1. Prof. Roshada Hashim School of Biological Sciences Room: 228 Ext

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

3. Enzymology

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

7. 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:
Lyase
4.1 Lyase C-C
Carboxy-Lyase (C-COO-)
Histidine carboxylase ie C-COO- in histidine

8. 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
Transferase
2.7 Transfer of phosporus grp.
Phosphotranferase with an alcohol group as an acceptor
ATP: D-glucose-6-phosphotransferase
If ATP: D-hexose-6-phosphotransferase

9. 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

10. 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 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. 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

12. 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 NH CO2

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. 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

15. 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

16. 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

17. 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

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

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
3. Promotes Acid Base Reactions