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Flashcards in Protein Folding 2 Deck (41):
1

What are two types of chaperonin proteins?

Type I and Type II.

2

Where are Type I chaperonins found?

Bacteria, mitochondria and chloroplasts - GroEL/GroES

3

Where are Type II chaperonins found?

Archaea and eukaryotes

4

What does HSP90 do in eukaryotes?

Facilitates late stage folding of signalling factors.

5

What do nucleoplasmins do?

Assemble nucleosomes.

6

What does HSP70 do?

Reverses denaturation/aggregation through forming a complex with HSP40.

7

How many proteins are in the E. coli 30S subunit and what rRNA is associated with it?

21 proteins and 16S rRNA

8

How many proteins are in the E. coli 50S subunit and what rRNA is associated with it?

31 proteins, 23rRNA and 5S rRNA

9

How much of the E. coli ribosome is RNA?

~2/3

10

Where do newly synthesised proteins leave the ribosome through?

Narrow tunnel - peptidyl transferase centre (PTC).

11

In elongation what are nascent protein chains sensitive to and why?

Aggregation and degradation - because emerge unfolded from ribosome.

12

Can co-translation folding occur in both prokaryotes and eukaryotes?

Yes.

13

Are trigger factors ATP dependent?

Yes

14

What 2 activities do trigger factors possess?

Chaperone and prolyl-cis-trans-isomerase activities.

15

Which protein of the ribosome does the trigger factor have affinity for?

L23

16

How does the trigger factor prevent proteases cleaving the nascent polypeptide?

Binds to L23 protein closing the channel and protecting the chain.

17

What happens once translation terminates?

Trigger factor either dissociates if protein can fold itself or passes polypeptide to DnaK (HSP70 in eukaroyotes).

18

What does DnaK do?

Decides if protein is to be folded (GroEL) or degraded.

19

What type of chaperone is GroEL/GroES?

Type 1

20

What part of the protein is GroES?

the caps.

21

How many proteins in each layer of GroEL?

7 proteins
(3 layers = 21 proteins)

22

What are the two conformations of GroEL?

Cis and trans

23

Which is elongated cis or trans?

Cis

24

Which conformation do unfolded proteins bind to and why in GroEL?

Trans - attracted to hydrophobic patches.

25

What happens once protein has bound to trans GroEL?

There is affinity for GroES (cap) to bind.

26

What binds alongside GroES?

ATP.

27

What does capping (GroES) cause?

Cis conformation to form.

28

How many ATPs are hydrolysed and what are they for?

7 and to assist protein folding?

29

When can (2nd chamber) trans conformation bind a polypeptide?

Once ATP has been hydrolysed.

30

What are the main targets of GroEL/GroES?

Alpha beta proteins.

31

How is selectivity determined in GroEL/GroES?

By size - there is limitation on what can fit.

32

What is a heat shock protein?

Type of chaperone protein.

33

When are HSPs expressed?

In heat shock stress - when cell becomes damaged due to aggregation.

34

What can HSPs do?

Sequester proteins from aggregates that can be still be refolded.

35

Describe function of PDI?

Randomises disulphide bonds (disrupts them) - when protein is correctly folded disulphide bonds will be protected. So assists protein in finding most stable conformation.

36

What is the rate limiting step of protein folding often?

Cis-trans prolyl isomerisation.

37

How does PPI accelerate cis-trans prolyl isomerisation?

Twists peptide that C,N,O atoms are no longer planar. (accelerates by 100 fold).

38

What is the pH of lysosome and how is it maintained?

5.5 and maintained by ATPase proton pump.

39

What proteins does lysosome normally degrade?

Extracellular proteins.

40

Which protein binds proteins that are tagged to be degraded by lysosomes?

Hsc73 - constitutively expressed HSP70 chaperone.

41

What protein does Hsc73 interact with?

LGP96 on lysosome membrane.