SandboxGenetic322-5 - Revision history

David O'Brochta at 14:14, 22 February 2017

David O'Brochta — Wed, 22 Feb 2017 14:14:17 GMT

←Older revision		Revision as of 14:14, 22 February 2017
Line 1:		Line 1:
-	~~'''Abby Mandelblatt'''~~	+	== Function ==

-	''Keratin'' proteins are expressed in epithelial cells and in epidermal cells and have a filamentous structure. They assemble to form cytoskeletal structures within the cell and epidermal derivatives such as hair and nails.

-	<Structure load='3TNU' size='350' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' />

-	The protein ~~chains~~ in ~~Keratin can bind to each other through covalent bonds (disulfide bonds between two cysteines), ionic bonds, hydrophobic interactions, and hydrogen bonds. Since~~ the ~~cysteines~~ in ~~this molecule are too far apart~~ to ~~bond covalently, ionic bonds, or salt bridges, form between~~ the ~~two chains~~.	+	The protein complex participates in placing the amino acids in their correct order when messenger RNA is translated into a protein sequence on the ribosome by promoting GTP-dependent binding of tRNA to the A site of the ribosome. In other words, it is involved with elongation during polypeptide synthesis.
-		+
-	* <scene name='55/559109/Acidic-residues/1'>Click here to see the acidic residues, ~~Asp and Glu~~.~~</scene>~~	+

-	* <~~scene name~~='~~55/559109/Basic-aas/1~~'~~>Click here to see the basic residues~~, ~~Arg and Lys.<~~/~~scene~~>	+	<Structure load='1ttt' size='350' frame='true' align='right' caption='Phe-tRNA, elongation factor EF-TU:GDPNP Ternary complex' />

-	This is the <scene name='75/750215/Helix/1'>helix</scene>.

		+	== Molecules it Interacts With and where ==

-	~~----~~	+	The protein binds to GDP as well as the following ligands in order to promote the attachment of the protein complex to the ribosome A site.

		+	''PHOSHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER''
		+

-	~~This is a Sandbox page that you can use for creating our discussion project.~~	+	''PHENYLALANINE''
		+	''MAGNESIUM ION''

-	I would like for you to watch the short training videos. Each is short and you can view them all in about 40 mins. These provide the basic knowledge you will need to our discussion sections.

-	~~I need you to get some basic familiarity with this package so you will be able to help students.~~	+	=='Origin'==

-	~~Our first three discussions will focus on~~ '~~structure~~'~~. Structure of DNA, proteins~~, and ~~RNA~~.	+	It has domains that are created in yeast (phenyl-transfer RNA) , in the heat resistant ''Thermus aquaticus'' (EF-Tu elongation factor, and can be synthetically manufactured.

-	The students will work in 2 person teams and will create a Proteopedia page on their assigned molecule and will be asked to research their molecule and create 'scenes' which are representations of the molecule that illustrates some key features.

-	~~There will be a work sheet the students will follow to help them through the project.~~	+	=='Structure'==

-	~~One of~~ the ~~objectives~~ is to ~~have~~ the ~~students manipulate structures~~ to ~~appreciate~~ the ~~3 dimensional nature~~ of the ~~molecules we are discussing and~~ to ~~begin to help them conceptualize how these molecule might interact etc~~.	+
		+	It has 3 domains. G proteins, Elongation Factors, and the EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain. It is composed of 6 chains, which combine in <scene name='75/751161/Hetero_domains/1'>Heterodimer </scene> alignment.
		+
		+
		+	Specific <scene name='75/751161/Ligand_site/1'>Ligand Sites</scene> are highlighted here. The ligands listed above, GDP, Phe, and Mg+2 ion each attach at these locations which are still being explored.
		+
		+	<scene name='75/751161/Basic_positive_residues/2'>Basic and Positive Residues</scene> which play a crucial role in binding to the ribosome during translation. They form positive pockets with which negative amino acids can bind to.
		+
		+	=='Molecules it Interacts With and where '==
		+
		+	The protein binds to GDP as well as the following ligands in order to promote the attachment of the protein complex to the ribosome A site.
		+
		+	''PHOSHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER''
		+
		+
		+	''PHENYLALANINE''
		+	''MAGNESIUM ION''

David O'Brochta at 20:55, 1 February 2017

David O'Brochta — Wed, 01 Feb 2017 20:55:21 GMT

←Older revision		Revision as of 20:55, 1 February 2017
Line 10:		Line 10:

	* <scene name='55/559109/Basic-aas/1'>Click here to see the basic residues, Arg and Lys.</scene>		* <scene name='55/559109/Basic-aas/1'>Click here to see the basic residues, Arg and Lys.</scene>
		+
		+	This is the <scene name='75/750215/Helix/1'>helix</scene>.

David O'Brochta at 16:29, 23 January 2017

David O'Brochta — Mon, 23 Jan 2017 16:29:51 GMT

←Older revision		Revision as of 16:29, 23 January 2017
Line 7:		Line 7:
	The protein chains in Keratin can bind to each other through covalent bonds (disulfide bonds between two cysteines), ionic bonds, hydrophobic interactions, and hydrogen bonds. Since the cysteines in this molecule are too far apart to bond covalently, ionic bonds, or salt bridges, form between the two chains.		The protein chains in Keratin can bind to each other through covalent bonds (disulfide bonds between two cysteines), ionic bonds, hydrophobic interactions, and hydrogen bonds. Since the cysteines in this molecule are too far apart to bond covalently, ionic bonds, or salt bridges, form between the two chains.

-	* <scene name='55/559109/Acidic-residues/1'>Click here to see the acidic residues, Asp and Glu ~~in Fig. 2~~.</scene>	+	* <scene name='55/559109/Acidic-residues/1'>Click here to see the acidic residues, Asp and Glu.</scene>

	* <scene name='55/559109/Basic-aas/1'>Click here to see the basic residues, Arg and Lys.</scene>		* <scene name='55/559109/Basic-aas/1'>Click here to see the basic residues, Arg and Lys.</scene>

David O'Brochta at 16:05, 23 January 2017

David O'Brochta — Mon, 23 Jan 2017 16:05:48 GMT

←Older revision		Revision as of 16:05, 23 January 2017
Line 1:		Line 1:
-	Abby Mandelblatt	+	'''Abby Mandelblatt'''
		+
		+	''Keratin'' proteins are expressed in epithelial cells and in epidermal cells and have a filamentous structure. They assemble to form cytoskeletal structures within the cell and epidermal derivatives such as hair and nails.

	<Structure load='3TNU' size='350' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' />		<Structure load='3TNU' size='350' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' />
		+
		+	The protein chains in Keratin can bind to each other through covalent bonds (disulfide bonds between two cysteines), ionic bonds, hydrophobic interactions, and hydrogen bonds. Since the cysteines in this molecule are too far apart to bond covalently, ionic bonds, or salt bridges, form between the two chains.
		+
		+	* <scene name='55/559109/Acidic-residues/1'>Click here to see the acidic residues, Asp and Glu in Fig. 2.</scene>
		+
		+	* <scene name='55/559109/Basic-aas/1'>Click here to see the basic residues, Arg and Lys.</scene>
		+
		+
		+	----
		+

	This is a Sandbox page that you can use for creating our discussion project.		This is a Sandbox page that you can use for creating our discussion project.

David O'Brochta at 15:18, 23 January 2017

David O'Brochta — Mon, 23 Jan 2017 15:18:37 GMT

←Older revision		Revision as of 15:18, 23 January 2017
Line 1:		Line 1:
	Abby Mandelblatt		Abby Mandelblatt

-	<Structure load='~~Image:Keratin.gif~~' size='350' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' />	+	<Structure load='3TNU' size='350' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' />

	This is a Sandbox page that you can use for creating our discussion project.		This is a Sandbox page that you can use for creating our discussion project.

David O'Brochta at 15:17, 23 January 2017

David O'Brochta — Mon, 23 Jan 2017 15:17:53 GMT

←Older revision		Revision as of 15:17, 23 January 2017
Line 1:		Line 1:
	Abby Mandelblatt		Abby Mandelblatt

-	<Structure load='Image:~~Lactase~~.~~jpeg~~' size='350' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' />	+	<Structure load='Image:Keratin.gif' size='350' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' />

	This is a Sandbox page that you can use for creating our discussion project.		This is a Sandbox page that you can use for creating our discussion project.

David O'Brochta at 06:26, 23 January 2017

David O'Brochta — Mon, 23 Jan 2017 06:26:40 GMT

←Older revision		Revision as of 06:26, 23 January 2017
Line 1:		Line 1:
	Abby Mandelblatt		Abby Mandelblatt
		+
		+	<Structure load='Image:Lactase.jpeg' size='350' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' />

	This is a Sandbox page that you can use for creating our discussion project.		This is a Sandbox page that you can use for creating our discussion project.

David O'Brochta at 06:20, 23 January 2017

David O'Brochta — Mon, 23 Jan 2017 06:20:24 GMT

←Older revision		Revision as of 06:20, 23 January 2017
Line 1:		Line 1:
		+	Abby Mandelblatt
		+
	This is a Sandbox page that you can use for creating our discussion project.		This is a Sandbox page that you can use for creating our discussion project.

David O'Brochta: New page: This is a Sandbox page that you can use for creating our discussion project. I would like for you to watch the short training videos. Each is short and you can view them all in about 40 ...

David O'Brochta — Wed, 04 Jan 2017 21:07:45 GMT

New page: This is a Sandbox page that you can use for creating our discussion project. I would like for you to watch the short training videos. Each is short and you can view them all in about 40 ...

New page

This is a Sandbox page that you can use for creating our discussion project.

I would like for you to watch the short training videos. Each is short and you can view them all in about 40 mins. These provide the basic knowledge you will need to our discussion sections.

I need you to get some basic familiarity with this package so you will be able to help students.

Our first three discussions will focus on 'structure'. Structure of DNA, proteins, and RNA.

The students will work in 2 person teams and will create a Proteopedia page on their assigned molecule and will be asked to research their molecule and create 'scenes' which are representations of the molecule that illustrates some key features.

There will be a work sheet the students will follow to help them through the project.

One of the objectives is to have the students manipulate structures to appreciate the 3 dimensional nature of the molecules we are discussing and to begin to help them conceptualize how these molecule might interact etc.