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Enzymes for Karnataka University Botany IV Semester

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  1. 1. 4th SEMESTER – BOTANY KARNATAKA UNIVERSITY, DHARWADModified from various internet resources by Dr. Jayakara Bhandary Associate Professor of Botany Government Arts & Science College Karwar, Uttara Kannada 1
  2. 2. Introduction & History Enzyme, in Greek means in living (en= in, zyme = living). Biocatalysts or Organic catalysts, usually high molecular weight proteins (exception- Ribozymes or RNA enzymes). Coined by Kuhne in 1878. First enzyme extract from Yeast cells by Buchner (1897). First purified enzyme is urease, by James B. Summer (1926). 2
  3. 3. Enzymes are Biological CatalystsEnzymes are proteins that: Increase the rate of reaction by lowering the energy of activation. Catalyze nearly all the chemical reactions taking place in the cells of the body. Have unique three- dimensional shapes that fit the shapes of reactants. 3
  4. 4. Activation EnergyThink of activation energy as theBARRIERrequired to make a product.Most stable product is the one withthe lowestenergy.Most reactions require a “push” toget themstarted! “Push” is called “energyof activation” forreaction - Also represented by EA 4
  5. 5. Trivial Names of EnzymesThe name of an enzyme: Usually ends in –ase. Identifies the reacting substance. For example, sucrase catalyzes the reaction of sucrose. Describes the function of the enzyme. For example, oxidases catalyze oxidation. Could be a common name, particularly for the digestion enzymes such as pepsin and trypsin. 5
  6. 6. IUB Classification of Enzymes Enzymes are classified according to the reaction they catalyze. Class Reactions catalyzed Oxidoreductases Oxidation-reduction Transferases Transfer groups of atoms Hydrolases Hydrolysis Lyases Add atoms/remove atoms to/from a double bond Isomerases Rearrange atoms Ligases Use ATP to combine molecules 6
  7. 7. Systematic Name According to the International union Of Biochemistry an enzyme name has two parts: -First part is the name of the substrates for the enzyme. -Second part is the type of reaction catalyzed by the enzyme.This part ends with the suffix “ase”.Example: Lactate dehydrogenase
  8. 8. EC numberEnzymes are classified into six different groups according to the reaction being catalyzed. The nomenclature was determined by the Enzyme Commission in 1961 (with the latest update having occurred in 1992), hence all enzymes are assigned an “EC” number. The classification does not take into account amino acid sequence (ie, homology), protein structure, or chemical mechanism.
  9. 9. EC numbers EC numbers are four digits, for example a.b.c.d, where “a” is the class, “b” is the subclass, “c” is the sub- subclass, and “d” is the sub-sub-subclass. The “b” and “c” digits describe the reaction, while the “d” digit is used to distinguish between different enzymes of the same function based on the actual substrate in the reaction. Example: for Alcohol:NAD+oxidoreductase EC number is
  10. 10. The Six Classes EC 1. Oxidoreductases EC 2. Transferases EC 3. Hydrolases EC 4. Lyases EC 5. Isomerases EC 6. Ligases
  11. 11. EC 1. Oxidoreductases Catalyze the transfer of hydrogen or oxygen atoms or electrons from one substrate to another. Since these are ‘redox’ reactions, an electron donor/acceptor is also required to complete the reaction. A H2 +B → A+ BH2 Ex. Oxidases, Dehydrogenases, Reductases.
  12. 12. EC 2. Transferases Catalyze group transfer reactions, excluding oxidoreductases (which transfer hydrogen or oxygen and are EC 1). These are of the general form: A-X + B ↔ BX + A Ex: Transaminases (transfer amino group), Kinases (transfer Phosphate group)
  13. 13. EC 3. Hydrolases Catalyze hydrolytic reactions. Includes. A-X + H2O ↔ X-OH + A-H Ex: lipases, esterases, Amylases, peptidases/proteases, etc.
  14. 14. EC 4. Lyases Catalyze non-hydrolytic (covered in EC 3) removal of functional groups from substrates, often creating a double bond in the product; or the reverse reaction, ie, addition of function groups across a double bond.A- X +B-Y → A=B + X-YEx: Decarboxylases, Aldolases, Dehydrases, Deaminases, Synthases, etc.
  15. 15. EC 5. Isomerases Catalyzes isomerization reactions, including epimerizations and cis-trans isomerizations. A →A’Ex: Isomerases (Cis-Trans),Epimerases (D—L)
  16. 16. EC 6. Ligases Catalyzes the synthesis of various (mostly C-X) bonds, coupled with the breakdown of energy- containing substrates, usually ATP . A+B → A-B ATP → ADP+iPEx: Synthetases, Carboxylases
  17. 17. Classification of Enzymes: Oxidoreductasesand Transferases 17
  18. 18. Classification: Hydrolases and Lyases 18
  19. 19. Classification: Isomerases and Ligases 19
  20. 20. Active SiteThe active site: Is a region within an enzyme that fits the shape of molecules called substrates. Contains amino acid R groups that align and bind the substrate. Releases products when the reaction is complete. 20
  21. 21. Enzyme Specificity Enzymes may recognize and catalyze: A single substrate. A group of similar substrates. A particular type of bond. 21
  22. 22. Mechanism ofEnzyme Catalyzed Reactions The proper fit of a substrate (S) in an active site forms an enzyme-substrate (ES) complex. E+S ES Within the ES complex, the reaction occurs to convert substrate to product (P). ES E+P The products, which are no longer attracted to the active site, are released. Overall, substrate is convert to product. E+S ES E+P 22
  23. 23. Mechanism of Enzyme Action 23
  24. 24. 24
  25. 25. Example of An Enzyme Catalyzed Reaction 25
  26. 26. Mechanism of Enzyme Action:1.Lock-and-Key ModelIn the lock-and-key model of enzyme action: The active site has a rigid shape. Only substrates with the matching shape can fit. The substrate is a key that fits the lock of the active site. 26
  27. 27. 2. Induced-fit ModelIn the induced-fit model of enzyme action: The active site is flexible, not rigid. The shapes of the enzyme, active site, and substrate adjust to maximum the fit, which improves catalysis. There is a greater range of substrate specificity. 27
  28. 28. IsoenzymesIsoenzymescatalyze the samereaction indifferent tissues inthe body.Lactatedehydrogenase,which convertslactate to pyruvate,(LDH) consists offive isoenzymes. 28
  29. 29. Temperature and Enzyme ActionEnzymes: Are most active at an optimum temperature (usually 37°C in humans). Show little activity at low temperatures. Lose activity at high temperatures as denaturation occurs. 29
  30. 30. pH and Enzyme ActionEnzymes: Are most active at optimum pH. Contain R groups of amino acids with proper charges at optimum pH. Lose activity in low or high pH as tertiary structure is disrupted. 30
  31. 31. Optimum pH Values Most enzymes of the body have an optimum pH of about 7.4. In certain organs, enzymes operate at lower and higher optimum pH values. 31
  32. 32. Enzyme Concentration The rate of reaction increases as enzyme concentration increases (at constant substrate concentration). At higher enzyme concentrations, more substrate binds with enzyme. 32
  33. 33. Substrate ConcentrationThe rate of reactionincreases assubstrateconcentrationincreases (atconstant enzymeconcentration).Maximum activityoccurs when theenzyme issaturated. 33