Biology Chapter 5: Topoisomerases and Nucleases
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Questions and Answers

What is the primary function of Type II topoisomerase in relation to helical turns of DNA?

  • It changes the DNA by two helical turns. (correct)
  • It fixes single-stranded breaks in DNA.
  • It introduces positive supercoils.
  • It unwinds DNA completely without cleaving.

    • What effect does negatively supercoiled DNA have on cellular processes?

  • It prevents transcription initiation.
  • It inhibits DNA replication.
  • It promotes strand separation. (correct)
  • It facilitates DNA denaturation.

    • Which of the following describes the end result of Type II topoisomerase cleavage and passage?

  • It religates both strands of the cleaved segment. (correct)
  • It forms a single-stranded break in DNA.
  • It prevents DNA tangling.
  • It creates two separate DNA molecules.

    • What is the structure of cellular DNA typically considered?

    <p>Negatively supercoiled.</p> Signup and view all the answers

    How does Type II topoisomerase achieve the passage of DNA strands?

    <p>Via a double-stranded break.</p> Signup and view all the answers

    Why is positively supercoiled DNA advantageous for thermophilic organisms?

    <p>It resists heat denaturation.</p> Signup and view all the answers

    What role does reverse gyrase play in thermophilic organisms?

    <p>It introduces positive supercoils.</p> Signup and view all the answers

    What happens to DNA during the bind-cleavage (double)-passage-religation mechanism of Type II topoisomerase?

    <p>Double-stranded breaks and strand passage occur.</p> Signup and view all the answers

    What effect do topoisomerases have on DNA supercoiling?

    <p>They can increase or decrease supercoiling.</p> Signup and view all the answers

    Which of the following best describes the function of Type I topoisomerase?

    <p>It creates a single-stranded break to relax supercoils.</p> Signup and view all the answers

    What is produced by each round of catalysis in Type I topoisomerase activity?

    <p>One helical turn change, relaxing one negative supercoil.</p> Signup and view all the answers

    What is the first step in the Type I topoisomerase mechanism?

    <p>Binds to a segment of double-stranded DNA.</p> Signup and view all the answers

    How does the Type I topoisomerase mechanism change DNA's structure?

    <p>It relaxes negative supercoils by changing DNA's helical turns.</p> Signup and view all the answers

    What role does the cleaved DNA strand play during the activity of Type I topoisomerase?

    <p>It passes through the break formed by the enzyme.</p> Signup and view all the answers

    Which type of topoisomerase is characterized by cutting both strands of DNA?

    <p>Type II topoisomerase.</p> Signup and view all the answers

    What happens during the 'reverse reaction' in Type I topoisomerase?

    <p>The cleaved strand is re-ligated, restoring DNA integrity.</p> Signup and view all the answers

    What happens to circular relaxed DNA when it is subjected to positive supercoiling?

    <p>It forms more helical turns.</p> Signup and view all the answers

    What role does topoisomerase I play in the context of DNA supercoiling?

    <p>It relaxes supercoiled DNA.</p> Signup and view all the answers

    In an agarose gel electrophoresis, how do DNA bands typically migrate?

    <p>From top to bottom.</p> Signup and view all the answers

    What is the visual marker used to stain DNA in agarose gel electrophoresis?

    <p>Ethidium bromide.</p> Signup and view all the answers

    What condition results in the formation of a negative supercoil in DNA?

    <p>If it has fewer helical turns.</p> Signup and view all the answers

    Which type of supercoil is produced when circular relaxed DNA is underwound?

    <p>Negative supercoil.</p> Signup and view all the answers

    What is the configuration of circular relaxed DNA in terms of helical turns?

    <p>It has one helical turn per 10.5 bp.</p> Signup and view all the answers

    What would be the effect of applying topoisomerase I to supercoiled DNA?

    <p>It would convert it to relaxed DNA.</p> Signup and view all the answers

    What is the product of RNA 5’ pApGpCpUpCpGpUpC 3’ after being digested with RNase T1?

    <p>pApGp + CpUpCpGp + UpC</p> Signup and view all the answers

    Which statement accurately reflects the action of DNase I on RNA-DNA fusion molecules?

    <p>It produces RNA fragments and non-selectively cleaves DNA.</p> Signup and view all the answers

    What distinguishes RNase A from RNase T1?

    <p>RNase A is specific for pyrimidines.</p> Signup and view all the answers

    What is a characteristic of alkaline hydrolysis of RNA?

    <p>It requires the presence of 2’-OH to act on RNA.</p> Signup and view all the answers

    What is the end product of RNA after its hydrolysis by concentrated NaOH?

    <p>RNA is completely hydrolyzed into nucleotides.</p> Signup and view all the answers

    What occurs when DNA is supercoiled?

    <p>The DNA strands partially relax.</p> Signup and view all the answers

    Which enzyme specifically degrades RNA?

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

    In the context of nucleases, what is the difference between an endonuclease and an exonuclease?

    <p>Endonucleases hydrolyze interior phosphodiester bonds.</p> Signup and view all the answers

    What characteristic does negatively supercoiled DNA exhibit in gel migration?

    <p>It migrates slower as it is less compact.</p> Signup and view all the answers

    Which statement about the nature of phosphodiester bond cleavage is true?

    <p>It produces both 5’-OH, 3’-P and 3’-OH, 5’-P ends based on the enzyme.</p> Signup and view all the answers

    How is the supercoiling state of DNA quantified?

    <p>Using the formula S = Lk - Lko.</p> Signup and view all the answers

    What is a key feature of a nuclease that exhibits substrate specificity?

    <p>It requires a specific type of nucleic acid to function.</p> Signup and view all the answers

    What type of cleavage does DNase I produce?

    <p>Only 3’-OH and 5’-P ends.</p> Signup and view all the answers

    Study Notes

    Topoisomerases

    • Topoisomerases alter DNA supercoiling; classified into type I and type II.
    • Type I topoisomerases relax DNA by cutting one strand (creating a single-stranded break) and allowing the other strand to pass through before re-ligating the cut strand.
    • Each action of type I topoisomerase results in the relaxation of one negative supercoil.

    Mechanism of Type I Topoisomerases

    • Binds to double-stranded DNA, cleaves, passes the unbroken strand through the break, and then religates the cut strand.
    • Each cycle changes the DNA by one helical turn, reducing supercoiling effectively.

    Type II Topoisomerases (DNA Gyrase)

    • Type II topoisomerases bind to two segments of DNA, cleave both strands at one segment (creating a double-stranded break), pass another segment through the break, and then religate both strands.
    • Catalysis results in changes of two helical turns, generating two negative supercoils and aiding in untangling DNA.

    DNA Supercoiling

    • Cellular DNA is typically negatively supercoiled, promoting easier strand separation which is necessary for replication and transcription.
    • Thermophilic organisms contain positively supercoiled DNA, providing structural stability at high temperatures. Reverse gyrase generates positive supercoils in these organisms.

    Experimental Analysis of Supercoiling

    • Circular DNA supercoiling can be visualized using agarose gel electrophoresis; relaxed DNA moves differently than supercoiled DNA.
    • Supercoiled DNA treated with topoisomerase I relaxes to a single supercoil, observable on a gel.

    Nucleases

    • Nucleases catalyze hydrolysis of phosphodiester bonds in nucleic acids, aiding in DNA and RNA degradation processes.
    • Types include ribonuclease (RNase) degrading RNA, deoxyribonuclease (DNase) degrading DNA, and non-specific nucleases acting on both.
    • Nucleases vary by position of attack: endonucleases cleave bonds within the chain, while exonucleases cleave from chain ends.

    Phosphodiester Bond Reactions

    • RNases and DNases produce 5'-OH and 3'-P or vice versa, depending on the specific nuclease.
    • Specificity can vary; some nucleases target specific bases while others can act more broadly.

    Alkaline Hydrolysis of RNA

    • Concentrated NaOH can hydrolyze RNA but does not affect DNA due to DNA's lack of a 2'-OH group, which prevents similar reactions.
    • Alkaline treatments lead to RNA denaturation by breaking hydrogen bonds without damaging DNA structurally.

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    Description

    Explore the functions and classifications of topoisomerases in DNA supercoiling through this quiz. Understand the differences between Type I and Type II topoisomerases and their roles in DNA manipulation. Test your knowledge on these essential enzymes crucial for DNA structure and function.

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