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Questions and Answers
Mutations at protein coding sequences or DNA regions that control mRNA expression can change the ______ of a cell.
Mutations at protein coding sequences or DNA regions that control mRNA expression can change the ______ of a cell.
phenotypes
Inaccuracy in DNA replication is one of the important sources of ______.
Inaccuracy in DNA replication is one of the important sources of ______.
mutations
A critical function of DNA repair mechanisms is to prevent errors in DNA ______ or transcription.
A critical function of DNA repair mechanisms is to prevent errors in DNA ______ or transcription.
replication
The simplest mutations include transitions, transversions, and ______ or deletions of a single nucleotide.
The simplest mutations include transitions, transversions, and ______ or deletions of a single nucleotide.
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Biodiversity depends on a balance between ______ and repair of DNA.
Biodiversity depends on a balance between ______ and repair of DNA.
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Exonuclease VII or RecJ degrades DNA in a 5’ to 3’ direction when DNA is cleaved on the ______ side of the mismatch.
Exonuclease VII or RecJ degrades DNA in a 5’ to 3’ direction when DNA is cleaved on the ______ side of the mismatch.
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If the nick is on the 3’ side, ______ is the exonuclease that degrades DNA in a 3’ to 5’ direction.
If the nick is on the 3’ side, ______ is the exonuclease that degrades DNA in a 3’ to 5’ direction.
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In eukaryotic cells, MSH protein is a homolog of ______.
In eukaryotic cells, MSH protein is a homolog of ______.
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Mutations can occur from damage to DNA and errors in ______.
Mutations can occur from damage to DNA and errors in ______.
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Environmental factors such as ______ can cause DNA damage.
Environmental factors such as ______ can cause DNA damage.
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The most frequent and important kind of hydrolytic damage involves the deamination of the base ______.
The most frequent and important kind of hydrolytic damage involves the deamination of the base ______.
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Deamination of adenine produces ______, which can hydrogen bond to cytosine.
Deamination of adenine produces ______, which can hydrogen bond to cytosine.
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DNA has thymine instead of ______ to help maintain its stability and integrity.
DNA has thymine instead of ______ to help maintain its stability and integrity.
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Thymine dimers can block DNA replication and ______.
Thymine dimers can block DNA replication and ______.
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Deamination of cytosine causes a C:G to ______ transition mutation.
Deamination of cytosine causes a C:G to ______ transition mutation.
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Excision repair removes the damaged ______ from the DNA.
Excision repair removes the damaged ______ from the DNA.
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Translesion Polymerase synthesizes DNA across the site of the ______.
Translesion Polymerase synthesizes DNA across the site of the ______.
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Photolyase captures energy from ______ to break covalent bonds linking pyrimidines.
Photolyase captures energy from ______ to break covalent bonds linking pyrimidines.
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A methyltransferase removes the methyl group from ______.
A methyltransferase removes the methyl group from ______.
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Base excision repair involves glycosylase hydrolyzing the ______ bond.
Base excision repair involves glycosylase hydrolyzing the ______ bond.
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Nucleotide excision repair recognizes distortions to the shape of the double ______.
Nucleotide excision repair recognizes distortions to the shape of the double ______.
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Extensive insertions or deletions and gross rearrangements of chromosome ______ cause more drastic changes in DNA.
Extensive insertions or deletions and gross rearrangements of chromosome ______ cause more drastic changes in DNA.
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The spontaneous mutation rate ranges from 10-6 to 10-______ per round of DNA replication.
The spontaneous mutation rate ranges from 10-6 to 10-______ per round of DNA replication.
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DNA microsatellites are examples of ______ that have repeats of di-, tri-, or tetranucleotide sequences.
DNA microsatellites are examples of ______ that have repeats of di-, tri-, or tetranucleotide sequences.
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Some replication errors escape ______ due to the limitations of the proofreading function.
Some replication errors escape ______ due to the limitations of the proofreading function.
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Mismatch repair increases the accuracy of DNA synthesis by correcting ______ that escape proofreading.
Mismatch repair increases the accuracy of DNA synthesis by correcting ______ that escape proofreading.
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In E. coli, the MutS dimer detects mismatches and induces a conformational change in ______.
In E. coli, the MutS dimer detects mismatches and induces a conformational change in ______.
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Dam methylase adds a methyl group on ______ residues to help identify parental strands during repair.
Dam methylase adds a methyl group on ______ residues to help identify parental strands during repair.
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MutH binds at ______ sites to initiate the mismatch repair process.
MutH binds at ______ sites to initiate the mismatch repair process.
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UvrA and UvrB scan the ______
UvrA and UvrB scan the ______
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UvrC creates two incisions, one located 4~5 nts ______ and the other 8 nts 5’ to the lesion.
UvrC creates two incisions, one located 4~5 nts ______ and the other 8 nts 5’ to the lesion.
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UvrD is known as a DNA ______.
UvrD is known as a DNA ______.
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RNA polymerase stalls when it detects ______ in the DNA.
RNA polymerase stalls when it detects ______ in the DNA.
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TFIIH unwinds the DNA template and includes ______ and XPD for helicase activity.
TFIIH unwinds the DNA template and includes ______ and XPD for helicase activity.
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Non-homologous end joining (NHEJ) protects and processes the broken ______.
Non-homologous end joining (NHEJ) protects and processes the broken ______.
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Excision repair uses undamaged DNA as a ______.
Excision repair uses undamaged DNA as a ______.
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DSBs are the most ______ of all DNA damage.
DSBs are the most ______ of all DNA damage.
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The proteins involved in Non-homologous end joining (NHEJ) include Ku70, Ku80, DNA-PKcs, and ______.
The proteins involved in Non-homologous end joining (NHEJ) include Ku70, Ku80, DNA-PKcs, and ______.
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DNA-PKcs forms a complex with ______.
DNA-PKcs forms a complex with ______.
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The ligation during NHEJ is performed by Ligase IV, XRCC4, and ______.
The ligation during NHEJ is performed by Ligase IV, XRCC4, and ______.
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Translesion synthesis is a highly ______ mechanism of DNA damage tolerance.
Translesion synthesis is a highly ______ mechanism of DNA damage tolerance.
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In E. coli, DNA pol IV is also known as ______.
In E. coli, DNA pol IV is also known as ______.
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Translesion DNA polymerase must be tightly ______ due to its mutagenic nature.
Translesion DNA polymerase must be tightly ______ due to its mutagenic nature.
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The SOS response in E. coli leads to the expression of translesion DNA polymerases after ______.
The SOS response in E. coli leads to the expression of translesion DNA polymerases after ______.
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Human DNA pol η inserts two ______ residues opposite a thymine dimer.
Human DNA pol η inserts two ______ residues opposite a thymine dimer.
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Study Notes
Chapter 10: The Mutability and Repair of DNA
- DNA mutability and repair are crucial for maintaining genetic material across generations
- Mutations at protein-coding sequences or mRNA expression control regions alter cell phenotypes
- Changes in DNA sequences play a vital role in evolutionary processes, including the emergence of new species like humans
- Biodiversity relies on a balance between mutation and repair
- Key sources of mutations include inaccuracies during DNA replication, chemical damages, and insertion of DNA elements (transposons)
Errors in DNA Replication and DNA Damage
- Replication errors and DNA damage result in permanent changes to DNA (mutations) and can prevent replication or transcription
- Key questions addressed in this chapter include how the cells detect mutations, how they are repaired, how cells distinguish parental and daughter strands, and how cells restore proper DNA sequences when original ones are damaged
Replication Errors and Their Repair
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The Nature of Mutations:
- Simple mutations include transitions (pyrimidine to pyrimidine, purine to purine) and transversions (pyrimidine to purine, purine to pyrimidine)
- Point mutations involve insertions or deletions of a single nucleotide
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Spontaneous Mutation Rate:
- Mutations arise at a frequency of 10-6 to 10-11 per round of DNA replication.
- "Hot spots" are regions where mutations arise frequently, including microsatellites.
- Microsatellites are regions containing di-, tri-, or tetranucleotide repeats
- CA repeats are found throughout eukaryotic genomes
- Variations in these regions can affect the number of copies and can be used as markers for inherited mutations
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Errors escaping proofreading:
- DNA replication machinery has a proofreading mechanism (3' to 5' exonuclease activity) but some errors still occur
- These errors lead to permanent changes in the DNA sequence.
- Mismatch repair is a system to correct mistakes that escape the proofreading mechanism
Mismatch Repair
- The mismatch repair system enhances DNA synthesis accuracy.
- Two key challenges for mismatch repair are rapidly scanning the genome for mismatches and accurately correcting the mismatch (specifically, the newly synthesized strand).
- In E. coli, MutS dimer recognizes mismatches (distorting the DNA structure)
- Induces a conformational change in MutS, recruiting MutL for the repair system
- MutL activates MutH to create an incision or nick in the unmethylated strand
- Exonucleases are used to remove the mismatched DNA segment. Methylation patterns are crucial
- In eukaryotes, similar mechanisms occur but MutH and Dam methylases are absent
- Additional proteins like MSH, MLH, and PMS are vital in the eukaryotic system.
DNA Damage
- DNA damage arises spontaneously from hydrolysis and deamination
- Mutations result from replication errors or DNA damage
- DNA damage occurs due to environmental factors (radiation) and chemical agents (mutagens)
- Examples of deamination are cytosine to uracil, adenine to hypoxanthine, and guanine to xanthine. The presence of uracil in DNA is not normal and can be dangerous
- DNA can be damaged by alkylation, oxidation, and radiation, which may include UV radiation, which leads to thymine dimer formation, and ionizing radiation
Repair and Tolerance of DNA Damage
- DNA damage compromises cell viability
- This chapter details how cells cope with various DNA damage types
- Excision repair, recombination repair, translesion synthesis are crucial components of the cell's defense mechanism against DNA damage
Other Repair Systems
- Base Excision Repair (BER): Damaged bases are removed and replaced with correct nucleotides.
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Nucleotide Excision Repair (NER): Damaged sections of DNA are removed and replaced with functional nucleotides.
- Critical in repairing thymine dimers and bulky adducts
- Transcription-Coupled Repair: RNA polymerase identifies sites of damage and recruits DNA repair enzymes.
- Other DNA Repair Systems: DNA breaks are repaired through recombination-based systems and by processes known as homologous end joining
- Non-homologous end joining is a critical pathway that uses specialized enzymes to repair double-strand breaks and restore the DNA sequence, though this process can lead to mutations
Translesion DNA Synthesis
- One mechanism for DNA damage tolerance that bypasses the damaged site.
- Involves specialized DNA polymerases, such as DNA poly IV or V in E. coli.
- The incorporation of a correct nucleotide depends on the fidelity of the polymerase involved
- Human DNA polymerase η inserts two A nucleotides opposite a thymine dimer.
- Translesion synthesis is mutagenic, often leading to errors that need additional repair mechanisms. Regulation of translesion synthesis is crucial.
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Description
Explore the critical concepts of DNA mutability and the mechanisms involved in DNA repair. This chapter delves into the implications of mutations on genetic material, evolutionary processes, and biodiversity. Understand how errors in DNA replication and damage influence genome stability and the strategies cells use to rectify these issues.
