Molec Bio Lecture 7

__________ is an enzyme in Base Excision Repair (BER) that cuts the sugar-phosphate backbone of DNA at an apurinic or apyrimidinic (AP) site where a base is missing.Answer:

AP Endonuclease

__________ is a homology-dependent repair pathway that fixes minor, "non-bulky" DNA damage that does not distort the double helix (e.g., missing bases from depurination/depyrimidation or altered bases from deamination/oxidation).Answer:

Base-Excision Repair (BER)

__________ are specialized error-prone DNA polymerases (at least 5 distinct types in eukaryotes) that temporarily replace stalled replicative polymerases (Pol D/E) to synthesize DNA directly across unrepaired damage during translesion synthesis.Answer:

Bypass Polymerase (Eukaryotes)

__________ is the specific prokaryotic error-prone bypass polymerase (DNA Polymerase V) that replaces Pol III at stalled replication forks to replicate across damage during translesion synthesis / SOS repair.Answer:

Bypass Polymerase = Pol V in Prokaryotes

__________ is an enzyme that works alongside superoxide dismutase (SOD) to convert hydrogen peroxide ($H_2O_2$) into water ($H_2O$), eliminating reactive oxygen species (ROS) that cause oxidative DNA damage.Answer:

Catalase

__________ is the central constricted region of a chromosome that separates the short arm (P arm) and the long arm (Q arm).Answer:

Centromere

__________ are the structural subdivisions of a chromosome demarcated by the centromere; the P arm refers to the short arm, and the Q arm refers to the long arm.Answer:

Chromosomes: P and Q Arms

__________ is a primary type of UV radiation-induced DNA lesion where a cyclobutane ring forms between adjacent pyrimidine bases, distorting the double helix; also known as CPP.Answer:

CPD (Cyclobutane Pyrimidine Dimers)

__________ is an alternative name for cyclobutane pyrimidine dimers (CPDs) caused by UV light exposure.Answer:

CPP (Cyclobutane Pyrimidine Pairs)

__________ are Cockayne Syndrome proteins A and B; proteins recruited when RNA polymerase stalls at bulky lesions during transcription-coupled NER. Defects in these proteins cause Cockayne syndrome.Answer:

CSA and CSB

__________ is severe DNA damage where both strands of the double helix are severed—caused by radiation, chemicals, ROS, or replication across a nick—and repaired via Non-Homologous End Joining (NHEJ) or homologous recombination.Answer:

Double Stranded Break (DSB)

__________ is a repair mechanism that directly undoes DNA damage without cutting the backbone or removing bases, such as CPD photolyase using visible light to reverse UV photodimers.Answer:

Direct Reversal

__________ is an enzyme in prokaryotic Base Excision Repair that cleaves phosphodiester bonds in the DNA backbone to remove adjacent nucleotides following AP endonuclease cleavage.Answer:

dRpase (Deoxyribose Phosphodiesterase)

__________ is an enzyme in Base Excision Repair that detects and cleaves out an incorrect or damaged base (e.g., deaminated or oxidized bases), leaving an apurinic/apyrimidinic (AP) site.Answer:

DNA Glycosylase

__________ is an enzyme that seals single-stranded nicks in the sugar-phosphate backbone across multiple repair pathways (BER, NER, MMR, and NHEJ).Answer:

DNA Ligase

__________ refers to chemical methyl tags present on the original parent DNA strand in prokaryotes, enabling MutH in mismatch repair to distinguish the parent strand from the newly synthesized, unmethylated daughter strand.Answer:

DNA Methylation

__________ is a eukaryotic DNA polymerase involved in repair synthesis during Nucleotide Excision Repair and Mismatch Repair, as well as replicative synthesis that stalls at DNA lesions prior to bypass polymerase recruitment.Answer:

DNA Polymerase D (Pol D)

__________ is an enzyme that cleaves internal phosphodiester bonds within a DNA strand, used in Base Excision Repair (AP endonuclease) and Nucleotide Excision Repair to cut around damaged DNA segments.Answer:

Endonuclease

__________ refers to last-resort repair mechanisms—specifically the SOS system / Translesion Synthesis and Non-Homologous End Joining (NHEJ)—that permit cell survival or replication past damage without correcting the underlying errors, often introducing mutations.Answer:

Error Prone Repair

__________ refers to pathways (including Base Excision Repair and Nucleotide Excision Repair) that excise damaged bases or nucleotide stretches and resynthesize the correct sequence using the undamaged complementary strand as a template.Answer:

Excision Repair

__________ is a pathway of Nucleotide Excision Repair that operates in transcriptionally silent regions of the genome; damage is recognized by XPC and XPE, which recruit the TFIIH complex.Answer:

Global Genomic Repair (GGR)

__________ refers to DNA repair mechanisms (Base Excision Repair, Nucleotide Excision Repair, Mismatch Repair) that rely on the complementary sequence of the undamaged opposite DNA strand to accurately remove and replace damaged bases.Answer:

Homology Dependent Repair

__________ refers to insertion or deletion mutations, which are inevitably generated during the trimming and ligation process of Non-Homologous End Joining (NHEJ).Answer:

Indel

__________ is a large-scale chromosomal modification where a segment is reversed end-to-end; can be produced during error-prone NHEJ repair of double-strand breaks.Answer:

Inversion

__________ is a heterodimer protein complex that binds to and stabilizes broken double-stranded DNA ends during NHEJ, subsequently recruiting other repair complex components.Answer:

Ku80 / Ku70

__________ refers to major structural chromosomal alterations—such as deletions, inversions, and translocations—typically arising from double-strand break repairs and frequently associated with syndromic diseases and cancers.Answer:

Large Scale DNA Damage

__________ is a post-replication, homology-dependent repair system that recognizes and corrects mispaired bases and small loops that escaped the 3' to 5' proofreading activity of replicative DNA polymerases.Answer:

Mismatch Repair (MMR)

__________ are bacterial mismatch repair proteins: MutS recognizes mismatched pairs and small loops; MutL positions MutH; MutH recognizes parent strand methylation and nicks the unmethylated daughter strand containing the error.Answer:

MutS / MutL / MutH

__________ is a homology-dependent pathway that fixes bulky, double-helix-distorting lesions (such as UV photodimers) via two initial pathways—Global Genomic Repair (GGR) or Transcription-Coupled Repair (TC-NER).Answer:

NER (Nucleotide-Excision Repair)

__________ is an error-prone repair mechanism of last resort for double-stranded breaks that trims and ligates broken DNA ends without requiring a homologous template strand.Answer:

NHEJ (Non-Homologous End Joining)

__________ is a structural protein component assembled into the multi-protein repair complex (along with DNA-PK, Artemis, XRCC4, and DNA ligase IV) during Non-Homologous End Joining.Answer:

NHEJ1 Protein

__________ is a lesion created when UV light induces covalent cross-linking between adjacent pyrimidine bases on a DNA strand (e.g., cyclobutane pyrimidine dimer).Answer:

Photodimer

__________ is the enzyme (CPD photolyase) that uses energy from visible light (350–450 nm) to directly reverse UV-induced photodimers back into normal bases (absent in placental mammals).Answer:

Photolyase

__________ refers to DNA repair pathways that operate during or after DNA replication to correct errors or damage, notably including mismatch repair.Answer:

Post-Replication Repair

__________ refers to replicative DNA polymerases with 3' to 5' exonuclease activity that detect and excise mismatched bases immediately as they are incorporated during replication; considered the most common mechanism for preventing errors.Answer:

Proof-Reading DNA Polymerase

__________ are the Y-shaped structures where DNA replication occurs; stalled replication forks caused by unrepaired lesions trigger repair pathways like NER or error-prone translesion synthesis.Answer:

Replication Forks

__________ is the enzyme that transcribes DNA into RNA; its stalling at bulky lesions distorts the double helix and recruits CSA/CSB to initiate transcription-coupled NER.Answer:

RNA Polymerase

__________ is a protein recruited during NER that binds to and stabilizes single-stranded DNA segments generated during unwinding.Answer:

RPA (Replication Protein A)

__________ is a eukaryotic sliding clamp protein that positions MutL/MutH homologs in mismatch repair, recruits Pol D/E and ligase in NER, and recruits error-prone bypass polymerases in translesion synthesis.Answer:

PCNA (Proliferating Cell Nuclear Antigen)

__________ are sequence variations (such as synonymous mutations like M5) that alter the DNA codon without changing the encoded amino acid, resulting in no effect on protein function.Answer:

Silent Mutations and Polymorphisms

__________ is an error-prone repair system of last resort utilized when NER fails, employing translesion synthesis to replicate past unrepaired damage at stalled replication forks.Answer:

SOS Repair

__________ is an antioxidant enzyme that neutralizes reactive oxygen species (ROS) into $H_2O_2$ to prevent oxidative DNA lesions like 8-oxo-dG and thymidine glycol.Answer:

SOD (Superoxide Dismutase)

__________ is a specialized NER pathway operating during active transcription, where stalled RNA polymerase recruits CSA and CSB proteins to swiftly repair bulky lesions in transcribed strands.Answer:

Transcription Coupled Repair (TC-NER)

__________ is an error-prone process where a specialized bypass polymerase replaces a stalled replicative DNA polymerase to synthesize DNA across an unrepaired damage site.Answer:

Translesion Synthesis (TLS)

__________ is a large-scale chromosomal defect involving the relocation of a genetic segment to another chromosome; can occur as an erroneous outcome of NHEJ.Answer:

Translocation

__________ refers to DNA lesions produced by ultraviolet radiation, primarily inducing cyclobutane pyrimidine dimers (CPDs) that disrupt double helix structure.Answer:

UV Light Damage

__________ are Xeroderma pigmentosum proteins B and D; helicase enzymes within the TFIIH complex that unwind DNA around a lesion during NER. Mutations in their genes lead to Xeroderma pigmentosum.Answer:

XPB / XPD

__________ is a protein component assembled with Artemis, DNA-PK, NHEJ1, and DNA Ligase IV in the repair complex during Non-Homologous End Joining.Answer:

XRCC4 (X-ray Repair Cross-Complementing Protein 4)

Homology dependent repair are….

high fidelity mechanisms

Base excision repair – triggered by…

non-bulky changes in DNA

Base excision repair uses….

1.) DNA glycosylase,

2.) AP endonuclease,

3.) dRPase (prokaryotes) or Flap endonuclease (eukaryotes)

4. DNA polymerase,

5. DNA ligase)

Nucleotide excision repair examples

(Global Genomic Repair/Global Genomic NER and Transcription-coupled NER)

Nucleotide excision repair Process

(Global Genomic Repair/Global Genomic NER and Transcription-coupled NER)

1. GGR – damaged bases recognized by

2. XPC/XPE o Transcription-coupled NER – stalled RNA pol recruits CSA/CSB

3. Both assemble TFIIH complex containing XPB/XPD, then RPA and endonucleases – cuts out a segment

4. PCNA and DNA polymerase D/E fill the gap

5. DNA ligase seals the nick

GGR –

damaged bases recognized by XPC/XPE

what is Transcription-coupled NER

stalled RNA pol recruits CSA/CSB o Both assemble TFIIH complex containing XPB/XPD, then RPA and endonucleases – cuts out a segment

PCNA and DNA polymerase D/E

fill the gap

DNA ligase

seals the nick

Mismatch repair – only following

DNA replication

MutS recognizes

mispaired bases or small loops (MutS homologues in eukaryotes)

MutH (only present in ———)

prokaryotes

MutH (only prokaryotes) fx?

recognizes parent strand by methylation and cuts new daughter strand.

MutL fx

holds DNA strands together and recruits other exonucleases to remove mutant strand.

MutS/MutL homologues in eukaryotes……..

do the same thing as MutL: holds DNA strands together and recruits other exonucleases to remove mutant strand.

In eukaryotes, ——— discriminates the strands.

PCNA

DNA polymerase D/E fx

fill the gap

DNA ligase fx

DNA ligase seals the nick

Mismatch repair

– only following DNA replication

o MutS recognizes mispaired bases or small loops (MutS homologues in eukaryotes)

o MutH (only prokaryotes) recognizes parent strand by methylation and cuts new daughter strand.

o MutL holds them together and recruits other exonucleases to remove mutant strand. MutS/MutL homologues in eukaryotes do the same thing.

o In eukaryotes, PCNA discriminates the strands.

o DNA polymerase D/E fill the gap

o DNA ligase seals the nick

Homology dependent repair – error-prone mechanisms

• Translesion synthesis (SOS system) – recruited if DNA polymerase stalls at DNA damage during replication

o Bypass polymerases recruited by the replication clamp (Beta Clamp in prokaryotes, PCNA in eukaryotes)

o Replicates across the damaged region – rescues cells from apoptosis

Homology dependent repair are…

error-prone mechanisms

Translesion synthesis (SOS system) – recruited if….

DNA polymerase stalls at DNA damage during replication

in Homology dependent repair, Bypass Polymerases are recuited by….

pro-?

eu-?

the replication clamp

Pro: Beta Clamp

Eu: PCNA

SOS system Replicates across the ——

damaged region – rescues cells from apoptosis

Homolgy-independent repair

• Non-homologous End Joining (NHEJ) – always results in indels. May result in chromosome translocations or inversions.

o Ku70/Ku80 heterodimers bind and stabilize broken DNA ends

o Repair complex assembles (DNA PK, Artemis, XRCC4, NHEJ1, DNA Ligase IV)

o Trims ends and ligates DNA together

Non-homologous End Joining (NHEJ) – ALWAYS results in …

INDELS

Non-homologous End Joining (NHEJ) may result in…

chromosome translocations or inversions.

Ku70/Ku80 heterodimers fx?

bind and stabilize broken DNA ends

Repair complex fx

assembles (DNA PK, Artemis, XRCC4, NHEJ1, DNA Ligase IV)

-Trims ends and ligates DNA together

Homologous Recombination happens…

only during replication- double-strand break repair that is high fidelity

In homologous recombination, exonucleases…

trim back 5’ ends of breaks, leaving exposed 3’ ends o 3’ end invades homologous chromosome and base pairs with homologous region forming a D-loop

Homologous Recombo: Exonucleases trim back 5’ ends of breaks, leaving exposed 3’ ends o 3’ end invades homologous chromosome and base pairs with homologous region forming a ——-

D-loop

Homologous Recombination: 3’ end is extended by DNA polymerase using ….

homologous chromosome as template

Homologous Recombination resolves in….

two ways

Homologous Recombination resolves by: Other 3’ end is also captured and extended on homologous chromosome in double D-loop. Ends are ligated and…

Holiday junction is resolved either with crossover or without crossover (involves cleaving two strands and ligating ends)

Homologous Recombination resolves by: Extended 3’ end is…

displaced and anneals with its own complementary strand. Gaps are filled by DNA polymerase and nicks ligated.