Lecture 6 - Proteins: Structure, Function, and Separation Strategies

Question 1

How can you tell if a protein has transited the ER?

Answer 1

It has a disulfide bridge.

Question 2

What is BiP bound to under normal circumstances that holds it to the ER membrane?

Answer 2

Ire1

Question 3

When does Ire1 dimerize? What does this result in?

Answer 3

Ire1 homodimerizes when Bip is associated with proteins instead of it. When this happens, a strange splicing event occurs that results in the production of a transcription factor that will activate the expression of a number of other chaperone proteins. This is referred to as the initiation of the unfolded protein response (UPR).

Question 4

What are ligands?

Answer 4

Ligands are proteins or other molecules that associated with a specific protein.

Question 5

What can we examine to get a measure of how strong an antibody binds to its ligand?

Answer 5

Dissociation Constant

Question 6

What does a drop in a protein complex’s dissociation constant indicate?

Answer 6

It indicates that the individual proteins are more likely to be in a complex than in single entities.

Question 7

What are catalysts?

Answer 7

Catalysts are molecules that make reactions take place but don’t get consumed in the reaction themselves.

Question 8

How do enzymes catalyze a reaction between two entities?

Answer 8

They reduce the activation energy needed for the reaction to proceed.

Question 9

Why does a reaction have a maximum velocity?

Answer 9

A reaction has a maximum velocity because the system will reach a point at which the active sites of all the enzymes are full and the reaction can’t go any faster.

Question 10

What is the concentration of a substrate at the half maximum velocity referred to as?

Answer 10

Km, the Michaelis Constant

Question 11

What happens to calmodulin when it binds calcium?

Answer 11

Calmodulin will immediately switch its conformation so that it can recognize specific regions of proteins to which it binds.

Question 12

Describe the GTPase cycle.

Answer 12

GTPase is bound to GTP in its active site. GTPase activating protein dephosphorylates the GTP to deactivate the complex. GEF will then replace the GDP with GTP to reactivate the complex.

Question 13

What kind of protein catalyzes phosphorylation?

Answer 13

Protein Kinases

Question 14

What kind of protein catalyzes dephosphorylation?

Answer 14

Phosphatases

Question 15

What are cyclins?

Answer 15

Cyclins are proteins that are very important for driving the cell cycle forward. They act by activating cyclin-dependent protein kinases (CDKs).

Question 16

How are cyclins modified?

Answer 16

Cyclins are modified through ubiquitination. The small protein ubiquitin (76 amino acids) becomes bound to the cyclin, which in turns binds another ubiquitin (at lysine46), which binds another, which binds another, etc.

Question 17

What does poly-ubiquitination lead to?

Answer 17

Protein Degradation

Question 18

What does the E1 enzyme do?

Answer 18

It uses ATP to set up ubiquitin so that you can add it on and utilize it in the final ubiquitination reaction. It links itself to ubiquitin through a thiolester bond with a cystine residue.

Question 19

What does the E2 enzyme do?

Answer 19

Ubiquitin is transferred to E2 to associate with the appropriate E3.

Question 20

What does the E3 enzyme do?

Answer 20

E3 directs the ubiquitin to the its correct final protein target and helps ligase the two.

Question 21

What recognizes polyubiquitinated proteins?

Answer 21

26S Proteasome