Protein Structure: Primary, Secondary, Tertiary, Quaternary

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

Molten globule

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

Low pH and high salt concentration

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

Intrinsically unstructured proteins

What is the function of molecular chaperones in protein folding?

Guide misfolded regions back into place

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

Hydrophobic effect

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

Hydrogen bonding, electrostatic interaction, and hydrophobic interaction

Which protein exhibits cooperativity in oxygen binding?

Hemoglobin

What is the primary structural component of hair and wool?

Keratin

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

Myoglobin

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

Tertiary structure

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

AlphaFold

Which yearly protein structure prediction challenge did AlphaFold win?

CASP

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

John Moult

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

Structure Prediction

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

CASP

What is denaturation in the context of proteins?

The loss of the structural order that gives a protein its biological activity

Which of the following can cause denaturation of proteins?

Changes in pH affecting side chain electrostatics

What is the role of molecular chaperones in protein folding?

Facilitate proper protein folding or restore misfolded proteins

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

Membrane proteins have hydrophobic residues in the membrane interior

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

Reduces entropy as water organizes around non-polar species

What is the main characteristic of globular proteins?

Folded to a more or less spherical shape

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

Describes the completely folded and compacted polypeptide chain

What is a common characteristic of fibrous proteins?

Contain substantial sections of α-helix and β-sheet

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

Fibrous proteins

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

Globular proteins

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

Primary structure

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

Hydrogen bonds

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

Tertiary structure

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?

They are parallel

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

Van der Waals interactions

What causes a bend in an alpha helix structure?

The presence of Proline with a cyclic structure

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

Proline

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

5.4 Å

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

Polypeptide chains

Which structural element causes steric crowding in an alpha helix?

Valine

What type of turn involves Glycine in protein structure?

Beta-turn

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

Lysine and Arginine side chains

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

Increase in temperature

Which type of protein structure prediction challenge did AlphaFold win?

Yearly challenge

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

Prevent protein misfolding

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

Membrane proteins have hydrophobic residues on the interior.

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

Drives proper folding through hydrophobic interactions

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

AlphaFold

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

Ionic bonds

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

Membrane proteins have hydrophobic residues on the exterior and interior.

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

Hydrophobic collapse

What is a common factor among fibrous proteins?

They consist of repeating structural motifs.

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?

Molten globule

What is the main challenge in predicting protein structures?

Resolving the tertiary structure

What is the role of molecular chaperones in protein folding?

Facilitating proper folding

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

Disruption of hydrophobic interactions

Which factor can lead to denaturation of proteins?

Chemical denaturants

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

Preventing misfolding and promoting correct folding

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

Membrane proteins have hydrophobic residues oriented towards the aqueous environment

Which type of proteins are often rich in hydrophobic residues?

Membrane proteins

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

Hydrophobic residues cluster together in the protein core to minimize contact with water

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

Promotes correct protein folding

What is the primary cause of denaturation in proteins?

Heat causing disruptive vibrations

What is the role of molecular chaperones in protein folding?

Aiding in the correct folding of proteins

Which factor is NOT involved in protein denaturation?

Proper protein folding

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

Membrane proteins have hydrophilic residues

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

Errors in protein folding

In protein folding, what role do chaperones play?

Ensuring proper protein folding or restoring misfolded proteins

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

Disulfide bonds and hydrophobic interactions

What distinguishes membrane proteins from globular proteins?

Location of hydrophobic residues in the membrane interior

What can cause denaturation of proteins?

Increase in pH

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

Causes protein aggregation

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

Steric crowding from bulky side chains

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

Glycine

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

Proximity of side chains with like charge

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

Proline residue creating a bend

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

Proximity of bulky Valine residues

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?

Secondary structure

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

$3.6$ amino acids per turn ratio

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

Secondary structure

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

Bulky Valine, Isoleucine, and Threonine residues

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.

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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