Protein Function

Question 1

What is a ligand?

Answer 1

any molecule that a protein can bind to in a reversible manner, Typically a smaller molecule

Question 2

What is a binding site?

Answer 2

A site on a protein where ligand binds; very specific!

Question 3

What does induced fit mean?

Answer 3

When both the ligand and the protein can change their conformations upon binding; makes binding site more complementary to ligand.

Question 4

What does affinity mean?

Answer 4

It is a measure of how tightly a protein P binds to ligand L.

Question 5

How is affinity measured?

Answer 5

Affinity is quantitatively expressed as a dissociation constant Kd, which is simply an equilibrium constant for the dissociation reaction. (Lower the Kd the higher the binding)

Question 6

Equation for Kd

Answer 6

Kd = [P] [L] / [PL]

Question 7

How would a protein have multiple binding sites?

Answer 7

If it has multiple subunits.

Question 8

What is cooperatively?

Answer 8

An interaction is cooperative if the binding of one ligand molecule affects the affinity of another ligand molecule on the same protein. It requires multiple domains or subunits.

Question 9

Positive cooperativity

Answer 9

occurs when the binding of a ligand increases the binding affinity of subsequent ligands.

Question 10

Negative cooperativity

Answer 10

occurs when the binding of a ligand decreases the binding affinity of subsequent ligands.

Question 11

What is an allosteric protein?

Answer 11

When binding of one ligand (the effector) affects the binding of another ligand to a different binding site on the same protein. DOES NOT ALWAYS REQUIRE MULTIPLE SUBUNITS!

Question 12

Myoglobin

Answer 12

Contains 1 subunit. Used for O2 storage. Contains 1 heme group.

Question 13

Hemoglobin

Answer 13

Contains 4 subunits - 2 alpha and 2 beta (multiple hetero binding sites). Used for O2 transport. Contains 4 heme groups (can bind 4 oxygens).