protein folding

Question 1

what was bovine spongiform encephalopathies commonly known as?

Answer 1

mad cows disease

Question 2

when was mad cows disease a public health issue?

Answer 2

1990’s

Question 3

what were the symptoms of BSE?

Answer 3

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

Question 4

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

Answer 4

weeks to months

Question 5

what was creutzfeldt-jakob disease?

Answer 5

human form of BSE

Question 6

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

Answer 6

68

Question 7

what was variant CJD?

Answer 7

resembled BSE

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

Question 8

what was Kuru?

Answer 8

a fatal neurodegenerative disorder similar vCJD

shaking disorder

Question 9

who was affected by Kuru?

Answer 9

a group of indigenous people in Papa New Guinea

women and children

Question 10

when was Kuru an issue?

Answer 10

1950’s

Question 11

why do proteins need to fold?

Answer 11

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

Question 12

what experiment did Christian Anfinsen conduct?

Answer 12

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%

Question 13

what was the key conclusion of the Anfinsen experiments?

Answer 13

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

Question 14

how can the configuration of a protein be changed?

Answer 14

only by breaking of covalent bonds

Question 15

how can the conformation of a protein be changed?

Answer 15

by rotating the bonds

Question 16

what is the meaning of an L isomer amino acid?

Answer 16

an amino acid that has a non superimposable mirror image counterpart

Question 17

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

Answer 17

ramachandran plot

Question 18

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

Answer 18

phi and psi

Question 19

what kind of bond characteristic does a peptide bond possess?

Answer 19

double bond characteristic

Question 20

what is a trans isomer?

Answer 20

R groups are on opposite sides of the peptide bond

Question 21

what is a cis isomer?

Answer 21

R groups are on the same side of the peptide bond

Question 22

what is a steric clash? which isomer induces these?

Answer 22

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

Question 23

what is the hydrophobic collapse also known as?

Answer 23

the hydrophobic effect

Question 24

what is the hydrophobic collapse?

Answer 24

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

Question 25

what causes the hydrophobic effect to come about?

Answer 25

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

Question 26

what stabilises the final protein structure?

Answer 26

hydrophobic effect hydrogen bonds salt bridges

Question 27

what can cause proteins to unfold?

Answer 27

extremes of pH | increased temperature

Question 28

what are examples of protein denaturants?

Answer 28

sodium dodecyl sulphate urea guanidine organic solvents

Question 29

how does sodium dodecyl sulphate act as a denaturant?

Answer 29

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

Question 30

how does guanidine act as a denaturant?

Answer 30

disrupts hydrogen bonding of water and deminishes the hydrophobic effect

Question 31

how do organic solvents act as a denaturant?

Answer 31

changes solubility of hydrophobic side chains

Question 32

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

Answer 32

conduct aliquots of refolding mixture and assay them and measure activity of proteins as they refold measure fluorescence, enhanced fluorescence in unfolded proteins

Question 33

what are the functions of chaperones?

Answer 33

facilitate folding prevent aggregation stabilize non-native conformations

Question 34

what are the functions of small heat shock proteins?

Answer 34

holders | protect against cellular stress

Question 35

what are the functions of Hsp 60 chaperones?

Answer 35

protein folding in chloroplasts and mitochondria | for difficult to fold proteins

Question 36

what are the functions of Hsp 70 chaperones?

Answer 36

stabilization of extended chains membrane translocation regulation of heat shock response

Question 37

what is an example of a Hsp 70 chaperone?

Answer 37

BiP

Question 38

what are the steps of the chaperonin cycle?

Answer 38

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

Question 39

what are type one protein misfolding diseases?

Answer 39

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

Question 40

what are type two protein folding diseases?

Answer 40

toxic folding | misfolding produces a conformation with toxic properties

Question 41

what are type three protein folding diseases?

Answer 41

due to improper trafficking incorrectly sorted misfolding causes mislocation of protein

Question 42

what are examples of type one protein folding diseases?

Answer 42

Cystic Fibrosis Marfan syndrome Gauchers disease

Question 43

what are examples of type two protein folding diseases?

Answer 43

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

Question 44

what are examples of type three protein folding diseases?

Answer 44

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

Question 45

what causes protein aggregation?

Answer 45

a change in pH or temperature

Question 46

why do beta sheets cause aggregation?

Answer 46

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

Question 47

what is responsible for CJD?

Answer 47

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

Question 48

how are amyloid fibrils formed?

Answer 48

native prion proteins start to aggregate to from long strands

Question 49

which area of the brain does BSE effect?

Answer 49

brain stem

Question 50

which area of the brain does CJD effect?

Answer 50

cerebral cortex

Question 51

which area of the brain does Kuru effect?

Answer 51

cerebellum