DNA Repair and Mutation

DNA Repair and Mutation

DNA Repair

• Proofreading by DNA Polymerases
    - DNA polymerases can detect and repair mistakes during DNA replication.

• Mismatch Repair
    - Involves a set of specialized proteins that scan for errors in DNA post-replication.
    - Errors are repaired by removing incorrect nucleotides and resynthesizing DNA.
    - The affected daughter strand is identifiable because it is not yet methylated.

• Damage Repair Mechanisms
    - DNA damage can be repaired at any point in the cell cycle through various mechanisms.
    - Common causes of DNA damage include:
      - Radiation (including UV).
      - Oxidation.
      - Chemical alterations to nucleotides.

• Direct Repair Enzymes
    - Enzymes that can convert altered bases back to the standard nucleotide forms (A, T, C, G).

• Base Excision Repair
    - Involves removing a single base that is damaged and replacing it with the appropriate nucleotide using DNA polymerase and ligase.

• Nucleotide Excision Repair
    - Removes a segment of damaged DNA on one strand and resynthesizes it utilizing DNA polymerase and ligase.

• Repair of Broken DNA Strands
    - Specific enzymes repair broken DNA strands.
    - In the G1 phase, Non-Homologous End-Joining (NHEJ) occurs:
      - In NHEJ, two closest broken DNA pieces are joined together.
      - This method can connect incorrect strands if multiple breaks are present, resulting in:
        - Inversions.
        - Translocations.
        - Insertions.
        - Deletions.
  
    - In the G2 phase, Homology Directed Repair (HDR) occurs:
      - Broken DNA pieces align to their sister chromatid, leading to far fewer mistakes.

Mutations

• Definition
    - Mutations arise when there is a change to the DNA sequence or chromosome structure that is not successfully repaired.

• Types of Mutations
    - Somatic Mutations: Occur in non-reproductive cells; affect the organism but are not heritable.
    - Germ-line Mutations: Occur in gamete-producing cells; are heritable and serve as the source of new alleles.

Types of DNA Sequence Mutations

• Transitions
    - Definition: A change from purine to purine (A <-> G) or pyrimidine to pyrimidine (T <-> C).
    - Note: More challenging to detect, as the diameter of the DNA remains unchanged.

• Transversions
    - Definition: A change between purine and pyrimidine (A <-> C, A <-> T, G <-> C, G <-> T).
    - Note: Alters the diameter of the DNA.

• Insertions and Deletions (Indels)
    - Definition: Involve the addition or removal of one or more nucleotides in the DNA sequence.

Consequences of Mutations in Protein Coding Regions

• Silent Mutations
    - Definition: Do not change the amino acid sequence.

• Missense Mutations
    - Definition: Result in a change of one amino acid in a protein.

• Nonsense Mutations
    - Definition: Create a premature stop codon in the protein sequence.

• Effects on Polypeptide Sequences
    - Neutral Mutations: Do not affect protein structure.
    - Loss-of-Function Mutations: Damage the protein structure leading to loss of function.
    - Gain-of-Function Mutations: Alter the protein structure, resulting in new functions.
    - Conditional Mutations: Only modify the protein structure under specific environmental conditions (e.g. heat, salinity).
    - Lethal Mutations: Cause lethality in offspring.

Causes of Mutations

• Varied insults can trigger mutations, including:
    - Radiation (including UV rays).
    - Oxidation.
    - Chemical Changes.
    - Transposons.
    - DNA Breaks.

• Specific Chemical Changes
    - Tautomers
      - Definition: Temporary alternate forms of nucleotides resulting from shifts in electron distribution.
      - Example: A carboxyl group might temporarily change to a hydroxyl group, altering hydrogen bonding patterns.
      - Consequence: Can attract incorrect base pairing during replication.

  - Depurination
    - Definition: Spontaneous loss of a purine base due to the breakage of the base-sugar bond.
    - Consequence: Allows a different base to be incorporated during replication.

  - Deamination
    - Definition: Loss of an amine group from a nucleotide, which may alter a Cytosine (C) to Uracil (U) or Thymine (T).

  - Mutagens
    - Definition: Chemicals that induce changes to nucleotide functional groups.

  - Free Radicals
    - Can oxidize nucleotide bases, leading to altered functional groups.

  - UV Light
    - Can provoke covalent bond formations between thymine bases, creating thymine dimers, resulting in structural DNA alterations.

• Transposons (Transposable Elements)
    - Definition: Mobile genetic elements that can relocate within the genome.
    - Consequences: Can damage regulatory regions or coding domains and may cause chromosomal rearrangements.