Protein Structure and Folding

Question 1

What are domains in relevance to protein structure?

Answer 1

They are responsible for a particular function or interaction

Question 2

What is a motif?

Answer 2

A sequence or structural element that contributes to the primary sequence of proteins.

Question 3

Two examples of proteins having quaternary structure

Answer 3

HIV Protease and Potassium Channel

Question 4

What is the impact of AlphaFold?

Answer 4

Predicts the protein structure

Question 5

What is the impact of PandaOmics?

Answer 5

This provides the protein of interest

Question 6

What is the impact of Chem42?

Answer 6

Generates molecules based on the structure provided by AlphaFold

Question 7

How do chaperone proteins help?

Answer 7

They form disulfide bonds, protect hydrophobic clusters from aggregation, and interconvert prolyl cis/trans peptide bonds.

Question 8

What are molecular chaperones?

Answer 8

These help proteins who are struggling to reach their native states by assisting protein folding

Question 9

T/F: Molecular chaperones interact with native proteins

Answer 9

FALSE

Question 10

What happens if protein folding not possible?

Answer 10

These proteins would become targeted for protein degradation to maintain protein homeostasis

Question 11

What are two pathways in which protein degradation occurs in?

Answer 11

Ubiquitin proteasome system(UPS) or the autophagy-lysosome pathway.

Question 12

Does entropy favor folded or unfolded state of proteins

Answer 12

Unfolded because this creates more disorder.

Question 13

How to measure stability of protein?

Answer 13

Kf = [Folded]/[Unfolded]

Question 14

What is protein folding

Answer 14

Polypeptide chain goes from linear chain to native, folded tertiary structure

Question 15

What is the significance of negative delta G?

Answer 15

Decrease in free energy for a process(reaction is favorable)

Question 16

What does delta H represent?

Answer 16

Change in enthalpy, meaning this reflects the number and kinds of chemical bonds in reactants and products

Question 17

What does delta S represent?

Answer 17

Change in entropy, an increase in disorder gives a positive number = favorable

Question 18

What are prions?

Answer 18

Type of infections agent that doesn’t carry any genetic material

Question 19

How many domains does the CFTR posess?

Answer 19

5 domains

Question 20

What are the 5 domains of the CFTR?

Answer 20

2 transmembrane domains(containing 6 hydrophobic alpha helices)
2 nucleotide binding domains(ATP)
1 regulatory domain that contains many phosphorylation sites

Question 21

What is the most prevalent mutation that affects 80% of CF patients?

Answer 21

DeltaF508

Question 22

What is the impact of deltaF508?

Answer 22

Reduces thermal and kinetic stability of NBD1, which prevents interdomain interactions

Question 23

What are the three defects of F508del-CFTR?

Answer 23

1) Inhibits trafficking
2) Enhances degradation
3) Reduces CFTR membrane channel function

Question 24

How many classes of CFTR mutations are there?

Answer 24

6 classes

Question 25

What is the purpose of Class 1 CFTR?

Answer 25

Rescue protein synthesis

Question 26

What is the purpose of Class 2 CFTR?

Answer 26

Correct protein folding

Question 27

What is the purpose of Class 3 and 4 CFTR?

Answer 27

Restore channel conductance

Question 28

What is the purpose of Class 5 CFTR?

Answer 28

Maturation/ Correct any splicing errors

Question 29

What is the purpose of Class 6 CFTR?

Answer 29

Promote protein stability

Question 30

What are the 3 main types of protein structure modulators?

Answer 30

Potentiators, Correctors, and Amplifiers

Question 31

What is the role of the potentiator?

Answer 31

Holds the CFTR chloride gate open(Ivacaftor does this)

Question 32

What is the role of the corrector?

Answer 32

Helps CFTR protein form the correct 3D shape so it can move towards the cell surface(Lumacaftor and Tezacaftor)

Question 33

What is the role of the amplifier?

Answer 33

Increase the amount of CFTR protein that the cell makes

Question 34

What is the purpose of CFTR?

Answer 34

a protein that plays a crucial role in maintaining the balance of salt and water on the surfaces of various epithelial cells in the body. Its primary function is to regulate the flow of chloride ions (Cl-) in and out of these cells, which, in turn, affects the movement of water across cell membranes.