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Biochemistry > Bioc 440: Protein Folding Enthalpy & Entropy; Aggregation; Post-translation Modifications > Flashcards

Bioc 440: Protein Folding Enthalpy & Entropy; Aggregation; Post-translation Modifications Flashcards

1
Q

What is entropy in the context of protein folding?

A

Entropy is a measure of the disorder or randomness in a system.

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2
Q

What is enthalpy in protein folding?

A

Enthalpy is the total heat content of a system, reflecting the energy needed to break and form bonds.

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3
Q

True or False: Higher entropy generally favors the folding of proteins.

A

False.

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4
Q

What is the relationship between entropy and the stability of a folded protein?

A

Lower entropy in the folded state contributes to the stability of the protein.

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5
Q

Fill in the blank: Protein folding is driven by the balance between enthalpy and __________.

A

entropy.

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6
Q

What role do hydrogen bonds play in protein folding?

A

Hydrogen bonds stabilize the folded structure and contribute to the enthalpic term.

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7
Q

Multiple Choice: Which factor increases the entropy during protein folding?

A

The release of water molecules from the protein surface.

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8
Q

Define the term ‘free energy’ in protein folding.

A

Free energy is the energy available to do work, determining the spontaneity of the folding process.

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9
Q

True or False: A negative change in enthalpy favors protein folding.

A

True.

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10
Q

What is the role of hydrophobic interactions in protein folding?

A

Hydrophobic interactions drive non-polar side chains to the interior, reducing system entropy.

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11
Q

How does temperature affect protein folding and stability?

A

Higher temperatures can increase entropy but may also lead to denaturation.

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12
Q

Fill in the blank: The process of protein folding can be described as a __________ energy landscape.

A

multi-dimensional.

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13
Q

What is the significance of the Gibbs free energy equation in protein folding?

A

It relates the change in free energy to changes in enthalpy and entropy during folding.

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14
Q

Multiple Choice: Which of the following increases the enthalpy of a folded protein?

A

Formation of covalent bonds.

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15
Q

What is the effect of disulfide bonds on protein structure?

A

Disulfide bonds provide stability by forming covalent links between cysteine residues.

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16
Q

True or False: Entropy is always unfavorable in the context of protein folding.

A

False.

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17
Q

What is a protein’s native state?

A

The native state is the most stable, functional conformation of a protein.

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18
Q

Fill in the blank: The transition state during protein folding is often considered a __________ state.

A

high-energy.

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19
Q

What does it mean when a protein is described as being ‘denatured’?

A

Denatured proteins are unfolded and lack their functional three-dimensional structure.

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20
Q

Multiple Choice: Which factor is NOT directly involved in the enthalpic contribution to folding?

A

Hydrophobic effect.

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21
Q

What are chaperone proteins?

A

Chaperone proteins assist in the proper folding of other proteins.

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22
Q

True or False: The process of protein folding is always spontaneous.

A

False.

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23
Q

What happens to the entropy of the solvent during protein folding?

A

The entropy of the solvent generally increases as water molecules are released.

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24
Q

Fill in the blank: The folding of proteins often involves __________ intermediates.

A

unfolded.

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25
Q

What is the primary driving force behind the folding of globular proteins?

A

The hydrophobic effect.

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26
Q

Multiple Choice: Which of the following is a characteristic of the transition state in protein folding?

A

It is high in energy and unstable.

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27
Q

What is the impact of mutations on protein folding?

A

Mutations can disrupt normal folding and stability of the protein.

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28
Q

True or False: All proteins fold into a single unique structure.

A

False.

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29
Q

What is the significance of the folding funnel model?

A

The folding funnel model illustrates how proteins navigate to their native state through various paths.

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30
Q

Fill in the blank: The __________ effect helps to drive protein folding by minimizing exposure of hydrophobic residues to water.

A

hydrophobic.

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31
Q

What is meant by ‘thermodynamic stability’ in proteins?

A

Thermodynamic stability refers to the tendency of a protein to remain in its folded state under physiological conditions.

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32
Q

Multiple Choice: Which process is energetically favorable for protein folding?

A

Formation of secondary structures.

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33
Q

How does pH affect protein folding?

A

Changes in pH can alter charge interactions and disrupt folding.

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34
Q

True or False: Protein folding is a purely enthalpic process.

A

False.

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35
Q

What is the role of molecular dynamics simulations in studying protein folding?

A

Molecular dynamics simulations help visualize the folding process and predict folding pathways.

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36
Q

Fill in the blank: The __________ principle states that the folded structure of a protein is determined by its amino acid sequence.

A

Anfinsen.

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37
Q

What is the main contribution of entropy to protein folding?

A

Entropy contributes by allowing more configurations and states in the unfolded state.

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38
Q

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

A

Increased entropy of the folded state.

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39
Q

What is the role of van der Waals forces in protein folding?

A

Van der Waals forces provide non-covalent interactions that help stabilize the folded structure.

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40
Q

True or False: The energy landscape of protein folding is typically rugged and complex.

A

True.

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41
Q

Fill in the blank: The __________ state of a protein is typically lower in free energy than the unfolded state.

A

folded.

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42
Q

What is the significance of the hydrophobic core in protein structure?

A

The hydrophobic core minimizes contact with water, contributing to the stability of the folded protein.

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43
Q

What is the native state of a protein?

A

The native state of a protein is its functional three-dimensional structure.

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44
Q

True or False: The native state of a protein is always the most thermodynamically stable form.

A

True

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45
Q

What are protein aggregates?

A

Protein aggregates are clusters of misfolded proteins that can lead to various diseases.

46
Q

Fill in the blank: The process of a protein adopting its native state is called __________.

A

folding

47
Q

What factors can influence protein folding?

A

Temperature, pH, ionic strength, and the presence of chaperones.

48
Q

Multiple choice: Which of the following is NOT a factor influencing protein aggregation? A) Temperature B) Protein concentration C) pH D) Molecular weight

A

D) Molecular weight

49
Q

What role do chaperone proteins play in protein folding?

A

Chaperone proteins assist in the proper folding of other proteins and prevent aggregation.

50
Q

True or False: All protein aggregates are harmful to cells.

A

False

51
Q

What is a common disease associated with protein aggregation?

A

Alzheimer’s disease.

52
Q

Define ‘denaturation’ in the context of proteins.

A

Denaturation is the process in which a protein loses its native structure and function.

53
Q

Fill in the blank: The __________ structure of a protein refers to its sequence of amino acids.

A

primary

54
Q

What is the secondary structure of proteins?

A

The secondary structure refers to local folding patterns like alpha helices and beta sheets.

55
Q

Multiple choice: Which level of protein structure is determined by hydrogen bonding? A) Primary B) Secondary C) Tertiary D) Quaternary

A

B) Secondary

56
Q

What is meant by ‘tertiary structure’ of a protein?

A

The tertiary structure is the overall three-dimensional shape of a single polypeptide chain.

57
Q

True or False: Quaternary structure involves multiple polypeptide chains.

A

True

58
Q

What can cause a protein to misfold?

A

Genetic mutations, environmental stress, and chemical modifications.

59
Q

Fill in the blank: Protein misfolding can lead to __________ diseases.

A

neurodegenerative

60
Q

What is the definition of ‘protein stability’?

A

Protein stability refers to the ability of a protein to maintain its native structure under varying conditions.

61
Q

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

A

D) All of the above

62
Q

What is ‘hydrophobic effect’ in protein folding?

A

The hydrophobic effect is the tendency of nonpolar side chains to avoid water, driving protein folding.

63
Q

True or False: Chaperonins are a type of chaperone protein that form large complexes.

A

True

64
Q

What is the role of disulfide bonds in protein structure?

A

Disulfide bonds stabilize the tertiary and quaternary structures of proteins.

65
Q

Fill in the blank: The __________ hypothesis suggests that proteins fold into their native state via a series of intermediate states.

A

framework

66
Q

What is the significance of the energy landscape in protein folding?

A

It describes the various energy states a protein can adopt during the folding process.

67
Q

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

A

B) Fibrous proteins

68
Q

What is amyloidosis?

A

Amyloidosis is a condition characterized by the accumulation of amyloid aggregates in tissues.

69
Q

True or False: Protein aggregates can form in both intracellular and extracellular environments.

A

True

70
Q

What is the importance of protein aggregation studies in medicine?

A

They help in understanding the mechanisms of diseases and developing therapies.

71
Q

Fill in the blank: __________ are proteins that assist in the folding and assembly of other proteins.

A

Chaperones

72
Q

What is the function of heat shock proteins?

A

Heat shock proteins help prevent misfolding and aggregation during stress conditions.

73
Q

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

A

B) Loss of function

74
Q

What are the two main types of protein aggregates?

A

Amorphous aggregates and fibrillar aggregates.

75
Q

True or False: Protein aggregation is a reversible process.

A

False

76
Q

What is a key characteristic of fibrillar aggregates?

A

Fibrillar aggregates are often long, unbranched fibers that can form in a highly ordered manner.

77
Q

Fill in the blank: The __________ model describes protein folding as a smooth, funnel-like process.

A

energy landscape

78
Q

What are the potential therapeutic strategies to combat protein aggregation?

A

Small molecules, antibodies, and enhancing chaperone activity.

79
Q

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

A) Protein aggregation

80
Q

What is the role of post-translational modifications in protein folding?

A

They can influence the folding process and affect protein stability and function.

81
Q

True or False: Protein aggregates can be beneficial in certain biological contexts.

A

True

82
Q

What is protein methylation?

A

Protein methylation is a post-translational modification where methyl groups are added to amino acids, typically lysine or arginine residues.

83
Q

True or False: Protein methylation can affect protein function and interactions.

A

True

84
Q

What enzyme typically catalyzes protein methylation?

A

Methyltransferases

85
Q

Fill in the blank: Protein __________ is the addition of ubiquitin molecules to a target protein.

A

ubiquitination

86
Q

What is the main function of ubiquitination?

A

To mark proteins for degradation by the proteasome.

87
Q

Which amino acid is most commonly involved in ubiquitination?

A

Lysine

88
Q

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

A

C) Tri-ubiquitination

89
Q

What role do sortase enzymes play in protein modification?

A

Sortase enzymes facilitate the covalent attachment of proteins to the cell wall in Gram-positive bacteria.

90
Q

True or False: Sortase linkage is important for the anchoring of surface proteins in bacteria.

A

True

91
Q

What is the target sequence recognized by sortase enzymes?

A

LPXTG motif

92
Q

Fill in the blank: Protein __________ refers to the cleavage of peptide bonds in proteins.

A

cleavage

93
Q

Which enzyme class is primarily responsible for protein cleavage?

A

Proteases

94
Q

What is the difference between endopeptidases and exopeptidases?

A

Endopeptidases cleave peptide bonds within the protein chain, while exopeptidases cleave terminal amino acids from the ends.

95
Q

Multiple Choice: Which of the following is a common type of protease? A) Kinase B) Phosphatase C) Serine protease D) Lipase

A

C) Serine protease

96
Q

True or False: Ubiquitination can result in both degradation and non-degradative signaling pathways.

A

True

97
Q

What is the role of E3 ligase in the ubiquitination process?

A

E3 ligase is responsible for transferring ubiquitin from the E2 enzyme to the substrate protein.

98
Q

Fill in the blank: The __________ pathway is a major route for protein degradation in eukaryotic cells.

A

ubiquitin-proteasome

99
Q

What is the significance of methylation on histones?

A

Methylation of histones can influence gene expression by altering chromatin structure.

100
Q

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

A) Activation of zymogens

101
Q

What does the term ‘zymogen’ refer to?

A

A zymogen is an inactive precursor of an enzyme that requires a biochemical change to become active.

102
Q

True or False: Protein methylation is reversible.

A

True

103
Q

Which type of protein modification can lead to the formation of protein aggregates?

A

Ubiquitination

104
Q

Fill in the blank: The __________ system is involved in the recognition and degradation of misfolded proteins.

A

ubiquitin-proteasome

105
Q

What is a common method for studying protein methylation?

A

Mass spectrometry

106
Q

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

A

C) They facilitate protein anchoring in bacteria

107
Q

What is the effect of lysine methylation on protein interactions?

A

Lysine methylation can create or disrupt binding sites for other proteins.

108
Q

True or False: All proteins undergo cleavage as part of their functional maturation.

A

False

109
Q

What is the significance of polyubiquitination?

A

Polyubiquitination typically signals for the protein to be directed to the proteasome for degradation.

110
Q

Fill in the blank: Protein __________ can play roles in cellular signaling pathways.

A

methylation

111
Q

What is the role of the proteasome in the cell?

A

The proteasome degrades ubiquitinated proteins and recycles amino acids.

Biochemistry (18 decks)

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