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

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|| 00:08
 
|| 00:08
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|| In this tutorial we will, Demonstrate '''Gene Expression-The Basics''', '''PhET Simulation'''.
+
|| In this tutorial, we will demonstrate '''Gene Expression-The Basics''', '''PhET Simulation'''.
  
 
|-
 
|-
 
|| 00:16
 
|| 00:16
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|| To follow this tutorial, Learners should be familiar with topics in high school Biology.
+
|| To follow this tutorial, learners should be familiar with topics in high-school biology.
  
 
|-
 
|-
 
|| 00:23
 
|| 00:23
−
|| Here I am using, Ubuntu Linux OS version 14.04
+
|| Here I am using: '''Ubuntu Linux OS''' version 14.04,
  
 
|-
 
|-
 
|| 00:30
 
|| 00:30
−
|| Java version 1.7.0.
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|| '''Java''' version 1.7.0,
  
 
|-
 
|-
 
|| 00:35
 
|| 00:35
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|| Firefox Web Browser version 53.02.2
+
|| '''Firefox Web Browser''' version 53.02.2
  
 
|-
 
|-
 
|| 00:41
 
|| 00:41
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|| Using this simulation we will learn,
+
|| Using this simulation, we will learn:
−
1.About steps involved in Protein Synthesis.
+
1. About steps involved in Protein Synthesis.
  
 
|-
 
|-
 
|| 00:48
 
|| 00:48
−
|| 2.Factors affecting Protein Synthesis and  
+
|| 2. Factors affecting Protein Synthesis and  
  
−
3.To observe the average level of '''Green Fluorescent Protein''' produced in cells.
+
3. To observe the average level of '''Green Fluorescent Protein''' produced in cells.
  
 
|-
 
|-
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|-
 
|| 01:23
 
|| 01:23
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|| '''Transcription''': is a process of making, '''mRNA'''.
+
|| '''Transcription''' is a process of making '''mRNA'''.
  
 
|-
 
|-
 
|| 01:28
 
|| 01:28
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|| '''Translation''': is a process by which '''mRNA''' directs protein synthesis.  
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|| '''Translation''' is a process by which '''mRNA''' directs protein synthesis.  
  
 
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|-
 
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|| 01:51
 
|| 01:51
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||To run the '''simulation''', open the terminal.
+
||To '''run''' the '''simulation''', open the '''terminal'''.
  
 
|-
 
|-
 
|| 01:55
 
|| 01:55
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||  At the prompt type, '''cd Downloads''' and press enter.
+
||  At the prompt, type: '''cd Downloads''' and press '''Enter'''.
  
 
|-
 
|-
 
|| 02:03
 
|| 02:03
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||Then type, '''java space  hyphen jar space gene hyphen expression hyphen basics underscore en dot jar''' and press enter.
+
||Then type: '''java space  hyphen jar space gene hyphen expression hyphen basics underscore en dot jar''' and press '''Enter'''.
  
 
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|| 02:25
 
|| 02:25
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|| The '''simulation''' screen shows 3 tabs at the top- '''Cell Gene Expression'''
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|| The '''simulation''' screen shows 3 tabs at the top- '''Cell Gene Expression''',
  
 
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|| 02:38
 
|| 02:38
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|| By default '''Cell Gene Expression''' screen opens.
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|| By default, '''Cell Gene Expression''' screen opens.
  
 
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|-
 
|-
 
|| 02:54
 
|| 02:54
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|| At the bottom of the screen a DNA strand is shown.
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|| At the bottom of the screen, a DNA strand is shown.
  
 
|-
 
|-
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|-
 
|-
 
|| 03:08
 
|| 03:08
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|| '''Regulatory Region''' is acted upon by, '''Positive''' and '''Negative Transcription Factors'''.
+
|| '''Regulatory Region''' is acted upon by '''Positive''' and '''Negative Transcription Factors'''.
  
 
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|-
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|-
 
|-
 
|| 04:07
 
|| 04:07
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|| Now click on '''RNA Polymerase''' from '''Biomolecule Toolbox'''.  
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|| Now, click on '''RNA Polymerase''' from '''Biomolecule Toolbox'''.  
  
 
|-
 
|-
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|-
 
|-
 
|| 04:43
 
|| 04:43
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|| '''Positive Transcription Factor''' is also known as an activator.  
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|| '''Positive Transcription Factor''' is also known as an '''activator'''.  
  
 
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|-
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|-
 
|-
 
|| 05:21
 
|| 05:21
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|| As an assignment, Select '''Negative Transcription Factor''' and Place it on '''Gene1'''.
+
|| As an assignment, select '''Negative Transcription Factor''' and place it on '''Gene1'''.
  
 
|-
 
|-
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|| 05:31
 
|| 05:31
 
|| See if '''RNA polymerase''' can pass through the '''transcribed region'''.
 
|| See if '''RNA polymerase''' can pass through the '''transcribed region'''.
−
 
+
And, explain the observation.
−
And Explain the observation.
+
  
 
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|-
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|-
 
|-
 
|| 06:01
 
|| 06:01
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|| About '''Ribosome'''.
+
|| Select '''mRNA destroyer''' from Biomolecule Toolbox.
  
 
|-
 
|-
−
|| 06:04
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|| 06:06
−
|| '''Ribosome''' is an RNA structure that reads '''mRNA''' strands to produce proteins.
+
||The position to fit mRNA destroyer is highlighted as dotted outline on mRNA.  
−
 
+
−
|-
+
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|| 06:13
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|| It clamps the RNA strand between its two subunits.
+
−
 
+
−
|-
+
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|| 06:19
+
−
|| Lets go back to the '''simulation'''.
+
−
 
+
−
|-
+
−
|| 06:22
+
−
|| Select '''mRNA destroyer''' from '''Biomolecule Toolbox'''.
+
−
 
+
−
|-
+
−
|| 06:27
+
−
|| The position to fit '''mRNA destroyer''' is highlighted as dotted outline on '''mRNA'''.
+
−
 
+
 
|-
 
|-
−
|| 06:35
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|| 06:14
 
|| Drag and place it on the highlighted area of '''mRNA'''.
 
|| Drag and place it on the highlighted area of '''mRNA'''.
  
 
|-
 
|-
−
|| 06:41
+
|| 06:20
 
|| '''mRNA''' is degraded into individual units.
 
|| '''mRNA''' is degraded into individual units.
  
 
|-
 
|-
−
|| 06:46
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|| 06:25
 
|| '''mRNA Destroyer''' stops '''mRNA''' from making additional proteins.
 
|| '''mRNA Destroyer''' stops '''mRNA''' from making additional proteins.
  
 
|-
 
|-
−
|| 06:52
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|| 06:31
 
|| '''Reset All''' button is available at the bottom-right corner of the screen.
 
|| '''Reset All''' button is available at the bottom-right corner of the screen.
  
 
|-
 
|-
−
|| 06:58
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|| 06:37
−
|| Click on it to reset the screen to default position.
+
|| Click on it to '''reset''' the '''screen''' to default position.
  
 
|-
 
|-
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|| 07:03
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|| 06:42
 
|| 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.
  
 
|-
 
|-
−
|| 07:10
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|| 06:49
 
|| This takes you to another gene which codes for a new type of protein.
 
|| This takes you to another gene which codes for a new type of protein.
  
 
|-
 
|-
−
|| 07:17
+
|| 06:56
 
|| 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.  
  
 
|-
 
|-
−
|| 07:24
+
|| 07:03
 
|| Click on '''Messenger RNA Production''' tab at the top.
 
|| Click on '''Messenger RNA Production''' tab at the top.
  
 
|-
 
|-
−
|| 07:29
+
|| 07:08
 
|| 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.
  
 
|-
 
|-
−
|| 07:36
+
|| 07:15
−
|| We can see two panels. '''Positive Transcription Factor''' and '''RNA Polymerase'''.
+
|| We can see two '''panel'''s. '''Positive Transcription Factor''' and '''RNA Polymerase'''.
  
 
|-
 
|-
−
|| 07:45
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|| 07:24
 
|| I will increase the '''Concentrations''' and '''Affinity''' of the '''Positive Transcription Factor'''.
 
|| I will increase the '''Concentrations''' and '''Affinity''' of the '''Positive Transcription Factor'''.
  
 
|-
 
|-
−
|| 07:53
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|| 07:32
 
|| Drag the slider of the '''Concentrations''' to '''Lots'''.
 
|| Drag the slider of the '''Concentrations''' to '''Lots'''.
  
 
|-
 
|-
−
|| 07:58
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|| 07:37
 
|| I will keep the '''Affinity''' to '''High'''.
 
|| I will keep the '''Affinity''' to '''High'''.
  
 
|-
 
|-
−
|| 08:02
+
|| 07:41
 
|| Also keep the '''RNA Polymerase Affinity''' to '''High'''.
 
|| Also keep the '''RNA Polymerase Affinity''' to '''High'''.
  
 
|-
 
|-
−
|| 08:07
+
|| 07:46
 
|| We can see that '''RNA polymerase''' can attach itself to the '''DNA''' strand easily.
 
|| We can see that '''RNA polymerase''' can attach itself to the '''DNA''' strand easily.
−
 
+
And, it produces '''mRNA'''.
−
And it produces '''mRNA'''.
+
  
 
|-
 
|-
−
|| 08:18
+
|| 07:57
−
|| Now we know that, Increase in the concentration of '''Positive Transcription Factor''', increases its binding, to the '''regulatory region'''.
+
|| Now we know that increase in the concentration of '''Positive Transcription Factor''' increases its binding to the '''regulatory region'''.
  
 
|-
 
|-
−
||08:29
+
||08:08
 
||It will in turn make '''RNA polymerase''' bind faster to '''DNA'''.
 
||It will in turn make '''RNA polymerase''' bind faster to '''DNA'''.
  
 
|-
 
|-
−
|| 08:35
+
|| 08:14
 
|| This results in faster production of '''mRNA'''.
 
|| This results in faster production of '''mRNA'''.
  
 
|-
 
|-
−
|| 08:40
+
|| 08:19
−
|| Explore '''Concentration''' and '''Affinity''' sliders. And observe the results.
+
|| Explore '''Concentration''' and '''Affinity''' sliders and observe the results.
  
 
|-
 
|-
−
|| 08:47
+
|| 08:26
−
|| Now Click on the '''Multiple Cells''' tab. On the right-hand side there are 3 options.
+
|| Now Click on the '''Multiple Cells''' tab. On the right-hand side there are 3 options-
  
 
|-
 
|-
−
|| 08:56
+
|| 08:35
 
|| '''Concentrations''', '''Affinities''' and '''Degradation'''.
 
|| '''Concentrations''', '''Affinities''' and '''Degradation'''.
  
 
|-
 
|-
−
|| 09:02
+
|| 08:41
−
|| Click on Green plus sign to open the panel.
+
|| Click on green plus sign to open the panel.
  
 
|-
 
|-
−
|| 09:06
+
|| 08:45
−
|| Drag the sliders to change '''Concentrations''', '''Affinities''' and '''Degradation'''.
+
|| Drag the '''slider'''s to change '''Concentrations''', '''Affinities''' and '''Degradation'''.
  
 
|-
 
|-
−
|| 09:16
+
|| 08:55
 
|| Observe the amount of '''Green Fluorescent''' protein produced in cells.
 
|| Observe the amount of '''Green Fluorescent''' protein produced in cells.
  
 
|-
 
|-
−
|| 09:22
+
|| 09:01
 
|| Drag the '''Cells''' slider from '''One''' to '''Many'''.
 
|| Drag the '''Cells''' slider from '''One''' to '''Many'''.
  
 
|-
 
|-
−
|| 09:27
+
|| 09:06
 
||Observe the '''green fluorescent''' protein cells.
 
||Observe the '''green fluorescent''' protein cells.
  
 
|-
 
|-
−
|| 09:31
+
|| 09:10
 
|| The brightness indicates the concentration of protein in cells.
 
|| The brightness indicates the concentration of protein in cells.
  
 
|-
 
|-
−
|| 09:37
+
|| 09:16
 
|| Let us summarize.
 
|| Let us summarize.
  
 
|-
 
|-
−
||09:40
+
||09:19
−
|| In this tutorial we have demonstrated, How to use '''Gene Expression-The Basics''' simulation.
+
|| In this tutorial, we have demonstrated how to use '''Gene Expression-The Basics''' simulation.
  
 
|-
 
|-
−
|| 09:49
+
|| 09:28
−
|| Using this '''simulation''', we have learnt, About steps involved in protein biosynthesis.
+
|| Using this '''simulation''', we have learnt: about steps involved in protein biosynthesis,
  
 
|-
 
|-
−
|| 09:56
+
|| 09:35
−
|| To create '''mRNA''' using transcription elements.
+
|| to create '''mRNA''' using transcription elements,
  
 
|-
 
|-
−
|| 10:01
+
|| 09:40
−
|| To create a protein using translation elements.
+
|| to create a protein using translation elements
  
 
|-
 
|-
−
|| 10:05
+
|| 09:45
−
||And to study the effect of factors influencing '''mRNA''' production.
+
||and to study the effect of factors influencing '''mRNA''' production.
  
 
|-
 
|-
−
|| 10:12
+
|| 09:51
−
|| As an Assignment, Using '''Cell Gene Expression''' screen, Transcribe gene 2 and put proteins in '''protein collection''' box.
+
|| As an Assignment: using '''Cell Gene Expression''' screen, transcribe gene 2 and put proteins in '''protein collection''' box.
  
 
|-
 
|-
−
|| 10:24
+
|| 10:03
 
|| Explore the '''Multiple Cells''' tab.
 
|| Explore the '''Multiple Cells''' tab.
  
 
|-
 
|-
−
|| 10:27
+
|| 10:06
 
|| Find the name of the cells used in this simulation.
 
|| Find the name of the cells used in this simulation.
  
 
|-
 
|-
−
|| 10:31
+
|| 10:10
 
|| Explain why cells are green in colour.
 
|| Explain why cells are green in colour.
  
 
|-
 
|-
−
|| 10:35
+
|| 10:14
 
|| The video at the following link summarizes the Spoken Tutorial project.
 
|| The video at the following link summarizes the Spoken Tutorial project.
  
Line 435: Line 417:
  
 
|-
 
|-
−
|| 10:44
+
|| 10:23
−
|| The '''Spoken Tutorial Project '''team: conducts workshops using spoken tutorials and Gives certificates on passing on line tests.
+
|| The '''Spoken Tutorial Project '''team: conducts workshops using spoken tutorials and gives certificates on passing on line tests.
  
 
|-
 
|-
−
|| 10:54
+
|| 10:33
 
|| For more details, please write to us.
 
|| For more details, please write to us.
  
 
|-
 
|-
−
|| 10:58
+
|| 10:37
 
|| Please post your timed queries on this forum.
 
|| Please post your timed queries on this forum.
  
 
|-
 
|-
−
|| 11:02
+
|| 10:41
 
|| This project is partially funded by '''Pandit Madan Mohan Malaviya National Mission on Teachers and Teaching.'''
 
|| This project is partially funded by '''Pandit Madan Mohan Malaviya National Mission on Teachers and Teaching.'''
  
 
|-
 
|-
−
||11:11
+
||10:50
−
|| Spoken Tutorial Project is funded by NMEICT, MHRD, Government of India.
+
|| Spoken Tutorial Project is funded by '''NMEICT, MHRD,''' Government of India.
  
 
More information on this mission is available at this link.
 
More information on this mission is available at this link.
  
 
|-
 
|-
−
|| 11:25
+
|| 11:04
 
|| This tutorial is contributed by spoken tutorial team from IIT Bombay.
 
|| This tutorial is contributed by spoken tutorial team from IIT Bombay.
  

Latest revision as of 16:58, 24 July 2019


Time Narration
00:01 Welcome to this tutorial on Gene-Expression-The Basics simulation.
00:08 In this tutorial, we will demonstrate Gene Expression-The Basics, PhET Simulation.
00:16 To follow this tutorial, learners should be familiar with topics in high-school biology.
00:23 Here I am using: Ubuntu Linux OS version 14.04,
00:30 Java version 1.7.0,
00:35 Firefox Web Browser version 53.02.2
00:41 Using this simulation, we will learn:

1. About steps involved in Protein Synthesis.

00:48 2. Factors affecting Protein Synthesis and

3. To observe the average level of Green Fluorescent Protein produced in cells.

01:00 Let us recall about Central Dogma of Genetics.
01:05 It was proposed by Francis Crick.
01:09 It states that the genetic information flows from DNA to mRNA to Protein.
01:19 Protein Synthesis involves two steps.
01:23 Transcription is a process of making mRNA.
01:28 Translation is a process by which mRNA directs protein synthesis.
01:35 Let us begin the demonstration.
01:38 Use the given link to download the simulation.
01:42 I have already downloaded Gene Expression-The Basics simulation to my Downloads folder.
01:51 To run the simulation, open the terminal.
01:55 At the prompt, type: cd Downloads and press Enter.
02:03 Then type: java space hyphen jar space gene hyphen expression hyphen basics underscore en dot jar and press Enter.
02:20 Gene Expression-The Basics Simulation opens.
02:25 The simulation screen shows 3 tabs at the top- Cell Gene Expression,
02:32 Messenger RNA Production and Multiple Cells.
02:38 By default, Cell Gene Expression screen opens.
02:43 Left side of the screen has a Biomolecule Toolbox.
02:48 It contains transcription and translation regulatory elements.
02:54 At the bottom of the screen, a DNA strand is shown.
02:59 It represents Gene 1.
03:02 Gene 1 has a Regulatory region and a Transcribed region.
03:08 Regulatory Region is acted upon by Positive and Negative Transcription Factors.
03:15 Transcribed Region is located after the Regulatory Region in the DNA strand.
03:22 It is used to create mRNA.
03:26 Information that mRNA strand contains, is found in the Transcribed Region.
03:33 On the right side, we have a box showing Protein Collection. It shows the type of protein which we make.
03:42 Now let us select Positive Transcription Factor from the Biomolecule Toolbox.
03:49 Click on the Positive Transcription Factor.
03:53 Observe the Regulatory Region on Gene1.
03:57 Shape of Positive Transcription Factor is highlighted.
04:02 Drag and place it on the highlighted Regulatory Region.
04:07 Now, click on RNA Polymerase from Biomolecule Toolbox.
04:13 Observe Gene1, shape of RNA polymerase is highlighted.
04:19 Drag and place it on the highlighted area of RNA Polymerase.
04:25 RNA Polymerase initiates the transcription process.
04:30 We can see mRNA is produced as the Transcription process is initiated.
04:38 Now let's see the roles of transcription elements.
04:43 Positive Transcription Factor is also known as an activator.
04:49 It positions itself on the Regulatory Region.
04:54 It encourages the binding of RNA polymerase to the Regulatory Region.
05:00 It allows RNA polymerase to produce mRNA.
05:05 RNA Polymerase is an enzyme.
05:09 It reads transcribed region of DNA to produce mRNA.
05:15 It zips down the strand by first passing through the regulatory region.
05:21 As an assignment, select Negative Transcription Factor and place it on Gene1.
05:28 Select RNA polymerase.
05:31 See if RNA polymerase can pass through the transcribed region.

And, explain the observation.

05:39 Back to the simulation.
05:42 Select a Ribosome from Biomolecule Toolbox.
05:47 Drag it on the highlighted area of free floating mRNA.
05:52 A type of protein is produced.
05:56 It is highlighted on Your Protein collection box.
06:01 Select mRNA destroyer from Biomolecule Toolbox.
06:06 The position to fit mRNA destroyer is highlighted as dotted outline on mRNA.
06:14 Drag and place it on the highlighted area of mRNA.
06:20 mRNA is degraded into individual units.
06:25 mRNA Destroyer stops mRNA from making additional proteins.
06:31 Reset All button is available at the bottom-right corner of the screen.
06:37 Click on it to reset the screen to default position.
06:42 Click on green Next Gene button at bottom right corner of the screen.
06:49 This takes you to another gene which codes for a new type of protein.
06:56 Explore and find how this second gene is different from the first one.
07:03 Click on Messenger RNA Production tab at the top.
07:08 Here we can see various factors that affect transcription that is mRNA production.
07:15 We can see two panels. Positive Transcription Factor and RNA Polymerase.
07:24 I will increase the Concentrations and Affinity of the Positive Transcription Factor.
07:32 Drag the slider of the Concentrations to Lots.
07:37 I will keep the Affinity to High.
07:41 Also keep the RNA Polymerase Affinity to High.
07:46 We can see that RNA polymerase can attach itself to the DNA strand easily.

And, it produces mRNA.

07:57 Now we know that increase in the concentration of Positive Transcription Factor increases its binding to the regulatory region.
08:08 It will in turn make RNA polymerase bind faster to DNA.
08:14 This results in faster production of mRNA.
08:19 Explore Concentration and Affinity sliders and observe the results.
08:26 Now Click on the Multiple Cells tab. On the right-hand side there are 3 options-
08:35 Concentrations, Affinities and Degradation.
08:41 Click on green plus sign to open the panel.
08:45 Drag the sliders to change Concentrations, Affinities and Degradation.
08:55 Observe the amount of Green Fluorescent protein produced in cells.
09:01 Drag the Cells slider from One to Many.
09:06 Observe the green fluorescent protein cells.
09:10 The brightness indicates the concentration of protein in cells.
09:16 Let us summarize.
09:19 In this tutorial, we have demonstrated how to use Gene Expression-The Basics simulation.
09:28 Using this simulation, we have learnt: about steps involved in protein biosynthesis,
09:35 to create mRNA using transcription elements,
09:40 to create a protein using translation elements
09:45 and to study the effect of factors influencing mRNA production.
09:51 As an Assignment: using Cell Gene Expression screen, transcribe gene 2 and put proteins in protein collection box.
10:03 Explore the Multiple Cells tab.
10:06 Find the name of the cells used in this simulation.
10:10 Explain why cells are green in colour.
10:14 The video at the following link summarizes the Spoken Tutorial project.

Please download and watch it.

10:23 The Spoken Tutorial Project team: conducts workshops using spoken tutorials and gives certificates on passing on line tests.
10:33 For more details, please write to us.
10:37 Please post your timed queries on this forum.
10:41 This project is partially funded by Pandit Madan Mohan Malaviya National Mission on Teachers and Teaching.
10:50 Spoken Tutorial Project is funded by NMEICT, MHRD, Government of India.

More information on this mission is available at this link.

11:04 This tutorial is contributed by spoken tutorial team from IIT Bombay.

Thank you for joining.

Contributors and Content Editors

PoojaMoolya, Sandhya.np14, Snehalathak

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