PoojaMoolya at 11:28, 24 July 2019

2019-07-24T11:28:39Z

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Sandhya.np14 at 10:29, 14 August 2018

2018-08-14T10:29:27Z

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Snehalathak at 06:55, 13 August 2018

2018-08-13T06:55:16Z

PoojaMoolya: Created page with " {|border=1 ||'''Time''' ||'''Narration''' |- || 00:01 || Welcome to this tutorial on '''Gene-Expression-The Basics simulation'''. |- || 00:08 || In this tutorial we will,..."

2018-07-31T09:52:38Z

Created page with " {|border=1 ||'''Time''' ||'''Narration''' |- || 00:01 || Welcome to this tutorial on '''Gene-Expression-The Basics simulation'''. |- || 00:08 || In this tutorial we will,..."

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{|border=1
||'''Time'''
||'''Narration'''

|-
|| 00:01
|| Welcome to this tutorial on '''Gene-Expression-The Basics simulation'''.

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|| 00:08
|| In this tutorial we will, Demonstrate '''Gene Expression-The Basics''', '''PhET Simulation'''.

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|| 00:16
|| To follow this tutorial, Learners should be familiar with topics in high school Biology.

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|| 00:23
|| Here I am using, Ubuntu Linux OS version 14.04

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|| 00:30
|| Java version 1.7.0.

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|| 00:35
|| Firefox Web Browser version 53.02.2

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|| 00:41
|| Using this simulation we will learn, About steps involved in Protein Synthesis.

|-
|| 00:48
|| Factors affecting Protein Synthesis and To observe the average level of '''Green Fluorescent Protein''' produced in cells.

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|| 01:00
|| Let us recall about '''Central Dogma of Genetics'''.

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|| 01:05
|| It was proposed by '''Francis Crick'''.

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|| 01:09
|| It states that the genetic information flows from '''DNA''' to '''mRNA''' to Protein.

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||01:19
|| Protein Synthesis involves two steps.

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|| 01:23
|| '''Transcription''': is a process of making, '''mRNA'''.

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|| 01:28
|| '''Translation''': is a process by which '''mRNA''' directs protein synthesis.

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||01:35
|| Let us begin the demonstration.

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||01:38
|| Use the given link to download the simulation.

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|| 01:42
|| I have already downloaded '''Gene Expression-The Basics''' simulation to my '''Downloads''' folder.

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|| 01:51
||To run the '''simulation''', open the terminal.

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|| 01:55
|| At the prompt type, '''cd Downloads''' and press enter.

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|| 02:03
||Then type, '''java space hyphen jar space gene hyphen expression hyphen basics underscore en dot jar''' and press enter.

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|| 02:20
|| '''Gene Expression-The Basics''' '''Simulation''' opens.

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|| 02:25
|| The '''simulation''' screen shows 3 tabs at the top- '''Cell Gene Expression'''

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|| 02:32
|| '''Messenger RNA Production''' and '''Multiple Cells'''.

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|| 02:38
|| By default '''Cell Gene Expression''' screen opens.

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|| 02:43
|| Left side of the screen has a '''Biomolecule Toolbox'''.

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|| 02:48
||It contains '''transcription''' and '''translation''' regulatory elements.

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|| 02:54
|| At the bottom of the screen a DNA strand is shown.

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|| 02:59
|| It represents '''Gene 1'''.

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|| 03:02
|| '''Gene 1''' has a '''Regulatory region''' and a '''Transcribed region'''.

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|| 03:08
|| '''Regulatory Region''' is acted upon by, '''Positive''' and '''Negative Transcription Factors'''.

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|| 03:15
|| '''Transcribed Region''' is located after the '''Regulatory Region''' in the DNA strand.

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||03:22
||It is used to create '''mRNA'''.

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|| 03:26
|| Information that '''mRNA''' strand contains, is found in the '''Transcribed Region'''.

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|| 03:33
|| On the right side, we have a box showing '''Protein Collection'''. It shows the type of protein which we make.

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|| 03:42
|| Now let us select '''Positive Transcription Factor''' from the '''Biomolecule Toolbox'''.

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|| 03:49
|| Click on the '''Positive Transcription Factor'''.

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|| 03:53
|| Observe the '''Regulatory Region''' on '''Gene1'''.

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|| 03:57
|| Shape of '''Positive Transcription Factor''' is highlighted.

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|| 04:02
|| Drag and place it on the highlighted '''Regulatory Region'''.

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|| 04:07
|| Now click on '''RNA Polymerase''' from '''Biomolecule Toolbox'''.

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|| 04:13
|| Observe '''Gene1''', shape of '''RNA polymerase''' is highlighted.

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||04:19
|| Drag and place it on the highlighted area of '''RNA Polymerase'''.

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|| 04:25
|| '''RNA Polymerase''' initiates the '''transcription''' process.

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||04:30
|| We can see '''mRNA''' is produced as the '''Transcription''' process is initiated.

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|| 04:38
|| Now let's see the roles of '''transcription''' elements.

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|| 04:43
|| '''Positive Transcription Factor''' is also known as an activator.

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|| 04:49
|| It positions itself on the '''Regulatory Region'''.

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|| 04:54
||It encourages the binding of '''RNA polymerase''' to the '''Regulatory Region'''.

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|| 05:00
|| It allows '''RNA polymerase''' to produce '''mRNA'''.

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|| 05:05
|| '''RNA Polymerase''' is an enzyme.

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|| 05:09
|| It reads '''transcribed region''' of '''DNA''' to produce '''mRNA'''.

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|| 05:15
|| It zips down the strand by first passing through the '''regulatory region'''.

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|| 05:21
|| As an assignment, Select '''Negative Transcription Factor''' and Place it on '''Gene1'''.

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|| 05:28
|| Select '''RNA polymerase'''.

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|| 05:31
|| See if '''RNA polymerase''' can pass through the '''transcribed region'''.

And Explain the observation.

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|| 05:39
|| Back to the '''simulation'''.

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|| 05:42
|| Select a '''Ribosome''' from '''Biomolecule Toolbox'''.

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|| 05:47
||Drag it on the highlighted area of free floating '''mRNA'''.

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||05:52
|| A type of protein is produced.

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|| 05:56
|| It is highlighted on '''Your Protein collection''' box.

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|| 06:01
|| About '''Ribosome'''.

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|| 06:04
|| '''Ribosome''' is an RNA structure that reads '''mRNA''' strands to produce proteins.

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|| 06:13
|| It clamps the RNA strand between its two subunits.

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|| 06:19
|| Lets go back to the '''simulation'''.

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|| 06:22
|| Select '''mRNA destroyer''' from '''Biomolecule Toolbox'''.

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|| 06:27
|| The position to fit '''mRNA destroyer''' is highlighted as dotted outline on '''mRNA'''.

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|| 06:35
|| Drag and place it on the highlighted area of '''mRNA'''.

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|| 06:41
|| '''mRNA''' is degraded into individual units.

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|| 06:46
|| '''mRNA Destroyer''' stops '''mRNA''' from making additional proteins.

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|| 06:52
|| '''Reset All''' button is available at the bottom-right corner of the screen.

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|| 06:58
|| Click on it to reset the screen to default position.

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|| 07:03
|| Click on green '''Next Gene''' button at bottom right corner of the screen.

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|| 07:10
|| This takes you to another gene which codes for a new type of protein.

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|| 07:17
|| Explore and find how this second gene is different from the first one.

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|| 07:24
|| Click on '''Messenger RNA Production''' tab at the top.

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|| 07:29
|| Here we can see various factors that affect '''transcription''' that is '''mRNA''' production.

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|| 07:36
|| We can see two panels. '''Positive Transcription Factor''' and '''RNA Polymerase'''.

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|| 07:45
|| I will increase the '''Concentrations''' and '''Affinity''' of the '''Positive Transcription Factor'''.

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|| 07:53
|| Drag the slider of the '''Concentrations''' to '''Lots'''.

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|| 07:58
|| I will keep the '''Affinity''' to '''High'''.

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|| 08:02
|| Also keep the '''RNA Polymerase Affinity''' to '''High'''.

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|| 08:07
|| We can see that '''RNA polymerase''' can attach itself to the '''DNA''' strand easily.

And it produces '''mRNA'''.

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|| 08:18
|| Now we know that, Increase in the concentration of '''Positive Transcription Factor''', increases its binding, to the '''regulatory region'''.

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||08:29
||It will in turn make '''RNA polymerase''' bind faster to '''DNA'''.

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|| 08:35
|| This results in faster production of '''mRNA'''.

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|| 08:40
|| Explore '''Concentration''' and '''Affinity''' sliders. And observe the results.

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|| 08:47
|| Now Click on the '''Multiple Cells''' tab. On the right-hand side there are 3 options.

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|| 08:56
|| '''Concentrations''', '''Affinities''' and '''Degradation'''.

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|| 09:02
|| Click on Green plus sign to open the panel.

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|| 09:06
|| Drag the sliders to change '''Concentrations''', '''Affinities''' and '''Degradation'''.

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|| 09:16
|| Observe the amount of '''Green Fluorescent''' protein produced in cells.

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|| 09:22
|| Drag the '''Cells''' slider from '''One''' to '''Many'''.

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|| 09:27
||Observe the '''green fluorescent''' protein cells.

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|| 09:31
|| The brightness indicates the concentration of protein in cells.

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|| 09:37
|| Let us summarize.

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||09:40
|| In this tutorial we have demonstrated, How to use '''Gene Expression-The Basics''' simulation.

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|| 09:49
|| Using this '''simulation''', we have learnt, About steps involved in protein biosynthesis.

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|| 09:56
|| To create '''mRNA''' using transcription elements.

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|| 10:01
|| To create a protein using translation elements.

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|| 10:05
||And to study the effect of factors influencing '''mRNA''' production.

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|| 10:12
|| As an Assignment, Using '''Cell Gene Expression''' screen, Transcribe gene 2 and put proteins in '''protein collection''' box.

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|| 10:24
|| Explore the '''Multiple Cells''' tab.

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|| 10:27
|| Find the name of the cells used in this simulation.

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|| 10:31
|| Explain why cells are green in colour.

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|| 10:35
|| The video at the following link summarizes the Spoken Tutorial project.

Please download and watch it.

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|| 10:44
|| The '''Spoken Tutorial Project '''team: conducts workshops using spoken tutorials and Gives certificates on passing on line tests.

|-
|| 10:54
|| For more details, please write to us.

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|| 10:58
|| Please post your timed queries on this forum.

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|| 11:02
|| This project is partially funded by '''Pandit Madan Mohan Malaviya National Mission on Teachers and Teaching.'''

|-
||11:11
|| Spoken Tutorial Project is funded by NMEICT, MHRD, Government of India.

More information on this mission is available at this link.

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|| 11:25
|| This tutorial is contributed by spoken tutorial team from IIT Bombay.

Thank you for joining.
|-
|}

@@ Line 31: / Line 31: @@
 |-
 || 00:41
-|| Using this simulation we will learn, About steps involved in Protein Synthesis.
+|| Using this simulation we will learn,
 |-
 || 00:48
-|| Factors affecting Protein Synthesis and To observe the average level of '''Green Fluorescent Protein''' produced in cells.
+|| 2.Factors affecting Protein Synthesis and
 |-

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

PoojaMoolya at 11:28, 24 July 2019

Sandhya.np14 at 10:29, 14 August 2018

Snehalathak at 06:55, 13 August 2018

PoojaMoolya: Created page with " {|border=1 ||'''Time''' ||'''Narration''' |- || 00:01 || Welcome to this tutorial on '''Gene-Expression-The Basics simulation'''. |- || 00:08 || In this tutorial we will,..."