If a mutation in the dna of an organism results in the replacement of an amino acid containing a polar r-group with another amino acid containing a nonpolar r-group how might

The R group of the proteins are side chains which are specific to each protein and which confer specific chemical properties to the proteins. The R group determines the size, polarity and the pH of the protein.
In the case of the protein where the amino acid containing a polar R group is replaced with another amino acid containing non polar R group, the TERTIARY structure of the protein might be affected. Structure will be affected if the protein is hydrophillic and the R group is hydrophobic. 

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