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MFoM > 01b: Protein Folding/misfolding > Flashcards

01b: Protein Folding/misfolding Flashcards

1
Q

T/F: proteins begin folding while they’re being synthesized.

A

True

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2
Q

Is protein folding into native configuration thermodynamically favorable or unfavorable?

A

Favorable (spontaneous)

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3
Q

Which polypeptide terminus is typically folded first?

A

N-terminal (since synthesized first)

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4
Q

What’s the mechanism of chaperones (how do they assist in folding)?

A

Restrict folding pathway (limit number of possible intermediate states).

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5
Q

Chaperones prevent interaction of:

A

Hydrophobic patches during folding process

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6
Q

Chaperones work (inter/intra)-molecularly to prevent inappropriate interactions.

A

Both!

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7
Q

T/F: Chaperones are ubiquitous among phyla.

A

True

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8
Q

Chaperonins are also known as:

A

Hsp60 proteins

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9
Q

T/F: chaperones are exclusively found in the cytosol.

A

False - cytosol, ER, mitochondria, chloroplasts

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10
Q

Chaperones were discovered in which organism?

A

Drosophila

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11
Q

T/F: Hsp70 chaperones are ATPases.

A

True

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12
Q

Which domains are present in Hsp70 chaperones?

A
  1. NT binding domain

2. Substrate binding domain (clamp)

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13
Q

What shuts the clamp in the Hsp70 chaperone?

A

ATP hydrolysis

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14
Q

What opens the clamp in the Hsp70 chaperone?

A

Exchange/release of ADP (and binding of ATP)

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15
Q

T/F: Hsp60 chaperonins are ATPases.

A

True

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16
Q

Describe Hsp60 structure

A
  1. Two independent folding channels (heptameric; called GroEL)
  2. Cap (GroES)
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17
Q

Proteins fold in which cellular compartment?

A

Multiple!

  1. Cytoplasm
  2. ER
  3. Mitochondrion
  4. Chloroplasts
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18
Q

How do folded proteins enter organelles?

A

They can’t; must be unfolded (enter via pores)

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19
Q

Name a key Hsp70 chaperone in the ER.

A

BiP

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20
Q

What’s UPR?

A

Unfolded Protein Response (compensatory mechanism for misfolded proteins)

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21
Q

List sensors for misfolded proteins. Where are they located?

A
  1. IRE1
  2. PERK
  3. ATF6

ER membrane

22
Q

UPR final outcome:

A

Activates genes to increase ER folding capacity

23
Q

What molecules are increased as result of UPR?

A

Chaperones and lipids

24
Q

What are the possible dates of newly synthesized proteins?

A
  1. Correct folding without help
  2. Correct folding with chaperone help
  3. Incompletely folded and digested by proteosome
  4. Protein aggregate
25
Q

Describe basic structure of proteosome

A

4 heptameric rings and a hexamer cap

26
Q

Name of proteosome cap

A

19S hexamer called “unfoldase”

27
Q

The proteosome active sites are present in (core/cap) and have (X)-like activities.

A

20S Core

X = trypsin-, chymotrypsin-, and peptidylglutamyl-

28
Q

Proteosome degrades proteins to how many AA peptides?

A

7-8

29
Q

How does ATP hydrolysis affect the proteosome cap?

A

Causes conformational change that strains ring and pulls substrate through

30
Q

How many AA in ubiquitin?

A

76

31
Q

Ubiquitin point of attachment is:

A

C terminal

32
Q

Ubiquitin attaches to which part(s) of proteins?

A

Lysine side chains

33
Q

The core of ubiquitin can be described as:

A

Globular and hydrophobic

34
Q

T/F: Transfer of ubiquitin to ubiquitin ligase is a passive process.

A

True

35
Q

In ubiquitin transfer, what is E1 formally called?

A

Ubiquitin-activating enzyme

36
Q

T/F: Binding of ubiquitin to ubiquitin-activating enzyme is a passive process.

A

False - converts ATP to AMP

37
Q

In ubiquitin binding, the (X) terminus of ubiquitin binds to (Y) group of E1.

A

X = C

Y = -SH (displaces H)

38
Q

In ubiquitin binding, the (X) terminus of ubiquitin binds to (Y) group of E2/E3.

A

X = C

Y = -SH (displaces H)

39
Q

The last AA of ubiquitin (X) connects to the AA (Y) on preceding ubiquitin, forming which type of bond?

A 
X = glycine 
Y = lysine (48)

Isopeptide bond

40
Q

Which path do misfolded proteins take to arrive at the (X) for degradation?

A

Retrotranslocation from ER to cytoplasm

X = proteosome

41
Q

Quality control mechanisms help the cell by:

A

Prevent accumulation of misfolded protein

42
Q

Proteostasis is:

A

Balance of protein synthesis, folding, and degradation (homeostasis)

43
Q

There are (few/many/unknown) genes involved in proteostasis.

A

Many

44
Q

It’s estimated that as many any (X)% of all polypeptide chains synthesizes in cell misfold.

A

X = 50

45
Q

Misfolding of protein can result in (gain/loss) of (X) function.

A
  1. Gain of toxic function
    OR
  2. Loss of normal biological function
46
Q

Dominant inheritance of protein misfolding typically results in:

A

Gain of toxic function

47
Q

Recessive inheritance of protein misfolding typically results in:

A

Loss of normal biological function

48
Q

What are amyloid fibrils?

A

Abnormal accumulation of protein

49
Q

In amyloid fibrils, (X) are perpendicular to fiber axis.

A

X = beta strands

50
Q

In amyloid fibrils, (X) are parallel to fiber axis.

A

X = beta sheets

51
Q

T/F: Amyloid may have physiological functions.

A

True

52
Q

Amyloid fibrils can be stained with:

A

Congo red or thioflavin

MFoM (20 decks)

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