Quaternary Protein Structure and Stability
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Quaternary Protein Structure and Stability

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Questions and Answers

What term describes complexes that have reciprocating mechanisms?

  • Quasisymmetry (correct)
  • Pseudosymmetry
  • Pleomorphism
  • Global asymmetry

    • Which type of asymmetry is rarely observed among identical subunits?

  • Pleomorphism
  • Global asymmetry (correct)
  • Reciprocating mechanisms
  • Pseudosymmetry

    • What is the concept where all subunits cycle through the same set of conformations?

  • Pseudosymmetry
  • Quasisymmetry
  • Pleomorphism (correct)
  • Global asymmetry

    • Which form of symmetry involves asymmetric structures that are similar but differing in conformation?

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

    What does pseudosymmetry imply about the symmetry of a complex?

    <p>The complex shows asymmetry yet retains aspects of symmetry.</p> Signup and view all the answers

    What is the arrangement of the subunits in the enzyme aspartate transcarbamoylase?

    <p>Homohexamer with six catalytic subunits</p> Signup and view all the answers

    What symmetry group does the homohexamer of aspartate transcarbamoylase belong to?

    <p>D3 symmetry group</p> Signup and view all the answers

    Which of the following statements is true about the structural representation of D3 symmetry?

    <p>The three closest subunits are shaded in different colors.</p> Signup and view all the answers

    Which type of symmetry do both the Norwalk virus capsid and mammalian ferritin display?

    <p>Cubic symmetry with multiple axes</p> Signup and view all the answers

    What is the primary function of the DNA polymerase delta processivity factor?

    <p>It acts as a sliding clamp during DNA replication.</p> Signup and view all the answers

    How many subunits make up the mammalian ferritin structure?

    <p>24 subunits</p> Signup and view all the answers

    What is the significance of the hollow core in the structure of ferritin?

    <p>It is used for the storage of iron as an iron oxide complex.</p> Signup and view all the answers

    What would you use to view the 3D structures of the proteins mentioned?

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

    What type of interactions stabilize quaternary structures of proteins?

    <p>Both covalent and noncovalent interactions</p> Signup and view all the answers

    Which of the following describes a structure with C3 symmetry?

    <p>A trimer requiring three 120-degree turns to return to the same view</p> Signup and view all the answers

    Which type of oligomer is characterized by having a defined limit to the number of subunits present?

    <p>Closed quaternary structure</p> Signup and view all the answers

    What does the hydrophobic effect contribute to in protein quaternary structures?

    <p>Oligomer formation through contact between nonpolar residues</p> Signup and view all the answers

    What is true about dihedral groups in protein oligomers?

    <p>They possess both a Cn axis and multiple C2 axes of symmetry</p> Signup and view all the answers

    Which of the following is an example of a closed quaternary structure?

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

    How many half turns does an oligomer with C2 symmetry take to reorient itself to the same view?

    <p>Two half turns</p> Signup and view all the answers

    Which of the following statements about oligomers with cyclic symmetry is correct?

    <p>They have a single axis of symmetry</p> Signup and view all the answers

    What aspect of biology is primarily addressed in the source content?

    <p>Role of structural symmetry in protein function</p> Signup and view all the answers

    Which type of publication is the source content taken from?

    <p>Annual review</p> Signup and view all the answers

    What is the primary focus of the article's authors?

    <p>David S. Goodsell and Arthur J. discuss structural symmetry and its relationship to proteins</p> Signup and view all the answers

    What type of symmetry is likely discussed concerning proteins based on the title?

    <p>Structural symmetry</p> Signup and view all the answers

    When was the publication issued?

    <p>April 20, 2000</p> Signup and view all the answers

    Which two fields are combined in the publication's subject matter?

    <p>Biophysics and Structural Biology</p> Signup and view all the answers

    The content's title suggests that it addresses the interplay between which two concepts?

    <p>Structural features and biological processes</p> Signup and view all the answers

    Who are the authors of the publication?

    <p>David S. Goodsell and Arthur J.</p> Signup and view all the answers

    What characteristic makes large proteins more stable against denaturation compared to smaller proteins?

    <p>Reduced surface area exposed to solvent</p> Signup and view all the answers

    Which of the following statements about large oligomeric proteins is true?

    <p>They consist of two or more subunits.</p> Signup and view all the answers

    Which type of proteins are less likely to denature due to their structural complexity?

    <p>Large symmetrical proteins</p> Signup and view all the answers

    In terms of stability against denaturation, how do large soluble proteins compare to membrane-bound proteins?

    <p>Large soluble proteins are more stable than membrane-bound proteins.</p> Signup and view all the answers

    What role do subunits play in the structure of large oligomeric proteins?

    <p>They contribute to the stability and functionality.</p> Signup and view all the answers

    How does the construction of large proteins generally affect their behavior in solvents?

    <p>They exhibit reduced susceptibility to solvating effects.</p> Signup and view all the answers

    What does the evolution of oligomeric complexes often favor?

    <p>The formation of dimers</p> Signup and view all the answers

    Which characteristic is NOT typical of large proteins?

    <p>Low molecular weight</p> Signup and view all the answers

    Which of the following statements about global asymmetry in complexes is true?

    <p>Global asymmetry is only rarely observed.</p> Signup and view all the answers

    What is the primary reason that large symmetrical proteins are constructed in a specific way?

    <p>To enhance stability and functionality</p> Signup and view all the answers

    What drives local asymmetry at the level of side chain conformation?

    <p>Reciprocating mechanisms within complexes</p> Signup and view all the answers

    How do subunits behave over time in asymmetric complexes?

    <p>They cycle through the same set of conformations.</p> Signup and view all the answers

    Which of the following best depicts the relationship between symmetry and the evolution of oligomeric complexes?

    <p>Dimers are preferred over more symmetrical complexes during evolution.</p> Signup and view all the answers

    What characterizes nearly all crystallographic point groups?

    <p>They can demonstrate functional local asymmetry.</p> Signup and view all the answers

    Which aspect is rarely observed in the study of complex symmetry?

    <p>Global asymmetry</p> Signup and view all the answers

    In the context of side chain conformation, what can drive functional local asymmetry?

    <p>Pre-positioned pairs of interacting residues</p> Signup and view all the answers

    Study Notes

    Quaternary Structure

    • Quaternary structure is the association of two or more protein chains to form a larger protein complex.
    • If the chains are identical, the protein is a homo-oligomer.
    • If the chains are different, the protein is a hetero-oligomer.
    • Examples include dimers, trimers, tetramers, hexamers, and octamers.
    • These structures have defined limits to the number of subunits present.

    Oligomeric Protein Types

    • Cyclic groups (Cn): Have one axis of symmetry (e.g., C2, C3).
    • Dihedral groups (Dn): Have one Cn axis and n C2 axes of symmetry perpendicular to the Cn axis (e.g., D3).

    Stability of Quaternary Structures

    • Quaternary structure is stabilized by the same interactions that drive protein folding, including covalent and noncovalent interactions.
    • Hydrophobic effect contributes to oligomer formation.
    • The association of subunits reduces surface area to volume ratio. (e.g., in alkaline phosphatase, dimer stability to higher temperatures)

    Protein Function

    • Some proteins have machine-like properties (e.g., DNA polymerase delta processivity factor).
    • Some proteins serve as containers (e.g., Norwalk virus capsid, ferritin).
    • Heterooligomeric proteins (e.g., ATP synthase) are common, with multiple different subunits.
    • Open oligomers can extend indefinitely (e.g., tubulin chains).

    Genetic Economy and Efficiency

    • Large proteins with multiple functions can be built from smaller, repeating units rather than one large protein. This reduces gene complexity and error rate, and increases stability and cooperativity.

    Cooperativity

    • Examples of cooperativity exist in Hemoglobin.
    • O2 binding to one site causes conformation changes affecting other binding sites (increasing their oxygen affinity).
    • Improves oxygen uptake and release in lungs and tissues.

    Additional Information

    • References are available for "Getting started with Structural Symmetry and Protein Function" and "Structural Symmetry & Protein Function" by Goodsell & Olson.
    • Various structural files can be viewed in PyMOL.
    • There are examples such as a movie of ferritin showing its differing perspectives, and a D3 symmetry movie.
    • A review article by Goodsell and Olson, as well as related .pdf files and .pse (PyMOL) files, are recommended for further study. This is part of a larger review, you are requested to only read certain section from it.

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    Description

    Explore the intricacies of quaternary protein structures, focusing on their formation, types, and stability. This quiz delves into the concepts of homo-oligomers, hetero-oligomers, and factors affecting the stability of these complex proteins. Test your knowledge on the classifications and interactions that drive oligomer formation.

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