Bioc 440: Protein Folding Enthalpy & Entropy; Aggregation; Post-translation Modifications Flashcards
What is entropy in the context of protein folding?
Entropy is a measure of the disorder or randomness in a system.
What is enthalpy in protein folding?
Enthalpy is the total heat content of a system, reflecting the energy needed to break and form bonds.
True or False: Higher entropy generally favors the folding of proteins.
False.
What is the relationship between entropy and the stability of a folded protein?
Lower entropy in the folded state contributes to the stability of the protein.
Fill in the blank: Protein folding is driven by the balance between enthalpy and __________.
entropy.
What role do hydrogen bonds play in protein folding?
Hydrogen bonds stabilize the folded structure and contribute to the enthalpic term.
Multiple Choice: Which factor increases the entropy during protein folding?
The release of water molecules from the protein surface.
Define the term ‘free energy’ in protein folding.
Free energy is the energy available to do work, determining the spontaneity of the folding process.
True or False: A negative change in enthalpy favors protein folding.
True.
What is the role of hydrophobic interactions in protein folding?
Hydrophobic interactions drive non-polar side chains to the interior, reducing system entropy.
How does temperature affect protein folding and stability?
Higher temperatures can increase entropy but may also lead to denaturation.
Fill in the blank: The process of protein folding can be described as a __________ energy landscape.
multi-dimensional.
What is the significance of the Gibbs free energy equation in protein folding?
It relates the change in free energy to changes in enthalpy and entropy during folding.
Multiple Choice: Which of the following increases the enthalpy of a folded protein?
Formation of covalent bonds.
What is the effect of disulfide bonds on protein structure?
Disulfide bonds provide stability by forming covalent links between cysteine residues.
True or False: Entropy is always unfavorable in the context of protein folding.
False.
What is a protein’s native state?
The native state is the most stable, functional conformation of a protein.
Fill in the blank: The transition state during protein folding is often considered a __________ state.
high-energy.
What does it mean when a protein is described as being ‘denatured’?
Denatured proteins are unfolded and lack their functional three-dimensional structure.
Multiple Choice: Which factor is NOT directly involved in the enthalpic contribution to folding?
Hydrophobic effect.
What are chaperone proteins?
Chaperone proteins assist in the proper folding of other proteins.
True or False: The process of protein folding is always spontaneous.
False.
What happens to the entropy of the solvent during protein folding?
The entropy of the solvent generally increases as water molecules are released.
Fill in the blank: The folding of proteins often involves __________ intermediates.
unfolded.
What is the primary driving force behind the folding of globular proteins?
The hydrophobic effect.
Multiple Choice: Which of the following is a characteristic of the transition state in protein folding?
It is high in energy and unstable.
What is the impact of mutations on protein folding?
Mutations can disrupt normal folding and stability of the protein.
True or False: All proteins fold into a single unique structure.
False.
What is the significance of the folding funnel model?
The folding funnel model illustrates how proteins navigate to their native state through various paths.
Fill in the blank: The __________ effect helps to drive protein folding by minimizing exposure of hydrophobic residues to water.
hydrophobic.
What is meant by ‘thermodynamic stability’ in proteins?
Thermodynamic stability refers to the tendency of a protein to remain in its folded state under physiological conditions.
Multiple Choice: Which process is energetically favorable for protein folding?
Formation of secondary structures.
How does pH affect protein folding?
Changes in pH can alter charge interactions and disrupt folding.
True or False: Protein folding is a purely enthalpic process.
False.
What is the role of molecular dynamics simulations in studying protein folding?
Molecular dynamics simulations help visualize the folding process and predict folding pathways.
Fill in the blank: The __________ principle states that the folded structure of a protein is determined by its amino acid sequence.
Anfinsen.
What is the main contribution of entropy to protein folding?
Entropy contributes by allowing more configurations and states in the unfolded state.
Multiple Choice: Which factor does NOT contribute to the stability of the folded protein? A) Vander waals interactions B) cysteine disulfide bonds C) Increased entropy of the folded state
Increased entropy of the folded state.
What is the role of van der Waals forces in protein folding?
Van der Waals forces provide non-covalent interactions that help stabilize the folded structure.
True or False: The energy landscape of protein folding is typically rugged and complex.
True.
Fill in the blank: The __________ state of a protein is typically lower in free energy than the unfolded state.
folded.
What is the significance of the hydrophobic core in protein structure?
The hydrophobic core minimizes contact with water, contributing to the stability of the folded protein.
What is the native state of a protein?
The native state of a protein is its functional three-dimensional structure.
True or False: The native state of a protein is always the most thermodynamically stable form.
True
What are protein aggregates?
Protein aggregates are clusters of misfolded proteins that can lead to various diseases.
Fill in the blank: The process of a protein adopting its native state is called __________.
folding
What factors can influence protein folding?
Temperature, pH, ionic strength, and the presence of chaperones.
Multiple choice: Which of the following is NOT a factor influencing protein aggregation? A) Temperature B) Protein concentration C) pH D) Molecular weight
D) Molecular weight
What role do chaperone proteins play in protein folding?
Chaperone proteins assist in the proper folding of other proteins and prevent aggregation.
True or False: All protein aggregates are harmful to cells.
False
What is a common disease associated with protein aggregation?
Alzheimer’s disease.
Define ‘denaturation’ in the context of proteins.
Denaturation is the process in which a protein loses its native structure and function.
Fill in the blank: The __________ structure of a protein refers to its sequence of amino acids.
primary
What is the secondary structure of proteins?
The secondary structure refers to local folding patterns like alpha helices and beta sheets.
Multiple choice: Which level of protein structure is determined by hydrogen bonding? A) Primary B) Secondary C) Tertiary D) Quaternary
B) Secondary
What is meant by ‘tertiary structure’ of a protein?
The tertiary structure is the overall three-dimensional shape of a single polypeptide chain.
True or False: Quaternary structure involves multiple polypeptide chains.
True
What can cause a protein to misfold?
Genetic mutations, environmental stress, and chemical modifications.
Fill in the blank: Protein misfolding can lead to __________ diseases.
neurodegenerative
What is the definition of ‘protein stability’?
Protein stability refers to the ability of a protein to maintain its native structure under varying conditions.
Multiple choice: Which of the following methods can be used to study protein folding? A) X-ray crystallography B) NMR spectroscopy C) Circular dichroism D) All of the above
D) All of the above
What is ‘hydrophobic effect’ in protein folding?
The hydrophobic effect is the tendency of nonpolar side chains to avoid water, driving protein folding.
True or False: Chaperonins are a type of chaperone protein that form large complexes.
True
What is the role of disulfide bonds in protein structure?
Disulfide bonds stabilize the tertiary and quaternary structures of proteins.
Fill in the blank: The __________ hypothesis suggests that proteins fold into their native state via a series of intermediate states.
framework
What is the significance of the energy landscape in protein folding?
It describes the various energy states a protein can adopt during the folding process.
Multiple choice: Which type of protein is most likely to aggregate? A) Globular proteins B) Fibrous proteins C) Membrane proteins D) All of the above
B) Fibrous proteins
What is amyloidosis?
Amyloidosis is a condition characterized by the accumulation of amyloid aggregates in tissues.
True or False: Protein aggregates can form in both intracellular and extracellular environments.
True
What is the importance of protein aggregation studies in medicine?
They help in understanding the mechanisms of diseases and developing therapies.
Fill in the blank: __________ are proteins that assist in the folding and assembly of other proteins.
Chaperones
What is the function of heat shock proteins?
Heat shock proteins help prevent misfolding and aggregation during stress conditions.
Multiple choice: Which of the following is a consequence of protein misfolding? A) Increased solubility B) Loss of function C) Enhanced stability D) None of the above
B) Loss of function
What are the two main types of protein aggregates?
Amorphous aggregates and fibrillar aggregates.
True or False: Protein aggregation is a reversible process.
False
What is a key characteristic of fibrillar aggregates?
Fibrillar aggregates are often long, unbranched fibers that can form in a highly ordered manner.
Fill in the blank: The __________ model describes protein folding as a smooth, funnel-like process.
energy landscape
What are the potential therapeutic strategies to combat protein aggregation?
Small molecules, antibodies, and enhancing chaperone activity.
Multiple choice: Which of the following is a hallmark of neurodegenerative diseases? A) Protein aggregation B) Increased cell division C) Enhanced protein folding D) None of the above
A) Protein aggregation
What is the role of post-translational modifications in protein folding?
They can influence the folding process and affect protein stability and function.
True or False: Protein aggregates can be beneficial in certain biological contexts.
True
What is protein methylation?
Protein methylation is a post-translational modification where methyl groups are added to amino acids, typically lysine or arginine residues.
True or False: Protein methylation can affect protein function and interactions.
True
What enzyme typically catalyzes protein methylation?
Methyltransferases
Fill in the blank: Protein __________ is the addition of ubiquitin molecules to a target protein.
ubiquitination
What is the main function of ubiquitination?
To mark proteins for degradation by the proteasome.
Which amino acid is most commonly involved in ubiquitination?
Lysine
Multiple Choice: Which of the following is NOT a type of ubiquitin modification? A) Mono-ubiquitination B) Poly-ubiquitination C) Tri-ubiquitination D) Multi-ubiquitination
C) Tri-ubiquitination
What role do sortase enzymes play in protein modification?
Sortase enzymes facilitate the covalent attachment of proteins to the cell wall in Gram-positive bacteria.
True or False: Sortase linkage is important for the anchoring of surface proteins in bacteria.
True
What is the target sequence recognized by sortase enzymes?
LPXTG motif
Fill in the blank: Protein __________ refers to the cleavage of peptide bonds in proteins.
cleavage
Which enzyme class is primarily responsible for protein cleavage?
Proteases
What is the difference between endopeptidases and exopeptidases?
Endopeptidases cleave peptide bonds within the protein chain, while exopeptidases cleave terminal amino acids from the ends.
Multiple Choice: Which of the following is a common type of protease? A) Kinase B) Phosphatase C) Serine protease D) Lipase
C) Serine protease
True or False: Ubiquitination can result in both degradation and non-degradative signaling pathways.
True
What is the role of E3 ligase in the ubiquitination process?
E3 ligase is responsible for transferring ubiquitin from the E2 enzyme to the substrate protein.
Fill in the blank: The __________ pathway is a major route for protein degradation in eukaryotic cells.
ubiquitin-proteasome
What is the significance of methylation on histones?
Methylation of histones can influence gene expression by altering chromatin structure.
Multiple Choice: Which of the following is a consequence of protein cleavage? A) Activation of zymogens B) Inhibition of protein functions C) Increased protein stability D) None of the above
A) Activation of zymogens
What does the term ‘zymogen’ refer to?
A zymogen is an inactive precursor of an enzyme that requires a biochemical change to become active.
True or False: Protein methylation is reversible.
True
Which type of protein modification can lead to the formation of protein aggregates?
Ubiquitination
Fill in the blank: The __________ system is involved in the recognition and degradation of misfolded proteins.
ubiquitin-proteasome
What is a common method for studying protein methylation?
Mass spectrometry
Multiple Choice: Which of the following is a characteristic of sortase enzymes? A) They are found only in eukaryotes B) They are involved in protein degradation C) They facilitate protein anchoring in bacteria D) They catalyze methylation reactions
C) They facilitate protein anchoring in bacteria
What is the effect of lysine methylation on protein interactions?
Lysine methylation can create or disrupt binding sites for other proteins.
True or False: All proteins undergo cleavage as part of their functional maturation.
False
What is the significance of polyubiquitination?
Polyubiquitination typically signals for the protein to be directed to the proteasome for degradation.
Fill in the blank: Protein __________ can play roles in cellular signaling pathways.
methylation
What is the role of the proteasome in the cell?
The proteasome degrades ubiquitinated proteins and recycles amino acids.
