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Protein Structure: Primary, Secondary, Tertiary, Quaternary
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Protein Structure: Primary, Secondary, Tertiary, Quaternary

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Questions and Answers

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

  • Molten globule (correct)
  • Hydrophobic effect
  • Denaturation
  • Chaperone

    • In which conditions was the molten globule phase first found in cytochrome c?

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

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

  • Intrinsically unstructured proteins (correct)
  • Membrane proteins
  • Denatured proteins
  • Chaperone-assisted proteins

    • Which strategy do chaperones use to guide misfolded regions of proteins back into place?

    <p>Various strategies</p> Signup and view all the answers

    What is the third phase of proteins mentioned in the text?

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

    What type of forces contribute to the tertiary (3°) structure of proteins?

    <p>H-bond, electrostatic interaction, hydrophobic interaction</p> Signup and view all the answers

    Which protein has a quaternary (4°) structure?

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

    What effect do changes in pH have on the binding of oxygen to hemoglobin?

    <p>pKa of His146 decreases when O2 binds</p> Signup and view all the answers

    Which protein molecule has no quaternary structure and binds only one oxygen molecule?

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

    What is the main structural role of proteins like keratin and collagen?

    <p>Providing mechanical strength</p> Signup and view all the answers

    Which type of protein structure is described as having polypeptide chains organized approximately parallel along a single axis?

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

    What stabilizes the tertiary (3°) structure of protein?

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

    Which type of protein structure is often approximated as spheres and tends to be water-soluble with polar residues on the exterior and non-polar residues inside?

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

    Which factor is NOT a cause of protein denaturation?

    <p>Disulfide bond formation</p> Signup and view all the answers

    Proteins that are folded to a more or less spherical shape and have polar side chains on the outside interacting with the aqueous environment belong to which category?

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

    What is the primary reason for protein aggregation in neurodegenerative diseases?

    <p>Hydrophobic residues in water</p> Signup and view all the answers

    Which interaction is primarily responsible for the burial of nonpolar side chains inside globular proteins?

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

    Which statement best describes the hydrophobic effect in protein folding?

    <p>Hydrophobic residues are exposed to the aqueous environment</p> Signup and view all the answers

    Which factor plays a role in ensuring proper protein folding?

    <p>Molecular chaperones</p> Signup and view all the answers

    What can lead to protein denaturation if not TOO severe?

    <p>Protein aggregation</p> Signup and view all the answers

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

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

    Who co-founded the biennial protein structure prediction challenge called CASP in 1994?

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

    What does CASP stand for in the protein structure prediction challenge context?

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

    Which challenge did AlphaFold outperform around 100 other teams in?

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

    What was the grand challenge that DeepMind's AlphaFold program managed to solve related to protein biology?

    <p>Determining a protein's 3D shape from its amino-acid sequence</p> Signup and view all the answers

    What is the primary structure of a protein?

    <p>The linear sequence of amino acids in a polypeptide chain</p> Signup and view all the answers

    Which type of structure in proteins involves a regular pattern of hydrogen bonds between nearby amino acids?

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

    What is the major type of secondary structure found in proteins that is described as 'extended flat sheets'?

    <p>β-sheets</p> Signup and view all the answers

    Which of the following is NOT a component of the secondary structure of proteins?

    <p>The sequence of amino acids in a polypeptide chain</p> Signup and view all the answers

    Which feature is characteristic of α-helices in proteins?

    <p>Parallel hydrogen bonds to the axis</p> Signup and view all the answers

    What type of bond is formed between the C=O of amino acid #1 and the N-H of amino acid #5 in a polypeptide chain?

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

    How many amino acids are present in each turn of an α-helix structure?

    <p>3.6 amino acids</p> Signup and view all the answers

    Which amino acid is known to disrupt α-helix structure due to its restricted rotation and lack of N-H for hydrogen bonding?

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

    Which factor can disrupt an α-helix by causing strong electrostatic repulsion?

    <p>Electrostatic repulsion from like-charged side chains</p> Signup and view all the answers

    What secondary structure consists of polypeptide chains lying adjacent to each other in a sheet-like structure?

    <p>β-pleated sheet</p> Signup and view all the answers

    What type of bonds form between the backbones of β-pleated sheets in proteins?

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

    Which amino acid is often found in reverse turns due to spatial reasons?

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

    Which type of secondary structure involves polypeptide chains changing direction and is stabilized by hydrogen bonds?

    <p>Reverse turn</p> Signup and view all the answers

    What causes a 'kink' or 'bend' in protein structure, disrupting the α-helix?

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

    Which factor contributes to the disruption of an α-helix due to the proximity of bulky side chains such as Valine, Isoleucine, and Threonine?

    <p>Steric crowding</p> Signup and view all the answers

    Study Notes

    Protein Structure

    • Proteins can have different types of structures, including:
      • Fibrous proteins: contain polypeptide chains organized approximately parallel along a single axis, often strong, insoluble, and have structural roles
      • Globular proteins: folded to a more or less spherical shape, tend to be soluble in water and salt solutions, and have polar side chains on the outside and non-polar side chains buried inside

    Primary Structure

    • Primary (1°) structure: the sequence of amino acids in a polypeptide chain, read from the N-terminal end to the C-terminal end
    • Refers to the linear amino acid sequence from N- to C-terminal end

    Secondary Structure

    • Secondary (2°) structure: local conformations maintained by extensive H-bonding that involves components of the peptide bond
    • Two major kinds of 2° structures found in proteins:
      • α-helices: helical, coiled, with C=O of one amino acid hydrogen bonded to N-H of an amino acid that is four down the chain
      • β-sheets: extended "flat" sheets, with polypeptide chains lying adjacent to one another, may be parallel or antiparallel
    • Factors that can disrupt an α-helix:
      • Proline: creates a bend due to restricted rotation and lack of N-H for hydrogen bonding
      • Strong electrostatic repulsion caused by proximity of side chains with like charge
      • Steric crowding caused by proximity of bulky side chains

    Tertiary Structure

    • Tertiary (3°) structure: describes the completely folded and compacted polypeptide chain
    • Stabilized by interactions of amino acid side chains in non-neighboring regions of the polypeptide chain
    • Forces involved in tertiary structure:
      • Non-covalent: H-bond, electrostatic interaction, hydrophobic interaction
      • Covalent: disulfide bond

    Quaternary Structure

    • Quaternary (4°) structure: the association of polypeptide chains
    • Several peptide chains (sub-units) combine together
    • Example: hemoglobin has 4 sub-units labeled α and β

    Protein Folding

    • Protein folding: the process of a polypeptide chain adopting its native 3D structure
    • Factors that influence protein folding:
      • Hydrophobic effect: non-polar species in water reduce entropy as water is forced to organize around them
      • Molecular chaperones: part of a quality control system that aims to ensure proper protein folding or restore proteins that have become misfolded
    • Errors in protein folding can contribute to diseases such as Alzheimer's and Diabetes type 2

    Denaturation

    • Denaturation: the loss of structural order that gives a protein its biological activity
    • Causes of denaturation:
      • pH changes
      • Mercaptoethanol
      • Detergent
      • Heat
      • Urea/guanidine
    • Denaturation may or may not be reversible

    Chaperones

    • Molecular chaperones: part of a quality control system that aims to ensure proper protein folding or restore proteins that have become misfolded
    • Examples: heat shock proteins, protein disulfide isomerase

    Structure Prediction

    • Structure prediction: determining a protein's 3D shape from its amino acid sequence
    • Techniques: bioinformatics, artificial intelligence (AI) networks
    • Example: AlphaFold, a program developed by Google AI offshoot DeepMind, has made a significant leap in solving protein structure prediction

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    Related Documents

    Chapter 4 - Protein structure.pptx

    Description

    Explore the different levels of protein structure including primary, secondary, tertiary, and quaternary structures. Learn about a-helices, b-sheets, forces involved in protein folding, and methods for structural determination.

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