1. ENZYMES: CLASSIFICATION, STRUCTURE

2. Enzymes - catalysts of biological reactions
Accelerate reactions by a millions fold

3. Common features for enzymes and inorganic catalysts:
1. Catalyze only thermodynamically possible reactions
2. Are not used or changed during the reaction.
3. Don’t change the position of equilibrium and direction of the reaction
4. Usually act by forming a transient complex with the reactant, thus stabilizing the transition state

4. Specific features of enzymes:
1. Accelerate reactions in much higher degree than inorganic catalysts
2. Specificity of action
3. Sensitivity to temperature
4. Sensitivity to pH

5. Structure of enzymes Enzymes
Complex or holoenzymes (protein part and nonprotein part – cofactor)
Simple (only protein)
Apoenzyme (protein part)
Cofactor
Prosthetic groups
usually small inorganic molecule or atom;
usually tightly bound to apoenzyme
Coenzyme
-large organic molecule
-loosely bound to apoenzyme

6. Example of prosthetic group
Example of metalloenzyme: carbonic anhydrase contains zinc
Metalloenzymes contain firmly bound metal ions at the enzyme active sites (examples: iron, zinc, copper, cobalt).

7. Coenzyme classification
Coenzymes
Coenzymes act as group-transfer reagents
Hydrogen, electrons, or groups of atoms can be transferred
Coenzyme classification
(1) Metabolite coenzymes - synthesized from common metabolites
Vitamin-derived coenzymes - derivatives of vitamins
Vitamins cannot be synthesized by mammals, but must be obtained as nutrients

8. Examples of metabolite coenzymes
ATP can donate phosphoryl group
ATP
S-adenosylmethionine
donates methyl groups in many biosynthesis reactions
S-adenosylmethionine

9. 5,6,7,8 - Tetrahydrobiopterin
Cofactor of nitric oxide synthase

10. Vitamin-Derived Coenzymes
Vitamins are required for coenzyme synthesis and must be obtained from nutrients
Most vitamins must be enzymatically transformed to the coenzyme
Deficit of vitamin and as result correspondent coenzyme results in the disease

11. NAD+ and NADP+
Nicotinic acid (niacin) an nicotinamide are precursor of NAD and NADP
Lack of niacin causes the disease pellagra
NAD and NADP are coenzymes for dehydro-genases

12. FAD and FMN
Flavin adenine dinucleotide (FAD) and Flavin mononucleotide (FMN) are derived from riboflavin (Vit B2)
Flavin coenzymes are involved in oxidation-reduction reactions
FMN (black), FAD (black/blue)

13. Thiamine Pyrophosphate (TPP)
TPP is a derivative of thiamine (Vit B1)
TPP participates in reactions of: (1) Oxidative decarboxylation (2) Transketo-lase enzyme reactions

14. Pyridoxal Phosphate (PLP)
PLP is derived from Vit B6 family of vitamins
PLP is a coenzyme for enzymes catalyzing reactions involving amino acid metabolism (isomerizations, decarboxylations, transamination)

15. Enzymes active sites Substrate usually is relatively small molecule
Enzyme is large protein molecule
Therefore substrate binds to specific area on the enzyme
Active site – specific region in the enzyme to which substrate molecule is bound

16. Characteristics of active sites
Specificity (absolute, relative (group), stereospecificity)
Small three dimensional region of the protein. Substrate interacts with only three to five amino acid residues. Residues can be far apart in sequence
Binds substrates through multiple weak interactions (noncovalent bonds)
There are contact and catalytic regions in the active site

17. Active site of lysozym consists of six amino acid residues which are far apart in sequence

18. Active site contains functional groups (-OH, -NH, -COO etc)
Binds substrates through multiple weak interactions (noncovalent bonds)

19. Theories of active site-substrate interaction
Fischer theory (lock and key model)
The enzyme active site (lock) is able to accept only a specific type of substrate (key)

20. Koshland theory (induced-fit model)
The process of substrate binding induces specific conformational changes in the the active site region

21. Specificity of enzymes
Properties of Enzymes
Specificity of enzymes
Absolute – one enzyme acts only on one substrate (example: urease decomposes only urea; arginase splits only arginine)
Relative – one enzyme acts on different substrates which have the same bond type (example: pepsin splits different proteins)
Stereospecificity – some enzymes can catalyze the transformation only substrates which are in certain geometrical configuration, cis- or trans-

22. Sensitivity to pH
Each enzyme has maximum activity at a particular pH (optimum pH)
For most enzymes the optimum pH is ~7 (there are exceptions)

23. Sensitivity to temperature
Each enzyme has maximum activity at a particular temperature (optimum temperature)
-Enzyme will denature above 45-50oC
-Most enzymes have temperature optimum of 37o

24. Naming of Enzymes Common names
are formed by adding the suffix –ase to the name of substrate
Example: tyrosinase catalyzes oxidation of tyrosine; cellulase catalyzes the hydrolysis of cellulose
Common names don’t describe the chemistry of the reaction
Trivial names
Example: pepsin, catalase, trypsin.
Don’t give information about the substrate, product or chemistry of the reaction

25. Principle of the international classification
All enzymes are classified into six categories according to the type of reaction they catalyze
Each enzyme has an official international name ending in –ase
Each enzyme has classification number consisting of four digits: EC:
First digit refers to a class of enzyme, second -to a subclass, third – to a subsubclass, and fourth means the ordinal number of enzyme in subsubclass

26. The Six Classes of Enzymes
1. Oxidoreductases
Catalyze oxidation-reduction reactions
- oxidases peroxidases dehydrogenases

27. 2. Transferases
Catalyze group transfer reactions

28. 3. Hydrolases
Catalyze hydrolysis reactions where water is the acceptor of the transferred group
- esterases peptidases glycosidases

29. 4. Lyases
Catalyze lysis of a substrate, generating a double bond in a nonhydrolytic, nonoxidative elimination

30. 5. Isomerases
Catalyze isomerization reactions

31. 6. Ligases (synthetases)
Catalyze ligation, or joining of two substrates
Require chemical energy (e.g. ATP)