#DNA damage

Environmental Effects - Ozone, Greenhouse and Safety

Why are UV rays harmful in large quantities?

**Ozone layer depletion** environmental concern related to increased UV-B reaching surface, causing skin cancer, cataracts, damage to crops and marine life, due to CFCs releasing Cl that catalytically destroys O₃, O₃ absorbs UV 200-320 nm, depletion increases UV transmission. The document mentions that UV rays in large quantities have harmful effects on humans, such as damaging skin cells and inducing excessive melanin production. Using c = fλ, E₀/B₀ = c, I_d = ε₀ dΦ_E/dt, and spectrum classification λ = c/f, evaluation yields They have harmful effects on humans, illustrating EM wave transvers

Ref: NCERT > Physics Book > Electromagnetic Waves > Environmental Effects - Ozone, Greenhouse and Safety

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Cell Cycle Regulation

Which component of the DNA damage response (DDR) is associated with single-strand DNA breaks?

Different lesions within DNA damage response activate distinct kinase cascades tailored to repair requirements. Single-strand breaks, gaps, and regions of single-stranded DNA generated when replication forks stall at UV photoproducts or chemical adducts expose stretches of RPA-coated ssDNA that recruit ATR-ATRIP complex and auxiliary proteins TopBP1 and ETAA1. ATR, ataxia telangiectasia and Rad3-related kinase, then phosphorylates CHK1 at serine 317 and 345, leading to degradation of Cdc25A and inhibition of CDK2 to slow S-phase progression and allow repair via homologous recombination or tran

Ref: Cimprich & Cortez, Nature Rev Mol Cell Biol 2008, ATR: Essential Regulator of Genome Integrity; Zou & Elledge, Science 2003, ATR Activation.

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Cell Cycle Regulation

Which kinase is activated in response to double-strand DNA breaks?

DNA double-strand breaks are among most deleterious lesions, potentially generating chromosomal translocations if unrepaired. Detection relies on sensor complex MRN composed of Mre11, Rad50, and Nbs1 that binds broken ends and recruits serine/threonine kinase ATM, ataxia telangiectasia mutated, member of PI3K-like kinase family. ATM exists as inactive dimer; upon recruitment and interaction with Nbs1 C-terminus, it autophosphorylates at serine 1981, dissociates into active monomers, and phosphorylates hundreds of targets including histone variant H2AX at serine 139 forming gamma-H2AX foci that

Ref: Abraham, Genes Dev 2001, ATM and ATR Kinases; Shiloh & Ziv, Nature Rev Mol Cell Biol 2013, ATM Signaling.

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Cell Cycle Regulation

What is the function of the G2 checkpoint?

After DNA replication in S phase, cells must verify that genome was fully and accurately duplicated and that any damage incurred during replication is repaired before segregating chromosomes in mitosis. G2 checkpoint serves this purpose at G2 to M transition, acting as final guardian before entry into prophase driven by CDK1-cyclin B activation. Central regulators include kinases ATR and ATM that sense single-stranded DNA and double-strand breaks, activating CHK1 and CHK2 which phosphorylate and inhibit Cdc25 phosphatase, thereby keeping CDK1 in inactive phosphorylated state bound to 14-3-3 pr

Ref: Lodish et al., Molecular Cell Biology, 9th ed., Chapter 13: DNA Damage Checkpoints; Hustedt & Durocher, Nature Cell Biol 2006, G2/M Control.

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Cell Cycle Regulation

Which checkpoint prevents cells with damaged DNA from entering S phase?

Cell cycle progression in eukaryotes is guarded by surveillance mechanisms that halt advance when conditions are unfavorable. At transition from G1 to S phase, cell must ensure adequate size, nutrients, growth factor signaling, and integrity of genome before committing to DNA replication, an irreversible step that duplicates entire genetic content. G1 checkpoint, often termed restriction point in mammalian cells, integrates signals from cyclin D-CDK4/6 and cyclin E-CDK2 that phosphorylate retinoblastoma protein Rb, releasing E2F transcription factors driving S-phase genes. If DNA damage, oxida

Ref: Alberts et al., Molecular Biology of the Cell, 7th ed., Chapter 17: Cell Cycle Control and Checkpoints; Sherr, Science 1996, G1 Progression.

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Repair Pathway

Stalled RNA polymerase during TCR recruits repair via

In bacterial transcription-coupled repair, stalled RNA polymerase at bulky lesion creates roadblock preventing repair access. Transcription-repair coupling factor Mfd, also known as TRCF, ATPase of superfamily 2, binds upstream DNA and uses ATP-driven translocation to displace stalled polymerase. Mfd contains UvrB homology module that directly recruits nucleotide excision repair machinery UvrA2B complex to damage site. By dissociating polymerase and loading Uvr proteins, Mfd couples transcription state to excision repair. MutS acts in mismatch repair, UvrD in unwinding, RecA in recombination,

Ref: NCBI Bookshelf TRCF Mfd function in TCR; Alberts et al. Chapter 6: Bacterial TCR mechanism; ScienceDirect Mfd UvrA recruitment

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Repair Pathway

Translesion DNA synthesis is

Translesion DNA synthesis represents damage tolerance mechanism allowing replication fork to bypass bulky adducts, pyrimidine dimers, cisplatin crosslinks, or apurinic sites that block high-fidelity replicative polymerases. Specialized Y-family polymerases Pol IV and Pol V possess capacious active sites accommodating distorted base pairs but lack 3' to 5' proofreading exonuclease and exhibit relaxed Watson-Crick selection. As result, they insert nucleotides opposite lesions with high misincorporation rates, generating targeted and untargeted mutations in SOS response. Though mutagenic, TLS pre

Ref: Friedberg et al., DNA Repair and Mutagenesis, 2nd ed., Chapter 15: TLS error-prone bypass mechanism; Alberts Ch.5 SOS translesion polymerases

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Repair Pathway

AP endonuclease cuts DNA at which position?

After glycosylase action, apurinic-apyrimidinic site lacks base but retains sugar-phosphate backbone. AP endonuclease family represented by E. coli exonuclease III and Xth and human APE1 incises phosphodiester immediately 5' to AP lesion generating 3'-hydroxyl and 5'-deoxyribose phosphate termini. This nick provides entry for DNA polymerase performing repair synthesis and dRP lyase activity removing sugar remnant. Cleavage strictly 5' side of lesion, not 3', creates appropriate primer for replacement synthesis. Defects in APE1 lead to accumulation of breaks and hypersensitivity to oxidizing ag

Ref: NCBI Bookshelf, Biochemistry, AP Endonuclease Incision 5' to AP Site

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Repair Pathway

Uracil in DNA is removed by

Cytosine deamination spontaneously generates uracil in DNA which pairs with adenine during replication causing C:G→T:A transition if unrepaired. Uracil-DNA glycosylase exemplifies BER initiation by flipping uracil out of helix into catalytic pocket, hydrolyzing N-glycosidic bond releasing free uracil and creating AP site. Pocket discriminates against thymine by methyl group exclusion and normal purines by size. Other glycosylases target 8-oxoguanine, alkyladenine, but uracil removal specifically handled by UNG family highly conserved. Subsequent AP endonuclease cuts, Pol I inserts cytosine, li

Ref: Lodish et al., Molecular Cell Biology, 9th ed., Chapter 12: Uracil Glycosylase Removal of Uracil

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Repair Pathway

Base excision repair is initiated by removal of

Base excision repair handles small non-helix-distorting lesions such as deaminated bases, oxidized bases, and alkylated bases. Pathway initiates with lesion-specific DNA glycosylase scanning minor groove hydrolyzing N-glycosidic bond linking damaged base to deoxyribose, leaving apurinic-apyrimidinic site with intact phosphodiester backbone. Monofunctional glycosylases generate AP site requiring AP endonuclease incision; bifunctional glycosylases additionally possess AP lyase activity. Removal strictly of base not nucleotide maintains backbone continuity distinguishing BER from NER which excise

Ref: Alberts et al., Molecular Biology of the Cell, 7th ed., Chapter 5: BER Initiation by Damaged Base Removal

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Repair Pathway

Direct repair of alkylated bases is carried out by

Alkylating agents add methyl or ethyl groups to oxygen atoms of guanine producing O6-methylguanine which mispairs with thymine leading to G:C→A:T transitions. O6-methylguanine-DNA methyltransferase encoded by MGMT in humans and Ada in bacteria directly reverses this lesion without excision. Cysteine thiol in active pocket performs stoichiometric suicide transfer of alkyl group from guanine O6 onto protein itself, restoring guanine and irreversibly inactivating enzyme that is then degraded. Each enzyme molecule acts only once. This direct reversal distinct from base excision glycosylases, UvrAB

Ref: Watson et al., Molecular Biology of the Gene, 7th ed., Chapter 10: MGMT Direct Repair of Alkylated Bases

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Repair Pathway

DNA photolyase requires which light for activation?

DNA photolyase contains light-harvesting cofactors such as methenyltetrahydrofolate and flavin adenine dinucleotide in reduced FADH- form. Enzyme flips out thymine dimer into active pocket where FADH- absorbs photons in blue region 350-450 nanometer. Upon photon absorption, excited FADH- donates electron to dimer splitting cyclobutane ring via radical mechanism returning dimers to monomeric thymines and restoring FAD radical which recaptures electron completing catalytic cycle. Absorption maximum around 384 nanometer and blue light requirement distinguishes photolyase from UV-C which itself cr

Ref: Lodish et al., Molecular Cell Biology, 9th ed., Chapter 12: Photolyase Blue Light Activation Mechanism

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