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Biochemistry > Protein folding > Flashcards

Protein folding Flashcards

1
Q

What does a sigmoid curve tell us about the mechanism?

A

That it is cooperative

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2
Q

Why do secondary structures happen before tertiary structures?

A

Because they are closer together

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3
Q

What structure does the folding start with?

A

Primary to secondary

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4
Q

What is progressive stabilisation?

A

You start with interaction of amino acids that are very close and then go on from there so it’s progressive

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5
Q

What is the native structure of a protein?

A

The active structure which is found in for example the body and is working

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6
Q

Where is there more entropy ? in a folded of unfolded protein?

A

Unfolded because there is more disorder

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7
Q

Is there any entropy in the native/folded protein?

A

Yes but very little as it is very ordered

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8
Q

What are the interaction occurring in proteins to form?

A

Hydrogen bonds,
Hydrophobic interaction (most important)
Disulphide bonds (second most important)
Hydrophilic interaction

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9
Q

Can we predict structure folding based on entropy?

A

If entropy is decreasing then the protein is folding in the right way. If it folds in a wrong way it won’t decrease that much

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10
Q

What is the main driving force of protein folding?

A

That the proteins are emerged in water and therefor have hydrophobic interactions

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11
Q

Why are disulphide bonds so important?

A

Because it makes it more difficult to denature protein with heat

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12
Q

What does Leinthal’s paradox say ?

A

Mathematically impossible for protein folding to occur by random trying every confirmation until lowest energy is found -> it is not random

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13
Q

Are there formation of intermediates in protein folding?

A

Yes

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14
Q

When is a reaction favorable, when ^G is positive or negative?

A

Negative

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15
Q

What is chain conformational entropy?

A

Entropy of the unfolded chain

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16
Q

When considering entropy and enthalpy (thermodynamics) which protein is more favoured? Folded or unfolded

A

From a thermodynamic point of view the folded protein is favorable because it’s ^G is negative

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17
Q

What is the ^G in the unfolding process compared to the folding process?

A

Positive, therefor it is not favoured

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18
Q

Does the hydrophobic effect have an effect on entropy?

A

Yes because it causes folding and thus decreases chaos

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19
Q

Does enthalpy decrease or increase when the protein is folded?

A

Increase

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20
Q

What does heat disrupt in a protein?

A

The hydrogen bonds

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21
Q

Can denaturing be reversible?

A

Yes but not always
In most enzymes yes but not in all (complex proteins are hard to reverse denaturing)

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22
Q

What are the 4 denaturing agents?

A

Heat
pH (extreme values)-> effects the charge
Detergents (Sodiumdisulphate)
Reagents (from H bonds competing the bonds in the protein)

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23
Q

What kind of primary bond makes denaturing unlikely to be reversible

A

Primarily disulphide it is unlikely to reversible denaturation

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24
Q

Does denaturing effect the primary structure?

A

No

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25
Q

What are the molecules (proteins) that help the folding?

A

Chaperones

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26
Q

What is the ubiquitin-proteasome system?

A

System that eliminates products produced by misfolding

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27
Q

What does failing to eliminate proteins that are misfolded result in?

A

Condition called amyloidosis where there are accumulation of amyloid fibrils (beta structures) which interact and form a big accumulation of waste

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28
Q

What is proteostasis?

A

Protein homestasis, continual maintenance of the active set of cellular proteins required under a given set of conditions

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29
Q

What is proteolysis?

A

Protein degradation, cut into pieces

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30
Q

What is the role of the proteostasis network?

A

Prevent the formation of toxic aggregates

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31
Q

Why are aggregates toxic?

A

They can form pores in the membrane
Deform membranes

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32
Q

What counteracts aggregates?

A

Chaperones

33
Q

What happens to concentration of chaperones with age?

A

It decreases

34
Q

What is renaturation of protein?

A

Proteins reforming after being denatured

35
Q

What is assisted folding?

A

Proteins assisted by chaperones and chaperonins in their folding

36
Q

For which proteins are chaperonins required by?

A

Proteins that don’t fold spontaneously

37
Q

How do chaperones work?

A

They are barrelled shaped and therefor push the amino acids close together, helping them form bonds

38
Q

What are some diseases resulted by misformed proteins?

A

Alzheiemer’s
Parkinson’s
Mad cow disease (prion)
Transthyretin amyloidosis

39
Q

What are abnormal prions?

A

Prions are misfolded protein with the ability to transmit their misfolded shape onto normal variants of the same proteins

40
Q

What is the normal prion called?

A

PrPc

41
Q

What is the abnormal prion called?

A

PrPSc

42
Q

Example of amyloidose diseases

A

Type 2 diabetes
Alzheimer’s
Huntington
Parkinson’s

43
Q

What are amyloid fibers?

A

Protein secreted in a misfolded state and converted to an insoluble extracellular fiber

44
Q

Do the functional groups in proteins play a role in the folding?

A

Yes

45
Q

What do proteins fold into?

A

A stable conformation that promotes favorable, non covalent interactions between the secondary structure elements, the R groups and water

46
Q

Where are hydrophobic R groups found?

A

On the interior of the protein (they are shielded from water there)

47
Q

Where are hydrophilic R groups found?

A

On the surface where they bond with water

48
Q

What happens if proteins are not folded properly?

A

It becomes toxic, accumulates and often lead to disease

49
Q

Is folding random?

A

No

50
Q

Why can heat denature proteins?

A

Because it interferes with interaction forces holding the protein together which causes denaturing

51
Q

4 example of things that can denature proteins

A

Heat
pH
Detergents
Reagents

52
Q

Can disulfide bonds be broken down?

A

Yes

53
Q

By what does protein folding occur?

A

Progressive stabilisation

54
Q

What does the folding funnel depict?

A

Thermodynamics of protein folding

55
Q

What is the entropy at the top of the folding funnel?

A

Max

56
Q

What is the structure of the protein at the top of the folding funnel?

A

Minimal

57
Q

Where on the folding funnel are the folded proteins found?

A

Bottom

58
Q

What are most neurological diseases characterised by?

A

Neuronal cells no longer being able to get rid of garbage

59
Q

What folds first?

A

Local secondary structures

60
Q

What plays an important role in local secondary structure folding?

A

Ionic interactions

61
Q

What plays an important role in longer range structure folding?

A

Hydrophobic effect

62
Q

Where does Hsp 70 bind?

A

Hydrophobic regions

63
Q

3 chaperone

A

Hsp70
Hsp60
Chaperonins

64
Q

What does Hsp stand for?

A

Heat shock proteins

65
Q

What does Hsp70 have an essential role in?

A

Protein folding, disaggregation and degradation

66
Q

How does Hsp60 help with protein folding?

A

It is shaped as a barrel wherein the protein is help until it is folded

67
Q

Where does amyloids occur?

A

Brain
Liver
Pancreas

68
Q

Is it a problem if the mutation of the protein occurs in the random coil?

A

No

69
Q

Is it a problem if the mutation of the protein occurs in the active site?

A

Yes

70
Q

What are senile plaques?

A

Bigger in size aggregates which distort nerve ramifications

71
Q

What kind of disease is cystic fibrosis?

A

Genetic disease

72
Q

What is cystic fibrosis caused by?

A

The malfunction of a chloride channel (cystic fibrosis transmembrane conductance regulator)

73
Q

What does misfolded beta amyloid promote?

A

Aggregation, forming an amyloid fibril

74
Q

2 reasons for mutations

A

DNA fails to copy accurately
External influences (chemicals, radiation or so on)

75
Q

What can a lack of vitamin K lead to?

A

Haemorrhaging

76
Q

Why can lack of vitamin K lead to haemorrhaging?

A

Because it prevents carboxylation of clotting proteins

77
Q

4 common covalent modifications of amino acid side chains

A

Hydroxyproline
Gamma carboxyglytamate
Carbohydrate-asparagine adduct
Phosphoserine

78
Q
A

Biochemistry (28 decks)

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