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Name: Alejandro
Status: Other
Grade:  Other
Location: N/A
Country: United States
Date: May 2007


Question:
I understand than when a dna-polymerase is making a copy of a dna strand, it attaches nucleosides that are present in it´s surroundings, but how does the enzyme "picks" or "catches" the nucleosides in order to attach them to the template strand if they are somehow "floating around" randomly?



Replies:
First, the nucleotides are nearby. They are floating around, and thanks to the natural vibrations of molecules (Brownian motion), they move back and forth and bump into the polymerase continuously. The way nucleotides attach has to do with the shape of the DNA polymerase and the shape of the nucleotide (here, they're nucleoTides, not nucleoSides).

As you may know, enzymes (DNA polymerase being one kind of enzyme) have very specific, special shapes to allow their target molecules to attach, or 'bind', to them. Not only the shape, but also the chemistry of the enzyme -- sometimes people use a lock-and-key analogy, but that's not the whole story; it's more like a lock that changes shape to fit the key, and rejects keys that aren't make of the right metal. DNA polymerase is shaped to attach to a strand of DNA and to have nucleotides attach as well. The exact mechanism of what-binds-to-what-and-when is a subject of current research, but it involves magnesium ions and several intermediate steps.

Generally speaking, though, the reason things bind is because they have lower energy. Things are 'happier' the lower energy they have, so they're always looking to reduce their energy. A free nucleotide floating in a cell has more energy than one bound in DNA polymerase (because the DNA polymerase is shaped just right).

When the DNA polymerase attempts to attach the next nucleotide to the DNA strand, if it is not the right nucleotide, it will have very high energy, and will resist binding (it will be 'unhappy'). The right nucleotide with fit just right (low energy = happy), and will bind more easily. Mistakes can occur occasionally. Some DNA polymerases can even go back and fix mistakes.

There's a lot more to this story than I shared (and I may be guilty of oversimplifying) -- you didn't list your grade level so I tried to give a medium amount of detail. If you still have a specific question, please ask.

Hope this helps,
Burr


Nucleotides are colliding with other molecules on the order of 1 million collisiRon Bakeons per second. When they collide with a complementary nucleotide in the template strand, they are held there long enough for the DNA polymerase to bond it to the previous nucleotide in the growing DNA strand. The nucleotide is held in position before incorporation by the specific Hydrogen bonding between the complementary base pairs (2 Hydrogen bonds between an AT base pair and 3 between a GC base pair). Less than 2 Hydrogen bonds are formed between either a GT base pair or a AC base pair.

Ron Baker, Ph.D.



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