How Do Mutations Happen?
Often, at some point in DNA replication or conversion into mRNA, one nucleotide can be swapped for another. When only one nucleotide is changed from its original form, it is called a substitution mutation. In the picture below, the original A nucleotide was substituted for a G nucleotide.
The Importance of Codons
During translation, codons are read by ribosomes to determine the order of amino acids in the developing protein. They decide what amino acid to place next in the chain by deciphering the codons one nucleotide at a time.
The codon chart below shows how ribosomes determine what amino acid to place next. You will notice that there are repeats of some amino acids such as leucine and arginine. There is also often more than one nucleotide combination in one box that codes for the same amino acid. This is called a redundancy. This happens when more than one code can lead to the same outcome.
What's a Silent Mutation?
This type of mutation happens when a change in the genetic code leads to the exact same amino acid being used. Due to the redundant nature of the genetic code and codon arrangement, there are many mutations that can occur on either the DNA or mRNA that will result in the same amino acid being used. This does not have any effect on the final protein's function.
For example, if we have an mRNA sequence AUG/UUC/CGA, the amino acid sequence will be Met/Phe/Arg. Now, let's say that there is a mutation that changes the mRNA sequence to AUG/UUU/CGA. The amino acid sequence would still be Met/Phe/Arg. There is no way to know the mRNA sequence was changed just by looking at the amino acid sequence, so this type of mutation is called "silent".