Prof. Roshada Hashim School of Biological Sciences Room: 228 Ext 3517 email: roshadahashim@gmail.com http://roshada.yolasite.com

Topic Dates Enzymology 29 March to 16 April Glycolysis 23 April – 26 April Gluconeogenesis 30 April + 3 May Test 28 May

Enzymology http://roshada.yolasite.com

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.

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

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 a b c d Main class Subclass Sub-subclass Individual enzymes

There are 6 classes of enzyme reactions: Main Class Number (EC No.) Systematic Name Type of Reaction 1 Oxidoreductase All types of oxidation and reduction reactions 2 Transferase Transfer of functional group 3 Hydrolase Hydrolysis reaction 4 Lyase Breaking of C-C, C-O and C-N bonds other than by hydrolysis or oxidation 5 Isomerase Isomerization reaction 6 Ligase Formation of bonds with ATP cleavage 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

2.7 Transfer of phosporus grp. 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

SIMILARITIES AND DIFFERENCES BETWEEN ENZYMES & CHEMICAL CATALYSTS 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

Enzymes are more efficient a. Most rxns take place at pH 7 and 37oC 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

Rate of hydrolysis (mol/min) Example: Hydrolysis of o-nitrophenol  galactosidase Substrate Enzyme Temp (oC) Rate of hydrolysis (mol/min) ONPG NaOH 20 6.9x10-6 HCl 6.6x10-4 β-galaktosidase 6.6x104

2. Enzymes are more Specific Absolute specificity 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

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

It will also attack ester bonds 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 HN CH C NH CH C (CH)4 O BUT It will also attack ester bonds HN CH C O CH3 (CH)4 O NH2

b. Stereochemical Specificity Type Example Optical 2 series of enzymes for the stereoisomers D and L. ie there is an L-amino acid oxidase and an D-amino acid oxidase

Chemical groups that are similar Type Example Geometric Succinate dehydrogenase catalyses the formation of trans-fumarate and not cis-malate Chemical groups that are similar Glycerolkinase phosphorylates glycerol to form L-glyseralphosphate and NOT D-glyseralphosphate

ZyMOGEN CONTROL (PRECURSOR) Versatile Enzymes can catalyse many types of rxns eg: hydrolysis polymerisation redox rxns dehydration acyl transfer rxns condensation d. Under cellular control Pepsinogen pepsin + peptida (BM 9000) Pepsin catalyses the above rxn 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) Autocatalysis Peptide (MWt 9000) is an inhibitor to control the number of molecules of pepsin produced GENETIC CONTROL ZyMOGEN CONTROL (PRECURSOR) PEPSIN: Synthesised in the form of pepsinogen PEPSINOGEN: NOT ACTIVE

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

Enzyme Structure E + S ES E + P

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

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

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

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.

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 3. Promotes Acid Base Reactions