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Questions and Answers
What term was first coined by A.Wada and M. Ohgushi in 1983?
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?
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?
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?
Which strategy do chaperones use to guide misfolded regions of proteins back into place?
What is the third phase of proteins mentioned in the text?
What is the third phase of proteins mentioned in the text?
What type of forces contribute to the tertiary (3°) structure of proteins?
What type of forces contribute to the tertiary (3°) structure of proteins?
Which protein has a quaternary (4°) structure?
Which protein has a quaternary (4°) structure?
What effect do changes in pH have on the binding of oxygen to hemoglobin?
What effect do changes in pH have on the binding of oxygen to hemoglobin?
Which protein molecule has no quaternary structure and binds only one oxygen molecule?
Which protein molecule has no quaternary structure and binds only one oxygen molecule?
What is the main structural role of proteins like keratin and collagen?
What is the main structural role of proteins like keratin and collagen?
Which type of protein structure is described as having polypeptide chains organized approximately parallel along a single axis?
Which type of protein structure is described as having polypeptide chains organized approximately parallel along a single axis?
What stabilizes the tertiary (3°) structure of protein?
What stabilizes the tertiary (3°) structure of protein?
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?
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?
Which factor is NOT a cause of protein denaturation?
Which factor is NOT a cause of protein denaturation?
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?
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?
What is the primary reason for protein aggregation in neurodegenerative diseases?
What is the primary reason for protein aggregation in neurodegenerative diseases?
Which interaction is primarily responsible for the burial of nonpolar side chains inside globular proteins?
Which interaction is primarily responsible for the burial of nonpolar side chains inside globular proteins?
Which statement best describes the hydrophobic effect in protein folding?
Which statement best describes the hydrophobic effect in protein folding?
Which factor plays a role in ensuring proper protein folding?
Which factor plays a role in ensuring proper protein folding?
What can lead to protein denaturation if not TOO severe?
What can lead to protein denaturation if not TOO severe?
What is the name of the artificial intelligence network developed by Google AI offshoot DeepMind for solving protein structure prediction?
What is the name of the artificial intelligence network developed by Google AI offshoot DeepMind for solving protein structure prediction?
Who co-founded the biennial protein structure prediction challenge called CASP in 1994?
Who co-founded the biennial protein structure prediction challenge called CASP in 1994?
What does CASP stand for in the protein structure prediction challenge context?
What does CASP stand for in the protein structure prediction challenge context?
Which challenge did AlphaFold outperform around 100 other teams in?
Which challenge did AlphaFold outperform around 100 other teams in?
What was the grand challenge that DeepMind's AlphaFold program managed to solve related to protein biology?
What was the grand challenge that DeepMind's AlphaFold program managed to solve related to protein biology?
What is the primary structure of a protein?
What is the primary structure of a protein?
Which type of structure in proteins involves a regular pattern of hydrogen bonds between nearby amino acids?
Which type of structure in proteins involves a regular pattern of hydrogen bonds between nearby amino acids?
What is the major type of secondary structure found in proteins that is described as 'extended flat sheets'?
What is the major type of secondary structure found in proteins that is described as 'extended flat sheets'?
Which of the following is NOT a component of the secondary structure of proteins?
Which of the following is NOT a component of the secondary structure of proteins?
Which feature is characteristic of α-helices in proteins?
Which feature is characteristic of α-helices in proteins?
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?
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?
How many amino acids are present in each turn of an α-helix structure?
How many amino acids are present in each turn of an α-helix structure?
Which amino acid is known to disrupt α-helix structure due to its restricted rotation and lack of N-H for hydrogen bonding?
Which amino acid is known to disrupt α-helix structure due to its restricted rotation and lack of N-H for hydrogen bonding?
Which factor can disrupt an α-helix by causing strong electrostatic repulsion?
Which factor can disrupt an α-helix by causing strong electrostatic repulsion?
What secondary structure consists of polypeptide chains lying adjacent to each other in a sheet-like structure?
What secondary structure consists of polypeptide chains lying adjacent to each other in a sheet-like structure?
What type of bonds form between the backbones of β-pleated sheets in proteins?
What type of bonds form between the backbones of β-pleated sheets in proteins?
Which amino acid is often found in reverse turns due to spatial reasons?
Which amino acid is often found in reverse turns due to spatial reasons?
Which type of secondary structure involves polypeptide chains changing direction and is stabilized by hydrogen bonds?
Which type of secondary structure involves polypeptide chains changing direction and is stabilized by hydrogen bonds?
What causes a 'kink' or 'bend' in protein structure, disrupting the α-helix?
What causes a 'kink' or 'bend' in protein structure, disrupting the α-helix?
Which factor contributes to the disruption of an α-helix due to the proximity of bulky side chains such as Valine, Isoleucine, and Threonine?
Which factor contributes to the disruption of an α-helix due to the proximity of bulky side chains such as Valine, Isoleucine, and Threonine?
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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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