Enzymes: Basic concepts and kinetics

Question 1

What are most catalysts in biological systems

Answer 1

Enzymes

Question 2

Enzymes

Answer 2

Nearly all are proteins. Highly specific. Can enhance reaction rates by 10^6 or more. They do not alter reaction equilibria, they increase the rate at which equilibrium is obtained.

Question 3

Cofactors

Answer 3

Many enzymes require these for activity. Can be metal ions or coenzymes (small, vitamin-derived organic molecules).

Question 4

When can a reaction take place spontaneously

Answer 4

If change in free energy (^G) is negative

Question 5

The standard free energy change (^G*)

Answer 5

The free -energy change of a reaction that takes place when reactants and products are at unit activity

Question 6

The standard free-energy change at pH 7

Answer 6

^G*’

Question 7

How do enzymes serve as catalysts?

Answer 7

By decreasing the free energy of activation of chemical reactions

Question 8

How do enzymes accelerate reactions?

Answer 8

By providing a reaction pathway in which the transition state (the highest energy species) has a lower free energy and so is more rapidly formed than in the uncatalyzed reaction

Question 9

What is the 1st step in catalysis?

Answer 9

The formation of an enzyme-substrate complex

Question 10

How are substrates bound to enzymes

Answer 10

At active site clefts from which water is largely excluded when the substrate is bound

Question 11

Where does the specificity of enzyme-substrate interactions arise from?

Answer 11

Mainly from hydrogen bonding, which is directional, and from the shape of the active site, which rejects molecules which do not have a complementary shape.

Question 12

How do enzymes facilitate formation of the transition state?

Answer 12

By a dynamic process in which the substrate binds to specific conformations of the enzyme, along with conformational changes at active sites that result in catalysis

Question 13

The Michaelis-Menten model

Answer 13

Describes the kinetic properties of many enzymes. An enzyme (E) combines with substrate (S) to form enzyme-substrate (ES) complex, which can form a product (P) or dissociate into E and S.

Question 14

The rate of the formation of product Vo is given by the Michaelis-Menten equation….

Answer 14

Vo = Vmax([S]/([S] + Km)).

Vmax = the reaction rate when the enzyme is fully saturated with substrate.
Km = The Michaelis constant. The substrate concentration at which the reaction rate is half maximal

Question 15

kcat/Km

Answer 15

Ratio providing a measure of enzyme efficiency and specificity

Question 16

3 facts about allosteric enzymes

Answer 16

1. Catalytic activity can be regulated
2. Do not conform to Michaelis-Menten kinetics
3. Have multiple active sites

Question 17

Allosteric enzyme active sites

Answer 17

Display cooperativity, as evidenced by a sigmoidal (s-shaped curve) dependence of reaction velocity on substrate concentration.

Question 18

Enzyme inhibition

Answer 18

Specific small molecules or ions can inhibit even nonallosteric enzymes

Question 19

Irreversible inhibition

Answer 19

Inhibitor is covalently linked to enzyme or bound so tightly that its dissociation from the enzyme is v.slow.

Question 20

How can enzymes active site be mapped?

Answer 20

With covalent inhibitors

Question 21

Reversible inhibition

Answer 21

More rapid and less stable interaction between enzyme and inhibitor.

Question 22

Competitive inhibitor

Answer 22

Prevents the substrate from binding the active site. Reduces the reaction velocity by diminishing the proportion of enzyme molecules that are bound to substrate

Question 23

How can competitive inhibition be overcome?

Answer 23

Raise the substrate concentration. Cannot overcome uncompetitive and noncompetitive in this way.

Question 24

Uncompetitive inhibition

Answer 24

Inhibitor combines only with ES complex.

Question 25

Noncompetitive inhibition

Answer 25

Inhibitor decreases turnover number.

Question 26

Transition state

Answer 26

Enzyme binds transition state more tightly than substrate

Question 27

Transition-state analogs

Answer 27

Stable compounds that mimic key features of this highest energy species. Potent and specific inhibitors of enzymes. Used as antigens, or immunogens, in generating catalytic antibodies.

Question 28

Enzymes can be studied at level of a single molecule (in singulo)

Answer 28

Yield info that is difficult to gain in studies of populations of molecules. Reveal a distribution of enzyme characteristics rather than an average value.