MadSci Network: Biochemistry
Query:

Re: Activation energy for DNA replication

Date: Sat May 3 12:38:42 2008
Posted By: Peter E. Hughes, Ph. D. Biochemistry, Faculty, Biochemistry, University System of New Hampshire
Area of science: Biochemistry
ID: 1205635182.Bc
Message:

Hi Sai,

This question inherently contains a very high level of complexity. I am sorry to say that a simple answer will not address all of the mechanisms of DNA stability. However, thanks to proteins, we may speak about stability of DNA.

Please notice we refer to DNA stability. In the demonstration that follows, please, please release the rubber band from your fingers if any sensation is discomforting.

Think of DNA and consider a rubber band. Take the rubber and rotate it many, many times between the fingers of one hand. It is coiled, like DNA. Now further rotate it so that the turns begin to knot up and form knots of bands, think of that as super-coiling. Super coiling of DNA may be thought of as chromosomes, although these are also associated with histones, a protein. Now, while the blood begins to be cut off in your fingers by the strength of the rubber band you will experience the incredible strength of DNA coiling and super-coiling. This stabilizing energy is huge.

Now please consider enzymes (your other hand) that are capable of unwrapping the supercoiled DNA. So use your hand to unwrap the rubber (DNA model) and you will very soon notice you need more than one finger (DNA enzymes) to do so.

When we speak about energy, how much energy did you just use in this simple demonstration? Muscles, two hands and a brain… one heck of a lot of energy! That is also true for the mechanistics of DNA. In terms of energy, we are incredibly expensive.

There are many such DNA enzymes and proteins that wrap and unwrap DNA in a very precise, quite stable fashion. When these proteins bind to DNA, they will effect a local (9 base) instability. However, that is carefully monitored by other enzymes and they correct the instability. What we know is that the instability is very fleeting.

Sai, we are really lucky that DNA is so stable.

I hope this helps! Thank you very much for your question!
Peter

• Watson, James D. The Double Helix: A Personal Account of the Discovery of the Structure of DNA (Norton Critical Editions). ISBN 0393950751
• Chomet, S. (Ed.), DNA Genesis of a Discovery, Newman-Hemisphere Press, London, 1994.
• Delmonte, C.S. and Mann, L.R.B. Variety in DNA secondary structure. Current Science, 85 (11), 1564–1570, 10 December 2003.

[Moderator's Note: Just to add a point to Peter's description of supercoiling, a DNA molecule can be positively or negatively supercoiled, essentially by twisting it one way or the other. Due to the symmetry of the DNA molecule, positive supercoils make it more difficult to pull apart the two strands, while negative supercoils make it easier for proteins to pull the strands apart, so areas of DNA that are "active" are negatively supercoiled, while "inactive" areas are positively supercoiled. -- Steve Mack]


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