Lecture 17 (exam 3)

Question 1

Protein folding in the cytoplasm and in the ER

Answer 1

Some proteins are translated straight into the cytoplasm

some proteins are translocated into the ER during translocation

Question 2

Protein folding in the cytoplasm

Answer 2

Some proteins begin to fold while being synthesized

Question 3

Problems with simplistic view of folding

Answer 3

• folding intermediated
• folding that requires distinct amino acids from different regions of the polypeptide
• folding that requires post-translational mdoification

Question 4

Molten Globule Structure

Answer 4

most newly synthesized proteins can form compact domain structures with most of the final secondary features (alpha-helices, beta-sheets)

quickly achieved, highly dynamic and flexible state

Question 5

Chaperone-mediated folding

Answer 5

most proteins probably don’t fold before synthesis is completed

Each domain of a newly synthesized protein quickly attains a molten globule state
—>
subsequent folding is slow; it involves multiple steps that require a chaperone

Question 6

chaperones and protein folding

Answer 6

protein folding occurs via multiple binding and release steps by the chaperones

many proteins need chaperones to fold into their final conformation

Question 7

common caperones

Answer 7

Hsp60, Hsp70, and lectin chaperones in the ER

Question 8

Hsp60 and Hsp70

Answer 8

chaperones

heat shock proteins Hsp60 and Hsp70 help protein to fold into their right conformation

structurally they are different

Question 9

Hsp60 and Hsp70 have high affinity

Answer 9

to hydrophobic patches on polypeptide chains

Question 10

Hsp60 and Hsp70 use _____ to regulate protein folding

Answer 10

ATP

Question 11

Hsp70 (____) and Hsp60 (____)

Answer 11

Hsp70 (early) and Hsp60 (later)

Question 12

Hsp70

Answer 12

acts early,
it binds the protein before it leaves the ribosome

Question 13

Hsp60

Answer 13

acts later,
only associates with fully synthesized proteins

Question 14

ROS

Answer 14

H2O2, OH-, O2

Hydroxyl radicals are the most damaging of all
ROS species in the cell.

Ultimately, keeping H2O2 levels low in the cell keeps us in good shape

Question 15

Antioxidants

Answer 15

peroxidases, superoxide dismutase

Question 16

Glutathione

Answer 16

most important antioxidant

Question 17

glutathione reductase

Answer 17

consumes vast amount of NADPH in order to re-reduce oxidized GSH back to reduced GSH.

this cycle continuously operates in order to keep hydrogen peroxide levels in check

NADPH ultimately reduces oxidized methionine and cystein in proteins keeping them reduced

Question 18

Proteasome

Answer 18

main machine for degradation

deliberately destroys aberrant proteins

Question 19

protein degradation

Answer 19

a regulated process brought about by a combination of cellular enzymes and proteins

Question 20

Two main systems for protein degradation in cells

Answer 20

1. Ubiquitin-mediated degradation
2. lysosomal protein degradation mediated by the autophagy pathway

Question 21

26S proteosome

Answer 21

is comprised of a 20S core catalytic particle and two 19S caps

core has multiple proteolytic activities and enables recycling of amino acids back into protein synthesis

dispersed throughout cytoplasm, mitochondria and nucleus

Question 22

polyubiquitinated proteins (proteosome)

Answer 22

are recognized by the 19S cap where numerous ATPase unfold proteins

Question 23

De-ubiquinated, unfolded proteins (proteosome)

Answer 23

transverse down the central cylinder and are degraded to amino acids and short peptide

Question 24

Ubiquitin

Answer 24

is a ~9 kDa polypeptide that can be ligated into target proteins either as a monomer or in a polymerized manner (poly-ubiquitination)

Question 25

Polyubiquitination of target proteins

Answer 25

occurs via sequential addition of ubiquitin monomers to the seeding ubiquitin via isopeptide bond formation between the epsilon-amino group of Lys48 with the c-terminus of ubiquitin

Question 26

How is regulated protein degradation induced?

Answer 26

1. Activation of a ubiquitin ligase
2. Activation of a degradation signal

Question 27

Protein folding and degradation in the ER

Answer 27

a “lectin chaperone”

Question 28

ER: N-linked Oligosaccharides

Answer 28

used as tags to mark the state of protein folding

Question 29

Three sensors for misfolded proteins

Answer 29

IRE1, PERK, ATF6

—-> activation of genes to increase protein folding capacity of ER

Question 30

The unfolded protein response

Answer 30

activates transcription of chaperone genes to help the
cell cope with misfolded proteins