Building a Proteome: Modification and Degradation

Question 1

What is covalent modification?

Answer 1

addition of a functional group

Question 2

List 4 examples of covalent modification.

Answer 2

Ubiquination
Acetylation
Phosphorylation
Glycosylation

Question 3

What does a protease do?

Answer 3

cleaves peptide bonds

Question 4

How is proinsulin processed?

Answer 4

A protease cleaves peptide bonds, leaving just insulin.

Question 5

Which amino acid do phosphate groups get added to (only evidenced by figure)?

Answer 5

Serine

Question 6

Which amino acid do acetyl groups get added to? (evidenced by example)

Answer 6

Lysine

Question 7

What are isoforms? Why do they exist?

Answer 7

Peptides with the same amino acid sequence, but different functional groups (after covalent modifications). They help increase molecular diversity, helping cells to regulate processes.

Question 8

Which amino acids can receive phosphate groups? What quality allows them to do so?

Answer 8

Serine, Threonine, and Tyrosine
Only amino acids with OH groups.

Question 9

Does phosphorylation turn a protein on or off?

Answer 9

Trick question! Can do either, depending on the identity of the protein in question.

Question 10

What does a protein kinase do?

Answer 10

Removes a phosphate group from ATP, adding it to a side chain (either serine, threonine, or tyrosine)

Question 11

What does a protein phosphatase do?

Answer 11

Cleaves inorganic phosphate from a side chain

Question 12

What are the three polypeptide degradation methods?

Answer 12

Via the proteosome
Via the lysosome
Via autophagosomes

Question 13

What is a proteosome and what does it do?

Answer 13

Large protein unit comprised of multiple; looks like a hollow tube; core receives 2 caps when operating
Degrades (chops up) polypeptides

Question 14

What determines which mechanism is used to degrade a protein?

Answer 14

The protein in question

Question 15

What must happen before a proteosome degrades a protein?

Answer 15

Ubiquination; ubiquitin must target a protein for destruction

Question 16

What is ubiquitin?

Answer 16

78 amino acid sequence that is added enzymatically to a protein being targeted for degradation

Question 17

What are the potential fates of a newly synthesized peptide? How often do they occur?

Answer 17

1/3 correctly folded without help
1/3 correctly folded with assistance from chaperones and chaperonins
Less than 1/3 incompletely folded are degraded via proteosome
Small amount aggregate and are unable to be destroyed

Question 18

Rank the time each fate of a newly synthesized peptide takes.

Answer 18

1. Correctly folding without help
2. Correctly folding with chaperone and chaperonin assistance
3. Degradation via proteosome
4. Aggregation

Question 19

What is turnover?

Answer 19

degradation of an existing molecule and replacement with a newly synthesized molecule of the same type

Question 20

What are the 3 ways to regulate protein activity?

Answer 20

1. Increase or decrease the steady-state level of a protein by changing its rate of synthesis, degradation, or both (changes protein concentration)
2. Change the location of a protein within a cell (or the volume of the compartment in which the protein resides).
3. Change the activity of a protein with non-covalent or covalent molecular interactions.

Question 21

What does a GTPase (small G protein) do?

Answer 21

When activated, noncovalently binds and hydrolyzes GTP (converting GTP to GDP) and binds to effector

Question 22

What does GAP stand for? What does a GAP protein do?

Answer 22

GTPase Activating Protein binds to G protein and stimulates hydrolysis of GTP; Activating the GTPase activity turns the G protein off (by cleaving the inorganic phosphate)

Question 23

What happens when GTP is hydrolyzed?

Answer 23

GTP loses a phosphate group and becomes GDP.
The small G protein (GTPase) can no longer bind to the effector protein.

Question 24

What turns the G protein on?

Answer 24

GEF (Guanine Nucleotide Exchange Factor)

Question 25

What turns the G protein off?

Answer 25

GAP (GTPase Activating Protein)

Question 26

What happens when GTP is on? When it’s off?

Answer 26

When on, it binds to the effector. When off, it can no longer be bound, so it deactivates.

Question 27

What does the GEF do?

Answer 27

adds the inorganic phosphate onto the GDP, activating the GTPase and allowing it to bind to the effector

Question 28

What does the GAP do?

Answer 28

binds to the G protein, stimulates the hydrolysis of GTP, deactivating the GTPase (prevents from it to bind to the effector)