BI 321 Genetics: Gene Mutation and DNA Repair

BI 321 Genetics Chapter 19: Gene Mutation and DNA Repair

1. Types of Changes Occurring in Mutations

  • Mutations are changes in the DNA sequence that can affect the structure and function of genes.
  • Changes may include alterations in nucleotide sequences, rearrangements of chromosome structures, and changes in chromosome number.
  • Common types of mutations:
    • Substitutions (point mutations)
    • Insertions
    • Deletions

2. Point Substitution

  • Definition: A point substitution is a mutation where one base pair in the DNA sequence is replaced by another.
  • Types of Point Substitutions:
    • Transition Mutation: A purine is substituted for another purine (A ↔ G) or a pyrimidine is substituted for another pyrimidine (C ↔ T).
    • Transversion Mutation: A purine is replaced by a pyrimidine or vice versa (A or G ↔ C or T).

3. Impact of Insertions and Deletions on DNA

  • Insertions: Addition of one or more nucleotide pairs.
  • Deletions: Loss of one or more nucleotide pairs.
  • Both can cause Frameshift Mutations, altering reading frames of genes, potentially leading to nonfunctional proteins.
  • Results depend on where the insertion or deletion occurs relative to the reading frame.

4. Types of Mutations Defined

  • Nonsense Mutation: A type of mutation that creates a premature stop codon (UAA, UAG, UGA) in the mRNA sequence, leading to truncated proteins.
  • Frameshift Mutation: Caused by insertions or deletions that shift the reading frame; alters downstream amino acid sequence, often leading to nonfunctional proteins.
  • Silent Mutation: A change in the nucleotide sequence that does not alter the amino acid produced due to redundancy in the genetic code.
  • Missense Mutation: A change in nucleotide sequence that results in a different amino acid being incorporated into the protein, which may affect protein function.

5. Mutations Outside of Coding Sequences

  • Promoter Mutations: Alterations in the regulatory regions affecting transcription rates.
  • Enhancer/Silencer Mutations: Changes in elements that modify expression levels of genes.
  • Intronic Mutations: Changes that may impact splicing processes.
  • Intergenic Mutations: Changes in the non-coding regions between genes that potentially affect genomic stability.

6. Suppressor Mutations

  • Definition: Mutations that counteract the effects of a previous mutation, restoring function.
  • Examples of Suppressor Mutations:
    • A second-site mutation in another gene can restore the original function (e.g., mutations that correct a frameshift mutation).
    • Intragenic Suppressor Mutations: occur within the same gene.
    • Extragenic Suppressor Mutations: occur in different genes that interact with the product of the mutated gene.

7. Position Effect

  • Definition: Change in gene expression due to alterations in the position of a gene within the genome.
  • Can affect gene expression if a gene is moved near an active promoter or near heterochromatin.
  • Implications can include activation or repression of genes, leading to varied phenotypic effects.

8. Spontaneous Mutations

  • Definition: Mutations that occur naturally without external influence.
  • Causes: Errors during DNA replication, spontaneous lesions, or human error in repair mechanisms.

9. Chemical Changes in Spontaneous Mutations

  • Various forms of spontaneous chemical changes include:
    • Deamination: Removal of an amino group from cytosine, resulting in conversion to uracil, which can lead to base substitutions during replication.
    • Depurination: Loss of purine base (A or G) leading to apurinic sites.
    • Oxidative Damage: Reactive oxygen species can modify bases, leading to mispairing during replication.

10. Oxidative Stress Effects on DNA

  • Impact: Can lead to modifications of guanine bases, forming 8-oxoguanine, which can pair with adenine instead of cytosine during DNA replication, causing mutations.
  • Cellular repair mechanisms may struggle to correct oxidative damage effectively.

11. Trinucleotide Repeats and Mutations

  • Definition: Expansions of repeating sequences of three nucleotides (e.g., CAG repeat in Huntington's disease).
  • Mechanism: During replication, slippage can occur, leading to further expansions during DNA synthesis, which can disrupt gene function or expression.

12. Chemical Mutagens Inducing Mutations

  • Chemical mutagens induce mutations through various mechanisms:
    • Alkylating Agents: Add alkyl groups to DNA bases, causing mispairing (e.g., EMS).
    • Acrylic Compounds: Can cause mispairing and lead to base substitutions.
    • Intercalating Agents: Insert between base pairs, causing frameshifts (e.g., ethidium bromide).
    • Base Analogs: Mimic natural bases and may pair incorrectly during replication (e.g., 5-bromouracil mimics thymine).

13. Effects of UV Light and Other Physical Mutagens

  • UV Light: Induces formation of pyrimidine dimers (thymine dimers), disrupting base pairing and leading to errors during DNA replication.
  • Other Physical Mutagens:** Includes ionizing radiation, which can cause double-strand breaks and base damage.

14. Testing for Mutagenicity in Bacteria

  • Ames Test: A biological assay to evaluate the mutagenic potential of chemical compounds by observing the rate of mutations in specific bacterial strains (e.g., Salmonella typhimurium).

15. Key Features of DNA Repair Mechanisms

  • Repair mechanisms target and fix damaged DNA to maintain genomic stability.
  • Several pathways exist to correct different types of DNA damage:
    • Accuracy and efficiency are essential in minimizing the risk of mutations.

16. Description of DNA Repair Mechanisms

  • Direct Repair: Repairs DNA without cutting the strand (e.g., photoreactivation repairing UV-induced dimers using light).
  • Base Excision Repair (BER): Removes and replaces damaged bases. Key steps include:
    • Recognition of damaged base
    • Cleavage of glycosidic bond
    • DNA polymerase fills in gap
    • DNA ligase seals the strand.
  • Nucleotide Excision Repair (NER): Removes bulky DNA adducts. Steps include:
    • Damage detection and unwinding
    • Endonuclease cuts on either side of the lesion
    • DNA polymerase synthesizes new strand
    • DNA ligase connects fragments.
  • Mismatch Repair: Restores the correct base pairs during DNA replication. Key steps include:
    • Recognition of mismatched base
    • Excision of incorrect base
    • DNA polymerase repair.
  • Homologous End Joining: Repairs double-strand breaks using the sister chromatid as template.
  • Non-homologous End Joining: Repairs double-strand breaks without a template, directly ligating ends together.

17. Translesions

  • Definition: DNA synthesized across a lesion instead of repairing it first, using specialized polymerases that can replicate overdamaged DNA but may introduce errors during the process. This mechanism allows for continued replication but increases the risk of mutations.