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Mutations in a gene’s regulatory region can alter the gene’s expression by regulating the frequency of transcription. Mutations that change non-coding regions of an mRNA can influence its half-life (stability) and/or interactions with the ribosome, while mutations in a gene’s coding region can, but generally do not influence transcription rate, unless of course regulatory regions are located within the coding region. Mutations can influence the sequence of the encoded polypeptide. We define three coding region mutations, involving a single base pair change as synonymous, mis-sense, or non-sense mutations. Because of the semi-redundant nature of the genetic code, it is possible that a single nucleotide change in a coding region will have no effect on the amino acid encoded – this is referred to as a synonymous mutation. That said, when different codons for the same amino acid are recognized by different tRNAs, these tRNAs may be present at different concentrations in the cell. The efficiency of translation is influenced by the rate of aa-tRNA binding. Different organisms can differ in the codons they use to encode particular amino acids, a fact that leads to what is known as "codon bias". Codon bias influences the efficiency of mRNA translation. Ribosome "stalling" can occur if the particular tRNA needed is present at low concentration. When genetically engineering the synthesis of a mRNA from one organism in another, translational efficiency can be increased by altering the gene that encodes the mRNA to reflect the codon bias of the host, rather than the codon bias of the donor.[339]
A second possibility is that the change of a single nucleotide will change the encoded amino acid; this is known as a mis-sense mutation. The effect of a mis-sense mutation depends upon where in the polypeptide it occurs and which amino acid is substituted. We can compare homologous polypeptides found in various organisms. Regions that are similar in terms of amino acid sequence and structure are referred to as conserved regions, compared to regions that are more variable, known (happily) as variable regions.[340] A mis-sense mutation that replaces an amino acid in a conserved region of a polypeptide is likely to have a more drastic effect on the polypeptide’s function than a similar change in a variable region. Similarly, a mutation that replaces a large hydrophobic amino acid with a highly hydrophilic amino acid is more likely to perturb polypeptide structure and function than replacing a large hydrophobic amino acid with a smaller one. Finally, a single nucleotide mutation can replace a codon that specifies an amino acid with a stop codon; this is known as a non-sense mutation. The result of a non-sense mutation is a truncated polypeptide. As a first guess, the effect of a non-sense mutation will be more severe the closer it is to the beginning of the coding region, compared to its effect near the end of the coding region – although other factors contribute to any particular mutation’s effect.
Mutations that influence splicing
While ignoring many details, a final class of point mutations are worth noting; these influence the "splicing" of a newly synthesized RNA molecule. Eukaryotic genes are generally broken up into coding regions, known as exons, and interspersed non-coding regions, known as introns. When a polypeptide-encoding gene is expressed, the initially 
synthesized RNA molecule contains both introns and exons. But ribosomes cannot distinguish between exon and intron sequences, probably one reason that prokaryotes do not have introns. In eukaryotes, introns are removed before the mature mRNA is exported across the nuclear envelope and into the cytoplasm (coming up). So the obvious question is, how exactly are introns recognized and removed, what molecular machines are used? As you may have guessed, there must be information present in the sequence of the newly synthesized RNA that identifies the intronic regions to be removed and the exons to be linked: where an exon ends and an intron starts, known as the 5’ splice site and where the intron ends and the next exon starts, the 3’ splice site. Finally, there is information within the intron known as the branch site (part A→). We can visualize this information through what are known as “sequence logo” plot.[341] Such a plot indicates the information associated within a sequence; where there is no preference, that is, where any of the four nucleotides are acceptable, the information present at that site is 0. Where either of two nucleotides are acceptable, the information is 1, and where only one particular nucleotide is acceptable, the information content is 2.
Splicing is carried out by a polypeptide-RNA complex known as the spliceosome. The spliceosome can recognize intron-exon boundary sequences and, using endonuclease and ligase activities, can cut out the intron and join the 3' end of one exon to the 5' of the next (B→), releasing the intron sequence in a looped form. Point mutations that disrupt the normal intron-exon boundary sequences (C→) can inhibit splicing, so that the intron remains in the final mRNA. Since introns do not encode polypeptides, there is little or no selection against the presence of stop codons in their sequence. A ribosome reading along a non-spliced RNA will likely add a series of inappropriate amino acids to the growing polypeptide before it encounters a stop codon, leading to the termination of polypeptide synthesis. Alternatively if, for example, the 3’ splice site is disabled, a “down-stream” exon may be used for splicing. The result can be that an exon normally included is lost from the spliced mRNA; the polypeptide sequence it encodes will be missing from the final polypeptide. The down-stream reading frame may also be altered, leading to the synthesis of incorrect amino acid sequences and the creation of stop codons. The result is that mutations that disrupt splicing can often have complex effects, and such mutations (alleles) have been associated with a number of human diseases.[342]
The complexity of eukaryotic genomes is greatly increased by the fact that most genes contain multiple exons and introns. Different sets of exons can be spliced together, a regulateable process known as alternative splicing, in different cells and within a single cell to produce mRNA molecules that encode variants of the "same" gene with different activities. These processes can lead to a range of complex behaviors that can muddy the interpretation of experimental manipulations.[343]
Insertions and deletions
Another class of mutations involves the insertion or deletion of nucleotide regions. Such insertions or deletions (known generically as indels) can disrupt or alter the binding of proteins to a gene’s regulatory region, influencing gene expression. If they occur within the coding region, they can alter both the polypeptide sequence and reading frame so that the sequence of the polypeptide downstream of the insertion site will be altered. If the reading frame is preserved, the final polypeptide may have a region of new or deleted amino acids, but retain the original sequence downstream of the insertion/deletion.
Questions to answer:
- What do the terms “up-stream” and “down-stream” mean in terms of gene structure.
- What effects on polypeptide synthesis arise from neglecting codon bias?
- Why doesn't release factor cause the premature termination of translation at non-stop codons?
- What might happen if a ribosome starts translating an mRNA at the "wrong" place?
- When analyzing the effects of a particular non- or mis-sense mutation, what factors would you consider first?
Question to ponder:
- How would you go about reengineering an organism to incorporate non-biological amino acids into its proteins.
References
[339] To learn more look at Codon Bias as a Means to Fine-Tune Gene Expression.
[340] A polypeptide assumes a 3D-dimensional that shape can be conserved.
[341] Sequence logos: a new way to display consensus sequences: http://www.ncbi.nlm.nih.gov/pubmed/2172928
[342] The pathobiology of splicing: https://www.ncbi.nlm.nih.gov/pubmed/19918805
[343] See Biological plasticity rescues target activity in CRISPR knock outs
This page titled 8.6: Effects of point mutations on polypeptides and proteins was last modified on Thu, 08 Jan 2026 23:37:44 GMT and is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by Michael W. Klymkowsky and Melanie M. Cooper.
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