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Chapter 15

Chapter 15. Enzymes. Enzyme Catalysis. Enzyme : a biological catalyst with the exception of some Ribozymes that catalyze their own splicing, all enzymes are proteins enzymes can increase the rate of a reaction by a factor of up to 10 20 over an uncatalyzed reaction

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Chapter 15

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  1. Chapter 15 Enzymes

  2. Enzyme Catalysis • Enzyme: a biological catalyst • with the exception of some Ribozymes that catalyze their own splicing, all enzymes are proteins • enzymes can increase the rate of a reaction by a factor of up to 1020 over an uncatalyzed reaction • Most are extremely specific. Some catalyze the reaction of only one compound • others are stereospecific; for example, enzymes that catalyze the reactions of only L-amino acids • others catalyze reactions of specific types of compounds or bonds; for example, trypsin catalyzes hydrolysis of peptide bonds on the carboxyl side of Lys and Arg

  3. Trypsin catalyses hydrolysis of peptide bonds on the carboxyl side of Lysine and Arginine. Helps to break down proteins in intestine. Fig. 22.1, p.554

  4. Classification of Enzymes • Enzymes are commonly named after the reaction or reactions they catalyze • example: lactate dehydrogenase, acid phosphatase • Enzymes are classified into six major groups • oxidoreductases: oxidation-reduction reactions • transferases: group transfer reactions • hydrolases: hydrolysis reactions • lyases: addition of groups to a double bond, or removal of groups to create a double bond • isomerases: isomerization reactions • ligases: the joining to two molecules

  5. Terms in Enzyme Chem • apoenzyme: the protein part of an enzyme • cofactor: a nonprotein portion of an enzyme that is involved in a chemical reaction; examples are metallic ions such as Zn2+ and Mg2+ • coenzyme: an organic cofactor; an example is heme • substrate: the compound or compounds whose reaction an enzyme catalyzes • active site: the specific portion of the enzyme to which a substrate binds during reaction

  6. Schematic of an Active Site

  7. Terms in Enzyme Chem • activation: any process that initiates or increases the activity of an enzyme • inhibition: any process that makes an enzyme less active or inactive • competitive inhibitor: an substance that binds to the active site of an enzyme thus preventing binding of substrate • noncompetitive inhibitor: any substance that binds to a portion of the enzyme other than the active site and thus inhibits the activity of the enzyme

  8. Enzyme Activity • Enzyme activity: a measure of how much a reaction rate is increased • We examine how the rate of an enzyme-catalyzed reaction is affected by • enzyme concentration • substrate concentration • temperature • pH

  9. Enzyme Concentration and Reaction Rate • The rate of reaction increases as enzyme concentration increases (at constant substrate concentration) • At higher enzyme concentrations, more enzymes are available to catalyze the reaction (more reactions at once) • There is a linear relationship between reaction rate and enzyme concentration (at constant substrate concentration)

  10. Substrate Concentration and Reaction Rate • The rate of reaction increases as substrate concentration increases (at constant enzyme concentration) • Maximum activity occurs when the enzyme is saturated (when all enzymes are binding substrate) • The relationship between reaction rate and substrate concentration is exponential, and asymptotes (levels off) when the enzyme is saturated

  11. Temperature and Enzyme Activity • Enzymes are most active at an optimum temperature (usually 37°C in humans) • They show little activity at low temperatures • Activity is lost at high temperatures as denaturation occurs

  12. pH and Enzyme Activity • Enzymes are most active at optimum pH • Amino acids with acidic or basic side-chains have the proper charges when the pH is optimum • Activity is lost at low or high pH as tertiary structure is disrupted

  13. Optimum pH for Selected Enzymes • Most enzymes of the body have an optimum pH of about 7.4 • However, in certain organs, enzymes operate at lower and higher optimum pH values

  14. Mechanism of Action • Lock-and-key model • the enzyme is a rigid three-dimensional body • the enzyme surface contains the active site

  15. Mechanism of Action • Induced-fit model • the active site becomes modified to accommodate the substrate

  16. Mechanism of Action • When a substrate (S) fits properly in an active site, an enzyme-substrate (ES) complex is formed: E + SES • Within the active site of the ES complex, the reaction occurs to convert substrate to product (P): ES E + P • The products are then released, allowing another substrate molecule to bind the enzyme - this cycle can be repeated millions (or even more) times per minute • The overall reaction for the conversion of substrate to product can be written as follows: E + SES E + P

  17. Enzyme Inhibitors • Inhibitors (I) are molecules that cause a loss of enzyme activity • They prevent substrates from fitting into the active site of the enzyme: E + S  ES  E + P E + I  EI  no P formed

  18. Reversible Inhibitors (Competitive Inhibition) • A reversible inhibitor goes on and off, allowing the enzyme to regain activity when the inhibitor leaves • A competitive inhibitor is reversible and has a structure like the substrate - it competes with the substrate for the active site - its effect is reversed by increasing substrate concentration

  19. Competitive Inhibition • the induced-fit model explains competitive inhibition • the inhibitor fits into the active site, preventing the substrate from entering

  20. Reversible Inhibitors (Noncompetitive Inhibition) • A noncompetitive inhibitor has a structure that is different than that of the substrate - it binds to an allosteric site rather than to the active site - it distorts the shape of the enzyme, which alters the shape of the active site and prevents the binding of the substrate • The effect can not be reversed by adding more substrate

  21. Noncompetitive Inhibition • the mechanism of noncompetitive inhibition

  22. Mechanism of Action • we can distinguish between competitive and noncompetitive inhibition by the enzyme kinetics in the absence and presence of the inhibitor

  23. Irreversible Inhibitors • An irreversible inhibitor destroys enzyme activity, usually by bonding with side-chain groups in the active site

  24. Catalytic Power of Enzymes • both the lock-and-key model and the induced-fit model emphasize the shape of the active site • however, the chemistry of the active site is the most important • just five amino acids participate in the active sites in more than 65% of the enzymes studies to date • these five are His > Cys > Asp > Arg > Glu • four these amino acids have either acidic or basic side chains; the fifth has a sulfhydryl group (-SH)

  25. Example of active site (pyruvate kinase) Cofactors K+ and Mg2+

  26. Catalytic Power of Enzymes • Enzymes increase the rate of reaction by lowering the activation energy of a reaction’s transition state

  27. Enzyme Regulation • Feedback control: an enzyme-regulation process where the product of a series of enzyme-catalyzed reactions inhibits an earlier reaction in a sequence • the inhibition may be competitive or noncompetitive

  28. Enzyme Regulation • Proenzyme (zymogen): an inactive form of an enzyme that must have part of its polypeptide chain cleaved before it becomes active • an example is trypsin, a digestive enzyme • it is synthesized and stored as trypsinogen, which has no enzyme activity • it becomes active only after a six-amino acid fragment is hydrolyzed from the N-terminal end of its chain • removal of this small fragment changes in not only the primary structure but also the tertiary structure, allowing the molecule to achieve its active form

  29. Enzyme Regulation • Allosterism: a type of enzyme regulation based on an event occurring on the enzyme at a place other than the active site but that creates a change in the active site • an enzyme regulated by this mechanism is called an allosteric enzyme • allosteric enzymes often have multiple polypeptide chains • negative modulation: inhibition of an allosteric enzyme • positive modulation: stimulation of an allosteric enzyme • regulator: a substance that binds to an allosteric enzyme

  30. The Allosteric Effect

  31. Enzyme Regulation • Protein modification: the process of affecting enzyme activity by covalently modifying it • the best known examples of protein modification involve phosphorylation/dephosphorylation • example: pyruvate kinase (PK) is the active form of the enzyme; it is inactivated by phosphorylation to pyruvate kinase phosphate (PKP)

  32. Enzyme Regulation • Isoenzyme: an enzyme that occurs in multiple forms; each catalyzes the same reaction • example: lactate dehydrogenase (LDH) catalyzes the oxidation of lactate to pyruvate • the enzyme is a tetramer of H and M chains • H4 is present predominately in heart muscle • M4 is present predominantly in the liver and in skeletal muscle • H3M, H2M2, and HM3 also exist • H4 is allosterically inhibited by high levels of pyruvate while M4 is not • H4 in serum correlates with the severity of heart attack

  33. Enzymes in Medicine • Enzyme assays useful in medical diagnosis

  34. Enzymes End Chapter 15

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