DNA Replication

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Questions and Answers

Why is accuracy crucial during DNA replication?

  • To reduce the number of nucleotides required for replication.
  • To ensure the process occurs at a high speed.
  • To facilitate the unwinding of the DNA double helix.
  • To prevent mutations that could lead to catastrophic cellular consequences. (correct)

What is the rate of DNA replication in E. coli?

  • 100 nucleotides/second
  • 10,000 nucleotides/second
  • 10 nucleotides/second
  • 1,000 nucleotides/second (correct)

What is the key difference between conservative and semiconservative DNA replication?

  • Conservative replication occurs at a slower rate than semiconservative replication.
  • Conservative replication uses RNA primers, while semiconservative uses DNA primers.
  • Semiconservative replication involves multiple origins of replication, while conservative replication uses a single origin.
  • Semiconservative replication results in one original and one new strand, while conservative replication leaves the original DNA intact and creates a new DNA molecule. (correct)

In the Meselson and Stahl experiment, what observation after the first round of replication supported semiconservative replication?

<p>DNA appeared as a single band of intermediate weight. (D)</p> Signup and view all the answers

What result would be expected in the Meselson-Stahl experiment after two rounds of replication in 14N medium, starting with DNA labeled in 15N, if replication was dispersive?

<p>One band at intermediate density (C)</p> Signup and view all the answers

Which characteristic is associated with theta replication?

<p>Involves a single origin of replication and forms a replication fork. (B)</p> Signup and view all the answers

Which mode of replication is characteristic of the F factor in E. coli?

<p>Rolling-circle replication (C)</p> Signup and view all the answers

What characterizes linear eukaryotic DNA replication?

<p>It involves the formation of a replication bubble at multiple origins. (B)</p> Signup and view all the answers

Which of the following is correct about a typical replicon in eukaryotic replication?

<p>Approximately 200,000-300,000 bp in length (B)</p> Signup and view all the answers

What is a key difference between theta replication and rolling-circle replication?

<p>Theta replication results in two circular molecules, while rolling-circle replication produces multiple circular DNA molecules. (C)</p> Signup and view all the answers

Why is a template strand essential for DNA replication?

<p>It ensures the newly synthesized strand has the correct sequence, complementary to the template. (B)</p> Signup and view all the answers

What is the role of the 3'-OH group in DNA replication?

<p>It is the site where DNA polymerase adds new nucleotides. (A)</p> Signup and view all the answers

If a region of a template strand has the sequence 5'-TTAGC-3', what is the sequence of the newly synthesized strand?

<p>5'-AATCG-3' (D)</p> Signup and view all the answers

Why does DNA polymerase only add nucleotides to the 3' end of a growing strand?

<p>Because the reaction involves the 3'-OH group attacking the 5'-phosphate of the incoming nucleotide. (A)</p> Signup and view all the answers

What is the direction of replication?

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

What characteristic of DNA leads to discontinuous replication?

<p>The antiparallel arrangement of DNA strands. (D)</p> Signup and view all the answers

What are Okazaki fragments?

<p>Short DNA fragments synthesized on the lagging strand (C)</p> Signup and view all the answers

During replication, what is the function of DNA helicase?

<p>Breaking hydrogen bonds to unwind the DNA double helix (D)</p> Signup and view all the answers

What is the correct sequence of enzyme action in bacterial DNA replication, starting at the origin?

<p>Initiator protein, DNA helicase, single-strand-binding protein, DNA gyrase (A)</p> Signup and view all the answers

Why are primers required for DNA replication?

<p>To provide a 3'-OH group for DNA polymerase to add nucleotides. (D)</p> Signup and view all the answers

On the lagging strand, where are primers synthesized?

<p>At the beginning of every Okazaki fragment (C)</p> Signup and view all the answers

During elongation, what are the roles of helicase, single-strand binding proteins, DNA gyrase, primase and DNA polymerase respectively?

<p>Unwind DNA, stabilize single strands, remove strain, synthesize primers, synthesize DNA (A)</p> Signup and view all the answers

What is the function of DNA polymerase I in bacterial DNA replication?

<p>To remove RNA primers and replace them with DNA (A)</p> Signup and view all the answers

What enzymatic activity is responsible for correcting incorrectly paired nucleotides during replication?

<p>3' → 5' exonuclease activity (D)</p> Signup and view all the answers

Which process relies on the ability to distinguish between newly synthesized and template strands of DNA?

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

What role do autonomously replicating sequences (ARSs) play in eukaryotic DNA replication?

<p>They initiate DNA replication. (D)</p> Signup and view all the answers

What binds to ARSs to initiate DNA replication in eukaryotes?

<p>Origin-recognition complex (ORC) (D)</p> Signup and view all the answers

Do eukaryotes need an initiator protein?

<p>No (A)</p> Signup and view all the answers

Why might a cell utilize an error-prone DNA polymerase instead of a more accurate one?

<p>Error-prone polymerases can bypass lesions in the DNA helix where accurate polymerases stall. (D)</p> Signup and view all the answers

What steps are required to create nucleosomes during eukaryotic DNA replication?

<p>Disruption of original nucleosomes, redistribution of pre-existing histones, addition of newly synthesized histones. (A)</p> Signup and view all the answers

What is the function of telomerase?

<p>To replicate the ends of linear chromosomes (D)</p> Signup and view all the answers

What would happen if telomeres were mutated and nonfunctional?

<p>Chromosomes would shorten each generation (B)</p> Signup and view all the answers

What process involves the exchange of genetic material between homologous DNA molecules?

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

Which of the following is a model for homologous recombination?

<p>Holliday junction, single-strand break, and double-strand break (B)</p> Signup and view all the answers

According to the Holliday model, what determines whether recombination results in crossover or noncrossover recombinants?

<p>Whether cleavage occurs in the horizontal or vertical plane of the Holliday structure (B)</p> Signup and view all the answers

In the double-strand break model of recombination, what is the first step following the double-strand break?

<p>Enzymatic removal of nucleotides to produce single-stranded DNA. (B)</p> Signup and view all the answers

Which of the following does not accurately describe conservative DNA replication?

<p>After replication, both daughter DNA molecules contain a mix of old and new DNA. (B)</p> Signup and view all the answers

In the Meselson-Stahl experiment, which outcome after the first generation of replication ruled out the conservative model?

<p>The DNA consisted of a single band at a density intermediate between 15N and 14N. (C)</p> Signup and view all the answers

What is the expected distribution of DNA molecules after three rounds of replication of a 15N-labeled DNA molecule in a 14N medium, assuming semiconservative replication?

<p>One-fourth of the DNA will be intermediate, and three-fourths will be light (14N). (D)</p> Signup and view all the answers

Which characteristic is unique to rolling circle replication compared to theta replication?

<p>Cleavage of a DNA strand to initiate replication. (C)</p> Signup and view all the answers

In linear eukaryotic replication, what event allows the numerous replicons to ultimately produce two identical DNA molecules?

<p>The replication forks of adjacent bubbles merge. (C)</p> Signup and view all the answers

What role would not be expected for a DNA template strand in replication?

<p>Providing the energy for nucleotide addition. (D)</p> Signup and view all the answers

What chemical property of the DNA molecule dictates the requirement for the 3'-OH group for replication?

<p>The phosphodiester bond formation mechanism (B)</p> Signup and view all the answers

If a DNA template strand is read in the 3'-to-5' direction, what will be the polarity (direction) of the newly synthesized strand?

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

Why is DNA replication considered a continuous and discontinuous process?

<p>Because DNA polymerase can only synthesize in one direction. (A)</p> Signup and view all the answers

What would likely occur if a mutation inactivated primase in a cell?

<p>DNA replication would cease because no new strands could be initiated. (A)</p> Signup and view all the answers

What is the function of single-strand binding (SSB) proteins during DNA replication?

<p>To prevent the formation of secondary structures in single-stranded DNA. (C)</p> Signup and view all the answers

If you are given the scenario where the DNA ligase enzyme is defective, what would you see?

<p>Incomplete joining of Okazaki fragments. (C)</p> Signup and view all the answers

Which activity is associated with DNA polymerase I that contributes to the fidelity of DNA replication?

<p>3' → 5' exonuclease activity (A)</p> Signup and view all the answers

Why is the mismatch repair system more effective if it can distinguish between the template and newly synthesized strand?

<p>It can correct errors on the newly synthesized strand using the template strand as a guide. (D)</p> Signup and view all the answers

In eukaryotes, where does the origin-recognition complex (ORC) bind to initiate DNA replication?

<p>Autonomously replicating sequences (ARSs) (D)</p> Signup and view all the answers

Which of the following accurately describes the function of the minichromosome maintenance (MCM) complex during DNA replication?

<p>It unwinds the DNA double helix at the replication fork. (A)</p> Signup and view all the answers

What is a key difference between eukaryotic and bacterial DNA polymerases?

<p>Eukaryotes have more types of DNA polymerases with specialized functions compared to bacteria. (A)</p> Signup and view all the answers

What is the primary role of error-prone DNA polymerases in eukaryotes?

<p>To bypass lesions or damage in the DNA template. (B)</p> Signup and view all the answers

What is the general process of nucleosome reassembly during eukaryotic DNA replication?

<p>Preexisting histones are recycled and assembled with newly synthesized histones onto the new DNA molecules. (D)</p> Signup and view all the answers

What unique challenge do linear chromosomes face during replication that is not a concern for circular chromosomes?

<p>The inability to fully replicate the ends of chromosomes during DNA replication. (C)</p> Signup and view all the answers

How does telomerase prevent the shortening of chromosomes after multiple rounds of replication?

<p>By extending the 3' end of the chromosome using an RNA template. (C)</p> Signup and view all the answers

Why is homologous recombination important for genetic diversity and DNA repair?

<p>It shuffles genetic information between homologous chromosomes and repairs damaged strands using homologous sequences as templates. (D)</p> Signup and view all the answers

What initiates the process of homologous recombination, according to the Holliday model?

<p>Alignment of homologous chromosomes and single-strand breaks. (D)</p> Signup and view all the answers

What is the term that describes the movement of the crossover point along the DNA during homologous recombination?

<p>Branch migration (B)</p> Signup and view all the answers

What is the role of the invading strand during the double-strand break model of homologous recombination?

<p>It serves as a template to repair the broken DNA molecule. (D)</p> Signup and view all the answers

How does the double-strand break repair (DSBR) model contribute to genetic diversity?

<p>By facilitating the exchange of genetic material between homologous chromosomes. (A)</p> Signup and view all the answers

What outcome is characteristic of homologous recombination?

<p>The creation of a mosaic DNA molecule. (D)</p> Signup and view all the answers

What would most likely happen if a cell lacked the enzyme responsible for resolving Holliday junctions during homologous recombination?

<p>The Holliday junction would persist, and the recombined chromosomes could not fully separate. (C)</p> Signup and view all the answers

During theta replication, what would be the most likely consequence of a mutation that inactivates the enzyme responsible for unwinding the DNA?

<p>DNA synthesis would cease due to the inability to separate the strands. (D)</p> Signup and view all the answers

During rolling circle replication, if the cycle is continuously repeated without termination, what would be the most likely outcome?

<p>The formation of multiple linear DNA copies from the original template. (D)</p> Signup and view all the answers

Flashcards

DNA Replication Accuracy

DNA replication must be exceptionally accurate to avoid catastrophic effects, with E. coli replicating at 1000 nucleotides/second.

DNA Replication Models

Proposed DNA replication models include conservative, dispersive, and semiconservative approaches.

Semiconservative Replication

The semiconservative replication model, where each new DNA molecule contains one original and one new strand.

Meselson and Stahl Experiment

Meselson and Stahl's experiment used isotopes of nitrogen to demonstrate semiconservative DNA replication in E. coli.

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Replicons

Replicons are units of replication that contain a replication origin, which marks the starting point.

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Theta Replication

Theta replication occurs in circular DNA with a single origin, forming a replication fork. Often bidirectional.

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Rolling-Circle DNA Replication

Rolling-circle replication occurs in viruses and the F factor of E. coli with a single origin of replication.

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Linear Eukaryotic Replication

Eukaryotic DNA replication that includes thousands of replication origins with the length of 200,000–300,000 bp in length.

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DNA Synthesis Direction

The direction of DNA synthesis is always 5' to 3', because DNA polymerase that adds to the 3' end of the growing strand.

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Okazaki Fragments

Okazaki fragments are discontinuously synthesized short DNA fragments forming the lagging strand.

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Bacterial DNA Replication Initiation

Bacterial DNA replication begins at the origin (oriC), contains 245 bp, and is initiated by the DnaA initiator protein.

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DNA Replication: Unwinding

DNA helicase unwinds DNA, single-strand-binding proteins stabilize single strands, and DNA gyrase reduces strain.

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Primers in DNA Replication

Primers, short RNA sequences that provide a 3'-OH group, are synthesized by primase, an RNA polymerase.

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Bacterial DNA Replication: Enzymes

DNA polymerase III elongates DNA, DNA polymerase I removes primers, and DNA ligase connects fragments.

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DNA Replication: Proofreading

DNA polymerase I has 3' 5' exonuclease activity removes incorrectly paired nucleotide.

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DNA Repair Mechanisms

Proofreading uses DNA polymerase and mismatch repair occurs after completion of replication.

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Eukaryotic Replication Initiation

Eukaryotic replication has ORC, autonomously replicating sequences(ARSs) licensing factors and does not need initiator protein.

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Eukaryotic Nucleosome Assembly

During Eukaryotic replication, the DNA is complexed to histone proteins in nucleosomes that require disruption, redistribution and addition to form.

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Eukaryotic DNA Polymerases

Eukaryotic nuclear DNA synthesis requires DNA polymerase alpha (initiation), delta(lagging), epsilon (leading).

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Telomerase Function

Telomerase uses an RNA template to extend chromosome ends, preventing shortening during replication.

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Homologous Recombination

Homologous recombination involves the exchange of genetic material between homologous DNA molecules.

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DNA Recombination Models

Holliday junction and double-strand break are mechanisms that promote genetic diversity or repair damaged DNA.

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Study Notes

Genetic Information Accuracy

  • Replication must be extremely accurate to avoid catastrophic errors during cell division
  • One error per million base pairs leads to 6400 mistakes every cell division
  • Replication must also occur at high speeds
  • E. coli replicates DNA at a rate of 1000 nucleotides per second

DNA Replication Models

  • Proposed DNA replication models include conservative, dispersive, and semiconservative

Meselson and Stahl's Experiment

  • The experiment used two isotopes of nitrogen: the common form 14N and the rare, heavy form 15N
  • E. coli were grown in 15N media and then transferred to 14N media
  • Cultured E. coli were then subjected to equilibrium density gradient centrifugation

Modes of Replication

  • Replicons are the units of replication
  • Replication origin refers to the specific location where replication starts
  • Theta replication occurs in circular DNA, such as in E. coli, and involves a single origin of replication that forms a replication fork, proceeding bidirectionally
  • Rolling-circle replication happens in viruses and the F factor of E. coli, using a single origin of replication

Linear Eukaryotic Replication

  • Occurs in eukaryotic cells
  • Requires thousands of origins
  • Involves a typical replicon of approximately 200,000–300,000 base pairs in length

Linear Eukaryotic Replication Requirements

  • These are template strands: nucleotides, enzymes, and other proteins

Direction of Replication

  • DNA polymerase adds nucleotides exclusively to the 3' end of the growing strand
  • Replication can only proceed in the 5' to 3' direction
  • Replication can be continuous or discontinuous

Linear Eukaryotic Replication Strands

  • The leading strand undergoes continuous replication
  • The lagging strand undergoes discontinuous replication
  • Okazaki fragments are short DNA fragments synthesized discontinuously, that make up the lagging strand

Bacterial DNA Replication

  • Bacterial DNA replication involves initiation
  • The oriC region, which is a single origin replicon, contains 245 base pairs
  • DnaA, an initiator protein in E. coli, is required for replication to be initiated

Bacterial DNA Replication Unwinding

  • Initiator proteins
  • DNA helicase
  • Single-strand-binding proteins (SSBs)
  • DNA gyrase (topoisomerase)

Elongation in Bacterial Replication

  • Primers are existing RNA nucleotide groups with a 3'-OH group where a new nucleotide can be added, and are typically 10–12 nucleotides long
  • Primase is an RNA polymerase

Elongation Components

  • Helicase to unwind the DNA
  • Single-strand-binding proteins to protect the single nucleotide strands and prevent secondary structures
  • DNA gyrase to remove strain ahead of the replication fork
  • Primase to synthesize primers with a 3'-OH group at the beginning of each DNA fragment
  • DNA polymerase to synthesize the leading and lagging nucleotide strands

Elongation Enzymes

  • Carried out by DNA polymerase III
  • Removing RNA primer: DNA polymerase I
  • Connecting nicks after RNA primers are removed: DNA ligase

Fidelity of DNA Replication

  • Proofreading: DNA polymerase I uses 3' → 5' exonuclease activity to remove incorrectly paired nucleotides
  • Mismatch repair: corrects errors after replication is complete

Eukaryotic DNA Replication

  • Autonomously replicating sequences (ARSs) are 100–120 bps long
  • Origin-recognition complex (ORC) binds to ARSs to initiate DNA replication
  • ORC recruits and loads helicase
  • Eukaryotes do not need initiator protein
  • License to (approval) of DNA replication by the replication licensing factor
  • With licensing factors to form the minichromosome maintenance(MCM)

DNA Polymerase Function

  • Synthesizes any sequence specified by the template strand, in the 5' → 3' direction by adding nucleotides to a 3'-OH group
  • Uses dNTPs to synthesize new DNA
  • Requires a 3'-OH group to initiate synthesis
  • Catalyzes the formation of a phosphodiester bond by joining the 5'-phosphate group of the incoming nucleotide to the 3'-OH group of the preceding nucleotide on the growing strand, the process cleaving off two phosphates
  • Produces newly synthesized strands that are antiparallel and complementary to the template strands
  • Is associated with a number of other proteins

Eukaryotic DNA Nucleosomes

  • Eukaryotic DNA is complexed to histone proteins in nucleosomes
  • Nucleosomes are reassembled quickly after replication
  • Disruption of original nucleosomes on the parental DNA
  • Redistribution of preexisting histones on the new DNA
  • Addition of newly synthesized histones to complete the formation of new nucleosomes

Chromosome Replication

  • The location of DNA replication is within the nucleus
  • The DNA polymerase is fixed in location and the template RNA is threaded through it
  • Replication at the ends of chromosomes involves telomeres and telomerase

Homologous Recombination

  • Homologous recombination involves the exchange between homologous DNA molecules during crossing over
  • Holliday junction and single-strand break are necessary for homologous recombination to occur
  • The double-strand break model of recombination

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