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Questions and Answers
What effect does Sae2 have on Mre11's endonuclease activity?
What effect does Sae2 have on Mre11's endonuclease activity?
What limitation does the Mre11 complex face during DNA end resection?
What limitation does the Mre11 complex face during DNA end resection?
Why can't 5’ to 3’ resection occur under certain circumstances?
Why can't 5’ to 3’ resection occur under certain circumstances?
What is the possible maximum limit of DNA end resection by Mre11 complex in human cells?
What is the possible maximum limit of DNA end resection by Mre11 complex in human cells?
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Which of the following mechanisms aids the initiation of DNA resection by the Mre11 complex?
Which of the following mechanisms aids the initiation of DNA resection by the Mre11 complex?
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What is the primary function of Exo1 in DNA resection?
What is the primary function of Exo1 in DNA resection?
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Which of the following statements is true regarding the role of Sgs1 in DNA resection?
Which of the following statements is true regarding the role of Sgs1 in DNA resection?
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What distinguishes the resection activity of Exo1 compared to the Mre11 complex?
What distinguishes the resection activity of Exo1 compared to the Mre11 complex?
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How does the Mre11 complex initiate DNA resection?
How does the Mre11 complex initiate DNA resection?
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What is the role of Dna2 in DNA resection?
What is the role of Dna2 in DNA resection?
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What is the primary product of B cells during their development?
What is the primary product of B cells during their development?
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What types of genes are encoded by each B cell?
What types of genes are encoded by each B cell?
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Which components are involved in forming double strand breaks during VDJ recombination?
Which components are involved in forming double strand breaks during VDJ recombination?
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What is the total number of potential VDJ combinations derived from the given parameters?
What is the total number of potential VDJ combinations derived from the given parameters?
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During homologous recombination, which step follows DNA resection?
During homologous recombination, which step follows DNA resection?
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What happens to the hairpin end during the VDJ recombination process?
What happens to the hairpin end during the VDJ recombination process?
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Which of the following accurately describes the nature of DNA replication on the leading strand?
Which of the following accurately describes the nature of DNA replication on the leading strand?
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Which mechanism is essential for generating antibody diversity in B cells?
Which mechanism is essential for generating antibody diversity in B cells?
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What process is initiated by the MRE11 complex during DNA repair?
What process is initiated by the MRE11 complex during DNA repair?
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What are the nucleolytic activities of Mre11p involved in DNA resection?
What are the nucleolytic activities of Mre11p involved in DNA resection?
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Which protein is essential for regulating the nuclease activities during DNA repair?
Which protein is essential for regulating the nuclease activities during DNA repair?
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During end resection, which of the following occurs first?
During end resection, which of the following occurs first?
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Which two components of the MRN complex interact to facilitate DNA repair?
Which two components of the MRN complex interact to facilitate DNA repair?
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In DNA digestion, what is the role of exonucleases?
In DNA digestion, what is the role of exonucleases?
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What is the digestion polarity during DNA digestion processes?
What is the digestion polarity during DNA digestion processes?
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Which structure is specifically linked to the initiation of homologous recombination?
Which structure is specifically linked to the initiation of homologous recombination?
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Study Notes
VDJ Recombination and Antibody Diversity
- The mammalian immune system generates an almost unlimited number of different light and heavy chain encoding genes during B cell development.
- Each B cell produces a single antibody with a unique antigen-binding site.
- Antibodies possess a variable and a constant region.
- The variable region is responsible for recognizing and binding to specific antigens.
VDJ Recombination
- VDJ recombination is a process that generates diverse antibody genes.
- DNA sequences of all stem cells are the same, but this process creates unique antibody genes encoding light and heavy chains.
- The variable region is composed of V, D, and J segments.
- During VDJ recombination, these segments are rearranged, resulting in a wide range of antibody diversity.
VDJ Recombination Steps
- VD recombination: The V and D segments are joined.
- DJ recombination: The D and J segments are joined.
- Transcription and splicing: The rearranged VDJ segment is transcribed into mRNA.
Number of VDJ Combinations
- The number of possible VDJ combinations is 150 x 9 x 4 = 5400.
VDJ Recombination and Non-Homologous End Joining (NHEJ)
- NHEJ is a DNA repair pathway that joins broken DNA ends.
- Recombinase: The RAG1 and RAG2 proteins are responsible for cutting the DNA and initiating the recombination process.
- Double-strand break (DSB) formation: The RAG proteins create DSBs with hairpin ends.
- Hairpin end removal: The Ku70/Ku80 complex and DNA-PK recruit Artemis to remove the hairpin ends.
- DSB end joining: XRCC4 and Ligase IV join the DSB ends.
Model for Homologous Recombination
- Homologous recombination is a DNA repair pathway that uses a homologous template to repair broken DNA.
- It starts with DNA resection to produce 3' single-stranded DNA (ssDNA).
- This 3' ssDNA searches for homologous sequences on the template DNA.
- DNA synthesis copies the homologous sequence from the template DNA to repair the damaged one.
- Ligation forms covalent bonds between the repaired DNA and the template, resulting in double Holliday junctions.
- Resolution separates the two joined DNA molecules, resulting in non-crossover or crossover events.
DNA Replication of the Leading Strand
- DNA replication occurs in one direction, from 5' to 3'.
- Pairing of ssDNA with the template DNA is essential for DNA extension.
DNA End Resection
- The process of producing 3' ssDNA tails from a DSB, essential for homologous recombination.
- This is achieved through nucleolytic degradation of the 5'-terminated strands, known as 5'-3' end resection.
Nucleolytic Degradation
- Cleavage of phosphodiester bonds within a DNA chain by deoxyribonuclease (DNase).
- Endonuclease: Cleaves the phosphodiester bond within a DNA chain.
- Exonuclease: Cleaves nucleotides one at a time from one end of a DNA chain.
- Digestion polarity: Can be 5' to 3' or 3' to 5' depending on the exonuclease.
Mre11 Complex
- The Mre11 complex, formed by MRE11, RAD50, and NBS1, is essential for homologous recombination.
- It binds to DSB sites at the early stages of repair.
- It possesses 3' to 5' exonuclease activity and endonuclease activity, both crucial for DNA resection.
DNA Digestion by Mre11 Complex
- The Mre11 complex uses both endonuclease and exonuclease activities to produce 3' ssDNA.
- The Sae2 protein regulates these activities, stimulating endonuclease activity but not exonuclease activity.
DNA Resection by Mre11 Complex
- The Mre11 complex initiates DNA resection by introducing a nick in the DNA, allowing the 3' to 5' exonuclease activity to create a 3' ssDNA tail.
- This pathway is more complicated than simply starting with 5' to 3' digestion because the 5' end might be blocked due to:
- Covalently-bound proteins at 5' end.
- Secondary structure at the end of DSB.
- The Mre11 complex-mediated resection is limited, typically 100-300 nt.
Extended DNA Resection Pathways
- Exo1: A 5' to 3' exonuclease that effectively extends the resection initiated by the Mre11 complex.
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Sgs1/Dna2:
- Sgs1 is a DNA helicase that unwinds dsDNA to create 5'-flap ssDNA, a substrate for Dna2.
- Dna2 is a 5'-flap endonuclease that cleaves within single-stranded regions of substrates forming flaps, thus extending the resection.
Exo1 Pathway
- Exo1 efficiently resects dsDNA with a short 3' ssDNA tail, which is the product of Mre11-mediated resection.
Sgs1/Dna2 Pathway
- Sgs1 unwinds dsDNA, creating a 5'-flap ssDNA for Dna2.
- Dna2 cleaves within single-stranded regions, extending the resection initiated by Mre11.
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Description
Explore the intricate processes of VDJ recombination and how they contribute to antibody diversity in the mammalian immune system. This quiz covers the steps involved in generating unique antibody genes and the structure of antibodies, emphasizing their importance in immune response.
