Question

BIOL 3020 Name Molecular Biology of Cell 7. Write the type or types of DNA alterations that are repaired by each of the following DNA repair mechanisms and how each repairs the alteration. a. Photoreactivation b. Base excision repair c. Nucleotide Excision repair: d. Mismatch repair: e. Homologous recombination

Answer 1

Answer: DNA is damaged by various factors such as UV/Ionizing radiation and chemical mutagens etc., These damages to DNA are repaired in the cell by various mechanisms.

a. Photoreactivation: It is the process of repairing the DNA damged by UV rays using visible light. In cells exposed to UV-rays, DNA is damaged by forming thymine dimers (T-T). Once, this dimers are formed, an enzyme called photolyase recognises the dimer and repairs the DNA by breaking the thymine dimers using the energy from visible light via FADH2. After breaking the dimers, thymine will normally pairs with adenine and the DNA returns to its normal conformational symmetry.

b. Base excision repair: It repairs the DNA that is damaged by oxidation, alkylation and deamination of bases. These modified bases pairs with incorrect base and forms mutation (non-helix-distorting base lesions) in the genome. In this repair mechanism, enzyme called DNA glycosyase recognises the damaged lesion, nicks and removes the damaged bases form the DNA forming AP (abasic) site. Afterwards, an enzyme called as AP endonuclease cleaves the DNA backbone at AP site and results in single-stranded break that is filled by DNA polymerase and the nick is sealed DNA ligase.

c. Nucleotide excision repair: It repairs the DNA that is damaged by chemical or by UV radiations. It generally removes and replaces the damaged DNA bases that distorts the double helix of the DNA. In bacteria, an enzyme complex called as UvrABC recognises the damaged bases from the DNA. Firstly, UvrA-B complex binds to DNA and scans for the damaged DNA. UvrA subunit recognises the damged base and leaves the site allowing UvrC to interact with UvrB, forming UvrBC complex. UvrB cuts the phosphodiester bond in the DNA four nucleotides downstream of the damaged base and UrvC cuts the phosphodiester bond in the DNA eight nucleotides upstream of the damaged base. Then helicase breaks the hygrogen bond between bases pairs of the 12 bases pair excision and removes the exicsed segment leaving a single stranded break that is repaired by DNA polymerase and the nick is sealed by DNA ligase.

D. Mismatch repair: It repairs the DNA damage caused by insertion and deltion of nucleotides during replication by DNA polymerase. Although DNA polymerase proof reading activity corrects errors during replication, some of the errors are missed and are repaired by mismatch repair mechanism. In this repair mechanism, mismatch repair machinery that consists of three proteins, MutS, MutH and MutL recognises damaged base and identify the daughter strand from template strand based on methylation (Parent strand methylated and daughter strand is not methylated). MutS recognises the mismatched base on the DNA and MutH nicks the DNA at the damaged site. Later, MutL recruits helicase (UvrD protein) and separates the two strands and excise damaged DNA forming a single strand gap that is synthesied by DNA polymerase and the nicks is sealed by DNA ligase.