protein folding, misfolding and degradation

Question 1

What is the significance of hydrophobic patches on
the surface of a protein?

Answer 1

Hydrophobic patches on the surface of a protein are
a sign of misfolding.

Question 2

What are chaperones?

Answer 2

Chaperones are proteins that assist in the folding of
other proteins, preventing misfolding and
aggregation.

Question 3

What is the difference between the native and
misfolded conformation of a protein?

Answer 3

The native conformation is the correct,
properly-folded conformation of a protein, while the
misfolded conformation is an incorrect,
improperly-folded conformation.

Question 4

What is the folding pathway?

Answer 4

The folding pathway is the process by which a
denatured protein spontaneously refolds into its
native conformation.

Question 5

When does the protein start folding?

Answer 5

The N-terminal region of a protein starts to fold
before the C-terminal region is synthesized,
allowing for proper folding to occur.

Question 6

What is protein aggregation?

Answer 6

Protein aggregation is the process by which misfolded proteins clump together, leading to the formation of insoluble aggregates.

Question 7

What conditions lead to the upregulation of
chaperones?

Answer 7

Conditions where misfolded proteins accumulate,
such as heat-shock.

Question 8

What is the function of chaperones? (5)

Answer 8

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

Question 9

How do chaperones recognize misfolded proteins?

Answer 9

Chaperones recognize exposed hydrophobic
patches on misfolded proteins.

Question 10

What is the mechanism of action of chaperones?

Answer 10

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 11

What are the two major classes of chaperones?

Answer 11

-molecular chaperones
-chaperonins

Question 12

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

Answer 12

Hsp70

Question 13

What is the meaning of Hsp in Hsp70?

Answer 13

Heat shock protein.

Question 14

What are chaperonins? (Hsp60)

Answer 14

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

Question 15

What is the difference between Group I and Group
II chaperonins?

Answer 15

Group I chaperonins are found in bacteria and
mitochondria, while Group II chaperonins are found
in eukaryotic cytoplasm.

Question 16

How do Group I chaperonins work?

Answer 16

The partially folded or misfolded protein binds in chamber. The Chaperonins is made up of two folding chambers (2 x 7 GroEL) and caps (GroEs). Following binding, GroES acts as a detachable lid for the cavity and creates a folding chamber that encloses polypeptide substrates. (requiring ATP). If the problem. If the exposed hydrophobic patch is no longer exposed, then it diffuses away. But if it’s if it’s still not fixed, there can be another cycle.

Question 17

How do Group II chaperonins work?

Answer 17

There are two rings they’re they’re made-up of eight protein subunits in each ring and they don’t have a separate cap. There is a reorientation from the open to closed position. Closing is just a reorientation of the subunits of the each individual protein. It can be open so client proteins can get in and it can be closed, so client proteins can be isolated from the cytoplasm and contained in a very special environment which is conducive to folding.

Question 18

Why are chaperones/chaperonins essential for life?

Answer 18

Chaperones/chaperonins are essential for life
because the majority of cellular proteins require
their assistance to adopt their proper 3-D structures
during synthesis or to properly refold if misfolded.

Question 19

Why are chaperones highly conserved in amino
acid sequence through evolution?

Answer 19

Chaperones are highly conserved in amino acid sequence through evolution because if they had not evolved, the cell would have a crippling burden of misfolded nonfunctional and aggregate-prone proteins.

Question 20

What happens to irretrievably misfolded proteins?

Answer 20

They are destroyed by proteolytic cleavage into small fragments.

Question 21

What is Ubiquitin?

Answer 21

a 76-residue protein that can
be covalently linked to lysine residues on
target proteins which plays a role in protein degradation.

Question 22

How does the step 1 of ubiquitin/proteasome system for protein degradation happen?
Step 1: Poly-ubiquitin “tags” damaged or misfolded proteins for degradation

Answer 22

1. ubiquitin is activated through the bond of the ubiquitin activating enzyme (E1), and the carboxyl terminus of ubiquitin.
2. Ubiquitin is then transferred to ubiquitin conjugases (E2),
3. and is finally conjugated to the N-terminal amino group (isopeptide bond), by an ubiquitin (E3) ligase, which recognizes specific motifs in the targeted protein.
4. Additional ubiquitin molecules are conjugated onto the first forming a chain.

Question 23

Whats happens in step 2 of ubiquitin/proteasome system for protein degradation

Answer 23

Ubiquitin-tagged proteins are fed into a multisubunit chamber in which the subunits form inward-facing proteases.

Question 24

What do E3 ubiquitin ligases recognize?

Answer 24

They recognize misfolded or damaged proteins (Exposed hydrophobic patches.)

Question 25

What other aberrant structures are recognized by
E3 ubiquitin ligases?

Answer 25

Oxidized amino acids.

Question 26

What is the purpose of E3 ubiquitin ligases recognizing and targeting for degradation
particular “normal” proteins that the cell needs to degrade?

Answer 26

for regulatory purposes,
ex: cyclins during cell cycle

Question 27

What triggers E3 recognition of cyclins?

Answer 27

Their regulated phosphorylation at a specific amino
acid residue.

Question 28

What is the function of the Proteasome? (4)

Answer 28

-To 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.

Question 29

What do the inward-facing proteases of the 20S
core subunits do?

Answer 29

Degrade proteins to amino acids or short
oligo-peptides.

Question 30

What is the benefit of isolating the active protease
from the cytoplasm in the Proteasome design?

Answer 30

It minimizes the “dangers” of an enzyme that
destroys proteins.

Question 31

What happens when the ubiquitin/proteasome mechanism fails?

Answer 31

It can lead to the accumulation of aggregates of
insoluble proteins.

Question 32

What is amyloid?

Answer 32

It is a certain form of misfolded protein accumulation which is an important aspect of several
neurodegenerative diseases.

Question 33

What is the similarity between the proteasome and
the chaperonins?

Answer 33

They independently evolved similar quaternary
structures.

Question 34

What are some common neurodegenerative
diseases associated with the accumulation of
misfolded protein aggregates?

Answer 34

Alzheimer’s and Parkinson’s diseases.