DNA Damage and Repair Study Notes

DNA Damage Response (DDR):
  - Component of a complex signal transduction pathway.
  - Recognizes when DNA is damaged.
  - Initiates the cellular response to the damage.
Cells cannot function if DNA damage corrupts essential information in the genome.
Variety of Repair Strategies:
  - Cells utilize the unmodified complementary strand of DNA or sister chromatid as a template to recover original information when possible.
  - Without a template, cells employ:
    - Photoreactivation.
    - Error-prone recovery method known as translesion synthesis.

Direct Reversal / Photoreactivation
Single Strand Damage Repair
   - 2.1 Base Excision Repair (BER)
   - 2.2 Nucleotide Excision Repair (NER)
   - 2.3 Mismatch Repair (MMR)
Double Strand Damage Repair
- 3.1 Non-homologous End Joining (NHEJ)
- 3.2 Homologous Recombination (HR)
Translesion Synthesis
SOS Response in Bacteria

UV-Induced Thymine Dimers:
- Thymine dimers caused by ultraviolet light can be repaired by an enzyme called photolyase.
Photolyase:
- A type of flavoprotein activated by visible light (300–600 nm).
- Binds to the pyrimidine dimer lesion and cleaves the covalent bonds between the dimer elements using light energy.

Spontaneous Depurination:
- Bases like cytosine, adenine, and guanine may transform into uracil, hypoxanthine, and xanthine.
Removal of Altered Bases:
- Carried out by base excision repair (BER).
Role of DNA Glycosylases:
- Recognize unwanted bases and cleave that region without affecting the DNA backbone.
Formation of AP-Site:
- Removal of the base creates a gap known as an apurinic/apyrimidinic (AP) site.
- An AP-endonuclease enzyme creates a nick in the damaged section.
DNA Polymerase-I:
- Cleaves the AP-site using its 3'-5' exonuclease activity and fulfills the gap through 5'-3' polymerization activity.
Final Step:
- DNA ligase seals the gap between the DNA fragments.

Function of NER:
- Removes long base adducts or whole nucleotide sequences; a type of long patch excision repair.
- Repairs UV-induced damage, oxidative damage, and large chemical adducts.
Formation of Thymine-Thymine Dimer:
- Initiated by UV radiation.
Uvr-BC Complex:
- Uvr-B enzyme binds with Uvr-C to form a Uvr-BC complex that removes the dimer.
- Energy from ATP hydrolysis is utilized.
Role of Uvr-D Helicase:
- Binds to the cleavage site and unwinds the damaged DNA segment, also utilizing ATP.
Final Step:
- DNA polymerase-I fulfills the gap created and DNA ligase seals it.

Purpose of MMR:
- Corrects mismatched base pairs occurring during DNA replication.
Recognition of Mismatches:
- Template strand is methylated; the newly synthesized strand is not, allowing MutS to identify damaged nucleotides.
Endonuclease Activity of MutH:
- Cuts the strand near a methylated GATC sequence followed by exonuclease digestion of the defective strand.
Replacement of Damaged Strand:
- New DNA strand synthesized by DNA polymerase I and sealed by DNA ligase.

Definition:
- Pathway for repairing double-strand breaks in DNA.
Mechanism:
- Direct ligation of break ends without a homologous template.
Cellular Activity:
- Active in both non-dividing and proliferating cells.
Key Proteins:
  - Ku70 and Ku80 form a heterodimer binding to broken DNA ends, recruiting DNA-PKcs.
  - DNA-PKcs recruits Artemis for processing broken ends.
  - Ligase IV, XRCC4, and Cernunnos-XLF facilitate join ends.

Definition and Mechanism:
- Requires an identical or nearly identical sequence as a template for repairing double-strand breaks.
Process Similarity:
- Enzymatic machinery is similar to chromosomal crossover during meiosis.
Template Sources:
- Affected chromosomes repaired using sister chromatids in G2 phase or homologous chromosomes.

Definition:
- Mechanism for bypassing DNA lesions blocking replication fork.
Specialized DNA Polymerase:
- Replaces blocked replicative polymerase at DNA damage site to extend nascent strand across damage.
Benefit:
- Allows time for damage repair before the replicase resumes genome duplication.

Description:
- An inducible system evolved by bacteria in response to sudden DNA damage increases.
Key Players:
- Induced by RecA and LexA.
UmuD and UmuC:
- Stimulate translesion synthesis; results in mutagenic yet nondetrimental gap repair.
Adaptive Mechanism:
- Facilitates genetic variation in bacteria under environmental stress conditions.