Mutations and DNA Damage Repair

Mutations and DNA Damage Repair: Comprehensive Study Notes

Consequences and Causes of Mutations

  • Definition & Impact: Mutations are changes in the DNA sequence that can have severe consequences for a cell or an organism.

    • Example: Sickle Cell Anemia: A single nucleotide change from A to T in the DNA causes sickle cell anemia. This substitution alters the amino acid at that position from Glutamic acid to Valine.

    • Sickle Cell Trait vs. Disease: Individuals with sickle cell trait carry one copy of the mutated gene, while those with sickle cell disease carry two. Both conditions can worsen under low oxygen conditions, but sickle cell disease is significantly more severe.

  • Sources of Nucleotide Changes in DNA:

    • Spontaneous Chemical Changes: Chemical modifications occur due to thermal collisions between DNA and other cellular molecules.

      • Depurination: Guanine and adenine commonly undergo depurination, where the purine base is lost from the nucleotide.

      • Deamination: Can occur in other bases, such as cytosine deaminating to uracil.

      • Consequences of Unrepaired Chemical Changes: If unrepaired, these modifications can lead to mutations, including deletions or substitutions during DNA replication.

        • A depurinated A (missing base) can lead to the deletion of an A-T nucleotide pair in subsequent replication, as the complementary base cannot be determined.

        • A deaminated C (which becomes U) will pair with A during replication, eventually leading to a C-G to T-A base pair substitution over two rounds of replication.

    • Replication Errors: Mistakes made by DNA polymerase during DNA replication.

    • Malfunctioning DNA Repair Enzymes: Errors in the cellular machinery designed to fix DNA damage can allow mutations to persist.

  • Types of Mutations at the Nucleotide Level:

    • Deletions: Removal of one or more nucleotides.

    • Additions (Insertions): Addition of one or more nucleotides.

    • Substitutions: Replacement of one nucleotide with another.

  • Impact on Amino Acid Sequence: These nucleotide changes can result in alterations to the amino acid sequence encoded by a gene.

    • Frameshift Mutations: Deletions and additions, particularly if not in multiples of three, cause frameshift mutations, drastically altering the downstream amino acid sequence from the point of mutation (connecting to the Translation topic).

Types of DNA Damage

  • UV Radiation Damage:

    • Mechanism: Ultraviolet (UV) rays in sunlight cause DNA damage by facilitating the formation of thymine dimers, where two adjacent thymine bases become covalently bonded.

    • Consequences: If these thymine dimers are not repaired, they can lead to errors during DNA replication, resulting in deletions or substitutions.

    • Clinical Relevance: Xeroderma Pigmentosum: Humans can develop Xeroderma pigmentosum (a rare genetic disorder characterized by extreme sensitivity to sunlight and a high risk of skin cancer) when they lack the necessary enzymes to repair thymine dimers.

  • Double-Stranded Breaks (DSBs):

    • Causes: DSBs are severe forms of DNA damage caused by ionizing radiation, oxidizing agents, or mishaps at replication forks.

    • Cellular Response: Cells have specific mechanisms to repair these breaks, which are critical for maintaining genomic integrity.

DNA Repair Mechanisms

  • General Principle: Most DNA damage creates structural abnormalities that are not found in undamaged DNA, which serve as recognizable targets for repair enzymes.

  • Basic Three-Step Mechanism of DNA Repair:

    1. Excision: Damaged nucleotides are recognized and precisely cut out by a variety of specific enzymes, each often specialized for different types of damage.

    2. Resynthesis: The gap created by excision is filled in by a DNA polymerase (often the same enzyme for various types of damage), using the complementary undamaged strand as a template.

    3. Ligation: The newly synthesized segment is joined to the existing DNA strand by DNA ligase (often the same enzyme for various types of damage), completing the repair.

DNA Replication Fidelity and Mismatch Repair

  • High Fidelity of DNA Replication: DNA replication inherently has a negligible error rate due to the proofreading activity of DNA polymerase.

  • Necessity of Repair: Despite high fidelity, errors do occur during replication and must be corrected to prevent mutations in the newly synthesized DNA.

  • Mismatch Repair (MMR):

    • Function: MMR is a post-replication repair system that eliminates replication errors that proofreading missed, ensuring the restoration of the original DNA sequence.

    • Mechanism: MMR identifies and corrects mispaired bases (mismatches) or short insertions/deletions on the newly synthesized strand, using the parental strand as a template to ensure accuracy.

Repair of Double-Stranded DNA Breaks

  • Cellular Strategies: Cells can repair double-stranded breaks (DSBs) through one of two main pathways:

    1. Non-Homologous End Joining (NHEJ): A 'quick and dirty' mechanism that directly ligates the broken ends, often resulting in small deletions or insertions, thus being error-prone.

    2. Homologous Recombination (HR) / Homologous End Joining: A more precise and 'flawless' repair mechanism.

  • Homologous Recombination for Repair:

    • Specificity: This mechanism allows for the accurate repair of double-stranded DNA breaks.

    • Timing: It occurs primarily between replicated, identical DNA duplexes, meaning it is active during the S (DNA synthesis) and G2 phases of the cell cycle, when sister chromatids are available as templates.

    • Mechanism: Uses the genetic information from an undamaged, identical sister chromatid to guide the repair, ensuring that no genetic information is lost or altered.

Genetic Rearrangements: Transposons and Viruses

  • Impact of Foreign DNA Insertion: The insertion of foreign DNA sequences into chromosomes can cause genetic rearrangements, leading to mutations or other functional changes.

    • Transposons (Jumping Genes / Mobile Genetic Elements):

      • Nature: Segments of DNA that can move from one position to another within the genome.

      • Consequences: These movements can cause genetic rearrangements, potentially leading to mutations or the generation of novel proteins.

    • Viruses:

      • Nature: Can integrate their genetic material into the host chromosome as a provirus.

      • Consequences: This integration can lead to abnormal protein expression, either in quantity or quality, potentially producing fusion hybrid proteins or non-functional proteins.

  • Historical Context: Barbara McClintock: Dr. Barbara McClintock was awarded the Nobel Prize in Medicine in 19831983 for her pioneering work on corn genetics, providing the explanation for the mottling of corn grains, which involved