Adrienne is a certified copyeditor but is more known for pulling together multifaceted projects created by teams in a form that suits both the learner and the learning environment. Learning about a wild array of subjects is part of the invigorating challenge that she loves about this work. Her title credits range from aircraft build specs to sea-kayaking guides, and from geophysics to Aboriginal knowledge. But the focus on maths and sciences is how she earned the moniker SciEditor.
She also developed a self-study program for editing with word. I would say that editors have dozens OK, maybe 1 dozen different words for types of edits. I think every editor has to come to grips with a taxonomy of edits and how to handle the various kinds, whether they be silent, invisible, substantive, etc. Maybe we can get a list going of all the categories of edits! Thanks for a thoughtful post, Adrienne! To me such a page does look cluttered, but I guess it gives the author a feeling of being in complete control of the text. And fair enough, as they sign it with their name.
Comments Adrienne, great article!
Silent mutations are base substitutions that result in no change of the amino acid or amino acid functionality when the altered messenger RNA mRNA is translated. For example, if the codon AAA is altered to become AAG, the same amino acid — lysine — will be incorporated into the peptide chain. This usually occurs because they come in "triplets" so a single nucleotide change will have no effect on the protein being produced. Mutations are often linked to diseases or negative impacts but silent mutations can be extremely beneficial in creating genetic diversity among species in a population.
Germ-line mutations are passed from the parent to the offspring.
Because silent mutations do not alter protein function they are often treated as though they are evolutionarily neutral. Many organisms are known to exhibit codon usage biases , suggesting that there is selection for the use of particular codons due to the need for translational stability. Transfer RNA tRNA availability is one of the reasons that silent mutations might not be as silent as conventionally believed.
There is a different tRNA molecule for each codon. If amino acid transport to the ribosome is delayed, translation will be carried out at a much slower rate. This can result in lower expression of a particular gene containing that silent mutation if the mutation occurs within an exon.
Silent changes – Eleanor Abraham • Editorial
Additionally, if the ribosome has to wait too long to receive the amino acid, the ribosome could terminate translation prematurely. A nonsynonymous mutation that occurs at the genomic or transcriptional levels is one that results in an alteration to the amino acid sequence in the protein product. A protein's primary structure refers to its amino acid sequence.
A substitution of one amino acid for another can impair protein function and tertiary structure, however its effects may be minimal or tolerated depending on how closely the properties of the amino acids involved in the swap correlate. Protein function and folding is dependent on the position in which the stop codon was inserted and the amount and composition of the sequence lost.
Conversely, silent mutations are mutations in which the amino acid sequence is not altered. This is permitted by the degeneracy of the genetic code.
Silent Changes: When and Why to Make Them
Historically, silent mutations were thought to be of little to no significance. However, recent research suggests that such alterations to the triplet code do effect protein translation efficiency and protein folding and function. Furthermore, a change in primary structure is critical because the fully folded tertiary structure of a protein is dependent upon the primary structure.
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The discovery was made throughout a series of experiments in the s that discovered that reduced and denatured RNase in its unfolded form could refold into the native tertiary form. The tertiary structure of a protein is a fully folded polypeptide chain with all hydrophobic R-groups folded into the interior of the protein to maximize entropy with interactions between secondary structures such as beta sheets and alpha helixes.
Since the structure of proteins determines its function, it is critical that a protein be folded correctly into its tertiary form so that the protein will function properly. However, it is important to note that polypeptide chains may differ vastly in primary structure, but be very similar in tertiary structure and protein function.
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. 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.
For example, if the mRNA molecule is relatively unstable, then it can be rapidly degraded by enzymes in the cytoplasm.
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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. 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. 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. 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 , or transcriptional control. Silent mutations affect protein folding and function. RNA typically produces two common misfolded proteins by tending to fold together and become stuck in different conformations and it has a difficulty singling in on the favored specific tertiary structure because of other competing structures. RNA-binding proteins can assist RNA folding problems, however, when a silent mutation occurs in the mRNA chain, these chaperones do not bind properly to the molecule and are unable to redirect the mRNA into the correct fold.
Recent research suggests that silent mutations can have an effect on subsequent protein structure and activity. Silent mutations have been employed as an experimental strategy and can have clinical implications. Steffen Mueller at the Stony Brook University designed a live vaccine for polio in which the virus was engineered to have synonymous codons replace naturally occurring ones in the genome. As a result, the virus was still able to infect and reproduce, albeit more slowly.
Mice that were vaccinated with this vaccine and exhibited resistance against the natural polio strain. In molecular cloning experiments, it can be useful to introduce silent mutations into a gene of interest in order to create or remove recognition sites for restriction enzymes. Mental disorders can be caused by silent mutations.
One silent mutation causes the dopamine receptor D2 gene to be less stable and degrade faster, underexpressing the gene. A silent mutation in the multidrug resistance gene 1 MDR1 , which codes for a cellular membrane pump that expels drugs from the cell, can slow down translation in a specific location to allow the peptide chain to bend into an unusual conformation.
Thus, the mutant pump is less functional. These two mutations are both shared by the low pain sensitivity and high pain sensitivity gene. Low pain sensitivity has an additional CTC to CTG silent mutation, while high pain sensitivity does not and shares the CTC sequence at this location with average pain sensitivity. MDR1 codes for the P-glycoprotein which helps get rid of drugs in the body.