Protein Modeling C

User avatar
eagerlearner102
Member
Member
Posts: 142
Joined: December 29th, 2017, 5:20 pm
Division: C
State: CA
Has thanked: 0
Been thanked: 0

Re: Protein Modeling C

Post by eagerlearner102 » February 27th, 2019, 8:14 pm

The research paper talks a lot about binary and ternary complex of sgRNA bound Spycas9. What is the major difference between the 2?
2019:Fermi Questions, Protein Modeling, Sounds of Music
2020: Designer Genes, Protein Modeling, Ping Pong Parachute
2021: Chem Lab, Experimental Design, Protein Modeling

ReallyConfused
Member
Member
Posts: 3
Joined: February 27th, 2019, 10:23 pm
Has thanked: 0
Been thanked: 0

Re: Protein Modeling C

Post by ReallyConfused » February 27th, 2019, 10:26 pm

Hi guys, I am frantically trying to get my pre-build model built and I am utterly confused. Do we need to literally put a mark for every amino acid? Also, when I viewed the protein, it seemed pretty small and only had 3-5 alpha helices. Is this right?
Thanks!

User avatar
JoeyC
Member
Member
Posts: 304
Joined: November 7th, 2017, 1:43 pm
Division: C
State: TX
Has thanked: 503 times
Been thanked: 72 times

Re: Protein Modeling C

Post by JoeyC » February 28th, 2019, 3:51 am

Yes. You do not need to mark every amino acid. It is recommended, but no one should take off points for it. (though I wouldn't consider 3-5 alpha helices small :P )
Ohayo!
Dynamic Planet, Protein Modeling, Fast Facts, Thermodynamics
Dynamic Planet, Machines, Ornith
John 14:15
Scientia Potentia Est
Has Gotten Coronavirus: No

In memory of Ravi Zacharias, a friend of Christ.

User avatar
CookiePie1
Exalted Member
Exalted Member
Posts: 393
Joined: February 15th, 2018, 5:05 pm
Division: C
State: NJ
Pronouns: He/Him/His
Location: South Brunswick
Has thanked: 87 times
Been thanked: 60 times

Re: Protein Modeling C

Post by CookiePie1 » February 28th, 2019, 7:40 am

JoeyC wrote:Yes. You do not need to mark every amino acid. It is recommended, but no one should take off points for it. (though I wouldn't consider 3-5 alpha helices small :P )
While you don't need to, it is still a good practice, and for 85 residues, should only take about 3-5 minutes. Use a sharpie. It is very difficult to accurately build a model without knowing where each specific amino acid is. It will also help when you start to add sidechains and creative additions.
South Brunswick High School Captain '22
2020 Events: Protein Modeling, Ping Pong Parachute, Wright Stuff, Sounds of Music

Reality is merely an illusion, albeit a very persistent one.
-Albert Einstein

Check out my userpage!

ReallyConfused
Member
Member
Posts: 3
Joined: February 27th, 2019, 10:23 pm
Has thanked: 0
Been thanked: 0

Re: Protein Modeling C

Post by ReallyConfused » February 28th, 2019, 10:39 am

Thank you for your help! When you say "mark" the amino acids, does that mean like putting a push pin for every one? i thought about doing that but worry that it might get too crowded

ReallyConfused
Member
Member
Posts: 3
Joined: February 27th, 2019, 10:23 pm
Has thanked: 0
Been thanked: 0

Re: Protein Modeling C

Post by ReallyConfused » February 28th, 2019, 10:58 am

Oh wait I just looked at previous protein models and I think I understand now. Thanks!

User avatar
TheMysteriousMapMan
Member
Member
Posts: 35
Joined: December 5th, 2018, 12:45 pm
Division: C
State: MI
Has thanked: 2 times
Been thanked: 0

Re: Protein Modeling C

Post by TheMysteriousMapMan » March 1st, 2019, 7:00 am

Hi all!

My coach just assigned me to be the third member of Protein Modeling. The other two and I have decided that I will focus on the test portion, as that is more of my forté. As I am new to this event, and biology events in general, where should I start studying? What should I know about CRISPR? Like I said, I know only what I learned in Bio classes as I don't normally do biology-focused events, so assume I know nothing.

Thanks for your help, in advance!
2020 Events: Astronomy, Experimental Design, Detector Building, Ornithology, Sounds of Music.

Unsuccessful Assassinator of Game 143.


User avatar
eagerlearner102
Member
Member
Posts: 142
Joined: December 29th, 2017, 5:20 pm
Division: C
State: CA
Has thanked: 0
Been thanked: 0

Re: Protein Modeling C

Post by eagerlearner102 » March 1st, 2019, 9:14 am

Go on http://cbm.msoe.edu/scienceOlympiad/ to get a good foundation on CRISPR. Once you are able to lecture about CRISPR, read the 2 research papers in DETAIL. I mean in detail as in know the exact residues, knowing which domains, and perhaps the methods they used in the research paper (SEC, enzymatic assays, etc.) Focus on the Yang and Patel research paper more on the other one because I took around 5 practice tests and there was more weight on the Yang and Patel one.
For the harder ones like MIT invitational that I practiced on, I noticed that these concepts were literally found on Klein Organic Chemistry textbook chapter 25 for amino acids. I also read MIT OCW lecture notes 5.07 and 7.012 about it just to get a better understanding.
2019:Fermi Questions, Protein Modeling, Sounds of Music
2020: Designer Genes, Protein Modeling, Ping Pong Parachute
2021: Chem Lab, Experimental Design, Protein Modeling

User avatar
eagerlearner102
Member
Member
Posts: 142
Joined: December 29th, 2017, 5:20 pm
Division: C
State: CA
Has thanked: 0
Been thanked: 0

Re: Protein Modeling C

Post by eagerlearner102 » March 1st, 2019, 9:16 am

There is an awesome video here to memorize the 20 amino acids properties and categories + abbreviations:
https://www.youtube.com/watch?v=m130s94pMjE

Once you memorize that, you have a basic understanding.
You should also have a good understanding of how DNA works.
For an interactive CRISPR, that can be found here:
https://www.hhmi.org/biointeractive/cri ... plications
Hope that helps! Good luck!
2019:Fermi Questions, Protein Modeling, Sounds of Music
2020: Designer Genes, Protein Modeling, Ping Pong Parachute
2021: Chem Lab, Experimental Design, Protein Modeling

jocoboxo
Member
Member
Posts: 4
Joined: March 23rd, 2018, 2:11 pm
Has thanked: 0
Been thanked: 0

Re: Protein Modeling C

Post by jocoboxo » March 1st, 2019, 9:23 am

Hey everyone,

when I read the articles, how do I know what's important and exactly where on the anti-CRISPR protein it should be?

Post Reply

Return to “2019 Lab Events”

Who is online

Users browsing this forum: No registered users and 4 guests