Question

BIOCHEMICAL CONNECTION What is a silent mutation? Why is the name "silent mutation" a bit of a misnomer?

Short answer

A silent mutation changes the DNA sequence without altering the protein sequence. However, it can still affect other biological processes, so the term 'silent' is somewhat misleading.

Step-by-step solution

Define a Silent Mutation

A silent mutation is a change in the nucleotide sequence of DNA that does not alter the amino acid sequence of the protein produced. This occurs due to the redundancy in the genetic code where multiple codons can code for the same amino acid.

Explain the Genetic Code Redundancy

The genetic code is composed of codons, which are sequences of three nucleotides that correspond to specific amino acids. Because there are 64 different codons but only 20 amino acids, several codons code for the same amino acid. For example, both UUU and UUC code for the amino acid phenylalanine.

Illustrate with an Example

Consider a mutation where the codon UUU (phenylalanine) changes to UUC (phenylalanine). Although there's a change in the nucleotide sequence, the resulting amino acid remains phenylalanine, hence the mutation is 'silent'.

Address the Misnomer

The term 'silent mutation' might be misleading because, although it does not change the protein sequence, it can still have other biological effects. These include influencing mRNA stability, altering splicing, and affecting the efficiency of translation.

Key concepts

Genetic Code Redundancy

Genetic code redundancy is a fascinating concept that explains why some changes in DNA do not always affect the resulting protein. The genetic code is made up of codons, which are sequences of three nucleotides. Each codon corresponds to a specific amino acid. But here's the interesting part: We have 64 different codons, but only 20 amino acids. This means multiple codons can code for the same amino acid.

For example, the codons UUU and UUC both code for the amino acid phenylalanine. Due to this redundancy, a change in the DNA from UUU to UUC won't change the protein that gets produced. This forms the basis for what we call silent mutations. It's like having multiple spellings for the same word; regardless of the spelling, the meaning stays the same.

This redundancy is nature's backup plan. It provides a buffer against mutations that might otherwise be harmful. Because of this, some genetic mutations do not cause a change in the protein and are termed 'silent'.

Codons

Codons are essential building blocks in our genetic code. Each codon is a sequence of three nucleotides, and together, they form the instructions for making proteins. Think of codons like words in a sentence; each 'word' instructs the cell machinery which amino acid to add next in the chain that forms a protein.

There are 64 possible combinations of these three-nucleotide sequences (from A, U, C, G in mRNA). Despite the large number of combinations, we have only 20 amino acids. Therefore, many codons code for the same amino acid, showcasing the redundancy in the genetic code.

For example:

• AUG - Methionine (also a start codon)
• UUU and UUC - Phenylalanine
• GAA and GAG - Glutamic Acid

This setup ensures that even if a mutation changes one codon to another that codes for the same amino acid, the resulting protein remains unaffected. Thus, this is the mechanism behind silent mutations.

Amino Acid Sequence

The amino acid sequence is the final output of the genetic code and determines the structure and function of proteins. Proteins are made up of long chains of amino acids, and the specific order of these amino acids is crucial. The sequence dictates how the protein folds, what shape it takes, and how it functions.

Let's look at how this works. Imagine the DNA as a cookbook and genes as recipes. The sequence of codons in a gene is the recipe's instructions, telling the cell's machinery which amino acids to string together to create a specific protein.

A change in the DNA sequence (mutation) can alter the amino acid sequence, potentially changing the protein's function. However, because of genetic code redundancy, some mutations - the silent ones - do not change the amino acid sequence. For example, changing the codon UUU to UUC will still incorporate phenylalanine into the protein. The protein remains the same because the amino acid sequence has not changed.

In conclusion, while silent mutations do not alter the amino acid sequence and therefore do not change the protein's function, they can still influence other aspects of gene expression and protein production.