Key Terms with Example Questions

Question 1

ubiquitin

Answer 1

a 76 amino acid polypeptide that acts as a tag to identify misfolded, obsolete, and damaged proteins to be degraded by proteases or repaired by polyubiquitylation,
depending on whether it binds to lys 48 for degradation or lys 63 for repair

Question 2

proteasome

Answer 2

has 3 parts (2 19s cap and 20s core)

Question 3

chaperonin

Answer 3

Hsp60; a class of chaperones that act post-translationally and facilitate folding by their small chamber

Question 4

degron

Answer 4

a sequence that marks a target protein as needing to be degraded; a signal to E3

Question 5

hsp 70

Answer 5

aka HSC (heat shock cognate); acts co-translationally and functions to bind and stabilize unfolded/partly folded proteins to prevent aggregation while the new protein is still being translated because it does not know how to fold until fully synthesized;

Question 6

• E3

Answer 6

ubiquitin ligase; attaches to the degron of a target protein to transfer ubiquitin from E2 to the lysine48 NH3 group, resulting with the polyubiquitin chain on the target protein

Question 7

20s core

Answer 7

protease; has the active sites to clip every peptide bond and keeps the entire substrate bound until it is converted into amino acids

Question 8

ubiquitin conjugating enzyme

Answer 8

E1; has a cysteine side chain (-SH) that attaches to ubiquitin (COO-) to form a thioester bond (S-C=O)

Question 9

target protein

Answer 9

a protein that is marked or needs to be marked for either degradation, repair, etc.

Question 10

For further thought: There are about 600 E3 ligases and 30 distinct E2 molecules. Why do you think there is such a big difference in the number of E3 and E2 molecules?

Question 11

Application: Components of the ubiquitin machinery were identified independently in genetic screens for genes that regulate the cell cycle. A mutation in genes required for chromosome segregation should cause cells to arrest in mitosis before chromosome segregation occurs. As it turns out, in some of these mutants that arrested in mitosis before chromosome segregation, the gene product was required for proteolytic destruction of specific proteins. What do you think these specific proteins do? What does the unmutated form of the gene encode?

Question 12

In your own words describe the overarching cell biology concept illustrated by these pathways?

Question 13

Ubiquitin can also regulate histones by

Answer 13

monoubiquitylation and endocytosis by multiubiquitylation; attaches as a tag by an isopeptide bond

Question 14

Ubiquitin receptor on 19s cap…

Answer 14

recognizes ubiquitin

Question 15

Ubiquitin hydrolase on 19s cap…

Answer 15

clips ubiquitin

Question 16

hexameric unfoldase ring on 19s cap…

Answer 16

unwinds protein strand by stretching and pulling the substrate by ATP hydrolysis; protein moves to 20s core (protease) that keeps the substrate bound until all peptide bonds are cut by active sites; amino acids exit the bottom 19s cap to re-assist the cell

Question 17

Hsp 60 functions to prevent…

Answer 17

aggregation by having a high affinity for the nonpolar side chains sticking out of the misfolded/incomplete proteins by binding and pulling them in

Question 18

Hsp 60 is capped by… with what in the cap…

Answer 18

GroEL/GroES; with ATP and the cap

Question 19

Hsp60 elongates to…

Answer 19

stretch and properly fold the protein

Question 20

Hsp 60 properly folded then what happens??

Answer 20

ADP is released and with the addition of another ATP, the cap is off and the newly folded protein is released

Question 21

activating the degron has different pathways: what are they??

Answer 21

phosphorylation by kinases, unmasked by protein dissociation, and creation of a destabilizing N-terminus

Question 22

Hsp 70 binds to

Answer 22

the SBD 9 substrate binding domain) on the nonpolar side chains with ATP (which is bound by the nucleotide binding domain); as ATP is hydrolyzed to ADP, SBD clamps down, folding the protein, and releases as new ATP s added