PhET/C3/Gene-Expression-The-Basics/English-timed
From Script | Spoken-Tutorial
| 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. |
