Protein folding Flashcards
What does a sigmoid curve tell us about the mechanism?
That it is cooperative
Why do secondary structures happen before tertiary structures?
Because they are closer together
What structure does the folding start with?
Primary to secondary
What is progressive stabilisation?
You start with interaction of amino acids that are very close and then go on from there so it’s progressive
What is the native structure of a protein?
The active structure which is found in for example the body and is working
Where is there more entropy ? in a folded of unfolded protein?
Unfolded because there is more disorder
Is there any entropy in the native/folded protein?
Yes but very little as it is very ordered
What are the interaction occurring in proteins to form?
Hydrogen bonds,
Hydrophobic interaction (most important)
Disulphide bonds (second most important)
Hydrophilic interaction
Can we predict structure folding based on entropy?
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
What is the main driving force of protein folding?
That the proteins are emerged in water and therefor have hydrophobic interactions
Why are disulphide bonds so important?
Because it makes it more difficult to denature protein with heat
What does Leinthal’s paradox say ?
Mathematically impossible for protein folding to occur by random trying every confirmation until lowest energy is found -> it is not random
Are there formation of intermediates in protein folding?
Yes
When is a reaction favorable, when ^G is positive or negative?
Negative
What is chain conformational entropy?
Entropy of the unfolded chain
When considering entropy and enthalpy (thermodynamics) which protein is more favoured? Folded or unfolded
From a thermodynamic point of view the folded protein is favorable because it’s ^G is negative
What is the ^G in the unfolding process compared to the folding process?
Positive, therefor it is not favoured
Does the hydrophobic effect have an effect on entropy?
Yes because it causes folding and thus decreases chaos
Does enthalpy decrease or increase when the protein is folded?
Increase
What does heat disrupt in a protein?
The hydrogen bonds
Can denaturing be reversible?
Yes but not always
In most enzymes yes but not in all (complex proteins are hard to reverse denaturing)
What are the 4 denaturing agents?
Heat
pH (extreme values)-> effects the charge
Detergents (Sodiumdisulphate)
Reagents (from H bonds competing the bonds in the protein)
What kind of primary bond makes denaturing unlikely to be reversible
Primarily disulphide it is unlikely to reversible denaturation
Does denaturing effect the primary structure?
No
What are the molecules (proteins) that help the folding?
Chaperones
What is the ubiquitin-proteasome system?
System that eliminates products produced by misfolding
What does failing to eliminate proteins that are misfolded result in?
Condition called amyloidosis where there are accumulation of amyloid fibrils (beta structures) which interact and form a big accumulation of waste
What is proteostasis?
Protein homestasis, continual maintenance of the active set of cellular proteins required under a given set of conditions
What is proteolysis?
Protein degradation, cut into pieces
What is the role of the proteostasis network?
Prevent the formation of toxic aggregates
Why are aggregates toxic?
They can form pores in the membrane
Deform membranes
What counteracts aggregates?
Chaperones
What happens to concentration of chaperones with age?
It decreases
What is renaturation of protein?
Proteins reforming after being denatured
What is assisted folding?
Proteins assisted by chaperones and chaperonins in their folding
For which proteins are chaperonins required by?
Proteins that don’t fold spontaneously
How do chaperones work?
They are barrelled shaped and therefor push the amino acids close together, helping them form bonds
What are some diseases resulted by misformed proteins?
Alzheiemer’s
Parkinson’s
Mad cow disease (prion)
Transthyretin amyloidosis
What are abnormal prions?
Prions are misfolded protein with the ability to transmit their misfolded shape onto normal variants of the same proteins
What is the normal prion called?
PrPc
What is the abnormal prion called?
PrPSc
Example of amyloidose diseases
Type 2 diabetes
Alzheimer’s
Huntington
Parkinson’s
What are amyloid fibers?
Protein secreted in a misfolded state and converted to an insoluble extracellular fiber
Do the functional groups in proteins play a role in the folding?
Yes
What do proteins fold into?
A stable conformation that promotes favorable, non covalent interactions between the secondary structure elements, the R groups and water
Where are hydrophobic R groups found?
On the interior of the protein (they are shielded from water there)
Where are hydrophilic R groups found?
On the surface where they bond with water
What happens if proteins are not folded properly?
It becomes toxic, accumulates and often lead to disease
Is folding random?
No
Why can heat denature proteins?
Because it interferes with interaction forces holding the protein together which causes denaturing
4 example of things that can denature proteins
Heat
pH
Detergents
Reagents
Can disulfide bonds be broken down?
Yes
By what does protein folding occur?
Progressive stabilisation
What does the folding funnel depict?
Thermodynamics of protein folding
What is the entropy at the top of the folding funnel?
Max
What is the structure of the protein at the top of the folding funnel?
Minimal
Where on the folding funnel are the folded proteins found?
Bottom
What are most neurological diseases characterised by?
Neuronal cells no longer being able to get rid of garbage
What folds first?
Local secondary structures
What plays an important role in local secondary structure folding?
Ionic interactions
What plays an important role in longer range structure folding?
Hydrophobic effect
Where does Hsp 70 bind?
Hydrophobic regions
3 chaperone
Hsp70
Hsp60
Chaperonins
What does Hsp stand for?
Heat shock proteins
What does Hsp70 have an essential role in?
Protein folding, disaggregation and degradation
How does Hsp60 help with protein folding?
It is shaped as a barrel wherein the protein is help until it is folded
Where does amyloids occur?
Brain
Liver
Pancreas
Is it a problem if the mutation of the protein occurs in the random coil?
No
Is it a problem if the mutation of the protein occurs in the active site?
Yes
What are senile plaques?
Bigger in size aggregates which distort nerve ramifications
What kind of disease is cystic fibrosis?
Genetic disease
What is cystic fibrosis caused by?
The malfunction of a chloride channel (cystic fibrosis transmembrane conductance regulator)
What does misfolded beta amyloid promote?
Aggregation, forming an amyloid fibril
2 reasons for mutations
DNA fails to copy accurately
External influences (chemicals, radiation or so on)
What can a lack of vitamin K lead to?
Haemorrhaging
Why can lack of vitamin K lead to haemorrhaging?
Because it prevents carboxylation of clotting proteins
4 common covalent modifications of amino acid side chains
Hydroxyproline
Gamma carboxyglytamate
Carbohydrate-asparagine adduct
Phosphoserine
