Difference between revisions of "PhET/C3/Gene-Expression-The-Basics/English-timed"
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| − | || | + | || Select '''mRNA destroyer''' from Biomolecule Toolbox. |
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| − | || 06: | + | || 06:06 |
| − | + | ||The position to fit mRNA destroyer is highlighted as dotted outline on mRNA. | |
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| − | || The position to fit | + | |
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| − | || 06: | + | || 06:14 |
|| Drag and place it on the highlighted area of '''mRNA'''. | || Drag and place it on the highlighted area of '''mRNA'''. | ||
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| − | || 06: | + | || 06:20 |
|| '''mRNA''' is degraded into individual units. | || '''mRNA''' is degraded into individual units. | ||
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| − | || 06: | + | || 06:25 |
|| '''mRNA Destroyer''' stops '''mRNA''' from making additional proteins. | || '''mRNA Destroyer''' stops '''mRNA''' from making additional proteins. | ||
|- | |- | ||
| − | || 06: | + | || 06:31 |
|| '''Reset All''' button is available at the bottom-right corner of the screen. | || '''Reset All''' button is available at the bottom-right corner of the screen. | ||
|- | |- | ||
| − | || 06: | + | || 06:37 |
|| Click on it to '''reset''' the '''screen''' to default position. | || Click on it to '''reset''' the '''screen''' to default position. | ||
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| − | || | + | || 06:42 |
|| Click on green '''Next Gene''' button at bottom right corner of the screen. | || Click on green '''Next Gene''' button at bottom right corner of the screen. | ||
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| − | || | + | || 06:49 |
|| This takes you to another gene which codes for a new type of protein. | || 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. | || Explore and find how this second gene is different from the first one. | ||
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| − | || 07: | + | || 07:03 |
|| Click on '''Messenger RNA Production''' tab at the top. | || Click on '''Messenger RNA Production''' tab at the top. | ||
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| − | || 07: | + | || 07:08 |
|| Here we can see various factors that affect '''transcription''' that is '''mRNA''' production. | || Here we can see various factors that affect '''transcription''' that is '''mRNA''' production. | ||
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| − | || 07: | + | || 07:15 |
|| We can see two '''panel'''s. '''Positive Transcription Factor''' and '''RNA Polymerase'''. | || We can see two '''panel'''s. '''Positive Transcription Factor''' and '''RNA Polymerase'''. | ||
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| − | || 07: | + | || 07:24 |
|| I will increase the '''Concentrations''' and '''Affinity''' of the '''Positive Transcription Factor'''. | || I will increase the '''Concentrations''' and '''Affinity''' of the '''Positive Transcription Factor'''. | ||
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| − | || 07: | + | || 07:32 |
|| Drag the slider of the '''Concentrations''' to '''Lots'''. | || Drag the slider of the '''Concentrations''' to '''Lots'''. | ||
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| − | || 07: | + | || 07:37 |
|| I will keep the '''Affinity''' to '''High'''. | || I will keep the '''Affinity''' to '''High'''. | ||
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| − | || | + | || 07:41 |
|| Also keep the '''RNA Polymerase Affinity''' to '''High'''. | || Also keep the '''RNA Polymerase Affinity''' to '''High'''. | ||
|- | |- | ||
| − | || | + | || 07:46 |
|| We can see that '''RNA polymerase''' can attach itself to the '''DNA''' strand easily. | || We can see that '''RNA polymerase''' can attach itself to the '''DNA''' strand easily. | ||
And, it produces '''mRNA'''. | 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'''. | || Now we know that increase in the concentration of '''Positive Transcription Factor''' increases its binding to the '''regulatory region'''. | ||
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| − | ||08: | + | ||08:08 |
||It will in turn make '''RNA polymerase''' bind faster to '''DNA'''. | ||It will in turn make '''RNA polymerase''' bind faster to '''DNA'''. | ||
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| − | || 08: | + | || 08:14 |
|| This results in faster production of '''mRNA'''. | || This results in faster production of '''mRNA'''. | ||
|- | |- | ||
| − | || 08: | + | || 08:19 |
|| Explore '''Concentration''' and '''Affinity''' sliders and observe the results. | || Explore '''Concentration''' and '''Affinity''' sliders and observe the results. | ||
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| − | || 08: | + | || 08:26 |
|| Now Click on the '''Multiple Cells''' tab. On the right-hand side there are 3 options- | || Now Click on the '''Multiple Cells''' tab. On the right-hand side there are 3 options- | ||
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| − | || 08: | + | || 08:35 |
|| '''Concentrations''', '''Affinities''' and '''Degradation'''. | || '''Concentrations''', '''Affinities''' and '''Degradation'''. | ||
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| − | || | + | || 08:41 |
|| Click on green plus sign to open the panel. | || Click on green plus sign to open the panel. | ||
|- | |- | ||
| − | || | + | || 08:45 |
|| Drag the '''slider'''s to change '''Concentrations''', '''Affinities''' and '''Degradation'''. | || Drag the '''slider'''s to change '''Concentrations''', '''Affinities''' and '''Degradation'''. | ||
|- | |- | ||
| − | || | + | || 08:55 |
|| Observe the amount of '''Green Fluorescent''' protein produced in cells. | || Observe the amount of '''Green Fluorescent''' protein produced in cells. | ||
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| − | || 09: | + | || 09:01 |
|| Drag the '''Cells''' slider from '''One''' to '''Many'''. | || Drag the '''Cells''' slider from '''One''' to '''Many'''. | ||
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| − | || 09: | + | || 09:06 |
||Observe the '''green fluorescent''' protein cells. | ||Observe the '''green fluorescent''' protein cells. | ||
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| − | || 09: | + | || 09:10 |
|| The brightness indicates the concentration of protein in cells. | || The brightness indicates the concentration of protein in cells. | ||
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| − | || 09: | + | || 09:16 |
|| Let us summarize. | || Let us summarize. | ||
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| − | ||09: | + | ||09:19 |
|| In this tutorial, we have demonstrated how to use '''Gene Expression-The Basics''' simulation. | || In this tutorial, we have demonstrated how to use '''Gene Expression-The Basics''' simulation. | ||
|- | |- | ||
| − | || 09: | + | || 09:28 |
| − | || Using this '''simulation''', we have learnt: | + | || Using this '''simulation''', we have learnt: about steps involved in protein biosynthesis, |
| − | about steps involved in protein biosynthesis, | + | |
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| − | || 09: | + | || 09:35 |
|| to create '''mRNA''' using transcription elements, | || to create '''mRNA''' using transcription elements, | ||
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| − | || | + | || 09:40 |
|| to create a protein using translation elements | || to create a protein using translation elements | ||
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| − | || | + | || 09:45 |
||and to study the effect of factors influencing '''mRNA''' production. | ||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. | || As an Assignment: using '''Cell Gene Expression''' screen, transcribe gene 2 and put proteins in '''protein collection''' box. | ||
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| − | || 10: | + | || 10:03 |
|| Explore the '''Multiple Cells''' tab. | || Explore the '''Multiple Cells''' tab. | ||
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| − | || 10: | + | || 10:06 |
|| Find the name of the cells used in this simulation. | || Find the name of the cells used in this simulation. | ||
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| − | || 10: | + | || 10:10 |
|| Explain why cells are green in colour. | || Explain why cells are green in colour. | ||
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| − | || 10: | + | || 10:14 |
|| The video at the following link summarizes the Spoken Tutorial project. | || The video at the following link summarizes the Spoken Tutorial project. | ||
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| − | || 10: | + | || 10:23 |
|| The '''Spoken Tutorial Project '''team: conducts workshops using spoken tutorials and gives certificates on passing on line tests. | || The '''Spoken Tutorial Project '''team: conducts workshops using spoken tutorials and gives certificates on passing on line tests. | ||
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| − | || 10: | + | || 10:33 |
|| For more details, please write to us. | || For more details, please write to us. | ||
|- | |- | ||
| − | || 10: | + | || 10:37 |
|| Please post your timed queries on this forum. | || 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.''' | || 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. | || Spoken Tutorial Project is funded by '''NMEICT, MHRD,''' Government of India. | ||
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| − | || 11: | + | || 11:04 |
|| This tutorial is contributed by spoken tutorial team from IIT Bombay. | || This tutorial is contributed by spoken tutorial team from IIT Bombay. | ||
Latest revision as of 16:58, 24 July 2019
| 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. |
