide Number 11'''

'''RNA Polymerase '''

|| '''RNA Polymerase''' is an enzyme.

It reads '''transcribed region''' of '''DNA''' to produce '''mRNA'''.

It zips down the strand by first passing through the '''regulatory region'''.
|-
|| '''Slide Number 12'''

'''Assignment'''
|| As an assignment,

Select '''Negative Transcription Factor''' and Place it on '''Gene1'''.

Select '''RNA polymerase'''.

See if '''RNA polymerase''' can pass through the '''transcribed region'''.

Explain the observation.
|-
|| Show in the interactive simulation.

|| Back to the simulation.
|-
|| Click on '''Ribosome ''' from '''Biomolecule Toolbox'''.
|| Select a '''Ribosome''' from '''Biomolecule Toolbox'''.

|-
|| Drag it on the highlighted area of free floating '''mRNA'''.

Point to protein on '''mRNA'''.

Point to protein in '''Your Protein collection''' box.
|| Drag it on the highlighted area of free floating '''mRNA'''.

A type of protein is produced.

It is highlighted on '''Your Protein collection''' box.
|-
|| '''Slide Number 13'''

'''Ribosome'''

|| About '''Ribosome'''.

'''Ribosome''' is an RNA structure that reads '''mRNA''' strands to produce proteins.

It clamps the RNA strand between its two subunits.
|-
|| Show in the interactive simulation.
|| Lets go back to the simulation.
|-
|| Click on '''mRNA destroyer''' from '''Biomolecule Toolbox'''.

Point to highlighted area on '''mRNA'''.

|| Select '''mRNA destroyer''' from '''Biomolecule Toolbox'''.

The position to fit '''mRNA destroyer''' is highlighted as dotted outline on '''mRNA'''.
|-
|| Drag and place it on the highlighted area of '''mRNA'''.

Point to '''mRNA'''.
|| Drag and place it on the highlighted area of '''mRNA'''.

'''mRNA''' is degraded into individual units.

'''mRNA Destroyer''' stops '''mRNA''' from making additional proteins.
|-
|| Show '''Reset All''' button.

Click on '''Reset All''' button.
|| '''Reset All''' button is available at the bottom-right corner of the screen.

Click on it to reset the screen to default position.
|-
|| Click on '''Next Gene''' button.

Cursor on simulation.
|| Click on green '''Next Gene''' button at bottom right corner of the screen.

This takes you to another gene which codes for a new type of protein.

Explore and find how this second gene is different from the first one.
|-
|| Click on the '''Messenger RNA Production''' tab.

Cursor on the simulation.

|| Click on '''Messenger RNA Production''' tab at the top.

Here we can see various factors that affect transcription that is mRNA production.
|-
|| Point to '''Positive Transcription Factor''' and '''RNA Polymerase'''.

Show Cursor at '''Concentrations''' & '''Affinity'''.
|| We can see two panels.

'''Positive Transcription Factor''' and '''RNA Polymerase'''.

I will increase the '''Concentrations''' and '''Affinity''' of the '''Positive Transcription Factor'''.
|-
|| Drag the slider of the '''Concentrations''' to '''Lots'''.
|| Drag the slider of the '''Concentrations''' to '''Lots'''.

|-
|| Point to '''Affinity''' at '''high'''.
|| I will keep the '''Affinity''' to '''High'''.

|-
|| Point to '''RNA Polymerase Affinity''' at '''high'''.
|| Also keep the '''RNA Polymerase Affinity''' to '''High'''.

|-
|| Point to '''RNA polymerase'''.
|| We can see that '''RNA polymerase''' can attach itself to the '''DNA''' strand easily.

And it produces '''mRNA'''.
|-
|| '''Slide Number 14 + 15'''

'''Factors influencing transcription'''

|| Now we know that,

Increase in the concentration of '''Positive Transcription Factor''', increases its binding, to the '''regulatory region'''.

It will in turn make '''RNA polymerase''' bind faster to DNA.

This results in faster production of '''mRNA'''.
|-
|| Cursor on the screen.
|| Explore '''Concentration''' and '''Affinity''' sliders.

Observe the results.

|-
|| Click on the '''Multiple Cells''' tab

Point to '''Concentrations''', '''Affinities''' and '''Degradation''' options.
|| Now Click on the '''Multiple Cells''' tab.

On the right-hand side there are 3 options.

'''Concentrations''', '''Affinities''' and '''Degradation'''.
|-
|| Click on Green plus sign.
|| Click on Green plus sign to open the panel.

|-
|| Drag the '''Concentrations''', '''Affinities''' and '''Degradation''' sliders.

Show the graph.
|| Drag the sliders to change '''Concentrations''', '''Affinities''' and '''Degradation'''.

English
Started Date

Observe the amount of Green Fluorescent protein produced in cells.
|-
|| Drag the '''Cells''' slider from '''One''' to '''Many'''.

Point to green fluorescent protein cells.
|| Drag the '''Cells''' slider from '''One''' to '''Many'''.

Observe the green fluorescent protein cells.

The brightness indicates the concentration of protein in cells.
|-
||
|| Let us summarize.

|-
|| '''Slide Number 16'''

'''Summary'''
|| In this tutorial we have demonstrated,

How to use '''Gene Expression-The Basics''' simulation.
|-
|| '''Slide Number 17'''

'''Summary'''

|| Using this simulation, we have learnt,

About steps involved in protein biosynthesis.

To create '''mRNA''' using transcription elements .

To create a protein using translation elements.

To study the effect of factors influencing '''mRNA''' production.
|-
|| '''Slide Number 18'''

'''Assignment 1'''

|| As an Assignment,

Using '''Cell Gene Expression''' screen,

Transcribe gene 2 and put proteins in '''protein collection''' box.
|-
|| '''Slide Number 19'''

'''Assignment 2'''
|| Explore the '''Multiple Cells''' tab.

Find the name of the cells used in this simulation.

Why the cells are green in colour.
|-
|| '''Slide Number 20'''

'''About Spoken Tutorial project'''
|| The video at the following link summarizes the Spoken Tutorial project.

Please download and watch it.
|-
|| '''Slide Number 21'''

'''Spoken Tutorial workshops'''
|| The '''Spoken Tutorial Project '''team:

conducts workshops using spoken tutorials and

gives certificates on passing on line tests.

For more details, please write to us.
|-
|| '''Slide Number 22'''

'''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 23'''

'''Acknowledgement'''

|| This project is partially funded by Pandit Madan Mohan Malaviya National Mission on Teachers and Teaching.

|-
|| '''Slide Number 24'''

'''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 spoken tutorial team from IIT Bombay.

Thank you for joining.

|}

@@ Line 247: / Line 247: @@
 It is highlighted on '''Your Protein collection''' box.
 |-
 || Show in the interactive '''simulation'''.

@@ Line 345: / Line 345: @@
 || Explore '''Concentration''' and '''Affinity''' sliders.
-Observe the results.
+And observe the results.
 |-
 || Click on the '''Multiple Cells''' tab.
@@ Line 365: / Line 365: @@
 || Drag the sliders to change '''Concentrations''', '''Affinities''' and '''Degradation'''.
-Observe the amount of Green Fluorescent protein produced in cells.
+Observe the amount of '''Green Fluorescent''' protein produced in cells.
 |-
 |-
@@ Line 371: / Line 371: @@
 || Drag the '''Cells''' slider from '''One''' to '''Many'''.
 |-
-|| Point to green fluorescent protein cells.
+|| Point to '''green fluorescent''' protein cells.
-||Observe the green fluorescent protein cells.
+||Observe the '''green fluorescent''' protein cells.
 The brightness indicates the concentration of protein in cells.
@@ Line 404: / Line 404: @@
 '''Summary'''
-||To study the effect of factors influencing '''mRNA''' production.
+||And to study the effect of factors influencing '''mRNA''' production.
 |-
 || '''Slide Number 19'''
@@ Line 423: / Line 423: @@
 Find the name of the cells used in this simulation.
-Why cells are green in colour.
+Explain why cells are green in colour.
 |-
 || '''Slide Number 21'''

@@ Line 318: / Line 318: @@
 And it produces '''mRNA'''.
 |-
-|| '''Slide Number 14 '''
+|| '''Slide Number 13 '''
 '''Factors influencing transcription'''
@@ Line 326: / Line 326: @@
 Increase in the concentration of '''Positive Transcription Factor''', increases its binding, to the '''regulatory region'''.
 |-
-|| '''Slide Number 15'''
+|| '''Slide Number 14'''
 '''Factors influencing transcription'''
@@ Line 372: / Line 372: @@
 |-
-|| '''Slide Number 16'''
+|| '''Slide Number 15'''
 '''Summary'''
@@ Line 379: / Line 379: @@
 How to use '''Gene Expression-The Basics''' simulation.
 |-
-|| '''Slide Number 17'''
+|| '''Slide Number 16'''
 '''Summary'''
@@ Line 391: / Line 391: @@
 To create a protein using translation elements.
 |-
-|| '''Slide Number 18'''
+|| '''Slide Number 17'''
 '''Summary'''
@@ Line 397: / Line 397: @@
 ||And to study the effect of factors influencing '''mRNA''' production.
 |-
-|| '''Slide Number 19'''
+|| '''Slide Number 18'''
 '''Assignment 2'''
@@ Line 407: / Line 407: @@
 Transcribe gene 2 and put proteins in '''protein collection''' box.
 |-
-|| '''Slide Number 20'''
+|| '''Slide Number 19'''
 '''Assignment 3'''
@@ Line 416: / Line 416: @@
 Explain why cells are green in colour.
 |-
-|| '''Slide Number 21'''
+|| '''Slide Number 20'''
 '''About Spoken Tutorial project'''
@@ Line 423: / Line 423: @@
 Please download and watch it.
 |-
-|| '''Slide Number 22'''
+|| '''Slide Number 21'''
 '''Spoken Tutorial workshops'''
@@ Line 434: / Line 434: @@
 For more details, please write to us.
 |-
-|| '''Slide Number 23'''
+|| '''Slide Number 22'''
 '''Forum for specific questions:'''
@@ Line 448: / Line 448: @@
 |-
-|| '''Slide Number 24'''
+|| '''Slide Number 23'''
 '''Acknowledgement'''
@@ Line 455: / Line 455: @@
 |-
-|| '''Slide Number 25'''
+|| '''Slide Number 24'''
 '''Acknowledgement'''

@@ Line 347: / Line 347: @@
 Observe the results.
 |-
-|| Click on the '''Multiple Cells''' tab
+|| Click on the '''Multiple Cells''' tab.
 Point to '''Concentrations''', '''Affinities''' and '''Degradation''' options.
@@ Line 396: / Line 396: @@
 About steps involved in protein biosynthesis.
-To create '''mRNA''' using transcription elements .
+To create '''mRNA''' using transcription elements.
 To create a protein using translation elements.