Mastering DNA Replication
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Questions and Answers

What are the three important functions of DNA polymerase?

The three important functions of DNA polymerase are: (1) Polymerase activity of adding Deoxyribonucleoside triphosphate (dNTPs) in a 5' to 3' direction while synthesizing a new DNA strand, (2) 3' to 5' exonuclease activity that removes the mismatched base, preventing DNA damage due to replication errors, and (3) 5' to 3' exonuclease activity that removes damaged or mismatched DNA segments in the double-stranded DNA.

What are the enzymes involved in elongation during replication, besides polymers?

The enzymes involved in elongation during replication, besides polymers, are DNA polymerase one, DNA polymerase three, single strand binding protein, topoisomerase of DNAbilase, and DNAbilase.

Which strand serves as the template for the leading strand during DNA replication?

  • The 3' to 5' strand (correct)
  • The 5' to 3' strand
  • Neither strand serves as the template for the leading strand
  • Both strands serve as templates for the leading strand

Which part of DNA Polymerase I is responsible for enhancing the accuracy of gene verification?

<p>3' to 5' exonuclease (B)</p> Signup and view all the answers

Explain the role of DNAA protein in the replication process of prokaryotes.

<p>The DNAA protein binds to the origin of replication and forms a replication bubble, which initiates the replication process in prokaryotes.</p> Signup and view all the answers

Explain how the sliding clamp or bitering structures increase replication efficiency.

<p>The sliding clamp or bitering structures loop around the DNA and increase processivity by keeping the polymerase enzyme attached to the template DNA, allowing for longer stretches of replication without dissociation.</p> Signup and view all the answers

What are the three parts of DNA Polymerase I and what are their specific functions?

<p>The three parts of DNA Polymerase I are polymerase, 3' to 5' exonuclease, and 5' to 3' exonuclease. The polymerase is responsible for adding nucleotides, while the exonucleases are responsible for removing nucleotides from the ends of DNA strands.</p> Signup and view all the answers

Describe the process of phosphodiester bond formation during DNA replication.

<p>The process of phosphodiester bond formation during DNA replication involves the formation of a covalent bond between the hydroxyl and phosphate groups, creating a phosphodiester bond.</p> Signup and view all the answers

Which protein is responsible for keeping the polymerase attached to the template DNA during replication?

<p>Beta clamp (D)</p> Signup and view all the answers

What is the role of the three prime exonuclease activity in DNA polymerase?

<p>It removes nucleotides from the three prime end of the growing chain and removes incorrect or mismatched bases (D)</p> Signup and view all the answers

What is the role of the single-strand binding protein in DNA replication?

<p>The single-strand binding protein stabilizes the exposed single-stranded DNA by stretching it out and keeping it in position.</p> Signup and view all the answers

What are the different subunits that make up the core enzyme of DNA polymerase 3 and what are their respective functions?

<p>The alpha subunit performs the 5' to 3' DNA polymerase activity, the epsilon subunit performs 3' to 5' proofreading activity, and the theta subunit acts as a stabilizer of epsilon.</p> Signup and view all the answers

What are the two types of exonuclease activities of DNA polymerase and what are their functions?

<p>The two types of exonuclease activities of DNA polymerase are the three prime exonuclease activity and the five prime exonuclease activity. The three prime exonuclease activity removes nucleotides from the three prime end of the growing chain and removes incorrect or mismatched bases, while the five prime exonuclease activity acts as an editor and removes about ten to twelve nucleotides at a time from the five prime end of double standard DNA. The five prime exonuclease activity also clears the path for the advancing polymerase by removing distorted segments.</p> Signup and view all the answers

What is the primary target of nalodexic acid and cyclophosphacel in DNA replication?

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

Which subunit of DNA polymerase 3 is responsible for proofreading activity?

<p>Epsilon subunit (B)</p> Signup and view all the answers

Which DNA polymerase enzyme is essential for bacterial replication?

<p>Polymerase three (B)</p> Signup and view all the answers

What is the direction of synthesis during DNA replication?

<p>5' to 3' (C)</p> Signup and view all the answers

Why is DNA polymerase one not suitable for the replication process?

<p>DNA polymerase one is loosely bound and not processed enough, which makes it unsuitable for the tightly controlled replication process.</p> Signup and view all the answers

Describe the composition of the primesome protein assembly and its function in DNA replication.

<p>The primesome protein assembly is composed of HELIKs, Primase, and five other subunits. Its function is to add ribonucleotides during DNA replication, but not to add or seal entities.</p> Signup and view all the answers

Describe the role of DNA helicase in the DNA replication process.

<p>DNA helicase binds to the DNA helix and gradually opens it up by breaking the hydrogen bonds. It also breaks hydrogen bonds and opens up DNA at the replication fork.</p> Signup and view all the answers

What is the function of DNA polymerase 1 in DNA replication?

<p>DNA polymerase 1 removes RNA primers and fills gaps with entities.</p> Signup and view all the answers

Describe the structure of DNA polymerase and its function in DNA synthesis.

<p>DNA polymerase is a large polypeptide made up of 928 amino acids and has a finger-like structure with a thumb. Its function is to hold the template DNA and add Deoxyribonucleoside triphosphates (DNTPs) in the 5' to 3' direction during DNA synthesis.</p> Signup and view all the answers

What happens when a replication fork encounters a smooth surface?

<p>The replication fork will stop and the DNA polymerase falls off.</p> Signup and view all the answers

Which enzyme is responsible for filling the gap at the end of DNA replication?

<p>DNA ligase (D)</p> Signup and view all the answers

What direction does DNA polymerase synthesize nucleotides in?

<p>Five prime to three prime direction (B)</p> Signup and view all the answers

What is the role of task protein in DNA replication termination?

<p>To stop the replication clock in one orientation (C)</p> Signup and view all the answers

What were the radioactive pulses used for in the DNA replication experiments conducted by Reiji and Tumiko Okazaki?

<p>The radioactive pulses were used to expose the DNA fragments and track the progress of replication.</p> Signup and view all the answers

Explain the process by which DNA polymerase synthesizes nucleotides.

<p>DNA polymerase synthesizes nucleotides in a five prime to three prime direction by forming a phosphodiester bond between the three prime hydroxy and the one possible group, following the ATTC rule and in an anti-parallel direction to the template structure.</p> Signup and view all the answers

Explain the role of DNA helicase in the DNA replication process.

<p>DNA helicase binds to the DNA helix and breaks the hydrogen bonds, gradually opening it up to initiate the replication process.</p> Signup and view all the answers

What did Reiji and Tumiko Okazaki discover during their DNA replication experiments?

<p>The presence of small DNA fragments in the gradient (C)</p> Signup and view all the answers

Which of the following is NOT a function of DNA polymerase?

<p>2' to 4' exonuclease activity (D)</p> Signup and view all the answers

Explain the role of DNA helicase in the DNA replication process.

<p>DNA helicase binds to the DNA helix and breaks the hydrogen bonds to gradually open it up. This allows other proteins and enzymes to access the DNA strands for replication.</p> Signup and view all the answers

Describe the mechanism of DNA replication on both the leading and lagging strands.

<p>DNA replication occurs simultaneously on both strands, with both daughter strands polymerized in the 5' to 3' direction. The leading strand is synthesized in one continuous molecule while the lagging strand is synthesized in small fragments that are joined later on.</p> Signup and view all the answers

What is the function of the gamma complex in DNA replication?

<p>To load the beta clamp (D)</p> Signup and view all the answers

What is the significance of circular chromosome in bacterial DNA replication?

<p>The circular chromosome in bacterial DNA indicates that the DNA has a double parent strand and two daughter strands, which are essential for the replication process.</p> Signup and view all the answers

What is the function of RNA primers in DNA replication?

<p>RNA primers are synthesized to provide a starting point for DNA polymerase to add DNTPs and extend the DNA strands. They provide a three prime hydroxy group, which is necessary for DNA polymerase to work.</p> Signup and view all the answers

Explain the importance of RNA primers in the DNA replication process.

<p>RNA primers synthesize a small strand of RNA, which acts as a primer for DNA polymerase to add DNTPs and extend the strands. They provide a primer with a three prime hydroxy group, which is needed by DNA polymerase.</p> Signup and view all the answers

Describe the function of RNA primers in DNA replication.

<p>RNA primers synthesize a small strand of RNA, which acts as a primer for DNA polymerase to add DNTPs and extend the strands. The three prime hydroxy group of the RNA primer is used by DNA polymerase to add new nucleotides.</p> Signup and view all the answers

How does the replication termination process occur, and what is the role of the test protein?

<p>The termination of replication happens with the help of two proteins, one of which is the test protein.</p> Signup and view all the answers

How do Zohai racks, nalidixic acid, and cifeloxacin inhibit DNA replication?

<p>Self-study is required to determine how these chemicals are impacting the DNA polymerase, DNA HIDs, or single-strand binding proteins.</p> Signup and view all the answers

Who discovered DNA polymerase and how was it discovered?

<p>Arthur Conbur discovered DNA polymerase in E. coli through an experiment involving extraction and purification. He added DNA polymerase to the extract and found that DNA strands were formed when treated with oxidants.</p> Signup and view all the answers

What are the essential components required for in vitro DNA synthesis, and what is the significance of a primer?

<p>The essential components required for in vitro DNA synthesis are primer, template DNA, DNTPs, and polymerase. The primer is significant because it provides a starting point for the polymerase to initiate DNA synthesis.</p> Signup and view all the answers

What is the function of RNA fragments in DNA synthesis?

<p>To provide a free three prime hydroxide group to build upon (B)</p> Signup and view all the answers

What is the role of RNA fragments in DNA synthesis?

<p>RNA fragments supply the oligonucleotide primer with a free three prime hydroxide group to build upon during DNA synthesis.</p> Signup and view all the answers

What is the main purpose of 3' to 5' exonuclease activity of DNA polymerase?

<p>To remove the mismatched base, preventing DNA damage due to replication errors (B)</p> Signup and view all the answers

Why is the polymerase activity of DNA polymerase crucial for DNA replication health?

<p>The polymerase activity of DNA polymerase is crucial for DNA replication health because it adds new nucleotides in a specific sequence to form a complementary strand to the original DNA template, which is essential for the accurate replication of genetic information.</p> Signup and view all the answers

Who discovered the small exocuclease fragment of DNA Polymerase I?

<p>Hans Clemens (C)</p> Signup and view all the answers

Who discovered the small exocuclease fragment of DNA Polymerase I and what is its significance in molecular biology?

<p>The small exocuclease fragment of DNA Polymerase I was discovered by Hans Clemens. It has been used in molecular biology labs before the discovery of Taq polymerase.</p> Signup and view all the answers

What is the replicative capacity of DNA polymerase I?

<p>It can add twenty nucleotides per second before falling off the DNA (C)</p> Signup and view all the answers

What is the maximum number of nucleotides that DNA polymerase I can add per second and what would happen if it was the replicative enzyme in E. Coli?

<p>DNA polymerase I can only add twenty nucleotides per second before falling off the DNA. If it was the replicative enzyme in E. Coli, the bacteria would take five point three days to divide.</p> Signup and view all the answers

What caused the mutation in the gene that codes for polymerase one?

<p>UV radiation exposure (A)</p> Signup and view all the answers

How did researchers identify a mutant e. Coli lacking polymerase one activity?

<p>Researchers identified a mutant e. Coli lacking polymerase one activity through UV radiation exposure, which caused a mutation in the gene that codes for the polymerase one enzyme.</p> Signup and view all the answers

Which DNA polymerase has 5' to 3' exonuclease activity?

<p>DNA polymerase 1 (A)</p> Signup and view all the answers

How does DNA polymerase 2 differ from DNA polymerase 3 in terms of their exonuclease activity?

<p>DNA polymerase 2 has 3' to 5' exonuclease activity, while DNA polymerase 3 has 5' to 3' exonuclease activity.</p> Signup and view all the answers

What is the role of the tau protein in DNA replication?

<p>The tau protein dimerizes and opens up the DNA helix to help with replication.</p> Signup and view all the answers

What is the chief DNA replicating enzyme of E. coli?

<p>Polymerase III (B)</p> Signup and view all the answers

What is the role of polymerase III in DNA replication in E. coli?

<p>Polymerase III is the chief DNA replicating enzyme of E. coli.</p> Signup and view all the answers

What happens when longer pulses of radioactive nucleotides are added during DNA replication experiments?

<p>More heavy bands and less short bands are produced (A)</p> Signup and view all the answers

How were the DNA strands separated in the replication experiments?

<p>The DNA strands were separated using either alkaline solution or sucrose density centrifugation.</p> Signup and view all the answers

What is the role of ATP in the process of DNA replication?

<p>It is used by DNA ligase to seal the gap at the end of replication (D)</p> Signup and view all the answers

What is the role of DNA ligase in DNA replication?

<p>DNA ligase seals the gap between 5' phosphate and 3' hydroxyl group using ATP.</p> Signup and view all the answers

What are the fragments called that are made on the lagging strand during DNA replication?

<p>Okazaki fragments (B)</p> Signup and view all the answers

What are Okazaki fragments and how do they differ from the leading strand during DNA replication?

<p>Okazaki fragments are short DNA fragments that are produced on the lagging strand during DNA replication. They differ from the leading strand in that they are made in the opposite direction.</p> Signup and view all the answers

Which protein blocks the replication fork due to reverse orientation facing beta sheets?

<p>Second task protein (A)</p> Signup and view all the answers

Which direction can the replication fork pass by the left-handed task protein?

<p>Both clockwise and anti-clockwise (C)</p> Signup and view all the answers

What is the role of the task protein in replication termination?

<p>The task protein is responsible for stopping replication in one orientation but not in the opposite orientation.</p> Signup and view all the answers

What is the role of 3' to 5' exonuclease activity of DNA polymerase?

<p>The role of 3' to 5' exonuclease activity of DNA polymerase is to remove any incorrectly paired nucleotides or mismatched bases that may have been incorporated during DNA replication. This activity helps to prevent DNA damage due to replication errors and maintains the accuracy of DNA replication.</p> Signup and view all the answers

What happens when the replication fork encounters a smooth surface during DNA replication?

<p>The fork will stop and the DNA polymerase falls off (B)</p> Signup and view all the answers

How is the lagging strand synthesized during DNA replication?

<p>In small fragments that are joined later on (C)</p> Signup and view all the answers

Why is polymerase activity crucial for DNA replication health?

<p>It adds Deoxyribonucleoside triphosphate (dNTPs) in a 5' to 3' direction while synthesizing a new DNA strand (D)</p> Signup and view all the answers

How does replication terminate and what is the role of casp proteins in this process?

<p>Replication terminates at a 350 base pair region with seven charged sequences that can stop replication. Casp proteins help to move the replication fork in different directions.</p> Signup and view all the answers

How are both daughter strands synthesized in the same direction despite having opposite template strands?

<p>DNA polymerase can only act in the 5' to 3' direction, which explains how both daughter strands are synthesized in the same direction despite having opposite template strands.</p> Signup and view all the answers

What are the three important features of DNA polymerase?

<p>The three important features of DNA polymerase are five prime to three prime polymerase activity, exonuclease activity, and a proofreading function.</p> Signup and view all the answers

How does DNA replication occur in two strands? Describe the leading and lagging strands.

<p>DNA replication occurs in two strands- the leading strand and the lagging strand- in the 5' to 3' direction. The leading strand is replicated continuously, while the lagging strand is replicated discontinuously in small fragments known as Okazaki fragments.</p> Signup and view all the answers

What are the possible ways in which small DNA fragments might have been formed during DNA replication experiments?

<p>All of the above (C)</p> Signup and view all the answers

What are the three important features of DNA polymerase?

<p>Five prime to three prime polymerase activity, endonuclease activity, and a proofreading function (D)</p> Signup and view all the answers

How does the replication process differ in prokaryotes and eukaryotes?

<p>Prokaryotic bacteria have a single replication origin, while eukaryotes have multiple origins due to their large DNA size. Additionally, the replication process in both involves DNA polymerase and DNA helicase proteins, but eukaryotic replication also involves other enzymes like DNA polymerase one, DNA polymerase three, single strand binding protein, topoisomerase of DNAbilase, and DNAbilase.</p> Signup and view all the answers

What is the significance of the presence of small DNA fragments in the replication experiments?

<p>Small DNA fragments indicate that they were either synthesized by DNA polymerase during replication or formed by breaking materials from bigger fragments.</p> Signup and view all the answers

What is the difference between PCR and DNA replication, and which enzyme is responsible for DNA replication?

<p>PCR is a precursor to DNA replication and is used to amplify specific DNA sequences, while DNA replication is the process of copying an entire DNA molecule. DNA polymerase 1 is the enzyme responsible for DNA replication.</p> Signup and view all the answers

Which compounds are important targets in DNA replication?

<p>Nalodexic acid (D)</p> Signup and view all the answers

What is the difference between the ligase used by bacteria and the one used in a molecular biology lab?

<p>Bacteria use NAD as a cofactor, whereas T4 ligase is used in a molecular biology lab (A)</p> Signup and view all the answers

When was DNA replication discovered and what was not yet known at that time?

<p>DNA replication was discovered in the 1950s, but the enzymes responsible for synthesizing DNA were not yet known.</p> Signup and view all the answers

Describe the process of replication bubble formation in DNA replication.

<p>The replication process begins with the formation of the replication bubble. This involves the DNA helicase breaking the hydrogen bonds and opening up the DNA strands. The replication bubble then opens up to form replication forks, which allow the DNA to be replicated in two strands- the leading strand and the lagging strand- in the 5' to 3' direction.</p> Signup and view all the answers

Why is ligase essential in cloning experiments and DNA synthesis?

<p>Ligase is essential in cloning experiments and DNA synthesis because it seals the gaps left after DNA polymerase 1 fills in the gaps, allowing for the creation of a complete strand of DNA.</p> Signup and view all the answers

Why is DNA polymerase one not suitable for the replication process?

<p>It is not processed enough (B)</p> Signup and view all the answers

What is the purpose of a small primer in DNA synthesis?

<p>A small primer of ten to twelve nucleotides is required to begin the synthesis, which is synthesized by RNA primes. After elongation, the primer is removed and replaced with DNA nucleotides. This process forms part of the initiation and elongation.</p> Signup and view all the answers

Which DNA polymerases are not involved in bacterial replication, and why is DNA polymerase three essential for survival?

<p>DNA polymerases one and two are not involved in bacterial replication, but DNA polymerase three is essential for survival because it is a multi-subunit complex and a hollow enzyme that is required for replication.</p> Signup and view all the answers

Is DNA polymerase I a replicative enzyme and why is it considered too abundant?

<p>DNA polymerase I is not a replicative enzyme. It is considered too abundant because it is present in large amounts in E. Coli cells, but it cannot effectively replicate DNA on its own.</p> Signup and view all the answers

How does the second task protein block the replication fork?

<p>The replication fork is blocked by the second task protein due to reverse orientation facing beta sheets.</p> Signup and view all the answers

What is the function of the sliding clamp in DNA polymerase 2?

<p>To hold the DNA (D)</p> Signup and view all the answers

What would be the consequence if E. Coli used DNA polymerase I as the replicative enzyme?

<p>E) Coli would take 5.3 days to divide (B)</p> Signup and view all the answers

How many charged sequences are there that can stop replication during DNA replication?

<p>7 (D)</p> Signup and view all the answers

What is the role of the sliding clamp in DNA replication and how many subunits does DNA polymerase 2 have that act as a clamp motor?

<p>The sliding clamp holds the DNA during replication, and DNA polymerase 2 has five subunits that act as a clamp motor.</p> Signup and view all the answers

How does the exonuclease activity of DNA Polymerase I enhance the accuracy of gene verification?

<p>The exonuclease activity of DNA Polymerase I allows for the removal of incorrect nucleotides that may have been added during DNA replication. This helps to ensure that the final DNA sequence is accurate and free from errors.</p> Signup and view all the answers

What is the direction of replication and how does it occur in both the leading and lagging strands?

<p>Replication occurs in the 5' to 3' direction. In the leading strand, DNA polymerase adds nucleotides continuously in the same direction as the replication fork. In the lagging strand, DNA polymerase adds nucleotides in the opposite direction to the replication fork, resulting in the formation of Okazaki fragments that are later joined by DNA ligase.</p> Signup and view all the answers

Which protein is responsible for keeping the strand open during replication so the polymerases can add nucleotides in the 5' to 3' direction?

<p>Single-stranded binding proteins (C)</p> Signup and view all the answers

What is the unique ability of DNA Polymerase I?

<p>It can both remove and add nucleotides (A)</p> Signup and view all the answers

What is the difference between the replication origin of prokaryotic bacteria and eukaryotes?

<p>Prokaryotic bacteria have a single replication origin while eukaryotes have multiple origins due to their large DNA size.</p> Signup and view all the answers

How do single-stranded binding proteins contribute to DNA replication?

<p>Single-stranded binding proteins keep the DNA strand open, allowing polymerases to add nucleotides in the 5' to 3' direction.</p> Signup and view all the answers

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Test your knowledge of DNA replication and the enzymes involved with this quiz. Learn about the role of DNA polymerases, topoisomerases, and single strand binding proteins in the replication process. Discover the difference between prokaryotic and eukaryotic replication origins and the proteins responsible for termination. Sharpen your understanding of DNA replication with this informative quiz.

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