Proteins Folding

Question 1

What is the molten Globule state?

Answer 1

-the intermediate ‘structure’ existing between the unfolded and native state of the protein.

Question 2

What causes a protein to denature?

Answer 2

pH, heat, mechanical motions, detergents (SDS), chaotropic agents (urea, guanidine hydrochloride)

Question 3

What methods allow to analyze protein denaturation?

Answer 3

• turbidity
• circular dichroism: differential absorption of Levo, dextro rotatory light.
• Fluorescence:tag aa to evaluate level of fluorescence.
• UV absoprtion: aromatic absorb light.

Question 4

protein disulfide isomerase

Answer 4

enzyme in certain location that guides cysteine to proper placement.

Question 5

peptidyl prolyl isomerases

Answer 5

alter the molecule to align in the proper orientation

Question 6

molecular chaperones

Answer 6

• ATP driven.

- provide environment for protein folding, try to fix misfolded proteins.

Question 7

chaperonins

Answer 7

• are chaperones
• group 1: circular with top lid, that protein enters.
• group 2: specific to eukaryotic cytosol
• mitochondria contains its own.

Question 8

What happens when a protein misfolds?

Answer 8

• collected by quality control mechanism

- if system is overfilled, can cause backup and potential for nucleation

Question 9

Amyloid plaque formation

Answer 9

• nucleation (seeding): misfolded proteins interact and stack on ehac other. this forms a crystal structure, as the alpha helices are converted to more rigid beta-sheets.
• then forms a fibril formation, which looks like actin.
• these deposit into different organ systems.

Question 10

Body’s defense to amyloid plaque

Answer 10

The body places the cells into ‘bags’ to prevent the growth of the structure.

Question 11

Amyloid

Answer 11

• comes from the molten globule, that takes too long to form.
• derived from cellular protein amyloid precursor protein.
• forms specifically from protein-protein interactions.

Question 12

Describe the process that misfolded proteins are removed from the system.

Answer 12

• protein is moved with chaperones HSP70/40 in order to tag it with ubiquitinin.
• ubiquitinin flagged protein has ATP applied and is transferred to a proteasome.
• proteasome destroys the misfolded protein.

Question 13

metallochaperones

Answer 13

-specifically adds metal to the proper locations to stabilize structure. also adds ability to perform other cellular tasks.

Question 14

What are the common categories of metalloproteins?

Answer 14

• enzymes

- transport and storage

Question 15

transport/storage metalloproteins sub category consist of?

Answer 15

• electron carriers: iron-sulfur protein, Fe is major metal
• metal management: ferritin (Fe binding protein) Fe
• oxygen management: myoglobin/hemoglobin, Fe

Question 16

Enzyme metalloproteins can be broken into…?

Answer 16

• hydroxylases: phosphatases-Mg, Zn
• oxidoreductases: oxidases, reductases- Fe, Cu
• isomerases/synthases: Vit B12

Question 17

What is an infectious protein?

Answer 17

-acts like a virus and is able to transfer from one cell to another.

Question 18

What are the transmittable agents of infectious proteins?

Answer 18

• prions
• alpha-synuclein
• beta-amyloids
• SOD1

Question 19

How do proteins generally fold?

Answer 19

-hydrophobic area is in the center and polar is faced towards the surface.

Question 20

hydrogen bond effect on protein folding.

Answer 20

-use NH and CO in hydrophobic region to form alpha helixes, or beta sheets.

Question 21

Van der waals interaction effects on protein folding?

Answer 21

-polarity of one molecule will influence another, can add stability with the proper alignment

Question 22

Short-range repulsion

Answer 22

-uses electrostatic forces to bind. If too far apart, then not strong enough to interact. If too close then repulsion pushes the molecules apart.

Question 23

Christian Anfinsen

Answer 23

-able to demonstrate that ‘directions’ for protein folding are contained in the aa sequence.

Question 24

Explain the folding funnel.

Answer 24

-graphical representation of the energy levels of a protein as it assembles itself from aa sequence to native form.

Question 25

What is essentially happening in the molten globule state?

Answer 25

• protein is ‘estimating’ its method of best fit.
• still 10-30% larger than native bc of loosely packed hydrophobic core.
• in transition state essentially.

Question 26

What does a binding site do for a protein?

Answer 26

-site causes conformational change, with the presence or absence of the fitted domain.

Question 27

What is common in tertiary structure?

Answer 27

-alpha helixes, as these are more flexible and allow more movement within the protein structure, over beta sheets.

Question 28

What are intrinsically unstructured proteins used for?

Answer 28

• generally signaling and play a role in regulatory pathway.

- at least 30 aa region within 50% of eukaryotic proteins.

Question 29

What is an intrinsically structured protein?

Answer 29

-protein with no discrete conformation, whose structure is based on other interactions with others.

Question 30

What are the characteristics of an infectious protein?

Answer 30

1. protein aggregates do not dissolve
2. protein is derived from a cellular protein
3. aggregates are formed by specific transmissible agents

Question 31

Prion aggregates form what transmissible agent?

Answer 31

PrP

Question 32

Amyloid Plaque aggregates form what transmissible agent?

Answer 32

b-amyloid

Question 33

Alpha-synuclein aggregates form what transmissible agent?

Answer 33

plaques

Question 34

SOD1 aggregates form what transmissible agent?

Answer 34

monomer SOD1 plaques

Question 35

Amyloid fibrils are transmissible by…..?

Answer 35

The same mechanisms that an infectious protein is