KH 04

Question 1

What is the oil drop model?

Answer 1

In properly-folded proteins,
hydrophobic amino acid
side-chains are not exposed
at the surface, but are buried
in the core.

Question 2

What can be a sign of misfolding in a protein?

Answer 2

Hydrophobic patches at the surface of a protein.

Question 3

Who received the 1972 Nobel Prize in chemistry in 1972 and what did they receive it for?

Answer 3

Anfinsen for his work on ribonuclease. He showed that the 3D structure is determined by the amino acid sequence

Question 4

Spontaneous refolding of a
denatured protein is thought to be
through a “_____ _____”.

Answer 4

folding pathway. Likewise for nascent proteins being
synthesized on ribosomes.

Question 5

Proteins are synthesized sequentially
from the ______ to the _____.

Answer 5

N-terminus (amino terminus), C-terminus (carboxy terminus)

Question 6

During protein synthesis, which terminal region starts to fold before the other terminal region is synthesized?

Answer 6

The N-terminal region folds before the C-terminal region is synthesized

Question 7

What is the folding of many proteins facilitated by?

Answer 7

Chaperones

Question 8

What are chaperones?

Answer 8

Chaperones are proteins that help guide protein folding along productive pathways, by permitting partially misfolded proteins to return to the proper folding pathway.

Question 9

What do chaperones recognize?

Answer 9

Exposed hydrophobic patches

Question 10

Many chaperones are upregulated under conditions where misfolded proteins accumulate. What is an example of a condition that misfolds proteins?

Answer 10

Heat-shoock

Question 11

How do chaperones work?

Answer 11

Chaperones work through ATP-dependent cycles of binding to, and release from, misfolded “client” molecules, at exposed hydrophobic patches. By blocking the exposed hydrophobic patches the chaperone keeps the folding or refolding protein ‘out of trouble’, while productive folding events occur.

Question 12

What can chaperones do?

Answer 12

Chaperones can fold newly made proteins into functional conformations, refold misfolded or unfolded proteins into functional conformations…..also disassemble potentially toxic protein aggregates that form due to protein misfolding, and assemble and dismantle large multiprotein complexes, and mediate transformations between inactive and active forms of some proteins.

Question 13

What are the 2 major classes of chaperones?

Answer 13

1. Molecular chaperones (operate as single molecules)
2. Chaperonins (form a multisubunit “refolding” chamber)

Question 14

What is an example of a major molecular chaperone that helps newly-synthesized proteins follow the correct
folding pathway?

Answer 14

Hsp70

Question 15

What does Hsp stand for?

Answer 15

Heat Shock Protein

Question 16

Chaperones work through a cycle of client protein binding and conformational change associated with _____ and _____.

Answer 16

ATP binding, hydrolysis

Question 17

What is an example of a chaperonin?

Answer 17

Hsp60

Question 18

How do chaperonins work?

Answer 18

They form an enclosed chamber made up of inward-facing protein-binding subunits that undergo concerted ATP-binding/hydrolysis and conformation change.

Question 19

Why are molecular chaperones and chaperonins essential for life?

Answer 19

Because although some proteins can fold and refold on their own without any help, the majority of cellular proteins require their assistance to adopt the proper 3D structure.

Question 20

What is an example of a protein that can fold and refold without any help?

Answer 20

Ribonuclease

Question 21

How have molecular chaperones and chaperonins evolved through evolution?

Answer 21

Chaperones are very ancient (found in both eukaryotes and prokaryotes) and their amino acid sequence has been very highly conserved through evolution. If they had not evolved, the cell would have a crippling burden of misfolded nonfunctional and aggregate-prone proteins.

Question 22

What happens to irretrievably misfloded proteins?

Answer 22

They are destroyed by proteolytic cleavage into small fragments.

Question 23

What is the ubiquitin/proteasome system for protein degradation?

Answer 23

Step 1: Poly-ubiquitin “tags” damaged or misfolded proteins for degradation.
Step 2: Ubiquitin-tagged proteins are fed into a multisubunit chamber in which the subunits form inward-facing proteases.

Question 24

What are ubiquitins?

Answer 24

76-residue proteins that can be covalently linked to lysine residues on target proteins.

Question 25

What is it that recognizes misfolded or damaged proteins?

Answer 25

E3 ubiquitin ligase

Question 26

How many genes encoding diverse E3 ubiquitin ligases does the human genome include?

Answer 26

About 600

Question 27

What can the genes that encode diverse E3 ubiquitin ligases cause?

Answer 27

Human diseases (when mutated)

Question 28

What is an example of a human disease caused by mutations in the U3 ubiquitin ligase?

Answer 28

Parkinson’s disease

Question 29

How do E3 ubiquitin ligases target misfolded proteins?

Answer 29

They recognize the exposed hydrophobic patches.

Question 30

Other than hydrophobic patches, what can E3 ubiquitin recognize?

Answer 30

Oxidized amino acids

Question 31

What is the function of proteasomes?

Answer 31

Proteins in cap that recognize and bind polyubiquitin, remove targeting ubiquitins by hydrolysis, unfold target proteins (using energy from ATP), and feed them into the central chamber of the 20S core. The 20S core subunits form inward-facing proteases that degrade proteins to amino acids or short oligopeptides. This design isolates the active protease from the cytoplasm,
thus minimizing the “dangers” of an enzyme that destroys proteins.

Question 32

Ideally, misfolded/aberrant proteins that cannot be properly refolded with chaperone assistance are degraded by the __________ mechanism.

Answer 32

multiubiquitination/proteasome. However, this system is imperfect in some situations, leading to the accumulation of aggregates of insoluble proteins.

Question 33

What is a form of accumulation of misfolded proteins?

Answer 33

Amyloid. It is an important aspect of several neurodegenerative diseases.

Question 34

Amyloid deposits in the brain are visible as lesions like _____ and ______ in the microscope.

Answer 34

plaques, tangles

Question 35

Is protein degradation an essential function for living cells?

Answer 35

Yes

Question 36

Did the proteasome mechanism evolve before or after the prokaryote/eukaryote divergence?

Answer 36

Before

Question 37

Is it true that some cellular regulatory mechanisms (like in cyclins during the cell cycle) require the controlled, rapid proteasomal removal of particular proteins?

Answer 37

Yes

Question 38

What is the E3 recognition of cyclins triggered by?

Answer 38

By their regulated phosphorylation at a specific amino acid residue.

Question 39

What are Alzheimer’s and Parkinson’s diseases associated with?

Answer 39

The accumulation, late in life, of insoluble and presumably toxic misfolded protein aggregates.

Question 40

The proteasome and the chaperonins independently evolved in similar _____ structures: capped multisubunit cylinders with a central chamber spatially isolated from the cytoplasm.

Answer 40

quaternary