PhET/C3/Gene-Machine-The-Lac-Operon/English-timed

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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