Bio 211 Intro Molecular Cell Biology

Lecture 7 and Lecture 8 “Enzymes”

Reading: Campbell Chap. 6 pp. 91-97

In the last lecture, we looked at the role of energy in the cell. Cells follow physical and chemical laws in their behavior: energy is conserved through biological processes although the products of metabolism produce altered forms of energy such as heat. The energy of cells is mostly in the form of chemical energy especially as ATP. In today’s lecture, we will look at the role of specialized proteins called enzymes in the cell.

Outline:

1. Role of enzymes

2. Substrate binding

3. Effects on enzyme activity

4. Enzyme regulation

Enzymes are catalysts, substances that speed up the rate of a reaction. They are nearly always proteins, although there are some enzymes such as the one that makes proteins (peptidyl transferase) which are catalytic RNAs. Enzymes like other catalysts are not themselves used up by the reaction.

How do enzymes speed up the rate of the reaction?

Reactions involve the breaking and reforming of chemical bonds. The breaking of bonds needs energy to get started even if the overall process is energetically favorable. The energy needed to get started is called the “activation energy”.

Activation energy = EA

Let’s look at the energy changes that take place in a given chemical reaction. (Fig. 6.9) Given a hypothetical reaction

AB+CD--->AC+ BD

In this reaction, the reactants (substrates) swap pieces with each other to give the products. The bonds of the reactants break only when the molecules have absorbed enough energy to be unstable.

The activation energy represents the uphill portion of the graph.

As the reactants absorb energy, they become unstable. This is the “transition state”. As new bonds are formed, energy is released into the surroundings. This is the downhill portion of the curve which indicates a loss of free energy by the products. The difference in free energy of the products vs. the reactants is G for the reaction which is negative for an exergonic reaction.

To overcome the activation energy requires energy input. For some chemical reactions, this can be accomplished by heating. Cells can be damaged by heat, therefore they use enzyme catalysts to lower the activation energy.

An enzyme cannot change the G for a reaction. They speed up reactions that would have occurred anyway, but perhaps at an extremely slow rate.

Fig. 6.10 shows how enzymes lower the EA without affecting G for the reaction.

2. Substrate binding

Enzyme catalyzed reactions can be summarized as follows:

enzyme

substrate---->products

substrate = reactant(s) acted on by an enzyme

Example

sucrase

sucrose + H2O---->glucose+ fructose

substratesproducts

Enzymes usually are highly specific for their substrates. The region of the enzyme responsible for binding to substrate is called the “active site”.

The active site is typically a pocket or groove created by some of the amino acids of the enzyme.

Fig. 6-11 (or equivalent) shows binding of the substrate (glucose) to the groove that makes up the active site of hexokinase.

Models that explain different aspects of substrate binding

1) lock and key

--good for explaining specificity

--doesn’t explain why substrates that resemble the transition state are the best fit

2) induced fit

--Substrate induces a conformational change that creates better fit of enzyme to substrate and places bonds in key positions to be acted on by the enzyme

.

Key features of enzyme/substrate interations:

--Substrate is bound to the enzyme by many weak interactions (hydrogen bonds, ionic bonds, hydrophobic interactions).

--Catalysis is begun by amino acids making up the active site of the enzyme; R groups are usually crucial in catalysis.

--Enzymes can catalyze thousands of reactions per second.

--The more substrate available, the more rapid the reaction, until the enzyme is saturated by substrate.

How do we measure the rate of an enzyme catalyzed reaction?

Mix--enzyme

--substrate (vary)

--buffer (maintain correct pH for enzyme activity)

Measure amount of product produced.

3. Factors that affect enzyme activity

a. Temperature: Most enzymes have optimal activity at body temperature (37C).

Enzymes from thermophilic organisms may have optimal activity at 70C. Fig. 6.13 (a)

b. pH: Most enzymes have optimal activity around pH 7.

Pepsin, digestive enzyme of stomach works best in the acid environment of the stomach, pH 2.0. Fig. 6.13 (b)

c. cofactors: Ions or coenzymes that are required by the enzyme for catalytic activity.

d. inhibitors: Chemicals that slow or stop the action of enzymes. Fig. 6.14 compares two types of inhibitors.

competitive inhibitors: Bind to active site, prevent access of substrate to active site.

noncompetitive inhibitors: Bind to enzyme somewhere other than the active site.

4. Enzyme regulation

Allows cell to respond to environmental signals and slow down or speed up steps in metabolism.

allosteric regulation: Binding of a small molecule to site other that the active site which changes the enzyme conformation.

Fig. 6.15 gives example

feedback inhibition: When end product in reaction signals to enzyme at beginning of pathway to slow down.

A ---> B ---> C ---> D

D is a feed back inhibitor of enzyme that converts A to B

Summary: Today our topic has been enzymes. Enzymes are mostly protein catalysts that speed up the rate of a chemical reaction in cells. Enzymes must be in their proper conformation to bind substrate and catalyze reactions. Changes in pH or temperature or presence of chemical inhibitors can inactivate enzymes. In the next group of lectures, we will observe the critical roles of enzymes in carrying out metabolism.

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