Enzymes

Question 1

Km - what is it?

Answer 1

• Km is a substrate concentration (units must be in concentration)
• Km is a property of every enzyme molecule…. it does NOT depend upon the enzyme concentration. Thus it is an intrinsic constant, in contrast to Vmax
• Km is inversely related to the affinity of an enzyme for its substrate: the higher the affinity the lower the Km

Question 2

K_m versus enzyme concentration and V_max

Answer 2

Question 3

Michaelis-Menten equation

With a very long and complex derivation, we can produce an equation which relates the K_m, the V₀, Vmax , and substrate concentration

Answer 3

Question 4

Lineweaver-Burke plot

Answer 4

Question 5

Lineweaver-Burk Plot (Double-Reciprocal)

The meaning of the reciprocal of Michaelis-Menten data

Answer 5

Question 6

K_cat = Catalytic constant or Turnover number

Answer 6

Represents the number of substrate molecules transformed to product by a single enzyme, E, per given time. Units = sec^-1

Question 7

Catalytic Efficiency

Answer 7

K_cat / K_m = Catalytic Efficiency, or how avidly the enzyme binds to its substrate and how rapidly it converts it to product.

Question 8

Irreversible inhibition

Answer 8

Bind to the enzyme so tightly that activity is blocked

“Suicide substrates” – enter the active site and fail to undergo the complete reaction – stuck in the active site. Chemical weapons.

Question 9

Competitive Inhibition

Answer 9

A substance directly competes with a substrate for binding to the active site.

Question 10

Competitive Inhibition, graphs.

Answer 10

• K_m increases: enzyme’s affinity for the substrate decreases, it takes a higher concentration of S to reach 1/2 V_max
• V_max stays the same: because S can still enter the active site, as [S] increases, Vo approaches Vmax

Question 11

Uncompetitive Inhibition

Answer 11

Inhibitor binds to the enzyme after substrate has bound: binds only to the ES complex.

Question 12

Uncompetitive Inhibition, graphs

Answer 12

• V_max decreases: enzyme-substrate-inhibitor complex does not form product
• K_m decreases proportionately (slope is the same!): binding of I to ES depletes ES complex causing more S to bind to E – lowering K_m

Question 13

Mixed Inhibition

Answer 13

Occurs when an inhibitor binds to an enzyme and alters the conformation such that both V_max and K_m are affected.

Question 14

Non-competitive inhibition

Answer 14

Question 15

Allosteric enzyme (Regulatory Enzymes)

Answer 15

• Regulate the flow of metabolites
• Activity is modulated through reversible, noncovalent binding of regulatory compounds
• Typically multisubunit proteins

Question 16

Allosteric effectors

Answer 16

small molecules that bind an enzyme at sites different than the substrate binding site and effects, positively or negatively, the activity of that enzyme

Question 17

Homotrophic and Heterotrophic enzymes

Answer 17

Homotrophic enzyme
1 molecule acts as both the ligand and the allosteric modulator

Heterotrophic enzyme
Modulators are different than ligands with different binding sites

Question 18

Kinetics of Allosteric Enzymes

Answer 18

Question 19

Percent of deprotenation given pKa and pH

Answer 19

pH = pKa + log(deprotenated/protenated)

Question 20

Gibbs Free Energy, given enthalpy, entropy, and temperature

Answer 20

∆G = ∆H - T∆S

Question 21

∆G˚

Answer 21

∆G˚ = -RT ln(K_eq)

Question 22

Gibbs free energy, given K and ∆G˚

Answer 22

∆G = ∆G˚ + RT ln([B]/[A])

Question 23

Non Polar AA

Answer 23

Glycine, Alanine, Proline, Valine, Leucine, Isoleucine, Methionine

Question 24

Polar AA

Answer 24

Serine, Threonine, Cysteine, Asparagine, Glutamine

Question 25

Aromatic AA

Answer 25

Phenylalanine, Tyrosine, Tryptophan

Question 26

Positively Charged AA

Answer 26

Lysine, Arginine, Histidine

Question 27

Negatively Charged AA

Answer 27

Aspartate, Glutamate