Supplemental Lecture (97/02/22 update) by Stephen T. Abedon (abedon.1@osu.edu)

  1. Chapter title: Mutation
    1. A list of vocabulary words is found toward the end of this document
    2. The object of DNA replication is the exact duplication of a single DNA double helix such that there are then two identical copies where previously their was only one. Thus, in DNA replication a DNA template is employed to produce a complementary DNA molecule, one which itself is capable of serving as a template. Given the replication of this second template, a DNA molecule identical to the original template is created. Though neat and clean in concept, in the real world as in so much of biology high fidelity DNA replication doesn't just happen. Instead (and analogous to the employment of the complex process of mitosis to effect chromosome segregation and avoid nondisjunction), organisms expend a great deal of energy and employ a large number of proteins to both prevent mistakes from happening during DNA replication and to repair any mistakes which occur despite these measures.
    3. Of those mistakes that occur during DNA replication, not all are always successfully repaired. We call these persisting mistakes mutations. A mutation is a change in a sequence of nucleotides. Specifically, however, it is a change which is itself heritable because it does not directly interfere with subsequent DNA replication. Mutations play an enormous role in the science of genetics. Mutations are also found at the center of a number of diseases and disease processes. Particularly, mutations (ultimately) are behind most genetic diseases, cancers, and pathogen evolution such as the development of antibiotic resistance. Indeed, mutations are the only source of novel variation within wild populations, and it is upon this variation that natural selection acts (i.e., evolution).
    4. In fact, it is fair to say that, without mutation, life itself could not exist. In this lecture we will broadly discuss mechanisms by which mutation can occur as well as what mutations look like at the level of the DNA sequence.
  2. Mutation
    1. A heritable change in nucleotide sequence.
    2. By definition, mutations are replicatable (i.e., they do not directly interfere with the action of DNA polymerase or any other protein involved in DNA replication).
    3. Though not necessarily without bias as to site of mutation or type of mutation that may occur at a given site, mutations nonetheless represent relatively random changes to complex (i.e., highly evolved), information-bearing structures.
    4. Thus, mutations tend to destroy existing information.
    5. Destroyers of information:
      1. Given sufficient time and rates of occurrence, however, mutations can also create useful information.
      2. In other words, random processes lead to useful information with low probability, but not with zero probability.
      3. An altered gene sequence that results in a protein having a novel function would be an example of an increase in information that occurs with low probability.
    6. At the root of everything:
      1. It is important to keep in mind during further studies of biology that all the information contained within biological systems originated as potentially information destroying change in nucleotide sequence (i.e., mutation).
      2. Furthermore, try to avoid discounting this concept of nucleotide sequence encoded information---biology, at its essence, is the study of such information.
  3. DNA damage [lesion, double-strand damage]
    1. Non-replicatable change:
      1. A non-heritable change in DNA, one which, by definition, directly interferes with DNA replication.
      2. DNA damages (a.k.a., lesions) tend to be chemical modifications of nitrogenous bases that prevent in some manner their recognition by DNA polymerase and, indeed, stop DNA replication from occurring at the point of the lesion.
    2. Lesions are often repairable (often by employing the information present on the complementary strand) though without repair cell death can occur.
    3. A half-measure than can often save an otherwise doomed cell is to place a random sequence opposite a not repaired lesion. Such random sequences are by definition mutations and DNA damage is a common route leading to mutation.
    4. Double-strand damage:
      1. DNA damage occurring to a nucleotide and the adjacent nucleotide on the complementary DNA molecule (i.e., as found in a double helix) is called double-strand damage.
      2. By definition, double-strand damage is not repairable by utilizing complementary strand information (since the information found on the complementary strand is also damaged).
      3. When double-strand DNA damage occurs, complementary strand information is subsequently only available in homologous chromosomes found in diploid cells (i.e., nearly identical second copies of chromosomes found in the same cell).
    5. Agents which can cause DNA damage and therefore can lead to mutation include X-rays, ultraviolet radiation (a component of sunlight), oxidizing chemical agents, etc.
  4. Mutagen
    1. A substance (chemical or physical), exposure to which increases the likelihood of mutation.
    2. Some mutagens act by inducing the formation of DNA lesions which are subsequently repaired but not with high fidelity.
    3. Alternatively, a mutagen might alter a nitrogenous base such that it remains replicatable but is recognized as a different nitrogenous base.
    4. General mechanisms of mutagenesis in addition to these two also exist.
  5. Carcinogen
    1. A substance, often a mutagen, exposure to which has been demonstrated in some manner to be associated with an increased likelihood of developing cancer.
    2. Semantically, a substance which has been demonstrated to be carcinogenic (i.e., cancer causing) is considered to be a carcinogen.
  6. Cancer
    1. A genetic disease of somatic cells.
    2. A cancer usually is the progeny of mutationally altered somatic cells, ones which have mutationally lost the ability to control their rate of growth.
  7. Point mutation
    1. A change in a single nitrogenous base such that the DNA retains the same number of nucleotides but has a slightly different sequence.
  8. Frameshift mutations [insertions, deletions]
    1. Frameshift mutations are changes in the number of nucleotides.
    2. This would be the addition (insertion) or deletion of one or more nucleotide at a single point.
    3. Particularly, a frameshift mutation involves the loss or gain of some number of nucleotides which is not divisible by three (i.e., one or more codons).
  9. Nonsense mutation
    1. A change of an amino acid-coding codon to a stop codon.
    2. Product of point as well as frame shift mutation:
      1. Though nonsense mutations tend to be the product of point mutations, it is worth noting that frameshift mutations also tend to lead to the creation of multiple stop codons.
      2. This is a consequence of the changing of a gene from one reading frame in which stop codons are very rare (a consequence of evolution) to a reading frame in which stop codons have not been eliminated by evolution (remember, on average a stop codon should be present in a random sequence of DNA every 20th codon: 63/3).
    3. FOLLOWING NEEDS TO BE INCORPORATED INTO LECTURE:
      1. A mutant is an organism who displays a mutation not displayed in its immediate ancestor(s).
      2. To mutagenize (a.k.a., mutate) is to treat an organism with chemicals (mutagens) that cause an increase in the rate of mutation.
      3. That is, mutagenesis is a means of creating mutants.
  10. Ames test
    1. A way of testing the ability of chemicals to induce mutations in microorganisms (and therefore allow the inference that the same chemical may induce mutations in humans).
    2. Outline of procedure:
      1. An auxotroph is placed in the presence of a chemical but in media in which it cannot grow due to a single mutation that affects its ability to synthesize some crucial organic compound. If the chemical induces mutations that reverse the original mutation, then the microorganisms can grow.
      2. Microorganism growth is thus used as a convenient marker for the ability of a given chemical to induce mutations. Such mutation inducing chemicals are often carcinogenic.
  11. Vocabulary
    1. Cancer
    2. Carcinogen
    3. Deletion
    4. DNA damage
    5. Double-strand damage
    6. Frameshift mutation
    7. Insertion
    8. Lesion
    9. Mutagen
    10. Mutation
    11. Nonsense mutation
    12. Point mutation
  12. Practice questions
    1. What's the difference between a mutation and DNA damage? (<20 word answer) [PEEK]
    2. An insertion of two nucleotides in the middle of a reading frame is an example of a __________[PEEK]
      1. point mutation
      2. frameshift mutation
      3. nonsense mutation
      4. deletion
      5. all of the above
      6. none of the above
    3. You are attempting to isolate novel alleles in a bacteriophage (a virus which has a bacterial host). To accomplish this you first expose a large number of these bacteriophage to 260nm wavelength ultraviolet (UV) radiation, a potent DNA damaging agent. You then examine the bacteriophage for heritable phenotypic novelty. Why did you first expose these bacteriophage to UV radiation? (note: to cause DNA damage is an insufficient explanation) [PEEK]
  13. Practice question answers
    1. the former can be replicated (mutation), the latter cannot (damage).
    2. frameshift mutation
    3. DNA damage can result in mutagenesis.
  14. References
    1. Raven, P.H., Johnson, G.B. (1995). Biology (updated version). Third Edition. Wm. C. Brown publishers, Dubuque, Iowa. pp. 320-335.