Editing Silent mutation (section)

=== Secondary structure ===
{{main|Biomolecular structure#Secondary structure}}
Silent mutations alter the [[secondary structure]] of [[mRNA]].

Secondary structure of proteins consists of interactions between the atoms of the backbone of a polypeptide chain, excluding the R-groups.&nbsp; One common type of secondary structures is the alpha helix, which is a right-handed helix that results from hydrogen bonds between the ''nth'' amino acid residue and the ''n+4th'' amino acid residue.&nbsp; The other common type of secondary structure is the beta sheet, which displays a right-handed twist, can be parallel or anti-parallel depending on the direction of the direction of the bonded polypeptides, and consists of hydrogen bonds between the carbonyl and amino groups of the backbone of two polypeptide chains.<ref>{{Cite web|url=https://www.khanacademy.org/science/biology/macromolecules/proteins-and-amino-acids/a/orders-of-protein-structure|title=Orders of protein structure|website=Khan Academy|language=en|access-date=2018-11-08}}</ref>

[[mRNA]] has a secondary structure that is not necessarily linear like that of DNA, thus the shape that accompanies complementary bonding in the structure can have significant effects. For example, if the mRNA molecule is relatively unstable, then it can be rapidly degraded by enzymes in the [[cytoplasm]]. If the RNA molecule is highly stable, and the complementary bonds are strong and resistant to unpacking prior to translation, then the gene may be under expressed.  Codon usage influences mRNA stability.<ref name="pmid21567958" />

Furthermore, since all organisms contain a slightly different genetic code, their mRNA structures differ slightly as well, however, multiple studies have been conducted that show that all properly folded mRNA structures are dependent on the primary sequence of the polypeptide chain and that the structure is maintained by dinucleotide relative abundances in the cell matrix.&nbsp; It has also been discovered that mRNA secondary structure is important for cell processes such as transcript stability and translation. The general idea is that the functional domains of mRNA fold upon each other, while the start and stop codon regions generally are more relaxed, which could aid in the signaling of initiation and termination in translation.<ref>{{cite journal | vauthors = Shabalina SA, Ogurtsov AY, Spiridonov NA | title = A periodic pattern of mRNA secondary structure created by the genetic code | journal = Nucleic Acids Research | volume = 34 | issue = 8 | pages = 2428–37 | date = 2006 | pmid = 16682450 | pmc = 1458515 | doi = 10.1093/nar/gkl287 }}</ref>

If the oncoming ribosome pauses because of a knot in the RNA, then the polypeptide could potentially have enough time to fold into a non-native structure before the [[tRNA]] molecule can add another [[amino acid]].  Silent mutations may also affect [[splicing (genetics)|splicing]], or [[Transcription (genetics)|transcriptional control]].