CC2_prelims_Lec: Intro to Enzymes

Enzyme

Biological protein that catalyzes biochemical reactions without altering the equilibrium point of the reaction or being consumed/changed in composition.

Enzyme nomenclature

The system used to name and classify enzymes; includes practical/trivial names and systematic/E.C. nomenclature.

Practical/Trivial Name

The commonly used or recommended name of an enzyme.

Substrate-based enzyme naming

An enzyme may be named according to its substrate by adding the suffix "-ase"; examples include lipase and protease.

Lipase

Enzyme that acts on lipids.

Protease

Enzyme that acts on proteins.

Reaction-based enzyme naming

Enzymes may be named according to the type of reaction they catalyze.

Transferase

Enzyme involved in transferring a chemical group from one substrate to another.

Kinase

Enzyme that transfers a phosphate group from a high-energy phosphate compound to its substrate.

Phosphatase

Enzyme that catalyzes hydrolysis of phosphate esters.

Dehydrogenase

Enzyme involved in removal of hydrogen atoms from its substrate.

Systematic/E.C. Nomenclature

Standardized enzyme naming system established by the Enzyme Commission under the International Union of Biochemistry.

E.C. number

An enzyme's numerical designation in the systematic classification system.

First number of E.C. number

Defines the general class to which the enzyme belongs.

Second and third numbers of E.C. number

Indicate the subclass and sub-subclass of the enzyme.

Last number of E.C. number

Specific serial number assigned to the enzyme within its subclass.

E.C. 1.1.1.7

Lactate dehydrogenase (LD/LDH).

E.C. 3.2.1.1

Amylase.

E.C. 2.6.1.2

Alanine aminotransferase (ALT).

Oxidoreductases

Enzymes involved in removal or addition of electrons in oxidation-reduction reactions.

Examples of oxidoreductases

Cytochrome oxidase, lactate dehydrogenase (LDH), malate dehydrogenase (MDH), and isocitrate dehydrogenase (ICD).

Transferases

Enzymes that transfer a chemical group other than hydrogen from one substrate to another.

Examples of transferases

AST/SGOT, ALT, creatine kinase/CPK, GGT, and ornithine carbamyl transferase (OCT).

AST

Aspartate aminotransferase; also called serum glutamic-oxaloacetic transaminase (SGOT).

ALT

Alanine aminotransferase.

Creatine kinase (CK/CPK)

Transferase involved in transferring phosphate groups; also called creatine phosphokinase.

GGT

Gamma-glutamyl transferase.

OCT

Ornithine carbamyl transferase.

Hydrolases

Enzymes that hydrolyze bonds by adding water.

Examples of hydrolases

Esterases, peptidases, and glycosidases.

Esterases

Hydrolases that act on ester bonds; examples include ACP, ALP, cholinesterase, and lipase.

Peptidases

Hydrolases that act on peptide bonds; examples include trypsin, pepsin, and leucine aminopeptidase.

Glycosidases

Hydrolases that act on glycosidic bonds; examples include amylase, amylo-1,6-glycosidase, and galactosidases.

ACP

Acid phosphatase.

ALP

Alkaline phosphatase.

CLS

Cholinesterase.

LPS

Lipase.

PTS

Trypsin.

PPS

Pepsin.

LAP

Leucine aminopeptidase.

AMS

Amylase.

Lyases

Enzymes that remove groups from substrates without hydrolysis, leaving a double bond in the product.

Examples of lyases

Aldolases, glutamate decarboxylase, pyruvate decarboxylase, and tryptophan decarboxylase.

Isomerases

Enzymes that catalyze interconversion of geometric, optical, or positional isomers.

Isomerases mnemonic

"Shape shifter" — they help molecules change into the correct form needed for their function.

Examples of isomerases

Glucose phosphate isomerase and ribose phosphate isomerase.

Ligases/Synthetases

Enzymes that join two substrate molecules using energy released from hydrolyzing a high-energy phosphate/pyrophosphate bond.

Energy required by ligases

ATP provides the energy needed for ligases to join two molecules.

Ligase example

Glutathione synthetase.

Glutathione synthetase

Helps form glutathione by attaching glycine to gamma-glutamyl cysteine.

Holoenzyme

Active enzyme formed by the combination of an apoenzyme and its cofactor/coenzyme.

Apoenzyme

Protein portion of an enzyme; catalytically inactive when its cofactor is removed.

Properties of apoenzymes

Protein portion is subject to denaturation and is heat labile.

Isoenzyme

Enzymes in an individual that have similar enzymatic activity but differ in physical, biochemical, and immunologic characteristics.

Metalloenzyme

Enzyme that requires a metal ion to function properly.

Common metal ions in metalloenzymes

Iron, zinc, and magnesium.

Intrinsic metal ions

Metal ions that are an integral part of the enzyme molecule; examples include catalase and cytochrome oxidase.

Proenzyme/Zymogen

Inactive precursor of an enzyme.

Zymogen example

Pepsinogen, which becomes pepsin.

Substrate

The material or molecule upon which an enzyme acts.

Cofactor

Non-protein substance required by an enzyme before enzymatic activity can occur; may be a metal ion or small molecule.

Properties of cofactors

Cofactors are thermostable and dialyzable and act as activators or enhancers of enzyme activity.

Types of cofactors

Organic molecules (coenzymes) and metal ions (activators).

Coenzyme

Organic molecule that helps an enzyme carry out a reaction.

NAD

Nicotinamide adenine dinucleotide; an example of a coenzyme.

NADP

Nicotinamide adenine dinucleotide phosphate; an example of a coenzyme.

Fate of coenzymes during reactions

Coenzymes hasten enzymatic reactions but undergo a change or are consumed and converted into another product.

Metal ion as a bridge

A metal ion can hold the substrate and enzyme together.

Metal ion as catalytic center

A metal ion can serve as the primary catalytic center of an enzyme.

Metal ion as stabilizing agent

A metal ion can stabilize the enzyme conformation needed for catalytic activity.

Amylase cofactor/activator

Chloride (Cl) and bromide (Br).

LDH metal activator

Zinc ion (Zn²⁺).

Lipase metal activator

Calcium ion (Ca²⁺).

Enzyme kinetics

Study of the rate at which enzyme-catalyzed reactions occur.

Enzyme-substrate complex (ES)

Complex formed when an enzyme combines with its substrate.

Fate of the ES complex

The ES complex can dissociate back into E + S or break down into product + free enzyme.

Michaelis-Menten equation

Equation describing the rate of enzyme-catalyzed reactions and the relationship between reaction velocity and substrate concentration.

V

Velocity or rate of the enzyme-catalyzed reaction.

Vmax

Maximum velocity or fastest rate an enzyme can achieve.

[S]

Substrate concentration.

Km

Michaelis-Menten constant; substrate concentration at which the reaction reaches half of its maximum velocity.

Importance of Michaelis-Menten equation

Helps describe how reaction velocity depends on substrate concentration and enzyme-substrate interaction.

Absolute specificity

An enzyme combines with only one substrate and catalyzes only one corresponding reaction.

Absolute specificity example

Urease, which breaks down urea into ammonia and carbon dioxide.

Group specificity

An enzyme acts on substrates containing a particular chemical group.

Bond specificity

An enzyme is specific for a particular type of chemical bond.

Bond specificity example

Pepsin recognizes and acts on peptide bonds.

Stereoisomeric specificity

An enzyme predominantly combines with only one optical or stereoisomer of a compound.

Stereoisomeric specificity example

Lactase acts on the beta anomer of lactose.

Lock-and-key theory

Emil Fischer's theory stating that the enzyme is rigid and the substrate fits the active site like a key fits a lock.

Induced-fit theory

Koshland's theory stating that substrate binding causes conformational changes in the enzyme.

Why induced-fit theory is more acceptable

The protein molecule is flexible and can undergo conformational changes; this also helps explain hormonal influences on enzyme activity.

Enzyme induction

Phenomenon in which an enzyme adapts to biochemical systems, helping the body process new substances.

Importance of enzyme induction

It can help the body break down drugs or harmful chemicals faster for elimination.

Effect of increased enzyme concentration

Increases reaction rate when other conditions are constant and substrate is present in constant excess.

Effect of doubling enzyme concentration

If substrate is in excess and other conditions remain constant, doubling enzyme concentration doubles the reaction rate.

Effect of increased substrate concentration

Initially increases reaction rate, but eventually reaches a maximum when enzyme active sites become saturated.

Saturation kinetics

Condition in which increasing substrate concentration beyond a certain point no longer increases reaction rate.

Temperature effect on enzyme reactions

The rate of a chemical reaction usually increases 2–3 times for every 10°C rise in temperature.

Why temperature increases reaction rate

Higher temperature increases molecular excitation and intermolecular collisions.