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

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|-
 
|-
 
|| 00:23
 
|| 00:23
−
|| Here I am using:
+
|| Here I am using:'''Ubuntu Linux OS''' version 14.04,
−
'''Ubuntu Linux OS''' version 14.04,
+
  
 
'''Java''' version 1.7.0,
 
'''Java''' version 1.7.0,
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|-
 
|-
 
|| 00:44
 
|| 00:44
−
||1.Lactose regulation
+
||Lactose regulation
  
 
|-
 
|-
 
|| 00:46
 
|| 00:46
−
|| 2. Genes involved in Lactose regulation
+
||Genes involved in Lactose regulation
  
 
|-
 
|-
 
|| 00:50
 
|| 00:50
−
|| 3. Factors affecting '''LacZ''' gene regulation.
+
||Factors affecting '''LacZ''' gene regulation.
  
 
|-
 
|-
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|-
 
|-
 
|| 01:40
 
|| 01:40
−
|| These genes are '''transcribe'''d as a single mRNA, under control of one promoter.
+
|| These genes are '''transcribed''' as a single mRNA, under control of one promoter.
  
 
|-
 
|-
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|-
 
|-
 
||01:55
 
||01:55
−
|| Genes of the '''Lac Operon''' can be expressed and their proteins '''translate'''d.
+
|| Genes of the '''Lac Operon''' can be expressed and their proteins '''translated'''.
  
 
|-
 
|-
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|-
 
|-
 
||02:47
 
||02:47
−
|| Then type: '''java space hyphen jar space gene hyphen machine hyphen lac hyphen operon undrenscore en  dot jar''' and press '''Enter'''.
+
|| Then type: '''java space hyphen jar space gene hyphen machine hyphen lac hyphen operon underscore en  dot jar''' and press '''Enter'''.
  
 
|-
 
|-
Line 197: Line 196:
  
 
|-
 
|-
−
||05:00
+
|| 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.
 
|| Notice that as soon as '''LacI protein''' is produced, '''Lactose injector''' appears on the top-left corner of the screen.
  
 
|-
 
|-
−
|| 05:18
+
|| 05:10
 
||Click on the '''Show Lactose Meter''' check-box at the bottom-left corner.
 
||Click on the '''Show Lactose Meter''' check-box at the bottom-left corner.
  
 
|-
 
|-
−
||05:24
+
||05:16
 
|| Meter will give an idea about interior lactose level.
 
|| Meter will give an idea about interior lactose level.
  
 
|-
 
|-
−
||05:29
+
||05:21
 
|| Next, assemble the '''LacZ''' gene.
 
|| Next, assemble the '''LacZ''' gene.
  
 
|-
 
|-
−
||05:32
+
||05:24
 
|| Drag and place
 
|| Drag and place
  
Line 227: Line 222:
  
 
|-
 
|-
−
|| 05:42
+
|| 05:34
 
|| '''LacI''' protein floating around will now bind to the Operator region of '''operon'''.
 
|| '''LacI''' protein floating around will now bind to the Operator region of '''operon'''.
  
 
|-
 
|-
−
|| 05:49
+
|| 05:41
 
|| Now place the '''LacZ gene''' on '''operon'''.
 
|| Now place the '''LacZ gene''' on '''operon'''.
  
 
|-
 
|-
−
|| 05:53
+
|| 05:45
−
|| Since the '''LacI''' is bound to the '''LacZ''' Operator region, it blocks the '''RNA polymerase''' to produce '''mRNA'''.
+
||In the absence of lactose, LacI binds to the operator region and prevents RNA polymerase from transcribing the operon.
  
−
Hence no '''LacZ''' enzyme is produced.
+
|-
 +
|| 05:55
 +
||Hence no LacZ enzyme is produced.  
  
 
|-
 
|-
−
|| 06:06
+
|| 05:59
 
|| Pump a few molecules of '''lactose''' on to the screen using '''Lactose injector'''.
 
|| Pump a few molecules of '''lactose''' on to the screen using '''Lactose injector'''.
  
 
|-
 
|-
−
||06:13
+
||06:06
 
|| There are 2 options for pumping, '''Manual''' and '''Auto'''.
 
|| There are 2 options for pumping, '''Manual''' and '''Auto'''.
  
 
|-
 
|-
−
||06:19
+
||06:12
 
|| Select '''Manual''' option.
 
|| Select '''Manual''' option.
  
 
|-
 
|-
−
||06:22
+
||06:15
 
||Press the red button on the '''injector'''.
 
||Press the red button on the '''injector'''.
  
 
|-
 
|-
−
||06:26
+
||06:19
 
|| Observe the Lactose level in '''lactose meter'''.
 
|| Observe the Lactose level in '''lactose meter'''.
  
 
|-
 
|-
−
|| 06:30
+
|| 06:23
 
|| '''LacI''' bound to the Operator, acts like '''Lactose''' sensor.  
 
|| '''LacI''' bound to the Operator, acts like '''Lactose''' sensor.  
  
 
|-
 
|-
−
||06:35
+
||06:28
 
|| '''Lactose''' molecule bind to the '''LacI''' and leaves the Operator region.
 
|| '''Lactose''' molecule bind to the '''LacI''' and leaves the Operator region.
  
 
|-
 
|-
−
|| 06:41
+
|| 06:34
 
|| The '''RNA Polymerase''' will now be able to transcribe the gene.
 
|| The '''RNA Polymerase''' will now be able to transcribe the gene.
  
 
|-
 
|-
−
||06:46
+
||06:39
 
|| This '''mRNA''' is in turn '''translate'''d to '''LacZ''' protein.
 
|| This '''mRNA''' is in turn '''translate'''d to '''LacZ''' protein.
  
 
|-
 
|-
−
|| 06:52
+
|| 06:45
 
|| '''LacZ''' is '''Beta-galactosidase''' enzyme.
 
|| '''LacZ''' is '''Beta-galactosidase''' enzyme.
  
 
|-
 
|-
−
||06:56
+
||06:49
 
|| It cleaves lactose into glucose and galactose.  
 
|| It cleaves lactose into glucose and galactose.  
  
 
|-
 
|-
−
|| 07:01
+
|| 06:54
 
|| Lactose molecules bind to '''LacZ''' protein.
 
|| Lactose molecules bind to '''LacZ''' protein.
  
 
|-
 
|-
−
||07:05
+
||06:58
−
|| '''LacZ''' protein dissociates lactose molecules as shown on the screen.
+
|| '''LacZ''' protein cleaves lactose molecules as shown on the screen.  
  
 
|-
 
|-
−
||07:11
+
||07:04
 
|| Observe the '''Interior Lactose Level''' meter, lactose level decreases.
 
|| Observe the '''Interior Lactose Level''' meter, lactose level decreases.
  
 
|-
 
|-
−
|| 07:17
+
|| 07:10
 
|| Click on '''Lactose Transport''' screen.
 
|| Click on '''Lactose Transport''' screen.
  
 
|-
 
|-
−
|| 07:21
+
|| 07:14
 
|| In addition to all the features of the '''Lactose regulation screen''',  '''Lactose Transport''' screen has '''Cell Membrane''' and '''LacY gene'''.
 
|| In addition to all the features of the '''Lactose regulation screen''',  '''Lactose Transport''' screen has '''Cell Membrane''' and '''LacY gene'''.
  
 
|-
 
|-
−
|| 07:31
+
|| 07:24
 
|| As demonstrated previously, assemble the Operon.
 
|| As demonstrated previously, assemble the Operon.
  
 
|-
 
|-
−
||07:36
+
||07:29
 
|| Drag and place all the components of the Operon in their respective places.
 
|| Drag and place all the components of the Operon in their respective places.
  
 
|-
 
|-
−
|| 07:52
+
|| 07:45
 
|| Click on '''Show Legend''' and '''Show Lactose Meter''' check box.
 
|| Click on '''Show Legend''' and '''Show Lactose Meter''' check box.
  
 
|-
 
|-
−
|| 07:58
+
|| 07:51
 
|| Pump-in few molecules of Lactose using Lactose injector.
 
|| Pump-in few molecules of Lactose using Lactose injector.
  
 
|-
 
|-
−
|| 08:03
+
|| 07:56
 
|| Click on '''Auto''' radio button on the '''Lactose injector'''.
 
|| Click on '''Auto''' radio button on the '''Lactose injector'''.
  
 
|-
 
|-
−
|| 08:08
+
|| 08:01
 
|| '''LacI''', '''LacZ''' and '''LacY''' proteins are produced.
 
|| '''LacI''', '''LacZ''' and '''LacY''' proteins are produced.
  
 
|-
 
|-
−
|| 08:14
+
|| 08:07
 
|| '''LacY''' is '''Beta-galactoside permease''' enzyme.
 
|| '''LacY''' is '''Beta-galactoside permease''' enzyme.
  
 
|-
 
|-
−
||08:19
+
||08:12
 
|| It enables transport of lactose into the cell.
 
|| It enables transport of lactose into the cell.
  
 
|-
 
|-
−
|| 08:24
+
|| 08:17
−
|| Observe that '''LacY''' protein binds to the '''Cell Membrane'''.
+
|| Observe that '''LacY''' protein is inserted into '''Cell Membrane'''.
  
 
|-
 
|-
−
|| 08:29
+
|| 08:23
 
|| Now lactose molecules permeate into cell with the help of '''LacY''' protein.
 
|| Now lactose molecules permeate into cell with the help of '''LacY''' protein.
  
 
|-
 
|-
−
|| 08:36
+
|| 08:30
 
|| Inside the cell, lactose molecules are metabolized by '''LacZ''' enzyme as shown on the screen.
 
|| Inside the cell, lactose molecules are metabolized by '''LacZ''' enzyme as shown on the screen.
  
 
|-
 
|-
−
|| 08:46
+
|| 08:40
 
|| Factors affecting '''LacZ''' gene regulation-
 
|| Factors affecting '''LacZ''' gene regulation-
  
 
|-
 
|-
−
||08:51
+
||08:45
 
|| The '''lac''' repressor acts as a lactose sensor.
 
|| The '''lac''' repressor acts as a lactose sensor.
  
 
|-
 
|-
−
||08:55
+
||08:49
 
|| It blocks transcription of the '''Lac operon'''  when there is no lactose present in the cell.
 
|| It blocks transcription of the '''Lac operon'''  when there is no lactose present in the cell.
  
 
|-
 
|-
−
|| 09:02
+
|| 08:56
 
|| When lactose is present, the ''lac'' repressor loses its ability to bind DNA.  
 
|| When lactose is present, the ''lac'' repressor loses its ability to bind DNA.  
  
 
|-
 
|-
−
|| 09:09
+
|| 09:03
 
|| It floats off the '''Operator''',  clearing the way for '''RNA polymerase''' to transcribe the '''operon'''.
 
|| It floats off the '''Operator''',  clearing the way for '''RNA polymerase''' to transcribe the '''operon'''.
  
 
|-
 
|-
−
|| 09:17
+
|| 09:11
 
|| Let us summarize.
 
|| Let us summarize.
  
Line 375: Line 372:
  
 
|-
 
|-
−
|| 09:29
+
|| 09:23
 
|| We have also learnt about: Lactose regulation,
 
|| We have also learnt about: Lactose regulation,
  
 
|-
 
|-
−
||09:35
+
||09:29
−
|| Genes involved in Lactose regulation,
+
|| Genes involved in Lactose regulation, and
  
 
|-
 
|-
−
||09:39
+
||09:33
 
|| Factors affecting '''LacZ gene '''regulation.
 
|| Factors affecting '''LacZ gene '''regulation.
  
 
|-
 
|-
−
|| 09:44
+
|| 09:38
 
|| An an assignment, remove some of the components of the '''Operon'''  such as Operator, Promoter and Genes.
 
|| An an assignment, remove some of the components of the '''Operon'''  such as Operator, Promoter and Genes.
  
 
|-
 
|-
−
||09:54
+
||09:48
 
|| '''Run''' the simulation. And observe the results and give explanation.
 
|| '''Run''' the simulation. And observe the results and give explanation.
  
 
|-
 
|-
−
|| 10:01
+
|| 09:55
 
|| 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
+
|| 10:04
 
|| The '''Spoken Tutorial Project '''team: conducts workshops using spoken tutorials and gives certificates on passing online tests.
 
|| The '''Spoken Tutorial Project '''team: conducts workshops using spoken tutorials and gives certificates on passing online tests.
  
 
|-
 
|-
−
||10:21
+
||10:15
 
|| For more details, please write to us.
 
|| For more details, please write to us.
  
 
|-
 
|-
−
||10:25
+
||10:19
 
|| Please post your timed queries on this forum.
 
|| Please post your timed queries on this forum.
  
 
|-
 
|-
−
|| 10:30
+
|| 10:24
 
|| 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.
  
 
|-
 
|-
−
|| 10:39
+
|| 10:33
 
|| Spoken Tutorial Project is funded by '''NMEICT, MHRD,''' Government of India.
 
|| Spoken Tutorial Project is funded by '''NMEICT, MHRD,''' Government of India.
  
Line 422: Line 419:
  
 
|-
 
|-
−
|| 10:53
+
|| 10:47
 
|| This tutorial is contributed by Snehalatha Kaliappan and Meenal Ghoderao from IIT Bombay.
 
|| This tutorial is contributed by Snehalatha Kaliappan and Meenal Ghoderao from IIT Bombay.
  

Latest revision as of 18:02, 24 July 2019

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 Lactose regulation
00:46 Genes involved in Lactose regulation
00:50 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 underscore 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 Notice that as soon as LacI protein is produced, Lactose injector appears on the top-left corner of the screen.
05:10 Click on the Show Lactose Meter check-box at the bottom-left corner.
05:16 Meter will give an idea about interior lactose level.
05:21 Next, assemble the LacZ gene.
05:24 Drag and place

Lac promoter,

Lac Operator

as prompted by the highlighted yellow portions on the operon.

05:34 LacI protein floating around will now bind to the Operator region of operon.
05:41 Now place the LacZ gene on operon.
05:45 In the absence of lactose, LacI binds to the operator region and prevents RNA polymerase from transcribing the operon.
05:55 Hence no LacZ enzyme is produced.
05:59 Pump a few molecules of lactose on to the screen using Lactose injector.
06:06 There are 2 options for pumping, Manual and Auto.
06:12 Select Manual option.
06:15 Press the red button on the injector.
06:19 Observe the Lactose level in lactose meter.
06:23 LacI bound to the Operator, acts like Lactose sensor.
06:28 Lactose molecule bind to the LacI and leaves the Operator region.
06:34 The RNA Polymerase will now be able to transcribe the gene.
06:39 This mRNA is in turn translated to LacZ protein.
06:45 LacZ is Beta-galactosidase enzyme.
06:49 It cleaves lactose into glucose and galactose.
06:54 Lactose molecules bind to LacZ protein.
06:58 LacZ protein cleaves lactose molecules as shown on the screen.
07:04 Observe the Interior Lactose Level meter, lactose level decreases.
07:10 Click on Lactose Transport screen.
07:14 In addition to all the features of the Lactose regulation screen, Lactose Transport screen has Cell Membrane and LacY gene.
07:24 As demonstrated previously, assemble the Operon.
07:29 Drag and place all the components of the Operon in their respective places.
07:45 Click on Show Legend and Show Lactose Meter check box.
07:51 Pump-in few molecules of Lactose using Lactose injector.
07:56 Click on Auto radio button on the Lactose injector.
08:01 LacI, LacZ and LacY proteins are produced.
08:07 LacY is Beta-galactoside permease enzyme.
08:12 It enables transport of lactose into the cell.
08:17 Observe that LacY protein is inserted into Cell Membrane.
08:23 Now lactose molecules permeate into cell with the help of LacY protein.
08:30 Inside the cell, lactose molecules are metabolized by LacZ enzyme as shown on the screen.
08:40 Factors affecting LacZ gene regulation-
08:45 The lac repressor acts as a lactose sensor.
08:49 It blocks transcription of the Lac operon when there is no lactose present in the cell.
08:56 When lactose is present, the lac repressor loses its ability to bind DNA.
09:03 It floats off the Operator, clearing the way for RNA polymerase to transcribe the operon.
09:11 Let us summarize.

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

09:23 We have also learnt about: Lactose regulation,
09:29 Genes involved in Lactose regulation, and
09:33 Factors affecting LacZ gene regulation.
09:38 An an assignment, remove some of the components of the Operon such as Operator, Promoter and Genes.
09:48 Run the simulation. And observe the results and give explanation.
09:55 The video at the following link summarizes the Spoken Tutorial project.

Please download and watch it.

10:04 The Spoken Tutorial Project team: conducts workshops using spoken tutorials and gives certificates on passing online tests.
10:15 For more details, please write to us.
10:19 Please post your timed queries on this forum.
10:24 This project is partially funded by Pandit Madan Mohan Malaviya National Mission on Teachers and Teaching.
10:33 Spoken Tutorial Project is funded by NMEICT, MHRD, Government of India.

More information on this mission is available at this link.

10:47 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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