Proteopedia - User contributions [en]

SandboxGenetic322-5

2017-02-22T14:14:17Z

David O'Brochta:

== 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.

<Structure load='1ttt' size='350' frame='true' align='right' caption='Phe-tRNA, elongation factor EF-TU:GDPNP Ternary complex' />

== 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''

SandboxGenetic322-5

2017-02-01T20:55:21Z

David O'Brochta:

'''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' />

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.</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>.

----

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.

SandboxGenetic322-6

2017-01-31T21:21:06Z

David O'Brochta:

<Structure load='1hmv' size='350' frame='true' align='right' caption='Structure of Reverse Transcriptase found in HIV-1' scene='Insert optional scene name here' />

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.

<StructureSection load='1bna' size='350' side='right' caption='Escherichia coli reca protein-bound DNA (PDB entry [[3rec]])' scene=''>

Anything in this section will appear adjacent to the 3D structure and will be scrollable.

</StructureSection>

'''HIV-1 Reverse Transcriptase'''
----
The <scene name='Reverse_transcriptase/Fingers/4'>Polymerase active site</scene> of Reverse Transcriptase is what recognizes the initial RNA molecule and begins Reverse Transcription of that molecule into DNA.

TA: ''' Ishan Shah'''

Template:Sandbox Reserved O'Brochta HLSC322

2017-01-27T14:54:31Z

David O'Brochta:

==HLSC322 Project: Exploring Structure/Function of Genetically Relevant Molecules==
'''Objective:''' You will investigate the structure and function of a genetically relevant molecule (you have been assigned a molecule).
You will use this page to create a short report that highlights the relevant structural features that relate to the molecule's function.

''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''

'''YOU ARE STRONGLY ENCOURAGED TO WORK WITH OTHER TEAMS TO COMPLETE THIS PROJECT!'''

For help along the way you should consult [[Proteopedia:Video Guide]] or [[Help:Getting Started in Proteopedia]] 
For more help on marking up a Wiki page you can check this Cheatsheet[https://en.wikipedia.org/wiki/Help:Cheatsheet] 
==
Instructions: ==

1. ALWAYS 'SAVE PAGE' FREQUENTLY WHILE YOU ARE WORKING. (this is a Wiki and all versions will be available) 
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. 
3. Load at least '''one applet''' of your molecule (place it and size it to your liking) 
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. 
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. 
6. Feel free to consult with you TA and Dr. O'Brochta. 
'''CAUTION: Make sure all of your writing is your's. Be mindful of even the appearance of plagerism.
'''

'''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.'''

OBrochtasSandbox

2017-01-26T19:29:30Z

David O'Brochta:

==Anopheles arabiensis Insulin Receptor like Protein==
<StructureSection load='Model.itasser.relax.pdb' side='right' caption='Anopheles arabiensis InR kinase domain model' scene='75/750300/Kinase_n_and_c_lobes/1'>

The Anopheles arabiensis Insulin Receptor's kinase domain was modeled by Brian Pierce for the 'An arab ts lethal project'

This shows the basic structure of the kinase domain with an <scene name='75/750300/Kinase_n_and_c_lobes/1'>N and C lobe</scene>. The ATP will sit between them just below Beta 1

<scene name='75/750300/Inr_atp-cat_loop/3'>This</scene> shows the ATP binding site (purple) and the catalytic loop (green).
Here it is as a <scene name='75/750300/Inr_atp-cat_loopspacefill/1'>spacefilled model</scene>.

These are <scene name='75/750300/Geneticmutations/1'>three ts mutations</scene> found in other RTKs.

G1000S (magenta), A1133G (orange), T1221I (teal)

And as a <scene name='75/750300/Geneticmutationsspacefilled/1'>spacefilled model</scene>

This <scene name='75/750300/T1221_spacefilled/1'>threonine</scene> when mutated to isoleucine resulted in ts lethal mutations in the sevenless and EGFR-like genes in D. melanogster

Using the software TS_pred (a ts mutation prediction program): these are the <scene name='75/750300/Geneticmutations-tspred_rosett/2'>5 best sites</scene> to mutate based on sequence and structure - L1236, I1071, V1196, L1197,I1258 (red)
Using Rosetta_ts_rbf (another ts mutation prediction program): these are the <scene name='75/750300/Geneticmutations-tspred_rosett/2'>top 5</scene> sites -W1173P, M1075K, Y1208G, L1197P, Y1208Asn (yellow)

Both TS_pred and Rosetta_ts_rbf had <scene name='75/750300/Tspredrosetta_spacefilled/1'>L1197</scene> in their top 5 (black)

Most but not all of the actual and predicted mutations are <scene name='75/750300/Tspred_rosett_burried_residues/1'>buried</scene>. Note that T1221 and G1000S are not buried.

Here are the <scene name='75/750300/Tspred_rosett_hydroph_residues/1'>hydrophobic residues</scene>.

</StructureSection>

OBrochtasSandbox

2017-01-26T19:27:35Z

David O'Brochta:

==Your Heading Here (maybe something like 'Structure')==
<StructureSection load='Model.itasser.relax.pdb' side='right' caption='Anopheles arabiensis InR kinase domain model' scene='75/750300/Kinase_n_and_c_lobes/1'>

The Anopheles arabiensis Insulin Receptor's kinase domain was modeled by Brian Pierce for the 'An arab ts lethal project'

This shows the basic structure of the kinase domain with an <scene name='75/750300/Kinase_n_and_c_lobes/1'>N and C lobe</scene>. The ATP will sit between them just below Beta 1

<scene name='75/750300/Inr_atp-cat_loop/3'>This</scene> shows the ATP binding site (purple) and the catalytic loop (green).
Here it is as a <scene name='75/750300/Inr_atp-cat_loopspacefill/1'>spacefilled model</scene>.

These are <scene name='75/750300/Geneticmutations/1'>three ts mutations</scene> found in other RTKs.

G1000S (magenta), A1133G (orange), T1221I (teal)

And as a <scene name='75/750300/Geneticmutationsspacefilled/1'>spacefilled model</scene>

This <scene name='75/750300/T1221_spacefilled/1'>threonine</scene> when mutated to isoleucine resulted in ts lethal mutations in the sevenless and EGFR-like genes in D. melanogster

Using the software TS_pred (a ts mutation prediction program): these are the <scene name='75/750300/Geneticmutations-tspred_rosett/2'>5 best sites</scene> to mutate based on sequence and structure - L1236, I1071, V1196, L1197,I1258 (red)
Using Rosetta_ts_rbf (another ts mutation prediction program): these are the <scene name='75/750300/Geneticmutations-tspred_rosett/2'>top 5</scene> sites -W1173P, M1075K, Y1208G, L1197P, Y1208Asn (yellow)

Both TS_pred and Rosetta_ts_rbf had <scene name='75/750300/Tspredrosetta_spacefilled/1'>L1197</scene> in their top 5 (black)

Most but not all of the actual and predicted mutations are <scene name='75/750300/Tspred_rosett_burried_residues/1'>buried</scene>. Note that T1221 and G1000S are not buried.

Here are the <scene name='75/750300/Tspred_rosett_hydroph_residues/1'>hydrophobic residues</scene>.

</StructureSection>=='''Anopheles arabiensis Insulin Receptor like Protein''' ==

This shows the basic structure of the kinase domain with an <scene name='75/750300/Kinase_n_and_c_lobes/1'>N and C lobe</scene>. The ATP will sit between them just below Beta 1

<scene name='75/750300/Inr_atp-cat_loop/3'>This</scene> shows the ATP binding site (purple) and the catalytic loop (green).
Here it is as a <scene name='75/750300/Inr_atp-cat_loopspacefill/1'>spacefilled model</scene>.

These are <scene name='75/750300/Geneticmutations/1'>three ts mutations</scene> found in other RTKs.

G1000S (magenta), A1133G (orange), T1221I (teal)

And as a <scene name='75/750300/Geneticmutationsspacefilled/1'>spacefilled model</scene>

This <scene name='75/750300/T1221_spacefilled/1'>threonine</scene> when mutated to isoleucine resulted in ts lethal mutations in the sevenless and EGFR-like genes in D. melanogster

Using the software TS_pred (a ts mutation prediction program): these are the <scene name='75/750300/Geneticmutations-tspred_rosett/2'>5 best sites</scene> to mutate based on sequence and structure - L1236, I1071, V1196, L1197,I1258 (red)
Using Rosetta_ts_rbf (another ts mutation prediction program): these are the <scene name='75/750300/Geneticmutations-tspred_rosett/2'>top 5</scene> sites -W1173P, M1075K, Y1208G, L1197P, Y1208Asn (yellow)

Both TS_pred and Rosetta_ts_rbf had <scene name='75/750300/Tspredrosetta_spacefilled/1'>L1197</scene> in their top 5 (black)

Most but not all of the actual and predicted mutations are <scene name='75/750300/Tspred_rosett_burried_residues/1'>buried</scene>. Note that T1221 and G1000S are not buried.

Here are the <scene name='75/750300/Tspred_rosett_hydroph_residues/1'>hydrophobic residues</scene>.

</StructureSection>

</StructureSection>

OBrochtasSandbox

2017-01-26T19:19:42Z

David O'Brochta:

== '''Anopheles arabiensis Insulin Receptor like Protein''' ==

<StructureSection load='Model.itasser.relax.pdb' size='800' side='right' caption='Anopheles arabiensis InR kinase domain model' scene='75/750300/Kinase_n_and_c_lobes/1' />

Anything in this section will appear adjacent to the 3D structure and will be scrollable.

The Anopheles arabiensis Insulin Receptor's kinase domain was modeled by Brian Pierce for the 'An arab ts lethal project'

This shows the basic structure of the kinase domain with an <scene name='75/750300/Kinase_n_and_c_lobes/1'>N and C lobe</scene>. The ATP will sit between them just below Beta 1

<scene name='75/750300/Inr_atp-cat_loop/3'>This</scene> shows the ATP binding site (purple) and the catalytic loop (green).
Here it is as a <scene name='75/750300/Inr_atp-cat_loopspacefill/1'>spacefilled model</scene>.

These are <scene name='75/750300/Geneticmutations/1'>three ts mutations</scene> found in other RTKs.

G1000S (magenta), A1133G (orange), T1221I (teal)

And as a <scene name='75/750300/Geneticmutationsspacefilled/1'>spacefilled model</scene>

This <scene name='75/750300/T1221_spacefilled/1'>threonine</scene> when mutated to isoleucine resulted in ts lethal mutations in the sevenless and EGFR-like genes in D. melanogster

Using the software TS_pred (a ts mutation prediction program): these are the <scene name='75/750300/Geneticmutations-tspred_rosett/2'>5 best sites</scene> to mutate based on sequence and structure - L1236, I1071, V1196, L1197,I1258 (red)
Using Rosetta_ts_rbf (another ts mutation prediction program): these are the <scene name='75/750300/Geneticmutations-tspred_rosett/2'>top 5</scene> sites -W1173P, M1075K, Y1208G, L1197P, Y1208Asn (yellow)

Both TS_pred and Rosetta_ts_rbf had <scene name='75/750300/Tspredrosetta_spacefilled/1'>L1197</scene> in their top 5 (black)

Most but not all of the actual and predicted mutations are <scene name='75/750300/Tspred_rosett_burried_residues/1'>buried</scene>. Note that T1221 and G1000S are not buried.

Here are the <scene name='75/750300/Tspred_rosett_hydroph_residues/1'>hydrophobic residues</scene>.

</StructureSection>

Genetics322 Sandbox DNA

2017-01-25T21:58:13Z

David O'Brochta:

3D DNA structure for class 1

==B DNA==

<StructureSection load='1bna' size='400' side='right' caption='B DNA' scene='75/751212/B_dna_stick/1'>

Anything in this section will appear adjacent to the 3D structure and will be scrollable.

This is the <scene name='75/751212/B_dna_stick/1'>B form of DNA</scene>

Here are the <scene name='75/751212/B_dna_stick/2'>bases</scene>.

Here are the <scene name='75/751212/B_dna_stick/4'>nucleotides dA (blue), dG (red), dC (green), dT</scene>

Here are the <scene name='75/751212/B_dna_stick/5'>Major and Minor grooves</scene>.

Here is the <scene name='75/751212/B_dna_stick/6'>surface of the grooves</scene>

<scene name='75/751212/B_dna_stick/7'>Methyl groups of dT</scene> in the major grove.

And here is the same view of the <scene name='75/751212/B_dna_stick/8'>surface.</scene>

</StructureSection>

<Structure load='1efa' size='400' frame='true' align='right' caption='Insert caption here' scene='75/751212/Lac_repressor_binding_dna/2' />

This is a transcriptional repressor protein from E. coli. It binds specifically to particular sequences. You can see how the parts of the protein interact with the edges of the bases in both the major and minor grooves.

Here it is showing the <scene name='75/751212/Lac_repressor_binding_dna/3'>surface of the protein</scene>. Look how it 'fits' into the major and minor grooves. This is a highly specific binding protein and only binds to this sequence. This is a chemical interaction.

</StructureSection>

Genetics322 Sandbox DNA

2017-01-25T21:57:21Z

David O'Brochta:

3D DNA structure for class 1

==B DNA==

<StructureSection load='1bna' size='300' side='right' caption='B DNA' scene='75/751212/B_dna_stick/1'>

Anything in this section will appear adjacent to the 3D structure and will be scrollable.

This is the <scene name='75/751212/B_dna_stick/1'>B form of DNA</scene>

Here are the <scene name='75/751212/B_dna_stick/2'>bases</scene>.

Here are the <scene name='75/751212/B_dna_stick/4'>nucleotides dA (blue), dG (red), dC (green), dT</scene>

Here are the <scene name='75/751212/B_dna_stick/5'>Major and Minor grooves</scene>.

Here is the <scene name='75/751212/B_dna_stick/6'>surface of the grooves</scene>

<scene name='75/751212/B_dna_stick/7'>Methyl groups of dT</scene> in the major grove.

And here is the same view of the <scene name='75/751212/B_dna_stick/8'>surface.</scene>

</StructureSection>

<Structure load='1efa' size='300' frame='true' align='right' caption='Insert caption here' scene='75/751212/Lac_repressor_binding_dna/2' />

This is a transcriptional repressor protein from E. coli. It binds specifically to particular sequences. You can see how the parts of the protein interact with the edges of the bases in both the major and minor grooves.

Here it is showing the <scene name='75/751212/Lac_repressor_binding_dna/3'>surface of the protein</scene>. Look how it 'fits' into the major and minor grooves. This is a highly specific binding protein and only binds to this sequence. This is a chemical interaction.

</StructureSection>

Genetics322 Sandbox DNA

2017-01-25T21:56:06Z

David O'Brochta:

3D DNA structure for class 1

==B DNA==

<StructureSection load='1bna' size='500' side='right' caption='B DNA' scene='75/751212/B_dna_stick/1'>

Anything in this section will appear adjacent to the 3D structure and will be scrollable.

This is the <scene name='75/751212/B_dna_stick/1'>B form of DNA</scene>

Here are the <scene name='75/751212/B_dna_stick/2'>bases</scene>.

Here are the <scene name='75/751212/B_dna_stick/4'>nucleotides dA (blue), dG (red), dC (green), dT</scene>

Here are the <scene name='75/751212/B_dna_stick/5'>Major and Minor grooves</scene>.

Here is the <scene name='75/751212/B_dna_stick/6'>surface of the grooves</scene>

<scene name='75/751212/B_dna_stick/7'>Methyl groups of dT</scene> in the major grove.

And here is the same view of the <scene name='75/751212/B_dna_stick/8'>surface.</scene>

</StructureSection>

<Structure load='1efa' size='500' frame='true' align='right' caption='Insert caption here' scene='75/751212/Lac_repressor_binding_dna/2' />

This is a transcriptional repressor protein from E. coli. It binds specifically to particular sequences. You can see how the parts of the protein interact with the edges of the bases in both the major and minor grooves.

Here it is showing the <scene name='75/751212/Lac_repressor_binding_dna/3'>surface of the protein</scene>. Look how it 'fits' into the major and minor grooves. This is a highly specific binding protein and only binds to this sequence. This is a chemical interaction.

</StructureSection>

Genetics322 Sandbox DNA

2017-01-25T21:53:22Z

David O'Brochta:

3D DNA structure for class 1

==B DNA==

<StructureSection load='1bna' size='500' side='right' caption='B DNA' scene='75/751212/B_dna_stick/1'>

Anything in this section will appear adjacent to the 3D structure and will be scrollable.

This is the <scene name='75/751212/B_dna_stick/1'>B form of DNA</scene>

Here are the <scene name='75/751212/B_dna_stick/2'>bases</scene>.

Here are the <scene name='75/751212/B_dna_stick/4'>nucleotides dA (blue), dG (red), dC (green), dT</scene>

Here are the <scene name='75/751212/B_dna_stick/5'>Major and Minor grooves</scene>.

Here is the <scene name='75/751212/B_dna_stick/6'>surface of the grooves</scene>

<scene name='75/751212/B_dna_stick/7'>Methyl groups of dT</scene> in the major grove.

And here is the same view of the <scene name='75/751212/B_dna_stick/8'>surface.</scene>

</StructureSection>

<Structure load='1efa' size='500' frame='true' align='right' caption='Insert caption here' scene='75/751212/Lac_repressor_binding_dna/2' />

==Your Heading Here (maybe something like 'Structure')==
<StructureSection load='3rec' size='350' side='right' caption='Escherichia coli reca protein-bound DNA (PDB entry [[3rec]])' scene=''>

Anything in this section will appear adjacent to the 3D structure and will be scrollable.

This is a transcriptional repressor protein from E. coli. It binds specifically to particular sequences. You can see how the parts of the protein interact with the edges of the bases in both the major and minor grooves.

Here it is showing the <scene name='75/751212/Lac_repressor_binding_dna/3'>surface of the protein</scene>. Look how it 'fits' into the major and minor grooves. This is a highly specific binding protein and only binds to this sequence. This is a chemical interaction.

</StructureSection>

Genetics322 Sandbox DNA

2017-01-25T21:52:08Z

David O'Brochta:

3D DNA structure for class 1

==B DNA==

<StructureSection load='1bna' size='600' side='right' caption='B DNA' scene='75/751212/B_dna_stick/1'>

Anything in this section will appear adjacent to the 3D structure and will be scrollable.

This is the <scene name='75/751212/B_dna_stick/1'>B form of DNA</scene>

Here are the <scene name='75/751212/B_dna_stick/2'>bases</scene>.

Here are the <scene name='75/751212/B_dna_stick/4'>nucleotides dA (blue), dG (red), dC (green), dT</scene>

Here are the <scene name='75/751212/B_dna_stick/5'>Major and Minor grooves</scene>.

Here is the <scene name='75/751212/B_dna_stick/6'>surface of the grooves</scene>

<scene name='75/751212/B_dna_stick/7'>Methyl groups of dT</scene> in the major grove.

And here is the same view of the <scene name='75/751212/B_dna_stick/8'>surface.</scene>

</StructureSection>

<Structure load='1efa' size='600' frame='true' align='right' caption='Insert caption here' scene='75/751212/Lac_repressor_binding_dna/2' />

==Your Heading Here (maybe something like 'Structure')==
<StructureSection load='3rec' size='350' side='right' caption='Escherichia coli reca protein-bound DNA (PDB entry [[3rec]])' scene=''>

Anything in this section will appear adjacent to the 3D structure and will be scrollable.

This is a transcriptional repressor protein from E. coli. It binds specifically to particular sequences. You can see how the parts of the protein interact with the edges of the bases in both the major and minor grooves.

Here it is showing the <scene name='75/751212/Lac_repressor_binding_dna/3'>surface of the protein</scene>. Look how it 'fits' into the major and minor grooves. This is a highly specific binding protein and only binds to this sequence. This is a chemical interaction.

</StructureSection>

Genetics322 Sandbox DNA

2017-01-25T21:49:47Z

David O'Brochta:

3D DNA structure for class 1

==B DNA==

<StructureSection load='1bna' size='600' side='right' caption='B DNA' scene='75/751212/B_dna_stick/1'>

Anything in this section will appear adjacent to the 3D structure and will be scrollable.

This is the <scene name='75/751212/B_dna_stick/1'>B form of DNA</scene>

Here are the <scene name='75/751212/B_dna_stick/2'>bases</scene>.

Here are the <scene name='75/751212/B_dna_stick/4'>nucleotides dA (blue), dG (red), dC (green), dT</scene>

Here are the <scene name='75/751212/B_dna_stick/5'>Major and Minor grooves</scene>.

Here is the <scene name='75/751212/B_dna_stick/6'>surface of the grooves</scene>

<scene name='75/751212/B_dna_stick/7'>Methyl groups of dT</scene> in the major grove.

And here is the same view of the <scene name='75/751212/B_dna_stick/8'>surface.</scene>

</StructureSection>

This is a transcriptional repressor protein from E. coli. It binds specifically to particular sequences. You can see how the parts of the protein interact with the edges of the bases in both the major and minor grooves.

<Structure load='1efa' size='600' frame='true' align='right' caption='Insert caption here' scene='75/751212/Lac_repressor_binding_dna/2' />

Here it is showing the <scene name='75/751212/Lac_repressor_binding_dna/3'>surface of the protein</scene>. Look how it 'fits' into the major and minor grooves. This is a highly specific binding protein and only binds to this sequence. This is a chemical interaction.

Genetics322 Sandbox DNA

2017-01-25T16:34:27Z

David O'Brochta:

3D DNA structure for class 1

==B DNA==

<StructureSection load='1bna' size='1200' side='right' caption='B DNA' scene='75/751212/B_dna_stick/1'>

Anything in this section will appear adjacent to the 3D structure and will be scrollable.

This is the <scene name='75/751212/B_dna_stick/1'>B form of DNA</scene>

Here are the <scene name='75/751212/B_dna_stick/2'>bases</scene>.

Here are the <scene name='75/751212/B_dna_stick/4'>nucleotides dA (blue), dG (red), dC (green), dT</scene>

Here are the <scene name='75/751212/B_dna_stick/5'>Major and Minor grooves</scene>.

Here is the <scene name='75/751212/B_dna_stick/6'>surface of the grooves</scene>

<scene name='75/751212/B_dna_stick/7'>Methyl groups of dT</scene> in the major grove.

And here is the same view of the <scene name='75/751212/B_dna_stick/8'>surface.</scene>

</StructureSection>

This is a transcriptional repressor protein from E. coli. It binds specifically to particular sequences. You can see how the parts of the protein interact with the edges of the bases in both the major and minor grooves.

<Structure load='1efa' size='1000' frame='true' align='right' caption='Insert caption here' scene='75/751212/Lac_repressor_binding_dna/2' />

Here it is showing the <scene name='75/751212/Lac_repressor_binding_dna/3'>surface of the protein</scene>. Look how it 'fits' into the major and minor grooves. This is a highly specific binding protein and only binds to this sequence. This is a chemical interaction.

Genetics322 Sandbox DNA

2017-01-25T14:59:46Z

David O'Brochta: New page: 3D DNA structure for class 1 ==B DNA== <StructureSection load='1bna' size='1200' side='right' caption='B DNA' scene='75/751212/B_dna_stick/1'> Anything in this section will appear adjac...

SandboxGenetic322-6

2017-01-23T16:42:32Z

David O'Brochta:

<Structure load='1hmv' size='350' frame='true' align='right' caption='Structure of Reverse Transcriptase found in HIV-1' scene='Insert optional scene name here' />

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.

'''HIV-1 Reverse Transcriptase'''
----
The <scene name='Reverse_transcriptase/Fingers/4'>Polymerase active site</scene> of Reverse Transcriptase is what recognizes the initial RNA molecule and begins Reverse Transcription of that molecule into DNA.

TA: ''' Ishan Shah'''

SandboxGenetic322-6

2017-01-23T16:42:17Z

David O'Brochta:

<Structure load='1hmv' size='350' frame='true' align='right' caption='Structure of Reverse Transcriptase found in HIV-1' scene='Insert optional scene name here' />

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.

'''HIV-1 Reverse Transcriptase'''
----
The <scene name='Reverse_transcriptase/Fingers/4'>Polymerase active site</scene> of Reverse Transcriptase is what recognizes the initial RNA molecule and begins Reverse Transcription of that molecule into DNA.

''' Ishan Shah'''

SandboxGenetic322-6

2017-01-23T16:41:36Z

David O'Brochta:

<Structure load='1hmv' size='350' frame='true' align='right' caption='Structure of Reverse Transcriptase found in HIV-1' scene='Insert optional scene name here' />

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.

'''HIV-1 Reverse Transcriptase'''
----
''' Ishan Shah
'''
The <scene name='Reverse_transcriptase/Fingers/4'>Polymerase active site</scene> of Reverse Transcriptase is what recognizes the initial RNA molecule and begins Reverse Transcription of that molecule into DNA.

SandboxGenetic322-6

2017-01-23T16:40:29Z

David O'Brochta:

<Structure load='1hmv' size='350' frame='true' align='right' caption='Structure of Reverse Transcriptase found in HIV-1' scene='Insert optional scene name here' />

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.

----
TA: Ishan Shah

The <scene name='Reverse_transcriptase/Fingers/4'>Polymerase active site</scene> of Reverse Transcriptase is what recognizes the initial RNA molecule and begins Reverse Transcription of that molecule into DNA.

SandboxGenetic322-6

2017-01-23T16:39:56Z

David O'Brochta:

<Structure load='1hmv' size='350' frame='true' align='right' caption='Structure of Reverse Transcriptase found in HIV-1' scene='Insert optional scene name here' />

TA: Ishan Shah
The <scene name='Reverse_transcriptase/Fingers/4'>Polymerase active site</scene> of Reverse Transcriptase is what recognizes the initial RNA molecule and begins Reverse Transcription of that molecule into DNA.
----
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.

SandboxGenetic322-6

2017-01-23T16:37:52Z

David O'Brochta:

<Structure load='1hmv' size='350' frame='true' align='right' caption='Structure of Reverse Transcriptase found in HIV-1' scene='Insert optional scene name here' />

TA: Ishan Shah
The active site of Reverse Transcriptase <scene name='Reverse_transcriptase/Fingers/4'>Polymerase active site</scene>
----
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.

SandboxGenetic322-5

2017-01-23T16:29:51Z

David O'Brochta:

'''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' />

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.</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.

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.

SandboxGenetic322-6

2017-01-23T16:27:51Z

David O'Brochta:

<Structure load='1hmv' size='350' frame='true' align='right' caption='Structure of Reverse Transcriptase found in HIV-1' scene='Insert optional scene name here' />

TA: Ishan Shah
----
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.

SandboxGenetic322-6

2017-01-23T16:17:58Z

David O'Brochta:

<Structure load='1hmv' size='350' frame='true' align='right' caption='Structure of HIV-1 Reverse Transcriptase' scene='Insert optional scene name here' />

TA: Ishan Shah
----
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.

SandboxGenetic322-5

2017-01-23T16:05:48Z

David O'Brochta:

'''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' />

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.

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.

SandboxGenetic322-5

2017-01-23T15:18:37Z

David O'Brochta:

Abby Mandelblatt

<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.

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.

SandboxGenetic322-5

2017-01-23T15:17:53Z

David O'Brochta:

Abby Mandelblatt

<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.

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.