Protein Modeling C

nmsciencemom
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Re: Protein Modeling C

Postby nmsciencemom » February 16th, 2016, 3:29 pm

Our toober did seem a bit short, but just a millimeter off for 100+ 2 cm segments and you come up short. Better to mark just under 2 cm and not run out.

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Re: Protein Modeling C

Postby SHS1 » February 17th, 2016, 8:52 pm

This event forum is pretty inactive but going to ask anyway.

So our team at the past several competitions has been getting perfect or near perfect on both the prebuild and the onsite build. But the test portion of this event we consistently do sub-par on. Does anyone have any tips on doing better on the exam for this event? Right now our plan is to read a lot more research papers and add more information to our reference sheet. Any help is much appreciated as our teams is starting to feel a little stuck.

Also feel free to PM me if you want
I've been having the same problem. We constantly see perfect scores on our models and then, like, 50% for our test. We're currently doing the same thing as you suggested. Make sure you have the obvious (a codon table, info about invitational, regional, state, and national proteins, amino acid table, structures of the neurotransmitters, etc.) if you don't already have it, because those can cost you a ton of points.

Check the wiki for some info as well, if you haven't already.
My team actually has the opposite problem of you guys, maybe we can swap tips? :D For the reference sheet, I basically swiped most of the diagrams made available on "The Beery Twin's Story" webpage http://cbm.msoe.edu/scienceOlympiad/participant2.php and wrote paragraphs summarizing what it all meant. The provided research papers, while hard to read, are actually essential for the test. At the very least, I'd include the abstracts of the relevant research papers in the reference sheet. I wish that I included more of the papers' structure-description for the Regional exam, especially for the on-site model questions. I'd have over half of the reference sheet dedicated to information about this year's proteins and neurotransmitters, and the other half dedicated to general protein information, like the codon and amino acid tables mentioned above. Hope that's helpful!

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Re: Protein Modeling C

Postby chl » February 22nd, 2016, 9:58 pm

For the state meet, I assume we need to know about the State Meet Protein and the prebuild protein. Is that it? Do we need to know any of the Molecule of the Month topics besides those that discuss those 2 proteins? Or the Invitational and Regional proteins?

It is not clear to me if any of the other Molecule of the Month topics are fair game for the test. Thank you for your advice.

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Re: Protein Modeling C

Postby Tesel » February 26th, 2016, 10:24 am

We have purchased the 3 D molecular design’s 2015-2016 Science Olympiad Protein Modeling Event Kit (pre- build Kit). The site says it is for 168 amino acids but this year’s protein needs 169 and we found the mini-toobers are short by 2 centimeters. Has anyone else ordered the kit and had the same problem? If so, how did you add the two centimeters?
A team from our state noticed the same issue. You can glue on your red and blue caps so they are only attached to 1 cm of the toober. Assuming that the caps are 2 cm each this will add 2 cm total to your protein.
There is no problem with the kit. The scale is 2 cm per amino acid, which really means that there are 2 cm between each amino acid. If you go on Jmol and color one amino acid you will see that the color covers one bend and halfway to the bend on either side. So each amino acid is represented by the turn - not the connection. The backbone structure connects amino acids linearly, rather than creating smooth turns like in the cartoon visualization. So, getting back to the kit, you need 2 cm between each amino acid. Say the protein was from amino acids 5 to 9 (hypothetically), that would mean your structure would be as follows with the dashes representing the 2 cm of tuber you need.
5 - 6 - 7 - 8 - 9
That's four dashes, 4 * 2 = 8 cm of tuber. More simply, (9-5) * 2 = 8. In the case of this years protein, we have to build amino acids 93 - 261. So, (261- 93) * 2 = (168) * 2 = 336 cm of tuber, which is what the kit provides.
I know it's confusing because there are 169 amino acids but you have to understand that the first and last amino acids are at the ends of the tuber. And when you restrict the amino acids visualized in Jmol, the program will eliminate one cm of backbone connecting to amino acid 92 and one cm of backbone connecting to amino acid 264, which is why the kit provides 2 cm less tuber than you might expect.
Thank you for the help, that explains it perfectly and should help me on my next invitational (tomorrow, glad I checked :)). That doesn't explain why the amino acid they had listed as an answer for our last invitational was 200 residues off, but what can you do...
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Re: Protein Modeling C

Postby ElementalClockwork » February 27th, 2016, 6:57 pm

Hey guys, I had posted this earlier but I haven't gotten a response yet. Just wondering if any teams out there label the substrate bindings sites on the protein? Would this be a good thing to include on the prebuild?

Thanks!
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Re: Protein Modeling C

Postby ScienceOlympian » February 27th, 2016, 7:26 pm

Welp, I incorrectly measured the protein so that I had 20 extra amino acids...
Does anyone have any advice in measuring the protein and removing sharpie from the foam? :/
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Re: Protein Modeling C

Postby llsrhayes » March 12th, 2016, 8:06 am

On the sequence page for the 1SEP protein, the second beta sheet that we have to fold goes from amino acids 150 to 156; however, on JSmol/Jmol that same beta sheet appears to run from amino acids 150-157. Is anyone else having this problem, and if so, which one should we follow when folding?

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Re: Protein Modeling C

Postby alisha » March 12th, 2016, 11:06 am

What sort of questions are they going to ask us about for the written test? I couldn't find any practice tests relevant to this year's protein

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Re: Protein Modeling C

Postby Uber » March 12th, 2016, 1:40 pm

What sort of questions are they going to ask us about for the written test? I couldn't find any practice tests relevant to this year's protein
Usually it's split into two parts: Protein general multiple choice and protein specific frq. Protein general is usually basic protein structure (where's the side chains in an a-helix?), amino acids (which amino acid might do x), or protein folding (what do chaperonins do?). Protein specific will be over sepiapterin reductase, the Beery Twins, and the competition specific protein (invitational, regional, state, or national level, depending on which one you're going to). The questions will be something like: What does this specific amino acid do in the reaction? How does inhibition work in the protein? How does this inhibitor differ from the other? etc. Make sure to read the entire paper, because some answers might be obscure.
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Re: Protein Modeling C

Postby chemmybear » March 12th, 2016, 3:09 pm

I'd say it hits the journals pretty heavy, moreso than it hits the onsite or generic protein info.


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