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 (D)</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. (B)</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 (A)</p> Signup and view all the answers

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

<p>D3 symmetry group (D)</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. (C)</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 (C)</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. (B)</p> Signup and view all the answers

How many subunits make up the mammalian ferritin structure?

<p>24 subunits (B)</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. (D)</p> Signup and view all the answers

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

<p>PyMOL (C)</p> Signup and view all the answers

What type of interactions stabilize quaternary structures of proteins?

<p>Both covalent and noncovalent interactions (C)</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 (A)</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 (D)</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 (D)</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 (B)</p> Signup and view all the answers

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

<p>Homohexamer (C)</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 (B)</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 (B)</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 (C)</p> Signup and view all the answers

Which type of publication is the source content taken from?

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

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

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

When was the publication issued?

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

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

<p>Biophysics and Structural Biology (A)</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 (D)</p> Signup and view all the answers

Who are the authors of the publication?

<p>David S. Goodsell and Arthur J. (A)</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 (B)</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. (A)</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 (A)</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. (A)</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. (C)</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. (C)</p> Signup and view all the answers

What does the evolution of oligomeric complexes often favor?

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

Which characteristic is NOT typical of large proteins?

<p>Low molecular weight (A)</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. (D)</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 (A)</p> Signup and view all the answers

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

<p>Reciprocating mechanisms within complexes (B)</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. (B)</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. (D)</p> Signup and view all the answers

What characterizes nearly all crystallographic point groups?

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

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

<p>Global asymmetry (C)</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 (D)</p> Signup and view all the answers

Flashcards

Quaternary Structure

The arrangement of multiple protein subunits.

Protein Subunit

An individual protein chain that contributes to a larger protein complex.

Oligomer

A protein complex formed by multiple subunits.

Homomer

A protein complex or oligomer composed of identical subunits.

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C2 symmetry

An axis of symmetry where a two-fold rotation brings the structure back to its initial orientation.

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C3 symmetry

An axis of symmetry where a three-fold rotation brings the structure back to its initial orientation.

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D3 symmetry

Oligomers with symmetry including a C3 axis and perpendicular C2 axes.

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Protein Folding Interactions

Covalent and noncovalent forces that stabilize protein structure, including quaternary structure (oligomerisation).

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Homohexamer

A protein complex composed of six identical subunits.

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D3 symmetry

A type of symmetry found in molecules with three-fold rotational axes and two-fold rotational axes in a specific arrangement.

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Oligomeric Protein

A protein composed of multiple subunits.

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DNA Polymerase Delta Processivity Factor

A protein that allows DNA polymerase delta to remain attached to DNA during replication.

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Ferritin

A protein that stores iron in the body.

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Norwalk Virus Capsid

A protein shell made of subunits forming a cubic structure that encloses viral DNA.

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Cubic Symmetry

A type of symmetry found in structures with multiple rotational axes of symmetry, like multiple 3-fold, 4-fold, or 6-fold axes.

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Protein Oligomer Shell

A protein structure formed of multiple identical protein subunits creating a protective shell-like assembly.

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Structural Symmetry

The arrangement of components within a structure that repeats after certain rotations and reflections.

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Protein Function

The job a protein does in a cell, often involving interactions with other molecules.

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Protein Structure

The 3D arrangement of atoms within a protein molecule that determines its function.

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Annual Reviews

A publication series that compiles top-tier reviews in scientific disciplines.

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Biophysical Structures

Arrangements and interactions of biological entities, like proteins, involving physical mechanisms.

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Protein Subunits

Individual protein chains, separate entities that form a larger protein complex.

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Oligomer

A protein complex built from multiple subunits.

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Quaternary Structure of Protein

The arrangement of multiple protein subunits in a protein complex.

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Large Proteins

Large proteins are often complexes made up of multiple subunits.

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Oligomeric Proteins

Proteins assembled from multiple individual protein subunits.

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Protein Subunits

Individual protein chains forming a larger protein structure.

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Protein Complexes

Structures formed when multiple proteins come together.

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Stability vs Size

Larger proteins are often more stable than individual smaller proteins.

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Protein Surface Area

The outer part of a protein complex that interacts with the environment.

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Solvent Solubility

Describes how well a protein dissolves in a liquid.

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Membrane-Bound Proteins

Proteins that are associated with cell membranes.

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Quasisymmetry

A type of symmetry where subunits have similar but different conformations over time, all subunits cycling through the same set of conformations.

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Pleomorphism

A state where identical subunits form different complexes over time.

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Global asymmetry

Structural differences that are common across the complete structure, are not typically observed in complexes.

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Reciprocating mechanisms

A type of mechanism where similar but different conformations of an asymmetric complex are adopted repeatedly over time.

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Identical subunits forming different complexes

Same subunits can create differing complexes in some processes.

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Crystallographic Point Groups

Different types of symmetrical arrangements in crystals

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Functional Local Need

Asymmetry in protein structure driven by the need for a specific function.

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Oligomeric Complex Evolution

Complex building blocks may form dimers (pairs) for easier evolution, instead of higher symmetry.

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Reciprocating Mechanisms

Parts of complexes cycle through conformations, even if the whole complex is asymmetric.

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Global Asymmetry

Overall asymmetry in a complex is rare in nature.

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Protein Side Chain Conformation

Shape of side chain influences complex structure

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Evolution of Symmetry

Protein complexes change shape through evolution.

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Symmetry in Complexes

Almost all types of symmetrical arrangements are seen in protein complexes.

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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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CHEM 3310H Lecture 18 - Protein Chemistry and Enzymology PDF

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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