DNA Replication Overview

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Questions and Answers

What is the typical size of a bacterial chromosome?

  • 4,000,000 bp (correct)
  • 8,000,000 bp
  • 2,000,000 bp
  • 6,000,000 bp

How many base pairs must a bacterium replicate per minute to keep up with its division rate?

  • 200,000 bp (correct)
  • 100,000 bp
  • 250,000 bp
  • 150,000 bp

What process was shown by the Meselson-Stahl experiment?

  • Semiconservative replication (correct)
  • Lagging strand replication
  • Dispersive replication
  • Conservative replication

What was used in the medium to label the DNA in the Meselson-Stahl experiment?

<p>15NH4Cl (C)</p> Signup and view all the answers

What method was used to distinguish between 15N-DNA and 14N-DNA?

<p>Density gradient centrifugation (A)</p> Signup and view all the answers

At what rate must the DNA molecule rotate during replication in a bacterium?

<p>20,000 revolutions per minute (A)</p> Signup and view all the answers

Which isotope of nitrogen was used in the experimentation to mark DNA?

<p>15N (D)</p> Signup and view all the answers

How often can a bacterium divide under the conditions described?

<p>Every 20 minutes (A)</p> Signup and view all the answers

What is the primary purpose of DNA replication?

<p>To ensure equal amounts of DNA are passed during cell division (B)</p> Signup and view all the answers

What type of replication produces two identical DNA strands, each containing one original strand?

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

Which enzymes are critical for resolving the unwinding of the DNA double helix during replication?

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

Why was semiconservative replication initially thought to be impossible?

<p>Because DNA is plectonemic and unwinding was deemed challenging (B)</p> Signup and view all the answers

What misconception about DNA replication was common in the 1950s?

<p>Semiconservative replication was thought to be impossible (D)</p> Signup and view all the answers

In which types of DNA structure is unwinding particularly problematic during replication?

<p>Circular DNA and plectonemic DNA (A)</p> Signup and view all the answers

What was the widely accepted theory of DNA replication before semiconservative replication was established?

<p>Dispersive replication was the main belief (D)</p> Signup and view all the answers

What is one consequence of defects in DNA replication?

<p>Development of various diseases, including cancer (B)</p> Signup and view all the answers

What is the primary function of DNA topoisomerases during DNA replication?

<p>To remove or prevent supercoiling of DNA (C)</p> Signup and view all the answers

Which segment of DNA is completely cut by a Type II DNA topoisomerase?

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

How does a Type I DNA topoisomerase function during DNA replication?

<p>By separating strands without unwinding the helix (D)</p> Signup and view all the answers

What is the role of the T Segment in the action of Type II DNA topoisomerase?

<p>It is the DNA strand that gets passed through (C)</p> Signup and view all the answers

What type of supercoiling occurs when DNA strands are separated?

<p>Positive supercoiling (B)</p> Signup and view all the answers

Which one of the following describes the main action of Type II DNA topoisomerases?

<p>They pass one DNA strand through another (A)</p> Signup and view all the answers

Which of the following best describes the mechanism of action for DNA topoisomerases?

<p>They cut and rejoin DNA strands to relieve tension (A)</p> Signup and view all the answers

What is required to initiate DNA synthesis during DNA-dependent DNA synthesis?

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

What direction does DNA synthesis occur in during DNA-dependent DNA synthesis?

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

Which type of exonuclease activity allows a DNA polymerase to correct errors it has just made?

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

What is the name of the enzyme that carries out DNA-dependent DNA synthesis?

<p>DNA-dependent DNA polymerase (B)</p> Signup and view all the answers

What happens if a DNA synthesis occurs without a primer?

<p>No DNA synthesis occurs (C)</p> Signup and view all the answers

What role do DNA polymerases play in DNA replication?

<p>They synthesize DNA strands from nucleotides. (C)</p> Signup and view all the answers

What distinguishes leading strand synthesis from lagging strand synthesis at the replication fork?

<p>Leading strands are synthesized continuously, while lagging strands are synthesized in fragments. (D)</p> Signup and view all the answers

What is the function of helicases during DNA replication?

<p>To break the hydrogen bonds between base pairs. (A)</p> Signup and view all the answers

Why is semiconservative replication considered an important mechanism?

<p>It ensures that each daughter DNA molecule contains one original and one new strand. (A)</p> Signup and view all the answers

What do mutations in DNA polymerases potentially lead to?

<p>Colorectal cancer. (A)</p> Signup and view all the answers

What is the primary role of single-strand binding proteins (SSBs) during DNA replication?

<p>To prevent DNA strands from re-attaching (C)</p> Signup and view all the answers

How does the initiation of DNA synthesis differ between bacteria and eukaryotes?

<p>Eukaryotes extend the RNA primer with DNA pol alpha before DNA pol delta, bacteria do not (A)</p> Signup and view all the answers

What is the main difference in the synthesis of the leading strand compared to the lagging strand?

<p>The leading strand is synthesized continuously, while the lagging strand is made in segments (D)</p> Signup and view all the answers

Which of the following statements about the RNA primer during DNA replication is correct?

<p>It serves as a starting point for DNA synthesis (D)</p> Signup and view all the answers

What direction does DNA synthesis occur during the replication process?

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

What are the short segments of DNA synthesized on the lagging strand called?

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

What must happen to Okazaki fragments after their formation?

<p>They must be joined together and RNA primers removed (B)</p> Signup and view all the answers

Why were small DNA fragments only observed at shorter timepoints in the discovery of Okazaki fragments?

<p>They were labeled with radioactive nucleotides (A)</p> Signup and view all the answers

Which enzyme is known for joining two Okazaki fragments in eukaryotes?

<p>FEN1 (B)</p> Signup and view all the answers

What is the primary characteristic of the lagging strand during DNA replication?

<p>It is synthesized in a non-linear fashion (D)</p> Signup and view all the answers

What is the primary reason for the incomplete DNA synthesis during replication?

<p>The lagging strand is copied discontinuously. (C)</p> Signup and view all the answers

What role does telomerase play in DNA replication?

<p>It elongates the telomeres to prevent DNA shortening. (A)</p> Signup and view all the answers

What are the small sections of DNA synthesized on the lagging strand called?

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

Which enzyme is responsible for creating the RNA primer in prokaryotes during DNA replication?

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

What enzyme prevents the shortening of chromosomes in eukaryotic cells?

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

What happens to the RNA primer after DNA pol III or DNA pol delta has extended the new strand?

<p>It is replaced by DNA nucleotides. (B)</p> Signup and view all the answers

What must occur to complete the synthesis of the lagging strand after Okazaki fragments are formed?

<p>Okazaki fragments must be joined together (C)</p> Signup and view all the answers

In which direction does DNA synthesis occur on both the leading and lagging strands?

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

What is the consequence of the inability to synthesize the final Okazaki fragment on a linear DNA molecule?

<p>Gradual shortening of DNA molecules (B)</p> Signup and view all the answers

What is a significant consequence of the end replication problem?

<p>Chromosomes become progressively shorter over generations. (A)</p> Signup and view all the answers

In eukaryotic cells, which enzyme is specifically involved in removing RNA primers during lagging strand synthesis?

<p>FEN1 (C)</p> Signup and view all the answers

How does the synthesis of the leading strand differ from that of the lagging strand?

<p>The leading strand synthesis is continuous and requires one primer. (D)</p> Signup and view all the answers

What additive sequence does telomerase add to the ends of chromosomes?

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

What is the role of RNA primers in the synthesis of Okazaki fragments?

<p>They provide a starting point for DNA synthesis (A)</p> Signup and view all the answers

During the synthesis of the leading strand, DNA is created in which manner compared to the lagging strand?

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

What is characteristic of senescent cells in culture during replication?

<p>They exhibit shortened ends of chromosomes. (B)</p> Signup and view all the answers

What role does telomerase play in Tetrahymena thermophila?

<p>It maintains the length of telomeres. (A)</p> Signup and view all the answers

Which pattern of DNA replication occurs first during the S phase?

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

Why might telomerase not be present in all cells in the body?

<p>Its presence may lead to abnormal cell behaviors. (A)</p> Signup and view all the answers

What is a result of DNA replication involving modified nucleotides?

<p>It enhances the ability to visualize DNA replication sites. (B)</p> Signup and view all the answers

In normal somatic cells, why do chromosomes shorten over time?

<p>Regular cell division processes. (A)</p> Signup and view all the answers

Which of the following best describes telomerase activity in cancer cells?

<p>Telomerase is activated leading to longer chromosome ends. (D)</p> Signup and view all the answers

What phase of the cell cycle is primarily concerned with DNA replication?

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

Flashcards

Semiconservative replication

DNA replication where each new DNA molecule contains one original strand and one newly synthesized strand.

Conservative replication

A type of DNA replication where the original DNA molecule remains intact, and a completely new copy is made.

Dispersive replication

A type of DNA replication where the original DNA molecule is broken down into small pieces, and each new DNA molecule is made up of a mixture of old and new DNA fragments.

Plectonemic DNA

A type of DNA structure where the two strands of the DNA helix are intertwined, like a twisted ladder.

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Topoisomerases

Enzymes that help to unwind and separate the two strands of the DNA helix during DNA replication.

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Circular DNA

DNA molecules that are circular in shape, such as those found in bacteria and some viruses.

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DNA replication

The process of copying DNA, which is essential for cell division and growth.

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How does semiconservative replication work?

The two strands of DNA are separated and each serves as a template for the synthesis of a new strand. This ensures that each daughter cell receives a complete copy of the genetic information.

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Density gradient centrifugation

A method used to separate molecules based on their density. Heavier molecules settle at the bottom of the tube, while lighter molecules remain near the top.

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Cesium chloride (CsCl)

A commonly used chemical in density gradient centrifugation. It forms a density gradient when centrifuged, allowing molecules to separate based on their weight.

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Heavy nitrogen (15N)

An isotope of nitrogen with an atomic weight of 15. It is heavier than the common nitrogen isotope (14N).

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Nitrogen in DNA

The nitrogen component of DNA bases, which can be labelled with either 14N or 15N allowing for tracking of DNA molecules in experiments.

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Meselson-Stahl experiment

The experiment conducted by Meselson and Stahl in 1959 to determine the mode of DNA replication.

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DNA unwinding

The process of unwinding the DNA double helix, exposing the individual strands for replication.

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Rotation of DNA during replication

The rate at which a circular DNA molecule would have to rotate if it were unwound linearly for replication.

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DNA topoisomerases

Enzymes that are responsible for relieving the torsional stress caused by DNA supercoiling during replication. They act by temporarily breaking and resealing DNA strands, allowing one strand to pass through the other.

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DNA supercoiling

The winding or coiling of double-stranded DNA upon itself, creating a more compact and tightly wound structure. This can occur during DNA replication, as unwinding one part of the strand creates tension elsewhere.

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Type I DNA topoisomerases

These topoisomerases work by cleaving one of the DNA strands, allowing the other strand to pass through the break, and then resealing the break.

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Type II DNA topoisomerases

These topoisomerases act by cleaving both strands of DNA simultaneously, forming a 'gate' that allows another portion of the DNA strand to pass through before resealing the break.

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Topoisomerase II mechanism

The complete breaking of one DNA strand (G segment) to allow another (T segment) to pass through the break.

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DNA helix unwinding

The unwinding of the DNA helix, breaking the hydrogen bonds between the base pairs, to expose the individual strands for replication.

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DNA Polymerase

The enzyme responsible for building new DNA strands during replication. It reads the existing strand and adds complementary nucleotides to the newly synthesized strand.

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Helicases

Enzymes that break the hydrogen bonds between complementary base pairs, allowing for the separation of the DNA double helix.

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Okazaki Fragments

Short DNA fragments synthesized on the lagging strand during replication, due to the discontinuous nature of synthesis.

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DNA-dependent DNA synthesis

DNA synthesis relies on a template strand of DNA to create a new complementary strand.

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5' to 3' synthesis

DNA synthesis always occurs in the 5' to 3' direction, meaning new nucleotides are added to the 3' end of the growing strand.

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Primer in DNA synthesis

A primer is a short sequence of RNA that initiates DNA synthesis. It provides a starting point for DNA polymerase.

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Exonuclease activity in DNA polymerase

DNA polymerases have exonuclease activity, which allows them to remove nucleotides from DNA. This activity is crucial for proofreading and repair.

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Proofreading in DNA synthesis

DNA polymerase's ability to remove incorrect nucleotides during synthesis, ensuring accuracy.

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DNA ligase

A special enzyme that joins Okazaki fragments together on the lagging strand during DNA replication.

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RNase H

The enzyme responsible for removing RNA primers from Okazaki fragments during DNA replication.

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FEN1

A specialized endonuclease that removes the 5' flap created during Okazaki fragment processing in eukaryotes.

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What are single-strand binding proteins (SSBs)?

Proteins that bind to and protect single-stranded DNA during replication, preventing degradation and re-attachment.

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What is the leading strand?

The leading strand is synthesized continuously in the 5' to 3' direction, following the replication fork.

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What is a primer in DNA replication?

A short RNA sequence that provides a starting point for DNA polymerase to begin synthesis.

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What is the lagging strand?

The lagging strand is synthesized discontinuously in short fragments called Okazaki fragments, moving away from the replication fork.

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What are Okazaki fragments?

The lagging strand is synthesized in short fragments called Okazaki fragments, each requiring a separate primer to initiate synthesis.

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Leading Strand

The leading strand is synthesized continuously in the 5' to 3' direction, following the replication fork. It requires only one primer to initiate synthesis.

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Lagging Strand

The lagging strand is synthesized discontinuously in the 5' to 3' direction, moving away from the replication fork. It requires multiple primers for each Okazaki fragment.

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Primers in DNA replication

Short sequences of RNA that provide a starting point for DNA polymerase to begin synthesis.

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What is FEN1?

A specialized endonuclease that removes the 5' flap created during Okazaki fragment processing in eukaryotes.

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What is telomerase?

A special enzyme that extends the parent DNA by adding the sequence TTAGGG several times, preventing the ends of chromosomes from being shortened.

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What happens when the end of a linear DNA molecule is reached?

The final Okazaki fragment cannot be made because its priming site would be after the end of the parent molecule; this leads to DNA molecules getting shorter with each replication.

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Why is the lagging strand synthesized discontinuously?

The lagging strand is synthesized discontinuously in fragments because DNA polymerase can only synthesize in one direction (5' to 3').

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What is the function of RNase H?

An endonuclease that cuts the 5' end of the RNA primer located at the beginning of an Okazaki fragment.

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What are DNA ligases?

Enzymes that join Okazaki fragments together on the lagging strand during DNA replication.

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How is the lagging strand different from the leading strand?

The leading strand is extended by more DNA synthesis, while the lagging strand has to be made in sections (Okazaki fragments) because of the antiparallel nature of DNA.

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What is the role of telomerase in maintaining chromosome ends?

The ends of chromosomes are protected and maintained by a special enzyme called telomerase. Telomerase adds repetitive DNA sequences to the ends of chromosomes, preventing them from shortening during DNA replication.

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Why do most cells not have telomerase?

Most cells in our body lack telomerase, leading to a gradual shortening of chromosome ends with each cell division. This shortening eventually triggers cellular senescence, where cells stop dividing and become inactive.

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What are telomeres and what is their function?

Telomeres are specialized structures located at the ends of chromosomes. They are composed of repetitive DNA sequences and protect the ends of chromosomes from degradation and fusion.

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During which phase of the cell cycle does DNA replication take place?

The S phase of the cell cycle is the stage during which the cell replicates its entire DNA content, effectively doubling its genetic material before cell division.

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Explain the basic process of DNA replication.

The process of replicating DNA involves the unwinding of the double helix structure, separating the two strands, and using each strand as a template to synthesize a new complementary strand. This results in two identical DNA molecules.

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What is the role of DNA polymerase in DNA replication?

Specialized enzymes called DNA polymerases are responsible for synthesizing new DNA strands during replication. They read the existing template strand and add complementary nucleotides, forming a new, identical DNA strand.

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Describe the process of replication fork formation.

The process of DNA replication involves the formation of two replication forks, where the DNA double helix is unwound and separated. These forks move along the DNA molecule, creating two new strands with the help of DNA polymerase.

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What is the significance of semi-conservative replication?

DNA replication is a semi-conservative process, meaning each newly formed DNA molecule contains one original strand and one newly synthesized strand. This ensures that each daughter cell receives a complete and accurate copy of the genetic information.

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Study Notes

DNA Replication

  • DNA replication is essential for cell division and life.
  • DNA needs to double to distribute equal amounts of DNA when cells divide.
  • Defects in DNA replication can cause diseases like cancer.
  • DNA topoisomerases are crucial for efficient and accurate DNA replication. They solve the problem of DNA double helix unwinding during strand separation.

Types of DNA Replication

  • Semiconservative replication: Each new DNA molecule consists of one original strand and one new strand. This was experimentally proven.
  • Conservative replication: Both parental strands remain together and create two new strands that form a new double helix.
  • Dispersive replication: Both parental strands are dispersed into new DNA strands.

Semiconservative replication proof

  • Meselson-Stahl experiment (1959): Distinguished semiconservative replication from other models by using isotopes of nitrogen.
  • Bacteria were grown in a medium containing heavy nitrogen (15N).
  • The bacteria's DNA was then transferred to a medium containing normal nitrogen (14N).
  • DNA was extracted and analyzed by density gradient centrifugation.
  • The results indicated that after one cycle of replication, the DNA was intermediate in density. This supported the semiconservative model.

The role of topoisomerases in DNA replication

  • DNA topoisomerases prevent supercoiling during DNA replication.
  • Supercoils form when DNA strands are separated.

How topoisomerases work

  • Type I Topoisomerases: Create a single-strand break in the DNA, allows another segment of DNA to pass through, and reseals the break. Type I topoisomerases allow the DNA to relieve twisting stress by making a single cut.
  • Type II Topoisomerases: Create a double-strand break, pass a segment of DNA through the gap, and then reseal the breaks. Type II topoisomerases resolve the knots formed by removing twists, and the DNA continues to unwind for replication.

DNA Supercoiling

  • Supercoiling occurs when DNA strands are separated.
  • Topoisomerases remove or prevent supercoiling.

Additional notes

  • A typical bacterial chromosome is a circular DNA molecule (approximately 4 million base pairs).
  • Bacteria can divide every 20 minutes.
  • A circular DNA molecule would have to rotate very rapidly to replicate its genome every 20 minutes (approximately 20,000 revolutions per minute).
  • DNA synthesis proceeds in the 5' to 3' direction.
  • Important enzymes involved in replication: DNA Polymerase I, DNA Polymerase III, DNA polymerase α, DNA polymerase δ, primase, FEN1.
  • Reading Materials: Brown, Chapter 10 (pages 187-191, 192-193) and Alberts, Chapter 6 (pages 199-205, 212).
  • Online resources are available on Blackboard.

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