Enzymes

Energy and Reaction Rate

• Many reactions in living systems are exergonic. Remember our word derivation:
  • Exer: out of
  • Ergon: work (i.e. energy)
  • Exergonic: making energy go out of the system
  • Therefore, they have a net release of “free energy.”
• Since exergonic reactions are “downhill,” it might seem like these reactions—in which reactants have more energy than products—should proceed spontaneously (like a ball rolling down a hill converting gravitational potential energy into kinetic energy).

Campbell's Biology, 5th Edition Study Partner CD, Activity 6.1

The Problem

• All reactions have an energy barrier that must be crossed in order to proceed forward: this is called the “activation energy” (E_A).
• If you were a chemist, the simplest way of getting around this problem would be to just heat the system!
  • This works because the heat energy causes the reactants to move faster.
  • This kinetic energy provides the necessary activation energy so the reaction can proceed forward.
• However, this solution does not work in living organisms.
  • If you heat a living organism its proteins will denature (unravel).
  • A protein's function is based on its structure. If you destroy its structure, you destroy its function!
  • “Devastating things will occur” (Chelsea Kolander, period 1 2005–2006)

Campbell's Biology, 5th Edition Study Partner CD, Activity 6.1

The Solution

• The solution for living organisms is enzymes.
• They are biological catalysts.
  • They lower the activation energy without increasing the temperature of the system.
  • By lowering the activation energy, they speed up reactions.

Figure 6.10, page 92, Campbell's Biology, 5th Edition

How Do Enzymes Work?

Lock and Key Model

• The first model developed to explain how enzymes work.
• Lock: the active site on the enzyme, where the molecules bind to.
• Key: the substrate molecules, i.e. the reactants.
• The idea:
  • Without the enzyme the reactants have a hard time reacting—they need to “get over” the activation energy hill.
  • The enzyme provides a physical place for the reactants to come together and react: they fit like a “key in a lock.”
  • This lowers the activation energy and speeds up the reaction.
• The enzyme is like a “matchmaker.”

Via Mr. Hammack's mad drawing skills

Induced Fit Hypothesis

• It was later discovered that enzyme activity was more complicated.
  • It turns out that the active site is not a perfect lock, nor the substrate a perfect key.
  • Instead, the active site's shape is modified by the substrate.
  • As the substrate enters the active site, it “induces a fit.”
• This would be similar to putting on a glove that is originally too big for your hand, but as your hand enters the glove, it conforms perfectly giving you a nice snug fit.
• Be sure to note that enzymes can break molecules apart as well as put them together.
  • They are not only like matchmakers; they are also like homewreckers.

Via Mr. Hammack's mad drawing skills

An Enzyme in Action

• This is a computer generated graphic of an enzyme in action.
  • Enzymes are proteins, so this is a protein.
  • It's specifically a tertiary (globular) protein, not a quaternary one.
• The enzyme is in blue; the substrate is in red.
• As the substrate molecule enters the active site, it induces a change in shape of the protein so the substrate “fits” in the enzyme.

Figure 6.11, page 92, Campbell's Biology, 5th Edition

Importance of Enzymes

• Every reaction in a living organism is catalyzed by an enzyme.
  • Think about that: it's amazing! There are so many reactions!
  • Enzymes are therefore the single most important group of macromolecules in living systems.
• Note that every enzyme has the suffix -ase, so you can easily tell if something is an enzyme.
• Below is a list of some of the different types of enzymes and what they do (hide).

  Aldolase

  Cleaves a carbon–carbon bond to create an aldehyde group.

  Carboxylase

  Adds CO₂ or HCO₃^- to its substrate to form a carboxyl group.

  Decarboxylase

  Cleaves a carboxyl group, e.g., from α-keto acids, liberating it as CO₂.

  Dehydrogenase

  Removes hydrogen atoms from its substrate.

  Esterase

  Hydrolyzes ester linkages to form an acid and an alcohol.

  Hydratase

  Adds water to a carbon–carbon bond without breaking the bond or, conversely, removes water to create a double bond.

  Hydrolase

  Adds water to break a bond (hydrolysis). The suffix “ase” alone often denotes a hydrolase; e.g., sucrase hydrolyzes sucrose.

  Hydroxylase

  Incorporates an oxygen atom from O₂ into its substrate to create a hydroxyl group.

  Isomerase

  Converts between cis and trans isomers, D and L isomers, or aldose and ketose.

  Kinase

  Transfers a phosphate group from a high-energy phosphate compound, such as ATP, to its substrate (in contrast, a phosphorylase adds inorganic phosphate, P_i, to its substrate).

  Ligase

  Joins two molecules together using energy released from hydrolyzing a pyrophosphate bond of a high-energy phophsate compound; also called synthetase.

  Lyase

  Adds groups to double bonds or removes groups to create double bonds, other than by hydrolysis.

  Mutase

  Shifts the position of a group, e.g. a methyl group, within a single molecule.

  Oxidase

  Adds O₂ to hydrogen atoms removed from the substrate (which is thereby oxidized) to generate H₂O, H₂O₂, or O₂^- (superoxide).

  Oxygenase

  Incorporates molecular O₂ into its substrates.

  Peptidase

  Hydrolyzes peptide bonds to yield free amino acids and peptides.

  Phosphatase

  Hydrolyzes substates, such as phosphoric esters, to liberate inorganic phosphate (P_i; at physiologic pH, a mixture of HPO₄^2- and H₂PO₄^-).

  Phosphorylase

  Adds inorganic phosphate (P_i) to split a bond (phosphorolysis).

  Reductase

  Catalyzes the reaction of its substrate, i.e., adds hydrogen atoms.

  Sulfatase

  Hydrolyzes substrates, such as sulfuric-acid esters, to liberate sulfate.

  Synthase

  Joins two molecules together without hydrolyzing a pyrophosphate bond (in contrast, ligase or synthetase requires the hydrolysis of such a bond).

  Synthetase

  Same as ligase.

  Transaminase

  Transfers amino groups from an amino acid to a keto acid (also known as aminotransferase).

  Transferase

  Transfers groups other than hydrogen atoms, such as phosphate groups for phosphotransferases or methyl groups for methyltransferases, from one molecule to another.

Why Your Parents Told You To Eat Your Vitamins and Minerals!

• Many enzymes require other, non-protein molecules in order to function—they need a “buddy” or “partner” to help them do their job.
• Cofactors
  • Inorganic metal ions that temporarily bind to certain enzymes and are essential for their function.
  • These are the “minerals” that your parents were concerned that you got in your diet.
• Coenzymes
  • Organic molecules (i.e. molecules that contain carbon) that are required for the action of certain enzymes.
  • They are generally much smaller than the enzyme (see illustration below).
  • Many vitamins are coenzymes, e.g. B₁, B₂, and B₃.

Unknown source

A Few Examples of Nonprotein Molecular “Partners” of Enzymes

Enzymes Can Be Inhibited

• As enzymes are critical for life, if they are “inhibited” metabolic activity can be slowed down or even stopped.
  • Whether inhibition is good or bad for an organism depends on the enzyme and what it does.
  • You will see an amazing example of the consequences of enzyme inhibition in the movie we will be watching in a few days, Lorenzo's Oil (which is based on a true story).
• An understanding of enzymes and enzyme inhibition is integral to life itself; it is more important than just passing a test.
• There are three types of enzyme inhibition:
  1. Competitive inhibition
  2. Noncompetetive inhibition
  3. Irreversible inhibition

1. Competitive Inhibition

• A chemical which mimics the substrate can compete with the substrate for access to the active site.
• If it blocks the active site, it inhibits the reaction, causing it to slow down or stop.
  • The substrate and the competitive inhibitor both “compete” for the active site.
  • The amount the reaction is slowed depends on the ratio of the concentrations of the two competitors.

Figure 6.18(a), Purves's Life: The Science of Biology, 7th Edition

2. Noncompetitive Inhibition

• A noncompetitive inhibitor binds to the enzyme at a location that is not the active site.
• This causes the enzyme to change shape, rendering the active site unable to bind the substrate.
• The enzyme is no longer able to function properly in catalysis.

Figure 6.18(b), Purves's Life: The Science of Biology, 7th Edition

3. Irreversible Inhibition

• A chemical binds permanently to the active site, causing the enzyme to be non-functional.
  • It is essentially the same as competitive inhibition, except the inhibitor will never be released from the active site.
  • Since the bond is permanent the enzyme will never function again to catalyze reactions.
  • This is catastrophic in living organisms since it stops metabolism.
• Example: nerve gas
  • A group of chemicals that bind irreversibly to the enzymes involved in the transmission of nerve impulses.
  • Breathing stops within minutes, since no nerve impulses tell the body to breathe.
  • Find out more (with animation)

Modified figure 6.18(a), Purves's Life: The Science of Biology, 7th Edition

Controlling Metabolism

• The key way metabolism is regulated is through the use of allosteric enzymes.
  • Allo: other
  • Steric: site
  • Allosteric: “other site”
• They regulate metabolism using an allosteric site, which is different from the active site (hence the name—“other site”).
  • Molecules bind to the allosteric site, causing a change in the 3D structure of the enzyme, that either inhibits or activates the active site.

Allosteric Enzymes: a Closer Look

• Allosteric enzymes are constructed from two or more protein subunits; therefore, they are quaternary proteins.
  • In the illustration below, the allosteric enzyme has four subunits.
  • Note how the allosteric site is different from the active site.
• Activation: An “activator” molecule binds to the allosteric site, allowing the enzyme to have its normal shape and therefore function properly.
• Inhibition: An “inhibitor” molecule binds to the allosteric site, causing the enzyme to change its shape and thereby inhibit its normal functioning.

Figure 6.15, page 96, Campbell's Biology, 5th Edition

Control of Enzyme Activity

• Proper temperature is critical.
  • Enzymes—since they are proteins—can easily be denatured, and therefore only work within an optimal temperature range.
  • The critical range can vary depending on the organism, as shown below.

Figure 6.13, page 94, Campbell's Biology, 5th Edition

Regulation of Enzyme Activity through Feedback Inhibition

• The process of feedback inhibition (negative feedback):
  • A product “down stream” in a metabolic pathway inhibits an allosteric enzyme “up stream,” so as to slow down the reaction and therefore reduce the amount of product.
  • As the reaction slows and less end-product is produced, the enzyme is no longer inhibited and the reaction rate increases—causing more end-product to be produced.
• This is similar, in principle, to how a thermostat works in controlling temperature in your home: it keeps it in a narrow range, working to change the temperature if it deviates from that range.
• Feedback inhibition is the primary way living organisms maintain homeostasis.
  • Word derivation:
    • Homeo: like, similar
    • Stasis: standing
  • Definition: the process of achieving a relatively stable internal environment

Figure 6.16, page 96, Campbell's Biology, 5th Edition