Podcast
Questions and Answers
What is the primary function of sliding DNA clamps in DNA replication?
What is the primary function of sliding DNA clamps in DNA replication?
- To remove RNA primers
- To increase the processivity of DNA polymerases (correct)
- To initiate DNA replication
- To unwind the DNA double helix
How do sliding DNA clamps achieve their processivity-enhancing function?
How do sliding DNA clamps achieve their processivity-enhancing function?
- By directly binding to the primer:template junctions and blocking dissociation
- By adding phosphate groups to the DNA polymerase
- By covalently linking to the DNA polymerase
- By forming a complex with the polymerase and encircling the DNA, allowing sliding movement (correct)
What is the typical processivity of DNA polymerases at the replication fork in the absence of sliding clamps?
What is the typical processivity of DNA polymerases at the replication fork in the absence of sliding clamps?
- 20-100 base pairs (correct)
- Millions of base pairs
- Hundreds of base pairs
- Thousands of base pairs
Which of the following describes the subunit structure of sliding DNA clamps?
Which of the following describes the subunit structure of sliding DNA clamps?
What is the approximate spacing between the DNA double helix and the sliding clamp?
What is the approximate spacing between the DNA double helix and the sliding clamp?
Which DNA polymerase in E. coli is primarily responsible for chromosome replication?
Which DNA polymerase in E. coli is primarily responsible for chromosome replication?
Which of the listed eukaryotic DNA polymerases is most closely related to leading strand synthesis?
Which of the listed eukaryotic DNA polymerases is most closely related to leading strand synthesis?
Which action is NOT directly related to the activities of the DNA polymerases listed?
Which action is NOT directly related to the activities of the DNA polymerases listed?
What is the primary effect of the sliding clamp on DNA polymerase processivity?
What is the primary effect of the sliding clamp on DNA polymerase processivity?
In the absence of a sliding clamp, approximately how often does a DNA polymerase dissociate from the template DNA?
In the absence of a sliding clamp, approximately how often does a DNA polymerase dissociate from the template DNA?
What causes a DNA polymerase to release from the sliding clamp and DNA?
What causes a DNA polymerase to release from the sliding clamp and DNA?
What is responsible for opening and placing the sliding clamp on DNA?
What is responsible for opening and placing the sliding clamp on DNA?
What happens to the sliding clamp after a DNA polymerase releases from it?
What happens to the sliding clamp after a DNA polymerase releases from it?
Which of the following best describes the conserved structure of sliding clamps across species?
Which of the following best describes the conserved structure of sliding clamps across species?
Which molecule's affinity for the sliding clamp is affected when a DNA polymerase encounters double-stranded DNA?
Which molecule's affinity for the sliding clamp is affected when a DNA polymerase encounters double-stranded DNA?
What is the approximate size of the opening in the sliding clamp, relative to the diameter of a DNA helix?
What is the approximate size of the opening in the sliding clamp, relative to the diameter of a DNA helix?
Which of the following is NOT a function associated with proteins that interact with sliding clamps on DNA?
Which of the following is NOT a function associated with proteins that interact with sliding clamps on DNA?
What is the state of the sliding clamp when it is in solution, before encircling the DNA?
What is the state of the sliding clamp when it is in solution, before encircling the DNA?
According to the provided text, what is the typical length of DNA synthesized by the DNA Pol α/primase complex?
According to the provided text, what is the typical length of DNA synthesized by the DNA Pol α/primase complex?
What kind of biological molecule is a sliding clamp?
What kind of biological molecule is a sliding clamp?
Which DNA polymerase is primarily used on the lagging-strand template?
Which DNA polymerase is primarily used on the lagging-strand template?
The affinity between the DNA polymerase and the sliding clamp is particularly low when the enzyme is associated with:
The affinity between the DNA polymerase and the sliding clamp is particularly low when the enzyme is associated with:
What type of energy molecule is utilized by clamp loaders when placing a sliding clamp on DNA?
What type of energy molecule is utilized by clamp loaders when placing a sliding clamp on DNA?
What structural feature of the DNA polymerase causes its release from the sliding clamp after synthesizing the template?
What structural feature of the DNA polymerase causes its release from the sliding clamp after synthesizing the template?
Which of the following is NOT a conserved feature of the sliding DNA clamps found across different organisms?
Which of the following is NOT a conserved feature of the sliding DNA clamps found across different organisms?
What is the primary function of AAA+ proteins within the context of sliding DNA clamp loading?
What is the primary function of AAA+ proteins within the context of sliding DNA clamp loading?
In the process of sliding clamp loading, what is the role of ATP binding to the clamp loader?
In the process of sliding clamp loading, what is the role of ATP binding to the clamp loader?
What triggers the release of the sliding clamp from the clamp loader during the loading process?
What triggers the release of the sliding clamp from the clamp loader during the loading process?
What specific feature of DNA does the clamp loader preferentially recognize when loading a sliding clamp?
What specific feature of DNA does the clamp loader preferentially recognize when loading a sliding clamp?
What happens to the sliding clamp once it's released from the clamp loader?
What happens to the sliding clamp once it's released from the clamp loader?
What is the consequence of a sliding clamp being bound to a DNA polymerase in terms of its removal?
What is the consequence of a sliding clamp being bound to a DNA polymerase in terms of its removal?
Which of the following is the primary function of sliding clamps?
Which of the following is the primary function of sliding clamps?
How does the process of loading a sliding clamp on DNA differ from the action of DNA helicases and topoisomerases?
How does the process of loading a sliding clamp on DNA differ from the action of DNA helicases and topoisomerases?
What is the role of the clamp loader's DNA-binding site?
What is the role of the clamp loader's DNA-binding site?
What is the initial state of the sliding clamp relative to the DNA when the clamp loader binds to it?
What is the initial state of the sliding clamp relative to the DNA when the clamp loader binds to it?
In the context of a primer:template junction, where exactly does the sliding clamp position itself?
In the context of a primer:template junction, where exactly does the sliding clamp position itself?
Which of the following would NOT prevent the removal of a sliding clamp from DNA?
Which of the following would NOT prevent the removal of a sliding clamp from DNA?
What is the final step in sliding clamp loading?
What is the final step in sliding clamp loading?
Flashcards
Sliding DNA Clamp
Sliding DNA Clamp
A protein complex that encircles DNA and increases the processivity of DNA polymerases.
Processivity
Processivity
The ability of an enzyme to perform multiple catalytic cycles without releasing its substrate. In DNA replication, it refers to the number of nucleotides a polymerase can add before detaching from the DNA template.
Association of Polymerases with Sliding Clamps
Association of Polymerases with Sliding Clamps
A key factor contributing to the high processivity of DNA polymerases at the replication fork. They associate with sliding DNA clamps, which act like a ring around the DNA.
High Processivity at Replication Fork
High Processivity at Replication Fork
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Sliding Clamp Mechanism
Sliding Clamp Mechanism
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Structure of Sliding DNA Clamp
Structure of Sliding DNA Clamp
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Binding of Sliding Clamp to Polymerase
Binding of Sliding Clamp to Polymerase
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Efficient Complex Movement
Efficient Complex Movement
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What is the sliding clamp?
What is the sliding clamp?
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What is processivity in DNA replication?
What is processivity in DNA replication?
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How does DNA polymerase behave without a sliding clamp?
How does DNA polymerase behave without a sliding clamp?
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How does the sliding clamp affect DNA polymerase processivity?
How does the sliding clamp affect DNA polymerase processivity?
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How does the sliding clamp prevent polymerase dissociation?
How does the sliding clamp prevent polymerase dissociation?
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What is the outcome of sliding clamp's action on processivity?
What is the outcome of sliding clamp's action on processivity?
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What is the structure of the sliding clamp?
What is the structure of the sliding clamp?
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What opens the sliding clamp and places it on the DNA?
What opens the sliding clamp and places it on the DNA?
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What energy source drives clamp loading?
What energy source drives clamp loading?
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When is the sliding clamp removed from the DNA?
When is the sliding clamp removed from the DNA?
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What other proteins interact with the sliding clamp?
What other proteins interact with the sliding clamp?
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What is the evolutionary significance of the sliding clamp?
What is the evolutionary significance of the sliding clamp?
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Sliding DNA Clamp Loader
Sliding DNA Clamp Loader
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Sliding DNA Clamp Removal
Sliding DNA Clamp Removal
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AAA+ Proteins
AAA+ Proteins
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Primer:Template Junction
Primer:Template Junction
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DNA Binding Specificity
DNA Binding Specificity
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Sliding DNA Clamp Opening and Closing
Sliding DNA Clamp Opening and Closing
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Closed Sliding DNA Clamp
Closed Sliding DNA Clamp
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Open Sliding DNA Clamp
Open Sliding DNA Clamp
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Pol δ
Pol δ
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Pol ε
Pol ε
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Clamp Loading
Clamp Loading
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Clamp Loader
Clamp Loader
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Clamp Removal
Clamp Removal
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Study Notes
DNA Polymerase Processivity and Sliding Clamps
- DNA polymerases replicate DNA, but without sliding clamps, they only synthesize 20-100 base pairs before detaching.
- Sliding clamps, doughnut-shaped proteins, increase processivity.
- The clamp's open structure encircles DNA, allowing it to slide along without detaching, with water molecules in the gap.
- Clamps bind tightly to DNA polymerases at primer-template junctions.
- This complex efficiently moves along DNA during synthesis.
How Sliding Clamps Increase Processivity
- Without clamps, polymerases detach and diffuse about every 20-100 base pairs.
- The clamp prevents diffusion, keeping polymerase close to the DNA.
- Thus, polymerase rebinds frequently, greatly enhancing the ability to extend the DNA chain.
- Polymerase release at the end of synthesis is triggered by conformation changes—when going past an Okazaki fragment, a double-stranded DNA in the active site causes a decreased affinity with the clamp.
Sliding Clamp Release and Interactions
- After a polymerase completes a stretch of DNA, it detaches from the clamp to initiate replication at a new site.
- The clamp remains on the replicated DNA until other proteins interact with it (Okazaki fragment repair proteins, chromatin assembly factors, etc.).
- This recruitment to recently replicated regions is needed, depending on the type of protein interacting and the function involved, for specific DNA repair, chromosomal assembly, etc.
Characteristics and Functions of Sliding Clamps
- Sliding clamps are found across various organisms (viruses, bacteria, yeast, humans).
- Their structure is conserved across diverse organisms (same symmetry, diameter).
- The subunits forming the clamp differ in various organisms.
Clamp Loading via Clamp Loaders
- Sliding clamps readily open and close to encircle DNA.
- Clamp loaders are proteins which catalyze this clamping process by using ATP.
- This ATP binding and hydrolysis lead to opening and positioning of the clamp around the primer-template junctions.
- The loader removes the clamp when no longer needed, releasing the position.
- ATP is also needed for DNA and sliding clamp binding by clamp loaders.
- Clamp loaders can be part of larger multi-protein complexes that have diverse functions.
Factors Controlling Clamp Loading and Removal
- Clamps are loaded at primer-template junctions wherever DNA replication or DNA repair occurs.
- The DNA polymerase binding to the clamp prevents its removal.
- Other enzymes involved in repair and chromatin structure—Okazaki fragment repair proteins, nucleosome assembly factors—take up same binding sites on the clamping protein preventing removal until they are ready.
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