DNA Repair Mechanisms

DNA Structure and Function

• DNA is like a library in the cell nucleus containing thousands of books.
• Genes are segments of DNA that contain recipes for proteins.
• DNA is composed of two strands of nucleotides.
• Each nucleotide contains:
  • A sugar (deoxyribose).
  • A phosphate group.
  • One of four nucleobases: adenine (A), cytosine (C), guanine (G), and thymine (T).
• Nucleotides on opposing strands pair via hydrogen bonds:
  • A pairs with T.
  • C pairs with G.
• DNA's primary functions:
  • Store information.
  • Pass on information to daughter cells.
  • Guide protein creation.

DNA Replication

• Occurs during the S phase of interphase in the cell cycle.
• Cell cycle consists of interphase (G1, S, G2) and mitosis.
• DNA replication ensures each daughter cell receives identical DNA.
• Process:
  • DNA helicase separates the two DNA strands.
  • DNA polymerase uses each strand as a template.
  • DNA polymerase adds complementary nucleotides to each strand.

Gene Expression

• Process of decoding DNA information to create proteins, involving transcription and translation.
• Transcription:
  • RNA polymerase copies the gene's nucleotide sequence.
  • Creates messenger RNA (mRNA).
  • mRNA has uracil (U) instead of thymine (T).
• Translation:
  • Ribosomes read mRNA in codons (three-nucleotide words).
  • Each codon codes for an amino acid.
  • Amino acids form a protein.

DNA Damage and Repair

• DNA must remain intact for proper function.
• Cells are exposed to endogenous and exogenous factors that can damage DNA.
• If DNA damage occurs, cells enter the G0 phase for DNA repair.
• If DNA damage is irreparable, cells may undergo:
  • Senescence (stop dividing).
  • Apoptosis (programmed cell death).
  • Uncontrolled cell division leading to tumor formation.

Types of DNA Damage

• Single-strand damage: caused by errors in DNA replication or by harmful chemical or physical agents.
• Double-strand damage: caused by ionizing radiation (X-rays, gamma rays).

Single-Strand Damage Repair Mechanisms

• Mismatch Repair (MMR)
  • Corrects errors made during DNA replication when DNA polymerase inserts the wrong nucleotide.
  • Error rate: 60,000 mismatches per replication (1 in 100,000 nucleotides).
  • Proofreading by DNA polymerase:
    • DNA polymerase checks for errors and corrects them immediately.
    • Functions as an exonuclease to remove incorrect nucleotides.
    • Reduces error rate to 600 mismatches per replication (1 in 10,000,000 nucleotides).
  • Mismatch repair process:
    • MSH proteins recognize mismatches in the newly synthesized strand.
    • Endonuclease severs nucleotide bonds.
    • Exonuclease removes the damaged DNA segment, creating a gap.
    • DNA polymerase fills the gap with correct nucleotides.
    • DNA ligase seals the bonds.
    • Final error rate: 6 errors per cell division (1 in 1,000,000,000 nucleotides).
• Base Excision Repair (BER)
  • Repairs damage caused by chemical exposure, such as nitrites and nitrosamines in cured or pickled foods.
  • Chemicals can cause deamination, altering the structure of nitrogen bases (e.g., cytosine to uracil).
  • Process:
    • Glycosylases remove the damaged base, creating an AP site (apurinic/apyrimidinic site).
    • AP endonuclease severs the bond between the phosphate and sugar.
    • Exonuclease removes the sugar-phosphate.
    • DNA polymerase fills the gap with new nucleotides.
    • DNA ligase seals the bonds.
• Nucleotide Excision Repair (NER)
  • Fixes damage from physical agents like UV radiation.
  • UV radiation causes pyrimidine dimers (e.g., two adjacent thymines bonding together).
  • Process:
    • Endonucleases make incisions on both sides of the damage (3' and 5' ends), removing a fragment of 12-24 nucleotides.
    • Exonucleases remove the nucleotides.
    • DNA polymerase inserts new nucleotides.
    • DNA ligase seals the bonds.

Double-Strand Damage Repair Mechanisms

• Caused by ionizing radiation (X-rays, gamma rays) that breaks the phosphate backbone of both DNA strands.
• Breaks are often jagged with single-stranded overhangs.
• Non-Homologous End Joining (NHEJ)
  • A DNA protein kinase complex binds to each end of the broken DNA.
  • Recruits Artemis to cut off single-stranded ends.
  • Ligase enzyme binds the two ends together.
  • Error-prone due to the loss of nucleotides.
• Homology Directed Repair (HDR) / Homologous Recombination
  • Uses the sister chromatid as a template for repair.
  • 46 chromosomes come in 23 pairs of homologous chromosomes with similar nucleotide sequences.
  • Process:
    • MRN protein complex binds to the broken DNA ends.
    • Exonucleases remove nucleotides from one strand, creating single-stranded ends (N1 and N2).
    • N1 pairs with a complementary sequence on the intact homologous sister chromatid, forming a loop.
    • DNA polymerase extends N1 until it aligns with N2.
    • The strand is released from the homologous DNA, and its last nucleotides bind to the last nucleotides of N2.
    • DNA polymerase fills any remaining gaps.
    • DNA ligase seals the bonds.
  • More reliable than NHEJ because there is no loss of nucleotides.

Recap

• DNA repair mechanisms prevent accumulation of DNA damage and avoid senescence, apoptosis, or uncontrolled cell division and tumor formation.
• Single-strand DNA breaks:
  • Mismatch repair: fixes nucleotide mismatches that DNA polymerase didn't correct.
  • Base excision repair: fixes deamination damage caused by chemicals.
  • Nucleotide excision repair: fixes pyrimidine dimers caused by UV radiation.
• Double-stranded DNA breaks:
  • Nonhomologous end joining.
  • Homologous recombination.