Protein Modeling C

fantasyfan
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Re: Protein Modeling C

Postby fantasyfan » November 2nd, 2014, 1:43 pm

What Jmol command would one use to display only this year's section of the fokI protein? (Chain A, residues 421 to 560)
restrict *A and 421-560
Edit: :oops: I didn't mean to go again so soon, I actually thought I was answering a question on the forum, and I only realized just now that I wasn't :oops: .
Looking forward to anatomy, protein, fossils, and optics (NYS trial) this year!

Gemma W
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Re: Protein Modeling C

Postby Gemma W » November 16th, 2014, 9:35 am

Whoops well good job anyway, go ahead and post another question if you wish
2015 events: WIDI, Protein Modeling, Geomapping, Chem Lab

2014 events: WIDI, Geomapping, Materials Science, Food Science
2013 events: WIDI, Mousetrap Vehicle, Heredity, Food Science, Metric Mastery

Best ever place: Nationals, 3rd in WIDI

fantasyfan
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Re: Protein Modeling C

Postby fantasyfan » December 3rd, 2014, 4:55 pm

Sorry, I entirely forgot about this :o

Describe the components of the Fok1 nuclear and how it functions.
Looking forward to anatomy, protein, fossils, and optics (NYS trial) this year!

nuclear reactor
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Re: Protein Modeling C

Postby nuclear reactor » December 27th, 2014, 5:24 pm

FokI is a restriction enzyme. It is a dimer that consists of a recognition domain which uses zinc-fingers to recognize a 5-base pair sequence, and then a cleavage domain which cuts the DNA strand 9 nucleotides downstream on the 3' end and 13 nucleotides downstream on the 5' end, thus creating sticky-ends which can be used to splice back more easily.

Slightly unrelated; does anyone know what the on-site build is supposed to be for invitationals? Is there one common or is that different every competition?

I suppose I should also pose a question:

Explain the mechanism by which a zinc-finger recognizes a DNA sequence.
only two things are infinite: the universe and human stupidity, though I'm not sure about the former.

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Re: Protein Modeling C

Postby Celestite » February 19th, 2015, 6:43 pm

The zinc finger binds to the major groove in the DNA, and specific amino acid residues reach out to bind to the DNA. Each zinc finger binds to three bases.

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Re: Protein Modeling C

Postby Celestite » February 19th, 2015, 6:44 pm

One for States:
What does the 12th and 13th residue in TAL Effectors do?

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Re: Protein Modeling C

Postby 09821qh » February 26th, 2015, 3:31 pm

They are essential for TALEs to recognize and bind to specific base pairs in the DNA sequence.


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