DNA Damage and Repair Mechanisms
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Questions and Answers

What type of mutation occurs when cytosine is deaminated to uracil?

  • TRANSVERSION
  • INSERTION
  • TRANSITION (correct)
  • DELETION

    • What is the role of DNA glycosylase in base excision repair?

  • Synthesizing new DNA strands
  • Ligating DNA strands
  • Removing the incorrect base and cleaving the sugar-phosphate backbone (correct)
  • Recognizing uracil in RNA

    • What type of damage can cause a GC to TA transversion?

  • Oxidative damage (correct)
  • Radiation
  • Deamination
  • Replication errors

    • What is the purpose of DNA methylation in bacteria?

    <p>To protect DNA from digestion by restriction endonucleases</p> Signup and view all the answers

    What is the difference between global genomic NER and transcription-coupled NER?

    <p>Proteins involved in the process</p> Signup and view all the answers

    What is the result of unrepaired DNA damage in xeroderma pigmentosum?

    <p>Cancer predisposition</p> Signup and view all the answers

    What is the role of homologous recombination in DNA repair?

    <p>To repair double-strand breaks</p> Signup and view all the answers

    What is the result of mutations in the MMR system?

    <p>Predisposition to colorectal cancer</p> Signup and view all the answers

    What is the role of the BRCA2 protein in DNA repair?

    <p>In homologous recombination</p> Signup and view all the answers

    What is the result of increased ability to repair radiation-induced breaks in some brain tumours?

    <p>Resistance to radiation</p> Signup and view all the answers

    Which enzyme helps to correct DNA misincorporation by proof-reading?

    <p>DNA polymerase</p> Signup and view all the answers

    What characterizes trinucleotide repeat diseases?

    <p>Repeat expansion</p> Signup and view all the answers

    What enzyme can reverse thymine dimers caused by UV light in bacteria?

    <p>DNA photolyases</p> Signup and view all the answers

    What process leads to Huntington’s disease when there are fewer than 30 repeats?

    <p>Anticipation</p> Signup and view all the answers

    Which type of DNA polymerase lacks proof-reading activity and is involved in bypassing damaged DNA sites?

    <p>TLS polymerase</p> Signup and view all the answers

    Which factor is NOT a cause of DNA damage?

    <p>Transient hairpin formation</p> Signup and view all the answers

    Which protein is involved in recruiting TLS polymerases to the 3'-end of the DNA strand?

    <p>PCNA</p> Signup and view all the answers

    What type of DNA damage is commonly caused by UV light exposure?

    <p>Thymine dimers</p> Signup and view all the answers

    What is the primary mechanism by which DNA pols correct misincorporation?

    <p>3'-5' exonuclease activity</p> Signup and view all the answers

    What is the consequence of mutations in the proof-reading domain of pol epsilon?

    <p>Hyper-mutation and cancer formation</p> Signup and view all the answers

    What is the approximate rate of error in DNA replication due to the high fidelity of DNA pols?

    <p>1 wrong nt/108-109 nts</p> Signup and view all the answers

    What is the role of MMR proteins in DNA replication?

    <p>To correct misincorporation when proof-reading fails</p> Signup and view all the answers

    What is the characteristic of DNA pols that enables them to correct misincorporation?

    <p>3'-5' exonuclease and proof-reading activity</p> Signup and view all the answers

    What is a consequence of the lack of proof-reading ability in TLS polymerases?

    <p>An increased chance of mistakes</p> Signup and view all the answers

    What is the role of the SLIDING CLAMP PCNA during DNA translesion synthesis?

    <p>To recruit TLS polymerases and swap them at the 3’-end of DNA strand</p> Signup and view all the answers

    Why can DNA replication proceed in the presence of damaged DNA sites?

    <p>Because TLS polymerases insert residues opposite the damaged sites</p> Signup and view all the answers

    At which end of the DNA strand does the SLIDING CLAMP PCNA coordinate polymerase swapping?

    <p>3’-end</p> Signup and view all the answers

    What main problem does the absence of proof-reading in TLS polymerases cause?

    <p>Elevated mutation rates</p> Signup and view all the answers

    What is the primary mechanism that leads to trinucleotide repeat diseases?

    <p>Expansion of repeat regions impairing gene function</p> Signup and view all the answers

    What is the characteristic of Huntington's disease that demonstrates anticipation?

    <p>Earlier onset of disease in offspring due to increased number of repeats</p> Signup and view all the answers

    What is the role of transient hairpin in trinucleotide repeat expansion?

    <p>Causing DNA polymerase to expand repeat regions</p> Signup and view all the answers

    What is the threshold for CAG repeats in the Huntingtin gene that leads to disease?

    <p>Over 40 repeats</p> Signup and view all the answers

    What is the consequence of trinucleotide repeat expansion in gene function?

    <p>Impaired gene function</p> Signup and view all the answers

    What is the result of deamination of cytosine to uracil in DNA?

    <p>Conversion of CG to TA</p> Signup and view all the answers

    What is the role of DNA photolyases in bacteria?

    <p>To reverse thymine dimers caused by UV light</p> Signup and view all the answers

    What is the function of UDG in base excision repair?

    <p>To recognise and remove uracil from DNA</p> Signup and view all the answers

    What is the result of oxidative damage to guanine in DNA?

    <p>A GC to TA transversion</p> Signup and view all the answers

    What is the role of DNA methylation in eukaryotes?

    <p>To control gene expression by methylating CpG islands</p> Signup and view all the answers

    What is the difference between LONG-PATCH BER and SHORT-PATCH BER?

    <p>The enzymes involved in the process</p> Signup and view all the answers

    What is the purpose of NER in eukaryotes and prokaryotes?

    <p>To repair pyrimidine dimers and distortions of double helix</p> Signup and view all the answers

    What is the result of mutations in genes encoding NER enzymes?

    <p>Xeroderma pigmentosum</p> Signup and view all the answers

    Why do bacteria methylate their DNA?

    <p>To excise non-methylated DNA</p> Signup and view all the answers

    What is the consequence of mutations in the MMR system?

    <p>Predisposition to colorectal cancer</p> Signup and view all the answers

    What is the difference between global genomic NER and transcription-coupled NER?

    <p>Different proteins are involved</p> Signup and view all the answers

    What is the primary consequence of using NHEJ to repair broken DNA ends?

    <p>Inherently mutagenic, leading to loss of DNA at the joining site</p> Signup and view all the answers

    In which phase of the cell cycle is NHEJ most important?

    <p>Resting G1 and G0 phases</p> Signup and view all the answers

    What is a consequence of mutations in NHEJ proteins?

    <p>Cancer</p> Signup and view all the answers

    What is the result of NHEJ-mediated DNA repair?

    <p>Loss of DNA at the joining site</p> Signup and view all the answers

    Why is NHEJ inherently mutagenic?

    <p>Because it can result in loss of DNA at the joining site</p> Signup and view all the answers

    What is the purpose of the extra copy of the chromosome in HR repair mechanism?

    <p>To act as a template for repair of damaged chromosome</p> Signup and view all the answers

    What is the outcome of the HR process if it leads to a crossed-over configuration?

    <p>DNA is swapped between the two chromosomes</p> Signup and view all the answers

    What is the role of RAD51 in HR?

    <p>Scanning the genome for identical dsDNA sequences</p> Signup and view all the answers

    What is the function of RubAB complex in HR?

    <p>Facilitating the sliding of Holliday junctions</p> Signup and view all the answers

    What is the outcome of the HR process if it leads to the restoration of 2 linear duplexes?

    <p>The parental DNA is regenerated</p> Signup and view all the answers

    Which protein mutation is commonly associated with inherited breast cancer?

    <p>BRCA2</p> Signup and view all the answers

    Which process contributes to antibody diversity by joining different DNA segments?

    <p>Non-homologous end joining</p> Signup and view all the answers

    What is the role of TERMINAL TRANSFERASE in the diversification of antibodies?

    <p>Adding extra nucleotides at junctions</p> Signup and view all the answers

    In which condition does translocation of parts of chromosome 9 and 22 play a significant role?

    <p>Chronic Myelogenous Leukemia</p> Signup and view all the answers

    Which of the following mutations can lead to immunodeficiency through failure in antibody diversity generation?

    <p>Mutations in NHEJ genes</p> Signup and view all the answers

    What is the principle behind using synthetic lethality in cancer treatment?

    <p>To inhibit specific pathways used more by cancer cells than normal cells</p> Signup and view all the answers

    Which drug is an example of a PARP inhibitor used in treating cancers with BRCA2 defects?

    <p>Olaparib</p> Signup and view all the answers

    What type of gene defect makes cancers particularly vulnerable to PARP inhibitors like Olaparib?

    <p>BRCA2 gene defect</p> Signup and view all the answers

    What is the main advantage of using synthetic lethality in cancer therapy?

    <p>It minimizes damage to normal cells by targeting specific repair pathways</p> Signup and view all the answers

    Which concept explains the mechanism by which Olaparib functions in BRCA2 deficient cancers?

    <p>Synthetic lethality</p> Signup and view all the answers

    Study Notes

    DNA Damage and Repair

    • DNA damage can occur due to various factors, including the release of aromatic bases, oxidative damage to bases, crosslinking of bases, and breaks in phospho-ester strands.
    • Humans have 150 genes that are responsible for DNA repair and maintaining genetic stability.

    Proof-Reading and Mismatch Repair

    • DNA polymerases have high fidelity and are accurate, with an error rate of 1 wrong nucleotide per 10^8-10^9 nucleotides.
    • DNA polymerases have 3'-5' exonuclease proof-reading activity, which corrects misincorporation.
    • Mismatch repair proteins act if proof-reading fails, correcting mismatches.

    Translesion Synthesis

    • Translesion synthesis (TLS) pols can insert residues opposite damaged sites, allowing DNA replication to proceed.
    • TLS pols lack proof-reading, increasing the chance of mistakes.
    • The recruitment of TLS pols is coordinated by the sliding clamp PCNA, which swaps pols at the 3'-end of the DNA strand.

    Trinucleotide Repeat Diseases

    • Short tandem repeats can display polymorphism, leading to errors in replication.
    • Trinucleotide repeat diseases occur when the expansion of repeats impairs the function or behavior of a gene product.
    • Huntington's disease is an example of a trinucleotide repeat disease, caused by the expansion of CAG repeats in the Huntingtin gene.

    UV Light-Induced Damage

    • UV light can crosslink adjacent thymine residues, forming cyclobutyl ring dimers that deform the double helix and obstruct DNA replication and RNA transcription.
    • This can be reversed in bacteria by DNA photolyases, which use light to split the dimer.

    Deamination and Base Excision Repair

    • Deamination of cytosine to uracil can convert CG to TA in later generations.
    • DNA glycosylase recognizes uracil in DNA and flips it out of the double helix, cleaving the glycosidic link to deoxyribose and leaving an abasic site.
    • This site is recognized by a nuclease, which cleaves the backbone and produces a 3'OH upstream of the abasic site, acting as a priming site for DNA pol to fill in.

    Oxidative Damage and Mismatch Repair

    • Oxidative damage can form 8-oxoGuanine, leading to GC to TA transversions if unrepaired.
    • A specific glycosylase removes oxidized bases.

    Methylation and Gene Expression

    • Methylation of DNA on C/A by Dam methyltransferase controls gene expression in bacteria.
    • In eukaryotes, methylation occurs at CpG islands to switch off nearby genes, which is the basis of genomic imprinting.

    Nucleotide Excision Repair

    • Nucleotide excision repair (NER) repairs pyrimidine dimers and distortions of the double helix in eukaryotes and prokaryotes.
    • NER exists as global genomic and transcription-coupled NER, which differ in proteins but have the same steps.

    Double-Strand Breaks

    • Double-strand breaks (DSBs) can be caused by radiation, reactive oxygen species, and during replication, leading to cell death or high mutagenicity.
    • There are two main repair mechanisms for DSBs: non-homologous end joining (NHEJ) and homologous recombination (HR).

    Non-Homologous End Joining

    • NHEJ sticks two broken ends of DNA together, restoring the original sequence, but can be inherently mutagenic.
    • NHEJ is important in resting G1 and G0 phases.

    Homologous Recombination

    • Homologous recombination is a more complex but potentially error-free mechanism that uses an extra copy of the chromosome as a template for repair.
    • The process generates Holliday junctions, which can slide up and down the DNA.

    DNA Repair and Cancer

    • Loss of NER protein function and DSB protein increases cancer predisposition.
    • Mutations in BRCA2, ATM, Chk2, p53, Nbs1, and Mre11 increase cancer risk.
    • Some cancers resist radiation by increasing their ability to repair radiation-induced breaks.

    Synthetic Lethality

    • Inhibiting specific DNA repair pathways used by cancer cells can have little impact on the rest of the cell, a concept known as synthetic lethality.
    • Examples include PARP inhibitors for BRCA2-deficient cancers.

    DNA Polymerase Accuracy

    • DNA polymerases are highly accurate, with an error rate of approximately 1 incorrect nucleotide per 108-109 nucleotides.
    • This accuracy is due to the 3'-5' exonuclease proof-reading activity of DNA polymerases, which allows them to correct errors during DNA replication.
    • In cases where proof-reading fails, Mismatch Repair (MMR) proteins can step in to correct errors.
    • Mutations in the proof-reading domain of DNA polymerase epsilon have been implicated in driving cancer formation through hyper-mutation.

    DNA Translesion Synthesis (TLS)

    • TLS polymerases (Pols) insert residues opposite damaged sites, allowing DNA replication to proceed despite the presence of unrepaired DNA damage.
    • TLS Pols lack proof-reading activity, which increases the chance of mistakes during DNA replication.
    • The recruitment of TLS Pols is coordinated by the Sliding Clamp PCNA, which facilitates the swapping of Pols at the 3’-end of the DNA strand.

    Trinucleotide Repeat Diseases

    • Trinucleotide repeat diseases occur when the expansion of repeats impairs the function or behavior of the gene product.
    • Repeat expansion can cause errors in replication, making some repeats more prone to errors.

    Huntington's Disease

    • Huntington's disease is caused by CAG repeats in the Huntingtin gene.
    • Individuals with fewer than 30 repeats do not develop the disease.
    • Individuals with over 40 repeats will develop the disease.
    • Huntington's disease demonstrates anticipation, where affected offspring develop the condition earlier due to an increased number of repeats.
    • The increase in repeat number is due to the transient hairpin formation in the repeat regions, causing the machinery to expand the region.

    Effects of UV Light on DNA

    • UV light can cause crosslinking of adjacent thymine residues, forming cyclobutyl ring dimers, which deform the double helix and obstruct DNA replication and RNA transcription

    DNA Repair Mechanisms

    • DNA photolyases can reverse thymine dimers using light
    • Deamination of cytosine to uracil can lead to CG to TA conversion in later generations, known as a transition
    • Uracil in DNA is recognized by DNA glycosylase (UDG), which flips it out of the double helix, cleaves the glycosidic link, and leaves an abasic site
    • Abasic site is recognized by a nuclease, which cleaves the backbone, producing a 3'OH upstream of the abasic site, acting as a priming site for DNA polymerase to fill in

    Base Excision Repair (BER)

    • BER can occur via Long-Patch BER or Short-Patch BER
    • Long-Patch BER involves the same proteins that process Okazaki fragments synthesizing over the abasic site
    • Short-Patch BER involves specialized DNA repair polymerase beta filling in the gap
    • DNA ligase seals the nick after repair

    Oxidative Damage and DNA Repair

    • Oxidative damage can form 8-oxoGuanine, leading to GC to TA transversion, commonly seen in cancers
    • A specific glycosylase removes the oxidized base to prevent mutations

    DNA Methylation and Gene Expression

    • DNA methylation by DAM methyltransferase (in bacteria) controls gene expression and protects DNA from digestion by restriction endonucleases
    • In eukaryotes, DNA methylation occurs at CpG islands, switching off nearby genes, which is the basis of genomic imprinting
    • Genomic imprinting results in parent-of-origin expression, where one copy of the gene is silent due to methylation

    Nucleotide Excision Repair (NER)

    • Repairs pyrimidine dimers and distortions of the double helix in both eukaryotes and prokaryotes.
    • The NER process involves the detection of a lesion, followed by the binding of protein machinery, unwinding of DNA, cleavage of the strand containing the lesion, and the creation of a short ssDNA gap.
    • The ssDNA gap is then filled by DNA polymerase.

    Global Genomic NER and Transcription-Coupled NER

    • Both types of NER follow the same steps, but differ in the proteins involved.

    Xeroderma Pigmentosum (XP)

    • A genetic disorder caused by mutations in genes encoding NER enzymes.
    • Characterized by autosomal recessive inheritance.

    Methyl-Directed Mismatch Repair (MMR) in Bacteria

    • Bacterial DNA is typically methylated, allowing for the identification of non-methylated DNA.
    • Non-methylated DNA is excised, and the resulting gap is filled by DNA polymerase.

    MMR System Defects and Cancer

    • Mutations in the MMR system are associated with a predisposition to colorectal cancer.

    DNA Repair

    • Sticking two broken ends of DNA together can restore the original sequence, but often requires cleaning, resulting in loss of DNA at the joining site, making it inherently mutagenic.

    Non-Homologous End Joining (NHEJ)

    • NHEJ is crucial in the resting G1 and G0 phases of the cell cycle.

    NHEJ and Cancer

    • Mutations in NHEJ proteins can lead to cancer, such as mutations in DNA ligase IV, which are associated with certain types of leukemia.

    Homologous Recombination (HR)

    • HR is a complex but potentially error-free mechanism for repairing damaged DNA.
    • It uses an extra copy of the chromosome as a template for repair.

    Process of HR

    • dsDNA break is processed, trimming the 5’ end and leaving an extended ssDNA 3’ end.
    • The ssDNA end is recognized by RecA (in bacteria) or RAD51 (in eukaryotes).
    • RecA/RAD51 scans the genome for identical dsDNA sequences.
    • Once a suitable target is found, it directs strand invasion, replacing one duplex strand with the ssDNA damaged strand.
    • The invaded end is primed for replication, copying DNA from the intact strand to fill the gap.

    Holliday Junctions

    • The process generates Holliday Junctions, which are mobile four-way junctions in DNA.
    • Holliday Junctions can slide up and down the DNA.
    • In bacteria, the sliding is facilitated by the RubAB complex, which uses ATP.

    Outcomes of HR

    • HR can restore two linear duplexes to regenerate parental DNA.
    • Alternatively, HR can lead to a crossed-over configuration (where DNA is swapped), which occurs in meiosis.
    • HR also restarts stalled or broken replication forks, which is essential for cell division (10 forks per eukaryotic cell cycle must be resolved).

    DSB Repair and Cancer

    • Loss of NER protein function and DSB protein can lead to cancer predisposition.
    • BRCA2 mutations are associated with sporadic and inherited breast cancer and play a role in Homologous Recombination (HR) repair.
    • Mutations in ATM, Chk2, p53, Nbs1, and Mre11, which are involved in DSB repair, increase cancer risk.

    Radiation Resistance and Cancer

    • Some brain tumors develop resistance to radiation by increasing their ability to repair radiation-induced DNA breaks.

    Positive and Negative Consequences of DSB Repair

    • DSB repair can be beneficial, such as in generating antibody diversity by joining different DNA segments, increasing variation.
    • However, DSB repair can also be detrimental, such as in the translocation of parts of chromosome 9 and 22, leading to Chronic Myelogenous Leukaemia.

    Antibody Diversity Generation

    • Enzymes like Terminal Transferase add extra nucleotides at junctions, increasing diversity by being sloppy in the number of bases added.
    • Non-Homologous End Joining (NHEJ) mediates antibody diversity generation, and mutations in NHEJ genes lead to immunodeficiency and failure to perform antibody diversity generation.

    Cancer Repair Mechanisms

    • Cancer cells inactivate certain repair mechanisms to gain a survival advantage.
    • Specific pathways are exploited by cancers more frequently, making them potential targets for inhibition.

    Synthetic Lethality

    • Synthetic lethality is a strategy to inhibit cancer-specific pathways with minimal impact on normal cells.
    • This approach is achieved by targeting specific pathways that are critical for cancer cell survival.

    PARP Inhibitors

    • Olaparib is a PARP (Poly ADP-ribose polymerase) inhibitor.
    • PARP inhibitors are effective against cancer cells with BRCA2 defect genes.
    • BRCA2 defect genes are associated with increased cancer susceptibility.

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    Description

    This quiz covers the various types of DNA damage and the mechanisms of DNA repair, including proof-reading and mismatch repair. Learn about the importance of DNA repair in maintaining genetic stability.

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