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Base pairs hold the actual information in DNA and RNA -- somewhat analogous to pits on a CD, or the magnetic coating on a hard disk. Each DNA nucleotide is made up of a sugar molecule, (S, below) a molecule of phosphoric acid (P), and another molecule (technically either a purine or pyrimidine) called the base. DNA bases are Adenine, Guanine, Thymine, or Cytosine; in RNA uracil replaces thymine. Each base pairs up with its opposite in a DNA molecule, guanine with cytosine, adenine with thymine, to form base pairs. Guanine-cytosine base pairs have two hydrogen bonds, while adenine-thymine pairs have three -- an excellent picture of this is available in jafuser's writeup under DNA.

Here is what each base pair would look like on a flattened strand of DNA:

    base pair                   
      _|_                       
P    /   \    P                 
 -           /                  
  S--A   T--S                   
 /           -                  
P             P                 
 -           /                  
  S--G   C--S                   
 /           -                  
P             P                 
 -           /                  
  S--T   A--S                   
 /           -                  
P             P                 
 -           /    _             
  S--C   G--S      \            
 /           -      } nucleotide
P             P   _/            

Insertion of the wrong base in a piece of DNA while it is being replicated is a mutation referred to as a base pair substitution. In most cases this causes there to be an incorrect amino acid to be inserted into the protein coded for by the effected gene, which may or may not hinder the function of the protein. Every once in a while, a base pair substitution will change the effected codon from coding for an amino acid to being a stop codon. When this happens, the protein that would've been made by the gene is only partially complete, and is most likely useless.

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