Do DNA codon and their complementary codon represent the same amino acids? If not, how do transcriptional proteins know which DNA strand actually codes for the correct amino acid and, ultimately, the correct protein?
Complementary DNA codons on a separated double helix do not encode for the same amino acids (and therefore the same proteins). For example, GGG encodes for glycine while the complementary codon CCC encodes for proline. So depending on which DNA strand is read and converted into a complementary RNA strand will determine exactly which protein is made. So how does the cell know which DNA strand to read when making a protein during the transcription phase? During the initiation phase, various proteins called transcription factors come together to allow RNA polymerase to bind to the DNA to start making the RNA strand. There are certain promoter sequences in the DNA that signal the cell to start the initiation phase. The most common initiator in eukaryotes is called a TATA box. It starts the whole process of the unwinding of the DNA and the transcription process. To my knowledge the complementary sequence ATAT does not carry any special meaning in terms of protein synthesis. This is how the two spearated strands are differentiated (by the presence of the TATA promoter sequence).