Silent mutation

The genetic code translates mRNA nucleotide sequences to amino acid sequences. Genetic information is coded using this process with groups of three nucleotides along the mRNA which are commonly known as codons. Most amino acids are specified by multiple codons demonstrating that the genetic code is degenerate–different codons result in the same amino acid. Scientists have predicted that people have approximately 5 to 10 deadly mutations in their genomes but this is essentially harmless because there is usually only one copy of a particular bad gene so diseases are unlikely. 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. For example, there is a specific tRNA molecule for the codon UCU and another specific for the codon UCC, both of which code for the amino acid serine. In this instance, if there was a thousand times less UCC tRNA than UCU tRNA, then the incorporation of serine into a polypeptide chain would happen a thousand times more slowly when a mutation causes the codon to change from UCU to UCC. 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. Additionally, if the ribosome has to wait too long to receive the amino acid, the ribosome could terminate translation prematurely. ==Structural consequences==

Primary structure 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. The premature insertion of a stop codon, a nonsense mutation, can alter the primary structure of a protein. In this case, a truncated protein is produced. 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. Furthermore, a change in primary structure is critical because the fully folded tertiary structure of a protein is dependent upon the primary structure.  The discovery was made throughout a series of experiments in the 1960s 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. 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.  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.  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. 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. 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. Tertiary structure Silent mutations affect protein folding and function. Recent research suggests that silent mutations can have an effect on subsequent protein structure and activity. The timing and rate of protein folding can be altered, which can lead to functional impairments. ==Research and clinical applications==

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. Deviations from average pain sensitivity are caused by both an ATG to GTG mutation (nonsynonymous), and a CAT to CAC mutation (synonymous). 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. Multi-Drug Resistance Gene 1 Around 99.8% of genes that undergo mutations are deemed silent because the nucleotide change does not change the amino acid being translated. Although silent mutations are not supposed to have an effect on the phenotypic outcome, some mutations prove otherwise like the Multi-Drug Resistance Gene 1. MDR1 codes for the P-glycoprotein which helps get rid of drugs in the body. It is located in the intestines, liver, pancreas, and brain. MDR 1 is located in the same places that CYP3A4 is located in, which is an enzyme that helps get rid of toxins or drugs from the liver and intestines. Silent mutations like MDR 1 do express a change in phenotypic response. A study done on mice showed when they did not have enough of the MDR 1 gene, their body did not recognize the ivermectin or cyclosporine drug, leading to the creation of toxins in their bodies. The multi-drug resistance genes at Exon 26 C3435T, exon 21 G2677T/A, and exon 12 C1236T have been studied to have SNP's that occur at the same time, therefore making the phenotypic "function "change. This suggests a haplotype dependency between exon 26 and other exon that have polymorphisms. For example, efavirenz and nelfinavir are two types of drugs that help decrease the HIV infection in a person's body. When the SNP from exon 26 is coupled with other SNP exons, the drugs have a lower chance of maintaining the HIV infection. Although, when the TT nucleotides in exon 26 are expressed the patient has a lower concentration of the virus but when the genotype morphs into CC or CT the infection is able to spread like normal leaving the MDR 1 gene almost defenseless. These changes in bases of exon 26 for MDR 1 show a correlation between the MDR 1 gene mutations and the ability of the antiretroviral drugs to suppress the HIV infection. Verapamil and cyclosporine A are common inhibitors for MDR 1. Other reasons behind MDR1's "silent mutation" occurs in messenger RNA. In mRNA, codons also work as exon splicing enhancers. Codons decide when to cut out introns based on the codon it is reading in mRNA. The mutated codons have a higher risk of making a mistake when splicing introns out of the mRNA sequence leading to the wrong exons being produced. Therefore, making a change to the mature messenger RNA. Mutations in the Multi-Drug Resistance Gene 1 show how silent mutations can have an effect on the outcome of the phenotype. == See also ==