01b: Protein Folding/misfolding

Question 1

T/F: proteins begin folding while they’re being synthesized.

Answer 1

True

Question 2

Is protein folding into native configuration thermodynamically favorable or unfavorable?

Answer 2

Favorable (spontaneous)

Question 3

Which polypeptide terminus is typically folded first?

Answer 3

N-terminal (since synthesized first)

Question 4

What’s the mechanism of chaperones (how do they assist in folding)?

Answer 4

Restrict folding pathway (limit number of possible intermediate states).

Question 5

Chaperones prevent interaction of:

Answer 5

Hydrophobic patches during folding process

Question 6

Chaperones work (inter/intra)-molecularly to prevent inappropriate interactions.

Answer 6

Both!

Question 7

T/F: Chaperones are ubiquitous among phyla.

Answer 7

True

Question 8

Chaperonins are also known as:

Answer 8

Hsp60 proteins

Question 9

T/F: chaperones are exclusively found in the cytosol.

Answer 9

False - cytosol, ER, mitochondria, chloroplasts

Question 10

Chaperones were discovered in which organism?

Answer 10

Drosophila

Question 11

T/F: Hsp70 chaperones are ATPases.

Answer 11

True

Question 12

Which domains are present in Hsp70 chaperones?

Answer 12

1. NT binding domain

2. Substrate binding domain (clamp)

Question 13

What shuts the clamp in the Hsp70 chaperone?

Answer 13

ATP hydrolysis

Question 14

What opens the clamp in the Hsp70 chaperone?

Answer 14

Exchange/release of ADP (and binding of ATP)

Question 15

T/F: Hsp60 chaperonins are ATPases.

Answer 15

True

Question 16

Describe Hsp60 structure

Answer 16

1. Two independent folding channels (heptameric; called GroEL)
2. Cap (GroES)

Question 17

Proteins fold in which cellular compartment?

Answer 17

Multiple!

1. Cytoplasm
2. ER
3. Mitochondrion
4. Chloroplasts

Question 18

How do folded proteins enter organelles?

Answer 18

They can’t; must be unfolded (enter via pores)

Question 19

Name a key Hsp70 chaperone in the ER.

Answer 19

BiP

Question 20

What’s UPR?

Answer 20

Unfolded Protein Response (compensatory mechanism for misfolded proteins)

Question 21

List sensors for misfolded proteins. Where are they located?

Answer 21

1. IRE1
2. PERK
3. ATF6

ER membrane

Question 22

UPR final outcome:

Answer 22

Activates genes to increase ER folding capacity

Question 23

What molecules are increased as result of UPR?

Answer 23

Chaperones and lipids

Question 24

What are the possible dates of newly synthesized proteins?

Answer 24

1. Correct folding without help
2. Correct folding with chaperone help
3. Incompletely folded and digested by proteosome
4. Protein aggregate

Question 25

Describe basic structure of proteosome

Answer 25

4 heptameric rings and a hexamer cap

Question 26

Name of proteosome cap

Answer 26

19S hexamer called "unfoldase"

Question 27

The proteosome active sites are present in (core/cap) and have (X)-like activities.

Answer 27

20S Core X = trypsin-, chymotrypsin-, and peptidylglutamyl-

Question 28

Proteosome degrades proteins to how many AA peptides?

Answer 28

7-8

Question 29

How does ATP hydrolysis affect the proteosome cap?

Answer 29

Causes conformational change that strains ring and pulls substrate through

Question 30

How many AA in ubiquitin?

Answer 30

76

Question 31

Ubiquitin point of attachment is:

Answer 31

C terminal

Question 32

Ubiquitin attaches to which part(s) of proteins?

Answer 32

Lysine side chains

Question 33

The core of ubiquitin can be described as:

Answer 33

Globular and hydrophobic

Question 34

T/F: Transfer of ubiquitin to ubiquitin ligase is a passive process.

Answer 34

True

Question 35

In ubiquitin transfer, what is E1 formally called?

Answer 35

Ubiquitin-activating enzyme

Question 36

T/F: Binding of ubiquitin to ubiquitin-activating enzyme is a passive process.

Answer 36

False - converts ATP to AMP

Question 37

In ubiquitin binding, the (X) terminus of ubiquitin binds to (Y) group of E1.

Answer 37

X = C Y = -SH (displaces H)

Question 38

In ubiquitin binding, the (X) terminus of ubiquitin binds to (Y) group of E2/E3.

Answer 38

X = C Y = -SH (displaces H)

Question 39

The last AA of ubiquitin (X) connects to the AA (Y) on preceding ubiquitin, forming which type of bond?

Answer 39

``` X = glycine Y = lysine (48) ``` Isopeptide bond

Question 40

Which path do misfolded proteins take to arrive at the (X) for degradation?

Answer 40

Retrotranslocation from ER to cytoplasm X = proteosome

Question 41

Quality control mechanisms help the cell by:

Answer 41

Prevent accumulation of misfolded protein

Question 42

Proteostasis is:

Answer 42

Balance of protein synthesis, folding, and degradation (homeostasis)

Question 43

There are (few/many/unknown) genes involved in proteostasis.

Answer 43

Many

Question 44

It's estimated that as many any (X)% of all polypeptide chains synthesizes in cell misfold.

Answer 44

X = 50

Question 45

Misfolding of protein can result in (gain/loss) of (X) function.

Answer 45

1. Gain of toxic function OR 2. Loss of normal biological function

Question 46

Dominant inheritance of protein misfolding typically results in:

Answer 46

Gain of toxic function

Question 47

Recessive inheritance of protein misfolding typically results in:

Answer 47

Loss of normal biological function

Question 48

What are amyloid fibrils?

Answer 48

Abnormal accumulation of protein

Question 49

In amyloid fibrils, (X) are perpendicular to fiber axis.

Answer 49

X = beta strands

Question 50

In amyloid fibrils, (X) are parallel to fiber axis.

Answer 50

X = beta sheets

Question 51

T/F: Amyloid may have physiological functions.

Answer 51

True

Question 52

Amyloid fibrils can be stained with:

Answer 52

Congo red or thioflavin