Difference between revisions of "PhET/C3/Gene-Machine-The-Lac-Operon/English-timed"

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|| 00:08
 
|| 00:08
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|| In this tutorial we will, Demonstrate '''Gene Machine - The Lac Operon, PhET simulation'''.
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|| In this tutorial, we will demonstrate '''Gene Machine - The Lac Operon, PhET simulation'''.
  
 
|-
 
|-
 
|| 00:16
 
|| 00:16
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|| To follow this tutorial, Learner should be familiar with topics in high school Biology.
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|| To follow this tutorial, learner should be familiar with topics in high-school biology.
  
 
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|-
 
|| 00:23
 
|| 00:23
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|| Here I am using, Ubuntu Linux OS version 14.04
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|| Here I am using:
 +
'''Ubuntu Linux OS''' version 14.04,
  
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Java version 1.7.0.
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'''Java''' version 1.7.0,
  
 
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|| 00:34
 
|| 00:34
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|| Firefox Web Browser version 53.02.2
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|| '''Firefox Web Browser''' version 53.02.2.
  
 
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|| 00:40
 
|| 00:40
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|| Using this simulation, students will learn about,
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|| Using this simulation, students will learn about:
  
 
|-
 
|-
 
|| 00:44
 
|| 00:44
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||1.Lactose regulation.
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||1.Lactose regulation
  
 
|-
 
|-
 
|| 00:46
 
|| 00:46
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|| 2.Genes involved in Lactose regulation.
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|| 2. Genes involved in Lactose regulation
  
 
|-
 
|-
 
|| 00:50
 
|| 00:50
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|| 3.Factors affecting '''LacZ''' gene regulation.
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|| 3. Factors affecting '''LacZ''' gene regulation.
  
 
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|| 01:17
 
|| 01:17
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|| '''Promoter''': Initiates transcription.
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|| '''Promoter''' initiates transcription.
  
 
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|| 01:20
 
|| 01:20
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|| '''Operator''': It is a Segment of DNA where repressor binds.
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|| '''Operator''': It is a segment of DNA where repressor binds.
  
 
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|| 01:31
 
|| 01:31
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|| The three structural genes in '''lac Operon''' are: '''lacZ''', '''lacY''', and '''lacA'''.  
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|| The three structural genes in '''lac Operon''' are '''lacZ''', '''lacY''', and '''lacA'''.  
  
 
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|| 01:40
 
|| 01:40
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|| These genes are transcribed as a single mRNA, under control of one promoter.
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|| These genes are '''transcribe'''d as a single mRNA, under control of one promoter.
  
 
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||01:55
 
||01:55
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|| Genes of the '''Lac Operon''' can be expressed and their proteins translated.
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|| Genes of the '''Lac Operon''' can be expressed and their proteins '''translate'''d.
  
 
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|| 02:08
 
|| 02:08
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|| '''lacY''' encodes '''Beta-galactoside permease''', It will enable transport of lactose into the cell.
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|| '''lacY''' encodes '''Beta-galactoside permease'''. It will enable transport of lactose into the cell.
  
 
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|| 02:23
 
|| 02:23
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|| Use the given link to download the simulation.
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|| Use the given '''link''' to download the simulation.
  
 
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|| 02:36
 
|| 02:36
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|| To run the simulation, open the terminal.
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|| To '''run''' the simulation, open the '''terminal'''.
  
 
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|| 02:40
 
|| 02:40
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|| At the prompt type, '''cd Downloads''' and press enter.
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|| At the prompt, type: '''cd Downloads''' and press '''Enter'''.
  
 
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||02:47
 
||02:47
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|| Then type, '''java space hyphen jar space gene hyphen machine hyphen lac hyphen operon undrenscore en  dot jar''' and press enter.
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|| Then type: '''java space hyphen jar space gene hyphen machine hyphen lac hyphen operon undrenscore en  dot jar''' and press '''Enter'''.
  
 
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|| 03:04
 
|| 03:04
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|| '''Gene-Machine-The Lac Operon''' Simulation opens.
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|| '''Gene-Machine-The Lac Operon''' simulation opens.
  
 
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|| 03:09
 
|| 03:09
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|| The simulation screen shows 2 tabs at the top,
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|| The simulation screen shows 2 tabs at the top-
  
 
'''Lactose Regulation''' and
 
'''Lactose Regulation''' and
  
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'''Lactose Transport'''
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'''Lactose Transport'''.
  
 
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|| 03:56
 
|| 03:56
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|| At the bottom of the screen we have, A slider to set the speed of the animation,
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|| At the bottom of the screen, we have- a slider to set the speed of the animation,
  
 
'''Play'''/'''Pause''',  
 
'''Play'''/'''Pause''',  
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|-
 
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||04:28
 
||04:28
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|| Similarly drag '''lacI gene''' and place it on the '''operon'''.
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|| Similarly, drag '''lacI gene''' and place it on the '''operon'''.
  
 
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|| 04:51
 
|| 04:51
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|| '''LacI''' is a '''lac''' repressor protein.
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|| '''LacI''' is a '''lac repressor protein'''.
  
 
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||05:29
 
||05:29
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|| Next assemble the '''LacZ''' gene.
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|| Next, assemble the '''LacZ''' gene.
  
 
|-
 
|-
 
||05:32
 
||05:32
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|| Drag and place,
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|| Drag and place
  
 
'''Lac promoter''',  
 
'''Lac promoter''',  
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|-
 
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||06:46
 
||06:46
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|| This '''mRNA''' is in turn translated to '''LacZ''' protein.
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|| This '''mRNA''' is in turn '''translate'''d to '''LacZ''' protein.
  
 
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||07:11
 
||07:11
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|| Observe the Interior Lactose Level meter, lactose level decreases.
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|| Observe the '''Interior Lactose Level''' meter, lactose level decreases.
  
 
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|| 08:03
 
|| 08:03
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|| Click on '''Auto''' radio button on the Lactose injector.
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|| Click on '''Auto''' radio button on the '''Lactose injector'''.
  
 
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|| 08:24
 
|| 08:24
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|| Observe that '''LacY''' protein, binds to the '''Cell Membrane'''.
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|| Observe that '''LacY''' protein binds to the '''Cell Membrane'''.
  
 
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||08:55
 
||08:55
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|| It blocks transcription of the '''Lac operon''', when there is no lactose present in the cell.
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|| It blocks transcription of the '''Lac operon'''  when there is no lactose present in the cell.
  
 
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|| 09:17
 
|| 09:17
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|| Let us summarize,
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|| Let us summarize.
  
−
In this tutorial we have demonstrated - How to use '''Gene Machine-The Lac Operon''', '''PhET simulation'''.
+
In this tutorial, we have demonstrated how to use '''Gene Machine-The Lac Operon''', '''PhET simulation'''.
  
 
|-
 
|-
 
|| 09:29
 
|| 09:29
−
|| We have also learnt about, Lactose regulation.
+
|| We have also learnt about: Lactose regulation,
  
 
|-
 
|-
 
||09:35
 
||09:35
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|| Genes involved in Lactose regulation.
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|| Genes involved in Lactose regulation,
  
 
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|| 09:44
 
|| 09:44
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|| An an assignment, Remove some of the components of the '''Operon'''  such as Operator, Promoter and Genes.
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|| An an assignment, remove some of the components of the '''Operon'''  such as Operator, Promoter and Genes.
  
 
|-
 
|-
 
||09:54
 
||09:54
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|| Run the simulation. And Observe the results and give explanation.
+
|| '''Run''' the simulation. And observe the results and give explanation.
  
 
|-
 
|-
 
|| 10:01
 
|| 10:01
−
|| The video at the following link summarizes the Spoken Tutorial project.
+
|| The video at the following link summarizes the '''Spoken Tutorial''' project.
−
 
+
 
Please download and watch it.
 
Please download and watch it.
  
 
|-
 
|-
 
|| 10:10
 
|| 10:10
−
|| The '''Spoken Tutorial Project '''team: conducts workshops using spoken tutorials and
+
|| The '''Spoken Tutorial Project '''team: conducts workshops using spoken tutorials and gives certificates on passing online tests.
−
 
+
−
gives certificates on passing online tests.
+
  
 
|-
 
|-
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|-
 
|-
 
|| 10:39
 
|| 10:39
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|| 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.

Revision as of 11:41, 14 August 2018

Time Narration
00:01 Welcome to this tutorial on Gene Machine - The Lac Operon simulation.
00:08 In this tutorial, we will demonstrate Gene Machine - The Lac Operon, PhET simulation.
00:16 To follow this tutorial, learner should be familiar with topics in high-school biology.
00:23 Here I am using:

Ubuntu Linux OS version 14.04,

Java version 1.7.0,

00:34 Firefox Web Browser version 53.02.2.
00:40 Using this simulation, students will learn about:
00:44 1.Lactose regulation
00:46 2. Genes involved in Lactose regulation
00:50 3. Factors affecting LacZ gene regulation.
00:55 The lac operon is a set of genes responsible for regulating lactose metabolism in E.coli bacteria.
01:05 An operon is made up of 3 basic DNA components: Promoter, Operator and Structural gene.
01:17 Promoter initiates transcription.
01:20 Operator: It is a segment of DNA where repressor binds.
01:26 Structural gene: A gene which codes for protein.
01:31 The three structural genes in lac Operon are lacZ, lacY, and lacA.
01:40 These genes are transcribed as a single mRNA, under control of one promoter.
01:47 Genes in the lac operon specify proteins that help the cell utilize lactose.
01:55 Genes of the Lac Operon can be expressed and their proteins translated.
02:01 The gene product of lacZ is β-galactosidase which cleaves lactose.
02:08 lacY encodes Beta-galactoside permease. It will enable transport of lactose into the cell.
02:17 lacA encodes for β-galactoside transacetylase.
02:23 Use the given link to download the simulation.
02:28 I have already downloaded Gene Machine-The Lac Operon simulation to my Downloads folder.
02:36 To run the simulation, open the terminal.
02:40 At the prompt, type: cd Downloads and press Enter.
02:47 Then type: java space hyphen jar space gene hyphen machine hyphen lac hyphen operon undrenscore en dot jar and press Enter.
03:04 Gene-Machine-The Lac Operon simulation opens.
03:09 The simulation screen shows 2 tabs at the top-

Lactose Regulation and

Lactose Transport.

03:19 On the Lactose Regulation screen, You will see two floating RNA polymerase in blue colour.
03:27 Observe an incomplete operon which needs to be assembled.
03:32 Here, you need to match each part given at the bottom, to it's specific place on the gene.
03:39 Click on the Show Legend check box at the bottom-right corner.
03:44 This will turn-on the Legend panel on the right-side of the screen.
03:49 The Legend panel helps you to identify the molecules present on the screen.
03:56 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.

04:10 Let us now start assembling the gene.
04:14 Click on lacI promoter.
04:17 The specific portions on the gene are highlighted in yellow color.
04:23 Drag lacI promoter and place it on the operon.
04:28 Similarly, drag lacI gene and place it on the operon.
04:33 The floating RNA Polymerase molecule binds briefly to the lacI promoter.
04:39 This will activate the lacI gene to produce mRNA.
04:44 This mRNA is translated to LacI protein which is seen floating on the screen.
04:51 LacI is a lac repressor protein.
04:55 It binds to the Lac operator region of the Operon.
05:00 In the absence of lactose, it will block the RNA polymerase to transcribe the LacZ gene.
05:08 Notice that as soon as LacI protein is produced, Lactose injector appears on the top-left corner of the screen.
05:18 Click on the Show Lactose Meter check-box at the bottom-left corner.
05:24 Meter will give an idea about interior lactose level.
05:29 Next, assemble the LacZ gene.
05:32 Drag and place

Lac promoter,

Lac operator

as prompted by the highlighted yellow portions on the operon.

05:42 LacI protein floating around will now bind to the operator region of operon.
05:49 Now place the LacZ gene on operon.
05:53 Since the LacI is bound to the LacZ Operator region, it blocks the RNA polymerase to produce mRNA.

Hence no LacZ enzyme is produced.

06:06 Pump a few molecules of lactose on to the screen using Lactose injector.
06:13 There are 2 options for pumping, Manual and Auto.
06:19 Select Manual option.
06:22 Press the red button on the injector.
06:26 Observe the Lactose level in lactose meter.
06:30 LacI bound to the operator, acts like Lactose sensor.
06:35 Lactose molecule bind to the LacI and leaves the Operator region.
06:41 The RNA Polymerase will now be able to transcribe the gene.
06:46 This mRNA is in turn translated to LacZ protein.
06:52 LacZ is Beta-galactosidase enzyme.
06:56 It cleaves lactose into glucose and galactose.
07:01 Lactose molecules bind to LacZ protein.
07:05 LacZ protein dissociates lactose molecules as shown on the screen.
07:11 Observe the Interior Lactose Level meter, lactose level decreases.
07:17 Click on Lactose Transport screen.
07:21 In addition to all the features of the Lactose regulation screen, Lactose Transport screen has Cell Membrane and LacY gene.
07:31 As demonstrated previously, assemble the Operon.
07:36 Drag and place all the components of the Operon in their respective places.
07:52 Click on Show Legend and Show Lactose Meter check box.
07:58 Pump-in few molecules of Lactose using Lactose injector.
08:03 Click on Auto radio button on the Lactose injector.
08:08 LacI, LacZ and LacY proteins are produced.
08:14 LacY is Beta-galactoside permease enzyme.
08:19 It enables transport of lactose into the cell.
08:24 Observe that LacY protein binds to the Cell Membrane.
08:29 Now lactose molecules permeate into cell with the help of LacY protein.
08:36 Inside the cell, lactose molecules are metabolized by LacZ enzyme as shown on the screen.
08:46 Factors affecting LacZ gene regulation-
08:51 The lac repressor acts as a lactose sensor.
08:55 It blocks transcription of the Lac operon when there is no lactose present in the cell.
09:02 When lactose is present, the lac repressor loses its ability to bind DNA.
09:09 It floats off the operator, clearing the way for RNA polymerase to transcribe the operon.
09:17 Let us summarize.

In this tutorial, we have demonstrated how to use Gene Machine-The Lac Operon, PhET simulation.

09:29 We have also learnt about: Lactose regulation,
09:35 Genes involved in Lactose regulation,
09:39 Factors affecting LacZ gene regulation.
09:44 An an assignment, remove some of the components of the Operon such as Operator, Promoter and Genes.
09:54 Run the simulation. And observe the results and give explanation.
10:01 The video at the following link summarizes the Spoken Tutorial project.

Please download and watch it.

10:10 The Spoken Tutorial Project team: conducts workshops using spoken tutorials and gives certificates on passing online tests.
10:21 For more details, please write to us.
10:25 Please post your timed queries on this forum.
10:30 This project is partially funded by Pandit Madan Mohan Malaviya National Mission on Teachers and Teaching.
10:39 Spoken Tutorial Project is funded by NMEICT, MHRD, Government of India.

More information on this mission is available at this link.

10:53 This tutorial is contributed by Snehalatha Kaliappan and Meenal Ghoderao from IIT Bombay.

Thanks for joining.

Contributors and Content Editors

PoojaMoolya, Sandhya.np14, Snehalathak

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