Feyza
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can someone plzz explain me in the simplest way...like treat me as if I have no idea ever about it ...the meaning of (-) and (+) supercoils that the topoisomerases insert and the consequences...over-under wound thing...
Its 2:34 PM and Ive been tryin to understand it for like 30 minutes ...startin to feel like a moron 
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| Jackofknives
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Ok, this concept is kind of hard to explain without pictures, so i borrowed some pics from google search. Mate, this is how I understood it, I can’t promise that it is 100% correct.
In order to understand this concepts of positive/negative supercoiling and DNA gyrase, you need to have an understanding about the following concepts:
Bacterial DNA double helix has a circular arrangement on the contrary to eukaryote DNA, which is a more linear one. In other words, look at figure1, the one on the top is a normal bacterial DNA “at rest”. This means that bacterial DNA is fixed, it cannot readily rotate as much as in the case of short stranded open ended DNA.
Now you want to replicate, how do you do that? Among others, you need a RNA polymerase inserted in the middle of the helix and unwound it and move forward. However because the above mentioned concept, the DNA wants to relief this extra tension, but it cannot just rotate, as a result, a supercoil is created. See figure 1, bottom picture. This is energetic favourable due to some physics concept.
Figure 1
http://genuex.unex.es/Genetica/tema4/supercoil.jp...
Now as the RNA polymerase move forward, it causes an excess of helical turns to accumulate in the DNA ahead of the protein (positive supercoiling) and a deficit of helical turns to arise in the DNA behind the protein (negative supercoiling).
(NOTE: supercoiling is a verb, this is not the same as supercoil, the noun, which I’m coming to shortly.)
You see, this is a problem, the more you move forward the more supercoils you are creating, making the further movements very difficult. In order to relief the tension, DNA gyras (another name for it is topoisomerase II) actively “pumps” supercoils behind the polymerase, making the tension ahead the polymerase constant.
Positive supercoil is the natural supercoil created when RNA polymerase move along the stretch of DNA. Negative supercoil is the one created by DNA gyrus, the difference is that negative supercoil has an opposite handedness in comparison to the positive one, no more to it as far as I know.
This is just an short text to help you get into it, you need have to reread the book to get the details. I really hope u understand it better now after reading this.
Edited by Jackofknives on 05/02/07 - 03:51 AM
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| Feyza
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ok...first thanx for your time Jack  now ...I was fine with this part when I was reading replication... DNA gyrase relax the (+) sc that form during elongation so the process is not inhibited ...thats ok...Im gonna try to summarize you the page that blew my brain up :
in DNA with a right handed helix :
(-) sc wrap the helix over itself to the right...so stabilizes an underwound helix...
(+) sc wrap the helix over itself to the left ...so stabilizes an overwound helix...
underwound helix more easily binds to proteins that initiate replication so fascilitates it so DNA gyrase add (-) sc to the helix to fascilitate replication...
adding (-) sc fascilitates....relaxing (-) sc inhibits replication...so actually DNA gyrase is relaxing the (+) SC
overwound helix is less able to bind to initiator proteins so no topoisomerase add (+) sc to the helix...
TO INTRODUCE (-) SC TO OVERWOUND DNA DESTABILIZE THE HELIX BY MAKING THE OVERWINDING WORSE  starting to go mad again !
well writing this summary and reading this nice exp of your made it settle more...I guess Ill be done if I read it once more tomorrow but that bold sentence still makes me feel like to throw my laptop down the window
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| Jackofknives
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BTW isn't this biochemistry?
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| Feyza
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Kaplan biochem is 3 parts...
1 Molecular biology ... theres the DNA RNA stuff and genetic testing
2 Biochemistry ...the metabolism stuff
3 Genetics
thats why I sent the topic to this forum but yes its in my biochem book
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O my Lord! Open my chest for me ( grant me self-confidence ) and ease my task for me.Ta-Ha 25-26.
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| Jackofknives
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No more I can do mate. I really suck at cell biochem, have to reread it all in the summer.
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| mytime
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HEY FEyzA check ur pm plz.
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