Lecture 7 concepts: Protein folding II

Question 1

Protein stability created by

Answer 1

Hydrophobic effect: keeps hydrophobic r chains on the inside and hydrophilic r chains on the outside through the release of water molecules from the nonpolar molecules (water disperses, thus increasing entropy of surroundings)

Disulfide linkages

“Ligameric structures” Subunit association: proteins associate with ligameric structures (quartenary structure) ie subunit associations: example- three polypeptide chains associating with one another.

Question 2

“fine tuning” bonds

Answer 2

1. secondary bonding such as hydrogen bonds and disulfide bonds, ionic bonds and van der waals interactions

Question 3

Symmetry: why C3 C4 etc?

Answer 3

important for protein stability

you can turn them around that number of times and see the same thing

Question 4

“Screw symmetry”

Answer 4

actin helical structures/ microtubules

Question 5

UPR

Answer 5

Unfolding Protein Response is a cellular response launched by the ER in response to UPS: halts elongation and degrades peptide. if this doesn’t work in clicks into apoptosis

Question 6

Protein Denaturation (Conditions)

Answer 6

Heat, pH, agitation

Heat: brings the hydrophobic interiors of egg whites to the outside, causing them to aggregate (making white color)

pH: breaks salt bonds and denatures

agitation: mechanical energy denatures proteins (frothing eggs for example)

Question 7

Protein Denaturation (Chemicals)

Answer 7

1) detergents
2) chaotropic agents (little molecules/metals that can disrupt bonds: urea and guanadinium chloride)
3) organic solvents (alcohol)

Question 8

Denaturing a protein: if you look at sample of denaturing protein at the midway point, what do you see?

Answer 8

50% denatured, 50% undenatured. Either/or, highly cooperative. Midway point is called “TN”

Question 9

“TN”

Answer 9

midway point of denatured proteins

Question 10

Methods of analyzing denatured proteins and related terms

Answer 10

1) turbidity (shaking around)
2) circular dichroism (CD: looking at secondary structure of protein itself, % of alpha helice and beta strand)
3) UV absorbance (aromatic, because they absorb
a) microenvironment will be different in the folded/unfolded state
4. biological activity (do these proteins have any activity?)

Question 11

Chaotropic Agents (name the one beginning with a G)

Answer 11

Guanidine (deprotonated)—–> Guanidinium (protonated)

Can reversibly bind a proton

Question 12

Chaotropic Agents II (name the one beginning with U)

Answer 12

Urea reducing agent, breaks down disulfide bonds

Question 13

Chaotropic bonds III (name the one beginning with b)

Answer 13

beta-mercaptoethanol, reducing again, completely breaks down disulfide bonds

Question 14

Where would you find chatropic agents? Where would they work? How?

Answer 14

They reduce disulfide bonds, so you would find them on extracellular proteins (because DSulfide bonds can withstand oxidative environments (already are oxidized)

They would work anywhere with disulfide bonds

They work through reduction: adding an H plus two electrons to their target

Question 15

Before you perform electrophoresis you would

Answer 15

reduce disulfide bonds

Question 16

Accessory Proteins: PDI

Answer 16

protein disulfide isomerases: fixes misses up disulfide bonds from misbonded proteins intended for export

they break the wrong ones and reform the correct ones

Question 17

Accessory Proteins: PPI

Answer 17

Proline has trans/cis, but energetically they are the same. PPI corrects the cis-trans depending on which it’s supposed to be

“protein cis-trans prolyl isomerases”

Question 18

Molecular chaperones: HSP 70 and 40

Answer 18

Reverse misfolds, ATP drive
participation in synthesizing new proteins
participate in delivery of proteins to mitochondria

Question 19

HSP 90

Answer 19

signal transduction proteins involved in folding IUP (intrinsically unstructured proteins)

Question 20

Nucleoplasmins

Answer 20

Involved in nucleus sole formation, ribogenesis as well

Question 21

Small-HSPs

Answer 21

25-50 exist depending on cell type
prevent aggregation of misfolded proteins,
work with the HSP 70 and HSP 40

Question 22

Chaperonins

Answer 22

basket like structure proteins that “catch” misfolded proteins and fix them

Question 23

Two Models (mechanisms) of Protein Folding

Answer 23

Passive Mechanism: unfolded protein is placed into a “cage” (protein) and allowed to reassemble itself by itself

Iterative Annealing: an accessory protein interacts with the unfolded protein to repair it

Question 24

Iterative Annealing

Answer 24

an accessory protein interacts with the unfolded protein to repair it: the inner part of the “basket” actually interacts with the unfolded protein. It’s an “active model”

Question 25

Passive Mechanism

Answer 25

“cage” model

unfolded protein is placed into a case and allowed to reassemble itself

Question 26

4 Steps of either the Iterative or the CAGE model

Answer 26

1) unfolded protein (UP) binds to apical domain of cage protein
a) the hydrophobic domain most likely

2) the GroES snaps shut
a) requires ATP input

3) Protein allowed to find itself OR the cage interacts with the protein to assist it
a) release of energy

4)GroES comes off and out goes the newly folded protein

Question 27

Presence of methionine sulfoxide means

Answer 27

Protein is worn out, thiol group can be reduced

Question 28

Chaperonins: name some

Answer 28

GroEs/El, group 1, hsp 60/10 mitochondrial: found in bacteria

CCTV group II found in eukaryotic cytosol

Both are dihedral

Question 29

Where might you find chaperonins?

Answer 29

Places where proteins are being broken down, muscle cells for example because your fibrous proteins are being broken down and reformed

Question 30

C7 is what

Answer 30

Cap to the group I chaperonins