Chapter 2

Enzyme

1. Properties of enzymes

2. Structural features of enzymes

3. Mechanism of enzyme-catalyzed reactions

4. Kinetics of enzyme-catalyzed reactions

5. Inhibition of enzymes

6. Regulation of enzymes

7. Clinical applications of enzymes

8. Nomenclature

Contents

Section 1

Properties of Enzymes

A + B → C + D

§ 1.1 General Concepts

GG0RTln[C][D][A][B]

• spontaneous reaction only if G is negative.

• at equilibrium if G is zero.

• spontaneously impossible if G is positive.

Reaction progress

Fre

e e

nerg

y

G forthe reaction

reactants

products

transition state, S

G+ (uncatalyzed)

Catalyzed reactions

• Reactants need to pass over the energy barrier, G+.

• Catalysts reduce the activation energy and assist the reactants to pass over the activation energy.

Reaction progress

Fre

e e

nerg

y

G forthe reaction

reactants

products

transition state, S

G+ (catalyzed)

G+ (uncatalyzed)

1. Fragile structures of the living systems

2. Low kinetic energy of the reactants

3. Low concentration of the reactants

4. Toxicity of catalysts

5. Complexity of the biological systems

Chemical reactions in living systems are quite different from that in the industrial situations because of

Need for special catalysts

• Enzymes are catalysts that have special characteristics to facilitate the biochemical reactions in the biological systems.

• Enzyme-catalyzed reactions take place usually under relatively mild conditions.

Enzymes

§ 1.2 Characteristics

Enzyme-catalyzed reactions have the following characteristics in comparison with the general catalyzed reactions:

• common features: 2 “do” and 2 “don’t”

• unique features: 3 “high”

• Do not consume themselves: no changes in quantity and quality before and after the reactions.

• Do not change the equilibrium points: only enhance the reaction rates.

• Apply to the thermodynamically allowable reactions

• Reduce the activation energy

Common features

• Enzyme-catalyzed reactions have very high catalytic efficiency.

• Enzymes have a high degree of specificity for their substrates.

• Enzymatic activities are highly regulated in response to the external changes.

Unique features

CatalystActivation energy

(cal/M)

No catalyst 18,000

Normal catalyst 11,700

Hydrogen peroxidase 2,000

§ 1.3.a High efficiency

Accelerated reaction rates

enzyme

Non-enzymatic

rate constant

(kn in s-1)

enzymatic

rate constant

(kn in s-1)

accelerated reaction rate

Carbonic anhydrase 10-1 106 8 x 106

Chymotrypsin 4 x 10-9 4 x 10-2 10-2107

Lysozyme 3 x 10-9 5 x 10-1 2 x 108

Triose phosphate isomerase

4 x 10-6 4 x 103 109

Urease 3 x 10-10 3 x 104 1014

Mandelate racemase 3 x 10-10 5 x 102 1.7 x 1015

Alkaline phosphatase

10-15 102 1017

• Absolute specificity

• Relative specificity

• Stereospecificity

§ 1.3.b High specificity

Unlike conventional catalysts, enzymes demonstrate the ability to distinguish different substrates. There are three types of substrate specificities.

Absolute specificity

Enzymes can recognize only one type of substrate and implement their catalytic functions.

O C

NH2

NH2

+ H2O 2NH3 + CO2

urea

urease

O C

NH

NH2

+ H2O

methyl urea

CH3

Enzymes catalyze one class of substrates or one kind of chemical bond in the same type.

Relative specificity

protein kinase Aprotein kinase Cprotein kinase G

To phopharylate the -OH group of serine and threonine in the substrate proteins, leading to the activation of proteins.

OH

OH

HH

OHH

OH

CH2OH

H

CH2OH

HCH2OH

OH H

H OH

O

O

1

1

OH

OH

HH

OHH

OH

CH2

H

CH2OH

HCH2OH

OH H

H OH

O

O

1

1

O

OOH

H

HH

OHH

OH

CH2OH

H 1

sucrose

raffinose

sucrase

StereospecificityThe enzyme can act on only one form of isomers of the substrates.

H

C

H3C COOHOH

H

C

H3C OHCOOH

AB C A

B C

Lactate dehydrogenase can recognize only the L-form but the D-form lactate.

• Enzyme-catalyzed reactions can be regulated in response to the external stimuli, satisfying the needs of biological processes.

• Regulations can be accomplished through varying the enzyme quantity, adjusting the enzymatic activity, or changing the substrate concentration.

§ 1.3.c High regulation

Section 2

Components of Enzymes

• Almost all the enzymes are proteins having well defined structures.

• Some functional groups are close enough in space to form a portion called the active center.

• Active centers look like a cleft or a crevice.

• Active centers are hydrophobic.

§ 2.1 Active Center

Lysozyme

Residues (colored ) in the active site come from different parts of the polypeptide chain .

• Binding group: to associate with the reactants to form an enzyme-substrate complex

• Catalytic group: to catalyze the reactions and convert substrates into products

Two essential groups

The active center has two essential groups in general.

+- Catalytic group

Binding group

Substratemolecule

Protein chain

Active center

Essential groupsoutside theactive center

Active centers

• Simple enzymes: consists of only one peptide chain

• Conjugated enzymes:

holoenzyme = apoenzyme + cofactor

(protein) (non-protein)

• Cofactors: metal ions; small organic molecules

§ 2.2 Molecular Components

Metal ions

• Metal-activated enzyme: ions necessary but loosely bound. Often found in metal-activated enzyme.

• Metalloenzymes: Ions tightly bound.

• Particularly in the active center, transfer electrons, bridge the enzyme and substrates, stabilize enzyme conformation, neutralize the anions.

• Small size and chemically stable compounds

• Transferring electrons, protons and other groups

• Vitamin-like or vitamin-containing molecule

Organic compounds

• Loosely bind to apoenzyme. Be able to be separated with dialysis.

• Accepting H+ or group and leaving to transfer it to others, or vise versa.

Coenzymes

Prosthetic groups• Tightly bind through either covalent or many n

on-covalent interactions.

• Remained bound to the apoenzyme during the course of reaction.

Section 3

Mechanism of Enzyme-Catalyzed Reactions

• Proximity and orientation arrangement

• Multielement catalysis

• Surface effect

To understand the molecular details of the catalyzed reaction.

Lock-and-key model

Both E and S are rigid and fixed, so they must be complementary to each other perfectly in order to have a right match.

Induced-fit model

The binding induces conformational changes of both E and S, forcing them to get a perfect match.

Hexokinase catalyzing glycolysis

• Hexokinase, the first enzyme in the glycolysis pathway, converted glucose to glucose-6-phosphate with consuming one ATP molecule.

• Two structural domains are connected by a hinge.

• Upon binding of a glucose molecule, domains close, shielding the active site for water.

Induced structural changes

Section 4

Kinetics of Enzyme- Catalyzed Reactions

§ 4.1 Reaction rate

Time (t)0

[P]

[P]

t

Initial slope = vo =[P]

t

• The reaction rate is defined as the product formation per unit time.

• The slope of product concentration ([P]) against the time in a graphic representation is called initial velocity.

• It is of rectangular hyperbolic shape.

Initial velocity

Reaction velocity curve

[S]0

Vmax

V0

Vmax/2

Km

Intermediate state

Forming an enzyme-substrate complex, a transition state, is a key step in the catalytic reaction.

initial intermediate final

k3k1

k2

E S E + PE + S

Reaction progress

Fre

e e

nerg

y

G forthe reaction

reactants

products

transition state, S

G+ (catalyzed)

G+ (uncatalyzed)

• K1 = rate constant for ES formation

• K2 = rate constant for ES dissociation

• K3 = rate constant for the product released from the active site

Rate constants

k3k1

k2

E S E + PE + S

• The mathematical expression of the product formation with respect to the experimental parameters

• Michaelis-Menten equation describes the relationship between the reaction rate and substrate concentration [S].

§ 4.2 Michaelis-Menten Equation

• [S] >> [E], changes of [S] is negligible.

• K2 is negligible compared with K1.

• Steady-state: the rate of E-S complex formation is equal to the rate of its disassociation (backward E + S and forward to E + P)

Assumptions

Describing a hyperbolic curve.

Km is a characteristic constant of E

[S] << Km 时， v [S]∝ [S] >> Km 时， v ≈ Vmax

Vmax=V Km + [S]

[S]

[S]0

Vmax

V0

First order withrespect to [S]

Zero order withrespect to [S]

• the substrate concentration at which enzyme-catalyzed reaction proceeds at one-half of its maximum velocity

• Km is independent of [E]. It is determined by the structure of E, the substrate and environmental conditions (pH, T, ionic strength, …)

Significance of Km

[S]0

Vmax

V0

Vmax/2

Km

• Km is a characteristic constant of E.

• The value of Km quantifies the affinity of the enzyme and the substrate under the condition of K3 << K2. The larger the Km， the smaller the affinity.

=Km k1

k3k2 +

Km for selected enzymes

Enzyme Substrate km

Catalase H2O225

Hexokinase ATP 0.4

D-Glucose 0.05

D-Fructose 1.5

Carbonic anhydrase HCO3- 9

Chemotrypsin Glycyltyrosinylglycine 108

N-Benzoyltyrosinamide 2.5

Galactosidase D-Lactose 4

Threonine dehydratase L-Threonine 5

• The reaction velocity of an enzymatic reaction when the binding sites of E are saturated with substrates.

• It is proportional to [E].

Significance of Vmax

• Vmax is the reaction rate when the enzymes are saturated, and is independent of the enzyme concentration.

• The number of the products converted in a unit time by one enzyme molecule which is saturated.

Turnover number

k3 = Vmax / [E]

• To determine Km and Vmax

• To identify the reversible repression

Lineweaver-Burk plot

1=

Km 1

[S]+

Vmax

1V Vmax

Slope = Km/Vmax

1/[S]

1/V

Intercept = 1/Vmax

Intercept = -1/ Km

Double-reciprocal plot

• Substrate concentration

• Enzyme concentration

• Temperature

• pH

• Inhibitors

• Activators

§ 4.3 Factors affecting enzyme-catalyzed reaction

§ 4.3.a Effect of substrate

• Has been described already.

• [E] affects the rate of enzyme-catalyzed reactions

• [S] is held constant.

• When [S] >> [E], V ≈ [E]

§ 4.3.b Effect of enzyme

Re

actio

n v

elo

city

Enzyme concentration

§ 4.3.c Effect of temperature

• Optimal temperature (To) is the characteristic T at which an enzyme has the maximal catalytic power.

• 35 ~ 40C for warm blood species.

• Reaction rates increase by 2 folds for every 10C rise.

• Higher T will denature the enzyme.

Temp. (C)

Enz

ymat

ic a

ctiv

ity

0.5

1.0

2.0

1.5

10 6050403020

§ 4.3.d Effect of pH

• Optimal pH is the characteristic pH at which the enzyme has the maximal catalytic power.

• pH7.0 is suitable for most enzymes.

• Particular examples: pH (pepsin) = 1.8 pH (trypsin) = 7.8

En

zym

atic

act

ivity

1.0

2.0

1.5

0.5

2.0 10.08.04.0 6.0 pH

pepsin

trypsin

Section 5

Inhibition of Enzyme

• Inhibitors are certain molecules that can decrease the catalytic rate of an enzyme-catalyzed reaction.

• Inhibitors can be normal body metabolites and foreign substances (drugs and toxins).

§ 5.1 Inhibitors

• The inhibition process can be either irreversible or reversible.

• The inhibition can be competitive, non-competitive, or un-competitive.

Inhibition processes

• Inhibitors are covalently bound to the essential groups of enzymes.

• Inhibitors cannot be removed with Inhibitors cannot be removed with simple dialysis or super-filtration. simple dialysis or super-filtration.

• Binding can cause a partial loss or complete loss of the enzymatic activity.

§ 5.2 Irreversible inhibition

Acetylcholine accumulation will cause excitement of the parasympathetic system: omitting, sweating, muscle trembling, pupil contraction

Pesticide poisoning

acetylcholine choline + acetic acid

choline esterase

+ E OHRO

PO

X

R'O

RO

PO

O

R'O

E

organophosphate inhibited AChE acid

E OH

OR

P

O OR'

N

CH3

CHNOH+

N

CH3

CHNO+

PAM

AChE

HX+

• Heavy metal containing chemicals bind to the –SH groups to inactivate the enzymes.

Heavy metal poisoning

E

SH

SH

E

S

S

Hg

E

SH

SH

ClAs

Cl

CH

CHCl As CH

CHClE

S

S

Hg2++ + 2H+

+ 2HCl+

• Inhibitors are bound to enzymes non-covalently.

• The reversible inhibition is characterized by an equilibrium between free enzymes and inhibitor-bound enzymes.

§ 5.3 Reversible inhibition

+

S P

I

ES E+

+

EI

E

§ 5.3.a Competitive inhibition

• Competitive inhibitors share the structural similarities with that of substrates.

• Competitive inhibitors compete for the active sites with the normal substrates.

• Inhibition depends on the affinity of enzymes and the ratio of [E] to [S].

V =Vmax [S]

Km(1 + + [S]Ki

[ I ])

Vmax

1=

Km 1

[S] +

Vmax

1 (1 + )

V

[ I ]

Ki

1/[S]

1/V

No inhibitor

Competitiveinhibitorincrease

-1/ Km

-1/ Km(1 + [I]/Ki)

1/Vmax

Lineweaver-Burk plot

• As [S] increases, the effect of inhibitors is reduced, leading to no change in Vmax.

• Due to the competition for the binding sites, Km rises, equivalent to the reduction of the affinity.

Inhibition features

• FH4 (tetrahydrofolate) is a coenzyme in the nucleic acid synthesis, and FH2 (dihydrofolate) is the precursor of FH4.

• Bacteria cannot absorb folic acid directly from environment.

• Bacteria use p-amino-benzoic acid (PABA), Glu and dihydropterin to synthesize FH2.

• Sulfanilamide derivatives share the structural similarity with PABA, blocking the FH2 formation as a competitive inhibitor.

Example-1: competitive inhibitor

Glu

H2N COOH

dihydropterin

FH2 synthetase

FH2 FH4

H2N SO2NHR

Sulfanilamide

Methotrexate

PABA FH2reductase

+

+

COOH

H2C

COOH

malonic acid

HC

COOH

CH

HOOC

succinate

succinate dehydrogenase

fumaric acid

CO-COOH

H2C

COOH

oxaloacetate

H2C

COOH

CH2

HOOC

Example-2: competitive inhibitor

+S P

I

+

+

E

EI

I

+

S+

E

ESI

ES

§ 5.3.b Non-competitive inhibition

• Inhibitors bind to other sites rather than the active sites on the free enzymes or the E-S complexes.

• The E-I complex formation does not affect the binding of substrates.

• The E-I-S complexes do not proceed to form products.

• Reducing the [E-S]

• Vmax↓; unchanged Km.

1/[S]

1/V

No inhibitor

noncompetitiveinhibitorincrease

-1/ Km

(1 + [I]/Ki)/Vmax

Vmax

1=

Km 1

[S] +

Vmax

1 (1 + )

V

[ I ]

Ki (1 + )

[ I ]

Ki

+S P

+E

I

+

E

ESI

ES

§ 5.3.c Uncompetitive inhibition

• Uncompetitive inhibitors bind only to the enzyme-substrate complexes.

• The E-I-S complexes do not proceed to form products.

• The E-I-S complexes do not backward to the substrates and enzymes.

• This inhibition has the effects on reducing both Vmax and Km.

• Commonly in the multiple substrate reactions.

1/[S]

1/V

No inhibitor

Uncompetitiveinhibitorincrease

-1/ Km

(1 + [I]/Ki)/Vmax

1/Vmax

-1/ Km(1 + [I]/Ki)

Vmax

1=

Km 1

[S] +

Vmax

1

V (1 + )

[ I ]

Ki

type binding target Km Vmax

Competitive E only =

Noncompetitive E or ES =

Uncompetitive ES only

Summary of inhibition

Activators are the compounds which bind to an enzyme or an enzyme-substrate complex to enhance the enzymatic activity without being modified by the enzymes.

Activator

• Metal ions

• essential activators: no enzymatic activity without it

Mg2+ of hexokinase

• non-essential activators: enhancing the catalytic power.

Activators

• Enzymatic activity is a measure of the capability of an enzyme of catalyzing a chemical reaction.

• It directly affects the reaction rate.

• International unit (IU): the amount of enzyme required to convert 1 µmol of substrate to product per minute under a designated condition.

Enzymatic activity

• Determination of the enzymatic activity requires proper treatment of enzymes, excess amount of substrate, optimal T and pH, …

• One katal is the amount of enzyme that converts 1 mol of substrate per second.

• IU = 16.67×10-9 kat

• In addition to enzymes, other chemical species often participate in the catalysis.

• Cofactor: chemical species required by inactive apoenzymes (protein only) to convert themselves to active holoenzymes.

§ 2.2 Molecular Components

Cofactors

Activator ions(loosely bound)

Metal ions ofmetalloenzymes(tightly bound)

Cosubstrates(loosely bound)

Prostheticgroups

(tightly bound)

Essential ions Coenzymes

Cofactors

• Activator ions: loosely and reversibly bound, often participate in the binding of substrates.

• Metal ions of metalloenzymes: tightly bound, and frequently participate directly in catalytic reactions.

Essential ions

• Transfer electron

• Linkage of S and E；• Keep conformation of E-S complex

• Neutralize anion

Function of metal ions

• Act as group-transfer reagents to supply active sites with reactive groups not present on the side chains of amino acids

• Cosubstrates:

• Prosthetic groups:

Coenzymes

• The substrates in nature.

• Their structures are altered for subsequent reactions.

• Shuttle mobile metabolic groups among different enzyme-catalyzed reactions.

Cosubstrates

• Supply the active sites with reactive groups not present on the side chains of AA residues.

• Can be either covalently attached to its apoenzymes or through many non-covalent interactions.

• Remained bound to the enzyme during the course of the reaction.

Prosthetic groups

• Metabolite coenzymes: they are synthesized from the common metabolites. – several NTP, ATP (most abundant), UDP-

glucose

• Vitamin-derived coenzymes: they are derivatives of vitamins, and can only be obtained from nutrients. – NAD and NADP+, FAD and FMN, lipid

vitamins, …

Coenzymes

• Until recently, all the enzymes are known to be proteins.

• Ribonucleic acids also demonstrate the catalytic ability.

• Ribozymes have the ability to self-cleave.

• They are highly conservative, an indication of the biological evolution and the primary enzyme.

§ 2.3 Ribozyme

Family of serine protease

Hydrolysissite

Trypsin ElastaseChymotrypsin

Hydrolysissite

Hydrolysissite

§ 5.3.a Competitive inhibition

E + S E + P+I

EI

ES

Ki

§ 5.3.b Non-competitive inhibition

E + S E + P+I

EI + S

ES

Ki

+I

EIS

Ki

§ 5.3.c Uncompetitive inhibition

E + S E + PES+I

EIS

Ki

Section 6

Regulation of Enzyme

• Many biological processes take place at a specific time; at a specific location and at a specific speed.

• The catalytic capacity is the product of the enzyme concentration and their intrinsic catalytic efficiency.

• The key step of this process is to regulate either the enzymatic activity or the enzyme quantity.

• Maintenance of an ordered state in a timely fashion and without wasting resources

• Conservation of energy to consume just enough nutrients

• Rapid adjustment in response to environmental changes

Reasons for regulation

Controlling an enzyme that catalyzes the rate-limiting reaction will regulate the entire metabolic pathway, making the biosystem control more efficient.

Rate limiting reaction is the reaction whose rate set by an enzyme will dictate the whole pathway, namely, the slowest one or the “bottleneck” step.

• Zymogen activation

• Allosteric regulation

• Covalent modification

§6.1 Regulation of E Activity

• Certain proteins are synthesized and secreted as an inactive precursor of an enzyme, called zymogen.

• Selective proteolysis of these precursors leads to conformational changes, and activates these enzymes.

• It is the conformational changes that either form an active site of the enzyme or expose the active site to the substrates.

§6.1.a Zymogen activation

• Hormones: proinsulin

• Digestive proteins: trypsinogen, …

• Funtional proteins: factors of blood clotting and clot dissolution

• Connective tissue proteins: procollagen

Wide varieties

Activation of chymotrypsin

1

1

S

14913 24514614 15 16

149 24514613 14 15 16

1 14616 149 24513

S S S

Pro-CT

CT

CT

• A cascade reaction in general

• To protect the zymogens from being digested

• To exert function in appropriate time and location

• Store and transport enzymes

Features of zymogen activation

• Allosteric enzymes are those whose activity can be adjusted by reversible, non-covalent binding of a specific modulator to the regulatory sites, specific sites on the surface of enzymes.

• Allosteric enzymes are normally composed of multiple subunits which can be either identical or different.

§6.1.b Allosteric regulation

• The multiple subunits are catalytic subunits regulatory subunits

• Kinetic plot of v versus [S] is sigmoidal shape.

• Demonstrating either positive or negative cooperative effect.

• There are two conformational forms, T and R, which are in equilibrium.

• Modulators and substrates can bind to the R form only; the inhibitors can bind to the T form.

Properties of allosteric enzymes

[S]

Allosteric enzyme

Allosteric represion

Allosteric activation

Allosteric curve

Activation of protein kinase

C: catalytic portions

R: regulatory portions

4 cAMP

protein kinase(inactive)

protein kinase(active)

+ +C

C

R

R

C

C

R

R

cAMP

cAMP

cAMP

cAMP

• A variety of chemical groups on enzymes could be modified in a reversible and covalent manner.

• Such modification can lead to the changes of the enzymatic activity.

§6.1.c Covalent modification

phosphorylation - dephosphorylation

adenylation - deadenylation

methylation - demethylation

uridylation - deuridylation

ribosylation - deribosylation

acetylation - deacetylation

Common modifications

Phosphorylation

E-OH E-O-PO3H2

ATP ADP

proteinkinase

phosphorylation

dephosphorylation

H2OPi

Mg2+

phosphatase

• Two active forms (high and low)

• Covalent modification

• Energy needed

• Amplification cascade

• Some enzymes can be controlled by allosteric and covalent modification.

Features of covalent modification

• Constitutive enzymes (house-keeping): enzymes whose concentration essentially remains constant over time

• Adaptive enzymes: enzymes whose quantity fluctuate as body needs and well-regulated.

• Regulation of enzyme quantity is accomplished through the control of the genes expression.

§6.2 Regulation of E Quantity

• Inducer: substrates or structurally related compounds that can initiate the enzyme synthesis

• Repressor: compounds that can curtail the synthesis of enzymes in an anabolic pathway in response to the excess of an metabolite

• Both are cis elements, trans-acting regulatory proteins, and specific DNA sequences located upstream of genes

Controlling the synthesis

• Enzymes are immortal, and have a wide range of lifetime. LDH4 5-6 days, amylase 3-5 hours.

• They degrade once not needed through proteolytic degradation.

• The degradation speed can be influenced by the presence of ligands such as substrates, coenzymes, and metal ions, nutrients and hormones.

Controlling the degradation

• Lysosomic pathway: – Under the acidic condition in lysosomes– No ATP required– Indiscriminative digestion – Digesting the invading or long lifetime proteins

• Non-lysosomic pathway:– Digest the proteins of short lifetime – Labeling by ubiquitin followed by hydrolysis– ATP needed

Degradation pathway

Enzymes/pathways in cellular organelles

organelle Enzyme/metabolic pathway

Cytoplasm Aminotransferases, peptidases, glycolysis, hexose monophosphate shunt, fatty acids synthesis, purine and pyrimidine catabolism

Mitochondria Fatty acid oxidation, amino acid oxidation, Krebs cycle, urea synthesis, electron transport chain and oxidative phosphorylation

Nucleus Biosynthesis of DNA and RNA

Endoplasmic reticulum

Protein biosynthesis, triacylglycerol and phospholipids synthesis, steroid synthesis and reduction, cytochrome P450, esterase

Lysosomes Lysozyme, phosphatases, phospholipases, proteases, lipases, nucleases

Golgi apparatus Glucose 6-phosphatase, 5’-nucleotidase, glucosyl- and galactosyl-transferase

Peroxisomes Calatase, urate oxidase, D-amino acid oxidase, long chain fatty acid oxidase

Section 7

Clinical Applications

• Plasma specific or plasma functional enzymes: Normally present in the plasma and have specific functions.

• High activities in plasma than in the tissues. Synthesized in liver and enter the circulation.

• Impairment in liver function or genetic disorder leads to a fall in the activities.

§7.1 Fundamental Concepts

• Non-plasma specific or plasma non-functional enzymes: either totally absent or at a low concentration in plasma

• In the normal turnover of cells, intracellular enzymes are released into blood stream.

• An organ damaged by diseases may elevate those enzymes

• A group of enzymes that catalyze the same reaction but differ from each other in their structure, substrate affinity, Vmax, and regulatory properties.

• Due to gene differentiation: the different gene products or different peptides of the same gene

• Present in different tissues of the same system, or subcellular components of the same cell

§7.2 Isoenzyme

• Synthesized from different genes (malate dehydrogenase in cytosol versus in mitochondria)

• Oligomeric forms of more than one type of subunits (lactate dehydrogenase)

• Different carbohydrate content (alkaline phosphatase)

Reasons for isoenzyme

• 5 isoenzymes, LDH1 – LDH5

• Tetramer– M subunits (M for muscle), basic – H subunits (H for heart), acidic

• Different catalytic activities

• Used as the marker for disease diagnosis

Lactate dehydrogenase (LDH)

H4

LDH1

M subunitH subunit

LDH2 LDH3 LDH4 LDH5

H1M3 M4H2M2H3M1

• LDH1 (H4) in heart muscle converts lactate to pyruvate, and then to acetyl CoA.

• LDH5 (M4) in skeletal muscle converts pyruvate to lactate.

H3CHC COOH

OH

H3C C COOH

O

LDH

NAD+ NADH + HLactate Pyruvate

• 3 isoenzymes, BB, BM, MM

• Dimeric form: M (muscle) or B (brain)

• CPK2 is undetectable (<2%) in serum for healthy individuals, and elevated to 20% in the first 6-18 hrs after myocardial infarction.

• Used as a earliest reliable indicator of myocardial infarction.

Creatine phosphokinase

• Usefulness:– Enzyme assays provide important information

concerning the presence and severity of diseases

– Provide a means of monitoring the patient’s response

• approaches:– Measuring the enzymatic activities directly

– Used as agents to monitor the presence of substrates

§7.3 Diagnostic Applications

Enzymatic activity changes

CK

act

ivity

1 2 3 4

Rat

io o

f LD

H1 to

LD

H2

LDH1 / LDH2

CM2

CM3

Days after myocardial infarction

1.00

1.25

0.75

Electrophoresis of LDH

Serum enzymes (elevated)

Diseases

Amylase Acute pancreatitis

Serum glutamate pyruvate transaminase (SGPT)

Liver diseases (hepatitis)

Serum glutamate oxaloacetate transaminase (SGOT)

Heart attack (myocardial infarction)

Alkaline phosphatase Rickets, obstructive jaundice

Acid phosphatase Cancer of prostate gland

Lactate dehydrogenase (LDH) Heart attack, liver diseases

γ-glutamyl transpeptidase (GGT) Alcoholism

5’-nucleotidase Hepatitis

Aldolase Muscular dystrophy

Enzymes for disease diagnosis

• Successful therapeutic uses– Steptokinase: treating myocardial infarction; preventing

the heart damage once administrated immediately after heart attack

– Asparaginase: tumor regression

• Several limits– Can be rapidly inactivated or digested

– May provoke allergic effects

§7.4 Therapeutic Applications

Section 8

Nomenclature

• Adding the suffix –ase to the name of the substrates (urease)

• Adding the suffix –ase to a descriptive term for the reactions they catalyze (glutemate dehydrogenase)

• For historic names (trypsin, amylase)

• Being named after their genes (Rec A –recA, HSP70)

§8.1 Conventional Nomenclature

• The International Union of Biochemistry and Molecular Biology (IUBMB) maintains the classification scheme.

• Categorize in to 6 classes according to the general class of organic reactions catalyzed

• Assigned a unique number, a systematic name, a shorter common name to each enzyme

§8.2 Systematic Nomenclature

1. Catalyzing a variety of oxidation-reduction reactions

AH2 + B → A + BH2

2. Alcohol dehydrogenase (alcohol:NAD+ oxidoreductase, E.C. 1.1.1.1.)

Cytochrome oxidase

L- and D-amino acid oxidase

§8.2.a Oxidoreductases

1. Catalyzing transfer of a groups between donors and acceptors

A-X + B → A + B-X

2. Hexokinase (ATP:D-hexose 6-phosphotransferase, E.C.2.7.1.1.)

Transaminase

Transmethylases

§8.2.b Transferases

1. Catalyzing cleavage of bonds by addition of water

A-B + H2O → AH + BOH

2. Lipase (triacylglycerol acyl hydrolase, E.C. 3.1.1.3.)Choline esteraseAcid and alkaline phosphatasesUrease

§8.2.c Hydrolases

1. Catalyzing lysis of a substrate and generating a double bond (nonhydrolytic, and non-oxidative reactions)

A-B + X-Y → AX + BY

2. Aldolase (ketose 1-phosphate aldehyde lysase, E.C. 4.1.2.7.)FumaraseHistidase

§8.2.d Lysases

1. Catalyzing recemization of optical or geometric isomers

A → A’

2. Triose phosphate isomerase (D-glyceraaldehyde 3-phosphate ketoisomerase, E.C. 5.3.1.1.)

Retinol isomerasePhosphohexose isomerase

§8.2.e Isomerases

1. Catalyzing synthetic reactions at the expense of a high energy bond of ATP

A + B → A-B

2. Glutamine synthetase (L-glutamate ammonia ligase, E.C. 6.3.1.2.)

Acetyl CoA carboxylase

Auccinate thiokinase

§8.2.f Ligases

• Blood clot formation and tissue repair are brought “on-line” only in response to pressing physiological or pathophysiological needs.