protein folding and stability

Question 1

intermolecular forces integral to protein folding and stability

Answer 1

-h bonding -van der waals -ionic bonds -covalent bonds (disulphide) HIVd -hydrophobic interactions

Question 2

Van der Waals

Answer 2

non covalent interactions between eelctrostatically neutral molecules- they arise from electrostatic interactions between permanent dipoles -much weaker than ionic -no positive or negative component -if molecules get too close and electrons overlap repulsion will occur - in terms of VDW, the proteins have to be packed closely to ensure that as many VDW form as possible- this means that the structures aren’t hollow and they fold tightly

Question 3

why are proteins not hollow

Answer 3

so that as many intermolecular forces can form as possible e.g. optimal length in VDW will ensure that as many form as possible giving stability

Question 4

proteins are held together by fairly weak forces however..

Answer 4

it it the accumulation of all these forces which increase stability - no protein will fold correctly due to just one of the forces (accept possibly not disulphide bridges)

Question 5

proteins can be denatured because..

Answer 5

incorrect pH incorrect temp

Question 6

proteins are used to existing in water and do not like..

Answer 6

organic solvents

Question 7

proteins fold spontaneously because..

Answer 7

the native conformation is the most energetically stable

Question 8

example of disease due to a defect in protein folding

Answer 8

CF involves the misfiling of a protein and results in the lack of the protein that involves the CL- transport mem.

Question 9

proteins fold to their energetically most..

Answer 9

energetically stable conformation

Question 10

why do proteins fold

Answer 10

proteins do not like organic solvents- therefore when the protein is folded less surface area (contact residues) is exposed to the solvent

Question 11

what describes the change in proteins being in the folded state to the unfolded state

Answer 11

protein folding is an equilibrium process

Question 12

hydrophobic interaction

Answer 12

in some proteins the amino acid side chains hydrophobic - these groups like to be on the inside of globular proteins (on the inside of the folded structure) -hydrophobic amino acids have methyl groups e.g. alanine and isoleucine or side chain or ring structures eg. phenylalanine

Question 13

physical basis from hydrophobic effect

Answer 13

entropically unfavourable- water molecules dislike becoming ordered- therefore the interaction between water an oil is as minimal as possible e.g. drops of old come together to make bigger droplets and therefore have less contact wit water - less hate rmoecule scan fit around it

Question 14

hydrophobic effect is driven by..

Answer 14

entropy

Question 15

three types of VDW

Answer 15

1) london dispersion forces 2) dipole induced dipole interactions (stronger) 3) interaction between permanent dipoles (strongest)

Question 16

london dispersion forces

Answer 16

due to one group having a greater attraction to electrons than the other- just dealt charges ( e.g. oxygen being more electronegative than carbon)

Question 17

hydrogen bonding

Answer 17

electrostatic interactions between weakly acidic donor groups and acceptor atoms that bear a lone pari of electrons -many H bonds in alpha and beta pleated sheets -O or N any molecule that can form hydrogen bonds to each other can also bond with water- therefore H bonds are found within folded and non-folded proteins - therefor their effect is only marginal

Question 18

ideal H bond length

Answer 18

2.7-3.1 A

Question 19

H bonds only have a marginal effect because…

Answer 19

folded and unfolded proteins have H bonds

Question 20

ionic interactions

Answer 20

electrostatic interactions between -ve and +ve charge amino acid like lysine and arginine. Can be many or single interactions

Question 21

in ionic bonding water must be stripped, otherwise the molecules would be salvage day water and this has a price to pay:

Answer 21

enthalpically unfavourable- energy must be provided and this is relayed by the forming of thee ionic binds

Question 22

disulphide bridges

Answer 22

only covalent bonds involve in protein structure

• e.g. 2 cysteine produce cystine
• mainly found in proteins which are secreted
• not found in cytoplasm which is a reducing environment.
• proteins with disulphide binding are very stable

Question 23

what are disulphide bridges also called

Answer 23

cysteine residues

Question 24

strongest intermolecular force

Answer 24

disulphide bridges

Question 25

mechanism of protein folding: the levinthal paradox

Answer 25

Lets assume that each amino acid has approx 10 possible diff conformations- a polypeptide of n amino acid therefore has 10n possible conformation -if a protein could try every possible combination the time period of 10^-14 seconds. -the time for a protein of n residues to explore all of it conformations would take 10^13 seconds. Therefore for a protein of 100 amino acid this would take 10^87 second–> the age of the universe is only 10^18sec. Therefore impossible to try out all diff conformations

Question 26

why is it impossible of a protein to try out all its confrmatons

Answer 26

-the time for a protein of n residues to explore all of it conformations would take 10^13 seconds. Therefore for a protein of 100 amino acid this would take 10^87 second–> the age of the universe is only 10^18sec. Therefore impossible to try out all diff conformations

Question 27

evidence for protein folding being a directive process and not random

Answer 27

the levinthal paradox

Question 28

Afisens experiment

Answer 28

1. when B-mercatoethanol and urea were removed slowly the protein refolded and the correct disulphide bonds were reformed- 100% activity
2. however when the B-mecatoethanol was removed, the cysteine formed random disulphides. Upon subsequent removal of urea only 1% of activity was restored. Scrambled ribonuclease spontaneously refolds and the sequence dictates its structure. If you only removed B mercatoethanol there is only 1% chance it will reform correctly.
   - 1/105 is the odd of getting the right disulphide to reform. Only those proteins who had the right disulphide combination could function properly.
   - However if you added slightly more b-mecaptoethanol the disulphide bonds will be re-broken and then reform to give the correct conformation and therefore now the protein will have 100% activity

Question 29

chaperones and protein folding

Answer 29

if there are many unfolded molecules, they can join together, which would prevent them from being functional. Chaperones job is to stop this from happening. They give the unfolded protein a nice environment in which they can fold on their own, without giving any direction. it protects them from unfolded molecules with which they may aggravate with.

Question 30

many ionic interactions

Answer 30

multiple charges from different amino acids forming interactions together

Question 32

example of ionic interaction between two amino acids

Answer 32

lysince and arginine

Question 33

cystine residues are formed as a result of

Answer 33

a condensation reaction: two cysteine are brought together and water is lost