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Name: Alfonso
Status: Other
Grade:  N/A
Location: AS
Country: United States
Date: February 2005

Go to 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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