Tuesday, March 24, 2009

Mutations

Describe the difference between synonymous and nonsynonymous mutations. Mathematically, which type of mutation is more common? In nature, which type of mutation do we see more often, and why is this so?
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2 comments:

  1. LockeMarch 31, 2009 at 11:36 AM

    Synonymous mutations are changes in a nucleotide base in DNA that does not necessarily change the sequence of the encoded protein. These changes "do not alter the 'meaning' of a triplet are called synonymous changes because the original and mutant triplet are synonyms that encode the same amino acid," (Carroll 80).

    Nonsynonymous mutations are changes in a nucleotide base in DNA that changes the meaning of a triplet - it causes "one amino acid in the protein to be replaced with another," (Carroll 80).

    In nature, the ratio that is found is approximately 1:3 in favor of synonymous changes (nonsynonymous:synonymous). According to Sean Carroll, "This ratio is ten-fold lower than what we expect from random base mutations," (80). This ratio is seen because natural selection acts upon each organism's DNA. It is a "purifying selection" which retains the "purity" of the genetic code, "...maintains the 'purity' of the amino acid sequences of proteins by ridding them of changes that would compromise their function," (Carroll 81). Natural selection is the driving force in "maintaining the purity" of heritable information (biological theme) in order to make the fittest survive and reproduce.

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  2. Jia GuoApril 5, 2009 at 4:49 AM

    The redundancy of the genetic code and the wobble effect make it possible for a synonymous mutation to occur in the genetic code. Synonymous mutation, “a change in nucleotide in the DNA sequence that does not result in a change in amino acid in the protein”, is also known as a silent mutation because it does not affect the protein’s form and function. (Campbell 322).

    Nonsynonymous mutations are changes in the codon that result in the substitution of an amino acid. This would consequentially change the protein’s primary structure and the protein’s overall conformation. Base-pair substitution creates missense mutation and its effect on protein conformation could be either profound or inconsequential, depending on the substituted amino acid. Nonsynonymous mutation could also be caused by a base pair insertion and deletion. This is known as a nonsense mutation and shifts the reading frame of the gene.

    Mathematically speaking, nonsynonymous mutations would be the more common. The sites for a nonsynonymous are the first and second codon of a triplet, thus the probability for a nonsynonymous mutation to occur would be 2/3. Furthermore, if an insertion or deletion of a base pair occurs, it would always be a nonsynonymous mutation. In order for a synonymous mutation to occur, the base pair substitution would have to be on the 3rd codon. Thus the probability for synonymous would be 1/3. However, some amino acids such as Ser and Asp, limits the kind of base that could be substituted on the 3rd codon. This would further lower the probability for a synonymous substation.

    In nature we see nonsynonymous mutations more often because it has a profound effect on the organism. Synonymous mutations have no effect on the phenotype thus it is invisible to the eye. In fact, all organisms are products of nonsynonymous mutations that have occurred along the evolutionary line.

    Although Sheikh mentioned that the relatively high ratio for synonymous mutations is a purifying selection to preserve the genome, I think that the 2/3 ratio for nonsynonymous mutation opens the possibility of change in the genome. Since animals are constantly interacting with their environment (5th theme), animals will naturally change and adapt (8th theme) to a condition that best fit the animal’s environment. Take the example of the rock pocket mice that Dr. Carroll mentioned. The mice, which live on sandy back grounds, are light color and blend into the environment. However, if the environmental disturbances, such as lava flow, the mice need to alter their coat color to blend into the darkened environment. A nonsynonymous mutation, which can occur on “10 sites on the MC1R gene”, is needed to produce a black mouse (62). With a 2/3 ratio for nonsynonymous mutation, Dr. Carroll calculated that there would be 1 black mouse in less than 2000 years, a short time in evolutionary terms.

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