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

From Script | Spoken-Tutorial
Revision as of 16:58, 24 July 2019 by PoojaMoolya (Talk | contribs)

(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)
Jump to: navigation, search


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:

1. About steps involved in Protein Synthesis.

00:48 2. Factors affecting Protein Synthesis and

3. 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 Select mRNA destroyer from Biomolecule Toolbox.
06:06 The position to fit mRNA destroyer is highlighted as dotted outline on mRNA.
06:14 Drag and place it on the highlighted area of mRNA.
06:20 mRNA is degraded into individual units.
06:25 mRNA Destroyer stops mRNA from making additional proteins.
06:31 Reset All button is available at the bottom-right corner of the screen.
06:37 Click on it to reset the screen to default position.
06:42 Click on green Next Gene button at bottom right corner of the screen.
06:49 This takes you to another gene which codes for a new type of protein.
06:56 Explore and find how this second gene is different from the first one.
07:03 Click on Messenger RNA Production tab at the top.
07:08 Here we can see various factors that affect transcription that is mRNA production.
07:15 We can see two panels. Positive Transcription Factor and RNA Polymerase.
07:24 I will increase the Concentrations and Affinity of the Positive Transcription Factor.
07:32 Drag the slider of the Concentrations to Lots.
07:37 I will keep the Affinity to High.
07:41 Also keep the RNA Polymerase Affinity to High.
07:46 We can see that RNA polymerase can attach itself to the DNA strand easily.

And, it produces mRNA.

07:57 Now we know that increase in the concentration of Positive Transcription Factor increases its binding to the regulatory region.
08:08 It will in turn make RNA polymerase bind faster to DNA.
08:14 This results in faster production of mRNA.
08:19 Explore Concentration and Affinity sliders and observe the results.
08:26 Now Click on the Multiple Cells tab. On the right-hand side there are 3 options-
08:35 Concentrations, Affinities and Degradation.
08:41 Click on green plus sign to open the panel.
08:45 Drag the sliders to change Concentrations, Affinities and Degradation.
08:55 Observe the amount of Green Fluorescent protein produced in cells.
09:01 Drag the Cells slider from One to Many.
09:06 Observe the green fluorescent protein cells.
09:10 The brightness indicates the concentration of protein in cells.
09:16 Let us summarize.
09:19 In this tutorial, we have demonstrated how to use Gene Expression-The Basics simulation.
09:28 Using this simulation, we have learnt: about steps involved in protein biosynthesis,
09:35 to create mRNA using transcription elements,
09:40 to create a protein using translation elements
09:45 and to study the effect of factors influencing mRNA production.
09:51 As an Assignment: using Cell Gene Expression screen, transcribe gene 2 and put proteins in protein collection box.
10:03 Explore the Multiple Cells tab.
10:06 Find the name of the cells used in this simulation.
10:10 Explain why cells are green in colour.
10:14 The video at the following link summarizes the Spoken Tutorial project.

Please download and watch it.

10:23 The Spoken Tutorial Project team: conducts workshops using spoken tutorials and gives certificates on passing on line tests.
10:33 For more details, please write to us.
10:37 Please post your timed queries on this forum.
10:41 This project is partially funded by Pandit Madan Mohan Malaviya National Mission on Teachers and Teaching.
10:50 Spoken Tutorial Project is funded by NMEICT, MHRD, Government of India.

More information on this mission is available at this link.

11:04 This tutorial is contributed by spoken tutorial team from IIT Bombay.

Thank you for joining.

Contributors and Content Editors

PoojaMoolya, Sandhya.np14, Snehalathak