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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
Q

Finish the sentence:

The more compact (folded) a protein the more…

A

Van der Waals interactions

26
Q

What is a hydrogen bond?

A

Electrostatic interaction between a weakly acidic donor group and accepter atom which has a lone pair of electrons

27
Q

What is the ideal bond length of hydrogen bond?

A

2.7 to 3.1 A

28
Q

When to amino acids react what is produced?

A

dipeptide and two water molecules

29
Q

What are the three types of van der Waals interactions?

A
  • interactions between permeant dipoles
  • Interaction between dipole-induced dipole interaction
  • London forces
30
Q

What is a disulfide bond?

A

Conalent bond between two cysteine amino acids in a protein chain

31
Q

Which out of the five different forces in protein correctly folds protein chains?

A

Disulfide bonds

32
Q

Where do you find disulfide bonds?

A
  • Proteins exported from the cell

- Proteins which need to be stable at high temperatures

33
Q

Are a disulfide bridge and disulfide bond the same thing?

A

No

34
Q

What is a disulfide bridge?

A

A cystine

35
Q

What happens to hydrophobic interactions if protein is unfolded?

A

Exposed to solvent

36
Q

What happens to hydrophobic interactions if protein is folded?

A

Shielded from solvent

37
Q

What happens to ionic interactions if protein is unfolded?

A

Charged groups are solvated

38
Q

What happens to ionic interactions if protein is folded?

A

Ionic bonds formed in protein

39
Q

What happens to van der Waals interactions if protein is unfolded?

A

Protein with water

40
Q

What happens to van der Waals interactions if protein is folded?

A

Protein with protein

41
Q

What happens to disulfide bonds interactions if protein is unfolded?

A

Not present

42
Q

What happens to disulfide bonds interactions if protein is folded?

A

Present

43
Q

What happens to hydrogen bonds interactions if protein is unfolded?

A

Protein with water

44
Q

What happens to hydrogen bonds interactions if protein is folded?

A

Protein with protein

45
Q

Can you predict the structure of a protein from primary sequence?

A

No

46
Q

What is a general rule about proteins folding?

A

The fold spontaneously

47
Q

What was the important findings from the Anfinsens’s experiment?

A

That proteins fold for themselves

48
Q

What was the first part of the Anfinsen’s experiment?

A

β-mercaptoethanol AND urea were removed

49
Q

What was the results of the first part of the Anfinsen’s experiment?

A

The protein refolded and the correct disulphide bonds reformed. 100% activity.

50
Q

What was the second part of the Anfinsen’s experiment?

A

Only the β-mercaptoethanol was removed

51
Q

What was the results of the second part of the Anfinsen’s experiment?

A

The cysteines formed random disulphides. Upon subsequent removal of urea only 1% activity was restored.

52
Q

What type of experiment is the Levinthal Paradox?

A

A thought exeperiment

53
Q

Describe the Levinthal Paradox:

A
  • 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
Q

What is the conclusion about the folding of proteins from the Levinthal Paradox?

A

Proteins fold their native conformation by a directed pathway rather than a random search method

55
Q

What does a chaperonins do?

A

Help proteins correctly fold in the cell

56
Q

Do chaperonins directly fold the protein?

A

No

57
Q

Are chaperonins assisting or directing the folding?

A

assisting

58
Q

Finish the sentence:

A chaperon stops the aggregation and gives an isolated polypeptide chain a ….

A

space to fold on its own

BIO1332 - Biochemistry (19 decks)

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