Which factor most affects the order of amino acids in a protein?

The correct answer is the arrangement of codon sequences on the DNA in the nucleus. Genes are composed of codon sequences, which are the three nucleotide sequences that code for an amino acid. These codons code for specific amino acids, therefore during the translation process in the ribosomes they determine the amino acid sequence in a a particular polypeptide as read by the anticodons in the transfer RNA.

The DNA in the nucleus of the cell affects the order of amino acids in a growing polypeptide chain. The DNA contains the genetic material wherein it is transcribe to messenger RNA so that the genetic code can be transported outside the nucleus to be translated. The order of nucleotides in the mRNA in triads called codons indicates the order of amino acids being translated as codons correspond to specific amino acids.