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

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.
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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