Final answer:
The existence of silent mutations due to the degeneracy of the genetic code explains why sequence differences in DNA may not lead to differences in protein sequences, as multiple codons can encode the same amino acid.
Step-by-step explanation:
The reason why there are multiple sequence differences in the coding segment DNA level but no observed differences in the protein sequence is likely due to the degeneracy of the genetic code. This means that multiple codons can code for the same amino acid. Thus, even though the DNA sequences of the two genes are different, the changes do not alter the amino acids encoded because the mutations fall at codons that result in the same amino acid — these are known as silent mutations.
Furthermore, considering the central dogma of molecular biology, the process of translation at the ribosome entails the reading of the mRNA sequence and the addition of the correct amino acids to form a polypeptide chain. If the silent mutations do not cause a change in the amino acids, the function and structure of the resulting protein will remain unchanged.