protein folding and translation Flashcards
protein folding location
cytosol
protein folding details
1) information is contained in primary aa sequence
2) initially driven by burial of hydrophobic domains
3) Chaperone proteins facilitate folding
Hsp chaperones
bind hydrophobic domains
DnaK aka
Hsp 70
DnaK recognizes…
exposed hydrophobic domains
co-translational recognition
accumulation of protein deposits leads to
Alzheimer’s disease (amyloid beta plaques and neurofibrillary tangles)
Parkinson’s disease (neurofibrillary tangles)
Huntington’s disease (polyQ aggregates of huntington protein)
where are gram-negative bacteria synthesized
cytoplasm, inner membrane, periplasm, outer membrane
proteins not going to the cytoplasm have
a leader sequence at the amino terminus
what removes leader sequence at amino terminus
leader peptidase
what synthesizing cytoplasmic proteins
soluble ribosomes in the cytosol
proteins destined for nucleus or mitochondria
also synthesized by soluble ribosomes in cytosol before being targeted for correct organelle
have special signals in primary aa sequence
proteins that are translated by ribosomes in the ER are
proteins with membrane-spanning domains or that are secreted or that reside in membrane-bound vesicles
protein translation in ER step 1
1) signal peptide at amino terminus directs ribosome to ER (for membrane-bound or secreted proteins)
2) signal peptidase removes the signal peptide
during nascent protein synthesis in ER lumen,
chaperone name BiP binds and maintains polypeptide in a state competent for subsequent folding
N-linked glycosylation
some proteins translated in ER undergo this
an oligomer of carbohydrates is covalently bound to nitrogen of Asn residues
(this is co-translational)
3 glucose residues are trimmed from oligomer (this allows proper folding
N-linked glycosylation and protein folding
oligosaccharide added to growing polypep chain in ER
stepwise cleavage of 3 glucose directions protein to chaperones in ER that assess folding
improperly folded proteins are kept in ER, properly folded proteins go to Golgi
where do misfolded proteins go
ER
where do properly folded proteins go
Golgi
O-linked glycosylation
in Golgi
adds carbohydrates to oxygen of Ser or Thr (no consensus sequences)
(post-translational)
carbs are added individually
post-translational processing of proteins
Proteolytic cleavage: - Removal of N-terminal Met - Pro-proteins - Removal of signal sequences Phosphorylation Glycosylation Acetylation Methylation SUMO-lation
protein turnover
proteins have different turnover rates
misfolded proteins must be recognized and removed
protein degradation common pathway
targeted for degradation by ubiquitin and sent to proteasomes
non-selective protein degradation
in lysosomes
lysosomes
membrane-bound compartments that contain proteolytic enzymes called cathepsins
active only at low pH (~5)
autophagy
helps degrade and recycle cellular components
how: enclosing large cellular components in a membrane that fuses with lysosomes
ubiquitination of proteins
ubiquitin can be linked to Lys residues
proteins must be poly-ubiquitinylated to be targeted to the proteasome
E1: ubiquitin-activating enzyme
cells have 1 E1
E2: ubiquitin-carrier protein
cells have a few E2s
E3: ubiquitin-protein ligase
recognizes targets for degradation and recognizes E2s
cells have many E3s
protein degradation RULES
Proteins with acidic amino terminus are targeted for degradation via an Arginine-modified intermediate
Proteins with PEST sequences also have short half-lives
proteasome structure
26S proteasome consists of a 20S central barrel plus 2 19S caps
- Degradation occurs in the barrel, which is made of rings of alpha and beta subunits
- Beta-subunits have proteolytic activity
protein degradation in proteasome: how?
1) Substrate is poly-ubiquitinylated by E1, E2, and E3 activities
2) 19S caps recognize the ubiquitinylated substrate
- Unfolding occurs in the caps
3) Unfolded proteins move into the barrel for degradation by the beta-subunits
4) Ubiquitin is not degraded but exits the proteasome intact
proteasome inhibitors
Yeast core proteasome bound to bortezomib
Used to treat multiple myeloma and mantle cell lymphoma
Blocking proteasome function disrupts cell cycle control and induces apoptosis
SUMO
small ubiquitin-like protein modifiers (SUMO)
small ubiquitin-like protein modifiers role
Can be covalently linked to Lyc residues
Uses similar E1, E2, and E3 enzymes
Sumoylated proteins are NOT targeted for degradation
consequences of sumoylation
Interactions with a partner may be prevented
Interactions with a partner may be permitted
Induction of a conformational change in the protein
protein quality control
unfolded/misfolded proteins are recognized by chaperons and by the ubiquitination system
Severely damaged proteins, or proteins that cannot be properly folded are targeted for degradation by the proteasome
