Prof. Roshada HashimSchool of Biological Sciences

Room: 228Ext 3517

email: roshadahashim@gmail.com

http://roshada.yolasite.com

Topic Dates

Enzymology 29 March to 16 AprilGlycolysis 23 April – 26 AprilGluconeogenesis 30 April + 3 May Test 28 May

Enzymologyhttp://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:

1. Catalytic power2. Specificity and 3. 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:

1. Named by adding a suffix: ~ase2. 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 dMain 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:

1. 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

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-phosphotransferaseIf 2.7.1.1 ATP: D-hexose-6-phosphotransferase

SIMILARITIES AND DIFFERENCES BETWEEN ENZYMES & CHEMICAL CATALYSTS

Similarities1.Influences the rate in achieving

equilibrium in a reaction DOES NOT influence the position of the equilibrium

2.Only a small amount is needed

3.Effectiveness can be reduced by poisons and inhibitors

Differences

1. 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

Example: Hydrolysis of o-nitrophenol galactosidase

Substrate Enzyme Temp (oC) Rate of hydrolysis (mol/min)

ONPG NaOH 20 6.9x10-6

ONPG HCl 20 6.6x10-4

ONPG β-galaktosidase 20 6.6x104

Differences

2. Enzymes are more Specific

a. Absolute specificity Recognises only one substrate; rare eg. Hydrolysis of urea by urease

H2N C = O + H2O 2NH3 + CO2

H2N

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

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 O

BUT It will also attack ester bonds

HN CH C O CH3

(CH)4O

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

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

c. VersatileEnzymes can catalyse many types of rxns eg:

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:SubstrateProductProtein synthesis can beInduced: in the presence of some metabolitesRepressed: 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 CONTROLZyMOGEN CONTROL (PRECURSOR)

PEPSIN: Synthesised in the form of pepsinogen PEPSINOGEN: NOT ACTIVE

hydrolysis polymerisation redox rxns

dehydration acyl transfer rxns condensation

Many enzymes rely on their protein structure for catalytic functions BUT there are others which require non protein components:

1. Cofactors: metal ions2. Coenzyme: a. non protein component is an organic molecule eg FAD,

NAD, CoA, Biotin b. serve as intermediate carriers of functional groups c. 3. Prosthetic group: coenzyme that is firmly attached (sometimes

covalent bond)

Therefore: The protein complex and the prosthetic group is called: HoloenzymeThe 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 : 35C - 37C

• 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?)

1. 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

2. 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.

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: -OHSulphydryl: -SHImidazole: from histidine

3. Promotes Acid Base Reactions