Difference between revisions of "PhET/C3/Gene-Machine-The-Lac-Operon/English-timed"
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Revision as of 11:57, 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. |
