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Re: Protein Modeling C

Posted: November 2nd, 2014, 1:43 pm
by fantasyfan
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: .

Re: Protein Modeling C

Posted: November 16th, 2014, 9:35 am
by Gemma W
Whoops well good job anyway, go ahead and post another question if you wish

Re: Protein Modeling C

Posted: December 3rd, 2014, 4:55 pm
by fantasyfan
Sorry, I entirely forgot about this :o

Describe the components of the Fok1 nuclear and how it functions.

Re: Protein Modeling C

Posted: December 27th, 2014, 5:24 pm
by nuclear reactor
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.

Re: Protein Modeling C

Posted: February 19th, 2015, 6:43 pm
by Celestite
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.

Re: Protein Modeling C

Posted: February 19th, 2015, 6:44 pm
by Celestite
One for States:
What does the 12th and 13th residue in TAL Effectors do?

Re: Protein Modeling C

Posted: February 26th, 2015, 3:31 pm
by 09821qh
They are essential for TALEs to recognize and bind to specific base pairs in the DNA sequence.