PhET/C3/Gene-Expression-The-Basics/English-timed

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Time Narration
00:01 Welcome to this tutorial on Gene-Expression-The Basics simulation.
00:08 In this tutorial we will, Demonstrate Gene Expression-The Basics, PhET Simulation.
00:16 To follow this tutorial, Learners should be familiar with topics in high school Biology.
00:23 Here I am using, Ubuntu Linux OS version 14.04
00:30 Java version 1.7.0.
00:35 Firefox Web Browser version 53.02.2
00:41 Using this simulation we will learn, About steps involved in Protein Synthesis.
00:48 Factors affecting Protein Synthesis and To observe the average level of Green Fluorescent Protein produced in cells.
01:00 Let us recall about Central Dogma of Genetics.
01:05 It was proposed by Francis Crick.
01:09 It states that the genetic information flows from DNA to mRNA to Protein.
01:19 Protein Synthesis involves two steps.
01:23 Transcription: is a process of making, mRNA.
01:28 Translation: is a process by which mRNA directs protein synthesis.
01:35 Let us begin the demonstration.
01:38 Use the given link to download the simulation.
01:42 I have already downloaded Gene Expression-The Basics simulation to my Downloads folder.
01:51 To run the simulation, open the terminal.
01:55 At the prompt type, cd Downloads and press enter.
02:03 Then type, java space hyphen jar space gene hyphen expression hyphen basics underscore en dot jar and press enter.
02:20 Gene Expression-The Basics Simulation opens.
02:25 The simulation screen shows 3 tabs at the top- Cell Gene Expression
02:32 Messenger RNA Production and Multiple Cells.
02:38 By default Cell Gene Expression screen opens.
02:43 Left side of the screen has a Biomolecule Toolbox.
02:48 It contains transcription and translation regulatory elements.
02:54 At the bottom of the screen a DNA strand is shown.
02:59 It represents Gene 1.
03:02 Gene 1 has a Regulatory region and a Transcribed region.
03:08 Regulatory Region is acted upon by, Positive and Negative Transcription Factors.
03:15 Transcribed Region is located after the Regulatory Region in the DNA strand.
03:22 It is used to create mRNA.
03:26 Information that mRNA strand contains, is found in the Transcribed Region.
03:33 On the right side, we have a box showing Protein Collection. It shows the type of protein which we make.
03:42 Now let us select Positive Transcription Factor from the Biomolecule Toolbox.
03:49 Click on the Positive Transcription Factor.
03:53 Observe the Regulatory Region on Gene1.
03:57 Shape of Positive Transcription Factor is highlighted.
04:02 Drag and place it on the highlighted Regulatory Region.
04:07 Now click on RNA Polymerase from Biomolecule Toolbox.
04:13 Observe Gene1, shape of RNA polymerase is highlighted.
04:19 Drag and place it on the highlighted area of RNA Polymerase.
04:25 RNA Polymerase initiates the transcription process.
04:30 We can see mRNA is produced as the Transcription process is initiated.
04:38 Now let's see the roles of transcription elements.
04:43 Positive Transcription Factor is also known as an activator.
04:49 It positions itself on the Regulatory Region.
04:54 It encourages the binding of RNA polymerase to the Regulatory Region.
05:00 It allows RNA polymerase to produce mRNA.
05:05 RNA Polymerase is an enzyme.
05:09 It reads transcribed region of DNA to produce mRNA.
05:15 It zips down the strand by first passing through the regulatory region.
05:21 As an assignment, Select Negative Transcription Factor and Place it on Gene1.
05:28 Select RNA polymerase.
05:31 See if RNA polymerase can pass through the transcribed region.

And Explain the observation.

05:39 Back to the simulation.
05:42 Select a Ribosome from Biomolecule Toolbox.
05:47 Drag it on the highlighted area of free floating mRNA.
05:52 A type of protein is produced.
05:56 It is highlighted on Your Protein collection box.
06:01 About Ribosome.
06:04 Ribosome is an RNA structure that reads mRNA strands to produce proteins.
06:13 It clamps the RNA strand between its two subunits.
06:19 Lets go back to the simulation.
06:22 Select mRNA destroyer from Biomolecule Toolbox.
06:27 The position to fit mRNA destroyer is highlighted as dotted outline on mRNA.
06:35 Drag and place it on the highlighted area of mRNA.
06:41 mRNA is degraded into individual units.
06:46 mRNA Destroyer stops mRNA from making additional proteins.
06:52 Reset All button is available at the bottom-right corner of the screen.
06:58 Click on it to reset the screen to default position.
07:03 Click on green Next Gene button at bottom right corner of the screen.
07:10 This takes you to another gene which codes for a new type of protein.
07:17 Explore and find how this second gene is different from the first one.
07:24 Click on Messenger RNA Production tab at the top.
07:29 Here we can see various factors that affect transcription that is mRNA production.
07:36 We can see two panels. Positive Transcription Factor and RNA Polymerase.
07:45 I will increase the Concentrations and Affinity of the Positive Transcription Factor.
07:53 Drag the slider of the Concentrations to Lots.
07:58 I will keep the Affinity to High.
08:02 Also keep the RNA Polymerase Affinity to High.
08:07 We can see that RNA polymerase can attach itself to the DNA strand easily.

And it produces mRNA.

08:18 Now we know that, Increase in the concentration of Positive Transcription Factor, increases its binding, to the regulatory region.
08:29 It will in turn make RNA polymerase bind faster to DNA.
08:35 This results in faster production of mRNA.
08:40 Explore Concentration and Affinity sliders. And observe the results.
08:47 Now Click on the Multiple Cells tab. On the right-hand side there are 3 options.
08:56 Concentrations, Affinities and Degradation.
09:02 Click on Green plus sign to open the panel.
09:06 Drag the sliders to change Concentrations, Affinities and Degradation.
09:16 Observe the amount of Green Fluorescent protein produced in cells.
09:22 Drag the Cells slider from One to Many.
09:27 Observe the green fluorescent protein cells.
09:31 The brightness indicates the concentration of protein in cells.
09:37 Let us summarize.
09:40 In this tutorial we have demonstrated, How to use Gene Expression-The Basics simulation.
09:49 Using this simulation, we have learnt, About steps involved in protein biosynthesis.
09:56 To create mRNA using transcription elements.
10:01 To create a protein using translation elements.
10:05 And to study the effect of factors influencing mRNA production.
10:12 As an Assignment, Using Cell Gene Expression screen, Transcribe gene 2 and put proteins in protein collection box.
10:24 Explore the Multiple Cells tab.
10:27 Find the name of the cells used in this simulation.
10:31 Explain why cells are green in colour.
10:35 The video at the following link summarizes the Spoken Tutorial project.

Please download and watch it.

10:44 The Spoken Tutorial Project team: conducts workshops using spoken tutorials and Gives certificates on passing on line tests.
10:54 For more details, please write to us.
10:58 Please post your timed queries on this forum.
11:02 This project is partially funded by Pandit Madan Mohan Malaviya National Mission on Teachers and Teaching.
11:11 Spoken Tutorial Project is funded by NMEICT, MHRD, Government of India.

More information on this mission is available at this link.

11:25 This tutorial is contributed by spoken tutorial team from IIT Bombay.

Thank you for joining.

Contributors and Content Editors

PoojaMoolya, Sandhya.np14, Snehalathak