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Estrutura e Função de Proteínas > Módulo 3 parte 1 > Flashcards

Módulo 3 parte 1 Flashcards

Barbara

1
Q

O domínio de uma proteína pode ser folded de forma independente da restante proteína. True or false?

A

True

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2
Q

What is the proteostatis boundary?

A

It’s a boundary which separates the proteins that have the correct conformation from the ones with an incorrect comformation.

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3
Q

Unstable/Misfolded/Mutated proteins can cause proteins that interact with it to be destabilized. This is why it’s said that these “incorrect” proteins have an additive effect. True or false?

A

False. They have a multiplicative effect.

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4
Q

Proteins outside the proteostasis boundary that interact with proteins close to the boundary can pull them “out” of the boundary. True or false?

A

True.

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5
Q

What happens when ATP binds with a chaperone?

A

It causes it to separate from the bound protein.

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6
Q

What are the three “classes” of chaperones?

A

Clamp-type, specialized surface and structural complementation.

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7
Q

For a protein to fold correctly, its folding constant must be higher than the chaperone association constant. True or false?

A

True.

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8
Q

The way chaperones work tends to be direct: They help a protein fold, and then they themselves get degradated, True or false?

A

False. Chaperones act in a cyclical way, helping proteins in folding and degradation in repeated cycles of binding/unbinding of proteins.

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9
Q

Name three families of chaperones and their function

A

Nucleoplasmines - Nucleosome assembly
Chaperonins (Hsp60) - Protein Folding
Hsp27/28 - Inhibition of aggregation under stress
Hsp40 (DnaJ) - Protein folding, oligomer assembly and transport
Hsp47 - Procollagen folding in the ER
Hsp70 (DnaK) - Protein folding, oligomer assembly and transport
Hsp90 - Folding/activation of hormone receptors and protein kinases
Hsp100/104 - Dissolution of insoluble aggregates
Disulphide isomerase - Folding of proteins with disulphide bonds
Calnexin/calreticulin - ER protein folding

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10
Q

Which chaperone family is in charge of the following function:
Protein folding, oligomer assembly and transport

A

Hsp40 (DnaJ) and Hsp70 (DnaK)

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11
Q

Not only is Hsp70 extremely common, but it is also able to act alone. True or false?

A

False. It needs a J protein and a NEF as partners.

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12
Q

Hsp70 is extremely versatile; it can change its function depending on what is needed at the time according to the partner protein bound to it. True or false?

A

True.

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13
Q

Chaperones have a higher affinity for hydrophobic regions of the protein. True or false?

A

True.

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14
Q

How many domains does Hsp70 have?

A

Three. ATPase domain, Substrate binding domain and C-terminal domain

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15
Q

Quickly go through the steps of how Hsp70 works

A
  1. Hsp70 is bound to ATP, which means it’s in its open conformation.
  2. With the help from the cochaperone J-protein (or J domain), an unfolded protein is bound to the Hsp70
  3. The binding of the J-protein and substrate binding causes the hydrolisis of ATP
  4. ATP is turned into ADP, which “closes” the chaperone.
  5. The protein gets folded correctly
  6. Dissassociation of J-protein and association of NEF, which converts ADP into ATP.
  7. Hsp70 is now bound to ATP, which means it’s in its open conformation, and lowers the affinity of the substrate for the chaperone, thus releasing the correctly folded protein.
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16
Q

What class of chaperones is Hsp70?

A

A clamp-type chaperone.

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17
Q

Why can the binding of Hsp70 be considered co-translational?

A

Because it binds to proteins as soon as an hydrophobic region is exposed while they’re being synthesized in the ribossome. This signals the binding of Hsp70 and reduces the ammount of undesired bonds between these areas and other areas.

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18
Q

What are the two types of co-chaperones? What sets them apart?

A

Productive co-chaperones and Degradative co-chaperones.
Productive ch-chaperones assist chaperones in promoting proper folding and maturation of client proteins
Degradative co-chaperones direct chaperone clients towards degradation pathways when folding attempts are unsuccessful

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19
Q

What is the function of the J-domain in Hsp40?

A

It stimulates the ATPase activity, leading to the conformational change in Hsp70.

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20
Q

Proteins either interact with one type of co-chaperones, never both. True or False?

A

False. When proteins bind to productive co-chaperones for too long, degradative co-chaperones are called to promote the degradation of those proteins.

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21
Q

GroEL can help fold any protein, no matter the size or form. True or false?

A

False. Proteins over 60 kDa will not be able to enter the chaperonin.

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22
Q

Chaperonins help proteins fold by providing a hydrophilic environment on which proteins can fold safely. This works since the exterior of a protein tends to be hydrophilic as well. True or false?

A

False. The inside of chaperonins is hydrophobic.

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23
Q

Even though prokaryotes and eukaryotes have different chaperonins, the chaperonins inside the mythochondria and chloroplasts are similar to the ones prokaryotes have. True or false?

A

True.

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24
Q

What are the differences between the two types of chaperonins?

A

Prokaryotic chaperonins have 7 rings and the “lid” is a separate entity from the chaperonin.
Eukaryotic chaperonins have 8 to 9 rings, and the “lid” is built-in,

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25
Q

In a chaperonin, ADP binds the protein and ATP closes the lid. True or false?

A

True

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26
Q

Hsp27 are special because of the fact that they are able to bind to non-native proteins, thus serving as a first line of defense. True or false?

A

True.

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27
Q

Name three characteristics of Hsp90

A

More complex than Hsp70
Prevents aggregation of unfolded proteins
Helps keep unfolded proteins in a folding-competent state

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28
Q

How can Hsp90 prevent aggregation of unfolded proteins?

A

It makes the unfolded proteins go to different compartiments.

29
Q

Hsp100 can be considered important for the degradation process. True or false?

A

True. (They help unfold and separate aggregated proteins so they can be more easily degradated by the proteossome)

30
Q

Hsp27 are extremely large. True or false?

A

False, they are small. (They can even be called sHsp)

31
Q

Molecular chaperones can help in the proteins in their translocation by keeping them unfolded, which facilitates crossing the membrane of certain organelles. True or false?

A

True

32
Q

Chaperones only exist in the cytosol. True or false?

A

False. They also exist inside organelles.

33
Q

Aside from the difference in chaperones structure, chaperone assistance in protein folding is roughly similar in both prokaryotes and eukaryotes. True or false?

A

False, it’s much more complex in eukaryotes.

34
Q

By default, in prokaryotes, most proteins fold spontaneously and only a smaller percentage needs assistance to fold correctly. However, if the stress level increases, the percentage of proteins in need of assistance to fold correctly increases. True or false?

A

True

35
Q

Eukaryotes have a protein that has the same function as the trigger factor in Prokaryotes. True or False?

A

True.

36
Q

During protein folding in Eukaryotes, at later stages, Hsp70 may be replaced by a chaperonin, and this switch is mediated by the protein HOP. True or false?

A

False. Hsp70 gets replaced by Hsp90

37
Q

How does Protein Disulfide Isomerase help with protein folding?

A

By promoting the oxidation of free sulfydril groups

38
Q

In what type of proteins can disulfide bonds be commonly found? And why?

A

In secretory pathway proteins, due to oxidating environment of the lumen of the ER.

39
Q

How is Protein Disulfide Isomerase regenerated?

A

A protein called ERO-1 regenerates the persulfide bond present in the PDI after it gives the one it has away to the protein catalyzed.

40
Q

Protein Disulfide Isomerase can not only create disulfide bonds, but it can correct incorrectly formed disulfide bonds in proteins. True or false?

A

True.

41
Q

What aminoacid does Peptidyl Prolyl Isomerase focus on? What does it do?

A

In proline, and it catalyzes the cis-trans isomerization, speeding up the folding.

42
Q

A protein that is destined to incorporate the plasmatic membrane will be first inserted in the ER membrane, and then transported through vesicles through the golgi complex and onto tthe membrane. True or false?

A

True.

43
Q

The lumen of the ER is similar to the outside environment of the cell, which means tbat when that protein is transported to the cell membrane, the parts that were facing the lumen of the ER will now be facing outwards. True or false?

A

True.

44
Q

The ER only produces proteins. True or False?

A

False. It also produces lipids.

45
Q

What types of proteins can the ER import? And from where are they imported?

A

They are imported from the cytosol, and these are:
- Transmembrane proteins (partially translocated and remain membrane-embedded)
- Soluble proteins (totally translocated and released into the lumen)

46
Q

The import of proteins to the ER happens after they are finished synthesizing but before they fold. True or false?

A

False. It happens as they are synthesized.

47
Q

ER membrane-anchored ribosomes produce…

A

proteins that are directly connected to the ER.

48
Q

Proteins that are being synthesized determine ribosome localization. True or false?

A

True.

49
Q

The smooth ER usually play the role of exits of the ER (ERES, ER exit sites) where transport vesicles are formed. True or False?

A

True.

50
Q

In cells that specialize in lipid metabolism we can see a bigger rugged ER. True or false?

A

False. The smooth ER is bigger in these sorts of cells.

51
Q

An ER membrane protein can never be produced by a free ribossome. True or false?

A

False. It’s the protein being synthesized that determines the ribossome localization. As such, if needs be, a free ribossome will move and bind to the ER membrane to form the protein.

52
Q

Microsomes can be split into two categories. Which are… and originate from…

A

Rugged microsomes, which form from the shattering of the rugged ER, and smooth microsomes, which can originate from the smooth ER, the plasmatic membrane, endossomes or mitochondria.

53
Q

Smooth microsomes can easily be distinguished from rugged microsomes due to the fact that smooth microsomes have specific proteins that rugged microsomes do not posess. True or false?

A

False. It’s the rugged microsomes that posess these specific proteins.

54
Q

If the signal hypothesis is correct, then how come no proteins that have been translocated posess this “signal sequence”?

A

Because it is cut by a signal peptidase

55
Q

Where is the signal sequence located in a protein?

A

In the N-terminus

56
Q

What happens to a protein that doesn’t have a signal sequence?

A

Doesn’t get translocated

57
Q

The signal sequence is a stretch of 6-12 hydrophobic residues associated with one (or more) positively charged aminoacids. True or false?

A

True

58
Q

I waited for my ribossomes to produce 40 residues, but strangely enough, the protein still wasn’t moving, despite translocation starting at about 40 aminoacids. What’s wrong?

A

The 40 residues need to be OUTSIDE the ribosome.

59
Q

The Signal Recognition Particle is composed of 6 subunits bound to a strand of RNA. The zone that recognises the signal sequence is a large cavity full of methionine residues. True or false?

A

True.

60
Q

The Signal Recognition Particle is extremely effecient as it allows the protein to continue being synthesized while it’s transported to the ER membrane. True or false?

A

False. It has a safety mechanism that stops the protein translation until the ribosomes are safely bound to the ER membrane.

61
Q

The SRP receptor is composed of two subunits: alpha which interacts with the signal sequence, and beta anchors the receptor to the ER membrane. True or false?

A

False. Alpha anchors and Beta interacts.

62
Q

The SRP receptor leads to the release of the SRP and anchors the ribosome to itself, which then allows the protein to start being synthesized inside the ER. True or false?

A

False. The SRP receptor and SRP released, and the protein:ribosome complex are anchored to the translocon.

63
Q

The hydrolisis of ATP is crucial for the SRP-SRP receptor transport due to the fact that the energy produced is important to release proteins with an incorrect sequence signal. True or false?

A

False. It’s not ATP it’s GTP, but the rest is correct.

64
Q

The nascent chain passes directly from the large ribosomal subunit to the central pore of the translocon, without being exposed in the cytosol. True or false?

A

True.

65
Q

The translocon is able of opening not only vertically, but also sideways. What is the advantage of this lateral opening?

A

Allows hydrophobic regions insertion into the membrane and is used for the insertion of transmembrane proteins

66
Q

Why is it said that the signal sequence has a dual role?

A

Because it directs the protein to the membrane and functions as a cleaving recognition site for the signal peptidase.

67
Q

What are the different classes of transmembrane proteins?

A

Type I: C-terminus is facing the cytosol and N-terminus is facing the lumen (Produced as expected)

Type II: C-terminus is facing the lumen and N-terminus is facing the cystosol (There’s an internal anchoring mechanism that causes the protein to “flip”. Imagine you’re pushing a string, and suddenly you hold a part of it and flip it)

Type III: Only a miniscule ammount of the protein is facing the lumen, most of it is in the membrane or facing the cytosol (Anchoring region basically prevents any further “expansion” into the lumen and pushes the protein out)

Type IV: Lots of regions in the membrane area

68
Q

Is it possible to predict a protein’s topology?

A

Yes. Through the use of a hydropathy profile, we can identify topogenic (sequences that are known to be in the membrane) sequences. It then identifies long hydrophobic segments and plots it. In the plot, major peaks identify topogenic sequences, their position and length.

69
Q

In a hydropathy profile, hydrophilic residues are given a positive score and hydrophobic residues are given a negative score. True or false?

A

False.
Hydrophobic residues – positive score (methionine, phenylalanine..)
Hydrophylic residues – negative score (ionizable,…)

Estrutura e Função de Proteínas (5 decks)

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