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Catching Nucleotide
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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Update: June 2012
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