DNA Replication: Lagging Strand and Okazaki Fragments
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Questions and Answers

What is the typical length of a bacterial gene?

  • 200 kb
  • 100 kb
  • 5 kb
  • 1 kb (correct)

    • Which type of DNA transfer is mediated by a virus that targets bacteria?

  • Horizontal transmission
  • Transformation
  • Transduction (correct)
  • Conjugation

    • What is the main function of plasmids in prokaryotic genomes?

  • Contain genes for antibiotic resistance (correct)
  • Promote natural transformation
  • Maintain the malleability of prokaryotic genetic information
  • Regulate the expression of structural genes

    • What phenomenon can introduce new functions to prokaryotic genomes?

    <p>Horizontal gene transfer</p> Signup and view all the answers

    What term is used for regions of the genome with signs of horizontal transfer?

    <p>Genomic islands</p> Signup and view all the answers

    What is the primary method by which genetic information can be transferred from the environment to bacteria?

    <p>Natural transformation</p> Signup and view all the answers

    In which type of genomes have microbial genomes undergone extensive gene loss and gain?

    <p>Prokaryotic genomes</p> Signup and view all the answers

    What is the number of loops into which the nucleoid forms chromosomes called?

    <p>~50 loops</p> Signup and view all the answers

    What is the primary factor contributing to the malleability of prokaryotic genomes?

    <p>Gene transfer processes</p> Signup and view all the answers

    What is the range of bacterial and archaeal chromosome size in kilobase pairs (kb)?

    <p>490 to 9,400 kb</p> Signup and view all the answers

    What is the nature of all microbial genomes, as revealed by bioinformatic studies?

    <p>Mosaic</p> Signup and view all the answers

    When was the first bacterial genome sequenced?

    <p>1995</p> Signup and view all the answers

    What is the term for the entire genetic complement of DNA in a cell?

    <p>Genome</p> Signup and view all the answers

    What is the range of genome size (in Mb) for bacteria?

    <p>0.12-9.4 Mb</p> Signup and view all the answers

    What is the number of genes in bacterial and archaeal chromosomes?

    <p>120-8000</p> Signup and view all the answers

    When comparing eukaryotic and bacterial genomes, what is a significant difference in chromosome size range?

    <p>Bacterial and archaeal chromosomes are smaller than eukaryotic chromosomes</p> Signup and view all the answers

    What was the publication where the microbial genome variability is mentioned?

    <p>Welch, et al. 2002, PNAS, 99:17020</p> Signup and view all the answers

    What experiment led to the discovery of transformation?

    <p>$\alpha$-hemolysis experiment</p> Signup and view all the answers

    'Genes and operons' were distinguished based on what criteria?

    <p>Function and location</p> Signup and view all the answers

    'Monophyletic vs polyphyletic ancestries for bacteria' refers to what aspect of bacterial evolution?

    <p>'Monophyletic' represents single ancestral lineage while 'polyphyletic' represents multiple ancestral lineages</p> Signup and view all the answers

    Which process involves the uptake of DNA directly from the environment?

    <p>Natural transformation</p> Signup and view all the answers

    What is the process called when bacteriophages carry host DNA from one cell that has been infected to another cell?

    <p>Transduction</p> Signup and view all the answers

    Which protein complex at the cell surface takes up foreign DNA during natural transformation?

    <p>Competence protein complexes</p> Signup and view all the answers

    What physiological state of cells greatly affects competence during natural transformation?

    <p>Early log phase growth</p> Signup and view all the answers

    What is the process called that involves the transfer of DNA from one bacterium to another following cell-to-cell contact?

    <p>Conjugation</p> Signup and view all the answers

    What process allows some bacteria to transfer genes across biological domains, such as Agrobacterium tumefaciens transferring genes to plant cells?

    <p>Conjugation</p> Signup and view all the answers

    Which type of recombination requires a short 10-20bp sequence recognized by a recombination enzyme (recombinase)?

    <p>Site-specific recombination</p> Signup and view all the answers

    What is the fate of plasmids entering the cell?

    <p>They coexist and replicate in the cell as extrachromosomal DNA</p> Signup and view all the answers

    What protein machine unwinds donor DNA during recombination?

    <p>RecBCD</p> Signup and view all the answers

    Which process involves viruses that attack bacteria and carry host DNA from an infected cell to another cell?

    <p>Transduction</p> Signup and view all the answers

    What is the function of restriction endonucleases in the restriction and modification system?

    <p>Cut foreign DNA at specific sequences</p> Signup and view all the answers

    In the restriction/modification system, what is the role of protective methylation?

    <p>Destroy foreign DNA without native DNA methylation pattern</p> Signup and view all the answers

    What is the function of CRISPR in bacterial defense against viral DNA?

    <p>Cuts up invading viral DNA and inserts pieces into the bacterial genome</p> Signup and view all the answers

    What happens to spacers in the CRISPR system after they are transcribed?

    <p>They are used by the Cas9 enzyme to monitor complementary DNA sequences</p> Signup and view all the answers

    What is the main function of restriction and modification system in bacteria?

    <p>Defend against transferred DNA</p> Signup and view all the answers

    How does the restriction/modification system protect host DNA from alien DNA?

    <p>By adding methyl groups to host DNA</p> Signup and view all the answers

    What is the role of Cas9 enzyme in the CRISPR system?

    <p>Uses transcribed spacers to monitor and degrade matching sequences</p> Signup and view all the answers

    How do bacteria defend against transferred DNA using CRISPR?

    <p>By cutting up invading viral DNA and inserting pieces into their own genome</p> Signup and view all the answers

    What is the protective role of restriction endonucleases in bacteria?

    <p>Cut foreign DNA at specific sequences (restriction sites)</p> Signup and view all the answers

    In the CRISPR system, what happens after spacers are transcribed?

    <p>They are used by Cas9 enzyme to monitor and degrade matching viral sequences</p> Signup and view all the answers

    What is the function of RNase H in DNA replication?

    <p>Recognizes DNA/RNA heteroduplexes and removes the RNA primers</p> Signup and view all the answers

    What is the primary role of DNA ligase in DNA replication?

    <p>Seals the junctions between Okazaki fragments</p> Signup and view all the answers

    What is the function of topoisomerase IV in DNA replication?

    <p>Passes the chromosomes through one another at defined termination sites</p> Signup and view all the answers

    What is the origin of replication in plasmids known as?

    <p>oriT (Origin of transfer)</p> Signup and view all the answers

    In plasmids, what is a replicon dependent on?

    <p>Chromosomal genes, such as DNA polymerases</p> Signup and view all the answers

    What is the term for the loss of plasmids if they no longer confer a benefit to the host cell?

    <p>Plasmid curing</p> Signup and view all the answers

    Which system in plasmids pushes plasmids to opposite ends of the dividing cell?

    <p>Segregation system</p> Signup and view all the answers

    What is the function of a toxin-antitoxin module in plasmids?

    <p>Self-maintenance of plasmids</p> Signup and view all the answers

    What type of replication does rolling circle replication involve?

    <p>&quot;Unidirectional&quot; replication</p> Signup and view all the answers

    'ParMRC' system is associated with which function in plasmids?

    <p>&quot;Segregation&quot;</p> Signup and view all the answers

    What process allows some bacteria to transfer genes across biological domains?

    <p>Transformation</p> Signup and view all the answers

    What is the role of Cas9 enzyme in the CRISPR system?

    <p>Targets and cleaves foreign DNA during bacterial defense mechanisms</p> Signup and view all the answers

    What is the function of DNA helicase in bacterial DNA replication?

    <p>It unwinds the two strands of DNA</p> Signup and view all the answers

    What is the role of DNA polymerase III in bacterial DNA replication?

    <p>It synthesizes new DNA strands</p> Signup and view all the answers

    Why are RNA primers required for DNA replication?

    <p>To provide the 3’-OH group for DNA polymerase III to synthesize new DNA strands</p> Signup and view all the answers

    What is the function of SSBs (single-stranded DNA binding proteins) in bacterial DNA replication?

    <p>To keep the single DNA strands apart during DNA synthesis</p> Signup and view all the answers

    Which enzyme is responsible for producing RNA primers in bacterial DNA replication?

    <p>DNA primase</p> Signup and view all the answers

    What evolutionary remnant is suggested by the fact that RNA was the first genetic material?

    <p>RNA primers</p> Signup and view all the answers

    Which component recruits DNA polymerase III and tethers it to the DNA during bacterial DNA replication?

    <p>Clamp loader and sliding clamps</p> Signup and view all the answers

    What is the main role of clamp loader and sliding clamps in bacterial DNA replication?

    <p>To recruit DNA polymerase III and tether it to the DNA</p> Signup and view all the answers

    What is the function of clamp loader in bacterial DNA replication?

    <p>Recruits DNA polymerase III and tethers it to the DNA</p> Signup and view all the answers

    Study Notes

    Bacterial Genomes

    • The typical length of a bacterial gene is not specified, but bacterial and archaeal chromosome sizes range from 0.5-12.2 megabase pairs (Mb).
    • Bacterial genomes have undergone extensive gene loss and gain in microbial genomes.

    DNA Transfer

    • The primary method of genetic information transfer from the environment to bacteria is through natural transformation.
    • Horizontal gene transfer can introduce new functions to prokaryotic genomes.
    • Regions of the genome with signs of horizontal transfer are referred to as genomic islands.
    • Transduction, mediated by a virus that targets bacteria, is a type of DNA transfer.
    • Conjugation, which involves the transfer of DNA from one bacterium to another following cell-to-cell contact, is another type of DNA transfer.
    • Some bacteria, such as Agrobacterium tumefaciens, can transfer genes across biological domains, such as to plant cells.

    Genome Structure

    • The nucleoid forms chromosomes into 4-10 loops.
    • The genetic complement of DNA in a cell is referred to as the genome.

    Plasmids

    • The main function of plasmids in prokaryotic genomes is to provide additional genetic information.
    • Plasmids can enter the cell through natural transformation.
    • The fate of plasmids entering the cell is to replicate and be maintained.
    • Some plasmids can transfer genes across biological domains.

    Restriction and Modification System

    • The restriction and modification system protects host DNA from alien DNA through the action of restriction endonucleases and protective methylation.
    • The function of restriction endonucleases is to cleave foreign DNA.
    • Protective methylation prevents the host DNA from being cleaved by restriction endonucleases.

    CRISPR System

    • The CRISPR system is a defense mechanism against viral DNA.
    • CRISPR involves the transfer of spacers from the host genome to the CRISPR array, which are then transcribed and used to target viral DNA.
    • The role of Cas9 enzyme is to cleave targeted viral DNA.
    • The main function of the CRISPR system is to defend against viral DNA.

    DNA Replication

    • The function of RNase H is to remove RNA primers during DNA replication.
    • The primary role of DNA ligase is to seal gaps between Okazaki fragments.
    • The function of topoisomerase IV is to relax DNA supercoiling.
    • The origin of replication in plasmids is known as the replicon.
    • The function of DNA helicase is to unwind DNA during replication.
    • The role of DNA polymerase III is to synthesize new DNA strands.
    • RNA primers are required for DNA replication because DNA polymerase cannot initiate synthesis de novo.
    • The function of SSBs is to protect single-stranded DNA during replication.
    • The enzyme responsible for producing RNA primers is primase.
    • The clamp loader and sliding clamps play a crucial role in recruiting DNA polymerase III and tethering it to the DNA during replication.

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    Description

    Test your knowledge of DNA replication with a focus on the lagging strand and Okazaki fragments. Explore the roles of DNA primase, DNA Polymerase III, RNase H, and DNA polymerase I in the process of completing DNA replication.

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