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Questions and Answers
What is the primary function of DNA polymerase proofreading?
What is the primary function of DNA polymerase proofreading?
Which type of replication ensures that new nucleotides are included on one of the strands of both double helices?
Which type of replication ensures that new nucleotides are included on one of the strands of both double helices?
What role do single-strand DNA-binding (SSB) proteins play during DNA replication?
What role do single-strand DNA-binding (SSB) proteins play during DNA replication?
How do topoisomerases help during DNA replication?
How do topoisomerases help during DNA replication?
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What is the function of the sliding clamp in DNA replication?
What is the function of the sliding clamp in DNA replication?
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Which process involves the removal of a nucleotide due to the incorrect incorporation during DNA synthesis?
Which process involves the removal of a nucleotide due to the incorrect incorporation during DNA synthesis?
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Which of the following components is specifically involved in forming bonds between phosphate and sugar in DNA?
Which of the following components is specifically involved in forming bonds between phosphate and sugar in DNA?
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What is the main outcome of somatic cell stability in multicellular organisms?
What is the main outcome of somatic cell stability in multicellular organisms?
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Which enzyme removes a damaged base in base excision repair?
Which enzyme removes a damaged base in base excision repair?
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What is the role of topoisomerase II during DNA replication?
What is the role of topoisomerase II during DNA replication?
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During which phase does the phosphorylation of the ORC and helicases occur?
During which phase does the phosphorylation of the ORC and helicases occur?
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Which repair mechanism is primarily responsible for fixing bulky lesions?
Which repair mechanism is primarily responsible for fixing bulky lesions?
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What occurs as a result of deamination in DNA?
What occurs as a result of deamination in DNA?
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What is the primary consequence of depurination in DNA?
What is the primary consequence of depurination in DNA?
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What is the typical gap created by nucleotide excision repair in human DNA?
What is the typical gap created by nucleotide excision repair in human DNA?
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Which process is characterized by low processivity and lacks proofreading?
Which process is characterized by low processivity and lacks proofreading?
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What leads to the formation of pyrimidine dimers in DNA?
What leads to the formation of pyrimidine dimers in DNA?
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What happens to cells without telomerase during replication?
What happens to cells without telomerase during replication?
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What is the primary role of DNA topoisomerase I during DNA replication?
What is the primary role of DNA topoisomerase I during DNA replication?
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How do phosphodiester bonds contribute to DNA structure?
How do phosphodiester bonds contribute to DNA structure?
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In which model of DNA replication are the new nucleotides interspersed throughout both double helices?
In which model of DNA replication are the new nucleotides interspersed throughout both double helices?
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What is the significance of exonucleatic proofreading in DNA replication?
What is the significance of exonucleatic proofreading in DNA replication?
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What function do single-strand DNA-binding (SSB) proteins serve during replication?
What function do single-strand DNA-binding (SSB) proteins serve during replication?
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What problem does DNA ligase specifically address during DNA replication?
What problem does DNA ligase specifically address during DNA replication?
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What role does the sliding clamp play in the process of DNA replication?
What role does the sliding clamp play in the process of DNA replication?
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Which statement accurately describes the main consequence of germ cell stability?
Which statement accurately describes the main consequence of germ cell stability?
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What do DNA helicases and single-strand DNA-binding proteins have in common during replication?
What do DNA helicases and single-strand DNA-binding proteins have in common during replication?
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Which statement accurately describes the role of topoisomerase II in DNA processing?
Which statement accurately describes the role of topoisomerase II in DNA processing?
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What is the primary function of glycosylases within the base excision repair mechanism?
What is the primary function of glycosylases within the base excision repair mechanism?
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During which phase is the ORC inactivated and what is the result of this inactivation?
During which phase is the ORC inactivated and what is the result of this inactivation?
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Which enzyme complex is responsible for recognizing bulky lesions in DNA during nucleotide excision repair?
Which enzyme complex is responsible for recognizing bulky lesions in DNA during nucleotide excision repair?
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How does translesion DNA polymerase function during DNA replication?
How does translesion DNA polymerase function during DNA replication?
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What type of DNA lesion occurs spontaneously through oxidative damage?
What type of DNA lesion occurs spontaneously through oxidative damage?
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Which statement best describes the replication origins in DNA?
Which statement best describes the replication origins in DNA?
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What is a consequence of the lack of telomerase in cells?
What is a consequence of the lack of telomerase in cells?
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What happens following the removal of a U-base by Uracil DNA Glycosylase?
What happens following the removal of a U-base by Uracil DNA Glycosylase?
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Study Notes
DNA Replication
- Germ cell stability is essential for maintaining genetic information for species perpetuation.
- Somatic cell stability prevents cancer by ensuring proper cell division and function.
- DNA polymerase and DNA primase catalyze the polymerization of nucleoside triphosphates, forming the DNA backbone.
- DNA helicases and single-strand DNA-binding proteins unwind the DNA helix, allowing replication to occur.
- DNA ligase and an enzyme that degrades RNA primers seal together the lagging strand DNA fragments.
- DNA topoisomerases relieve helical winding and DNA tangling problems.
- Phosphodiester bond forms between phosphate and sugar in the DNA backbone; DNA polymerase forms a tight grip around the active site when the correct nucleotide enters.
- DNA polymerase proofreading ensures accuracy by checking and correcting base pairing before catalyzing the reaction.
- Exonucleatic proofreading removes incorrectly incorporated nucleotides, stopping further elongation.
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Models of replication:
- Conservative replication: The new double helix is made from entirely new nucleotides.
- Dispersive replication: New nucleotides are dispersed across both double helices.
- Semiconservative replication: The new nucleotides are incorporated on one of the two strands of both double helices.
- Single-stranded DNA binding (SSB) proteins stabilize single-stranded DNA during replication and prevent re-annealing.
- A sliding clamp is a circular protein complex that encircles DNA, assisting DNA polymerase to bind to the DNA.
- Supercoils are loops of DNA double helix wrapped around the straight-lined double helix.
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Topoisomerases prevent DNA tangling and supercoiling during replication.
- Topoisomerase I relieves torsional stress by breaking one phosphodiester bond in the DNA molecule, allowing the two ends of the helix to rotate.
- Topoisomerase II reduces supercoiling by recognizing entanglement, creating a protein gate that allows another DNA double helix to pass through.
- Topoisomerase II requires ATP for its function.
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Base excision repair is a mechanism to repair damaged bases.
- Glycosylases remove damaged bases by excising the sugar-phosphate bond.
- Uracil DNA glycosylase removes uracil (U) bases, creating a gap.
- AP endonuclease removes the phosphate, allowing DNA polymerase to add a new base.
- Ligase seals the nick in the DNA.
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Nucleotide excision repair repairs bulky lesions (large areas of errors).
- An enzyme complex recognizes bulky lesions that distort the helix.
- Endonuclease cuts on both sides of the DNA backbone.
- Helicase removes the fragment containing the bulky lesion, creating a gap.
- DNA polymerase and Ligase resynthesize and seal the DNA, removing the bulky lesion.
- Replication origins are AT-rich regions on the DNA where replication starts, easier to destabilize due to only 2 H-bonds.
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Replication initiation phases:
- G1-Phase: Non-phosphorylated ORC (Origin Recognition Complex) binds to the origin. ORC loads nearby helicases onto the DNA.
- S-Phase: ORC and helicases become phosphorylated. ORC is inactivated, and helicases are activated. The replication bubble opens, and the replication fork begins.
- G2-Phase: ORC is phosphorylated and inactive.
- M-Phase: ORC is dephosphorylated, and the cycle repeats.
- Reverse transcriptase is a protein that utilizes an RNA template to elongate a DNA strand, then converts it into DNA nucleotides.
- Telomere repeats are sequences added to the ends of chromosomes by telomerase, preventing the loss of genetic information during replication.
DNA Repair
- Proofreading is a high-specificity error-correcting process that occurs during replication.
- Strand-directed mismatch repair recognizes and corrects mismatched base pairs in DNA by detecting distortions in the DNA helix.
- DNA lesions can be spontaneous or induced.
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Spontaneous DNA lesions:
- Oxidative damage: Damage caused by reactive oxygen species.
- Hydrolytic attack: Removal of a DNA base, leaving a gap in the backbone.
- Depurination: The loss of purine bases (adenine and guanine) from DNA.
- Methylation: Accidental modification of bases that can inactivate them.
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Induced DNA Lesions:
- Chemical inducers: Chemicals that react with DNA and cause damage.
- Physical inducers: Physical agents like radiation that cause DNA damage.
- Bulky lesions: Occur when two bases are crosslinked together, distorting the helix.
- Deamination: Removal of an amino group from DNA bases.
- Depurination: Loss of a purine base from DNA.
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Translesion repair is a mechanism to repair DNA damage not addressed by other repair pathways.
- Translesion DNA polymerase takes over when normal DNA polymerase encounters unrepaired damage.
- Translesion polymerases are less accurate and lack proofreading abilities. They have a low processivity and are quickly replaced by normal DNA polymerase.
Other Key Concepts
- Replication origins: Specific sequences on the DNA where replication begins.
- Histone chaperones: Help break apart nucleosomes ahead of the replication fork to allow access to DNA.
- Without telomerase, cells lose 100-200 base pairs (bp) with each round of replication.
- UV radiation leads to the formation of pyrimidine dimers, bulky lesions involving two adjacent pyrimidine bases.
DNA Replication
- Germ cell stability ensures the accurate transmission of genetic information across generations, crucial for species perpetuation.
- Somatic cell stability prevents uncontrolled cell growth and the development of cancer.
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DNA replication involves a complex interplay of enzymes and proteins:
- DNA polymerase and DNA primase catalyze the polymerization of nucleoside triphosphates, forming the DNA backbone.
- DNA helicases and single-strand DNA-binding proteins unwind the DNA helix, allowing access for replication machinery.
- DNA ligase and RNA primer degrading enzymes seal together the lagging strand fragments, ensuring continuous DNA synthesis.
- DNA topoisomerases prevent DNA tangling and supercoiling, maintaining the structural integrity of the DNA helix.
- Phosphodiester bond forms between the phosphate group of one nucleotide and the sugar of the next nucleotide, linking the DNA backbone.
- DNA polymerase proofreading enhances accuracy by double-checking the newly incorporated nucleotide before moving on to the next one.
- Exonucleatic proofreading removes incorrectly incorporated nucleotides, ensuring high fidelity of DNA replication.
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Models of replication:
- Conservative model: The original DNA strand remains intact, and a completely new double helix is synthesized.
- Dispersive model: The new nucleotides are dispersed randomly throughout both new DNA strands.
- Semiconservative model: Each new double helix contains one strand from the original DNA and one newly synthesized strand – this is the accepted model.
- Single-stranded DNA-binding (SSB) proteins stabilize single-stranded DNA during replication, preventing re-annealing and tangling.
- Sliding clamp circular protein complex encircles the DNA and binds DNA polymerase, ensuring efficient processivity and preventing polymerase dissociation.
- Supercoils are loops of DNA helix that form due to the unwinding of the double helix.
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Topoisomerases relieve supercoiling and prevent DNA tangling during replication.
- Topoisomerase I relieves torsional stress by breaking and re-ligating one strand of the DNA helix, allowing rotation.
- Topoisomerase II resolves entanglement by passing one DNA double helix through a transient gate formed by another double helix, relying on ATP hydrolysis for energy.
DNA Repair
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Base excision repair corrects mutations arising from single-base damage:
- Glycosylases remove damaged bases by detaching the sugar-phosphate bond.
- Uracil DNA glycosylase specifically removes uracil bases, preventing erroneous incorporation.
- AP endonuclease removes the remaining sugar-phosphate residue, creating a gap.
- DNA polymerase fills the gap with the correct nucleotide.
- Ligase seals the nick in the DNA backbone, completing the repair.
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Nucleotide excision repair repairs bulky lesions, larger areas of DNA damage:
- Enzyme complex recognizes the bulky lesion, which distorts the helix.
- Endonucleases cut on both sides of the damaged region.
- Helicase removes the damaged segment, creating a gap of 12 nucleotides in bacteria and 30 nucleotides in humans.
- DNA polymerase fills the gap with correct nucleotides.
- Ligase seals the nick, restoring the DNA sequence.
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Translesion repair handles replication encountering unrepaired DNA damage:
- Translesion DNA polymerase takes over when regular polymerase stalls.
- Less accurate: prone to errors due to relaxed base pairing requirements.
- No proofreading: lacks the error-checking capability of regular polymerase.
- Low processivity: quickly replaced by regular polymerase once damage is bypassed.
DNA Replication Origins
- Replication origins are specific DNA sequences, rich in AT base pairs due to their weaker hydrogen bonding, where DNA replication initiates.
- Histone chaperones aid in nucleosome disassembly ahead of the replication fork, allowing access for replicative machinery.
Telomeres and Telomerase
- Telomeres are repetitive DNA sequences at the ends of chromosomes, acting as protective caps.
- Telomerase is an enzyme that adds telomere repeats, counteracting the shortening of chromosomes during replication.
- Without telomerase, cells lose 100-200 base pairs with each replication cycle.
DNA Damage
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DNA damage can be spontaneous or induced by environmental factors:
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Spontaneous lesions:
- Oxidative damage: Reactive oxygen species can chemically modify DNA bases.
- Hydrolytic attack: Water molecules can detach bases from the DNA backbone (e.g., depurination).
- Methylation: Accidental addition of methyl groups to DNA bases can alter their function.
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Spontaneous lesions:
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Induced lesions:
- Chemical inducers: Certain chemicals can directly modify DNA bases.
- Physical inducers: Radiation (e.g., UV) can cause DNA damage (e.g., pyrimidine dimer formation).
Types of DNA Damage
- Bulky lesions: Two DNA bases become covalently linked, distorting the DNA helix.
- Deamination: Removal of an amino group from a DNA base, altering base pairing properties.
- Depurination: Loss of a purine base (adenine or guanine) from the DNA backbone, creating a gap in the sequence.
Repair during replication
- Proofreading: DNA polymerase's inherent error-correcting mechanism.
- Strand-directed mismatch repair (MMR): Detects distortions in the DNA helix caused by mismatched base pairs and corrects them.
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Description
This quiz covers essential topics related to DNA replication, including the roles of various enzymes like DNA polymerase, helicase, and ligase. You'll explore the mechanisms that ensure genetic stability in both germ and somatic cells, as well as the biochemical processes involved in forming the DNA backbone. Test your understanding of how these elements work together to maintain genetic fidelity.
