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Biochemistry > Protein folding and stability > Flashcards

Protein folding and stability Flashcards

Hydrogen bonds, disulphide bonds, ribonuclease refolding, interactions.

1
Q

Cystic fibrosis involves misfolding and resulting lack of a protein involved in chloride ion transport across membranes.
Many neurodivergence disorders involve abnormal protein…

A

Aggregation.

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2
Q

List a few of these neurodivergence disorders.

A

Prion diseases (creutzfeldt-Jakob disease)
Alzheimer’s disease
Parkinson’s disease

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3
Q

How are toxic aggregates formed?

A

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

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4
Q

How are proteins held together?

A

By an accumulation of weak forces.

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5
Q

Why are proteins described as only marginally stable?

A

They are not that much more stable than their unfolded states.

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6
Q

How are proteins normally denatured?

A

By extremes of pH (most only stable from pH 5-9).
By high temperatures.

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7
Q

Proteins are not usually stable in organic solvents.
Why?

A

This strips essential water.

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8
Q

What is protein folding based on?

A

Primary structure.

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9
Q

Protein folding is difficult to accurately predict based on…

A

Amino acid sequence.

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10
Q

What kind of a process is protein folding?

A

equilibrium

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11
Q

How do proteins fold?

A

To their most energetically favourable conformation and spontaneously.

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12
Q

What external factor has a major role in folding proteins?

A

The solvent.

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13
Q

When is a protein’s contact with the solvent maximal?

A

In unfolded states.

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14
Q

List all the forces and interactions that stabilise the 3D structure of proteins.

A
  • hydrophobic interactions
  • ionic interactions
  • van der waals interactions
  • hydrogen bonds
  • disulphide bonds
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15
Q

Why do proteins tend to be quite stable if they have disulphide bonds?

A

These are the only covalent interactions.

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16
Q

Why are hydrophobic amino acids found inside of globular proteins? Why do pro

A

They repel water.

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17
Q

Hydrophobic amino acids have side chains that are…

A

non-polar.

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18
Q

What kind of core do proteins usually have?

A

Hydrophobic

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19
Q

When do clathrate structures of water molecules form?

A

During the hydrophobic effect water molecules form a cage like structure when they hydrogen bond with each other but (oil) droplets limit hydrogen bonds.

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20
Q

What does protein folding do for hydrophobic residues?

A

Minimises the contact with water for the hydrophobic residues.

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21
Q

What is a salt bridge?

A

Bonds between oppositely charged residues that are sufficiently close to each other to experience electrostatic attraction.

For instance, an amino acid with a positive side chain can form an ionic bond with an amino acid with a negative side chain.

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22
Q

For an ionic bond to form, it requires the removal of a…

A

solvation shell (where water molecules meet the polypeptide).

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23
Q
A
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24
Q

Why?

A

To offset (balance) energy liberated (set free) when bond is made.

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25
Q

What are van der Waals interactions?

A

Non-covalent interactions between electrically neutral molecules arising from electrostatic interactions between permanent dipoles and/or instantaneous dipoles and/or induced dipoles.

26
Q

Describe the formation of London dispersion forces (a type of van der Waal interaction).

A

Chance charge separation creates an instantaneous dipole and a second molecule has a charge separation induced by the first molecule.
Positive side of first molecule attracted to negative side of second molecule.

27
Q

How do van der Waals forces compare with ionic interactions within a protein?

A

Much weaker (but there are many of them within a protein).

28
Q

Interactions have a positive component and a…

A

negative component.

29
Q

What happens when molecules get too close?

A

Electron clouds repel.

30
Q

What is the van der Waals distance?

(If confused, look at PowerPoint).

A

The optimal distance between 2 atoms.

31
Q

What is the net force a result of?

A

The Leonard-Jones potential (energy = A/r^12 - B/r^6).

r^-12 = repulsive energy
r^-6 = attractive energy

32
Q

How do you find the optimal distance on a graph?

A

Distance (in angstroms) from 0 to when net energy (in kcal/mol) line reaches lowest energy point on graph.

33
Q

What determines the optimal van der Waals radius?

A

Attractive and repulsive forces.

34
Q

Order the following van der Waals forces in terms of strength.

A

interactions between permanent dipoles > dipole-induced dipole interactions > London dispersion forces

35
Q

What can maximise van der Waal interactions between atoms?

A

optimal packing

36
Q

What are hydrogen bonds?

A

Electrostatic interactions between a weakly acidic donor, D, group (hydrogen partially letting go of) and an acceptor atom, A, that bears a lone pair of electrons.

37
Q

In a hydrogen bond, the hydrogen atom is sandwiched between…

A

two electronegative atoms (usually O or N).

38
Q

There are many hydrogen bonds in alpha-helices and beta-sheets.

What is the ideal bond length?

A

2.7 - 3.1 Å

39
Q

How many residues is an alpha helix turn?

A

3.6

40
Q

What is the pitch distance of an alpha helix (the distance the helix rises along its axis per turn)?

A

5.4 Å

41
Q

How is hydrogen bonding arranged in a helix to result in the optimal length 2.8 Å?

A

The peptide C=O group of the nth residue points along the helix towards the peptide N-H group of the (n+4)th residue.

42
Q

Where do the R-groups point in an alpha helix?

A

outwards

43
Q

Any molecules that can form hydrogen bonds with each other can from hydrogen bonds with…

A

water molecules.

44
Q

Due to competition with water molecules, the hydrogen bonds formed between two molecules dissolved in water are relatively…

A

weak.

45
Q

What are disulphide bonds?

A

Covalent bonds between two cysteine amino acids in the protein chain.

Only covalent bond found to hold protein in its correct fold.

46
Q

What kind of proteins are disulphide bonds mainly found in?

A

Proteins which are exported from the cell and have to be stable at high temperatures.

47
Q

Although some forces may be strong, why do they only make weak contributions to protein stability in the unfolded state?

A

Similar strength interactions are made with the solvent.

48
Q

When are hydrophobic forces exposed to the solvent and shielded from the solvent?

A

Exposed = unfolded.
Shielded = folded.

49
Q

When are charged groups solvated (interact with solvent) in the protein?

A

In the proteins unfolded state.

50
Q

What happens to charged groups in the folded state of a protein?

A

Ionic bonds form within the protein.

51
Q

What do van der Waals forces form between in terms of proteins in their folded and unfolded states?

A

Unfolded = protein and water.
Folded = within protein.

52
Q

What do hydrogen bonds form between in terms of proteins in their folded and unfolded states?

A

Unfolded = protein and water.
Folded = within protein.

53
Q

When are disulphide bonds present in terms of the state of a protein?

A

Only present in protein’s folded state.

54
Q

Who conducted the ribonuclease refolding experiment?

A

Christian B. Anfinsen

55
Q

What was the ribonuclease refolding experiment?

A

When beta-mercaptoethanol and urea are added, the ribonuclease is denatured so there is no enzymatic activity.

When beta-mercaptoethanol and urea were slowly removed, the protein refolded and correct disulphide bonds reformed giving 100% activity.

When only beta-mercaptoethanol was removed, cysteines formed random disulphides and upon subsequent removal of urea approximately 1% of activity is restored.

56
Q

How many cysteines are in ribonuclease?

A

8

57
Q

Using the question above, where does the 1% come from?

(If confused, look at summary sheet).

A

1/7 x 1/5 x 1/3 x 1/1 = 1/105 ~ 1%

58
Q

Correct protein folding is helped in the cell by proteins called…

A

chaperonins.

59
Q

Why do chaperonins exist if proteins can fold spontaneously?

A

To stop proteins aggregating with other unfolded proteins (not to tell proteins how to fold).

60
Q

What is the Levinthal paradox?

A

Finding the native folded state of a protein by a random search among all possible configurations.

This would take longer than the apparent age of the universe.

61
Q

How long does it take for a protein to fold?

A

Less than or equal to seconds.

62
Q

How do proteins fold to native conformations?

A

By directed pathways rather than random search methods.

The protein forms secondary structure elements to make a core.

Biochemistry (10 decks)

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