DNA Structure and Stability
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Questions and Answers

What is responsible for minimizing the repulsion between nearby phosphate groups in DNA's sugar-phosphate backbone?

  • Van der Waals forces between phosphate groups
  • Hydrogen bonding between phosphate groups
  • Electrostatic interactions between phosphate groups
  • Divalent cations such as Mg2+ and polycationic molecules (correct)

    • What is the characteristic of the double helix formed due to base stacking interactions?

  • A planar structure with hydrophilic sugar-phosphate backbones
  • A linear structure with exposed hydrophilic bases
  • A spiral structure with exposed hydrophobic backbones
  • A twisted structure with a hydrophobic interior (correct)

    • Why are molecules able to interact with specific base pairs without disrupting the double helix?

  • Because the sugar-phosphate backbones are exposed to the aqueous environment
  • Because the hydrophobic bases are located on the outside of the helix
  • Because the base pairs are exposed on the surface of the helix
  • Because the base pairs are accessible in the major and minor grooves (correct)

    • What type of interactions between the upper and lower surfaces of each base pair contribute to the stability of DNA?

    <p>Cooperative, non-covalent interactions</p> Signup and view all the answers

    What is the primary source of stability for large DNA molecules?

    <p>Van der Waals contacts</p> Signup and view all the answers

    What is the orientation of the base pairs in B-DNA?

    <p>Perpendicular to the long axis of the molecule</p> Signup and view all the answers

    What is the characteristic of the sugar-phosphate backbone in the double helix?

    <p>Hydrophilic and wound around the outside of the helix</p> Signup and view all the answers

    What is the purpose of the major and minor grooves in the double helix?

    <p>To provide a binding site for proteins</p> Signup and view all the answers

    What is the distance between adjacent base pairs in DNA?

    <p>0.34 nm</p> Signup and view all the answers

    What type of bonding interaction contributes to the stability of DNA's structure by minimizing the interactions of base components with water?

    <p>Hydrophobic interactions</p> Signup and view all the answers

    What is the approximate number of base pairs in one turn of the double helix?

    <p>10.4</p> Signup and view all the answers

    Which of the following is NOT a type of non-covalent bonding interaction that contributes to the stability of DNA's structure?

    <p>Covalent bonds</p> Signup and view all the answers

    What is the approximate distance between the two polynucleotide strands in the DNA double helix?

    <p>2.4 nm</p> Signup and view all the answers

    What is the diameter of the double helix?

    <p>2.4 nm</p> Signup and view all the answers

    How many hydrogen bonds are formed between GC pairs?

    <p>3</p> Signup and view all the answers

    Which of the following is NOT a base pair in DNA?

    <p>Guanine-Thymine</p> Signup and view all the answers

    What is the primary force responsible for the stability of the DNA double helix?

    <p>Hydrogen bonding</p> Signup and view all the answers

    What type of interaction is responsible for the 'clustering' of base components within the double helix?

    <p>Hydrophobic interactions</p> Signup and view all the answers

    What is the term for the specific pairing of bases in DNA?

    <p>Base pairing</p> Signup and view all the answers

    What type of forces are responsible for the weak contacts between stacked base pairs?

    <p>Van der Waals forces</p> Signup and view all the answers

    What is the shape of the DNA double helix?

    <p>Right-handed spiral</p> Signup and view all the answers

    Which of the following is a characteristic of the B-DNA conformation?

    <p>The polynucleotide strands are antiparallel</p> Signup and view all the answers

    What is the result of the antiparallel orientation of the polynucleotide strands?

    <p>Hydrogen bonding between the nitrogenous bases</p> Signup and view all the answers

    What is the term for the attractive forces between the stacked nitrogenous bases in DNA?

    <p>Base stacking</p> Signup and view all the answers

    What is the pKa of each phosphate group that participates in a phosphodiester linkage?

    <p>about 2</p> Signup and view all the answers

    Which of the following is true about the base composition of DNA?

    <p>A and T are present in equimolar amounts, as are G and C</p> Signup and view all the answers

    What is the directionality of the tetra-nucleotide in Figure 4?

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

    What is the term for the negative charge carried by nucleic acids under physiological conditions?

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

    What is the significance of Chargaff's rules in understanding DNA structure?

    <p>They reveal the base composition of DNA</p> Signup and view all the answers

    What is the result of the negative charge carried by phosphate groups in nucleic acids?

    <p>Repulsion between nearby phosphate groups</p> Signup and view all the answers

    What is the ratio of purines to pyrimidines in DNA?

    <p>1:1</p> Signup and view all the answers

    What is the arrangement of the two strands in a DNA double helix?

    <p>Antiparallel and oriented in opposite directions</p> Signup and view all the answers

    What is the result of the base pairing between guanine and cytosine?

    <p>Three hydrogen bonds are formed</p> Signup and view all the answers

    What is the spacing between adjacent base pairs in a DNA double helix?

    <p>0.34 nm</p> Signup and view all the answers

    What is the characteristic of the interior space of the DNA double helix?

    <p>It is suitable for pairing a purine and a pyrimidine</p> Signup and view all the answers

    What is the effect of the base stacking interactions in DNA?

    <p>It forms weak van der Waals contacts</p> Signup and view all the answers

    What is the role of hydrophobic interactions in DNA?

    <p>They minimize the interactions of base components with water</p> Signup and view all the answers

    What is the length of one turn of the DNA double helix?

    <p>3.4 nm</p> Signup and view all the answers

    What is the main reason why the sugar-phosphate backbone of DNA is twisted?

    <p>Due to the hydrophobic interactions between the stacked base pairs</p> Signup and view all the answers

    What is the result of the cooperative, non-covalent interactions between the upper and lower surfaces of each base pair?

    <p>The base pairs are brought closer together</p> Signup and view all the answers

    What is the characteristic of the double helix that allows molecules to interact with specific base pairs without disrupting the helix?

    <p>The grooves on the double helix</p> Signup and view all the answers

    What is the reason for the unequal width of the major and minor grooves in the double helix?

    <p>Because of the way the base pairs stack and the sugar-phosphate backbones twist</p> Signup and view all the answers

    What is the building block of DNA?

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

    What is the orientation of the sugar-phosphate backbone in the double helix?

    <p>It is twisted around the outside of the helix</p> Signup and view all the answers

    What type of bond links nucleotides together in DNA?

    <p>Phosphodiester bond</p> Signup and view all the answers

    What is the characteristic of the base pairs in the interior of the helix?

    <p>They are hydrophobic and shielded from water</p> Signup and view all the answers

    What is the role of divalent cations and polycationic molecules in the DNA structure?

    <p>They shield the phosphate groups from water</p> Signup and view all the answers

    What is the directionality of a polynucleotide chain?

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

    What is the primary structure of a nucleic acid?

    <p>The sequence of nucleotides</p> Signup and view all the answers

    What is the basis of the information that specifies the primary structure of a protein?

    <p>The sequence of nucleotides in DNA</p> Signup and view all the answers

    What is the name of the sugar molecule in DNA?

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

    What is the type of nitrogenous base found in DNA?

    <p>Purine and pyrimidine</p> Signup and view all the answers

    What is the role of transcription in protein synthesis?

    <p>Copying DNA into RNA</p> Signup and view all the answers

    What is the flow of biological information in a cell?

    <p>DNA to RNA to protein</p> Signup and view all the answers

    Study Notes

    DNA Structure and Stability

    • The cumulative effect of weak van der Waals contacts between individual stacked base pairs contributes to the stability of large DNA molecules.
    • Electrostatic interactions between negatively charged phosphate groups in the sugar-phosphate backbone are minimized by the shielding effects of divalent cations and polycationic molecules.

    DNA Base Pair Stacking

    • In B-DNA, base pairs are stacked one above the other, nearly perpendicular to the long axis of the molecule.
    • Cooperative, non-covalent interactions between the upper and lower surfaces of each base pair bring the pairs closer together, creating a hydrophobic interior.
    • This stacking interaction creates the familiar double helix structure.

    The Double Helix Structure

    • The sugar-phosphate backbone winds around the outside of the helix, exposed to the aqueous environment.
    • The stacked, relatively hydrophobic bases are located in the interior of the helix, shielded from water.
    • The double helix has two grooves of unequal width, the major groove and the minor groove, due to the way base pairs stack and the sugar-phosphate backbones twist.

    Base Pairing and Grooves

    • Functional groups on the edges of the base pairs are exposed to water and are chemically distinguishable within the grooves.
    • The base pairs are accessible in the grooves, allowing molecules to interact with specific base pairs without disrupting the helix.

    Dimensions of Crystalline DNA

    • One turn of the double helix spans 3.4 nm and consists of approximately 10.4 base pairs.
    • The diameter of the double helix is 2.4 nm.
    • The interior space of the double helix is only suitable for base pairing a purine and a pyrimidine.
    • The distance between adjacent base pairs is 0.34 nm.

    Non-Covalent Bonding Interactions

    • Hydrophobic interactions between stacked purine and pyrimidine bases contribute to the stability of the DNA structure.
    • Hydrogen bonds form between base pairs, with three between GC pairs and two between AT pairs.
    • Base stacking interactions also contribute to the stability of the DNA structure.

    Watson-Crick Model

    • The Watson-Crick model accounts for the equal amounts of purines and pyrimidines by proposing a double-stranded DNA with specific base pairing.
    • The model suggests that DNA consists of two polynucleotide strands wound around each other to form a right-handed double helix.

    Base Composition of DNA

    • The base composition of DNA can vary between organisms, with different ratios of purines to pyrimidines.
    • Table 1 shows the base composition of DNA in various organisms, including E. coli, M. tuberculosis, yeast, cow, pig, and human.

    Nucleotides and Phosphodiester Linkages

    • A tetra-nucleotide can be referred to as 5' pApGpTpC 3', or even AGTC
    • Phosphate groups have a pKa of about 2 and bear a negative charge at neutral pH
    • Nucleic acids are polyanions under physiological conditions

    Double-Stranded (ds) DNA Structure

    • Erwin Chargaff observed that in DNA, A and T are present in equimolar amounts, as are G and C
    • The percentage of purine bases always equals the percentage of pyrimidine bases in DNA
    • The ratio of purines to pyrimidines in DNA is always 1:1
    • The DNA of some organisms, such as yeast, is relatively deficient in G+C, whereas the DNA of other organisms, such as Mycobacterium tuberculosis, is rich in G+C
    • The DNAs of closely related species, such as cows, pigs, and humans, have similar base compositions
    • Guanine (a purine) pairs with cytosine (a pyrimidine)
    • One turn of the double helix spans 3.4 nm and consists of approximately 10.4 base pairs
    • The diameter of the double helix is 2.4 nm
    • The distance between adjacent base pairs is 0.34 nm
    • The two strands run in opposite directions, and the order of bases in one strand determines the sequence of bases of the other strand

    Forces Stabilizing DNA Structure

    • Hydrophobic interactions between stacked purine and pyrimidine bases
    • Hydrogen bonds between base pairs (3 between GC pairs and 2 between AT pairs)
    • Base stacking interactions between stacked base pairs
    • Electrostatic interactions between negatively charged phosphate groups and divalent cations

    B-DNA Structure

    • Base pairs are stacked one above the other and are nearly perpendicular to the long axis of the molecule
    • The cooperative, non-covalent interactions between the upper and lower surfaces of each base pair bring the pairs closer together
    • The stacking interactions create a hydrophobic interior that causes the sugar-phosphate backbone to twist
    • The double helix has two grooves of unequal width, the major groove and the minor groove

    Single-Stranded (ss) DNA Structure

    • Nucleotides are the building blocks of DNA
    • Each nucleotide monomer in DNA is composed of a nitrogenous base, a deoxyribose sugar, and phosphate
    • Nucleotides are linked to each other by 3' to 5' phosphodiester bonds
    • The primary structure of a nucleic acid is the sequence of residues connected by 3', 5'-phosphodiester bonds linkages

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    Description

    This quiz covers the structural stability of DNA, including the roles of van der Waals contacts, electrostatic interactions, and divalent cations.

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