KH4

Question 1

describe protein folding - proper vs not proper

Answer 1

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

Question 2

can proteins denature and renature easily

Answer 2

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

Question 3

are misfolded proteins soluble

Answer 3

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

Question 4

describe spontaneous refolding of a denatured protein

Answer 4

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

Question 5

what facilitates protein folding

Answer 5

chaperones

Question 6

what are chaperones

Answer 6

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

Question 7

what do chaperones recognize

Answer 7

exposed hydrophobic patches
how it decides if its misfolded

Question 8

what are many chaperones (many chaperones are…)

Answer 8

upregulated under conditions where misfolded proteins accumulate

Question 9

describe heat shock proteins - gen/informal

Answer 9

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

Question 10

name all the functions of chaperones (5)

Answer 10

• 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)

Question 11

how do chaperones work

Answer 11

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

Question 12

name the 2 major classes of chaperones

Answer 12

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

Question 13

what is hsp70

Answer 13

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

Question 14

what is hsp

Answer 14

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

Question 15

what do chaperones bind to

Answer 15

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

Question 16

what do chaperones work through

Answer 16

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

Question 17

what are chaperonins

Answer 17

hsp60’s

Question 18

what do hsp60’s form

Answer 18

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

Question 19

describe chaperonins - generally

Answer 19

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

Question 20

describe group II chaperonins

Answer 20

eukaryotic cytoplasm

Question 21

describe group I chaperonins

Answer 21

bacteria
mitochondria

Question 22

do proteins need chaperones/chaperonins often

Answer 22

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

Question 23

why are chaperones/chaperonins important for evoluton

Answer 23

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

Question 24

can chaperones fix all misfolded proteins

Answer 24

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

Question 25

how are proteins degraded

Answer 25

ubiquitin proteasome system

Question 26

describe how group I/II chaperonins work

Answer 26

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

Question 27

describe step 1 ubiquitin proteasome system

Answer 27

poly ubiquitin tags damaged or misfolded proteins for degradation

Question 28

describe step 2 ubiquitin proteasome system

Answer 28

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

Question 29

what is ubiquitin

Answer 29

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

Question 30

what is E1

Answer 30

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

Question 31

what is E2

Answer 31

ubiquitin conjugating enzyme

Question 32

what is E3

Answer 32

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)

Question 33

what can a mutation in E3 cause

Answer 33

familial parkinsons disease neurodegenerative disorder

Question 34

does E3 only recognize misfolded or damaged proteins

Answer 34

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

Question 35

describe role of proteasome

Answer 35

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

Question 36

what does 20S core subunits form

Answer 36

inward facing proteases degrade proteins to aas or short oligopeptides

Question 37

why is design of proteasome good

Answer 37

isolates proteases from cytoplasm minimize dangers of enzyme that destroys proteins

Question 38

describe proteasome process informally

Answer 38

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

Question 39

describe protein quality control failure

Answer 39

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

Question 40

what does accumulation of misfolded proteins cause

Answer 40

in form of amyloid - aspect of neurodegenerative diseases

Question 41

name diseases caused by amyloid

Answer 41

parkinsons alzheimers mad cow

Question 42

describe how amyloid accumulation happens (steps kinda)

Answer 42

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

Question 43

describe amyloid deposits

Answer 43

visible as lesions in microscope plaques and tangles

Question 44

is protein degradation important

Answer 44

YUH essential function for living cellsss

Question 45

describe how proteasome and chaperonins developed

Answer 45

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

Question 46

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

Answer 46

chaperone will help ub will just mark you FOR DEATH