enzymes: classification, structure. accelerate reactions by a millions fold enzymes - catalysts of...

ENZYMES: CLASSIFICATION, STRUCTUREENZYMES: CLASSIFICATION, STRUCTURE

Accelerate reactions by a millions fold

Enzymes - catalysts of biological reactions

1. Catalyze only thermodynamically possible reactions

2. Are not used or changed during the reaction.

3. Don’t change the position of equilibrium and direction of the reaction

4. Usually act by forming a transient complex with the reactant, thus stabilizing the transition state

Common features for enzymes and inorganic catalysts:

Specific features of enzymes:

1. Accelerate reactions in much higher degree than inorganic catalysts

2. Specificity of action

3. Sensitivity to temperature

4. Sensitivity to pH

Structure of enzymesEnzyme

sComplex or holoenzymes

(protein part and nonprotein part – cofactor)

Simple (only protein)

Apoenzyme (protein part)

Cofactor

Prosthetic groups

-usually small inorganic molecule or

atom;

-usually tightly bound to apoenzyme

Coenzyme

-large organic molecule

-loosely bound to apoenzyme

Example of prosthetic group

Metalloenzymes contain firmly bound metal ions at the enzyme active sites (examples: iron, zinc, copper, cobalt).

Example of metalloenzyme: carbonic anhydrase contains

zinc

Coenzymes

• Coenzymes act as group-transfer reagents

• Hydrogen, electrons, or groups of atoms can be transferred

Coenzyme classification

(1) Metabolite coenzymes - synthesized from common metabolites

(2) Vitamin-derived coenzymes - derivatives of vitamins

Vitamins cannot be synthesized by mammals, but must be obtained as nutrients

Examples of metabolite coenzymes

ATP

S-adenosylmethionine

ATP can donate phosphoryl group

S-adenosylmethioninedonates methyl groups in many biosynthesis reactions

Cofactor of nitric oxide synthase

5,6,7,8 - Tetrahydrobiopterin

Vitamin-Derived Coenzymes

•Vitamins are required for coenzyme synthesis and must be obtained from nutrients

•Most vitamins must be enzymatically transformed to the coenzyme

•Deficit of vitamin and as result correspondent coenzyme results in the disease

• Nicotinic acid (niacin) an nicotinamide are precursor of NAD and NADP

• Lack of niacin causes the disease pellagra

NAD+ and NADP+

NAD and NADP are coenzymes for dehydro-genases

FAD and FMN• Flavin adenine dinucleotide (FAD) and Flavin

mononucleotide (FMN) are derived from riboflavin (Vit B2)

• Flavin coenzymes are involved in oxidation-reduction reactions

FMN (black), FAD (black/blue)

Thiamine Pyrophosphate (TPP)

• TPP is a derivative of thiamine (Vit B1)

• TPP participates in reactions of: (1) Oxidative decarboxylation(2) Transketo-lase enzyme reactions

Pyridoxal Phosphate (PLP)

• PLP is derived from Vit B6 family of vitamins

PLP is a coenzyme for enzymes catalyzing reactions involving amino acid metabolism (isomerizations, decarboxylations, transamination)

Enzymes active sites

Active site – specific region in the enzyme to which substrate molecule is bound

Substrate usually is relatively small molecule

Enzyme is large protein molecule

Therefore substrate binds to specific area on the enzyme

Characteristics of active sites

Specificity (absolute, relative (group), stereospecificity)

Small three dimensional region of the protein. Substrate interacts with only three to five amino acid residues. Residues can be far apart in sequence

Binds substrates through multiple weak interactions (noncovalent bonds)

There are contact and catalytic regions in the active site

Active site of lysozym consists of six amino acid residues which are far apart in sequence

Active site contains functional groups (-OH, -NH, -COO etc)

Binds substrates through multiple weak interactions (noncovalent bonds)

Theories of active site-substrate interaction

Fischer theory (lock and key model)

The enzyme active site (lock) is able to accept only a specific type of substrate (key)

Koshland theory (induced-fit model)

The process of substrate binding induces specific conformational changes in the the active site region

Properties of Enzymes

Specificity of enzymes

1.Absolute – one enzyme acts only on one substrate (example: urease decomposes only urea; arginase splits only arginine)

2.Relative – one enzyme acts on different substrates which have the same bond type (example: pepsin splits different proteins)

3.Stereospecificity – some enzymes can catalyze the transformation only substrates which are in certain geometrical configuration, cis- or trans-

Sensitivity to pHEach enzyme has maximum activity at a particular pH (optimum pH)

For most enzymes the optimum pH is ~7 (there are exceptions)

-Enzyme will denature above 45-50oC

-Most enzymes have temperature optimum of 37o

Each enzyme has maximum activity at a particular temperature (optimum temperature)

Sensitivity to temperature

Naming of EnzymesCommon names

are formed by adding the suffix –ase to the name of substrate

Example: - tyrosinase catalyzes oxidation of tyrosine; - cellulase catalyzes the hydrolysis of cellulose

Common names don’t describe the chemistry of the reaction Trivial names

Example: pepsin, catalase, trypsin.

Don’t give information about the substrate, product or chemistry of the reaction

Principle of the international classification

All enzymes are classified into six categories according to the type of reaction they catalyze

Each enzyme has an official international name ending in –ase

Each enzyme has classification number consisting of four digits: EC: 2.3.4.2

First digit refers to a class of enzyme, second -to a subclass, third – to a subsubclass, and fourth means the ordinal number of enzyme in subsubclass

The Six Classes of Enzymes

1. Oxidoreductases

• Catalyze oxidation-reduction reactions

- oxidases - peroxidases - dehydrogenases

2. Transferases

•Catalyze group transfer reactions

3. Hydrolases

•Catalyze hydrolysis reactions where water is the acceptor of the transferred group

- esterases - peptidases - glycosidases

4. Lyases

•Catalyze lysis of a substrate, generating a double bond in a nonhydrolytic, nonoxidative elimination

5. Isomerases

•Catalyze isomerization reactions

6. Ligases (synthetases)

•Catalyze ligation, or joining of two substrates

•Require chemical energy (e.g. ATP)