What's 5' end and 3' end of mRNA? What are they used for?
An RNA nucleotide has as part of its structure the sugar ribose. It is a
pentose sugar, ie. it forms a five sided ring structure. 4 of the 5 points
on the ring are carbon atoms. The fifth carbon atom is attached to the left
point of the ring. The carbons are numbered starting with the right point.
RNA also has a phosphate group in its structure. The phosphate is attached
to the 5' carbon (the one attached to the left point). There is also a
nitrogen base in the structure of an RNA nucleotide. There are 4 kinds of
nitrogen bases in RNA: adenine, guanine, ctyosine and uracil. The nitrogen
base is attached to the number 1 carbon (the right point of the sugar). This
leaves the 2' and 3' carbons free. When the enzyme RNA polymerase is
stringing RNA nucleotides together to make mRNA, it looks for a free 3' end
to add them to. Think of RNA nucleotides as puzzle pieces. Think of the 5'
end of a nucleotide as the part of the puzzle piece that has the "plug" or
the protruding part that will fit into the next piece. Think of the 3' end
as the part that has the notch that the other piece will fit into. The RNA
polymerase enzyme can only join a 5' plug end into an available 3' notch end
of the previous nucleotide. You can fit a 5' end to a 5' end or a 3' end to
a 3' end.
The naming identifies the ends of the DNA molecule and the orientation of
the opposite strands (DNA is typically double stranded in mammals). DNA is
mad up of a series of nucleotides. The nucleotide (a nucleotide is made of 5
carbon sugar called ribose a phosphate and one of 4 different bases with
abbreviations A, T, C, and G) at the beginnig of the DNA molecule has a
phosphate group on the 5th carbon of its sugar therefor the 5' end. The
other end has the free hydroxyl group on the 3rd carbon of the ribose sugar
thereffor the 3' end. This is noteworthy because when DNA is growing new
nucleotides are added only to the 3' (pronounced three prime) end so a new
strand of DNA is created in a 5' to 3' direction.
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Update: June 2012