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Name: Sue
Status: Educator
Grade:  9-12
Location: NJ
Country: United States
Date: February 2006

What does the 3' and 5' side of a gene mean?

3' and 5' refer to the number 3 and 5 carbon atoms of the sugar molecule deoxyribose. The first nucleotide in a strand of DNA has a 5' carbon atom that is not bonded to another nucleotide; it is therefore said to be free, thus the term free 5' end. The last nucleotide in a strand of DNA has a 3' carbon atom that is not attached to another nucleotide, thus the term free 3' end. When you look at a double-stranded DNA molecule that is in the vertical position, if the strand on the left has a free 5' nucleotide at the bottom, the strand on the right will have a free 3' at the bottom. The two strand are said to be anti-parallel, i.e. parallel but running in opposite direction 5' > 3' directions. DNA and mRNA is synthesized in the 5' > 3' direction so that means the template strands of DNA are read from the 3' to 5' during replication and transcription. So there is 5' and 3' *side* of DNA but rather 5' and 3' ends.

Ron Baker, Ph.D.

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