ENZYMES

1. ENZYMES IB TOPICS: SL 2.3.1 - 2.3.5 HL 6.6.1 - 6.6.5

2. OBJECTIVES: • Define enzyme, substrate, active site, and allosteric site. • Explain how enzymes affect the rate of metabolic reactions in an organism • Explain enzyme substrate specificity (Lock and Key Model, Induced-Fit Model) • Define denaturing • Describe the effects of temperature, pH, and substrate concentration on enzyme activity • Describe, compare and contrast competitive and non- competitive inhibition of enzymes. • Define metabolic pathway and how allosteric enzymes regulate these pathways by non-competitive inhibition by an end product of the specific pathway. • Explain the industrial uses and biotechnological uses of enzymes. • Define co-enzymes and co-factors, give examples and describe their role in enzymatic activity.

3. Enzymes • Enzymes are organic catalysts. Catalyst are molecules which speed up the rate of a chemical reaction (catabolic or anabolic) by lowering the energy of activation (the energy needed to bring reactants into close enough proximity for contact and often enough for the reaction to occur). • All enzymes are composed of proteins. • Because enzymes are composed of proteins, their shape is important to their function. If you change the shape of the protein that composes the enzyme you alter or destroy the enzyme. • Enzymes are specific to which molecules they act upon. The substances they act upon are called substrates. • Most enzymes end with the suffix –ase. Typically it is a portion of the substrate’s name + -ase. For example the enzyme found in saliva which begins the chemical hydrolysis of amylose is called amylase. • Enzymes are not used up or destroyed in the reaction process and at the end of their reaction will bind with more substrate molecules and repeat the same chemical process. Therefore, small numbers of these molecules can have a great effect.

4. Reaction Forms Energy of Activation products E E reactants E Free energy Free energy E E E E E reactants products Rate of reaction Rate of reaction The reaction above is an endergonic reaction. Energy is being put in to drive the reaction. Ex. Photosynthesis The reaction above is an exergonic reaction. After the reaction begins energy is released. Ex. Cellular Respiration

5. How Enzymes Affect Reaction Rates • Enzymes affect the rates of reactions by lowering the amount of energy of activation required for the reactions to begin. Therefore processes can occur in living systems at lower temperatures or energy levels than it would require for these same reactions to occur without the enzymes present.

6. How Enzymes Affect Reaction Rates C6H1206 + 602 6CO2 + 6H20 + Above is the formula for the complete combustion of glucose. This reaction can be carried out in a laboratory at several hundred degrees Celsius. The same reaction occurs during the process of cellular respiration in living cells. In humans at a temperature of 37o Celsius. What makes the difference? Energy ENZYMES!

7. Enzyme Structure • All enzymes have an active site where the substrate binds. The active site and the substrate have complimentary shapes. • Some enzymes have a second site called an allosteric site to which molecules other than substrate bind to activate the enzyme or deactivate the enzyme. Enzymes with this structure are called allosteric enzymes. If the molecule activates the enzyme it is called an allosteric activator. If the molecule binds to the site and deactivates the enzyme it is called an allosteric inhibitor. When they bind they cause a change in the shape of the active site of the enzyme. These molecules are important in the regulation of enzyme activity. Allosteric sites can be thought of as “on and off” switches, depending on the effect they have on the active site.

8. How Enzymes Bind to Substrates • There are two proposed methods by which enzymes bind to their substrate molecules: a. Lock and Key Model b. Induced-Fit Model

9. enzyme enzyme enzyme Lock and Key Model • The lock and key model states that the enzyme’s active site shape is specific and complimentary in shape to a specific substrate. If the substrate does not fit the active site, no enzymatic reaction can occur. Just as a specific key fits a specific lock, each substrate has a specific enzyme with a complimentary active site. Products P Active site P S2 S1 S2 S1 ENZYME SUBSTRATE COMPLEX SUBSTRATE MOLECULES Enzyme returns from the reaction unchanged and can now react with more substrate.

10. Induced-Fit Model The induced model states that the substrate binds to the active site and induces or causes a change in shape of the active site so that it is a complimentary fit. This model explains why some enzymes can act on more than one substrate. Substrate induces a change in active site so that it is complimentary Products Active site in inactive state P1 P1 SUBSTRATE MOLECULES S3 S2 S1 S1 ENZYME ENZYME SUBSTRATE COMPLEX The active site of the enzyme returns to the inactive state after the products are released and now can react with more substrate.

11. Induced-Fit Model

12. Enzyme Cooperativity Some enzymes have multiple active site. It has been observed that when one substrate molecule binds to a single active site in the inactive form or tense state of the enzyme, a configurational change occurs in the other active sites making them more receptive to other substrate molecules.

13. Regulation of Enzyme Activity To regulate enzyme activity, there must be some form of prevention of binding of substrate with active site. This is called enzymatic inhibition. There are two forms of inhibition: 1. Competitive inhibition 2. Noncompetitive inhibition

14. Competitive Inhibition This type of inhibition occurs when another molecule is structurally similar to the substrate and can bind to the active site of the substrate. However, since it is not the actual substrate, there is no reaction and the substance remains in the active site, disabling the enzyme. This is a non-reversible process and the enzyme is no longer functional. The “mimic” molecule competes with the substrate for the active site. These “mimic” molecules are commonly called poisons! The pesticide DDT works in this manner. The miracle antibiotic penicillin works in the same manner. It inhibits the enzyme certain types of pathogenic bacteria use to build their cell walls. Without the functional enzyme the bacterial cell walls are defective and weak or rupture. If the bacteria survive, this makes them weak and easy targets for antibodies and our white blood cells. Penicillin has little or no effect on human cells because we don’t have cell walls, therefore no enzyme that produces cell walls!

15. Noncompetitive Inhibition This type of inhibition is common in metabolic pathways. A metabolic pathway is a series of interconnected enzymatic steps where the products of one reaction becomes the substrates for subsequent enzymatic reactions in the pathway. This process is reversible and the enzymes are undamaged by the inhibitor molecules. This process is best observed in allosteric enzymes, where the inhibitor molecules bind to the allosteric site to deactivate the enzyme. This is called negative-feedback inhibition. This form of inhibition prevents the build up of excess products and the use of energy to produce them.

16. Negative-Feedback Inhibition This example demonstrates how an end product can inhibit the first step in its production. Isoleucine binds to the allosteric site of threonine deaminase and prevents threonine from binding to the active site because the shape of the active site is altered. When the level of isoleucine drops in the cell’s cytoplasm, the isoleucine is removed from the allosteric site on the enzyme, the active site resumes the activated shape and the pathway is “cut back on” and isoleucine begins to be produced.

17. Environmental Factors Which Affect Enzyme Activity Since enzymes are protein any environmental change that can affect their structure affects their activity. All protein shape determine their function. Their structure is due primarily to hydrogen bonding at the various levels. If any thing disrupts or interferes with the hydrogen bonding the protein’s level of structure begins to breakdown and the protein “unravels” or “unfolds” and becomes non-functional. Denaturingis the destruction of a protein’s function due to the breakdown or loss of its structure. Denaturing is an irreversible process (ex. egg albumin before and after cooking)Any environmental factor that has an effect of hydrogen bonding can denature proteins. Temperature and pH both effect hydrogen bonding and can denature proteins. Therefore they would have a definite effect on enzyme activity.

18. Environmental Factors Which Affect Enzyme Activity: Temperature All enzymes have an optimum temperature at which they work best. If you observe the enzyme’s activity below the specific temperature it will steadily increase until it reaches the optimum. After the optimum temperature is reached the enzymes activity drops dramatically due to denaturing. Depending on the species, the range of optimum activity is very broad. Above is a comparison of human enzyme activity with that of bacteria found in hot springs and oceanic vents.

19. Environmental Factors Which Affect Enzyme Activity: pH In the human body’s digestive tract there are variations in pH from area to area. The stomach’s juices’ pH is around 2 (acidic), the enzyme pepsin found in the gastric juices has optimum activity at a pH of 2. The small intestine’s juice’s pH is around 8 (basic). The enzyme trypsin found in the small intestine’s juices has optimum activity at a pH of 8. All enzymes have an optimum pH at which they work best. If the pH falls below or rises above the optimum value, enzymatic activity decreases as a result of denaturing.

20. Environmental Factors Which Affect Enzyme Activity: Substrate Concentration The concentration of substrate also has an affect on the rate of enzyme activity. If the concentration of substrate is increased while the concentration of enzyme is constant, the level of enzyme activity will increase until a point of saturation is reached. At this point there are no enzymes available to react with excess substrate and the rate of the reaction stabilizes. No matter if you continue to add substrate, the reaction rate will not increase! Point of Saturation, all active sites are filled with substrate. Rate of Reaction Increasing Substrate Concentration

21. Co-Enzymes and Co-Factors Some enzymes require another organic molecule or substance to be present before they can function. These organic molecules or substances are called Co-enzymes or Co-factors. Co-enzymes are organic molecules (usually vitamins) and co-factors are inorganic substance (minerals). This is one of the reasons it is so important to eat a well balanced diet. For example, Vitamin K is necessary for the enzyme responsible for blood clot formation. A lack of vitamin K leads to easy bruising and prolonged bleeding when injuries occur. Calcium is a co-factor which is required by several enzymes for their activation.