Lecture 4

Question 1

entropy

Answer 1

measure of the different ways something can be arranged

Question 2

multiple protein conformational states favour or disfavour folding? and why?

Answer 2

disfavour
unfolded state = many conformations = high entropy = favourable

Question 3

does a folded or unfolded protein have higher energy?

Answer 3

unfolded

Question 4

what does the formation of weak bonds release?

Answer 4

energy

Question 5

does the formation of new weak interactions favour or disfavour folding? and why?

Answer 5

favour
as new hydrogen bonds are formed in protein - new van der waal interactions are made

Question 6

does the hydrophobic effect favour or disfavour folding? and why?

Answer 6

favour
during protein folding hydrophobic side chains go inside protein

Question 7

when water around the protein is fluid, is entropy high/low and is this state favoured/unfavored

Answer 7

high
favoured

Question 8

protein creation steps
(native protein –> ________ protein —–> misfolded protein —–> _______ —–> amorphous aggregate/protofibrils —–> ______)

Answer 8

native protein —-> unfolded protein —-> misfolded protein —> oligomers —-> amorphous aggregate/protofibrils —–> fibrils

Question 9

what are metamorphic protein?

Answer 9

low energy barriers and signalling molecules in immune system

Question 10

protein creation steps
(_________ protein —-> unfolded protein —-> _________ protein —> oligomers —-> _________ ________/___________ —–> fibrils )

Answer 10

native protein –> ________ protein —–> misfolded protein —–> _______ —–> amorphous aggregate/protofibrils —–> ______

Question 11

when normal proteins fold do they attain low or high energy?

Answer 11

low

Question 12

pH ___ pKa = predominantly the protonated form

pH ___ pKa = 50/50 mixture of protonated and deprotonated

pH ___ pKa = predominantly deprotonated)

Answer 12

pH<pKa = predominantly the protonated form

pH=pKa = 50/50 mixture of protonated and deprotonated

pH>pKa = predominantly deprotonated)