Country: United States
Date: February 2005
Go to google.com and set it to images. Google an image of a DNA nucleotide.
You will see that the sugar, deoxyribose, has 5 carbons in its structure.
The "3 o'clock" point, is carbon #1. Carbon #2 and #3 are on the bottom,
carbon #4 is on the "9 o'clock" point, and the #5 carbon is attached off the
ring. These are also referred to as 1-5 Prime ( ie. 5' ) carbons. A phosphate
group is attached to the 5' carbon in the nucleotide.
The phosphate group of the second nucleotide in a growing chain of DNA
attaches to the 3' carbon of the first nucleotide. Then the phosphate of the
third nucleotide attaches to the 3' end of the second nucleotide and so on.
If you look at the 3' carbon on a nucleotide, you will notice that there is
an -OH attached there. The enzyme DNA polymerase can only add a new
nucleotide to the 3' end of a nucleotide. Remember that enzymes have a lock and key
fit with their substrates. The nucleotide is the substrate and the DNA
polymerase needs to be able to fit with the -OH group for the chemical reaction to
take place. So if you look at a new strand of DNA, the "top" end has a
phosphate (5' ) and the "bottom" has OH (3' )
Because enzymes that replicate or repair DNA can only move along the template
strand of DNA in the 3' to 5' direction. Remember the two complementary
strands have opposite polarity. If you are asking why a strand of DNA has
a 5' and a 3' end, it is because the deoxyribose molecule that is attached
to every nitrogen base is asymmetric and therefore cannot be the same at
both ends of a DNA strand.
Regards, Ron Baker, Ph.D.
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Update: June 2012