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BIO1332 - Biochemistry > Protein Folding and Stability > Flashcards

Protein Folding and Stability Flashcards

1
Q

What can defects in protein folding cause?

A

Diseases

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2
Q

What is an example of disease resulted from a misfolding and resulting in lack of protein involved in Cl- transport across membrane?

A

Cystic fibrosis

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3
Q

Give three examples of neurodegenerative disorder abnormal protein
aggregation:

A

-Prion diseases (e.g.Creutzfeldt-
Jakob disease)
-Alzheimer’s disease
-Parkinson’s disease

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4
Q

What are toxic aggregates?

A

Partly folded or misfolded polypeptides or fragments may sometimes associate with similar chains

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5
Q

How stable is a protein?

A

Marginally stable

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6
Q

Why is proteins marginally stable?

A

accumulation of week forces

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7
Q

When do proteins denature in respect to pH?

A

At extreme pH levels

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8
Q

When do proteins denature in respect to temperature?

A

High temperature

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9
Q

Why are proteins not usually stable in organic solvents?

A

Strips the essential water

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10
Q

Why is protein folding an equilibrium process?

A

Fold to their energetically most favourable conformation

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11
Q

What interaction plays a major role in the folding of proteins?

A

With a solvent as contact with the solvent is maximal in the inflated states

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12
Q

What are the five forces which stabilise 3D protein structure?

A
  • Hydrophobic interactions
  • Ionic interactions
  • Van der Waals interactions
  • Hydrogen bonds
  • Disulfide bridges
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13
Q

What causes hydrophobic interactions?

A

the side chains of amino acids are hydrophobic

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14
Q

Where do you find hydrophobic interactions?

A

Inside globular proteins

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15
Q

What causes side chains to be hydrophobic?

A

They have a methyl group

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16
Q

Describe the clathrate model:

A
  • Water molecules surround the non-polar solvent in an ordered network
  • Causing an entropic penalty making system want to cause maximal disorder
  • aggrevating the non-polar molecule to become a bigger molecule
  • This frees up water molecules
  • No entropically favourable
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17
Q

What does hydrophobic interactions cause the protein to do?

A

Unfolded proteins become more folded

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18
Q

What is ionic interactions?

A

electrostatic interactions between a positive charged amino acid and a negative charged amino acid

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19
Q

Is there a set number to how many ionic interactions can be occurring?

A

No there could be a single or multiple cluster of interactions occurring

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20
Q

What is a van der Waals interaction?

A

Non-covalent interactions between neutral molecules and permanent or induced dipoles

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21
Q

Which is weaker ionic or van der Waals interactions?

A

Van der Waals

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22
Q

What must there be in order to have a van der Waals interactions?

A

positive and negative components

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23
Q

What determines the optimal van der Waals radius?

A

The attractive and repulsive forces

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24
Q

Finish the sentence: The optimal distance between the two atoms is described as?

A

Van der Waals distance

25
Finish the sentence: | The more compact (folded) a protein the more...
Van der Waals interactions
26
What is a hydrogen bond?
Electrostatic interaction between a weakly acidic donor group and accepter atom which has a lone pair of electrons
27
What is the ideal bond length of hydrogen bond?
2.7 to 3.1 A
28
When to amino acids react what is produced?
dipeptide and two water molecules
29
What are the three types of van der Waals interactions?
- interactions between permeant dipoles - Interaction between dipole-induced dipole interaction - London forces
30
What is a disulfide bond?
Conalent bond between two cysteine amino acids in a protein chain
31
Which out of the five different forces in protein correctly folds protein chains?
Disulfide bonds
32
Where do you find disulfide bonds?
- Proteins exported from the cell | - Proteins which need to be stable at high temperatures
33
Are a disulfide bridge and disulfide bond the same thing?
No
34
What is a disulfide bridge?
A cystine
35
What happens to hydrophobic interactions if protein is unfolded?
Exposed to solvent
36
What happens to hydrophobic interactions if protein is folded?
Shielded from solvent
37
What happens to ionic interactions if protein is unfolded?
Charged groups are solvated
38
What happens to ionic interactions if protein is folded?
Ionic bonds formed in protein
39
What happens to van der Waals interactions if protein is unfolded?
Protein with water
40
What happens to van der Waals interactions if protein is folded?
Protein with protein
41
What happens to disulfide bonds interactions if protein is unfolded?
Not present
42
What happens to disulfide bonds interactions if protein is folded?
Present
43
What happens to hydrogen bonds interactions if protein is unfolded?
Protein with water
44
What happens to hydrogen bonds interactions if protein is folded?
Protein with protein
45
Can you predict the structure of a protein from primary sequence?
No
46
What is a general rule about proteins folding?
The fold spontaneously
47
What was the important findings from the Anfinsens's experiment?
That proteins fold for themselves
48
What was the first part of the Anfinsen's experiment?
β-mercaptoethanol AND urea were removed
49
What was the results of the first part of the Anfinsen's experiment?
The protein refolded and the correct disulphide bonds reformed. 100% activity.
50
What was the second part of the Anfinsen's experiment?
Only the β-mercaptoethanol was removed
51
What was the results of the second part of the Anfinsen's experiment?
The cysteines formed random disulphides. Upon subsequent removal of urea only 1% activity was restored.
52
What type of experiment is the Levinthal Paradox?
A thought exeperiment
53
Describe the Levinthal Paradox:
- Assume each amino acid has about 10 possible conformations - polypeptide of n amino acid then has 10^n possible conformations - assume that a protein could explore a new conformation every 10^-13 seconds - time = 10^n/10^13 - For a protein of 100 amino acids it would be 10^87 seconds
54
What is the conclusion about the folding of proteins from the Levinthal Paradox?
Proteins fold their native conformation by a directed pathway rather than a random search method
55
What does a chaperonins do?
Help proteins correctly fold in the cell
56
Do chaperonins directly fold the protein?
No
57
Are chaperonins assisting or directing the folding?
assisting
58
Finish the sentence: | A chaperon stops the aggregation and gives an isolated polypeptide chain a ....
space to fold on its own

BIO1332 - Biochemistry (19 decks)

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