DNA Polymerase and Sliding Clamps Quiz

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Questions and Answers

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?

  • 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?

  • 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?

<p>They are composed of multiple identical subunits forming a doughnut shape (B)</p> Signup and view all the answers

What is the approximate spacing between the DNA double helix and the sliding clamp?

<p>Space for roughly one to two water molecules (C)</p> Signup and view all the answers

Which DNA polymerase in E. coli is primarily responsible for chromosome replication?

<p>Pol III (A)</p> Signup and view all the answers

Which of the listed eukaryotic DNA polymerases is most closely related to leading strand synthesis?

<p>Pol ε (C)</p> Signup and view all the answers

Which action is NOT directly related to the activities of the DNA polymerases listed?

<p>ATP hydrolysis (D)</p> Signup and view all the answers

What is the primary effect of the sliding clamp on DNA polymerase processivity?

<p>It ensures that the DNA polymerase rebinds quickly to the same primer:template junction after dissociation. (D)</p> Signup and view all the answers

In the absence of a sliding clamp, approximately how often does a DNA polymerase dissociate from the template DNA?

<p>Every 20-100 bp synthesized. (C)</p> Signup and view all the answers

What causes a DNA polymerase to release from the sliding clamp and DNA?

<p>A change in the affinity between the DNA polymerase and the sliding clamp, triggered by double-stranded DNA in its active site. (D)</p> Signup and view all the answers

What is responsible for opening and placing the sliding clamp on DNA?

<p>Sliding clamp loaders. (C)</p> Signup and view all the answers

What happens to the sliding clamp after a DNA polymerase releases from it?

<p>It remains on the DNA and interacts with other proteins. (B)</p> Signup and view all the answers

Which of the following best describes the conserved structure of sliding clamps across species?

<p>They have the same sixfold symmetry and diameter, but differ in their subunit composition. (D)</p> Signup and view all the answers

Which molecule's affinity for the sliding clamp is affected when a DNA polymerase encounters double-stranded DNA?

<p>The DNA polymerase. (C)</p> Signup and view all the answers

What is the approximate size of the opening in the sliding clamp, relative to the diameter of a DNA helix?

<p>The opening is significantly larger than the DNA helix, allowing room for water molecules. (C)</p> Signup and view all the answers

Which of the following is NOT a function associated with proteins that interact with sliding clamps on DNA?

<p>DNA methylation. (C)</p> Signup and view all the answers

What is the state of the sliding clamp when it is in solution, before encircling the DNA?

<p>It is a closed ring. (B)</p> Signup and view all the answers

According to the provided text, what is the typical length of DNA synthesized by the DNA Pol α/primase complex?

<p>Approximately 50-100 bp. (C)</p> Signup and view all the answers

What kind of biological molecule is a sliding clamp?

<p>A protein. (C)</p> Signup and view all the answers

Which DNA polymerase is primarily used on the lagging-strand template?

<p>DNA polymerase delta. (C)</p> Signup and view all the answers

The affinity between the DNA polymerase and the sliding clamp is particularly low when the enzyme is associated with:

<p>Double stranded DNA at the active site. (D)</p> Signup and view all the answers

What type of energy molecule is utilized by clamp loaders when placing a sliding clamp on DNA?

<p>ATP. (C)</p> Signup and view all the answers

What structural feature of the DNA polymerase causes its release from the sliding clamp after synthesizing the template?

<p>The absence of a primer:template junction. (D)</p> Signup and view all the answers

Which of the following is NOT a conserved feature of the sliding DNA clamps found across different organisms?

<p>Specific protein subunit used in configuration. (D)</p> Signup and view all the answers

What is the primary function of AAA+ proteins within the context of sliding DNA clamp loading?

<p>To load proteins, assemble and disassemble complex protein structures. (B)</p> Signup and view all the answers

In the process of sliding clamp loading, what is the role of ATP binding to the clamp loader?

<p>It enables the clamp loader to bind to both the sliding clamp and the DNA. (D)</p> Signup and view all the answers

What triggers the release of the sliding clamp from the clamp loader during the loading process?

<p>Hydrolysis of ATP by the clamp loader. (A)</p> Signup and view all the answers

What specific feature of DNA does the clamp loader preferentially recognize when loading a sliding clamp?

<p>A primer:template junction. (B)</p> Signup and view all the answers

What happens to the sliding clamp once it's released from the clamp loader?

<p>It spontaneously closes around the double-stranded DNA. (D)</p> Signup and view all the answers

What is the consequence of a sliding clamp being bound to a DNA polymerase in terms of its removal?

<p>It prevents the clamp from being removed from the DNA by the clamp loader. (C)</p> Signup and view all the answers

Which of the following is the primary function of sliding clamps?

<p>To enhance the processivity of DNA polymerases. (A)</p> Signup and view all the answers

How does the process of loading a sliding clamp on DNA differ from the action of DNA helicases and topoisomerases?

<p>Sliding clamp loading alters the structure and conformation of the clamp, but not its chemical composition. (C)</p> Signup and view all the answers

What is the role of the clamp loader's DNA-binding site?

<p>To bring the open sliding clamp ring to the primer:template junction. (C)</p> Signup and view all the answers

What is the initial state of the sliding clamp relative to the DNA when the clamp loader binds to it?

<p>The clamp ring is open, ready to encircle the DNA. (C)</p> Signup and view all the answers

In the context of a primer:template junction, where exactly does the sliding clamp position itself?

<p>The double-stranded region of the primer:template junction. (B)</p> Signup and view all the answers

Which of the following would NOT prevent the removal of a sliding clamp from DNA?

<p>The presence of a primer:template junction. (D)</p> Signup and view all the answers

What is the final step in sliding clamp loading?

<p>ATP hydrolysis by the clamp loader. (B)</p> Signup and view all the answers

Flashcards

Sliding DNA Clamp

A protein complex that encircles DNA and increases the processivity of DNA polymerases.

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

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

The DNA polymerase at the replication fork synthesizes many nucleotides before it releases from the DNA template.

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Sliding Clamp Mechanism

The mechanism by which the sliding DNA clamp helps improve the processivity of DNA polymerases.

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Structure of Sliding DNA Clamp

The sliding DNA clamp encircles the DNA double helix, leaving room for water molecules between the clamp and the DNA.

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Binding of Sliding Clamp to Polymerase

The sliding clamp binds tightly to the DNA polymerase attached to the primer-template junction.

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Efficient Complex Movement

The complex of DNA polymerase and sliding clamp moves smoothly along the DNA template during DNA synthesis.

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What is the sliding clamp?

A protein complex that encircles DNA, holding the DNA polymerase in place and increasing its processivity.

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What is processivity in DNA replication?

DNA polymerase is an enzyme that synthesizes new DNA. The processivity of DNA polymerase is its ability to continuously add nucleotides to the growing DNA chain without dissociating from the template.

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How does DNA polymerase behave without a sliding clamp?

In the absence of the sliding clamp, DNA polymerase dissociates from the template after synthesizing only a short stretch of DNA (20-100 base pairs).

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How does the sliding clamp affect DNA polymerase processivity?

The sliding clamp binds to the DNA polymerase and keeps it in close proximity to the DNA template, greatly increasing its ability to synthesize long stretches of DNA.

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How does the sliding clamp prevent polymerase dissociation?

The sliding clamp prevents the DNA polymerase from diffusing away from the DNA template, even though the polymerase may temporarily detach from the 3' end of the growing strand.

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What is the outcome of sliding clamp's action on processivity?

The sliding clamp makes the DNA polymerase rebind to the same primer-template junction quickly after disengaging, increasing its processivity.

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What is the structure of the sliding clamp?

The sliding clamp is a closed ring in solution, but it needs to open to encircle the DNA helix.

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What opens the sliding clamp and places it on the DNA?

Special protein complexes called clamp loaders catalyze the opening of the sliding clamp and its assembly onto the DNA.

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What energy source drives clamp loading?

Clamp loaders couple ATP binding and hydrolysis to the process of loading the clamp onto the DNA.

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When is the sliding clamp removed from the DNA?

The sliding clamp is removed from the DNA when the DNA polymerase completes a stretch of replication.

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What other proteins interact with the sliding clamp?

Other proteins involved in DNA replication, repair, and chromatin assembly can interact with the sliding clamp, accumulating at sites of active DNA synthesis.

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What is the evolutionary significance of the sliding clamp?

The sliding clamp is a conserved component of DNA replication machinery found in various organisms, from viruses to humans. Its structure is also conserved.

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Sliding DNA Clamp Loader

A protein complex that loads the sliding DNA clamp onto DNA.

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Sliding DNA Clamp Removal

The process by which a sliding DNA clamp is removed from DNA.

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AAA+ Proteins

A protein complex that binds to and hydrolyzes ATP, providing energy for various cellular processes.

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Primer:Template Junction

A specific DNA sequence recognized by the sliding DNA clamp loader for clamp loading. This sequence is found at the junction between the primer and template strands.

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DNA Binding Specificity

The ability of a protein to bind specifically to a particular DNA sequence.

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Sliding DNA Clamp Opening and Closing

The process by which a sliding DNA clamp is opened and closed.

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Closed Sliding DNA Clamp

The state of a sliding DNA clamp when it is bound to DNA.

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Open Sliding DNA Clamp

The state of a sliding DNA clamp when it is not bound to DNA.

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Pol δ

The type of DNA polymerase that is responsible for replicating the lagging strand during eukaryotic DNA replication.

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Pol ε

The type of DNA polymerase that is responsible for replicating the leading strand during eukaryotic DNA replication.

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Clamp Loading

The process by which the sliding DNA clamp is loaded onto DNA at the primer:template junction.

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Clamp Loader

A protein complex that binds to and hydrolyzes ATP, providing energy for clamp loading.

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Clamp Removal

The process by which the sliding DNA clamp is removed from DNA.

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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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