The Stream of Nucleic Acids

An important thing to keep in mind is that we are studying how the sequence of bases in nucleic acid is translated into a sequence of amino acids in a protein, or polypeptide. Since both of these molecule classes are polymers and they have a polarity, when we talk about the sequence we need to know which direction we are reading.

Although DNA is a double stranded molecule, one strand is sufficient to code the information for translation of an amino acid sequence. As we will see, the sequence of bases is always read in the 5' to 3' direction along the coding strand. Therefore, you will usually see nucleic acid sequence given in this direction - and if the direction is not indicated then you can assume that it is 5' to 3'.

Proteins are synthesized from the Amino (NH2) terminus to the Carboxyl (COOH) terminus as the cell reads the base sequence 5' to 3' so you always see amino acid sequences given in this direction.

Two terms to know since they are related to the information "flow":

Upstream: in a DNA molecule this refers to the 3' to 5' direction, that is, against the flow of information along a specified strand (almost always the coding strand of a gene). If you refer to a specific nucleotide, everything in the 5' direction is upstream from that nucleotide.

Downstream: in a DNA molecule this refers to the 5' to 3' direction, that is, with the flow of information along a specified strand (almost always the coding strand of a gene). If you refer to a specific nucleotide, everything in the 3' direction is downstream from that nucleotide.