Difference between revisions of "PhET/C3/Gene-Expression-The-Basics/English"

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[http://phet.colorado.edu/ http://phet.colorado.edu]
 
[http://phet.colorado.edu/ http://phet.colorado.edu]
 
|-
 
|-
−
|| Point to the file in Downloads folder.
+
|| Point to the file in '''Downloads''' folder.
 
|| I have already downloaded '''Gene Expression-The Basics''' simulation to my '''Downloads''' folder.
 
|| I have already downloaded '''Gene Expression-The Basics''' simulation to my '''Downloads''' folder.
  
 
|-
 
|-
−
|| Press '''ctrl''', '''Alt''' and '''T''' keys simultaneously.
+
|| Press '''ctrl''', '''Alt''' and '''T''' keys.
  
 
At the prompt type,
 
At the prompt type,
  
 
'''cd Downloads''' and press enter.
 
'''cd Downloads''' and press enter.
 +
||To run the '''simulation''', open the terminal.
  
−
Then type, '''java -jar gene-expression-basics_en.jar''' and press enter.
+
At the prompt type, '''cd Downloads''' and press enter.
 +
|-
  
−
Point to the simulation.
+
|| Type:
−
|| To run the simulation, open the terminal.
+
  
−
At the prompt type, '''cd Downloads''' and press enter.
+
'''java -jar gene-expression-basics_en.jar'''
 +
press enter.
  
−
Then type, '''java -jar gene-expression-basics_en.jar''' and press enter.
+
Point to the '''simulation'''.
 +
||Then type, '''java -jar gene-expression-basics_en.jar''' and press enter.
  
−
'''Gene Expression-The Basics''' Simulation opens.
+
'''Gene Expression-The Basics''' '''Simulation''' opens.
 
|-
 
|-
−
|| Cursor on simulation.
+
|| Cursor on '''simulation'''.
  
 
Point the cursor on each tab.
 
Point the cursor on each tab.
−
|| The simulation screen shows 3 tabs at the top-
+
|| The '''simulation''' screen shows 3 tabs at the top-
  
 
'''Cell Gene Expression'''
 
'''Cell Gene Expression'''
Line 117: Line 120:
 
|| Cursor on the '''Biomolecule Toolbox'''.
 
|| Cursor on the '''Biomolecule Toolbox'''.
 
|| Left side of the screen has a '''Biomolecule Toolbox'''.
 
|| Left side of the screen has a '''Biomolecule Toolbox'''.
−
 
+
|-
−
It contains '''transcription''' and '''translation''' regulatory elements.
+
|| Cursor on the '''Biomolecule Toolbox'''.
 +
||It contains '''transcription''' and '''translation''' regulatory elements.
 
|-
 
|-
 
|| Cursor on the '''DNA''' strand.
 
|| Cursor on the '''DNA''' strand.
Line 139: Line 143:
  
 
|| '''Transcribed Region''' is located after the '''Regulatory Region''' in the DNA strand.
 
|| '''Transcribed Region''' is located after the '''Regulatory Region''' in the DNA strand.
−
 
+
|-
−
It is used to create '''mRNA'''.
+
||Cursor on the screen.
 +
||It is used to create '''mRNA'''.
  
 
Information that '''mRNA''' strand contains, is found in the '''Transcribed Region'''.
 
Information that '''mRNA''' strand contains, is found in the '''Transcribed Region'''.
Line 177: Line 182:
 
|| Drag and place it on the highlighted area of '''RNA Polymerase'''.
 
|| Drag and place it on the highlighted area of '''RNA Polymerase'''.
  
−
'''RNA Polymerase''' initiates the transcription process.
+
'''RNA Polymerase''' initiates the '''transcription''' process.
 
|-
 
|-
 
|| Point to '''mRNA''' on screen.
 
|| Point to '''mRNA''' on screen.
Line 211: Line 216:
 
|| '''Slide Number 12'''
 
|| '''Slide Number 12'''
  
−
'''Assignment'''
+
'''Assignment 1'''
 
|| As an assignment,
 
|| As an assignment,
  
Line 222: Line 227:
 
Explain the observation.
 
Explain the observation.
 
|-
 
|-
−
|| Show in the interactive simulation.
+
|| Show in the interactive '''simulation'''.
  
−
|| Back to the simulation.
+
|| Back to the '''simulation'''.
 
|-
 
|-
 
|| Click on '''Ribosome ''' from '''Biomolecule Toolbox'''.
 
|| Click on '''Ribosome ''' from '''Biomolecule Toolbox'''.
Line 232: Line 237:
 
|| Drag it on the highlighted area of free floating '''mRNA'''.
 
|| Drag it on the highlighted area of free floating '''mRNA'''.
  
−
Point to protein on '''mRNA'''.
+
||Drag it on the highlighted area of free floating '''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'''
+
||Point to protein on '''mRNA'''.
  
−
|| About '''Ribosome'''.
+
Point to protein in '''Your Protein collection''' box.
 +
|| A type of protein is produced.  
  
−
'''Ribosome''' is an RNA structure that reads '''mRNA''' strands to produce proteins.
+
It is highlighted on '''Your Protein collection''' box.
  
−
It clamps the RNA strand between its two subunits.
 
 
|-
 
|-
−
|| Show in the interactive simulation.
+
|| Show in the interactive '''simulation'''.
−
|| Lets go back to the simulation.
+
|| Lets go back to the '''simulation'''.
 
|-
 
|-
 
|| Click on '''mRNA destroyer''' from '''Biomolecule Toolbox'''.
 
|| Click on '''mRNA destroyer''' from '''Biomolecule Toolbox'''.
Line 263: Line 261:
 
|-
 
|-
 
|| Drag and place it on the highlighted area of '''mRNA'''.
 
|| Drag and place it on the highlighted area of '''mRNA'''.
−
 
−
Point to '''mRNA'''.
 
 
|| Drag and place it on the highlighted area of '''mRNA'''.
 
|| Drag and place it on the highlighted area of '''mRNA'''.
−
 
+
|-
−
'''mRNA''' is degraded into individual units.
+
|| Point to '''mRNA'''.
 +
|| '''mRNA''' is degraded into individual units.
  
 
'''mRNA Destroyer''' stops '''mRNA''' from making additional proteins.
 
'''mRNA Destroyer''' stops '''mRNA''' from making additional proteins.
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|| Click on '''Next Gene''' button.
 
|| Click on '''Next Gene''' button.
  
−
Cursor on simulation.
 
 
|| Click on green '''Next Gene''' button at bottom right corner of the screen.
 
|| 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.
+
|| Cursor on '''simulation'''.
 +
|| 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.  
 
Explore and find how this second gene is different from the first one.  
Line 289: Line 286:
 
|| Click on the '''Messenger RNA Production''' tab.
 
|| Click on the '''Messenger RNA Production''' tab.
  
−
Cursor on the simulation.
+
Cursor on the '''simulation'''.
  
 
|| Click on '''Messenger RNA Production''' tab at the top.
 
|| Click on '''Messenger RNA Production''' tab at the top.
  
−
Here we can see various factors that affect transcription that is mRNA production.
+
Here we can see various factors that affect '''transcription''' that is '''mRNA''' production.
 
|-
 
|-
 
|| Point to '''Positive Transcription Factor''' and '''RNA Polymerase'''.
 
|| Point to '''Positive Transcription Factor''' and '''RNA Polymerase'''.
  
−
Show Cursor at '''Concentrations''' & '''Affinity'''.
+
Show Cursor at '''Concentrations''' and '''Affinity'''.
 
|| We can see two panels.  
 
|| We can see two panels.  
  
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And it produces '''mRNA'''.
 
And it produces '''mRNA'''.
 
|-
 
|-
−
|| '''Slide Number 14 '''
+
|| '''Slide Number 13 '''
  
 
'''Factors influencing transcription'''
 
'''Factors influencing transcription'''
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Increase in the concentration of '''Positive Transcription Factor''', increases its binding, to the '''regulatory region'''.
 
Increase in the concentration of '''Positive Transcription Factor''', increases its binding, to the '''regulatory region'''.
 
|-
 
|-
−
|| '''Slide Number 15'''
+
|| '''Slide Number 14'''
  
 
'''Factors influencing transcription'''
 
'''Factors influencing transcription'''
−
||It will in turn make '''RNA polymerase''' bind faster to DNA.
+
||It will in turn make '''RNA polymerase''' bind faster to '''DNA'''.
  
 
This results in faster production of '''mRNA'''.
 
This results in faster production of '''mRNA'''.
Line 339: Line 336:
 
|| Explore '''Concentration''' and '''Affinity''' sliders.
 
|| Explore '''Concentration''' and '''Affinity''' sliders.
  
−
Observe the results.
+
And observe the results.
 
|-
 
|-
−
|| Click on the '''Multiple Cells''' tab
+
|| Click on the '''Multiple Cells''' tab.
  
 
Point to '''Concentrations''', '''Affinities''' and '''Degradation''' options.
 
Point to '''Concentrations''', '''Affinities''' and '''Degradation''' options.
Line 352: Line 349:
 
|| Click on Green plus sign.
 
|| Click on Green plus sign.
 
|| Click on Green plus sign to open the panel.
 
|| Click on Green plus sign to open the panel.
−
 
 
|-
 
|-
 
|| Drag the '''Concentrations''', '''Affinities''' and '''Degradation''' sliders.
 
|| Drag the '''Concentrations''', '''Affinities''' and '''Degradation''' sliders.
  
 
Show the graph.
 
Show the graph.
 +
 
|| Drag the sliders to change '''Concentrations''', '''Affinities''' and '''Degradation'''.
 
|| 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.
 +
|-
 
|-
 
|-
 
|| Drag the '''Cells''' slider from '''One''' to '''Many'''.
 
|| Drag the '''Cells''' slider from '''One''' to '''Many'''.
−
 
−
Point to green fluorescent protein cells.
 
 
|| Drag the '''Cells''' slider from '''One''' to '''Many'''.
 
|| Drag the '''Cells''' slider from '''One''' to '''Many'''.
 +
|-
 +
|| 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.
 
The brightness indicates the concentration of protein in cells.
Line 374: Line 372:
  
 
|-
 
|-
−
|| '''Slide Number 16'''
+
|| '''Slide Number 15'''
  
 
'''Summary'''
 
'''Summary'''
Line 381: Line 379:
 
How to use '''Gene Expression-The Basics''' simulation.
 
How to use '''Gene Expression-The Basics''' simulation.
 
|-
 
|-
−
|| '''Slide Number 17'''
+
|| '''Slide Number 16'''
  
 
'''Summary'''
 
'''Summary'''
  
−
|| Using this simulation, we have learnt,  
+
|| Using this '''simulation''', we have learnt,  
  
 
About steps involved in protein biosynthesis.
 
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.
 
To create a protein using translation elements.
 +
|-
 +
|| '''Slide Number 17'''
 +
 +
'''Summary'''
  
−
To study the effect of factors influencing '''mRNA''' production.
+
||And to study the effect of factors influencing '''mRNA''' production.
 
|-
 
|-
 
|| '''Slide Number 18'''
 
|| '''Slide Number 18'''
  
−
'''Assignment 1'''
+
'''Assignment 2'''
  
 
|| As an Assignment,
 
|| As an Assignment,
Line 407: Line 409:
 
|| '''Slide Number 19'''
 
|| '''Slide Number 19'''
  
−
'''Assignment 2'''
+
'''Assignment 3'''
 
|| Explore the '''Multiple Cells''' tab.
 
|| Explore the '''Multiple Cells''' tab.
  
 
Find the name of the cells used in this simulation.
 
Find the name of the cells used in this simulation.
  
−
Why the cells are green in colour.
+
Explain why cells are green in colour.
 
|-
 
|-
 
|| '''Slide Number 20'''
 
|| '''Slide Number 20'''
Line 464: Line 466:
  
 
Thank you for joining.
 
Thank you for joining.
−
 
+
|-
 
|}
 
|}

Latest revision as of 16:37, 1 July 2019


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

[1]

Use the given link to download the simulation.

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.

At the prompt type,

cd Downloads and press enter.

To run the simulation, open the terminal.

At the prompt type, cd Downloads and press enter.

Type:

java -jar gene-expression-basics_en.jar press enter.

Point to the simulation.

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.
Cursor on the 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.
Cursor on the screen. 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

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.

Slide Number 10

Positive Transcription Factor

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 1

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. Drag it on the highlighted area of free floating mRNA.
Point to protein on mRNA.

Point to protein in Your Protein collection box.

A type of protein is produced.

It is highlighted on Your Protein collection box.

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. Drag and place it on the highlighted area of mRNA.
Point to 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. Click on green Next Gene button at bottom right corner of the screen.
Cursor on simulation. 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 and 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 13

Factors influencing transcription

Now we know that,

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

Slide Number 14

Factors influencing transcription

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.

And 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.

Observe the amount of Green Fluorescent protein produced in cells.

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

The brightness indicates the concentration of protein in cells.

Let us summarize.
Slide Number 15

Summary

In this tutorial we have demonstrated,

How to use Gene Expression-The Basics simulation.

Slide Number 16

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.

Slide Number 17

Summary

And to study the effect of factors influencing mRNA production.
Slide Number 18

Assignment 2

As an Assignment,

Using Cell Gene Expression screen,

Transcribe gene 2 and put proteins in protein collection box.

Slide Number 19

Assignment 3

Explore the Multiple Cells tab.

Find the name of the cells used in this simulation.

Explain why 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.

Contributors and Content Editors

Meenalghoderao, Snehalathak

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