protein folding and translation

Question 1

protein folding location

Answer 1

cytosol

Question 2

protein folding details

Answer 2

1) information is contained in primary aa sequence
2) initially driven by burial of hydrophobic domains
3) Chaperone proteins facilitate folding

Question 3

Hsp chaperones

Answer 3

bind hydrophobic domains

Question 4

DnaK aka

Answer 4

Hsp 70

Question 5

DnaK recognizes…

Answer 5

exposed hydrophobic domains

co-translational recognition

Question 6

accumulation of protein deposits leads to

Answer 6

Alzheimer’s disease (amyloid beta plaques and neurofibrillary tangles)
Parkinson’s disease (neurofibrillary tangles)
Huntington’s disease (polyQ aggregates of huntington protein)

Question 7

where are gram-negative bacteria synthesized

Answer 7

cytoplasm, inner membrane, periplasm, outer membrane

Question 8

proteins not going to the cytoplasm have

Answer 8

a leader sequence at the amino terminus

Question 9

what removes leader sequence at amino terminus

Answer 9

leader peptidase

Question 10

what synthesizing cytoplasmic proteins

Answer 10

soluble ribosomes in the cytosol

Question 11

proteins destined for nucleus or mitochondria

Answer 11

also synthesized by soluble ribosomes in cytosol before being targeted for correct organelle

have special signals in primary aa sequence

Question 12

proteins that are translated by ribosomes in the ER are

Answer 12

proteins with membrane-spanning domains or that are secreted or that reside in membrane-bound vesicles

Question 13

protein translation in ER step 1

Answer 13

1) signal peptide at amino terminus directs ribosome to ER (for membrane-bound or secreted proteins)
2) signal peptidase removes the signal peptide

Question 14

during nascent protein synthesis in ER lumen,

Answer 14

chaperone name BiP binds and maintains polypeptide in a state competent for subsequent folding

Question 15

N-linked glycosylation

Answer 15

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

Question 16

N-linked glycosylation and protein folding

Answer 16

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

Question 17

where do misfolded proteins go

Answer 17

ER

Question 18

where do properly folded proteins go

Answer 18

Golgi

Question 19

O-linked glycosylation

Answer 19

in Golgi
adds carbohydrates to oxygen of Ser or Thr (no consensus sequences)
(post-translational)
carbs are added individually

Question 20

post-translational processing of proteins

Answer 20

Proteolytic cleavage:
- Removal of N-terminal Met
- Pro-proteins
- Removal of signal sequences
Phosphorylation
Glycosylation
Acetylation
Methylation
SUMO-lation

Question 21

protein turnover

Answer 21

proteins have different turnover rates

misfolded proteins must be recognized and removed

Question 22

protein degradation common pathway

Answer 22

targeted for degradation by ubiquitin and sent to proteasomes

Question 23

non-selective protein degradation

Answer 23

in lysosomes

Question 24

lysosomes

Answer 24

membrane-bound compartments that contain proteolytic enzymes called cathepsins
active only at low pH (~5)

Question 25

autophagy

Answer 25

helps degrade and recycle cellular components

how: enclosing large cellular components in a membrane that fuses with lysosomes

Question 26

ubiquitination of proteins

Answer 26

ubiquitin can be linked to Lys residues

proteins must be poly-ubiquitinylated to be targeted to the proteasome

Question 27

E1: ubiquitin-activating enzyme

Answer 27

cells have 1 E1

Question 28

E2: ubiquitin-carrier protein

Answer 28

cells have a few E2s

Question 29

E3: ubiquitin-protein ligase

Answer 29

recognizes targets for degradation and recognizes E2s

cells have many E3s

Question 30

protein degradation RULES

Answer 30

Proteins with acidic amino terminus are targeted for degradation via an Arginine-modified intermediate
Proteins with PEST sequences also have short half-lives

Question 31

proteasome structure

Answer 31

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

Question 32

protein degradation in proteasome: how?

Answer 32

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

Question 33

proteasome inhibitors

Answer 33

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

Question 34

SUMO

Answer 34

small ubiquitin-like protein modifiers (SUMO)

Question 35

small ubiquitin-like protein modifiers role

Answer 35

Can be covalently linked to Lyc residues
Uses similar E1, E2, and E3 enzymes
Sumoylated proteins are NOT targeted for degradation

Question 36

consequences of sumoylation

Answer 36

Interactions with a partner may be prevented
Interactions with a partner may be permitted
Induction of a conformational change in the protein

Question 37

protein quality control

Answer 37

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