Enzymes: Catalysts in Biochemical Reactions

1. Biochemistry Chapter 23 Enzymes

2. Problem Sets • PS #1 • Sections 23.1 – 23.4 • # 1, 4, 5, 6, 7, 9, 10, 12, 14, 15, 16, 17, 20 • PS #2 • Sections 23.5 – 23.8 • # 21, 23, 25, 26, 27, 28, 29, 30, 32, 34, 41, 43, 45, 48

3. 23.1 Enzymes • Large molecules that catalyze reactions • Increase reaction rate without taking part in reaction • Biological reactions are too slow to maintain life without enzymes • Most enzymes are globular proteins • How catalysts work • Reduce activation energy of reaction • Do not alter equilibrium position, just rate

4. 23.1 Enzymes • Enzymes are extremely effective catalysts • Increase reaction rates 109 to 1020 times • Example: glucose sits in air (O2) for months or years without reacting, yet the enzyme catalyzed reaction occurs in seconds in a living cell • Most enzymes are extremely specific • Called substrate specificity • Some enzymes work on a class of compounds (alcohol dehydrogenase), others work on one specific substance (trypsin)

5. 23.2 Classification of Enzymes • Oxidoreductases • catalyze redox reactions • Transferases • catalyze transfers of functional groups from one molecule to another • Hydrolases • catalyze hydrolysis reactions • Lyases • Catalyze the forming or breaking of double bonds

6. 23.2 Classification of Enzymes • Isomerases • Catalyze isomerization reactions • Ligases • Catalyze the joining of molecules • Also called synthetases • Note many enzyme names end in –ase • Some have older names (e.g., pepsin)

8. 23.3 Some Enzyme Terminology • Apoenzyme – polypeptide part of enzyme • Cofactor – non-polypeptide portion • Can be a metal ion or an organic (coenzyme) • Substrate • compound on which the enzyme operates • Active site – area of enzyme where substrate binds • Activation • Process that increases enzyme action • Activator – cofactor that activates enzyme

9. 23.3 Some Enzyme Terminology • Inhibition • Process that makes enzyme less active • Inhibitor – compounds that inhibit enzymes • Competitive inhibitors • Bind to active site of enzyme • Prevent it from binding to substrate • Noncompetitive inhibitors • Bind elsewhere to enzyme • Change tertiary structure so it is less effective

10. 23.4 Enzyme Activity Measure of how much the enzyme increases the reaction rate Depends on 3 factors: 1. Concentrations Enzyme Concentration Substrate Concentration Linear Curve Saturation Curve Enzyme concentration is low, so it all gets involved Activity rises until all available Enzyme molecules are bound

11. 23.4 Enzyme Activity 2. Temperature 3. pH Shows an optimal temperature Shows an optimal pH Too acidic or too basic denatures the enzyme Too low or too high causes steric changes

12. 23.5 Mechanisms of Enzyme Action • Theories that explain how enzymes work • Must explain catalytic action • Must explain substrate specificity • Basic idea – • Enzyme combines with substrate to form an intermediate compound • Called the enzyme-substrate complex • Two major theories exist • Lock-and-key model, Induced-fit model

13. 23.5 Lock-and-Key Model Enzyme is a rigid, three-dimensional body Active site has a restricted opening that only allows the proper substrate to enter Amino acid sequence is important because it creates the exact shape needed to hold the substrate First model to attempt to explain enzymes Flaws: Enzyme molecules are not static Active sites have some flexibility Perfect fit = too stable to react

14. 23.5 Induced-Fit Model Enzyme modifies the shape of the active site to accommodate the substrate Enzyme molecule is in constant motion More flexible model that allows us to explain more features of enzyme action For example, both models can explain competitive inhibitors, but only Induced-Fit can explain noncompetitive inhibitors

15. 23.5 Induced-Fit Model Competitive Inhibitor Noncompetitive Inhibitor Binds to active site Binds elsewhere Competes with substrate for active site Conformational changes limit effectiveness of active site

16. 23.5 Induced-Fit Model Competitive Reaches same vmax Requires higher conc. LeChatelier’s Principle Noncompetitive Reaches lower vmax Inhibitor cannot be displaced by excess substrate no matter the concentration

17. 23.5 Catalytic Power of Enzymes • Chemistry of active site is the most important factor • Five amino acids often used at active site • His, Cys, Asp, Arg, Glu • Most are acidic or basic • Acid-base chemistry is important in the function of active sites

18. 23.5 Catalytic Power of Enzymes Enzymes reduce activation energy by forming a different, lower energy transition state

19. 23.6 Regulation of Enzymes • Feedback Control • Formation of a product inhibits an earlier reaction in the sequence • E1 E2 E3A  B  C  D • Let’s say D is an inhibitor for E1 • As the reaction progresses, D builds up • E1 is inhibited, shutting down the chain

20. 23.6 Proenzymes • Also called zymogens • Enzymes manufactured with extra amino acid sequences, making them inactive • Excess polypeptides must be removed in order to activate • Often used for digestive enzymes so that they don’t digest our own body tissues! • Example – trypsinogen  trypsin

21. 23.6 Allosterism • Regulation of an enzyme by binding at a site other than the active site • Enzyme – allosteric enzyme • Binding substance – regulator • Site where it attaches is the regulatory site • Regulator can inhibit (negative modulation) or stimulate (positive modulation)

22. 23.6 Allosterism R form Relaxed form More active T form Taut form Less active Both forms exist in equilibrium

23. 23.6 Protein Modification • Change in the protein’s primary structure • Often done by adding a functional group • Phosphorylation of serine or tyrosine residues is a common approach • Can be used to activate or deactivate an enzyme • Glycogen phosphorylase is activated by the addition of a phosphate • Nerve agents deactivate acetylcholinesterase by phosphorylating serine residues

24. 23.6 Isoenzymes • Two or more forms of the same enzyme • Each isoenzyme has the same function, but is made up of different combinations of subunits (different quaternary structure) • Allows the enzymes to operate in slightly different ways in different tissues • Example – lactate dehydrogenase • Heart muscle has a form that requires aerobic ox. • Skeletal muscle has form that allows anaerobic ox.

25. 23.7 Medical Uses of Enzymes • Most enzymes are found within cells and are not useful for diagnosis • Some enzymes found in body fluids • Fluid enzyme levels can be used as indicators of abnormal activity • Sometimes enzymes can be administered as part of therapy

27. 23.8 Transition State Analogs • Enzyme active sites best fit the transition states in a reaction, not the substrates or products • Transition state analogs – molecules that mimic the shape of the transition state of a substrate • Acts as an inhibitor because it binds to the active site • Used as drugs to fight enzymatic diseases