Enzymes
Biological catalysts
- Typically are very large proteins.
- Permit reactions to 'go' at conditions that the body can tolerate.
- Can process millions of molecules every second.
- Are very specific - react with one or only a few types of molecules (substrates).

Enzyme Nomenclature
Naming is easy compared to other compounds.
Name is based on:
- what it reacts with
- how it reacts
- add -ase ending
Examples
- enzyme that reacts lactose.
- removes carboxyl from pyruvate.

Classification of Enzymes
Based on type of reaction

Oxireductase	catalyze a redox reaction
Transferase	transfer a functional group
Hydrolase	cause hydrolysis reactions
Lyase	break C-O, C-C or C-N bonds
Isomerases	rearrange functional groups
Ligase	join two molecules

Effect of Enzymes on Activation Energy
For all reactions you must get over the activation energy hurdle.
Enzymes change how a reaction will proceed.
This reduces the activation energy.
It makes it faster.

Effect of Substrate Concentration
For non-catalyzed reactions
Reaction rate increase with concentration.
Enzyme catalyzed reactions
Also increase but only to a certain point .
Vmax, maximum velocity
At Vmax , the enzyme is working as fast as it can.
So, the rate is limited by the concentration of both the substrate and enzyme.

The Active Site
Enzymes are typically HUGE proteins, yet only a small part are actually involved in reaction.
The active site has two basic components.
- catalytic site
- binding site

Characteristics of Enzyme Active Sites
Catalytic site
- Where the reaction actually occurs.
Binding site
- Area that holds substrate in proper place.
- Enzymes use weak, non-covalent interactions to hold the substrate in place based on R groups of amino acids.
Shape is complementary to the substrate and determines the specificity of the enzyme.
Sites are pockets or clefts on the enzyme surface.

Steps in an Enzymatic Reaction
1. Enzyme and substrate combine to form a complex.
2. Complex goes through a transition state - not quite substrate or product.
3. A complex of the enzyme and the product is produced.
4. Finally the enzyme and product separate.
All of these steps are equilibria.
The Players
- binding site
- catalytic site
- enzyme
- substrate
Formation of the Enzyme-Substrate Complex
- First step in an enzyme catalyzed reaction
- Enzyme + Substrate = Complex
Formation of the transition state
- An intermediate species is then formed.
Formation of the enzyme-product complex
- The enzyme-product complex is then formed.
Formation of the product
- The product is finally made and the enzyme is ready for another substrate.

Enzyme Classes
Absolutely specific
- Only reacts with a single substrate.
Group specific
- Works with similar molecules with the same functional group.
Linkage specific
- Catalyzes a specific combination of bonds.
Stereochemically specific
- Only will work with the proper D- or L- form.

Cofactors and Coenzymes
Some enzymes require a second species to be present in order to do their job.
For Cofactor type enzymes.
Apoenzyme
- protein portion of enzyme.
- almost ready to work.
Cofactor
- prosthetic group need to 'activate' the apoenzyme.
- usually a metal ion that holds protein in the proper shape.
Coenzymes
- A second enzyme that temporarily binds to the apoenzyme in order for it to work.
- Apoenzyme + coenzyme = holoenzyme
Vitamins are often converted to coenzymes

Vitamin	Coenzyme made	Function
B1	thiamine pyrophosphate	decarboxylation
B2	flavin mononucleotide	carries hydrogen
folic acid	tetrahydrofolic acid	amino acid metabolism
biotin	biocytin	CO2 fixation
tpantothenic	Coenzyme A	acyl group carrier
acid

Effect of pH & Temperature on Enzymatic Reactions
Exceeding normal pH and temperature ranges always reduces enzyme reaction rates.
Optimum temperature is usually 25-40C.
For pH, most enzymes work best near pH 7
- not all though.

Regulation of Enzyme Activity
Unlike other catalysts, enzymes are often regulated by the cell.
Cells use several methods to control when an enzyme will be able to work and how well.

Methods of Enzyme Regulation
End product inhibition
- Enzyme - substrate reaction is an equilibrium
- If product builds up, the reaction slows.
- Equilibrium shifts to left if product starts to build up
Use of allosteric enzyme
- Similar to coenzymes.
- The presence of an effector molecule alters how an enzyme will act.
- Positive allosterism - activates the enzyme.
- Negative allosterism - deactivates the enzyme.
A type of allosteric effect where the product acts as the effector molecule.
Inactive forms of an enzyme.
Cell activates them on demand using another enzyme.
Release materials that block off the active site of the enzyme. May be reversible or not.

Specific Enzyme Examples
Let's look at role of some specific enzymes.
Two good examples are:
- A proteolytic enzyme (protein-cleaving).
- Used in digestion of dietary protein in the small intestines.e
- Used for hydrolysis of acetylcholine.
- Needed for operation of nerves.
Chymotrypsin
This enzyme is a proteolytic enzyme. It cleaves peptide bonds.
This enzyme only works on amino acids containing an aromatic ring.
- phenylalanine, tyrosine and tryptophan.
Acetylcholinesterase and nerve transmission
- This enzyme is needed to transmit a nerve signal at a neuromuscular junction.
- Arrival of nerve signal causes Ca2+ levels to increase.
- This causes acetylcholine containing vesicles to release acetylcholine into synapse.
- Acetylcholine then diffuses across synapse to pass the signal to the muscle.
- Acetylcholinesterase then destroys the acetylcholine to stop the signal.
- Presence of acetylcholine at receptor causes a flow of sodium and potassium ions. This causes a muscle contraction.
- Without the enzyme, muscles would continue to contract causing spasms.
Acetylcholinesterase inhibitors are used as drugs and poisons.
Organo fluorophosphates
- bind to the enzyme. Death can occur.
- Succinylcholine
Acts like acetylcholine and binds to sites on the muscle. Used as a muscle relaxant.
Another Example
- Blood Clotting - formation of fibrin.
- Process requires a series of enzymatic steps.
- Many of the enzymes are made in an inactive form. This prevents blood from clotting on its own.
Two pathways can be used to start the process.
- Extrinsic - Activated by tissue damage outside the blood vessel.
- Intrinsic - Activated by damage within a blood vessel.

Drug Interactions
Drugs can be administered to alter the clotting mechanism.
Example: - an anticoagulant.
Acts by accelerating the action of the existing inhibitor of thrombin - antithrombin III
- Antithrombin III inhibits activating the clotting factors that have a reactive serine residue at their enzymatically active centers.
Heparin interaction
- Addition of heparin makes it easier for trombin to interact with antithrombin - positive allosteric effect.

Defective Enzymes and Disease
A number of hereditary diseases result from the absence of an enzyme or a defective one.

Disease	Defective enzyme
Albinism	tyrosinase
Glactosemia	glactose 1-phosphate uridyltransferase
Phenylketonuria	phenylalanine hydroxylase (PKU)
Tay-Sachs disease	hexosaminidase A

Phenylketonuria (PKU)
Genetic defect that results in a defect of the enzyme phenylalanine hydroxylase.
Affects about 1 baby per 13,000.
Federal way requires screening at birth.
Can result in retarded physical and mental development if untreated.
PKU is one of a family of enzymatic/genetic disorders related to phenylalanine metabolism.
Treatment - restrict phenylalanine until age 10 (until brain is developed).