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MSF1 > Protein Folding 3 > Flashcards

Protein Folding 3 Flashcards

1
Q

What is the size of ubiquitin?

A

76aa

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2
Q

What is ubiquitin used for?

A

Tagging proteins for degradations in the proteasome pathway.

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3
Q

How ubiquitin linked to proteins?

A

Using an isopeptide bond via Lys 48, Lys 63 and N terminus.

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4
Q

Which protein complex tags protein with ubiquitin?

A

E1-E2-E3.

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5
Q

Which protein in the complex provides specificity and how?

A

E3 (protein ligase complex) - interacts with protein and ubiquitin.

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6
Q

What can give variability given to the tag?

A

poly-ubiquitination

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7
Q

What protein does HPV encode and what does it target?

A

E3 - specific to p53 tumour suppressor protein.

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8
Q

What proteins recognise misfolded or damaged proteins?

A

Hsp40-Hsp70 complex.

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9
Q

What does recognition by the Hsp40-Hsp70 complex lead to?

A

This will lead to E1-E2-E3 complex where poly-ubiquitination will occur via Lys 48 – tagged for degradation.

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10
Q

What is the structure of the proteasome?

A

central chamber - 28 proteins and 2 lids.

Four rings make up central chamber.

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11
Q

Which part of proteasome recognise the poly-U tag?

A

The two lids.

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12
Q

Where are proteasomes found?

A

eukaroyotes, archaea and some bacteria.

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13
Q

Which rings function as the gate?

A

outer two rings.

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14
Q

Which proteins recognise misfolded proteins in aggresome-autophagy pathway?

A

Parkin, Ubc13 and Uev1a.

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15
Q

How are misfolded proteins in aggresome-autophaphy pathway tagged?

A

Ubiquitin via Lys 63.

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16
Q

What does the ubiquitin Lys 63 tag promote?

A

The binding of p62 which recruits autophagic membranes to aggresome to form autophagosome - fuses with lysosome.

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17
Q

What can form amyloid fibrils?

A

Partially folded intermediates/degraded fragments.

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18
Q

Can all types of proteins form amyloids?

A

yes.

19
Q

What does the fact that all proteins can form amyloid fibrils suggest?

A

That amyloid fibrils are the real thermodynamic minimum in folding.

20
Q

What % of people have Alzheimers +65 years?

A

10%

21
Q

What % of people have Alzheimers +85years?

A

50%

22
Q

What happens to brain tissue that contain amyloid plaques?

A

they form neurofibrillary tangles.

23
Q

What do protein causes amyloids?

A

Amyloid Beta peptide.

24
Q

Which protein is Amyloid Beta peptide derived from?

A

Amyloid beta precursor protein (AbetaPP) - it undergoes proteolysis to form this.

25
Q

What is the pathway of amyloid fibril formations?

A

Native –> amyloidgenic intermediate –> oligomers –> protofibrils –> amyloid fibrils.

26
Q

What is the most toxic species in pathway?

A

Oligomers - not structurally defined.

27
Q

Are amyloidgenic precursors (protein monomers) transient?

A

Yes.

28
Q

Are amyloid fibrils resistant to detergents/unfolding agents?

A

Yes.

29
Q

What do oligomers have the ability to do?

A

penetrate cellular membranes.

30
Q

What secondary structure are amyloids made of?

A

Extended beta sheets.

31
Q

What is distance between beta strands in amyloids?

A

4.7A

32
Q

What is distance between beta sheets in amyloids?

A

10.7A

33
Q

What is the steric zipper model referring to in amyloids?

A

Tight hydrogen bonding between beta strands that excludes water.

34
Q

What did more recent analysis of amyloid structure show?

A

That they are hollow in middle and this is water filled.

35
Q

What the size of Prion protein and what is it bound to?

A

208aa and membrane bound.

36
Q

Is prion protein self propagating and what does this mean?

A

Yes - can convert normal cellular prion protein to scrapie protein.

37
Q

Give examples of diseases caused by Prion gene mutation?

A

Familial CJD

Fatal familial insomnia.

38
Q

Do IDPs have a large number of minimum energy conformations?

A

Yes.

39
Q

What are the main properties of IDPs?

A

Tend to be charged with low hydrophobicity - this drives folding.

40
Q

Why is not good to crystallise IDPs?

A

Even if possible would only be viewing one possible conformation.

41
Q

What can be used to monitor IDPs?

A

NMR.

42
Q

Can IDPs have residual secondary structure?

A

Yes - partial alpha helix, partial beta strand, partial poly-proline helix.

43
Q

What type of helix is a poly proline helix?

A

Left handed helix - makes turn every 3 residues - pro every 3 residues.

44
Q

What does NMR spectra of IDPs look like?

A

Limited dispersion - sharp peaks (long T2 - has little dipolar coupling as is unfolded).

MSF1 (12 decks)

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