Difference between revisions of "PhET/C3/Gene-Machine-The-Lac-Operon/English-timed"
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|| 00:08 | || 00:08 | ||
− | || In this tutorial we will | + | || In this tutorial, we will demonstrate '''Gene Machine - The Lac Operon, PhET simulation'''. |
|- | |- | ||
|| 00:16 | || 00:16 | ||
− | || To follow this tutorial, | + | || To follow this tutorial, learner should be familiar with topics in high-school biology. |
|- | |- | ||
|| 00:23 | || 00:23 | ||
− | || Here I am using | + | || Here I am using:'''Ubuntu Linux OS''' version 14.04, |
− | Java version 1.7.0 | + | '''Java''' version 1.7.0, |
|- | |- | ||
|| 00:34 | || 00:34 | ||
− | || Firefox Web Browser version 53.02.2 | + | || '''Firefox Web Browser''' version 53.02.2. |
|- | |- | ||
|| 00:40 | || 00:40 | ||
− | || Using this simulation, students will learn about | + | || Using this simulation, students will learn about: |
|- | |- | ||
|| 00:44 | || 00:44 | ||
− | || | + | ||Lactose regulation |
|- | |- | ||
|| 00:46 | || 00:46 | ||
− | || | + | ||Genes involved in Lactose regulation |
|- | |- | ||
|| 00:50 | || 00:50 | ||
− | || | + | ||Factors affecting '''LacZ''' gene regulation. |
|- | |- | ||
Line 51: | Line 51: | ||
|- | |- | ||
|| 01:17 | || 01:17 | ||
− | || '''Promoter''' | + | || '''Promoter''' initiates transcription. |
|- | |- | ||
|| 01:20 | || 01:20 | ||
− | || '''Operator''': It is a | + | || '''Operator''': It is a segment of DNA where repressor binds. |
|- | |- | ||
Line 63: | Line 63: | ||
|- | |- | ||
|| 01:31 | || 01:31 | ||
− | || The three structural genes in '''lac Operon''' are | + | || The three structural genes in '''lac Operon''' are '''lacZ''', '''lacY''', and '''lacA'''. |
|- | |- | ||
|| 01:40 | || 01:40 | ||
− | || These genes are transcribed as a single mRNA, under control of one promoter. | + | || These genes are '''transcribed''' as a single mRNA, under control of one promoter. |
|- | |- | ||
Line 75: | Line 75: | ||
|- | |- | ||
||01:55 | ||01:55 | ||
− | || Genes of the '''Lac Operon''' can be expressed and their proteins translated. | + | || Genes of the '''Lac Operon''' can be expressed and their proteins '''translated'''. |
|- | |- | ||
Line 83: | Line 83: | ||
|- | |- | ||
|| 02:08 | || 02:08 | ||
− | || '''lacY''' encodes '''Beta-galactoside permease''' | + | || '''lacY''' encodes '''Beta-galactoside permease'''. It will enable transport of lactose into the cell. |
|- | |- | ||
Line 91: | Line 91: | ||
|- | |- | ||
|| 02:23 | || 02:23 | ||
− | || Use the given link to download the simulation. | + | || Use the given '''link''' to download the simulation. |
|- | |- | ||
Line 99: | Line 99: | ||
|- | |- | ||
|| 02:36 | || 02:36 | ||
− | || To run the simulation, open the terminal. | + | || To '''run''' the simulation, open the '''terminal'''. |
|- | |- | ||
|| 02:40 | || 02:40 | ||
− | || At the prompt | + | || At the prompt, type: '''cd Downloads''' and press '''Enter'''. |
|- | |- | ||
||02:47 | ||02:47 | ||
− | || Then type | + | || Then type: '''java space hyphen jar space gene hyphen machine hyphen lac hyphen operon underscore en dot jar''' and press '''Enter'''. |
|- | |- | ||
|| 03:04 | || 03:04 | ||
− | || '''Gene-Machine-The Lac Operon''' | + | || '''Gene-Machine-The Lac Operon''' simulation opens. |
|- | |- | ||
|| 03:09 | || 03:09 | ||
− | || The simulation screen shows 2 tabs at the top | + | || The simulation screen shows 2 tabs at the top- |
'''Lactose Regulation''' and | '''Lactose Regulation''' and | ||
− | '''Lactose Transport''' | + | '''Lactose Transport'''. |
|- | |- | ||
Line 147: | Line 147: | ||
|- | |- | ||
|| 03:56 | || 03:56 | ||
− | || At the bottom of the screen we have | + | || At the bottom of the screen, we have- a slider to set the speed of the animation, |
'''Play'''/'''Pause''', | '''Play'''/'''Pause''', | ||
Line 173: | Line 173: | ||
|- | |- | ||
||04:28 | ||04:28 | ||
− | || Similarly drag '''lacI gene''' and place it on the '''operon'''. | + | || Similarly, drag '''lacI gene''' and place it on the '''operon'''. |
|- | |- | ||
Line 189: | Line 189: | ||
|- | |- | ||
|| 04:51 | || 04:51 | ||
− | || '''LacI''' is a '''lac''' | + | || '''LacI''' is a '''lac repressor protein'''. |
|- | |- | ||
||04:55 | ||04:55 | ||
− | || It binds to the '''Lac | + | || It binds to the '''Lac Operator''' region of the '''Operon'''. |
|- | |- | ||
− | ||05:00 | + | || 05:00 |
− | + | ||
− | + | ||
− | + | ||
− | + | ||
|| 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: | + | || 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: | + | ||05:16 |
|| Meter will give an idea about interior lactose level. | || Meter will give an idea about interior lactose level. | ||
|- | |- | ||
− | ||05: | + | ||05:21 |
− | || Next assemble the '''LacZ''' gene. | + | || Next, assemble the '''LacZ''' gene. |
|- | |- | ||
− | ||05: | + | ||05:24 |
− | || Drag and place | + | || Drag and place |
'''Lac promoter''', | '''Lac promoter''', | ||
− | '''Lac | + | '''Lac Operator''' |
as prompted by the highlighted yellow portions on the '''operon'''. | as prompted by the highlighted yellow portions on the '''operon'''. | ||
|- | |- | ||
− | || 05: | + | || 05:34 |
− | || '''LacI''' protein floating around will now bind to the | + | || '''LacI''' protein floating around will now bind to the Operator region of '''operon'''. |
|- | |- | ||
− | || 05: | + | || 05:41 |
|| Now place the '''LacZ gene''' on '''operon'''. | || Now place the '''LacZ gene''' on '''operon'''. | ||
|- | |- | ||
− | || 05: | + | || 05:45 |
− | || | + | ||In the absence of lactose, LacI binds to the operator region and prevents RNA polymerase from transcribing the operon. |
− | Hence no | + | |- |
+ | || 05:55 | ||
+ | ||Hence no LacZ enzyme is produced. | ||
|- | |- | ||
− | || | + | || 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: | + | ||06:06 |
|| There are 2 options for pumping, '''Manual''' and '''Auto'''. | || There are 2 options for pumping, '''Manual''' and '''Auto'''. | ||
|- | |- | ||
− | ||06: | + | ||06:12 |
|| Select '''Manual''' option. | || Select '''Manual''' option. | ||
|- | |- | ||
− | ||06: | + | ||06:15 |
||Press the red button on the '''injector'''. | ||Press the red button on the '''injector'''. | ||
|- | |- | ||
− | ||06: | + | ||06:19 |
|| Observe the Lactose level in '''lactose meter'''. | || Observe the Lactose level in '''lactose meter'''. | ||
|- | |- | ||
− | || 06: | + | || 06:23 |
− | || '''LacI''' bound to the | + | || '''LacI''' bound to the Operator, acts like '''Lactose''' sensor. |
|- | |- | ||
− | ||06: | + | ||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: | + | || 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: | + | ||06:39 |
− | || This '''mRNA''' is in turn | + | || This '''mRNA''' is in turn '''translate'''d to '''LacZ''' protein. |
|- | |- | ||
− | || 06: | + | || 06:45 |
|| '''LacZ''' is '''Beta-galactosidase''' enzyme. | || '''LacZ''' is '''Beta-galactosidase''' enzyme. | ||
|- | |- | ||
− | ||06: | + | ||06:49 |
|| It cleaves lactose into glucose and galactose. | || It cleaves lactose into glucose and galactose. | ||
|- | |- | ||
− | || | + | || 06:54 |
|| Lactose molecules bind to '''LacZ''' protein. | || Lactose molecules bind to '''LacZ''' protein. | ||
|- | |- | ||
− | || | + | ||06:58 |
− | || '''LacZ''' protein | + | || '''LacZ''' protein cleaves lactose molecules as shown on the screen. |
|- | |- | ||
− | ||07: | + | ||07:04 |
− | || Observe the Interior Lactose Level meter, lactose level decreases. | + | || Observe the '''Interior Lactose Level''' meter, lactose level decreases. |
|- | |- | ||
− | || 07: | + | || 07:10 |
|| Click on '''Lactose Transport''' screen. | || Click on '''Lactose Transport''' screen. | ||
|- | |- | ||
− | || 07: | + | || 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: | + | || 07:24 |
|| As demonstrated previously, assemble the Operon. | || As demonstrated previously, assemble the Operon. | ||
|- | |- | ||
− | ||07: | + | ||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: | + | || 07:45 |
|| Click on '''Show Legend''' and '''Show Lactose Meter''' check box. | || Click on '''Show Legend''' and '''Show Lactose Meter''' check box. | ||
|- | |- | ||
− | || 07: | + | || 07:51 |
|| Pump-in few molecules of Lactose using Lactose injector. | || Pump-in few molecules of Lactose using Lactose injector. | ||
|- | |- | ||
− | || | + | || 07:56 |
− | || Click on '''Auto''' radio button on the Lactose injector. | + | || Click on '''Auto''' radio button on the '''Lactose injector'''. |
|- | |- | ||
− | || 08: | + | || 08:01 |
|| '''LacI''', '''LacZ''' and '''LacY''' proteins are produced. | || '''LacI''', '''LacZ''' and '''LacY''' proteins are produced. | ||
|- | |- | ||
− | || 08: | + | || 08:07 |
|| '''LacY''' is '''Beta-galactoside permease''' enzyme. | || '''LacY''' is '''Beta-galactoside permease''' enzyme. | ||
|- | |- | ||
− | ||08: | + | ||08:12 |
|| It enables transport of lactose into the cell. | || It enables transport of lactose into the cell. | ||
|- | |- | ||
− | || 08: | + | || 08:17 |
− | || Observe that '''LacY''' protein | + | || Observe that '''LacY''' protein is inserted into '''Cell Membrane'''. |
|- | |- | ||
− | || 08: | + | || 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: | + | || 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: | + | || 08:40 |
|| Factors affecting '''LacZ''' gene regulation- | || Factors affecting '''LacZ''' gene regulation- | ||
|- | |- | ||
− | ||08: | + | ||08:45 |
|| The '''lac''' repressor acts as a lactose sensor. | || The '''lac''' repressor acts as a lactose sensor. | ||
|- | |- | ||
− | ||08: | + | ||08:49 |
− | || It blocks transcription of the '''Lac operon''' | + | || 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. | || When lactose is present, the ''lac'' repressor loses its ability to bind DNA. | ||
|- | |- | ||
− | || 09: | + | || 09:03 |
− | || It floats off the ''' | + | || It floats off the '''Operator''', clearing the way for '''RNA polymerase''' to transcribe the '''operon'''. |
|- | |- | ||
− | || 09: | + | || 09:11 |
− | || Let us summarize | + | || Let us summarize. |
− | In this tutorial we have demonstrated | + | In this tutorial, we have demonstrated how to use '''Gene Machine-The Lac Operon''', '''PhET simulation'''. |
|- | |- | ||
− | || 09: | + | || 09:23 |
− | || We have also learnt about | + | || We have also learnt about: Lactose regulation, |
|- | |- | ||
− | ||09: | + | ||09:29 |
− | || Genes involved in Lactose regulation | + | || Genes involved in Lactose regulation, and |
|- | |- | ||
− | ||09: | + | ||09:33 |
|| Factors affecting '''LacZ gene '''regulation. | || Factors affecting '''LacZ gene '''regulation. | ||
|- | |- | ||
− | || 09: | + | || 09:38 |
− | || An an assignment, | + | || An an assignment, remove some of the components of the '''Operon''' such as Operator, Promoter and Genes. |
|- | |- | ||
− | ||09: | + | ||09:48 |
− | || Run the simulation. And | + | || '''Run''' the simulation. And observe the results and give explanation. |
|- | |- | ||
− | || | + | || 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: | + | || 10:04 |
− | || 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. | + | |
|- | |- | ||
− | ||10: | + | ||10:15 |
|| For more details, please write to us. | || For more details, please write to us. | ||
|- | |- | ||
− | ||10: | + | ||10:19 |
|| Please post your timed queries on this forum. | || Please post your timed queries on this forum. | ||
|- | |- | ||
− | || 10: | + | || 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: | + | || 10:33 |
− | || 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. | ||
|- | |- | ||
− | || 10: | + | || 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. |