Exam I

Question 1

Oxidoreductases

Answer 1

catalyses oxidation-reduction reactions.

Question 2

Transferases

Answer 2

Catalyses transfers of C- N , or P containing groups.

Question 3

Hydrolases

Answer 3

Catalyze cleavage of bonds by addtion of water.

Question 4

Isomerases

Answer 4

Catalyzes racemization of optical or geometric isomers.

Question 5

Ligases

Answer 5

Catalyzes the formation of bonds between Carbon, O, S, N, coupled to hydrolysis of high energy phosphates. (ATP goes to ADP-Pi)

Question 6

Why biocatalysis?

Answer 6

Higher reaction rates, greater reaction specificity, capacity for regulation, metabolites have many potential pathways of decomposition, enzymes make the desired one most favorable.

Question 7

Lyases

Answer 7

Catalyzes cleavege of C-C , C-S, and certains C-N bonds.

Question 8

What does enzymes do to the Rate of the reaction?

Answer 8

Rate acceleration

The enzymes lower the activation barrier compared to the uncatalyzed aqueous reaction. Enzymes do not change free energies of reactants and products, and therefore, do not change the equilibrium of the reaction

Question 9

Enzymes catalyze biological reactions by

1- Increasing entropy of a system

2- Increasing substrate energy

3- Altering reaction equilibrium

4- Lowering total energy levels of reactants

5-Decreasing free energy of activation

Answer 9

5-Decreasing free energy of activation

Question 10

What are inhibitors?

Name a type of Inhibitor

Answer 10

Inhibitors are compounds that decrease the rate of an enzematic reaction.

Transition-state analogs are extremely potent and specific inhibitors of enzymes because they bind more tightly to the enzyme than do substrates or products.

Question 11

How does penicillin works?

Answer 11

The antibiotic peniciliin is a transition state analog that binds tightly to glycopeptidyl transferase, the enzyme required by bacteria for synthesis of the cell wall.

Question 12

What kind of curve does Michaellis-Menten show?

What kind of curve do allosteric enzymes show?

Answer 12

Enzymes following Michaellis-Mentes show hyperbolic curve.

Allosteric enzymes show sigmoidal curves.

Question 13

What means to affinity when you have a large Km? what about a small Km?

Answer 13

If we have a large Km, it means the enzyme affinity to the substrate is low. If we have a small Km it means the enzyme affinity to the subtrate is high.

Question 14

What is K_cat?

Answer 14

The turn over number- How many substrate molecules can one ezyme conver per second.

Question 15

What does the K_m refers to?

Answer 15

An approximate measure of substrate’s affinity for enzyme.

Question 16

What are irreversible inhibitors?

Answer 16

They are inactivators, react with the enzyme. One inhibitor molecule can permanently shut off one enzyme molecule. They are often powerful toxins but may also be used as drugs.

Question 17

How do reversible inhibitors work?

Answer 17

Reversible inhibitors are often structural analogs of substrates of products. They can bind to, and can dissociate from the enzyme. They are usually used as drugs to slow down the enzyme.

Question 18

How does the K_m change with a competitive inhibitor?

Answer 18

K_m increases when there is a competitive inhibitor.

Question 19

What happens to K_m with non-competitive inhibitors?

Answer 19

K_m stays the same. But V_max decreases.

Question 20

What kind of inhibitor appears in this Lineweaver-Burk graph?

Answer 20

Non-competitive, K_m doesn’t change. Only V_max decreases.

Question 21

How is the enzyme synthesis controlled?

Answer 21

The rate of enzyme synthesis is regulated by increasing or decreasing the rate of gene transcription.

Question 22

How is protein degredation achieved?

Answer 22

Protein in the cell can be degraded with characteristic half-life within lysosomes, or via two specialized systems, proteosomes and caspases, which are highly selective and regulated.

Question 23

LOCK-AND-KEY MODEL FOR SUBSTRATE BINDING

Answer 23

The substrate-binding site contains amino acid residues arranged in a complemen- tary three-dimensional surface that “recognizes” the substrate and binds it through multiple hydrophobic interactions, electrostatic interactions, or hydrogen bonds (Fig. 8.5). The amino acid residues that bind the substrate can come from very dif- ferent parts of the linear amino acid sequence of the enzyme, as seen in glucokinase. The binding of compounds with a structure that differs from the substrate even to a small degree may be prevented by steric hindrance and charge repulsion. In the lock-and-key model, the complementarity between the substrate and its binding site is compared to that of a key fitting into a rigid lock.

Question 24

What is a holoenzyme?

Answer 24

It is an active enzyme with its nonprotein component.

Question 25

What is an Apoenzyme?

Answer 25

An enzyme without its nonprotein moiety, and it is inactive.

Question 26

What are coenzymes? Explain the two types of coenzymes?

Answer 26

Coenzymes are small organic molecules that interact with the enzymes. **Cosubstrate:** coenzymes that are only trasiently associated with the enzyme. They dissociate from the enzyme in an altered state. **Prosthetic group:** coenzymes that are permanently associated with the enzyme, and returned to its original form.

Question 27

When do enzymes show sigmoidal curve when plotted against substrate concentration?

Answer 27

When the substrate itself serves as an effector, the effect is said to be homotropic. Most often, an allosteric substrate functions as a positive effector. In such a case, the presence of a substrate molecule at one site on the enzyme enhances the catalytic properties of the other substrate-binding sites. That is, their binding sites exhibit cooperativity. These enzymes show a sigmoidal curve when reaction velocity (vo) is plotted against substrate concentration ([S]), as shown in Figure 5.16. This contrasts with the hyperbolic curve characteristic of enzymes following Michaelis-Menten kinetics, as previously discussed. [Note: The concept of cooperativity of substrate binding is analogous to the binding of oxygen to hemoglobin.