Gene Mutation and DNA Repair Lecture Flashcards

Overview of Mutations and DNA Repair

• The term mutation refers to a heritable change in the genetic material of an organism.

• Functions and impacts of mutations:     - They provide allelic variations within a population.     - They serve as the foundation for evolutionary change.     - They can be detrimental if they result in an allele that functions more poorly than the original wild-type version.

• DNA Damage (DNA Lesion) vs. Mutation:     - DNA damage refers to an abnormal change in DNA structure.     - A mutation is a heritable change in the sequence.     - DNA damage that is not repaired in dividing cells can result in a permanent mutation.

Effects of Mutations on Gene Structure and Function

• Mutations occur at two primary levels:     - Chromosomal changes: Variations in structure or number that generally affect more than one gene.     - Gene mutations: DNA changes that typically affect only one gene.         - These include changing one nucleotide to another, deleting nucleotides, or inserting nucleotides.

Point Mutations

• A point mutation is a change in a single base pair involving a base substitution.

• Transition: A change of a pyrimidine ($C, T$) to another pyrimidine, or a purine ($A, G$) to another purine. Transitions are more common than transversions.

• Transversion: A change of a pyrimidine ($C, T$) to a purine ($A, G$) or vice versa.

Mutations Within the Coding Sequence

• Silent Mutations: These do not alter the amino acid sequence of the polypeptide due to the degeneracy of the genetic code (multiple codons code for the same amino acid).

• Missense Mutations: These alter the amino acid sequence.     - Example: Sickle-cell anemia results from a missense mutation in the beta-globin gene, changing the 6th amino acid from Glutamine to Valine.     - Neutral Mutation: A missense mutation that does not significantly affect the protein's function.

• Nonsense Mutations: These change a sense codon to a stop codon ($UAA, UAG, UGA$), producing a truncated (shortened) polypeptide.

• Frameshift Mutations: These involve the addition or deletion of nucleotides in numbers not divisible by three, shifting the reading frame and altering all subsequent amino acids.

Gene Mutations in Noncoding Sequences

• These mutations can disrupt gene expression even if they do not change the protein's primary sequence:     - Promoter Mutations:         - Up promoter mutations: Increase the rate of transcription.         - Down promoter mutations: Decrease the rate of transcription.     - Regulatory Element/Operator Site: May disrupt the ability of the gene to be properly regulated by transcription factors.     - 5′-UTR and 3′-UTR: May alter mRNA stability or the ability of mRNA to be translated.     - Splice Recognition Sequences (Splice Junctions): In eukaryotes, these may alter the ability of pre-mRNA to be properly spliced.

Effects on Genotype, Phenotype, and Environment

• Wild-type: The most common genotype or phenotype in a natural population. Many genes have multiple wild-type alleles.

• Mutant Allele: A mutation that is rare in a population.

• Reverse Mutation (Reversion): A second mutation that changes a mutant allele back to the wild-type sequence.

• Consequences for Survival:     - Deleterious mutation: Lowers the chance of survival and reproduction.     - Lethal mutation: Results in the death of the cell or organism.     - Beneficial mutation: Enhances survival or reproductive success.

• Environmental Influence:     - The benefit or harm of a mutation may depend on the environment. For example, the sickle-cell allele is deleterious in most environments but provides a survival advantage (resistance to malaria) to heterozygotes in regions where malaria is prevalent.

• Conditional Mutations: Affect the phenotype only under specific conditions.     - Example: Temperature-sensitive ($ts$) mutants. E. coli with a $ts$ mutation may grow normally at $33$ to $38^{\circ}\text{C}$ but fail to grow at $40$ to $42^{\circ}\text{C}$.

Suppressor Mutations

• A suppressor is a second mutation that affects the phenotypic expression of a first mutation at a different site (not a reversion).

• Intragenic Suppressor: The second mutation occurs in the same gene as the first. Example: A first mutation inhibits lactose transport, and a second mutation in the same protein restores the function.

• Intergenic Suppressor: The second mutation occurs in a different gene.     - Possible mechanisms:         - A second protein takes on the role of the first.         - Proteins act in the same cellular pathway.         - Polypeptides are subunits of the same multimeric (protein-protein interaction) protein.         - A mutant transcription factor activates a compensatory gene.

Position Effects

• A gene's expression may be altered because of its new location on a chromosome, even if the gene remains intact. This is called a position effect.

• Common causes:     - Movement near proximity to regulatory sequences: A gene is moved next to the regulatory sequences of a different gene.     - Movement to a heterochromatic region: A gene is moved to a highly compacted (inactive) region, such as occurs in Drosophila eye color variegation (moving the red-eye gene to a heterochromatic area results in variegated red/white eyes).

Germ-Line vs. Somatic Mutations

• Germ-line mutations: Occur in sperm, egg, or precursor cells. These are passed to future generations; the mutation will be present in every cell of the offspring.

• Somatic mutations: Occur in non-reproductive cells at any stage of development.     - The size of the affected region depends on the timing; earlier mutations produce larger patches.     - Genetic Mosaic: An individual with somatic cells that are genotypically different from each other.

Spontaneous Mutations

• Spontaneous mutations result from abnormalities in biological processes (e.g., DNA replication errors, aberrant recombination, aberrant segregation, or transposable elements).

• Depurination: The most common chemical change. The covalent bond between deoxyribose and a purine base ($A$ or $G$) breaks, creating an apurinic site.     - If unrepaired, DNA polymerase may add any of the four bases, leading to a 75\text{%} chance of mutation.

• Deamination:     - Cytosine to Uracil: Easily recognized and repaired because Uracil is not a standard DNA base.     - 5-methylcytosine to Thymine: This creates a "hot spot" for mutation because Thymine is a normal DNA base, and repair enzymes cannot readily identify which strand is incorrect.

• Tautomeric Shifts: Bases can interconvert between forms ($\text{keto} \rightleftharpoons \text{enol}$ for $T$ and $G$; $\text{amino} \rightleftharpoons \text{imino}$ for $A$ and $C$).     - Rare forms promote mismatched base pairs (e.g., $A-C$ or $G-T$).

• Oxidative Stress: Aerobic metabolism produces Reactive Oxygen Species (ROS) (e.g., peroxides, free radicals).     - ROS can cause oxidative DNA damage, such as converting Guanine to 8-oxoguanine (8-oxoG).     - 8-oxoG base pairs with Adenine, causing a $G-C$ to $T-A$ transversion.

Trinucleotide Repeat Expansion (TNRE)

• Certain genes contain tandem repeats of three nucleotides. TNRE occurs when the number of repeats increases significantly between generations.

• Clinical Features:     - Anticipation: The severity of the disease worsens and/or occurs earlier in future generations.     - Severity can depend on which parent transmits the allele (e.g., paternal inheritance for Huntington disease, maternal for myotonic dystrophy).

• Mechanism: The repeat sequences (e.g., $CAG$) can form a hairpin (stem-loop) during replication, causing DNA polymerase to slip and subsequently synthesize more repeats via gap repair.

• TNRE Disorders:     - Huntington Disease (HD): $CAG$ repeat in the coding sequence; causes protein aggregation. Individuals have $27-121$ repeats (unaffected have $6-37$).     - Fragile X Syndrome (FRAXA): $CGG$ repeat in the $5'\text{-UTR}$; causes mental impairment.     - Myotonic Muscular Dystrophy (DM): $CTG$ repeat in the $3'\text{-UTR}$.

Induced Mutations and Mutagens

• Mutagens are environmental agents (chemical or physical) that permanently alter DNA structure.

• Chemical Mutagens:     - Base modifiers: Covalently modify bases. Example: Nitrous acid replaces amino groups with keto groups ($C \rightarrow U$, $A \rightarrow \text{hypoxanthine}$).     - Alkylating agents: Covalently attach methyl or ethyl groups to bases. Examples: Nitrogen mustard and Ethyl methanesulfonate (EMS).     - Intercalating agents: Flat planar structures that wedge into the DNA helix, causing frameshifts. Example: Proflavine.     - Base analogs: Incorporated into DNA during replication. Example: 5-bromouracil (5BU) acts as a Thymine analog but can undergo a tautomeric shift to pair with Guanine.

• Physical Mutagens:     - Ionizing Radiation ($X\text{-rays}, \text{gamma rays}$): Short wavelength, high energy. Causes double-strand breaks, deletions, and free radicals.     - Nonionizing Radiation ($UV\text{ light}$): Less energy, cannot penetrate deeply. Specifically causes thymine dimers, which are cross-linked thymines that interfere with replication.

DNA Repair Systems

• Cells utilize multi-step processes: Detection of the irregularity, Removal of abnormal DNA, and Synthesis of normal DNA.

Questions & Discussion

• Question 1: A researcher identifies a novel mutation in a gene that results in a protein only half its normal length. Based on this information, which type of mutation is the most likely cause?     - Answer: c) A nonsense mutation.

• Question 2: Explain the relationship between the degeneracy of the genetic code and the occurrence of silent mutations.     - Answer: d) The degeneracy of the genetic code means that multiple codons can code for the same amino acid, so a mutation in the DNA sequence may not change the amino acid sequence of the protein.

• Question 3: How does the length of the CAG repeat in the huntingtin gene affect the disease progression of HD?     - Answer: b) Longer CAG repeats result in earlier onset and more severe symptoms.

• Question 4: The mutagen nitrous acid causes cytosine to be converted to uracil. If this mutation is not repaired, which base will be incorporated into the newly synthesized DNA strand during DNA replication?     - Answer: c) Adenine (because Uracil pairs with Adenine like Thymine).