enzyme introduction by dr. ashok kumar j

04/13/2023 Dr. Ashok Kumar J; Professor; Department of Biochemistry. 1

Introduction to enzymeDr. Ashok Kumar. J.

International Medical SchoolManagement Science University

Malaysia

04/13/2023 Dr. Ashok Kumar J; Professor; Department of Biochemistry. 2

Objectives: To learn…….

• What are enzymes?• How Catalysts function ?• Coenzymes and their importance• Substrates and enzyme substrate complex• Active site and its characteristics• Free energy of activation • Why enzymes increase the rate of the reaction

04/13/2023 Dr. Ashok Kumar J; Professor; Department of Biochemistry. 3

ENZYMEProtein in nature

Themolabile

Increase the speed of the reaction

Biocatalysts

04/13/2023 Dr. Ashok Kumar J; Professor; Department of Biochemistry. 4

CATALYSTS

Bind to substances form highly reactive and

unstable intermediate

Remain unchanged in mass and form on completion of the reaction they catalyze

Small amount of catalyst may be repeatedly used to increase the speed of the reaction

04/13/2023 Dr. Ashok Kumar J; Professor; Department of Biochemistry. 5

Cannot initiate any reaction that does not

occur spontaneously

Equilibrium constant of the reaction is not altered, but helps to attain it faster

Catalyze the reaction by decreasing the activation energy

04/13/2023 Dr. Ashok Kumar J; Professor; Department of Biochemistry. 6

Coenzymes Enzyme proteins may be • simple proteins

or • conjugated proteins

Non protein part of the enzyme protein is called cofactor

• Organic molecule - it is called coenzyme• Inorganic (metal) ion metal – frequently termed cofactor

04/13/2023 Dr. Ashok Kumar J; Professor; Department of Biochemistry. 7

Apo-enzyme + Coenzyme = Holo-enzyme

04/13/2023 Dr. Ashok Kumar J; Professor; Department of Biochemistry. 8

Coenzymes

Small organic molecules

Derivatives of B complex vitamin

Bind loosely and transiently

If they bind tightly and permanently associated with the enzyme it is called prosthetic group

04/13/2023 Dr. Ashok Kumar J; Professor; Department of Biochemistry. 9

Coenzymes may be divided in to two groupsFirst group• Coenzymes taking part in reactions catalyzed by oxidoreductases by

donating or accepting hydrogen atom or electron

e.g. Lactate dehydrogenase

Lactate Pyruvate

NAD+ NADH+H+

• These coenzymes can be considered as co-substrates• Changes occurring in the substrate is counterbalanced by the

co-enzyme

04/13/2023 Dr. Ashok Kumar J; Professor; Department of Biochemistry. 10

e.g. Lactate dehydrogenase

Lactate Pyruvate

NAD+ NADH+H+

• Two hydrogens are removed from lactateTwo electrons and one hydrogen are accepted by NAD+ to

form NADH Remaining H+ is released to the surrounding

Coenzyme transferring hydrogen • NAD+, NADP+• FMN, FAD

04/13/2023 Dr. Ashok Kumar J; Professor; Department of Biochemistry. 11

Second group• Coenzymes taking part in transferring groups other than hydrogen

Alanine αKetoglutarate

Pyruvate Glutamate

Transaminase (amino transferase)Pyridoxal phosphate (PLP)

04/13/2023 Dr. Ashok Kumar J; Professor; Department of Biochemistry. 12

Coenzyme • Pyridoxal Phosphate• Thiamine pyrophosphate (TPP)• Biotin• Coenzyme A• Tetrahydrofolate

Group transferred• Amino group• Hydroxy ethyl group• Carbon dioxide• Acyl group• One carbon group

04/13/2023 Dr. Ashok Kumar J; Professor; Department of Biochemistry. 13

• Once the reaction is completed – coenzyme is released from the apo-enzyme• Can bind to another enzyme molecule

Lactate dehydrogenase

Glyceraldehyde- 3- phosphate

NAD+NADH+H+

Lactate Pyruvate

1,3 bisphosphoglycerate

Glyceraldehyde-3-phosphate dehydrogenase

04/13/2023 Dr. Ashok Kumar J; Professor; Department of Biochemistry. 14

Cofactors

Non-protein moiety it is called cofactor if it is a metal ion such as Zn2+ , Mg 2+, Cu2+, Mn2+ or Fe2+

Metal activated enzymes: Loose and easily dissociable complex with

specific metal

Metalloenzymes:Higher affinity for specific metals; holds

the metal tightly in the molecules

04/13/2023 Dr. Ashok Kumar J; Professor; Department of Biochemistry. 15

SUBSTRATE

Substance on which enzyme acts is called substrate

Substrate binds to enzyme at a specific site on the enzyme

Forms Enzyme substrate-complex

Substrate is modified to product

04/13/2023 Dr. Ashok Kumar J; Professor; Department of Biochemistry. 16

Enzyme activity depends upon Three dimensional (3D) structure of the enzyme protein

04/13/2023 Dr. Ashok Kumar J; Professor; Department of Biochemistry. 17

Enzymes are the most specific catalyst known

Tertiary structure of the enzyme folded in such a way as to create a region that has

- correct molecular dimensions- appropriate topology- optimum alignment of counter ion

groups and hydrophobic regions to accommodate a specific substrate

04/13/2023 Dr. Ashok Kumar J; Professor; Department of Biochemistry. 18

Active site

Is due to tertiary structure of protein Are regarded as clefts or cervices Is not rigid it is flexible Generally has a substrate binding site and a

catalytic site Coenzymes or cofactors on which some enzymes depend are part of the active site

04/13/2023 Dr. Ashok Kumar J; Professor; Department of Biochemistry. 19

Substrate binds to active site by forming weak non-covalent bonds Of the 20 amino acids, some of them are repeatedly found in active site

e.g. cysteine, serine, aspartate, histidine, lysine, arginine, glutamate, tyrosine

• Enzymes are larger in size compared to substrates

04/13/2023 Dr. Ashok Kumar J; Professor; Department of Biochemistry. 20

SO ENZYME ACTIVITY DEPENDS ON

pH temperature ionic strength

binding of specific substance to enzyme

?

04/13/2023 Dr. Ashok Kumar J; Professor; Department of Biochemistry. 21

ENZYME SUBSTRTAE COMPLEX

04/13/2023 Dr. Ashok Kumar J; Professor; Department of Biochemistry. 22

+ S P P

Lock and Key ModelFischer’s Template Model

• Active site is pre-shaped • Rigid• Does not explains allostearic modulation

S

EE E

04/13/2023 Dr. Ashok Kumar J; Professor; Department of Biochemistry. 23

• Flexible• Explains allostearic modulation, competitive inhibition• Accepted

Koshland’s Induced Fit Model

04/13/2023 Dr. Ashok Kumar J; Professor; Department of Biochemistry. 24

All reactions have an energy barrier separating the reactants and the products

‘Free energy of activation’

Energy difference between the energy of the reactants and high energy intermediates

(transition state) that occur during formation of product

04/13/2023 Dr. Ashok Kumar J; Professor; Department of Biochemistry. 25

04/13/2023 Dr. Ashok Kumar J; Professor; Department of Biochemistry. 26

Thank you