Lecture 2

Question 1

Ligand

Answer 1

Any molecule that binds to any site on a protein; isn’t the active site on a protein, however. When it binds to the protein its structure does NOT get changed. doesn’t have to be the active site of an enzyme, the protein doesn’t even need to be an enzyme?

Question 2

Kd

Answer 2

Dissociation constant. It is the concentration of L needed for exactly one half of the protein/enzyme population to be saturated at a given concentration of protein/enzyme.
- Is an indication of “fit” of a ligand to its site: the better the fit, the tighter the binding, and the lower the Kd.

Question 3

isotherm

Answer 3

s

Question 4

rectangular hyperbola

Answer 4

The shape of the graph that is formed by ligand interactions. An example of a molecule that follows this kind of plot is myoglobin. Hemoglobin, which is allosterically regulated, does not follow this type of graph..
- Occurs when K is constant?

Question 5

enzyme-substrate complex

Answer 5

e

Question 6

saturablility

Answer 6

As more ligand is introduced with the same amount of protein present, the more saturated it becomes until it is at its absolute saturation point where every protein is bound to a ligand.

Question 7

Michaelis-Menten equation

Answer 7

d

Question 8

Vmax

Answer 8

e

Question 9

Km

Answer 9

d

Question 10

kcat

Answer 10

f

Question 11

turnover number

Answer 11

d

Question 12

Lineweaver-Burk plot

Answer 12

d

Question 13

inhibitor

Answer 13

d

Question 14

competitive inhibitor

Answer 14

Binds to the same place on the protein as our ligand.

- The binding curve still has the L/(L+K) form

Question 15

uncompetitive inhibitor

Answer 15

e

Question 16

catalytic triad

Answer 16

d

Question 17

induced fit

Answer 17

e

Question 18

cooperativity

Answer 18

Occurs when the concentration of a ligand alters the binding properties of a protein that recognizes it. An example of positive cooperativity is seen in hemoglobin

Question 19

allosteric enzyme

Answer 19

d

Question 20

sigmoidal isotherm

Answer 20

d

Question 21

allosteric inhibitor

Answer 21

Binding of it to one subunit decreases the chance of substrate binding to another subunit of the same enzyme

Question 22

allosteric activator

Answer 22

Binding of it to one subunit increases the chance of substrate binding to another subunit of the same enzyme

Question 23

phosphorylation

Answer 23

• Phosphorylation is the addition of a phosphate group to a molecule (typically a protein) by an enzyme ( a protein called a kinase)
• In some cases, adding a phosphate increases activity/activates the molecule, while in other cases, it decreases activity/deactivates it
• Specific amino acids of an enzyme are phosphorylated, so its not just random
• Phosphatases are what remove a phosphate group, and this can also have an activating or deactivating effect, depending on the protein

Question 24

modification

Answer 24

e

Question 25

inhibitable (paper)

Answer 25

e

Question 26

Entropy Reduction Catalysis

Answer 26

• A mechanism of enzyme catalysis
• Decreases the
• Enzymes do this through non-covalent interactions and binding

Question 27

Acid-Base Catalysis

Answer 27

d

Question 28

Metal-Ion Catalysis

Answer 28

d

Question 29

Chymotrypsin

Answer 29

• An example of the covalent intermediate catalysis mechanism

Question 30

Relationship between change in activation energy and increase in reaction rate

Answer 30

k(new)=K(old) x e^(d/RT)
- When deltaGdagger is lowered by amount d, the rate constant is increased by a factor of e^(d/RT), giving us an exponential relationship

Question 31

Binding Isotherm

Answer 31

d