Exercises: Mutations

What is a mutation? Explain the difference between a gene (or point) mutation and a chromosome mutation, giving an example of each.

Name two mutagenic agents, one physical and one chemical, and briefly explain how they damage DNA.

Mutations can be spontaneous or induced. Explain the difference between them and give an example of a cause of each type.

Are all mutations harmful? Reason your answer and give an example of a mutation that has turned out to be beneficial for a species.

Explain what the mutation rate is and reason why living beings maintain low but non-zero mutation rates, relating it to the balance between genetic stability and variability.

Explain the difference, in terms of their consequences and their transmission to offspring, between a mutation occurring in a somatic cell and one occurring in a germ cell.

Mutations are said to be the primary source of genetic variability. Explain the relationship between mutations, the evolution of species and biodiversity.

Cells possess DNA repair systems that correct many of the lesions that escape DNA polymerase. Explain what happens when a lesion is not repaired and reason why people with xeroderma pigmentosum, who have a defective system for repairing the thymine dimers caused by ultraviolet light, show such a high risk of skin cancer.

Down syndrome is due to the presence of an extra copy of chromosome 21 (trisomy 21). Explain what type of mutation it is, how it can originate through non-disjunction during meiosis and reason why mutations of this type affect many traits simultaneously.

A mutation located in the regulatory region of a gene prevents it from being transcribed, even though its coding sequence is completely normal. Explain how this is possible and compare the effect of this mutation with that of a substitution within an exon of the same gene.

Retroviruses, such as HIV, copy their genome using reverse transcriptase, an enzyme with no proofreading activity. Reason why these viruses show very high mutation rates and explain what consequences this fact has for the treatment of the infections they cause and for the development of vaccines.

In a region where malaria is endemic, the frequency of the mutant allele $Hb^S$ (responsible for sickle cell anemia in homozygosity) remains stable at around 0.12 due to the selective advantage it confers on heterozygotes against infection by Plasmodium.

1. a) Following an intensive health campaign, malaria is completely eradicated in that region. Reasonably predict how the frequency of the $Hb^S$ allele will evolve over the following generations.
2. b) Justify why the $Hb^S$ allele will not immediately disappear from the population despite being lethal or severely deleterious in homozygosity.
3. c) A person states: "Now that malaria has disappeared, the $Hb^S$ mutation has ceased to exist in the population." Refute this statement by clearly distinguishing between the origin of a mutation and its adaptive value depending on the environment.

During bacterial DNA replication, DNA polymerase mistakenly incorporates a guanine (G) deoxyribonucleotide opposite a thymine (T) on the template, giving rise to a G-T mismatch in one of the newly synthesized strands that is not detected by immediate proofreading activity.

1. a) Deduce what percentage of descendant double-stranded DNA molecules will carry a permanent mutation fixed in both strands after two successive rounds of replication starting from that initial molecule.
2. b) Justify how the resulting base pairs are distributed in each of the four final DNA molecules, assuming that the initial pair was A-T and no subsequent repair system acts.
3. c) The mismatch repair system is only effective if it acts before the newly synthesized strand is methylated. Justify what consequence it would have on genome stability if this system repaired the methylated template strand instead of the newly formed daughter strand.

To study the origin of antibiotic resistance, an experiment inspired by the Luria-Delbrück fluctuation test was designed: 20 independent tubes were inoculated with an identical and very low number of ampicillin-sensitive bacteria, allowing them to grow to saturation. Simultaneously, a large flask with a volume equivalent to that of the 20 tubes combined was cultured. Equal aliquots were then plated on ampicillin-containing plates:

• Samples from the large flask yielded a very similar number of resistant colonies to one another (mean of 24 colonies, with very low variance).

• Samples from the 20 independent tubes showed enormous fluctuation: most tubes yielded 0 or 1 resistant colony, while a few yielded more than 300 colonies.

1. a) Interpret these results: do they demonstrate that resistance is induced by exposure to the antibiotic or that it is due to pre-existing spontaneous mutations? Justify your answer by explaining the cause of the high variance among the independent tubes.
2. b) Predict what result would have been observed on the plates from the 20 tubes if the presence of the antibiotic were the direct stimulus triggering the mutation in a small, constant fraction of bacteria.

When sequencing whole genomes of a species, it is observed empirically that the rate of spontaneous transitions is twice that of transversions (2:1 ratio), even though the number of theoretically possible transversions is twice that of transitions (theoretical 1:2 ratio).

1. a) Justify at the stereochemical level why DNA polymerase makes and overlooks a transition more frequently than a transversion during DNA replication.
2. b) Examine the third position of codons in four-codon families in the genetic code (for example, valine: GUU, GUC, GUA, GUG). Justify why a transition at that position has a neutral effect on the polypeptide sequence and predict whether a transversion at that same position would have the same biological harmlessness.
3. c) Predict what alteration in mutation rates a cell would undergo if a mutation selectively inactivated the 3'→5' exonuclease domain of its main DNA polymerase.

Genomic analysis of a completely healthy newborn reveals that they carry approximately 70 de novo point mutations absent from their parents' genomes. Their relatives fear that these mutations will lead to the development of serious diseases in the future.

1. a) Using the organization of the human genome and the features of the genetic code, justify why the vast majority of these 70 point mutations have no discernible phenotypic effect.
2. b) Suppose that one of these point mutations is located in the conserved dinucleotide that marks the splicing site of the first intron of an essential gene. Predict and justify the molecular consequences for the mature mRNA and the translated protein.
3. c) Can a point mutation located in a non-coding intergenic region alter the amount of protein synthesized by an adjacent gene? Justify your answer by proposing a specific molecular mechanism.

In an experimental evolution assay in the laboratory, two bacterial populations (standard strain with a normal mutation rate and mutator strain with a 150-fold higher mutation rate due to a defect in DNA repair) are subjected to increasing lethal doses of a novel toxic drug.

1. a) During the initial cycles of exposure, the mutator strain generates viable resistant clones significantly faster than the standard strain. Interpret this result in terms of genetic variability and natural selection.
2. b) After one thousand generations in an optimal and constant medium, without the presence of any toxic compound, the mutator strain experiences a marked decrease in its biological fitness and a population decline compared to the standard strain. Justify this decline based on the nature of the majority of mutations and the concept of mutational load.
3. c) Based on the above results, formulate a hypothesis explaining why natural selection has favored very low mutation rates, but not strictly equal to zero, in living organisms.

Unit challenge. As a genetic counselor, you must analyze the molecular impact of a real mutation in the human $HBB$ gene (responsible for sickle cell anemia) and propose a biotechnological solution.

1. Data collection: Access the public NCBI ClinVar or Ensembl database, locate the $HBB$ gene, and extract the original triplet of codon 6 versus the pathogenic hemoglobin S variant (c.20A>T, p.Glu7Val in ClinVar; Glu6Val in classical numbering).

2. Flow of genetic information: Prepare a comparative table showing the replication of the DNA fragment (template and complementary strands), its transcription into mRNA, and translation into the resulting peptide. Classify the mutation at the molecular level and predict how this amino acid change affects the three-dimensional conformation of hemoglobin.

3. Regulation and therapeutic report: Write a reasoned report (1.0-1.5 pages) explaining why the pathology does not manifest during the fetal stage (gene silencing and regulation of $HBB$ versus fetal globins). Propose a well-founded hypothesis on how to reactivate fetal globin expression using gene editing to treat the disease.

Evaluation criteria:

• Rigor and accuracy in deducing the processes of replication, transcription, and translation from real NCBI data.

• Proper classification of the mutation and its correlation with protein structure.

• Critical integration of gene expression regulation mechanisms into the therapeutic proposal.