Template:Sandbox Reserved O'Brochta HLSC322

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==HLSC322 Project: Exploring Structure/Function of Genetically Relevant Molecules==
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==genetics is ok==
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'''Objective:''' You will investigate the structure and function of a genetically relevant molecule (you have been assigned a molecule).
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You will use this page to create a short report that highlights the relevant structural features that relate to the molecule's function.
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''We are exploring structure to help us appreciate the chemical basis of heredity and to begin to understand how structures of proteins is tied to their functions''
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=='Molecules it Interacts With and where '==
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'''YOU ARE STRONGLY ENCOURAGED TO WORK WITH OTHER TEAMS TO COMPLETE THIS PROJECT!'''
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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.
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For help along the way you should consult [[Proteopedia:Video Guide]] or [[Help:Getting Started in Proteopedia]] <br>
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''PHOSHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER''
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For more help on marking up a Wiki page you can check this Cheatsheet[https://en.wikipedia.org/wiki/Help:Cheatsheet]<br><br>
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==
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Instructions: ==
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1. ALWAYS 'SAVE PAGE' FREQUENTLY WHILE YOU ARE WORKING. (this is a Wiki and all versions will be available)<br>
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''PHENYLALANINE''
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2. '''Introduction:''' This should be a brief (≤250 words), clear exposition that orients the reader to the genetic process involved and the role of your molecule in this process.<br>
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''MAGNESIUM ION''
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3. Load at least '''one applet''' of your molecule (place it and size it to your liking)<br>
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4. '''About ''your molecule's name''''': Here you will write a paragraph or two that describes structural aspects of the molecule that are relevant to its function. You will create at least '''3 Scenes''' that help readers visualize these feature. <br>
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5. '''Your Scenes:''' You can design your scenes in anyway you wish but you should try to use the full potential of the visualization tools available for Scene creation. This is about exploring structure more than about writing. <br>
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6. Feel free to consult with you TA and Dr. O'Brochta.<br>
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'''CAUTION: Make sure all of your writing is your's. Be mindful of even the appearance of plagerism.
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'''
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'''THE SPACE BELOW IS CURRENTLY FILLED WITH SAMPLE TEXT AND AN APPLET OF A MOLECULE. YOUR SHOULD REMOVE ALL OF THIS BEFORE YOU START WORKING.'''
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=='Origin'==
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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.
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=='Structure'==
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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.
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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.
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<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.
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=='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.
 +
 
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''PHOSHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER''
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''PHENYLALANINE''
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''MAGNESIUM ION''
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 +
 
 +
=='Origin'==
 +
 
 +
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.
 +
 
 +
 
 +
=='Structure'==
 +
 
 +
 
 +
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.
 +
 
 +
<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.
 +
 
 +
=='Function"==
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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.
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<Structure load='1ttt' size='350' frame='true' align='right' caption='Phe-tRNA, elongation factor EF-TU:GDPNP Ternary complex'
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=='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''
 +
 
 +
 
 +
=='Origin'==
 +
 
 +
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.
 +
 
 +
 
 +
=='Structure'==
 +
 
 +
 
 +
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''
 +
 
 +
 
 +
=='Origin'==
 +
 
 +
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.
 +
 
 +
 
 +
=='Structure'==
 +
 
 +
 
 +
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.
 +
 
 +
<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.

Current revision

Contents

genetics is ok

'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


'Origin'

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.


'Structure'

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 alignment.


Specific are highlighted here. The ligands listed above, GDP, Phe, and Mg+2 ion each attach at these locations which are still being explored.

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


'Origin'

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.


'Structure'

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 alignment.


Specific are highlighted here.

which play a crucial role in binding to the ribosome during translation.

'Function"

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.

Phe-tRNA, elongation factor EF-TU:GDPNP Ternary complex

Drag the structure with the mouse to rotate
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