Protein Structure: Primary, Secondary, Tertiary, Quaternary
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Questions and Answers

What term was first coined in 1983 by A. Wada and M. Ohgushi?

  • Intrinsically unstructured protein
  • Molecular chaperone
  • Molten globule (correct)
  • Denatured protein

    • Under what conditions was the molten globule first found in cytochrome c?

  • High pH and low salt concentration
  • Neutral pH and moderate salt concentration
  • Low pH and low salt concentration
  • Low pH and high salt concentration (correct)

    • Which type of proteins lack a well-structured three-dimensional fold?

  • Intrinsically unstructured proteins (correct)
  • Fibrous proteins
  • Membrane proteins
  • Globular proteins

    • What is the function of molecular chaperones in protein folding?

    <p>Guide misfolded regions back into place</p> Signup and view all the answers

    Which phenomenon describes the tendency of nonpolar molecules to aggregate in an aqueous environment?

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

    What type of interactions are involved in the tertiary structure of proteins?

    <p>Hydrogen bonding, electrostatic interaction, and hydrophobic interaction</p> Signup and view all the answers

    Which protein exhibits cooperativity in oxygen binding?

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

    What is the primary structural component of hair and wool?

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

    Which protein is found in muscle and tissue and binds only one oxygen molecule?

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

    Proper protein folding is essential for the creation of which protein structure?

    <p>Tertiary structure</p> Signup and view all the answers

    What is the name of the Google AI offshoot that developed the AI network for protein structure prediction?

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

    Which yearly protein structure prediction challenge did AlphaFold win?

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

    Who co-founded CASP in 1994 to improve computational methods for predicting protein structures?

    <p>John Moult</p> Signup and view all the answers

    Which term refers to determining a protein’s 3D shape from its amino-acid sequence?

    <p>Structure Prediction</p> Signup and view all the answers

    What is the name of the biennial protein structure prediction challenge that AlphaFold participated in?

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

    What is denaturation in the context of proteins?

    <p>The loss of the structural order that gives a protein its biological activity</p> Signup and view all the answers

    Which of the following can cause denaturation of proteins?

    <p>Changes in pH affecting side chain electrostatics</p> Signup and view all the answers

    What is the role of molecular chaperones in protein folding?

    <p>Facilitate proper protein folding or restore misfolded proteins</p> Signup and view all the answers

    How do membrane proteins differ from globular proteins in terms of hydrophobic residues?

    <p>Membrane proteins have hydrophobic residues in the membrane interior</p> Signup and view all the answers

    What effect does the hydrophobic effect have on proteins in water?

    <p>Reduces entropy as water organizes around non-polar species</p> Signup and view all the answers

    What is the main characteristic of globular proteins?

    <p>Folded to a more or less spherical shape</p> Signup and view all the answers

    Which statement best describes the tertiary (3°) structure of proteins?

    <p>Describes the completely folded and compacted polypeptide chain</p> Signup and view all the answers

    What is a common characteristic of fibrous proteins?

    <p>Contain substantial sections of α-helix and β-sheet</p> Signup and view all the answers

    Which type of protein structure contains polypeptide chains organized approximately parallel along a single axis?

    <p>Fibrous proteins</p> Signup and view all the answers

    What type of proteins are often approximated as spheres, tend to be water-soluble, and have polar residues on the exterior?

    <p>Globular proteins</p> Signup and view all the answers

    Which term refers to the sequence of amino acids in a polypeptide chain?

    <p>Primary structure</p> Signup and view all the answers

    What type of bonds are primarily responsible for maintaining local conformations in secondary protein structures?

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

    Which of the following is NOT a type of secondary protein structure?

    <p>Tertiary structure</p> Signup and view all the answers

    In an α-helix, how is the C=O of one amino acid oriented with respect to the N-H of an amino acid four residues down the chain?

    <p>They are parallel</p> Signup and view all the answers

    Which type of interaction is primarily responsible for the hydrophobic effect in protein folding?

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

    What causes a bend in an alpha helix structure?

    <p>The presence of Proline with a cyclic structure</p> Signup and view all the answers

    Which amino acid is known to disrupt the alpha helix structure?

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

    What is the distance for one turn in an alpha helix structure?

    <p>5.4 Å</p> Signup and view all the answers

    In beta-pleated sheets, hydrogen bonds form between the backbone of which component?

    <p>Polypeptide chains</p> Signup and view all the answers

    Which structural element causes steric crowding in an alpha helix?

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

    What type of turn involves Glycine in protein structure?

    <p>Beta-turn</p> Signup and view all the answers

    What disrupts the alpha-helix structure due to strong electrostatic repulsion?

    <p>Lysine and Arginine side chains</p> Signup and view all the answers

    What is a major factor contributing to the denaturation of proteins?

    <p>Increase in temperature</p> Signup and view all the answers

    Which type of protein structure prediction challenge did AlphaFold win?

    <p>Yearly challenge</p> Signup and view all the answers

    In protein folding, what is the role of molecular chaperones?

    <p>Prevent protein misfolding</p> Signup and view all the answers

    What distinguishes membrane proteins from globular proteins in terms of hydrophobic residues?

    <p>Membrane proteins have hydrophobic residues on the interior.</p> Signup and view all the answers

    What effect does the hydrophobic effect have on protein folding in aqueous environments?

    <p>Drives proper folding through hydrophobic interactions</p> Signup and view all the answers

    What is the name of the AI network developed by Google AI offshoot DeepMind for protein structure prediction?

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

    In protein folding, what disrupts the native structure leading to denaturation due to strong electrostatic repulsion?

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

    How do membrane proteins typically differ from globular proteins in terms of hydrophobic residues?

    <p>Membrane proteins have hydrophobic residues on the exterior and interior.</p> Signup and view all the answers

    Which phenomenon describes the tendency of nonpolar molecules to aggregate in an aqueous environment?

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

    What is a common factor among fibrous proteins?

    <p>They consist of repeating structural motifs.</p> Signup and view all the answers

    What term was first coined by A.Wada and M.Ohgushi in 1983 to describe a phase of proteins that conserves a native-like secondary structure content without the tightly packed protein interior?

    <p>Molten globule</p> Signup and view all the answers

    What is the main challenge in predicting protein structures?

    <p>Resolving the tertiary structure</p> Signup and view all the answers

    What is the role of molecular chaperones in protein folding?

    <p>Facilitating proper folding</p> Signup and view all the answers

    Which factor is most likely to contribute to the denaturation of a protein?

    <p>Disruption of hydrophobic interactions</p> Signup and view all the answers

    Which factor can lead to denaturation of proteins?

    <p>Chemical denaturants</p> Signup and view all the answers

    What role do molecular chaperones play in the context of protein folding?

    <p>Preventing misfolding and promoting correct folding</p> Signup and view all the answers

    How do membrane proteins differ from globular proteins in terms of hydrophobic residues?

    <p>Membrane proteins have hydrophobic residues oriented towards the aqueous environment</p> Signup and view all the answers

    Which type of proteins are often rich in hydrophobic residues?

    <p>Membrane proteins</p> Signup and view all the answers

    Which of the following statements best describes the hydrophobic effect in protein folding?

    <p>Hydrophobic residues cluster together in the protein core to minimize contact with water</p> Signup and view all the answers

    What effect does the hydrophobic effect have on protein folding in aqueous environments?

    <p>Promotes correct protein folding</p> Signup and view all the answers

    What is the primary cause of denaturation in proteins?

    <p>Heat causing disruptive vibrations</p> Signup and view all the answers

    What is the role of molecular chaperones in protein folding?

    <p>Aiding in the correct folding of proteins</p> Signup and view all the answers

    Which factor is NOT involved in protein denaturation?

    <p>Proper protein folding</p> Signup and view all the answers

    How do membrane proteins differ from globular proteins in terms of hydrophobic residues?

    <p>Membrane proteins have hydrophilic residues</p> Signup and view all the answers

    What contributes to diseases like Alzheimer's and Type 2 Diabetes?

    <p>Errors in protein folding</p> Signup and view all the answers

    In protein folding, what role do chaperones play?

    <p>Ensuring proper protein folding or restoring misfolded proteins</p> Signup and view all the answers

    What type of interactions are involved in the tertiary structure of proteins?

    <p>Disulfide bonds and hydrophobic interactions</p> Signup and view all the answers

    What distinguishes membrane proteins from globular proteins?

    <p>Location of hydrophobic residues in the membrane interior</p> Signup and view all the answers

    What can cause denaturation of proteins?

    <p>Increase in pH</p> Signup and view all the answers

    What effect does the hydrophobic effect have on proteins in water?

    <p>Causes protein aggregation</p> Signup and view all the answers

    What structural element causes a bend or kink in an alpha helix?

    <p>Steric crowding from bulky side chains</p> Signup and view all the answers

    Which amino acid is primarily responsible for disrupting the alpha helix structure due to the lack of an N-H group for hydrogen bonding?

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

    What is the primary cause of disruption in an alpha helix structure due to strong electrostatic repulsion?

    <p>Proximity of side chains with like charge</p> Signup and view all the answers

    Which factor disrupts the alpha helix due to restricted rotation from its cyclic structure?

    <p>Proline residue creating a bend</p> Signup and view all the answers

    What causes disruption in an alpha helix structure due to steric crowding?

    <p>Proximity of bulky Valine residues</p> Signup and view all the answers

    Which type of protein structure is significantly impacted by proline due to its cyclic structure and lack of an N-H group for hydrogen bonding?

    <p>Secondary structure</p> Signup and view all the answers

    Which component of an alpha helix structure is disrupted by the absence of N-H groups for hydrogen bonding?

    <p>$3.6$ amino acids per turn ratio</p> Signup and view all the answers

    In protein structures, what does proline disrupt due to strong electrostatic repulsion?

    <p>Secondary structure</p> Signup and view all the answers

    What disrupts an alpha helix structure due to steric crowding caused by bulky side chains proximity?

    <p>Bulky Valine, Isoleucine, and Threonine residues</p> Signup and view all the answers

    Study Notes

    Protein Structure

    • Primary (1°) structure: the sequence of amino acids in a polypeptide chain, read from the N-terminal end to the C-terminal end.
    • Secondary (2°) structure: local conformations, maintained by extensive hydrogen bonding that involves components of the peptide bond.
      • 2 types of 2° structures: α-helices and β-sheets.
      • α-helices: helical, coiled structures formed by hydrogen bonds between C=O and N-H groups of amino acids.
      • β-sheets: extended, flat structures formed by hydrogen bonds between amino acids.
    • Tertiary (3°) structure: the completely folded and compacted polypeptide chain, stabilized by interactions of amino acid side chains.
      • Forces involved: hydrogen bonding, electrostatic interactions, hydrophobic interactions, and disulfide bonds.
    • Quaternary (4°) structure: the association of polypeptide chains (sub-units) combining together.
      • Example: hemoglobin has 4 sub-units (α and β) that bind 4 O2 molecules.

    Protein Folding

    • Chaperones: part of a quality control system that ensures proper protein folding or restores misfolded proteins after stress.
    • Denaturation: the loss of structural order that gives a protein its biological activity.
      • Caused by: pH changes, Mercaptoethanol, detergents, heat, and urea/guanidine.
    • Renaturation: the process of returning to the native structure after denaturation.

    Protein Folding and Disease

    • Protein aggregation: linked to numerous neurodegenerative diseases.
    • Molten globule: a third phase of proteins, characterized by a native-like secondary structure content but without a tightly packed protein interior.

    Prediction of Protein Structure

    • Structure prediction challenge: a biennial challenge to predict protein structures from amino acid sequences.
    • AlphaFold: an AI network developed by Google AI that outperformed other teams in the CASP challenge.

    Protein Functions

    • Globular proteins: water-soluble, spherical proteins with polar side chains on the outside and non-polar side chains inside.
    • Fibrous proteins: insoluble, strong, and structurally important proteins, such as keratin and collagen.

    Hemoglobin and Myoglobin

    • Hemoglobin: a protein in blood with 4 sub-units, binds 4 O2 molecules, and exhibits cooperativity and pH-dependent O2 binding.
    • Myoglobin: a protein in muscle and tissue, binds 1 O2 molecule, and has no quaternary structure.

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    Chapter 4 - Protein structure.pptx

    Description

    Explore the components of protein structure including primary, secondary, tertiary, and quaternary structures. Learn about a-helices, b-sheets, protein folding, and the levels of protein structure.

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