KH4 Flashcards
describe protein folding - proper vs not proper
proper = hydrophobic amino acid side chains are not exposed at the surface - buried in core
sign of misfolding is when hydrophobic patches are at the surface of a protein
can proteins denature and renature easily
sometimes
some can go between native and denatured conformations but most do not remember and end up as misfolded (like hard boiled egg)
are misfolded proteins soluble
NOOO
a protein that is misfolded like with a hydrophobic patch is insoluble
they are prone to aggregation
describe spontaneous refolding of a denatured protein
refolding is like a folding pathway
(likewise for nascent proteins being synthesized on ribosomes)
proteins are synthesized from N terminus to C terminus, N terminal region comes out and starts to fold before C terminal end is synthesized
what facilitates protein folding
chaperones
what are chaperones
proteins that help guide protein formation along productive pathways
permits partially misfolded proteins to return to proper folding pathway
what do chaperones recognize
exposed hydrophobic patches
how it decides if its misfolded
what are many chaperones (many chaperones are…)
upregulated under conditions where misfolded proteins accumulate
describe heat shock proteins - gen/informal
heat shock or stress induced proteins
shock partially denatures and unfolds protein
cell upregulates chaperons and heat shock protein tries to get it back on track
name all the functions of chaperones (5)
- fold newly made proteins into functional conformations
- refold misfolded or unfolded proteins into functional conformations
- disassemble potentially toxic protein aggregates (form due to misfolding)
- assemble and dismantle large multiprotein complexes
- mediate transformations between inactive and active forms of some proteins (help them get through transition without irreversible misfolding)
how do chaperones work
work through ATP dependent cycles of binding to and release from misfolded (client) molcules at exposed hydrophobic patches
binding to it and blocks exposed patches - keeps folding or refolding protein out of trouble - while productive folding events occur
name the 2 major classes of chaperones
molecular chaperones - operate as single molecules
chaperonins - form a multisubunit refolding chamber
what is hsp70
molecular chaperon that helps newly synthesized proteins follow correct folding pathway
can help renature protein that has denatured
what is hsp
heat shock protein
upregulated under conditions that promote misfolding, like high temp
many chaperones were discovered this way
what do chaperones bind to
exposed hydrophobic residues of nascent polypeptides
protect from aggregation until properly folded
what do chaperones work through
cycle of client protein binding and conformational change associated with ATP binding and hydrolysis
what are chaperonins
hsp60’s
what do hsp60’s form
enclosed chamber made up of inward facing protein binding subunits
undergo concerted ATP binding and hydrolysis and conformation change
describe chaperonins - generally
7 proteins
unfolded protein binds to material and enters chamber
then cap binds and then atp hydrolysis cycles
isolate protein and its possible that conditions in chamber mimic cytoplasm and cause folding
entropy change in water (moiety) - hydrophobic effect
could be another cycle if protein comes out wrong
describe group II chaperonins
eukaryotic cytoplasm
describe group I chaperonins
bacteria
mitochondria
do proteins need chaperones/chaperonins often
yesss
majority of cellular proteins need them to adopt their 3d structures during synthesis or to refold if misfolded
except like ribonuclease - can fold and refold without any help
why are chaperones/chaperonins important for evoluton
essential to life
highly conserve in aa sequence through evolution
cell would have crippling burden of misfolded nonfunctional and aggregate prone proteins
can chaperones fix all misfolded proteins
nooooo
Irretrievably misfolded proteins are destroyed by proteolytic cleavage into small fragments
how are proteins degraded
ubiquitin proteasome system
describe how group I/II chaperonins work
2 chambers barrel shaped place - subunits of proteins
client enters
atp binds
shape change and rotates and closes chamber at top
refolding events happen
twists back to open and protein comes out
describe step 1 ubiquitin proteasome system
poly ubiquitin tags damaged or misfolded proteins for degradation
describe step 2 ubiquitin proteasome system
ubiquitin tagged proteins are fed into multisubunit chamber in which the subunits from inward facing proteases
what is ubiquitin
76 residue protein that can be covalently linked to lysine residues on target proteins
what is E1
ubiquitin activating enzyme
hydrolyzes ATP and takes energy and attaches ub to itself through terminal at end of ub
E1 transfers to E2 and to E3
what is E2
ubiquitin conjugating enzyme
what is E3
ubiquitin ligases
recognizes protein to be destroyed (misfolded or damaged) and calls in E2 and attaches to target protein
thought to recognize hydrophobic patches (also oxidized aas)
what can a mutation in E3 cause
familial parkinsons disease
neurodegenerative disorder
does E3 only recognize misfolded or damaged proteins
no they can recognize normal proteins that the cell needs to degrade for regulatory needs
like cyclins during cell cycle - E3 recognition of cyclins is triggered by regulated phosphorylation at specific aa residue
describe role of proteasome
proteins in cap recognize and bind polyubiquitin
remove targeting ubiquitin by hydrolysis
unfold target proteins = using energy from ATP
and feed them into central chamber of 20S core
what does 20S core subunits form
inward facing proteases
degrade proteins to aas or short oligopeptides
why is design of proteasome good
isolates proteases from cytoplasm
minimize dangers of enzyme that destroys proteins
describe proteasome process informally
proteins inside barrel
only protein threaded through cap into 20S core
cap = multisubunit quaternary structure
describe protein quality control failure
polyubiquitin/proteasome mechanism can fail and causes accumulation of aggregates of insoluble proteins
bad outcome!! but also takes long
what does accumulation of misfolded proteins cause
in form of amyloid - aspect of neurodegenerative diseases
name diseases caused by amyloid
parkinsons
alzheimers
mad cow
describe how amyloid accumulation happens (steps kinda)
amyloid precursor –> (cleavage) –> alpha helix –> beta sheet (changes structure to be short) –> aggregation into filaments resistant to proteolysis (amyloids!)
describe amyloid deposits
visible as lesions in microscope
plaques and tangles
is protein degradation important
YUH
essential function for living cellsss
describe how proteasome and chaperonins developed
independently evolved similar quaternary structures = capped multisubunit cylinders with central chamber isolated from cytoplasm
similar structure but different function
if you were a misfolded protein would you want chaperone or ubiquitin to find you first
chaperone will help
ub will just mark you FOR DEATH
