01b: Protein Folding/misfolding Flashcards
T/F: proteins begin folding while they’re being synthesized.
True
Is protein folding into native configuration thermodynamically favorable or unfavorable?
Favorable (spontaneous)
Which polypeptide terminus is typically folded first?
N-terminal (since synthesized first)
What’s the mechanism of chaperones (how do they assist in folding)?
Restrict folding pathway (limit number of possible intermediate states).
Chaperones prevent interaction of:
Hydrophobic patches during folding process
Chaperones work (inter/intra)-molecularly to prevent inappropriate interactions.
Both!
T/F: Chaperones are ubiquitous among phyla.
True
Chaperonins are also known as:
Hsp60 proteins
T/F: chaperones are exclusively found in the cytosol.
False - cytosol, ER, mitochondria, chloroplasts
Chaperones were discovered in which organism?
Drosophila
T/F: Hsp70 chaperones are ATPases.
True
Which domains are present in Hsp70 chaperones?
- NT binding domain
2. Substrate binding domain (clamp)
What shuts the clamp in the Hsp70 chaperone?
ATP hydrolysis
What opens the clamp in the Hsp70 chaperone?
Exchange/release of ADP (and binding of ATP)
T/F: Hsp60 chaperonins are ATPases.
True
Describe Hsp60 structure
- Two independent folding channels (heptameric; called GroEL)
- Cap (GroES)
Proteins fold in which cellular compartment?
Multiple!
- Cytoplasm
- ER
- Mitochondrion
- Chloroplasts
How do folded proteins enter organelles?
They can’t; must be unfolded (enter via pores)
Name a key Hsp70 chaperone in the ER.
BiP
What’s UPR?
Unfolded Protein Response (compensatory mechanism for misfolded proteins)
List sensors for misfolded proteins. Where are they located?
- IRE1
- PERK
- ATF6
ER membrane
UPR final outcome:
Activates genes to increase ER folding capacity
What molecules are increased as result of UPR?
Chaperones and lipids
What are the possible dates of newly synthesized proteins?
- Correct folding without help
- Correct folding with chaperone help
- Incompletely folded and digested by proteosome
- Protein aggregate
Describe basic structure of proteosome
4 heptameric rings and a hexamer cap
Name of proteosome cap
19S hexamer called “unfoldase”
The proteosome active sites are present in (core/cap) and have (X)-like activities.
20S Core
X = trypsin-, chymotrypsin-, and peptidylglutamyl-
Proteosome degrades proteins to how many AA peptides?
7-8
How does ATP hydrolysis affect the proteosome cap?
Causes conformational change that strains ring and pulls substrate through
How many AA in ubiquitin?
76
Ubiquitin point of attachment is:
C terminal
Ubiquitin attaches to which part(s) of proteins?
Lysine side chains
The core of ubiquitin can be described as:
Globular and hydrophobic
T/F: Transfer of ubiquitin to ubiquitin ligase is a passive process.
True
In ubiquitin transfer, what is E1 formally called?
Ubiquitin-activating enzyme
T/F: Binding of ubiquitin to ubiquitin-activating enzyme is a passive process.
False - converts ATP to AMP
In ubiquitin binding, the (X) terminus of ubiquitin binds to (Y) group of E1.
X = C
Y = -SH (displaces H)
In ubiquitin binding, the (X) terminus of ubiquitin binds to (Y) group of E2/E3.
X = C
Y = -SH (displaces H)
The last AA of ubiquitin (X) connects to the AA (Y) on preceding ubiquitin, forming which type of bond?
X = glycine Y = lysine (48)
Isopeptide bond
Which path do misfolded proteins take to arrive at the (X) for degradation?
Retrotranslocation from ER to cytoplasm
X = proteosome
Quality control mechanisms help the cell by:
Prevent accumulation of misfolded protein
Proteostasis is:
Balance of protein synthesis, folding, and degradation (homeostasis)
There are (few/many/unknown) genes involved in proteostasis.
Many
It’s estimated that as many any (X)% of all polypeptide chains synthesizes in cell misfold.
X = 50
Misfolding of protein can result in (gain/loss) of (X) function.
- Gain of toxic function
OR - Loss of normal biological function
Dominant inheritance of protein misfolding typically results in:
Gain of toxic function
Recessive inheritance of protein misfolding typically results in:
Loss of normal biological function
What are amyloid fibrils?
Abnormal accumulation of protein
In amyloid fibrils, (X) are perpendicular to fiber axis.
X = beta strands
In amyloid fibrils, (X) are parallel to fiber axis.
X = beta sheets
T/F: Amyloid may have physiological functions.
True
Amyloid fibrils can be stained with:
Congo red or thioflavin
