ENZYMESOutline

DefinitionCharacteristics of enzymes

Types of enzymesFactors effecting enzyme activity

The Definition and Characteristics of Enzymes

• Enzymes are catalysts that increase the rate of a reaction without being changed themselves.

• Characters: a protein Catalyst effects rate of reaction and not the equilibrium unchanged at the end of reaction effective in smaller quantities efficient and specific reaction can be reversed activities affected by surroundings may need helpers – cofactors/coenzymes involve in multiple steps of biochemical pathways

Classification of enzymes

6 main classes according to International Union of Biochemistry and Molecular Biology (IUBMB):

1. Oxidoreductase2. Transferase

3. hydrolase4. lyase

5. isomerase6. ligase

Function: catalyzes oxidation-reduction reactions (transfer of electrons)

e.g. alcohol dehydrogenase

Other e.g. Biliverdin reductase; Glucose oxidase

1.OXIDOREDACTASES1.OXIDOREDACTASES

Function: catalyzes reactions involving transfer of functional groups

e.g. Hexokinase

Other e.g. Glycoaldehyde transferase; DNA nucleotidylexotransferase

2.TRANSFERASES2.TRANSFERASES

Function: catalyzes hydrolytic reactions involving use of water mol.

e.g. Triacylglycerol lipase

Other e.g. -amino acid esterase; Oxaloacetase; trypsin

H2O

3. HYDROLASES3. HYDROLASES

Function: catalyzes cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation.

e.g. Lysine decarboxylase

other e.g.: threonine aldolase [EC 4.1.2.5]; Other e.g. cystine lyase, pyruvate decarboxylase

4. LYASES4. LYASES

Function: catalyzes intramolecular transfer of groups

e.g. Maleate isomerase

Other e.g. Inositol-3-phosphate synthase; Maltose epimerase]

5. ISOMERASES5. ISOMERASES

Function: catalyzes the joining of two molecules with concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate

e.g. Pyruvate carboxylase

Other e.g. GMP synthase; DNA ligase

6. LIGASES6. LIGASES

Enzymes are protein and all proteins are not enzyme

exhibits characteristics like other proteins primary structure

amino acid sequence

e.g.: human pancreatic lipase (467 amino acids)N-Met1-…-Ser171-...-Asp194-...-His281-…-Cys467-C

human trypsin (247 amino acids) N-Met1-…-His63-…-Asp107-…-Ser200-…-Ser247-C

Lysozyme’s tertiary structure

Anti-parallel

-sheet

(3)

-helix

(5)

Aspartate carbamoyltransferase’s quartenary structure

2 catalytic trimers

3 regulatory dimers

Active site of Enzyme:• The active site is the region of the enzyme that binds the

substrate, to form an enzyme–substrate complex, and transforms it into product (Binding site).

• The active site is a three-dimensional entity, often a cleft or crevice on the surface of the protein, in which the substrate is bound by multiple weak interactions (non-covalent bond).

• Two models have been proposed to explain how an enzyme binds its substrate: the lock-and-key model and the induced-fit model.

Lock and Key hypothesis

E + S ES E + P

Proposed by Emil Fischer (1894): the shape of the substrate and the active site of the enzyme are thought to fit together like a key into its lock.

Induced fit hypothesisproposed in 1958 by Daniel E. Koshland, Jr.: the binding of substrate induces a conformational change in the active site of the enzyme. In addition, the enzyme may distort the substrate, forcing it into a conformation similar to that of the transition state

For example, the binding of glucose to hexokinase induces a conformational change in the structure of the enzyme such that the active site assumes a shape that is complementary to the substrate (glucose) only after it has bound to the enzyme.

Coenzyme and Cofactor

Many enzymes require the presence of small, nonprotein units to carry out their particular reaction. Coenzyme: complex organic moleculeCofactor: inorganic ions, such as Zn2+ or Fe2+

Holoenzyme: A complete catalytically-active enzyme together with its coenzyme or metal ion (cofactor) is called as holoenzyme.

Apoenzyme: The protein part of the enzyme on its own without its cofactor/ coenzyme is termed as apoenzyme.

Enzyme Kinetics

Activation energy: For a biochemical reaction to proceed, the energy barrier needed to transform the substrate molecules into the transition state has to beovercome. The energy required to overcome this energy barrier is known as activation energy.It is the magnitude of the activation energy which determines just how fast the reaction will proceed. It is believed that enzymes increase the rate of reaction by lowering the activation energy for the reaction they are catalyzing.

Enzyme Kinetics

Factors affecting enzyme activity1. Substrate concentration2. Enzyme concentration3. pH4. Temperature5. Inhibitors

1. Substrate concentration

A

B

At low substrate concentrations a doubling of substrate concentration leads to a doubling of reaction rate, whereas at higher substrate concentration the enzyme becomes saturated and there is no further increase in reaction rate (hyperbolic curve)

2. Enzyme concentration

When substrate concentrations is saturating, a doubling of the enzyme concentration leads to a doubling of rate of reaction

3. pHEach enzyme has an optimum pH at which the rate of the reaction that it catalyzes is at its maximum. Slight deviations in the pH from the optimum lead to a decrease in the reaction rate.

AC

B

4. TemperatureElevated temperature increases the rate of an enzyme-catalyzed reaction by increasing the thermal energy of the substrate molecules which helps to overcome energy barrier or achieve activation energy.However, a second effect comes into play at higher temperatures.which causes denaturation of the enzyme and decrease the rate of reaction.

Substances which bind to enzyme & disrupt the enzyme activity by blocking the production of ES-complex or E + P

Many inhibitors exist, including normal body metabolites, foreign drugs and toxins.

Enzyme inhibition can be of two main types: irreversibleor reversible.

Reversible inhibition can be subdivided into competitiveand noncompetitive.

5. Enzyme Inhibition

Irreversible Inhibition

An irreversible inhibitor binds tightly, often covalently, to the active site of the enzyme, permanently inactivating theenzyme. They often form covalent bond with amino acid at active site.Examples: diisopropylphosphofluoridate (DIPF), iodoacetamide and penicillin.

Reversible Inhibition

Involves the noncovalent links between inhibitor and enzyme

Reversible Competitive Inhibition

A competitive inhibitor competes with the substrate molecules for binding to the active site of the enzyme due to close structural similarities with the substrate molecule. At high substrate concentration, the effect of a competitive inhibitor can be overcome.

e.g.: succinate dehydrogenase (E); succinate (S); malonate (I)

Reversible Non-competitive Inhibition

A noncompetitive inhibitor binds at a site other than the active site of theenzyme and decreases its catalytic rate by causing a conformationalchange in the three-dimensional shape of the enzyme.Inhibitor dont have any structural similarities with the substrate molecule

e.g.: prostaglandin synthase (E); arachidonate (S); aspirin (I)

Enzyme inhibitor: harmful or beneficial? Sarin – the nerve gasAction – inhibits acetylcholinesterase from hydrolyzing

acetylcholine to acetate & cholineEffect – acetylcholine gather at end of nerve, causing

symptoms such as fuzzy eyesight, extreme sweating, loss of motor functions control & paralysis

acetylcholinesterase – enzyme in the body which has an important function in nerve regulation and control

Penicillin – antibacterial agentAction – covalently attaches to bacterial glycoprotein

peptidase active site, preventing peptidoglycanpeptide bond cross-linking

Effect – prevents cell wall synthesis; exposing bacterial cell to osmotic lysis; bacteria cannot reproduceglycoprotein peptidase – bacterial enzyme catalyzing cross-linking

of peptidoglycan peptide bonds, the main cell wall polymer

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