Lecture 10 - Enzymes I - Substrate Binding

Question 1

What are the major classifications of enzymes and their functions?

L10 S3-11

Answer 1

Oxidoreductases:
-moves electrons; oxidation/reduction

Transferases:
-transfers a functional group

Hydrolases:
-break a bond by adding water

Lyases:
-break a bond without water

Isomerases:
-isomerization

Ligases:
-make a new chemical bond using ATP

Question 2

What are the main metabolic reaction types and what occurs in each?

L10 S12

Answer 2

Nucleophilic substitution:
-swap of functional groups

Nucleophilic addition:
-addition of functional group

Carbonyl condensation:
-changes # of C’s

Elimination:
-increased bond order

Oxidation-reduction:
-moves electrons

Question 3

What are the key features affecting how an enzyme interacts with another substance?

L10 S13-14

Answer 3

Noncovalent interactions:

• non-polar (Van der Waals)
• charge-charge
• H-bonding

Shape/size

Question 4

What are the characteristics of an active site?

L10 S14

Answer 4

Binding site for substrate
Specific for substrate by creating unique micro environment favorable for interaction with substrate.
Specificity is caused by only a few AAs

Question 5

What is an allosteric binding site and what binds at this location?

L10 S15

Answer 5

A binding site located somewhere other than the active site.

Activators or inhibitors can bind here.

Question 6

Differentiate between apoenzymes and holoenzymes.

L10 S18

Answer 6

Apoenzyme:

• enzyme that lacks necessary cofactor/coenzyme
• inactive

Holoenzyme:

• apoenzyme that now has required cofactor/coenzyme
• active

Question 7

What are the association and dissociation constants?

L10 S22

Answer 7

K(A):

• [E*S]/[E][S]
• 1/K(D)

K(D):

• [E][S]/[E*S]
• 1/K(A)
• the concentration of ligand at which half the available binding sites are full

Question 8

What is fractional saturation and how do you calculate it for an enzyme with one binding site?

L10 S23

Answer 8

Fractional saturation, Y, the fraction of enzyme bound by ligand.

Y= [S]/(K(D) + [S])

Question 9

What is a Scatchard plot?
What do the intercepts represent on this plot?

L10 S26

Answer 9

Linear adaptation of the graph of fractional saturation and [S].

Y-intercept:
-1/K(D)

X-intercept:
-[E], total amount of enzyme present

Question 10

What does the term “cooperativity” mean with regards to enzymes?

L10 S28

Answer 10

When a ligand binds to a an enzyme and affects the strength of interaction of the next ligand to bind.