SCHOCH

Question 1

Cells control the balance between ________/_________ & degradation to respond to changing cellular environments and stimuli.

Answer 1

transcription/translation

Question 2

The balance between transcription/translation & degradation is specific to each ________/________.

Answer 2

gene/protein

Question 3

List three reasons why a protein might be degraded.

Answer 3

Damage, Aggregation/Misfolding, Not currently needed

Question 4

Amino acids may be needed for _________ generation (muscle) or for biosynthesis of other molecules.

Answer 4

energy

Question 5

Protein half-lives can depend on the protein’s _______________ properties.

Answer 5

physicochemical

Question 6

List four physicochemical properties that can affect a protein’s half-life.

Answer 6

-Amount of secondary structure
-Number of cellular binding partners
-Catalytic activity level
-Tissue type

Question 7

Degradation can be coordinated between multiple proteins in a ________.

Answer 7

complex

Question 8

How many E1, E2, and E3 enzymes are there in the ubiquitin proteasome system?

Answer 8

1 E1 enzyme, 30 E2 enzymes, >700 E3 enzymes

Question 9

True or False: Each E3 recognizes only one protein for degradation.

Answer 9

False, less E3s than proteins

Question 10

What is the size of ubiquitin?

Answer 10

8.6 kD

Question 11

Ubiquitin has many ________ residues which serve as sites for poly-ubiquitin chain formation.

Answer 11

lysine

Question 12

Ubiquitin is highly _________: between human, yeast, and oat there are only 3 amino acid changes.

Answer 12

conserved

Question 13

The C-terminal ________ of ubiquitin is the residue that will be esterified to the E1 and E2 enzymes.

Answer 13

glycine

Question 14

The E1 enzyme is comprised of two halves – each containing an ___________ domain and a catalytic _________ domain.

Answer 14

adenylation, cysteine

Question 15

What stabilizes the interaction between ubiquitin and the E1 enzyme?

Answer 15

The flexible C-terminal tail extends under a loop connecting the two domains (“the crossover loop”)

Question 16

________ and ________ are two structurally related proteins to ubiquitin that tag proteins for processes other than degradation.

Answer 16

Nedd8, SUMO

Question 17

The E1 enzyme for ubiquitin has a negatively charged groove that binds ________ in the tail of ubiquitin.

Answer 17

arginine

Question 18

The E1 enzyme for Nedd8 has a ___________ groove that binds alanine in the tail of Nedd8.

Answer 18

hydrophobic

Question 19

The E1 enzyme for SUMO has an arginine and tyrosine-filled groove that binds __________ in the tail of SUMO.

Answer 19

glutamate

Question 20

True or False: Nedd8 and SUMO do not lead to degradation by the proteosome.

Answer 20

True

Question 21

The E2 enzyme acts as a ______________ binding both the E1 and E3 enzyme.

Answer 21

middle-man

Question 22

The E2 enzyme depends upon the E1 having bound the correct ________ or ____________________.

Answer 22

ubiquitin, ubiquitin-like protein

Question 23

What are the two major families of E3 ligases?

Answer 23

HECT-containing, RING-containing

Question 24

RING-containing E3 ligases can be either _________ subunit or ______________.

Answer 24

single, multi-unit

Question 25

HECT E3s contain a catalytic _________ residue in their C-lobe that accepts Ub from the E2.

Answer 25

cysteine

Question 26

RING E3s transfer Ub directly to the __________.

Answer 26

substrate

Question 27

One RING E3 recognizes the _________________ residue of a protein to target it for degradation.

Answer 27

N-terminal

Question 28

Degradation rates in the N-end rule pathway are dependent on the N-terminal ___________ or on a modified N-terminus such as _______________.

Answer 28

amino acid, acetylation

Question 29

_____ (___________) Ligases are the largest family of RING E3s.

Answer 29

SCF (Skp1-Cullin1-Fbox)

Question 30

What are the four components of SCF ligases?

Answer 30

RING domain (ex. Rbx1), Scaffolding protein (Cullin1), Adaptor protein (Skp1), The E3 ligase which contains an Fbox domain

Question 31

Flexibility in the ________ scaffold disrupts ubiquitination of substrates.

Answer 31

Cullin1

Question 32

Binding to SCF ligase substrate binding domains is almost always regulated by requiring ______________________ modification or an _______________ protein.

Answer 32

post-translational, accessory.

Question 33

RING E3s need to be _______(rigid/flexible).

Answer 33

rigid

Question 34

The goal of SCF ligases is to bring a substrate ________ into the right proximity to catalyze Ub transfer from the E2 or E3.

Answer 34

lysine

Question 35

Sites of ubiquitin chain attachment (on the substrate) affects the rate of substrate _____________.

Answer 35

degradation

Question 36

Ubiquitination targets the protein to the ___________.

Answer 36

proteosome

Question 37

The core particle of the proteasome consists of 4 ___________ rings, 2⍺ and 2β.

Answer 37

heptameric

Question 38

The RPT hexamer is an __________ enzyme.

Answer 38

unfoldase

Question 39

Degradation by the proteasome requires the Ub chain + an _____________ region of 20-30 aa that is positioned near the RPT hexamer.

Answer 39

unstructured

Question 40

The proteasome is regulated by requiring assembly of the _____ regulatory particle.

Answer 40

19S

Question 41

Fbxw7 is the most frequently mutated member of the UPS. Mutations in Fbxw7 abolish binding with all its substrates, and many of these substrates are ___________.

Answer 41

oncogenes

Question 42

_____________ is the process by which cytosolic components are encapsulated within a single membrane which then fuses with the lysosome to degrade its components.

Answer 42

Autophagy

Question 43

Specific autophagy requires ___ modification.

Answer 43

Ub (ubiquitin)

Question 44

________________ is the term used to describe the balance between transcription/translation and degradation that cells use to respond to changing cellular environments and stimuli.

Answer 44

Proteostasis

Question 45

A protein that is ________________ and/or misfolded may be degraded.

Answer 45

aggregated

Question 46

The _________ of a protein is the time it takes for half of the protein to be degraded.

Answer 46

half-life

Question 47

________________ E3 ligases contain a catalytic cysteine residue in their C-lobe that accepts ubiquitin from the E2 enzyme.

Answer 47

HECT

Question 48

The _________ between the two lobes of HECT E3s is flexible, allowing the C-lobe to rotate into the proper proximity to transfer ubiquitin to the substrate.

Answer 48

linker

Question 49

________________ E3 ligases transfer ubiquitin directly to the substrate.

Answer 49

RING

Question 50

In the N-end rule degradation pathway, the protein is targeted for degradation based on its ________________ amino acid.

Answer 50

N-terminal

Question 51

SCF ligases are the __________ family of RING E3s.

Answer 51

largest

Question 52

The RING domain of an SCF ligase is also called _________.

Answer 52

Rbx1

Question 53

_______________________ modification or the presence of an accessory protein is often required for binding to SCF ligase substrate binding domains.

Answer 53

Post-translational

Question 54

The ____________ is a large protein complex responsible for degrading proteins that have been tagged with ubiquitin.

Answer 54

Proteasome

Question 55

For a protein to be degraded by the proteasome, it must be tagged with a _______________ chain of a certain type.

Answer 55

poly-ubiquitin

Question 56

True or False: Proteins that are more unfolded (less structured) are degraded faster than globular proteins.

Answer 56

True

Question 57

If all lysines in a ubiquitin chain are linked through the same lysine, the chain is called __________.

Answer 57

Homotypic