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Questions and Answers
What is the primary mechanism used to separate heavy and light DNA during the Meselson-Stahl experiment?
What is the primary mechanism used to separate heavy and light DNA during the Meselson-Stahl experiment?
What is the name of the technique that separates DNA molecules based on their density in a CsCl gradient?
What is the name of the technique that separates DNA molecules based on their density in a CsCl gradient?
What does the presence of DNA hybrid (heavy and light isotopes) after one generation of bacterial growth indicate?
What does the presence of DNA hybrid (heavy and light isotopes) after one generation of bacterial growth indicate?
What is the purpose of heating the DNA hybrid before centrifugation in the Meselson-Stahl experiment?
What is the purpose of heating the DNA hybrid before centrifugation in the Meselson-Stahl experiment?
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What is the main function of initiator proteins in DNA replication?
What is the main function of initiator proteins in DNA replication?
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What is the primary role of DNA replication in the context of cellular processes?
What is the primary role of DNA replication in the context of cellular processes?
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Which of the following statements accurately describes the relationship between the two strands of a DNA double helix?
Which of the following statements accurately describes the relationship between the two strands of a DNA double helix?
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How does the structure of DNA allow for its efficient replication?
How does the structure of DNA allow for its efficient replication?
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What is the role of replication origins in the process of DNA replication?
What is the role of replication origins in the process of DNA replication?
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What is the central idea behind the semiconservative model of DNA replication?
What is the central idea behind the semiconservative model of DNA replication?
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Which of the following is a characteristic of the 'replication machine' involved in replicating DNA?
Which of the following is a characteristic of the 'replication machine' involved in replicating DNA?
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Why is DNA replication considered a highly accurate process?
Why is DNA replication considered a highly accurate process?
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Which of the following is NOT a characteristic of telomeres?
Which of the following is NOT a characteristic of telomeres?
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What is the rate of DNA replication in humans?
What is the rate of DNA replication in humans?
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What is the direction of DNA synthesis?
What is the direction of DNA synthesis?
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What is the function of the replication fork?
What is the function of the replication fork?
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What molecule is released during DNA synthesis?
What molecule is released during DNA synthesis?
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Which of the following statements about DNA polymerase is TRUE?
Which of the following statements about DNA polymerase is TRUE?
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What is the size of each chromosome in the human genome?
What is the size of each chromosome in the human genome?
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How many replication origins are there in each chromosome?
How many replication origins are there in each chromosome?
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What is the function of the replication machine?
What is the function of the replication machine?
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What is the primary function of single-strand DNA binding proteins during DNA replication?
What is the primary function of single-strand DNA binding proteins during DNA replication?
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Which of the following enzymes is responsible for unwinding the parental DNA double helix during replication?
Which of the following enzymes is responsible for unwinding the parental DNA double helix during replication?
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What is the primary role of the 3' to 5' exonuclease activity of DNA polymerase during DNA replication?
What is the primary role of the 3' to 5' exonuclease activity of DNA polymerase during DNA replication?
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What is the role of the sliding clamp in DNA replication?
What is the role of the sliding clamp in DNA replication?
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What happens when DNA polymerase makes an error and adds the wrong nucleotide during DNA replication?
What happens when DNA polymerase makes an error and adds the wrong nucleotide during DNA replication?
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Which of the following statements accurately describe the function of the clamp loader in DNA replication?
Which of the following statements accurately describe the function of the clamp loader in DNA replication?
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What is the direction of DNA synthesis by DNA polymerase?
What is the direction of DNA synthesis by DNA polymerase?
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Which of the following statements accurately describes the role of primase in DNA replication?
Which of the following statements accurately describes the role of primase in DNA replication?
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Why is it necessary to have a short length of RNA as a primer for DNA polymerase to initiate DNA synthesis?
Why is it necessary to have a short length of RNA as a primer for DNA polymerase to initiate DNA synthesis?
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What is the significance of the fact that DNA polymerase can only synthesize DNA in the 5'-to-3' direction?
What is the significance of the fact that DNA polymerase can only synthesize DNA in the 5'-to-3' direction?
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Which of the following proteins is NOT part of the replication machine?
Which of the following proteins is NOT part of the replication machine?
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How does the proofreading function of DNA polymerase contribute to the high fidelity of DNA replication?
How does the proofreading function of DNA polymerase contribute to the high fidelity of DNA replication?
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What is the approximate error rate of DNA polymerase during DNA replication?
What is the approximate error rate of DNA polymerase during DNA replication?
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How does the replication machine ensure the accuracy of DNA replication?
How does the replication machine ensure the accuracy of DNA replication?
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How does DNA polymerase ensure that the correct nucleotide is added to the growing DNA strand?
How does DNA polymerase ensure that the correct nucleotide is added to the growing DNA strand?
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What is the significance of the fact that DNA polymerase has separate sites for DNA synthesis and proofreading?
What is the significance of the fact that DNA polymerase has separate sites for DNA synthesis and proofreading?
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What is the main consequence of shortening telomeres in cells?
What is the main consequence of shortening telomeres in cells?
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What is the primary function of telomeres in protecting linear chromosomes?
What is the primary function of telomeres in protecting linear chromosomes?
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Which of these cell types would you expect to have a high level of telomerase activity?
Which of these cell types would you expect to have a high level of telomerase activity?
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Why is it important to distinguish between natural chromosome ends and accidental double-strand breaks?
Why is it important to distinguish between natural chromosome ends and accidental double-strand breaks?
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How do telomeres contribute to the maintenance of telomere length?
How do telomeres contribute to the maintenance of telomere length?
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Flashcards
CsCl gradient
CsCl gradient
A density gradient used to separate DNA based on its heavy and light isotopes.
Equilibrium density centrifugation
Equilibrium density centrifugation
A method to isolate DNA by spinning samples in a density gradient until equilibrium is reached.
Semiconservative replication
Semiconservative replication
The model where each new DNA molecule consists of one old strand and one new strand.
Replication origins
Replication origins
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Initiator proteins
Initiator proteins
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DNA replication
DNA replication
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Base-pairing
Base-pairing
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Telomeres
Telomeres
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Telomerase
Telomerase
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DNA transcription
DNA transcription
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Replication machine
Replication machine
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DNA Helicase
DNA Helicase
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Single-Strand Binding Proteins
Single-Strand Binding Proteins
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DNA Polymerase
DNA Polymerase
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Sliding Clamp
Sliding Clamp
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Clamp Loader
Clamp Loader
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ATP Dependence
ATP Dependence
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5'-to-3' Direction
5'-to-3' Direction
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Function of Telomeres
Function of Telomeres
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Telomere-binding proteins
Telomere-binding proteins
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Telomerase activity
Telomerase activity
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Telomere length variation
Telomere length variation
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Consequence of shortened telomeres
Consequence of shortened telomeres
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Self-Correcting
Self-Correcting
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Proofreading
Proofreading
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Exonuclease Activity
Exonuclease Activity
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RNA Primer
RNA Primer
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Primase
Primase
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Leading Strand
Leading Strand
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Replication Fork
Replication Fork
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Bidirectional Replication
Bidirectional Replication
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synthesis direction
synthesis direction
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Phosphodiester Bond
Phosphodiester Bond
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Nucleotide Addition
Nucleotide Addition
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Irreversibility of Polymerization
Irreversibility of Polymerization
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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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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.