In addition to the principles we have already discussed, there are basic rules that govern the translation of the genetic code into a protein. There are three principle rules we will discuss:
The first rule is somewhat basic. It says that since mRNA is translated in the 5' to 3' direction, the codon sequences must occur in a similar orientation so that they will be properly translated. This simply means that the first base of a codon must be located at the 5'-most end of the codon. Codons must always be read from 5' to 3'.
The second rule means that any one nucleotide can only be a part of one codon. It cannot be a part of two different codons. Therefore, successive codons are composed of adjacent, not over-lapping, trinucleotides. For example, given the code AACT, AAC could be a codon with T starting a new codon or ACT could be a codon with the first A the last letter of a previous codon. But AAC and ACT cannot both be codons at the same time.
The final rule states that once you begin reading the code from a specific nucleotide, you continue reading it by threes until the end. The beginning of an amino acid sequence is specified by a start codon located somewhere in the mRNA sequence, this is usually an AUG, but can also be a GUG. The end of a sequence is specified by one of three stop codons: UAA, UAG, or UGA. A consequence of this rule is that the genetic code can be read in three different reading frames depending on which base one begins with. For example, the sequence: ACGACGACGACGACG can be read in the three following ways.
1.) ACG ACG ACG ACG ACG (each codon specifies the amino acid threonine)
2.) A CGA CGA CGA CGA CG (each codon specifies the amino acid arginine)