Biology 335 - Molecular Genetics

DNA Structure

 
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These basic building blocks, phosphate, sugar and N-base,
are linked together at specific positions to form the substrates used by the cell in polymerizing nucleic acids
(as well as serving other functions).

First, hooking the N-base onto the 1' position of the sugar results in the nucleoside.

Then, the 5' position of the sugar is mono-, di- or tri-phosphorylated to generate the nucleotides.

 
 

Figure 6a: Structure of Nucleosides

 
 

Figure 6b: Structure of Nucleotides
(the alpha-, beta- and gamma- phospates are indicated on GTP)

 
Note: when ordering reagents from a catalog it will be important to be able to identify the exact compound you want - it does little good to try and incorporate 32P into DNA by random primed synthesis if the 32P label is in the gamma-position. It is important to read the catalogs carefully if you are ordering compounds for specific purposes.

The polymerization of nucleotide triphosphates into RNA or DNA is an enzymatic prcess catalysed by various RNA or DNA polymerases. In each case, the polymerization proceeds in a 5' to 3' direction.

The a-phosphate forms a 5'-3' phosphodiester linkage between the adjacent sugars
while the beta and gamma phosphates (pyrophosphate) are hydrolysed to provide
the energy source driving the polymerization reaction.

 
 

Figure 7: Polymerization of Nucleic Acids

 
Notice that nucleic acid polymers have an inherent directionality (5' to 3').

This can lead to confusion when writing out sequence.
By convention, when writing sequence always write 5' to 3', left to right.
Several conventional styles are shown below.

 
 

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