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Estrutura e Função de Proteínas > Módulo 2 > Flashcards

Módulo 2 Flashcards

Claudio

1
Q

A peptide bond is a covalent bond that is able to rotate slightly. True or false?

A

True.

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2
Q

The peptide bonds are double bonds. True or false?

A

False. They are partial double bonds.

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3
Q

In a peptide bond, what are phi and psi?

A

The angles at which the bond can rotate

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4
Q

When do we have a beta turn?

A

Because of proline, which forms a turn

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5
Q

What is the difference between aa alpha/Beta topology and an alpha+Beta?

A

a/B are in sequence (a-B-a-B) and a+B just means it has both. (Normally segregated)

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6
Q

There are multiple kinetic pathways for a protein’s native conformation. True or false?

A

True.

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7
Q

The only proteins that aren’t marginally stable are enzymes. True or false?

A

False. It’s structure proteins that are extremely stable.

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8
Q

Why do proteins constantly appear to be “vibrating”?

A

Because of thermal energy.

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9
Q

Internal areas of the protein have aminoacids that are able to rotate less. True or false?

A

True. (steric hindrance)

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10
Q

Local motions of aminoacids affect the movement of nearby aminoacids. True or false?

A

False. Rapid local motions are harmonic (symetric vibrations) and uncorrelated (one does not influence the other)

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11
Q

Why doesn’t the internal motions of one domain affect other domains of the same protein?

A

Because of Linker regions

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12
Q

The motion of a residue depends solely on the residue itself. True or false?

A

False. it also depends on the environment.

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13
Q

How does the size of an aminoacid residue affect it’s motion?

A

Smaller residues move faster.

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14
Q

Buried waters reduce protein mobility due to stabilization, as the residues form Hydrogen bonds with the water and have less reason to move. True or false?

A

False. Water molecules in protein cavities increases protein mobility due to entropic effects.

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15
Q

With buried waters, although water entropy is decreased, the entropy of the protein is increased. True or false?

A

True. Rotation of water molecules inside cavity allows protein to reorganize some of its H-bonding

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16
Q

The more secondary structures a protein has, the less it wobbles. True or false?

A

True

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17
Q

What is Enthalpy?

A

Enthalpy is the measurement of energy in a thermodynamic system

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18
Q

What is Entropy?

A

Entropy is a measure of disorder

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19
Q

What does a reducing agent do to proteins?

A

Denatures them by reducing and breaking the dissulphide bonds.

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20
Q

What did Anfisen conclude?

A

All the information necessary for a protein to fold correctly in encoded within the primary structure of the protein. In other words, the native structure is a unique, stable and kinetically accessible minimum of the free energy

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21
Q

What does Urea do to proteins?

A

Denatures them by breaking noncovalent interactions.

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22
Q

What are the conditions for the thermodynamic hypothesis?

A

Uniqueness: A sequência irá dar origem ao mínimo de energia livre mais óbvio, ou seja, qualquer outra conformação que a proteína possa ter terá mais energia livre.

Stability: Small changes in the environment cannot give rise to changes in the minimum folded configuration.

Kinetic accessability: The pathway from unfolded to unfolded is simple and does not involve any complex shape changes in the protein.

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23
Q

The native conformation corresponds to minimum free energy and entropy, which gives the protein high stability. True or false?

A

True

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24
Q

The native conformation provides the highest free energy and entropy. True or false?

A

False. That is actually the unfolded conformation.

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25
Q

The folded state is more favourable than the unfolded state because there’s a reduction in the entropy of the system brought by the reduction of the hydrophobic effect. True or false?

A

True.

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26
Q

How is the hydrophobic effect lowered in the folded state?

A

By shielding the hydrophobic side chains into the interior of the proteins

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27
Q

What is a globular protein?

A

Hydrophobic interior and polar exterior.

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28
Q

The angle of an Hydrogen bond dictates its strength. True or false?

A

True.

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29
Q

Name six things that help make proteins stable.

A

Hydrogen bonds, Electrostatic forces, Van der Walls forces, Dissulfide bridges, PTMs and Cofactors.

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30
Q

Give three examples of ways proteins can overcome the “rugged bumps” in a rugged energy landscape.

A

Thermal energy, the protein’s own dynamics, and chaperones.

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31
Q

The amplitude of the top of the folding funnel is proportional to the enthalpy of the system. True or false?

A

False. It’s proportional to te entropy.

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32
Q

Why are short peptides unable to form tertiary structures?

A

While they can form secondary structures, they are unable to form tertiary structures due to the fact that they cannot form a hydrophobic core.

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33
Q

Intrinsically disordered regions appear because they possess low hidrophobicity and lots of polar aminoacids. True or false?

A

True.

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34
Q

The order by which aminoacid appears in the primary sequence is the only deciding factor when it comes to the generation of intrinsically disordered regions. True or false?

A

False. It’s the order by which they appear AND their hidrophobicity and polarity.

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35
Q

The order by which aminoacid appears in the primary sequence is one of the deciding factors when it comes to the generation of intrinsically disordered regions. True or false?

A

True.

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36
Q

Proteins that have a large net charge and low hydrophobic content usually lack ordered structure. True or false?

A

True

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37
Q

What is a fuzzy complex?

A

It’s the result of a bond between an IDR protein and a partner (normally other proteins).

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38
Q

The domain is the unit of stable folding. True or false?

A

True

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39
Q

Why is a flat energy landscape incorrect when it comes to visualizing protein folding pathways?

A

Because if an energy landscape is “flat”, all pathways are equal, and random search is unlikely to find the pathway leading to the native state

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40
Q

What is first event during protein folding?

A

Hydrophobic collapse/Formation of the hydrophobic core

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41
Q

What is the Molten Globule state?

A

Molten globules are compact, partially folded conformations of proteins that are thought to be common intermediates in protein folding.

42
Q

What is phi-value analysis?

A

How much each aminoacid contributes to the folding of a protein.

43
Q

Molten globules are characterized by their substantial secondary and tertiary structure, and their exposed hydrophilic surface area. True or false?

A

False. They have little to no tertiary structure and they hydroPHOBIC surface area is exposed.

44
Q

In what sorts of conditions can molten globules and other partially folded intermidiates be found?

A

Marginally destabilizing ones.

45
Q

What characteristics of a MG can we detect? And through what means?

A
  • Native-like secondary structure, can be measured by CD and NMR proton exchange rate
  • It has a slowly fluctuating tertiary structure which gives no detectable near UV CD signal and gives quenched fluorescence signal with broadened NMR chemical peaks
  • Non-specific assembly of secondary structure and hydrophobic interactions, which allows ANS to bind and gives an enhanced ANS fluorescence
46
Q

Is the MG state bigger or smaller than the native state?

A

MG is about a 10% increase in size than the native state (Bigger)

47
Q

Size exclusion chromatography can tell us how compact a cell is. True or false?

A

True

48
Q

During the MG state, the hydrophobic core isn’t shielded, which means hydrophilic protein surfaces can bind and mess with its folding. True or false?

A

False. During the MG state, the hydrophobic core isn’t shielded, which means hydroPHOBIC protein surfaces can bind and mess with its folding.

49
Q

What’s the problem with proline isomerization?

A

Depending on whether it’s cis or trans, the angles it forms are different, which creates different conformations that can be considered a local minimum, delaying the folding by tens of seconds.

50
Q

Why are stopped flow kinnetics used to study protein folding?

A

Reactions are too fast (subsecond).

51
Q

Where does the cooperativity of the folding reaction comes from?

A

The cooperativity of the folding reaction comes from the fact that the “first bond” to be estabilished in a protein (between itself) is very easy to make (doesn’t require very complicated movements), and causes the protein to acquire a new comformation. In this new conformation, there’s an even better bond to be estabilished, and so the protein estabilishes the bond and gets a new conformation, leading to a new favorable bond to be found and estabilished, and so on and so forth.

52
Q

If a folding reaction is cooperative, then at 50% denaturant added, half the proteins will be completely folded, and half will be completely unfolded. True or false?

(Assuming that at 0% denaturant all proteins are folded completely and at 100% all proteins are unfolded completely)

A

True

53
Q

If a folding reaction is cooperative, then at 50% denaturant added, all proteins will be half folded. True or false?

(Assuming that at 0% denaturant all proteins are folded completely and at 100% all proteins are unfolded completely)

A

False. The only way for proteins to be half folded is if the folding reaction is not cooperative.

54
Q

The flatter the melting curve, the higher the chances of a folding reaction being cooperative. True or false?

A

False. A flatter melting curve (gradual increase) is typical of non cooperative folding reactions.

55
Q

How would you describe the melting curve of a cooperative folding reaction?

A

As a sharp increase or an “all or nothing” folding

56
Q

What is a Chaotropic agent?

A

A denaturant that disrupt the H-bonding network between water molecules and reduce the stability of the native state of proteins by weakening the hydrophobic effect.

57
Q

Chaotropic agents work by disordering water structure and dynamics, which causes hydrophobic molecules to be more easily solvated. In other words, it increases the hydrophobic effect. True or false?

A

False. It DECREASES the hydrophobic effect.

58
Q

If there is no signal from a Circular dichroism analysis, then that means the protein is unfolded. True or False?

A

True.

59
Q

What does Circular dichroism detect?

A

Secondary structure

60
Q

Given two denaturation curves of protein A and B, with protein A having a maior declive NO GRÁFICO DE DESNATURAÇÃO and lower transition point than Protein B, we can assume that Protein B is more stable than A because is requires more denaturant to denature 50% of the proteins. True or false?

A

A proteína B parece ser mais estável, uma vez que apresenta um ponto de transição maior. Contudo uma vez que apresenta um maior declive, o ∆G é menor e, por isso é menos estável. Por outro lado, a proteína A apresenta em virtude um menor declive, que lhe confere um maior ∆G e consequentemente é mais estável.

61
Q

In a denaturation curve, the maior declive the higher the ∆G. True or false?

A

True.

62
Q

In a denaturation curve, the higher the ∆G, the less stable a protein is. True or false?

A

False. higher the ∆G, the more stable a protein is.

63
Q

At midpoint, [D]50% = ∆G(H20) / m
What does the “m” represent?

A

It represents the “m-value”, which is related to how cooperative the transition is. It also represents the slope of the curve.

64
Q

The variation in slope (m) is believed to be due to change in the solvent accessible area of hydrophobic residues. True or false?

A

True.

65
Q

The m-value is inversely proportional to the size of a protein; in other words, the more residues a protein has, the small the m-value will be. True or false?

A

False. It is DIRECTLY proportional, so a larger protein has a larger m-value.

66
Q

There are two major models for protein unfolding: A two-state model and via an intermediate state model.
If the protein is a dimer, the intermediate state can be either two partially denatured monomers or one partially denatured dimer. True or false?

A

True

67
Q

When proteins are heated, they become more extended. What is a consequence of this?

A

The conformational entropy increases.

68
Q

The energy supplied to the system in the form of heat, disrupts H-bonds and other interactions, increasing enthalpy. True or false?

A

False, it decreases enthalpy.

69
Q

Define Differential scanning calorimetry.

A

Differential Scanning Calorimetry (DSC) is a technique used to characterize the stability of a protein or other biomolecule directly in its native form. It does this by measuring the heat change (be it heat released or absorbed) associated with the molecule’s thermal denaturation when heated at a constant rate.

70
Q

Tryptophan residues in the inside of a protein emit at a much higher wavelength than Tryptophan residues on the outside of a protein. True or false?

A

False. They emit at a lower wavelength on the inside.

71
Q

Tryptophan is important for protein studies due to their intrinsic fluorescence. True or false?

A

True.

72
Q

If use fluorescence spectroscopy and relying on Tryptophan, after a chemical denaturation we can still see some leftover structure conformation. The same cannot be said about thermal denaturation. True or false?

A

True

73
Q

The protein hydration layer is essential for protein function and folding. Why?

A

It provides thermal energy to proteins and H-bonding to charged groups and backbone.

74
Q

The contact between a water molecule and a protein is long lasting. True or false.

A

False. It’s incredibly short.

75
Q

The water molecules hydrating proteins have roughly the same behaviour as any other water molecule. True or false?

A

False. They are very different.

76
Q

A protein in a tight space has greater folding stability, because its denatured state has fewer conformations and thus less conformational entropy. True or false?

A

True.

77
Q

Macromolecular crowding favors protein assembly since the components to build protein complexes are closer together. True or false?

A

False. High association makes proteins more sticky so the rate at which protein complexes assemble is retarded.

78
Q

What mechanisms does the cell have to ensure the protein is folded correctly while still inside the ribossome?

A

The use of rare codons to slow down protein synthesis and give the protein enough time to fold correctly, and the fact that the ribossomes exit all point towards different places, thus reducing the number of interactions between proteins being synthesized.

79
Q

Name four ways biology modulates the protein folding reaction.

A
  1. Control of the transcription rate through rare codon usage
  2. Folding regulation at the ribossome (co-translational folding)
  3. Use of protein folding catalysts (Molecular chaperones)
  4. Quality Control of protein folding (degradation machinery)
80
Q

Name 1 factor promoting protein misfolding in vitro and another on in vivo.

A

Pick two from this list:

  • Aggregation from Equilibrium Partially Folded States
  • Aggregation from Intermediates of folding
  • Native-State Fluctuations
  • Intrinsic Disorder within Proteins
  • Mutations
  • Altered physicochemical conditions (pH, metal ions)
  • High Protein Concentrations
  • Unfolded States formed from Globular Proteins
  • Protein modifications (including oxidative stress)
  • Interactions with bio-surfaces - Lipid Membranes
  • Macromolecular Crowding
  • Aging increases the probability of Protein Aggregation due to less efficent quality control
81
Q

How can mutations (normally) worsen the protein folding landscape.

A

They broaden the native basin (a parte de baixo) of the folding funnel, which results in lower energetic barriers, between native conformers, which can be easily populated through dynamic fluctuations. In other words, the proteins can go from the correct state to an incorrect folded state more easily. This incorrect folded state may have different stabilizing properties, or have impaired function.

82
Q

What is a “Kinetic trap”?

A

It’s a state in which the protein misfolds into an incorrect state and not the native state, but the necessary energy to surpass this trap is too large.

83
Q

The results of intramolecular contacts during protein folding (such as amyloid fibrils and amorphous aggregates) are as stable as the protein in their native conformation. As such, these incorrect forms of folding only happen when the safety mechanisms of protein folding fail. True or false?

A

False. The results of intramolecular contacts during protein folding are much more stable than a protein’s natural conformation.

84
Q

Protein aggregation is a ____ process and relies on the ______________ of protein present.

A

slow, concentrarion.

85
Q

Give three characteristics for each Misfolded protein state.

A

Destabilized protein:
Low stability conformational state * May have locally altered secundary structure or poored tertiary interactions. * It usually retains some biological function * More susceptible to proteolysis than native

Protein Aggregate:
Amorphous * insoluble protein conglomerate * Results from intermolecular hydrophobic interactions between misfolded proteins * Readily resolubilized in buffer in native like conditions

Amyloid Fibril:
Highly ordered * Insoluble fibril-shaped protein aggregates * formed from b-sheet stacking in a cross-b motif * Highly resistent to proteolysis * Require high concentrations of denaturant or detergent to resolubilize

86
Q

Inclusion bodies only exist in prokaryotes. True or false?

A

False, they exist in eukaryotes as well.

87
Q

Chaperones are important molecules involved in protein folding as they provide additional guidance for how the protein should fold. True or false.

A

False. They merely avoid protein aggregation.

88
Q

What are APRs? Where can they be found in high quality?

A

These are aggregation prone regions. Intrinsically disordered proteins have a high level on unconcealed APRs.

89
Q

Why are amyloid fibrils so toxic to the cell?

A

Because the cell cannot degrade them.

90
Q

Protein topology and size are uninportant for amyloid formation. True or false?

A

True.

91
Q

Under conditions that promote exposure of aggregation prone regions, any protein will self assemble into an amyloid fibril. True or false?

A

True.

92
Q

APRs have a high tendency to from alpha-helixes. True or False?

A

False. They tend to form Beta sheets.

93
Q

What is the “fuzzy coat” in an APR?

A

It’s the rest of the protein that isn’t the stacked beta sheets. (See notes to understand better)

94
Q

If an amyloid fybril is placed under an X-ray, there is difraction at two distinct lengths, which correspond to:

A

The distance between beta sheets and the Hydrogen bonds estabilished between them.

95
Q

The primary structure of the protein also holds the tendency a protein has to form amyloid fibrils. True or false?

A

True.

96
Q

What are some characteristics that make a protein more susceptible to forming an amyloid?

A

Aminoacids that tend to form Beta sheets
Short sequences that lead to oligomerization when exposed
High hidrophobicity
Low liquid content/cargo

97
Q

What is a way proteins have evolved to avoid amyloid formation?

A

Proteins have evolved to hide these segments that can lead to amyloid formation. For example in dimers, the protein tends to hide the hydrophobic regions.

98
Q

Why do proteins that tend to have high tendency to form amyloid aggregation also tend to be rich in proline?

A

Because proline leads to steric hindrance which tends to discourage amyloid formation. The proline is located at the start and finish of the APRs.

99
Q

All amyloids are toxic to the human body. True or false?

A

False. There exists functional amyloids that act as natural storage of peptide hormones in pituitary secretory granules.

100
Q

What are the three major classes of protein folding diseases?

A

Diseases resulting from protein misfolding and destabilization with no aggregation

Diseases resulting from protein misfolding with amyloid aggregation

Diseases resulting from defects in molecular chaperones - chaperonopathies

101
Q

Pharmacological chaperons are able to correct and fix incorrectly folded proteins by permanently binding to them and forcing them to get their correct folded state. True or false?

A

False. They don’t bind permanently (but the rest is correct)

102
Q

How do chemical chaperones help protein folding?

A

They stabilize proteins through excluded volume effects and preferential hidration

Estrutura e Função de Proteínas (5 decks)

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