Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

BIOC212 > MVU4 PROTEIN FOLDING IN THE CELL -3 > Flashcards

MVU4 PROTEIN FOLDING IN THE CELL -3 Flashcards

1
Q

what is the nature of many chaperones?

A

they are heat shock proteins
all HSP are chaperones but not all chaperones are HSP

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

how do cells respond to stress that causes protein misfolding?

A

increase the expression of chaperones and other specialized proteins

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

where does the heat shock response happen and what does it do?

A

happens in cytosolic and nuclear proteins
protects against cell death

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

where does the unfolded protein response (UPR) happens and what does it do?

A

happens in ER proteins
can promote cell death if the stress is too severe

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

what are inducible chaperones?

A

the heat shock proteins
heat induces the transcriptional activation of specific genes, which induces the transcription of certain proteins

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

what are constitutive chaperones?

A

assist in protein folding
proteins that facilitate the folding of others
hold or stabilise the hydrophobic residues
universal mechanism of protein homeostasis

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

what can cause unfolded cytosolic proteins?

A

heat stress
oxidative damage
proteasome inhibition

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

how long after the stress is removed does the stress response continue?

A

only after 24 hours does the cell return to normal

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

what transcription factor mediates the heat shock response?

A

HSF1

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

what domains does HSF1 have?

A

DNA binding domain
regulatory domain
transcription activation domain

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

what are the active and inactive forms of HSF1?

A

inactive = monomeric
active = trimer

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

what sequence in the DNA does active HSF1 recognise?

A

recognises heat shock element promoters (HSE)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

what does the regulatory domain of HSF1 do?

A

allows it to become a trimer

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

how is HSF1 regulated? (before, during and after the heat shock)

A

before the heat shock: monomeric HSF1 is folded, but mimics unfolded proteins and is bound by Hsp90 (has exposed hydrophobic patches)
after: unfolded proteins compete with HSF1 for Hsp90 binding
free HSF1, liberated from Hsp90, trimerises and activates transcription
chaperones, included Hsp90 are expressed and help fold or degrade unfolded protein
after: HSF1 is down regulated by binding excess Hsp90 to the monomer form

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

what do some substrates require?

A

some require specific chaperones or combination of chaperones

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

what do ATP dependent chaperones do?

A

actively promote folding
substrate binding and release is regulate by ATPase cycles

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

what do ATP independent chaperones do?

A

prevent aggregation and can catalyse some folding steps

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

how do chaperones work?

A

in networks, cooperate

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

what do different families of chaperone proteins use?

A

different biochemical mechanisms

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

what are the 3 different families of ATP dependent chaperones?

A

Hsp70 family
monomers
locking pliers

Hsp90 family
dimers
nutcrackers

chaperonins (Hsp60)
trimer
cage

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

which two chaperones from the HSP70 family are present in the cytosol?

A

HSC70 (constitutive)
HSP70 (inducible)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

which two chaperones from the HSP90 family are present in the cytosol?

A

HSP90 alpha and beta

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

which chaperonin (HSP60) is present in the cytosol?

A

TRiC

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

which protein from the HSP70 family is present in the ER?

A

BiP

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

which protein from the HSP90 family is present in the ER?

A

GRP94

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

what chaperone in E.coli works like HSP60?

A

GroEL

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

which is the one chaperone that is not expressed constitutively?

A

HSP70

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
28
Q

how do HSP70 chaperones work?

A

70kDa monmers
the ATPase domain controls substrate binding domain
ATP bound: no substrate peptide binding
ADP bound: the substrate binding domain is closed tightly on the peptide
binds short hydrophobic sequences

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
29
Q

what are co chaperones?

A

co chaperones are proteins which contact chaperones to regulate their activity
some can bind to polypeptide themselves and are both chaperones and co chaperones

30
Q

what are some HSP70 co chaperones?

A

DNAJ (HSP40) promoter HSP70 substrate binding
nucleotide exchange factors (NEFs) promote substrate release

31
Q

what is the HSP70 functional cycle?

A
  1. HSP40 mediated delivery of substrate to ATP bound HSP70
  2. hydrolysis of ATP to ADP mediated by HSP40 results in closing of the alpha helical lid and tight binding of substrate by HSP70
  3. NEF catalyses exchange of ADP for ATP
  4. opening of the alpha helical lid induced by ATP binding, results in substrate release
  5. released substrate either folds to native state or given to another HSP
32
Q

what do DNAJs do?

A

regulate HSP70 function

33
Q

how many genes code for DNAJs?

A

at least 53

34
Q

what are the different domains of DNAJs?

A

all have a conserved J domain
bind transiently to HSP70, activate it to hydrolyse ATP and bind polypeptide
do not bind substrate
other domains determine their specific biological function
substrate binding (only some have this, bind to hydrophobic sequences)
dimerization domain

35
Q

what do DNAJ co chaperones do?

A

homodimers: 2 subunits of 40-50kDa
bind short hydrophobic sequences
transfer substrate to HSP70 during ATP hydrolysis

36
Q

what do DNAJs that bind substrates act as?

A

bind through specific domains
act as ATP independent chaperones

37
Q

what do DNAJs that do not bind substrates do?

A

specific domains attach DNAJ to a protein complex or intracellular membrane
recruit HSP70 to the complex or the membrane

38
Q

what do NEFs do?

A

remove ADP from HSP70 and allow ATP to bind
NEF binding opens up HSP70 ATPase domain and weakens interaction with the nucleotide
ATP binds when NEF dissociates
ATP bound HSP70 releases the polypeptide
there are several NEF families in humans

39
Q

how does HSP70 help folding?

A

HSP70 binds hydrophobic regions of folding intermediates and prevents incorrect proteins from forming
release of the polypeptide from the HSP70 provides a chance for it to fold

40
Q

the balance between which two things provides an optimal rate for HSP70?

A

DNAJs and NEFs

41
Q

what is the structure of HSP90 chaperones?

A

homodimers, 2 identical subunits joined at the C termini
human HSP90= 2x90kDa= 180kDa

42
Q

what is the analogy of how the dimer works

A

can open and close like a nutcracker

43
Q

what controls the opening and closing of the HSP90 dimer?

A

ATP

44
Q

what stabilises the closed form of the HSP90 dimer?

A

co chaperone p23

45
Q

at what stage of folding does HSP90 bind? and what does it bind to?

A

late stage folding
binds to hydrophobic and polar surfaces, stabilises intermediate folded states
substrate is bound along the sides of the subunit
different substrates can bind to different sites on the sides, unlike HSP70 and chaperonins

46
Q

what do HSP70 and HSP90 form?

A

a multi chaperone system
they cooperate to assist substrates
released from HSP70 and bound by HSP90
HSP70 dissociates when HSP90 binds ATP

47
Q

what assists in the formation of the HSP70 and HSP90 complex?

A

HOP
co chaperones provide flexibility, have folding and non folding functions

48
Q

what is the similarity between HSP70 and HSP90?

A

not homologous but have similar C terminal sequence motif
EEVD-COO-

49
Q

what domain recognises these EEVD motifs?

A

TPR domains in HOP proteins
can be specific for HSC70, HSP90 or both

50
Q

what are TPR domains?

A

adaptors to HSP70 and HSP90

51
Q

what do TPR co chaperones often have?

A

other domains which interact with substrate directly

52
Q

what specific domains does HOP have?

A

domains that bind HSP70 and HSP90

53
Q

what TPR domains does FKBP52 have?

A

HSP90 binding domain and PPIase domains
peptidyl-propyl isomerase: chaperone specific to prolines

54
Q

what does CHIP bind?

A

either HSP70 or HSP90
and has a ubiquitin ligase domain that helps degrade proteins

55
Q

what types of proteins are many HSP90 substrates?

A

signal transduction proteins
kinases, receptors, transcription factors

56
Q

what do those signal transduction proteins also require and what is the exception?

A

many require HSC70 as well
except kinases, HSP90 binds to them without needing HSC70

57
Q

what do mutations in signaling proteins cause?

A

cancer

58
Q

what chaperones are often drug targets for cancer treatment?

A

HSP90 and HSC70

59
Q

what is the difference btween c-src and v-src

A

c-src (cellular) is the normal kinase involved in signaling cell growth
it is auto regulated and not always active
v-src (viral) is a mutant kinase that causes cancer
HSP90 helps it stay active and make tumors

60
Q

how can you treat cancer caused by v-src?

A

v-src expressed in fibroblast epithelial cells causes them to become cancerous
treat cells with HSP90 inhibitor
HSP90 cannot chaperone v-src anymore
cells revert from cancer to normal growth

61
Q

how does the HPS90 functional cycle work? (steps)

A
  1. the C terminus of the proteins is the dimerisation domain, the middle region recognises the client, and the N terminus is the ATP binding domain
  2. the client binds to HSP90, accompanied by HSP40 and HSP70, with the help of the co chaperone HOP
  3. ATP binds to the N terminus of the protein, and the p23 stabilises that binding and closes the conformation
  4. FKBP52 also stabilises the dimer
  5. ATP is hydrolysed to ADP, and the client and other proteins are liberated
  6. ADP is now bound to the protein, but ADP needs to be liberated so that HSP90 can bind to the next client
62
Q

what is the structure of the E.coli GroEL?

A

2 rings x 7 identical subunits x 60kDa = 840kDa
2 cages, one up and one down with alternative cycles

63
Q

what is the structure of the E.coli GroES cap co chaperone?

A

7 subunits x 10 kDA= 70kDa

64
Q

what are the different domains of the HSP60?

A

substrate binding domain
ATPase domain
substrate binding domain
+GroES cap

65
Q

how does ATP change the conformation of HSP60?

A

ATP binding changes the size of the cage

66
Q

what is the conformation of the down position of the HSP60?

A

no nucleotide
smaller
hydrophobic subunits around the ring bind to the hydrophobic polypeptide

67
Q

what is the conformation of the up position of the HSP60?

A

ATP bound
subunits bind to GroES cap instead of the substrate
large cavity with polar surface is formed
doesn’t interact with polypeptide, gives it space to fold
released into the cavity

68
Q

what are the domains in each of the GroEL subunits and their functions during down and up positions?

A

ATPase domain (hydrolyses ATP)
linker region
substrate binding region
in the down conformation the substrate binding region has a hydrophobic residue that points towards the center
the movement of the substrate binding domain is controlled by the ATPase domain
in the up conformation the subunit is taller, the hydrophobic residue binds to the GroES

69
Q

what is the GroEL functional cycle (for one ring)

A

the protein is in its down conformation
ATP binds to it
switches to up conformation, gets bigger
binds the cap
releases the protein inside the cavity, gives it space to fold
ATP is hydrolysed to ADP
releases the protein

70
Q
A

BIOC212 (32 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions