Lecture 15

Question 1

What is the protein half life?

Answer 1

this is the time that half the population of protein remains or the time that half of the original populations of protein has been degraded

Question 2

What are 5 reasons that proteins are degraded?

1. to regulate the ________/________ of a ________ and therefore the ________ eg. ______ channels and transporters in epithelia to change _______ transport pathways
2. to allow _______ with new proteins
3. to _________ them e.g., ligands, cell cycle proteins
4. to recycle ________ ________ of ___________ proteins e.g., _________ or _________ proteins in the ER
5. as they are _______ proteins from pathogens

Answer 2

1. to regulate the function/activity of a protein and therefore the cell eg. ion channels and transporters in epithelia to change ion transport pathways
2. to allow replacement with new proteins
3. to inactivate them e.g., ligands, cell cycle proteins
4. to recycle amino acids of nonfunctional proteins e.g., misfolded or misassembled proteins in the ER
5. as they are extracellular proteins from pathogens

Question 3

What does the lifetime of a protein depend on?

Answer 3

the function of the protein and the cellular pathway it is involved in

Question 4

Where are proteins degraded?

Answer 4

in the lysosome or the proteasome

Question 5

What do lysosomes break down?

Answer 5

• extracellular or transmembrane proteins brought into the cell and
• aged or defective organelles (autophagy)

(tyrosine, leucine motifs and ubiquitination)

Question 6

What do lysosomes contain?

Answer 6

enzymes that work best at acidic pH

Question 7

What do the enzymes in the lysosomes breakdown?

Answer 7

proteins, sugars and nucleic acids

Question 8

Two transport proteins pump H+ and Cl- into the lysosome to do what?

Answer 8

maintain low pH

Question 9

Describe the process of autophagy

Answer 9

• there is uptake of a random area of cytoplasm of cytoplasm or defective organelles (this is called the phagophore)
• the phagophore forms a complete vesicle called the autophagosome
• the autophagosome begins to fuse with the lysosome
• an autophagosome is formed and degradation begins
• organelles and any uptake substances degraded and recycled

Question 10

What is the ubiquitin-proteasome system for protein degradation?

Answer 10

this is a highly controlled process for degrading unwanted proteins, terminating or activating signalling pathways, regulating the cell cycle and providing an important source of amino acids for new protein synthesis

Question 11

What is ubiquitination?

Answer 11

this is when proteins are covalently tagged with a small 8kDa protein called ubiquitin

Question 12

Ubiquitination occurs through a series of enzymes called what? What do these enzymes do?

Answer 12

E1 (activating enzyme)
E2 (conjugating enzyme)
E3 (ligase)
these catalyse the covalent attachment of ubiquitin to target proteins

Question 13

Describe how the ubiquitination process occurs

Answer 13

E1 catalyses the breakdown of ATP to AMP which will transfer ubiquitin to E2, then this repeats to get it to E3 and then E3 transfers it to the protein

Question 14

During endocytosis, proteins are deubiquitinated. What is involved in this?

Answer 14

this is done by deubiquitinating enzymes or DUBS which remove ubiquitin from proteins

Question 15

Describe the role of the proteasome in the process of degradation

Answer 15

Ubiquitin binds to the proteasome and orients the protein. The protein is degraded in the proteasome by a peptidase (break the peptide bonds between amino acids) and the peptides and amino acids are recycled

Question 16

What does ubiquitin tagging promote?

Answer 16

endocytosis of ion channels

Question 17

Give an example of Ubiquitin tagging promoting endocytosis of ion channels?

Answer 17

1. ENaC and ROMK1 are monoubiquitinated, promoting endocytosis to the apical sorting endosome
2. Ubiquitinated proteins trafficked onto common endosome where fate of the channel is determined
3. Deubiquitination leads to recycling. If they are not deubiquitinated, the ubiquitinated proteins move on to lysosome for degradation

Question 18

What happens in Liddle’s syndrome?

Answer 18

ENaC cannot be tagged with ubiquitin due to loss of the binding site for an E3 ubiquitin ligase. Therefore less ENaC endocytosis, more ENaC at the plasma membrane and more Na+ reabsorption leading to high ECF volume and pressure

Question 19

What are the 3 main types of ubiquitination?

Answer 19

1. monoubiquitination
2. multiubiquitination
3. polyubiquitination

Question 20

Describe monoubiquitination

Answer 20

This is the single addition of ubiquitin

Question 21

What is multiubiquitination?

Answer 21

The single addition of ubiquitin at multiple different sites

Question 22

What is polyubiquitination?

Answer 22

the binding of a ubiquitination chain on a single site

Question 23

How and to what is ubiquitin binded?

Answer 23

It is covalently linked to lysines or to the N-terminal amino acid of the target/substrate protein

Question 24

What is ubiquitination a signal for?

Answer 24

endocytosis

Question 25

What is polyubiquitination a signal for?

Answer 25

degradation in the proteosome

Question 26

Where can a good summary and comparison on lysosome, autophagy and proteosome-mediated degradation be found?

Answer 26

slide 13 lecture 15

Question 27

Which method of degradation involves E1, E2, E3?

Answer 27

proteasome

Question 28

Lysosomes only degrade proteins BECAUSE monoubiquitin is used as a tag for degradation in the endocytosis pathway.
A. Both statements true and causal.
B. Both statements true but not causal.
C. First statement true, second false.
D. First statement false, second true.
E. Both statements are false

Answer 28

false, true

Question 29

What enzymes are in lysosomes?

Answer 29

Acid hydrolases

Question 30

What enzymes are in Proteasomes?

Answer 30

Peptidases

Question 31

What enzymes are involved in Autophagy?

Answer 31

Acid hydrolases

Question 32

What do lysosomes degrade?

Answer 32

proteins, sugars, DNA/RNA

Question 33

What do proteasomes degrade?

Answer 33

Proteins (ubiquitin recycled)

Question 34

What does autophagy degrade?

Answer 34

Damaged organelles, microbes, cytosolic components

Question 35

Describe the regulation of the lysosome degradation

Answer 35

it is Somewhat random, ubiquitin tagging

Question 36

Describe the regulation of the proteasome degradation

Answer 36

Highly regulated

Question 37

Describe the regulation of the autophagy degradation

Answer 37

Random, but some regulation

Question 38

What are the cofactors required in lysosome degradation?

Answer 38

NA

Question 39

What are the cofactors required in proteasome degradation?

Answer 39

Requires a series of three enzymes: E1,E2 and E3

Question 40

What are the cofactors required in autophagy degradation?

Answer 40

NA

Question 41

What are the general targets for lysosome degradation?

Answer 41

Cell surface and extracellular proteins

Question 42

What are the general targets for proteasome degradation?

Answer 42

Cytoslic, nuclear, ER proteins (ERAD)

Question 43

What are the general targets for autophagy degradation?

Answer 43

Cytosolic components

Question 44

Describe the structure of the autophagy

Answer 44

Double- membraned autophagosome