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biomedical biochemistry > protein folding > Flashcards

protein folding Flashcards

1
Q

what was bovine spongiform encephalopathies commonly known as?

A

mad cows disease

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2
Q

when was mad cows disease a public health issue?

A

1990’s

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3
Q

what were the symptoms of BSE?

A

cattle would exhibit abnormal behaviour
couldnt mobilise
hind legs would give way

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4
Q

what was the onset of symptoms to death time period of BSE?

A

weeks to months

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5
Q

what was creutzfeldt-jakob disease?

A

human form of BSE

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6
Q

what was the median age of onset of creutzfeldt-jakob disease?

A

68

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7
Q

what was variant CJD?

A

resembled BSE

had a lower age of onset compared to CJD and had a longer illness duration

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8
Q

what was Kuru?

A

a fatal neurodegenerative disorder similar vCJD

shaking disorder

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9
Q

who was affected by Kuru?

A

a group of indigenous people in Papa New Guinea

women and children

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10
Q

when was Kuru an issue?

A

1950’s

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11
Q

why do proteins need to fold?

A

to assume active, functional conformation
folded proteins more stable
folded structure determines function

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12
Q

what experiment did Christian Anfinsen conduct?

A

renaturation experiments with RNase
denatured proteins with heat and reducing agents and then incubated the unfolded proteins under milder conditions
yeild of spontaneous refolding was more than 90%

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13
Q

what was the key conclusion of the Anfinsen experiments?

A

demonstrated that proteins encode all the information neccessary to fold
no cellular mechanisms are needed
3D conformation is determined by amino acid sequence

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14
Q

how can the configuration of a protein be changed?

A

only by breaking of covalent bonds

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15
Q

how can the conformation of a protein be changed?

A

by rotating the bonds

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16
Q

what is the meaning of an L isomer amino acid?

A

an amino acid that has a non superimposable mirror image counterpart

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17
Q

what is the name of the graph that can be used to determine the angles of rotation in an amino acid?

A

ramachandran plot

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18
Q

what are the names of the two torsion angles present in an amino acid?

A

phi and psi

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19
Q

what kind of bond characteristic does a peptide bond possess?

A

double bond characteristic

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20
Q

what is a trans isomer?

A

R groups are on opposite sides of the peptide bond

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21
Q

what is a cis isomer?

A

R groups are on the same side of the peptide bond

22
Q

what is a steric clash? which isomer induces these?

A

the unnatural overlapping of two non-bonding atoms in a protein structure
induced by cis isomers

23
Q

what is the hydrophobic collapse also known as?

A

the hydrophobic effect

24
Q

what is the hydrophobic collapse?

A

the tendency for hydrophobic molecules to isolate themselves from contact with water
as a result hydrophobic side chains tend to become buried in the interior of the protein

25
Q

what causes the hydrophobic effect to come about?

A

the increasing entropy of surrounding aqueous environment as non-polar molecules interact and cluster

26
Q

what stabilises the final protein structure?

A

hydrophobic effect
hydrogen bonds
salt bridges

27
Q

what can cause proteins to unfold?

A

extremes of pH

increased temperature

28
Q

what are examples of protein denaturants?

A

sodium dodecyl sulphate
urea
guanidine
organic solvents

29
Q

how does sodium dodecyl sulphate act as a denaturant?

A

disrupts the hydrophobic core and non-covalent interactions increasing the negative charge of the polypeptide

30
Q

how does guanidine act as a denaturant?

A

disrupts hydrogen bonding of water and deminishes the hydrophobic effect

31
Q

how do organic solvents act as a denaturant?

A

changes solubility of hydrophobic side chains

32
Q

how can you detect the difference between folded and unfolded proteins?

A

conduct aliquots of refolding mixture and assay them and measure activity of proteins as they refold

measure fluorescence, enhanced fluorescence in unfolded proteins

33
Q

what are the functions of chaperones?

A

facilitate folding
prevent aggregation
stabilize non-native conformations

34
Q

what are the functions of small heat shock proteins?

A

holders

protect against cellular stress

35
Q

what are the functions of Hsp 60 chaperones?

A

protein folding in chloroplasts and mitochondria

for difficult to fold proteins

36
Q

what are the functions of Hsp 70 chaperones?

A

stabilization of extended chains
membrane translocation
regulation of heat shock response

37
Q

what is an example of a Hsp 70 chaperone?

A

BiP

38
Q

what are the steps of the chaperonin cycle?

A
  1. improperly folded protein binds to cis ring
  2. cap associates causing a conformational change. the cis ring is bigger so proteins begin to refold. there is a weakened interaction between GroES cap and GroEL
  3. second improperly folded protein binds to trans ring
  4. cis ring releases GroES cap along with better folded protein
  5. chamber rotates 180 degrees, trans ring becomes cis ring and the process restarts
39
Q

what are type one protein misfolding diseases?

A

inability to fold
partial proteins sent for degradation but there is improper degradation
results in a lack of functioning protein

40
Q

what are type two protein folding diseases?

A

toxic folding

misfolding produces a conformation with toxic properties

41
Q

what are type three protein folding diseases?

A

due to improper trafficking
incorrectly sorted
misfolding causes mislocation of protein

42
Q

what are examples of type one protein folding diseases?

A

Cystic Fibrosis
Marfan syndrome
Gauchers disease

43
Q

what are examples of type two protein folding diseases?

A

APOE4 allele, associated with Alzheimers disease. It is a polymorphic version of the APOE gene which plays a role in brain injury repair

44
Q

what are examples of type three protein folding diseases?

A

alpha anti trypsin deficiency, mutant form is misfolded and retained in the ER in hepatocytes so the lung cant be protected from protease damage and accumulation in the hepatocytes causes liver damage

45
Q

what causes protein aggregation?

A

a change in pH or temperature

46
Q

why do beta sheets cause aggregation?

A

when parallel sheets line up there are lots of hydrogen bond acceptors and donors on the edges
this association promotes aggregation

47
Q

what is responsible for CJD?

A

normal prion protein acquires a different conformation producing amyloid prion proteins
these contain more beta sheets which promote aggregation and cause brain damage
prion proteins can bind to other proteins and change them

48
Q

how are amyloid fibrils formed?

A

native prion proteins start to aggregate to from long strands

49
Q

which area of the brain does BSE effect?

A

brain stem

50
Q

which area of the brain does CJD effect?

A

cerebral cortex

51
Q

which area of the brain does Kuru effect?

A

cerebellum

biomedical biochemistry (7 decks)

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