Biology Chapter on DNA Replication Mechanics
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Questions and Answers

What is the primary mechanism used to separate heavy and light DNA during the Meselson-Stahl experiment?

  • Chromatography
  • Centrifugation (correct)
  • Filtration
  • Electrophoresis
  • What is the name of the technique that separates DNA molecules based on their density in a CsCl gradient?

  • Equilibrium density gradient centrifugation (correct)
  • Atomic force microscopy
  • Gel electrophoresis
  • High-performance liquid chromatography
  • What does the presence of DNA hybrid (heavy and light isotopes) after one generation of bacterial growth indicate?

  • Conservative replication
  • Dispersive replication
  • Semiconservative replication (correct)
  • None of the above
  • What is the purpose of heating the DNA hybrid before centrifugation in the Meselson-Stahl experiment?

    <p>To break the hydrogen bonds between the DNA strands (A)</p> Signup and view all the answers

    What is the main function of initiator proteins in DNA replication?

    <p>To bind to specific DNA sequences called replication origins (A)</p> Signup and view all the answers

    What is the primary role of DNA replication in the context of cellular processes?

    <p>To create copies of the genetic material for cell division. (A)</p> Signup and view all the answers

    Which of the following statements accurately describes the relationship between the two strands of a DNA double helix?

    <p>They are complementary in nucleotide sequence. (B)</p> Signup and view all the answers

    How does the structure of DNA allow for its efficient replication?

    <p>The double helix structure provides a template for creating a new strand. (B)</p> Signup and view all the answers

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

    <p>They mark the starting points for the synthesis of new DNA strands. (D)</p> Signup and view all the answers

    What is the central idea behind the semiconservative model of DNA replication?

    <p>Each new DNA molecule contains one original strand and one newly synthesized strand. (D)</p> Signup and view all the answers

    Which of the following is a characteristic of the 'replication machine' involved in replicating DNA?

    <p>It is a complex of multiple proteins that work together to replicate DNA. (D)</p> Signup and view all the answers

    Why is DNA replication considered a highly accurate process?

    <p>DNA polymerase has a proofreading mechanism to correct errors during replication. (A)</p> Signup and view all the answers

    Which of the following is NOT a characteristic of telomeres?

    <p>They are composed of protein, not DNA. (D)</p> Signup and view all the answers

    What is the rate of DNA replication in humans?

    <p>100 nt/s (B)</p> Signup and view all the answers

    What is the direction of DNA synthesis?

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

    What is the function of the replication fork?

    <p>The replication fork is a Y-shaped junction where DNA synthesis occurs. (C)</p> Signup and view all the answers

    What molecule is released during DNA synthesis?

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

    Which of the following statements about DNA polymerase is TRUE?

    <p>DNA polymerase catalyzes the formation of a phosphodiester bond between the 3’ end of the growing DNA chain and the 5’-phosphate group of the incoming nucleotide. (B)</p> Signup and view all the answers

    What is the size of each chromosome in the human genome?

    <p>Approximately 220 million nucleotides per chromosome (D)</p> Signup and view all the answers

    How many replication origins are there in each chromosome?

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

    What is the function of the replication machine?

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

    What is the primary function of single-strand DNA binding proteins during DNA replication?

    <p>To prevent the unwound single strands of DNA from re-annealing (B)</p> Signup and view all the answers

    Which of the following enzymes is responsible for unwinding the parental DNA double helix during replication?

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

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

    <p>To remove incorrectly incorporated nucleotides. (A)</p> Signup and view all the answers

    What is the role of the sliding clamp in DNA replication?

    <p>To maintain the association of DNA polymerase with the DNA template (A)</p> Signup and view all the answers

    What happens when DNA polymerase makes an error and adds the wrong nucleotide during DNA replication?

    <p>The error is automatically corrected by a separate proofreading mechanism. (D)</p> Signup and view all the answers

    Which of the following statements accurately describe the function of the clamp loader in DNA replication?

    <p>It attaches the sliding clamp to the DNA template. (C)</p> Signup and view all the answers

    What is the direction of DNA synthesis by DNA polymerase?

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

    Which of the following statements accurately describes the role of primase in DNA replication?

    <p>Primase synthesizes short RNA primers that provide a starting point for DNA polymerase. (B)</p> Signup and view all the answers

    Why is it necessary to have a short length of RNA as a primer for DNA polymerase to initiate DNA synthesis?

    <p>Because DNA polymerase can only add nucleotides to an existing 3' end. (D)</p> Signup and view all the answers

    What is the significance of the fact that DNA polymerase can only synthesize DNA in the 5'-to-3' direction?

    <p>It necessitates the use of Okazaki fragments on the lagging strand. (D)</p> Signup and view all the answers

    Which of the following proteins is NOT part of the replication machine?

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

    How does the proofreading function of DNA polymerase contribute to the high fidelity of DNA replication?

    <p>It removes any mismatched nucleotides that might be incorporated during synthesis. (A)</p> Signup and view all the answers

    What is the approximate error rate of DNA polymerase during DNA replication?

    <p>1 error in 10^8 nucleotides (B)</p> Signup and view all the answers

    How does the replication machine ensure the accuracy of DNA replication?

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

    How does DNA polymerase ensure that the correct nucleotide is added to the growing DNA strand?

    <p>It checks the base pairing between the incoming nucleotide and the template strand before adding it to the growing strand. (A)</p> Signup and view all the answers

    What is the significance of the fact that DNA polymerase has separate sites for DNA synthesis and proofreading?

    <p>It allows the polymerase to perform both functions simultaneously, speeding up the replication process. (C)</p> Signup and view all the answers

    What is the main consequence of shortening telomeres in cells?

    <p>Increased risk of DNA damage (B)</p> Signup and view all the answers

    What is the primary function of telomeres in protecting linear chromosomes?

    <p>Preventing the loss of genetic information during DNA replication (A)</p> Signup and view all the answers

    Which of these cell types would you expect to have a high level of telomerase activity?

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

    Why is it important to distinguish between natural chromosome ends and accidental double-strand breaks?

    <p>To activate the repair machinery for broken DNA (D)</p> Signup and view all the answers

    How do telomeres contribute to the maintenance of telomere length?

    <p>By attracting telomere-binding proteins that prevent degradation (B)</p> Signup and view all the answers

    Flashcards

    CsCl gradient

    A density gradient used to separate DNA based on its heavy and light isotopes.

    Equilibrium density centrifugation

    A method to isolate DNA by spinning samples in a density gradient until equilibrium is reached.

    Semiconservative replication

    The model where each new DNA molecule consists of one old strand and one new strand.

    Replication origins

    Specific DNA sequences where DNA replication begins.

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    Initiator proteins

    Proteins that bind to replication origins to start DNA unwinding.

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    DNA replication

    The process of duplicating genetic material before cell division.

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    Base-pairing

    A mechanism where nucleotides on one DNA strand pair with complementary nucleotides on the opposite strand.

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    Telomeres

    Repeating DNA sequences at the ends of chromosomes that protect them from deterioration.

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    Telomerase

    An enzyme that extends telomeres, maintaining chromosome stability during replication.

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    DNA transcription

    The process in which a single strand of DNA serves as a template for the synthesis of RNA.

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    Replication machine

    A cluster of proteins that work together to perform DNA replication efficiently.

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    DNA Helicase

    An enzyme that unwinds the DNA double helix during replication, using ATP.

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    Single-Strand Binding Proteins

    Proteins that bind to single-stranded DNA to prevent it from re-forming a double helix.

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    DNA Polymerase

    An enzyme that synthesizes new DNA strands in the 5’-to-3’ direction.

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    Sliding Clamp

    A protein that keeps DNA polymerase attached to the DNA template.

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    Clamp Loader

    A protein complex that locks the sliding clamp around the DNA double helix, utilizing ATP.

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    ATP Dependence

    The need for ATP to fuel specific enzymatic processes in DNA replication.

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    5'-to-3' Direction

    The direction in which DNA polymerase synthesizes new DNA strands.

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    Function of Telomeres

    Telomeres allow replication of chromosome ends and mark true ends of chromosomes.

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    Telomere-binding proteins

    Proteins that bind to telomeres to protect chromosome ends and maintain length.

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    Telomerase activity

    Telomerase prevents telomere shortening in rapidly dividing cells by extending telomeres.

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    Telomere length variation

    Telomere length varies by cell type and decreases with age in non-dividing cells.

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    Consequence of shortened telomeres

    Cells cease dividing when telomeres disappear after many divisions.

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    Self-Correcting

    DNA polymerase's ability to fix its own errors during replication.

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    Proofreading

    The process where DNA polymerase checks and corrects errors in DNA sequences.

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    Exonuclease Activity

    Involves the removal of mismatched nucleotides by DNA polymerase.

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    RNA Primer

    A short RNA sequence required to initiate DNA synthesis.

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    Primase

    An enzyme that synthesizes RNA primers for DNA replication.

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    Leading Strand

    The continuously synthesized DNA strand during replication.

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    Replication Fork

    A Y-shaped junction where DNA synthesis occurs during replication.

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    Bidirectional Replication

    A process where two replication forks move away from the origin in opposite directions.

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    synthesis direction

    DNA synthesis occurs in the 5' to 3' direction.

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    Phosphodiester Bond

    A connection formed between the 3' end of one DNA strand and the 5' phosphate of another.

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    Nucleotide Addition

    The process by which DNA polymerase adds deoxyribonucleotides to a growing DNA strand.

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    Irreversibility of Polymerization

    The polymerization reaction is effectively irreversible due to the hydrolysis of pyrophosphate.

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    Study Notes

    DNA Replication Overview

    • Base-pairing enables DNA replication
    • DNA synthesis starts at replication origins
    • DNA replicates semi-conservatively
    • DNA replication process details
    • Telomeres and telomerase function

    DNA Replication Details

    • Cell survival and proliferation depend on accurate genetic duplication
    • DNA replication happens before cell division to create two identical daughter cells
    • DNA replication happens during the synthesis phase
    • Each DNA strand is a template for a complementary strand

    Base-Pairing Enables DNA Replication

    • Each strand of a DNA double helix has a nucleotide sequence complementary to its partner strand
    • Each strand acts as a template to produce a complementary strand

    DNA Copying Mechanisms

    • Three models of DNA replication exist (Watson and Crick, Delbrück, Model #3)
    • Semiconservative: After replication, the new DNA molecule consists of one original (parental) strand and one newly synthesized strand
    • Dispersive: During replication, segments of parental strand mix with newly synthesized DNA
    • Conservative: Two original parental DNA strands and two newly synthesized DNA strands are produced

    Labelling DNA with Stable Isotopes

    • Meselson and Stahl used E. coli, heavy 15N-containing DNA and light 14N-containing DNA
    • Centrifugation in CsCl gradient separates heavy and light DNA
    • Equilibrium density centrifugation was used

    Testing DNA Replication Hypotheses

    • Various conditions and results were tested to identify the correct replication model.
    • Results from various methods support the semiconservative model

    DNA Synthesis Begins at Replication Origins

    • DNA double helix is usually stable
    • Opening the helix requires energy, like heat
    • Initiator proteins bind to specific replication origins.
    • Replication origins are locations in the genome where replication begins
    • Bacteria have circular chromosomes with 1 origin
    • Humans have linear chromosomes with many origins ( ~220 per chromosome/ ~10,000 total)

    Two Replication Forks Form at Each Replication Origin

    • DNA synthesis occurs at Y-shaped junctions called replication forks
    • Two forks are produced at the origin
    • At each fork, the replication machine moves along the DNA, using each strand as a template to make a new daughter strand.
    • Replication is bidirectional
    • Speed = ~1,000 nt/sec (bacteria) and ~100 nt/sec (humans)

    DNA Polymerase Synthesizes DNA Using a Parent Strand as a Template

    • The replication machine uses DNA polymerase
    • DNA polymerase uses one parent DNA strand as a template
    • Catalyses nucleotide additions at the 3' end of the growing DNA strand
    • DNA is synthesized in a 5' to 3' direction

    DNA Polymerase Adds Deoxyribonucleotide to the 3' end of a Growing DNA Strand

    • Formation of phosphodiester bonds joining the 3' end of the growing chain to the 5' phosphate group of the incoming nucleotide
    • Pyrophosphate is hydrolyzed, making the polymerization reaction irreversible

    DNA Polymerase Proofreads its Own Work During DNA Synthesis

    • DNA polymerase has high accuracy (~1 error in 107 nucleotides)
    • Monitoring base pairing between incoming nucleotide and template helps ensure accuracy
    • When a mistake occurs, the polymerase corrects it through proofreading

    Initiation of DNA Synthesis Requires

    • DNA polymerase needs a base-paired 3' end before adding nucleotides.
    • A separate enzyme, primase, provides this starting point.
    • Primase synthesizes RNA primers for DNA replication

    Multiple Enzymes Required for Discontinuous DNA Synthesis

    • New RNA primers are laid down at intervals along the lagging strand.
    • DNA polymerase adds deoxyribonucleotides to the 3' end of each primer to form Okazaki fragments
    • Three other enzymes are needed to generate a continuous new DNA strand from Okazaki fragments

    DNA Ligase

    • Joins the 5' phosphate end of one fragment to the 3' hydroxyl end of the next
    • Joins Okazaki fragments on the lagging strand

    Proteins at Replication Fork Cooperate to Form a Replication Machine

    • DNA replication requires the double helix to be continually separated by DNA helicase (ATP dependent)
    • Single-strand DNA binding proteins (SSBs) latch onto ssDNA to prevent re-annealing

    Replication Machine

    • DNA synthesis is carried out by a group of proteins.
    • DNA polymerase operates in the 5' to 3' direction.
    • Sliding clamp to keep DNA polymerase attached to the template.
    • Clamp loader assists in locking the sliding clamp onto the DNA.

    Replication Machine in Cells

    • Proteins in the replication machine are held together in a large unit
    • Clamp loader locks the sliding clamp around the newly formed DNA template
    • ATP is required in this process

    Does Localized Unwinding of DNA Double Helices Present a Problem?

    • As helicase moves, the DNA ahead of the replication fork tightens.
    • Tension builds up, but this problem is relieved by DNA topoisomerases

    DNA Topoisomerases

    • Enzymes that relieve tension by making transient single-strand breaks in the DNA.
    • Breaks are resealed to release tension.

    Various Proteins and their Activities in DNA Replication

    • Summary of various proteins and their roles in DNA replication

    DNA Replication in Living Cells

    • The given website is a resource for advanced information on DNA replication

    Telomerase Replicates the Ends of Eukaryotic Chromosomes

    • Leading strand replication is completed but lagging strand replication cannot
    • Telomeres are required to finish lagging strand replication.
    • RNA primer is removed and replaced by DNA using a mechanism of proofreading
    • Telomerase carries its own RNA template and uses it add copies to the lagging strand template

    Dealing with "End-Replication Problem"

    • Telomeres are repetitive nucleotide sequences at the ends of chromosomes
    • Provide extra DNA for lagging-strand replication completion
    • Telomerase carries its own RNA template, adding repetitive DNA sequences to the lagging strand template

    Telomeres and Telomerases

    • Telomeres prevent linear eukaryotic chromosomes from shortening after each cell division
    • Repetitive DNA sequences draw telomere-binding proteins to protect chromosome ends and maintain telomere length

    Telomeres and Telomerases

    • Telomere length varies with age and cell type.
    • Rapidly dividing cells maintain high telomerase activity, whereas many other cell types gradually reduce their telomerase activity over cell divisions.
    • Telomeres shorten, eventually causing cell division to cease.

    Lecture 3 Reading

    • Chapter 6 covers DNA replication and repair, on pages 179-225 of the textbook

    Upcoming Lecture 4 Reading

    • Chapter 6 covers DNA replication and repair, on pages 225-236

    Room Changes for Labs 55 and 60

    • Room changes for labs 55 and 60 are to be found on UWinsite

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    DNA Replication Lecture 3 PDF

    Description

    Explore key concepts regarding DNA replication in this quiz, focusing on the Meselson-Stahl experiment and its implications. Test your understanding of DNA structure, replication origins, and the role of initiator proteins. This quiz will enhance your knowledge of molecular biology and the processes involved in DNA replication.

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