Chapter 3

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

Components of Enzymes

• Simple enzymes: consists of only one peptide chain

• Conjugated enzymes:

holoenzyme = apoenzyme + cofactor

(protein) (non-protein)

• Cofactors: metal ions; small organic molecules

§ 1.1 Molecular Components

Only holoenzyme possesses catalytic acticity

Metal ions

• Metal-activated enzyme: ions necessary but loosely bound.

• Metalloenzymes: Ions tightly bound.

1. Particularly in the active center, transfer electrons;

2. bridge the enzyme and substrates;

3. stabilize enzyme conformation;

4. 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.

• 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.

§ 1.2 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

• A group of enzymes that catalyze the same reaction but differ from each other in their structure, physicochemical property, and Immune properties.

§1.3 Isoenzyme同工酶

• 同：催化的化学反应• 异：酶蛋白分子结构、

理化性质、

免疫学性质

Reasons for isoenzyme

• 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

同一基因编码的不同产物

同一个体不同组织或同一细胞不同亚细胞结构

Lactate dehydrogenase (LDH)乳酸脱氢酶

• 5 isoenzymes, LDH1 – LDH5

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

H4

LDH1

M subunitH subunit

LDH2 LDH3 LDH4 LDH5

H1M3 M4H2M2H3M1

Used as the marker for disease diagnosis

Section 2

Properties of Enzymes

1. Fragile structures of the living systems 结构易被破坏

2. Low kinetic energy of the reactants 反应物动能低

3. Low concentration of the reactants 反应物浓度低

4. Toxicity of catalysts 化学催化剂对机体有毒性

5. Complexity of the biological systems 生物系统的复杂性

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

§ 2.1 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.

Common features

不改变自身的质和量

不改变反应平衡点

催化热力学允许的反应

降低反应的活化能

• Apply to the thermodynamically allowable reactions

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

• Reduce the activation energy

• 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

高催化效率

高度特异性

高度可调节

§ 2.1.a High efficiency

enzyme

Non-enzymatic

rate constant

(kn in s-1)

enzymatic

rate constant

(kn in s-1)

accelerated reaction rate

Carbonic anhydrase 10-1 106 107

Chymotrypsin 4 x 10-9 4 x 10-2 107

Lysozyme 3 x 10-9 5 x 10-1 1.7 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 1012

Alkaline phosphatase

10-15 102 1017

Accelerated reaction rates

• Absolute specificity 绝对特异性

• Relative specificity 相对特异性

• Stereospecificity 立体异构特异性

§ 2.1.b High specificity

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

Absolute specificity 绝对特异性

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 相对特异性

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

Stereospecificity 立体异构特异性The 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.

绝对专一性 一种酶只能催化一种底物。如 6- 磷酸葡萄糖磷酸酯酶。

立体专一性 一种酶只能对一种立体异构体起催化作用。

相对专一性

键专一性

一种酶只作用于一定的化学键，对键两侧的基团无要求。如酯酶。

基团专一性

不仅要求底物具有一定的化学键，还对键某一侧的基团有选择性。如磷酸单酯酶。

酶的专一性及其类型（ Summary ）

• 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.

§ 2.1.c High regulation

1 、对酶生成与降解量的调节。2、酶催化活性的调节。3、通过改变底物浓度对酶进行调节等。

§2.2 Mechanism of Enzyme-Catalyzed Reactions

Reaction progress

Fre

e ene

rgy

G forthe reaction

reactants

products

transition state, S

G+ (catalyzed)

G+ (uncatalyzed)

§2.2.a lower the activation energy than the other catalyst 酶比一般催化剂更有效地降低反应的活化能

§2.2.b Induced-fit model 诱导契合效应

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

§2.2.c Proximity and orientation arrangement

临近效应与定向排列

§2.2.d Surface effect表面效应

§2.2.e Multielement catalysis多元催化作用

• General acid-base catalysis

酸 -碱催化• Covalent catalysis

共价催化• Nucleophilic catalysis

亲核催化

Section 3

Kinetics of Enzyme- Catalyzed Reactions

• Substrate concentration 底物浓度• Enzyme concentration 酶浓度• Temperature 温度• pH pH 值• Inhibitors 抑制剂• Activators 激活剂

Factors affecting enzyme-catalyzed reaction

§3.1 Effect of substrate

[S]0

Vmax

V0

Vmax/2

Km

• It is of rectangular hyperbolic shape.

Zero order with respect to [s]

First order with respect to [s]

当底物浓度较低时反应速度与底物浓度成正比；

反应为一级反应。

EEE

E E

EE

EEE

EE

表示 S

V

[S]

a

EEE

E E

EE

EEE

EE

随着底物浓度的增高

反应速度不再成正比例加速；反应为混合级反应。

V

[S]

b

当底物浓度高达极大时

反应速度不再增加，达最大速度；反应为零级反应。

EEE

E E

EE

EEE

EE

V

[S]

c

§3.1.a Intermediate state 中间产物学说

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

• 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].

反应酶促反应速率和底物浓度的关系。

§3.1.b Michaelis-Menten Equation米 - 曼氏方程

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

Vmax=V Km + [S]

[S]

[S]0

Vmax

V0

Vmax/2

Km

Describing a hyperbolic curve.

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

Km值等于酶促反应速率为最大速率一半时的底物浓度 .

§3.1.c Significance of Km

• Km is a characteristic constant of E.

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

• 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 +

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

Vmax是酶完全被底物饱和时的反应速率。

§3.1.d Significance of Vmax

• It is proportional to [E].

与酶浓度呈正比。

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

单位时间内每个酶分子催化生成的产物数。

§3.1.e Turnover number 转换数

k3 = Vmax / [E]

• To determine Km and Vmax

• To identify the reversible repression

§3.1.f Lineweaver-Burk plot林 - 贝式作图

1=

Km 1

[S]+

Vmax

1V Vmax

Slope = Km/Vmax

1/[S]

1/V

Intercept = 1/Vmax

Intercept = -1/ Km

Double-reciprocal plot 双倒数作图

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

• [S] is held constant.

• When [S] >> [E], V ≈ [E]

§3.2 Effect of enzyme

Re

actio

n v

elo

city

Enzyme concentration

§3.3 Effect of temperature

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

酶促反应速率最快时反应体系的温度。

• 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

§3.4 Effect of pH

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

酶催化活性最高时反应体系的 pH值。

• 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 4

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).

§ 4.1 Inhibitors

• The inhibition process can be either irreversible or reversible.

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

Inhibition processes

酶的抑制作用分为不可逆性抑制与可逆性抑制两类。

可逆性抑制作用包括竞争性抑制作用、非竞争性抑制作用、反竞争性抑制作用 3类。

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

抑制剂与酶活性中心必需基团共价结合。

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

抑制剂不能通过透析、超滤等方法去除。

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

结合后导致酶失活。

§ 4.2 Irreversible inhibition

Acetylcholine accumulation will cause excitement of the parasympathetic system: omitting, sweating, muscle trembling, pupil contraction乙酰胆碱的积蓄会造成迷走神经的毒性兴奋状态。

1. Pesticide poisoning 有机磷化合物中毒

acetylcholine choline + acetic acid

choline esterase 胆碱酯酶

乙酰胆碱

+ 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+

解磷定

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

2. Heavy metal poisoning 重金属离子及砷中毒

Lewisite inhibited

BAL

E

S

As

S

CH CHCl + E

SH

SH

CH2

CH2

CH

SH

SH

OH

+

CH2

CH2

CH

S

S

OH

As CH CHCl

• Inhibitors are bound to enzymes non-covalently.

抑制剂通过非共价键与酶和（或）酶 -底物复合物可逆性结合。

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

特点：在酶与酶 -抑制剂复合物之间保持平衡。

§ 4.3 Reversible inhibition

+

S P

I

ES E+

+

EI

E

§ 4.3.a Competitive inhibition

E + S E + P+I

EI

ES

Ki

• 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].

抑制剂与底物结构相似。

抑制剂与底物竞争酶的活性中心。

抑制程度取决于抑制剂与酶的相对亲和力和底物浓度的相对比例。

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

动力学特点： Vmax 不变， Km 增大。

Glu

H2N COOH

dihydropterin

FH2 synthetase

FH2 FH4

H2N SO2NHR

Sulfanilamide

Methotrexate

PABA FH2reductase

+

+

Example-1: competitive inhibitor

二氢蝶呤啶

对氨基苯甲酸

磺胺类药物 氨甲喋呤

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

琥珀酸 延胡索酸

丙二酸

琥珀酸脱氢酶

草酰乙酸

+S P

I

+

+

E

EI

I

+

S+

E

ESI

ES

§ 4.3.b Non-competitive inhibition

E + S E + P+I

EI + S

ES

Ki

+I

EIS

Ki

• 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.

抑制剂与酶活性中心外的必需基团结合。

酶 -抑制剂复合物的形成不影响酶与底物的结合。

酶 -抑制剂 -底物复合物不能进一步释放产物。

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

• Vmax↓; unchanged Km.

+S P

+E

I

+

E

ESI

ES

§ 4.3.c Uncompetitive inhibition

E + S E + PES+I

EIS

Ki

• 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.

抑制剂仅与酶 -底物复合物结合。

酶 -抑制剂 -底物复合物不能释放出产物。

酶 -抑制剂 -底物复合物不能再解离出游离的酶和底物。

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

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

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.

§ 4.4 Activator

• Metal ions （ mainly ）• essential activators: no enzymatic activit

y without it.

eg ： Mg2+ of hexokinase

• non-essential activators: enhancing the catalytic power.

Activators

Section 5

Regulation of Enzyme

• Zymogen activation 酶原激活

• Allosteric regulation 变构调节

• Covalent modification 共价修饰

§5.1 Regulation of E Activity

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

§5.1.a Zymogen activation 酶原激活

有些酶在细胞内合成或初分泌时无活性，此无活性前体称为酶原。

• 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.

§5.1.a Zymogen activation

酶原在一定条件下，水解掉一个或几个短肽，形成或暴露出活性中心，转化为有活性酶的过程。

Activation of chymotrypsin

赖缬 天天天天

甘异赖缬 天天天天 缬组

丝

SSSS

SS

SS4646

183183

甘异缬

组丝

SSSS

SS

SS

肠激酶肠激酶 胰蛋白酶胰蛋白酶

active site

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

酶原激活是一个级联放大的过程

避免对自身组织细胞的消化

使酶在特定的时间和场所发挥作用

酶原可作为酶的储存和转运的形式

• 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.

§5.1.b Allosteric regulation 变构调节

一些代谢物可与某些酶分子活性中心外的某部分可逆地结合，使酶构象改变，从而改变酶的催化活性，此种调节方式称变构调节。

• The multiple subunits are catalytic subunits 催化亚基 regulatory subunits 调节亚基

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

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

Allosteric curve Allosteric activationAllosteric activation

Allosteric represion

[S] [S]

VV Allosteric enzyme

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

• Demonstrating either positive or negative cooperative effect.

• 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.

§5.1.c Covalent modification 共价修饰

在其他酶的催化作用下，某些酶蛋白肽链上的一些基团可与某种化学基团发生可逆的共价结合，从而改变酶的活性，此过程称为共价修饰。

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

§5.2 Regulation of E Quantity

1. Controlling the synthesis

• Induction

• Repression

2. Controlling the degradation

• Lysosomic pathway

• Non-lysosomic pathway

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

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.