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

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	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 sub-units.
06:19	Let's 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