DNA Repair, Oncogenes, and Tumor Suppressors

DNA structure is susceptible to damage from chemicals or radiation.
Uncorrected damage is copied and passed to daughter cells.
Damage includes:
- Breaks in the DNA backbone.
- Structural/spontaneous alterations of bases.
- Incorporation of incorrect bases during replication.
Defects increase cancer risk; cells have processes to catch errors to maintain genome integrity.

Mutated genes can lead to cancer. Cancer cells:
- Proliferate excessively without external stimulation.
- Escape normal cell proliferation controls.
- Migrate via local invasion or metastasis (through bloodstream/lymphatic system).
Over time cells accumulate mutations, cancer-causing mutated genes are termed oncogenes.
- Encode cell cycle-related proteins.
- Proto-oncogenes are normal versions before mutation.
- SRC (named after sarcoma) was the first oncogene discovered.
Abnormal alleles encode overactive proteins, accelerating cell cycle.
- Mutation in one copy is sufficient for tumor growth (dominant).
Tumor suppressor genes (e.g., p53, RB/retinoblastoma)
- Encode proteins that inhibit the cell cycle or participate in DNA repair.
- Function to stop tumor progression (anti-oncogenes).
- Mutations result in loss of tumor suppression, promoting cancer.
Inactivation of both alleles is usually necessary for loss of function (multiple hits required).

DNA polymerase builds complementary strand with high accuracy but occasionally makes errors.
Proofreading:
- During synthesis, double-stranded DNA passes through a proofreading part of DNA polymerase.
- Unstable hydrogen bonds indicate incorrectly paired bases.
- Incorrect base is excised and replaced.
- Enzyme discriminates template vs. daughter strand by methylation.
- Template strand is more heavily methylated due to longer existence in the cell.
- Methylation also plays a role in transcriptional activity of DNA.
- Corrects most errors during replication.
DNA ligase lacks proofreading ability, increasing mutation likelihood in the lagging strand.
Mismatch repair: Occurs in G2 phase.
- Enzymes (encoded by genes MSH2 and MLH1) detect and remove errors missed during S phase.
- Homologous to MUTS and MUTL in prokaryotes.

Repair mechanisms involve lesion recognition, removal, and gap filling using the complementary strand as a template.
Cell machinery recognizes and fixes two types of DNA damage in G1 and G2 phases through:
- Nucleotide excision repair (NER)
- Base excision repair (BER)

Ultraviolet light induces thymine dimer formation.
- Interferes with DNA replication, gene expression distorting the double helix shape.
Thymine dimers are eliminated by NER (cut and patch process).
- Specific proteins scan DNA and recognize lesions (bulges).
- Excision endonuclease nicks phosphodiester backbone on both sides of the dimer and removes the defective oligonucleotide.
- DNA polymerase fills the gap (5' to 3') using the undamaged strand as a template.
- DNA ligase seals the nick.

Thermal energy can lead to cytosine deamination (loss of an amino group), converting cytosine to uracil.
- Uracil is easily detected as an error (not normally in DNA).
Detection systems also exist for small, non-helix-distorting mutations.
Base excision repair:
- Affected base is recognized and removed by a glycosylase enzyme, leaving an apyrimidinic (AP) or abasic site.
- AP site recognized by AP endonuclease that removes the damaged sequence.
- DNA polymerase and DNA ligase fill the gap and seal the strand.