Secondary Messenger RNA Structure
Silent mutations change the secondary structure of RNA. Since RNA has a secondary structure that is not necessarily linear like that of DNA, the shape that goes along with the complementary bonding in the structure can have significant effects. For example, if the RNA molecule is not very stable, then it can be broken down quickly by enzymes in the cytoplasm. Alternatively, if the RNA molecule is too stable, and the complementary bonds are too strong for unpacking before translation, then the gene can also be under expressed.
Also, if the oncoming ribosome pauses because of a knot in the RNA, then the polypeptide can have time to fold into an unusual structure before the tRNA molecule has time to add another amino acid.
Read more about this topic: Silent Mutation
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