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3.9: The origins of polymorphisms

So what produces the genomic variations between individuals found within current populations? Are these processes still continuing to produce genotypic and phenotypic variations or have they ended? First, as we have alluded to (and will return to again and again), the sequence of letters in an organism’s genome corresponds to the sequence of characters in DNA molecules. A DNA molecule in water (and over ~70% of a typical cell is water) is thermodynamically unstable and can undergo various types of reactions that lead to changes in the sequences of characters within the molecule.77 In addition, we are continually bombarded by radiation that can damage DNA (although not to worry, the radiation energy associated with cell phones, bluetooth, and wifi devices is too low to damage DNA). Mutagenic radiation, that is, the types of radiation capable of damaging the genome, comes from various sources, including cosmic rays that originate from outside of the solar system, UV light from the sun, the decay of naturally occurring radioactive isotopes found in rocks and soil, including radon, and the ingestion of naturally occurring isotopes, such as potassium-40. DNA molecules can absorb such radiation, which can lead to chemical changes (mutations). Many but not all of these changes can be identified and repaired by cellular systems, which we will consider later in the book.

The second, and major source of change to the genome involves the process of DNA replication. DNA replication happens every time a cell divides and while remarkably accurate it is not perfect. Copying creates mistakes. In humans, it appears that replication creates one error for every ~100,000,000 (108) characters copied. A proof-reading error repair system corrects ~99% of these errors, leading to an overall error rate during replication of 1 in 1010 bases replicated. Since a single human cell contains about 6,400,000,000 (> 6 billion) bases of DNA sequence, that means that less than one new mutation is introduced per cell division cycle. Given the number of generations from fertilized egg to sexually active adult, that ends up producing ~100-200 new mutations (changes) added to an individual’s genome per generation.78 These mutations can have a wide range of effects, complicated by the fact that essentially all of the various aspects of an organism’s phenotype are determined by the action of hundreds to thousands of genes working in a complex network. And here we introduce our last new terms for a while; when a mutation leads to change in a gene, it creates a new version of that gene, which is known as an allele of the gene. When a mutation changes the DNA’s sequence, whether or not it is part of a gene, it creates what is known as a sequence polymorphism (a different DNA sequence). Once an allele or polymorphism has been generated, it is stable - it can be inherited from a parent and passed on to an offspring. Through the various processes associated with reproduction, which we will consider in detail later on, each organism carries its own distinctive set of alleles and its own unique set of polymorphisms. Taken together these genotypic differences (different alleles and different polymorphisms) produce different phenotypes. The DNA tests used to determine paternity and forensic identity work because they identify the unique polymorphisms (and alleles) present within an individual’s genome. We will return to and hopefully further clarify the significance of alleles and polymorphisms when we consider DNA in greater detail later on in this book.

Two points are worth noting about genomic changes or mutations. First, whether produced by mistakes in replication or chemical or photochemical reactions, it appears that these changes occur randomly within the genome. With a few notable and highly specific exceptions there are no known mechanisms by which the environment (or the organism) can specify where a mutation will occur. The second point is that a mutation may or may not influence an organism’s phenotype. The effects of a mutation will depend on a number of factors, including exactly where the mutation is in the genome, its specific nature, the role of the mutated gene within the organism, the rest of the genome (the organism’s genotype), and the environment in which the organism finds itself.

References

77 Instability and decay of the primary structure of DNA: http://www.nature.com/nature/journal...f/362709a0.pdf and DNA has a 521-year half-life: http://www.nature.com/news/dna-has- a-521- year-half- life-1.11555

78 Human mutation rate revealed: http://www.nature.com/news/2009/0908....2009.864.html

Contributors

  • Michael W. Klymkowsky (University of Colorado Boulder) and Melanie M. Cooper (Michigan State University) with significant contributions by Emina Begovic & some editorial assistance of Rebecca Klymkowsky.