roshada.yolasite

1. Prof. Roshada HashimSchool of Biological SciencesRoom: 228Ext 3517email: roshadahashim@gmail.com http://roshada.yolasite.com

3. Enzymology http://roshada.yolasite.com

4. All biochemical reactions that occur in the cell involves enzymes • Enzymes are found in all parts of the cell All enzymes are proteins (with some exceptions) but not all proteins are enzymes • 3 distinct features: • Catalytic power • Specificity and • regulation Definition of an enzyme: A biological catalyst that increases the rate of a chemical reaction to reach equilibrium and does not become one of the products.

5. NOMENCLATURE: • Named by adding a suffix: ~ase • Naming is based on the type of reaction catalysed and the substrate involved: • eg. Histidine decarboxylase: This enzyme catalyses the decarboxylation of histidine

6. Systematic Classification of Enzymes According to the Enzyme Commission Follows a numbering system in which an enzyme will have a series of 4 numbers: EC a.b.c.d

7. There are 6 classes of enzyme reactions: • Examples of Enzymes: • Histidine Carboxylase: • 4. Lyase • 4.1 Lyase C-C • 4.1.1 Carboxy-Lyase (C-COO-) • 4.1.1.22 Histidine carboxylase ie C-COO- in histidine

8. ATP + D-Glucose ADP + D-Glucose 6- P A phosphate group is transferred from ATP to the C-6 –OH group of glucose. So the enzyme is a transferase 2. Transferase 2.7 Transfer of phosporus grp. 2.7.1 Phosphotranferase with an alcohol group as an acceptor 2.7.1.2 ATP: D-glucose-6-phosphotransferase If 2.7.1.1 ATP: D-hexose-6-phosphotransferase

9. SIMILARITIES AND DIFFERENCES BETWEEN ENZYMES & CHEMICAL CATALYSTS • Similarities • Influences the rate in achieving equilibrium in a reaction DOES NOT influence the position of the equilibrium • Only a small amount is needed • Effectiveness can be reduced by poisons and inhibitors

10. Differences • Enzymes are more efficient • a. Most rxns take place at pH 7 and 37oC • b. Rate of rxns are increased 108-1011 times • c. Turnover number (total number of substrates that are metabolsied by a molecule of enzyme in 1 minit is higher: • Enzymes: 1 million • Chemical catalyst: 1000

11. Example: Hydrolysis of o-nitrophenol  galactosidase

12. Differences • 2. Enzymes are more Specific • Absolute specificity • Recognises only one substrate; rare • eg. Hydrolysis of urea by urease • H2N • C = O + H2O 2NH3 + CO2 • H2N

13. b. Absolute group specificity Recognises a certain group of chemicals eg. alcohol and alcohol dehydrogenase CH3CH2OH + NAD+ CH2CHO + NADH BUT It recognises other alcohols as substrate

14. O O O HN CH C NH CH C (CH)4 HN CH C O CH3 (CH)4 NH2 c. Absolute relative group specificity Trypsin hydrolyses peptide bonds but will attack peptide bonds where the -C=O portion is donated by the basic amino acids: Lys, His, Arg BUT It willalso attack ester bonds

15. b. Stereochemical Specificity

17. Versatile • Enzymes can catalyse many types of rxns eg: d. Under cellular control ZyMOGEN CONTROL (PRECURSOR) GENETIC CONTROL Autocatalysis Peptide (MWt 9000) is an inhibitor to control the number of molecules of pepsin produced • Rate of synthesis and the final concentration of enzyme under genetic control is influenced by: • Substrate • Product • Protein synthesis can be • Induced: in the presence of some metabolites • Repressed: fail to synthesise in the presence of certain metabolites • (differenct from inhibitors) PEPSIN: Synthesised in the form of pepsinogen PEPSINOGEN: NOT ACTIVE Pepsinogen pepsin + peptida (BM 9000) Pepsin catalyses the above rxn

18. Many enzymes rely on their protein structure for catalytic functions BUT there are others which require non protein components: • Cofactors: metal ions • Coenzyme: a. non protein component is an organic molecule eg FAD, NAD, CoA, Biotin • b. serve as intermediate carriers of functional groups • c. • Prosthetic group: coenzyme that is firmly attached (sometimes covalent bond) • Therefore: • The protein complex and the prosthetic group is called: Holoenzyme • The protein without the prosthetic group is called Apoenzyme; catalytically inactive

19. Enzyme Structure E + S ES E + P

20. Substrat binds at a specific site: Active Site • Active site is only about 5% of the whole enzyme • Usually a crevice or a pit • Shape of the active site must complement the shape of the substrate • Amino acids that are far apart can form the active site • Usually amino acids involved have R-grps that are ionic, nucleophillic and reactive • There groups participate in the binding of substrate and the formation of product

21. The optimum conformation of the active site depends on: • Temperature : 35C - 37C • pH between 6.5 – 7.5 ( but there are some exceptions • Ionic strength: 0.15

22. www.biologyreference.com/Dn-Ep/Enzymes.html www.chemistry.wustl.edu/~edudev/LabTutorials/...

23. 3 factors that contribute towards enzyme efficiency • (How does an enzyme increase the rate of chemical reaction?) • Proximity: • The active site brings the reactants together (proximity) for collision. The effective concentration of the reactants is increased significantly at the active site and favors transition state formation • Orientation: Substrate collisions in solution are random and are less likely to be the specific orientation that promotes the approach to the transition state. The amino acids in the active site play a significant role in orientating the substrate. Substrate interaction with these specific amino acid side chains promotes strain such that some of the bonds are easier to break and thus the new bonds can form.

24. 3. Promotes Acid Base Reactions The amino acids that form the active site have functional side chains that are poised to donate or accept hydrogen ions from the substrate. The loss or the addition of a portion (H ) can destabilize the covalent bonds in the substrate to make it easier for the bonds to break. Hydrolysis and electron transfers also work by this mechanism. The functional groups that are involved in this function are: Carboxyl: -COOH Amino: -NH3 Hydroxyl: -OH Sulphydryl: -SH Imidazole: from histidine