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BIOL 200 > KH4 > Flashcards

KH4 Flashcards

1
Q

describe protein folding - proper vs not proper

A

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

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2
Q

can proteins denature and renature easily

A

sometimes
some can go between native and denatured conformations but most do not remember and end up as misfolded (like hard boiled egg)

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3
Q

are misfolded proteins soluble

A

NOOO
a protein that is misfolded like with a hydrophobic patch is insoluble
they are prone to aggregation

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4
Q

describe spontaneous refolding of a denatured protein

A

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

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5
Q

what facilitates protein folding

A

chaperones

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6
Q

what are chaperones

A

proteins that help guide protein formation along productive pathways
permits partially misfolded proteins to return to proper folding pathway

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7
Q

what do chaperones recognize

A

exposed hydrophobic patches
how it decides if its misfolded

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8
Q

what are many chaperones (many chaperones are…)

A

upregulated under conditions where misfolded proteins accumulate

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9
Q

describe heat shock proteins - gen/informal

A

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

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10
Q

name all the functions of chaperones (5)

A
  • 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)
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11
Q

how do chaperones work

A

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

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12
Q

name the 2 major classes of chaperones

A

molecular chaperones - operate as single molecules
chaperonins - form a multisubunit refolding chamber

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13
Q

what is hsp70

A

molecular chaperon that helps newly synthesized proteins follow correct folding pathway
can help renature protein that has denatured

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14
Q

what is hsp

A

heat shock protein
upregulated under conditions that promote misfolding, like high temp
many chaperones were discovered this way

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15
Q

what do chaperones bind to

A

exposed hydrophobic residues of nascent polypeptides
protect from aggregation until properly folded

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16
Q

what do chaperones work through

A

cycle of client protein binding and conformational change associated with ATP binding and hydrolysis

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17
Q

what are chaperonins

A

hsp60’s

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18
Q

what do hsp60’s form

A

enclosed chamber made up of inward facing protein binding subunits
undergo concerted ATP binding and hydrolysis and conformation change

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19
Q

describe chaperonins - generally

A

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

20
Q

describe group II chaperonins

A

eukaryotic cytoplasm

21
Q

describe group I chaperonins

A

bacteria
mitochondria

22
Q

do proteins need chaperones/chaperonins often

A

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

23
Q

why are chaperones/chaperonins important for evoluton

A

essential to life
highly conserve in aa sequence through evolution
cell would have crippling burden of misfolded nonfunctional and aggregate prone proteins

24
Q

can chaperones fix all misfolded proteins

A

nooooo
Irretrievably misfolded proteins are destroyed by proteolytic cleavage into small fragments

25
Q

how are proteins degraded

A

ubiquitin proteasome system

26
Q

describe how group I/II chaperonins work

A

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

27
Q

describe step 1 ubiquitin proteasome system

A

poly ubiquitin tags damaged or misfolded proteins for degradation

28
Q

describe step 2 ubiquitin proteasome system

A

ubiquitin tagged proteins are fed into multisubunit chamber in which the subunits from inward facing proteases

29
Q

what is ubiquitin

A

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

30
Q

what is E1

A

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

31
Q

what is E2

A

ubiquitin conjugating enzyme

32
Q

what is E3

A

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)

33
Q

what can a mutation in E3 cause

A

familial parkinsons disease
neurodegenerative disorder

34
Q

does E3 only recognize misfolded or damaged proteins

A

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

35
Q

describe role of proteasome

A

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

36
Q

what does 20S core subunits form

A

inward facing proteases
degrade proteins to aas or short oligopeptides

37
Q

why is design of proteasome good

A

isolates proteases from cytoplasm
minimize dangers of enzyme that destroys proteins

38
Q

describe proteasome process informally

A

proteins inside barrel
only protein threaded through cap into 20S core
cap = multisubunit quaternary structure

39
Q

describe protein quality control failure

A

polyubiquitin/proteasome mechanism can fail and causes accumulation of aggregates of insoluble proteins
bad outcome!! but also takes long

40
Q

what does accumulation of misfolded proteins cause

A

in form of amyloid - aspect of neurodegenerative diseases

41
Q

name diseases caused by amyloid

A

parkinsons
alzheimers
mad cow

42
Q

describe how amyloid accumulation happens (steps kinda)

A

amyloid precursor –> (cleavage) –> alpha helix –> beta sheet (changes structure to be short) –> aggregation into filaments resistant to proteolysis (amyloids!)

43
Q

describe amyloid deposits

A

visible as lesions in microscope
plaques and tangles

44
Q

is protein degradation important

A

YUH
essential function for living cellsss

45
Q

describe how proteasome and chaperonins developed

A

independently evolved similar quaternary structures = capped multisubunit cylinders with central chamber isolated from cytoplasm
similar structure but different function

46
Q

if you were a misfolded protein would you want chaperone or ubiquitin to find you first

A

chaperone will help
ub will just mark you FOR DEATH

BIOL 200 (29 decks)

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