Silent Mutation

Silent Mutation Definition

Silent mutations occur when nucleotide bases in DNA are changed without affecting amino acids or overall protein function. A single amino acid can change, but if it has the same properties as the amino acid it replaces, little to no change will occur. There are many ways in which a silent mutation can occur, but the main thing is that it doesn’t change the function of the amino acid or subsequent protein. Silent mutations are those that do nothing significant, not making a sound in the orchestra of the cell.

Silent Mutation Examples

The Redundant Genome

Codons, which are made up of three nucleotides, are used to read DNA. A codon specifies an amino acid, with a few reserved as stop and start signals. There are times when different codons specify the same amino acid. Genetic code flexibility is enabled by this redundancy. It is for this reason that a silent mutation is usually completely unnoticed by society. 

There is a comparison between a silent mutation and both a nonsense mutation as well as a missense mutation in this case study. A silent mutation occurs when a thymine is changed to a cytosine at the DNA level, which is an actual change at the level of the DNA. 

The mutation that caused this could have been caused either by an error in the DNA replication process, or by some sort of repair that took place after the DNA had been damaged in some way. No matter what, both of these three nucleotide codons tell the ribosome and the machinery within it to go ahead and attach a lysine amino acid to the molecule.

As a result, even though there has been a silent mutation, the entire structure of the protein will remain the same, regardless of what the mutation is. As long as the amino acid structure of the protein remains the same, the protein will not behave differently from one environment to another, except if it is placed in a different environment. The function of a protein can also be altered by a silent mutation, which occurs at the protein level but does not affect its functionality.

Amino Acid Groups

The 4 nucleotides, in groups of three codons, can call for all 21 amino acids. Seen below, the amino acids are grouped by their structure and side chains. These features directly impact how they interact with other amino acids, and what effects they have on molecules in the environment.

A silent mutation, which could easily include more than one nucleotide, could easily change an entire amino acid, or even series of amino acids. If a serine changed into a threonine, the effect might be minimal. The two amino acids are in the same category and are very similar shapes. This means that they will have a similar chemical reaction on the molecules around them. This will influence the shape and effect of the total protein. If the effect is negligible, the change is considered a silent mutation.

Place within Protein Structure

Several amino acids can be key to the entire structure or functionality of a protein. Many proteins have an active site, to which other molecules must bind. This site is constructed from a specific sequence of amino acids. When folded just right, certain amino acids and their side chains will have the exclusive ability to interact with another molecule. If these amino acids are changed by a mutation, the functionality of bonding may be seriously impaired. This can change the function or utility of a protein.

Other proteins, on the inside of the molecule, have complex structures which must be present to preform specific functions. Many proteins undergo a conformational change, which is a change in shape. This is driven by electrical stimulation or the binding of a molecule like a coenzyme or a substrate to the protein. The conformational change, literally changing the shape of the protein, can press molecules together or tear them apart. 

The energy supplied is dependent upon the internal structure and specific bonds within the protein. Sometimes, a single amino acid can be a key piece of this. If this amino acid is changed for a non-functional one, the mutation is not a silent mutation. The change on the inside of the protein can also affect the functionality of the protein. Regardless of what a silent mutation changes, it should not change the functionality of the resulting protein.

Within Non-coding DNA

Many portions of the DNA are used structurally, and their full purpose is not understood. There are many cases in which parts of the DNA are vastly different between individuals, yet their phenotypes seem the same. These changes, especially small structural changes in the DNA, do not become significant until they begin to change the interaction of the coding DNA with the environment. A silent mutation could easily happen in these areas without notice, yet over time many mutations may begin to change a population.

Bacteria, interestingly, usually have a single circle of DNA, which carries all the information they need. By contrast, the human genome is separated on multiple chromosomes, which are bundled and managed by specialized proteins so they can be wound up during cell division. One hypothesis as to how this much more complex DNA came about was that certain silent mutations began forming structures of DNA. 

In a more compact genome, more information can be stored, which may have led to the complexity of life from single celled organisms to more complex forms. The folding and protection of various parts of DNA is part of normal cell differentiation in eukaryotes. Supposedly, these could have arisen through silent mutation until they became useful and were selected for.


What is a silent mutation?

A silent mutation is a type of genetic mutation that occurs when a change in the DNA sequence does not result in a change in the amino acid sequence of the protein that the DNA codes for. This is because the genetic code is degenerate, meaning that some amino acids can be coded for by more than one codon.

How does a silent mutation differ from other types of mutations?

Unlike other types of mutations, such as missense mutations that change the amino acid sequence of a protein, silent mutations do not affect the function of the protein. This is because the same amino acid is still produced, even if the DNA sequence has changed.

Can silent mutations be harmful?

Although silent mutations do not directly affect protein function, they can still have an impact on gene expression and regulation. In rare cases, a silent mutation may disrupt splicing or regulatory elements and lead to disease.

How are silent mutations detected?

Silent mutations can be detected through genetic testing and sequencing. Since they do not produce a change in the protein, they can be difficult to detect and may require specific analysis of the DNA sequence.

Are silent mutations common?

Silent mutations are relatively common, as the genetic code is degenerate and multiple codons can code for the same amino acid. They are estimated to occur in about one-third of all mutations in protein-coding genes. However, the frequency of silent mutations can vary depending on the organism and the specific gene being analyzed.

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