enzyme

Classification of Enzymes Chemistry (A) According to Chemical Nature Enzymes are Divided into: (1) Simple Enzymes & (2) Conjugated Enzymes Simple Enzymes Conjugated Enzyme Formed of Protein Only Formed of Protein part & Non-protein part Do Not Need Additional Components for Full Activity Need Additional Components for Full Activity e.g. Proteolytic Peptidases (Pepsin, Trypsin) Urease e.g. Most Enzymes ** A Large Number of Enzymes Require an Additional Non-Protein Component ** To Carry Out its Catalytic Functions. Simple Enzyme: - Simple Enzymes are Also Called Proteozyme. Conjugated Enzymes: - Conjugated Enzymes are Also Called Complex Enzymes. - Protein part + Non-protein part = Conjugated enzyme - Apoenzyme + Cofactor = Holoenzyme - The Enzyme Without its Non-protein Moiety is Termed an Apoenzyme & is Inactive. - The Complete Structure of Apoenzyme & Cofactor is Termed Holoenzyme & is Active. - Enzyme -- Cofactor = Apoenzyme. - Enzyme + Cofactor = Holoenzyme. Cofactor Definition: - It is the Non-protein Part of an Enzyme, Required for Full Enzymatic Activity. Site: - It Binds to Active site of Enzyme. Classification: - Cofactors can be Inorganic or Organic. Inorganic Cofactor Complex Organic Cofactor Metals & Ions (Iron-Sulfur Clusters) & (Essential Ions) Vitamins, Heme, Flavin (WSV + Vitamin K) Takes Part in Catalysis Doesn’t Take Part in Catalysis Helps in Carrying ions & Groups ** Organic Cofactor are Called Coenzyme ** Enzymes Consist of: (1) Apo-Enzyme, (2) Co-Factor, (3) Co-Enzyme, (4) Holo-enzyme, (5) Active Site, (6) Substrate. Cofactor Inorganic Cofactors: - Some Enzymes Bind Metals More Tightly than Others. - Metals can be Loosely Bound or Tightly Bound. Loosely Bound (Activator Ions) Tightly Bound (Prosthetic Group) Easily Removed Not Easily Removed Without Causing Damage Cause Damage Called Metal Activated Enzyme Called Metalloenzyme e.g. Salivary Amylase & Cl & Ca ATP Requiring Enzymes Mg e.g. Cu, Co, Mn, Mg, Se, Zn Catalase & Mn Alcohol dehydrogenase & Zn Organic Cofactors: - Some Enzymes Bind Coenzymes More Tightly than Others. - Coenzymes can be Loosely Bound or Tightly Bound. Loosely Bound (Cosubstrate) Tightly Bound (Prosthetic Group) They Transiently Associate with the Enzyme. They Permanently Associate With the Enzyme They Dissociate From the Enzyme in an Altered State During Catalysis Cycle They Remain Bound and Returned to its Original Form During Catalysis Cycle e.g. ATP UDP SAM (B3) NAD⁺, NADP⁺ (B5) CoA (B9) THF e.g. (B1) TPP (B2) FMN, FAD (B6) PLP (B7) Biotin (B12) DA-Cobalamin Lipoic Acid - Cofactors can be Distinguished by the Strength of Interaction with their Apoenzyme Cofactor Organic Cofactors: - Coenzymes can be are Classified Based on the Source Into: (1) Metabolite Coenzymes & (2) Vitamin-Derived Coenzymes Metabolite Coenzymes Vitamin-Derived Coenzymes They are Synthesized from Common Metabolites They are Derived from Vitamins e.g. ATP UDP SAM (S-Adenosyl-Methionine) e.g. Frequently are Derived from Water-Soluble Vitamins (B1) (B2) (B3) (B5) (B6) (B7) (B9) (B12) Lipoic Acid ** Vitamins Cannot be Synthesized by Mammals, but Must be Obtained as Nutrients ** Prosthetic Groups (PG): - Are Tightly Bound Inorganic or Organic Cofactor is Called a Prosthetic Group. - PG are Difficult to Remove Without Damage (Denaturation). - PG Can't be Removed from Enzyme Until Structure of Enzyme gets Denatured. - They Are Tightly (Permanently) Integrated Into an Enzyme’s Structure. - They are have Tight, Stable Incorporation into Protein. - They Use Covalent or Non-covalent Forces. Cofactor Examples of Enzymes & Their Inorganic Cofactors (Metal): Coenzyme Metal Pyruvate Kinase Potassium (K + ) Pyruvate Kinase Hexokinase Glucose-6-Phosphatase Magnesium (Mg2+) Arginase, Ribonucleotide Reductase Manganese (Mn2+) Dinitrogenase Molybdenum (Mo) Urease Nickel (Ni2+) Glutathione Reductase Selenium (Se) Alcohol Dehydrogenase Carbonic Anhydrase Carboxypeptidase A,B Zinc (Zn) Cofactor Examples of Enzymes & Their Organic Coenzyme (Carriers): - Coenzymes Function as Transient Carriers of Specific Functional Groups: - Electrons, Hydrogen, or Groups of Atoms Can be Transferred Vitamin Active Form (Coenzyme) Function (Carries) Reactions Dependent Enzyme B1 (Thiamin) Thiamin Pyrrophosphate (TPP) Aldehydes Oxidative Decarboxylation Transketolase B2 (Riboflavin) Flavin Mononucleotide (FMN) Electrons (Hydrogen) Oxidation & Reduction L-amino acid Oxidase B2 (Riboflavin) Flavin Adenine Dinucleotide (FAD) Electrons (Hydrogen) Oxidation & Reduction D-amino acid Oxidase B3 (Niacin) Nicotinamide Adenine Dinucleotide (NAD) Electrons (Hydrogen) Oxidation & Reduction Lactate Dehydrogenase B5 (Pantothenic Acid) Coenzyme A (CoA) Fatty Acid (Acyl Groups) Acylation Acyl group Transfer Thiokinase B6 (Pyridoxine) Pyridoxal Phosphate (PLP) Amino Groups Transamination Transfer of Groups To & From a.a Alanine Transaminase B7 (H) (Biotin) Biotin Co2 Carboxylation Pyruvate Carboxylase B9 (Folic Acid) Tetrahydrofolate (THF) 1 Carbon Unit 1 Carbon Transfer Reaction Formyl Transferase B12 (Cobalamin) 5' Deoxyadenosyl Cobalamin Hydrogen & Alkyl Intramolecular Rearrangement -------------- Lipoic acid Lipoic acid Hydrogen & Acyl Oxidation & Acylation -------------- Coenzyme Q Coenzyme Q Electrons (Hydrogen) Oxidation & Reduction -------------- Cofactor Coenzymes can be Classified According to the Group whose Transfer they Facilitate - FMN, FAD, NAD, NADP, Lipoic, Coenzyme Q: Transfer Hydrogen. - TPP, CoA, PLP, Biotin, Folate, Lipoic, ATP: Transfer Groups Other than Hydrogen. Coenzyme A is derived from the vitamin B5 (Pantothenic acid). Coenzyme A (CoASH or CoA) itself is a complex and highly polar molecule. Consisting of 4-phosphopantothenic acid, adenosine 3',5'-diphosphate & β-mercaptoethylamine, β-mercaptoethylamine directly involved in acyl transfer reactions. adenosine 3’ ,5’-diphosphate functions as a recognition site it increases the affinity for CoA binding to enzymes. B12 is Important for Carb, Fat, Amino acid Metabolism. it is a very important naturally accruing organometallic compound it is the only vitamin that contain ion metal. it is a co-enzyme and act as prostatic group. Conezymes of Vit B12 are methylcobalamin & 5′-deoxyadenosylcobalamin Active Site Definition: - It Is a Small Special Pocket or Cleft in an Enzyme where Binding & Catalysis occurs. Sites: - The Active Site Consists of 2 Sites: Binding site Catalytic site Contains amino acid Residues that form Temporary bond with Substrate Contains amino acid Residues that Catalyse Reaction of Substrate Binding: - The Active Site can Binds & Orients to: (1) Substrate, (2) Cofactor or Prosthetic Group, (3) Competitive Inhibitor. Properties: (1) Small, (2) Active (3) Specific, (4) Reversible. Property Explanation Small Active site Represent <5% of Total Surface Area of Enzyme Active Active site has Active amino acids like Ser & Cys. These amino acids Have Special groups such as -NH₂, -COOH, -SH. Reversible - Active site Binds to Substrate by Weak Non-covalent bonds like (H-bond, Electrostatic, Wan der Waal, Hydrophobic) Specific The Set, Sequence & 3D Positions of amino acids in Active Site Give the Active Site a Very Specific Size, Shape, Tertiary Structure & Chemical Behavior. - The Active site is Groove or Pocket that is Located in a Deep Tunnel within Enzyme. - A Change in Shape of Protein Affects Shape of Active Site & Function of Enzyme. Active Site Specificity: - The Specificity of an Enzyme is Determined by Active Site. - There are Two Models that Explain how Enzymes Bind to their Substrate. Lock & Key Model Hand & Glove Model Rigid Model Induced-Fit Model Fischer Model Koshland Model Old Restrictive Theory (1890’s) New Non-Restrictive Theory (1963) Active site Rigid. Active site is Flexible. Active Site Does Not Require Any Changes to Bind Active Site Requires Some Change to Bind Active site is Perfect & Complementary Fit For Substrate Active site is Almost Perfect & Complementary Fit For Substrate Substrate Doesn’t Induce Conformational Change In Active site Substrate Induce Conformational Change In Active site Induced-Fit Model: - The Active Site is Almost Complementary to Substrate. - But When it Binds, the Enzyme Undergoes Conformational Changes. - To Make its Active Site’s Shape Better Fit. - The Conformational Changes Ensure an Ideal Binding Arrangement Between Enzyme & Substrate. - This Maximizes the Ability of the Enzyme to Catalyze the Reaction. This Theory is More Generally Accepted than the Lock and Key Model.