Enzymes PDF

ENZYMES  Enzymes  Catalysts = substances that speed up chemical reactions.  Organic catalysts (contain carbon) are called enzymes  Enzymes are specific for one particular reaction or group of related reactions.  Many reactions cannot occur without the correct enzyme pre...

ENZYMES  Enzymes  Catalysts = substances that speed up chemical reactions.  Organic catalysts (contain carbon) are called enzymes  Enzymes are specific for one particular reaction or group of related reactions.  Many reactions cannot occur without the correct enzyme present.  Enzymes are often named by adding "ase" to the name of the substrate. Example: Dehydrogenases are enzymes that remove hydrogen.  Enzymes- Key Terms Enzyme: protein molecules that acts catalysts in biochemical reactions (organic catalysts) Substrate: the reactant(s) that an enzyme acts upon when it catalyzes a reaction Active site: A specific area on an enzyme where the substrate binds to the enzyme Enzyme-Substrate complex: an enzyme with its substrate attached to the active site  Lock and Key Model  An enzyme-substrate complex forms when the enzyme’s active site binds with the substrate like a key fitting a lock.  The shape of the enzyme must match the shape of the substrate molecule  Enzymes are therefore very specific; they only function if the shape of the substrate matches the active site  Examples of Enzyme-Substrate Complexes Ex. 1 Ex. 2 Ex. 3  Induced Fit Theory  The substrate molecule does not fit exactly in the active site. This induces a change in the enzyme’s conformation to make a closer fit.  In reactions that involve breaking bonds, the inexact fit puts stress on certain bonds, lowering the amount of energy needed to break them (easier to break)  In reactions that involve making bonds, the inexact fit may hold specific parts of the molecules closer together, lowering the amount of energy needed to make the bond (easier to make)  Induced Fit Theory The enzyme does NOT form a chemical bond with the substrate After the reaction, the products are released and the enzyme returns to its normal shape (enzyme remains unchanged) Therefore enzymes can be reused Only a small amount of enzyme is needed because they can be used repeatedly.  Substrate Enzyme s Enzymes are 1 organic Active Site catalysts. Enzyme Product Enzyme-Substrate Complex 3 2 Enzyme Menu  Activation Energy Activation Energy: the minimum amount of energy that is needed for a chemical reaction to occur Amount of activation energy that is required is considerably less when an enzyme is present Therefore, enzymes LOWER activation energy  Activation Energy HOW EXACTLY DO ENZYMES LOWER ACTIVATION ENERGY? – Remember the induced fit theory! – In anabolic reactions, enzymes hold/position the reactants in a way that makes the bond more likely to form (less energy needed) – In catabolic reactions, enzymes hold/position the reactants in a way that makes the bond more likely to break (less energy needed)  Activation Energy Note: Ea = activation energy  Rate of Reaction Reactions with enzymes are up to 10 billion times faster than those without enzymes. Enzymes typically react with between 1 and 10,000 molecules per second. Fast enzymes catalyze up to 500,000 molecules per second. Factors that affect rate of reaction include: – Substrate Concentration – Enzyme Concentration – Temperature – pH  Substrate Concentration At low substrate concentrations, the active sites on most enzyme molecules are empty because there is not much substrate. Higher substrate concentration results in more collisions and makes it more likely that an enzyme will encounter a substrate molecule. The maximum rate of a reaction is reached when the active sites are almost continuously filled. Increased substrate concentration after this point will not increase the rate.  Substrate Concentration Reaction rate therefore increases as substrate concentration increases Once all the active sites are filled the reaction rate levels off  Enzyme Concentration  If there is insufficient enzyme present, the reaction will not proceed very fast because there is not enough enzyme for all of the substrate molecules.  As the amount of enzyme is increased, the rate of reaction increases.  If there are more enzyme molecules than are needed, adding additional enzyme will not increase the rate.  Enzyme Concentration Reaction rate therefore increases as enzyme concentration increases but then it levels off.  Denaturation  If the hydrogen bonds within an enzyme are broken, the enzyme may unfold or take on a different shape. The enzyme is denatured.  A denatured enzyme will not function properly because the shape of the active site has changed.  If the denaturation is not severe, the enzyme may regain its original shape and become functional.  The following will cause denaturation: › Heat › Changes in pH › Heavy-metal ions (lead, arsenic, mercury) › UV radiation  Temperature Higher temperatures generally cause molecules to move faster. This increased movement results in more collisions among the molecules. More collisions increase the likelihood that the substrate will collide with the active site of the enzyme, thus increasing the rate of an enzyme- catalyzed reaction.  Temperature If the temperature gets too high, the bonds that determine the enzyme’s overall shape may be disrupted. If the shape changes, then the enzyme may not be functional (i.e. denaturation) Increasing the temperature causes more collisions between substrate and enzyme molecules. The rate of Temperature reaction therefore increases as temperature increases. Rate of Reaction 30 40 50 Temperature  Temperature Enzymes denature when the temperature gets too high. The rate of reaction decreases as the enzyme Rate of Reaction becomes nonfunctional. 30 40 50 Temperature  pH  Each enzyme has an optimal pH.  Optimal pH value depends on where that enzyme is normally found in the body.  Changing the pH can alter the ionization of the R-groups of the amino acids that make up the enzyme. When the charges on the amino acids change, hydrogen bonding within the protein molecule change and the molecule changes shape. The new shape may not be effective.  pH Each enzyme has its own optimum pH. Pepsin Trypsin Rate of Reaction 2 3 4 5 6 7 8 9 pH  pH Why do pepsin and trypsin have different optimal pH values? Pepsin is found in the stomach and thus functions best in an acidic environment (low pH due to hydrochloric acid). Trypsin is found in the duodenum (small intestine), and thus its optimum pH is in the neutral range to match the pH of the duodenum.  Metabolic Pathways Metabolism = the sum of all the chemical reactions that occur within cells. Reactions occur in a sequence and a specific enzyme catalyzes each step.  Notice that C can produce either D or F. This substrate has two different enzymes that work on it. A B C D E enzyme 1 enzyme 2 enzyme 3 enzyme 4 F enzyme 5 Enzymes are very specific. In this case enzyme 1 will catalyze the conversion of A to B only.  A Cyclic Metabolic Pathway In this pathway, substrate “A” enters the reaction. After several steps, product “E” is produced. A B A+FB F C BCD DF+E E D  Regulation of Enzymes Cells have built in control mechanisms to regulate enzyme concentration and activity For example, it may be necessary to decrease the activity of certain enzymes if the cell no longer needs the product produced by the enzymes.  Regulation of Enzymes genetic regulation of enzymes regulation already produced Enzymes are proteins. Recall the central dogma: DNA mRNA Proteins Proteins can be regulated by making more or less of them as needed. The topic of regulating protein synthesis (manufacture) is deferred to a later chapter.  Regulation of Enzymes genetic regulation of enzymes regulation already produced competitive Inhibition (illustrated on the next slide)  Competitive Inhibition In competitive inhibition, a similar-shaped molecule competes with the substrate for active sites.  Competitive Inhibition Substrate is physically “blocked” from the active site  Regulation of Enzymes genetic regulation of enzymes regulation already produced competitive noncompetitive inhibition (allosteric) inhibition (next slide)  Noncompetitive/Allosteric Inhibition Active site Inhibitor Altered active site Enzyme Another form of inhibition involves an inhibitor that binds to an allosteric site of an enzyme. An allosteric site is a different location than the active site. The binding of an inhibitor to the allosteric site alters the shape of the enzyme, resulting in a distorted active site that does not function properly.  Noncompetitive/Allosteric Inhibition The binding of an inhibitor to an allosteric site is usually temporary. Poisons are inhibitors that bind irreversibly. For example, penicillin inhibits an enzyme needed by bacteria to build the cell wall. Bacteria growing (reproducing) without producing cell walls eventually rupture.  Allosteric Regulation - Activators Binding an allosteric ACTIVATOR to an allosteric site stabilizes the active form of the enzyme This keeps all the active sites available for the substrates to bind to them.  Allosteric Regulation - Inhibitors Binding of an allosteric INHIBITOR stabilizes the inactive form of the enzyme  Regulation of Enzymes genetic regulation of enzymes regulation already produced competitive noncompetitive feedback inhibition (allosteric) inhibitioninhibition (next slide)  Example of Feedback Inhibition In this example of feedback inhibition, heat (the product) inhibits its production. This keeps the temperature constant. Cold Thermostat Heater Heat inhibits  Feedback Inhibition The goal of this hypothetical metabolic pathway is to produce chemical D from A. A B C D enzyme 1 enzyme 2 enzyme 3 B and by Enzyme regulation C are intermediates. negative feedback inhibition is similar to the thermostat example. As an The next several slides will show how enzyme's product accumulates, it turns off the feedback inhibition regulates the amount enzyme just as heat causes a thermostat to turn off of D produced. the production of heat.  C and D will decrease Feedback Inhibition because B is needed to The amount of B in the cell will produce C and C is decrease if enzyme 1 is inhibited. needed to produce D. A BX XC XD X enzyme 1 enzyme 2 enzyme 3 Enzyme 1 is structured in a way that causes it to interact with D. When the amount of D increases, the enzyme stops functioning.  Feedback Inhibition A X BB XC C XD D enzyme 1 enzyme 2 enzyme 3  Feedback Inhibition A B C D X enzyme 1 enzyme 2 enzyme 3 As D begins to increase, it inhibits enzyme 1 again and the cycle repeats itself.  Ribozymes Ribozymes are molecules of RNA that function like enzymes, that is, they have an active site and increase the rate of specific chemical reactions.  Cofactors Many enzymes require a cofactor to assist in the reaction. These "assistants" are nonprotein and may be metal ions such as magnesium (Mg++), potassium (K+), and calcium (Ca++). The cofactors bind to the enzyme and participate in the reaction by removing electrons, protons , or chemical groups from the substrate.  Coenzymes Cofactors that are organic molecules are coenzymes. In oxidation-reduction reactions, coenzymes often remove electrons from the substrate and pass them to different enzymes. In this way, coenzymes serve to carry energy in the form of electrons (or hydrogen atoms) from one compound to another.  Coenzymes Coenzyme Enzyme Enzyme Coenzymes bind to the enzyme and also participate in the reaction by carrying electrons or hydrogen atoms.  Many Vitamins are Coenzymes Vitamin Coenzyme Name Niacin NAD+ B2 (riboflavin) FAD B1 (thiamine) Thiamine pyrophosphate Pantothenic acid Coenzyme A (CoA) B12 Cobamide coenzymes  Examples of Important Coenzymes The next few slides discuss specific coenzymes known as electron carriers. They are included here simply because they are coenzymes They will be discussed in detail during the cellular respiration/photosynthesis notes You do NOT have to know this info for the test  Electron Carriers (coenzymes) Electron carriers function in photosynthesis and cellular respiration. Three major electron carriers are listed below. Cellular Respiration – NAD+ – FAD Photosynthesis – NADP+  NAD+ (Nicotinamide Adenine Dinucleotide) Organic Molecule + NAD+ NAD+ NAD+ + 2H NADH + H+ NAD+ functions in cellular respiration by carrying two electrons. With two electrons, it becomes NADH. NAD+ oxidizes its substrate by removing two hydrogen atoms. One of the hydrogen atoms bonds to the NAD+. The electron from the other hydrogen atom remains with the NADH molecule but the proton (H+) is released. NAD+ + 2H NADH + H+ NADH can donate two electrons (one of them is a hydrogen atom) to another molecule. Menu  NAD + 2H NADH + H + + NADH + H+ Energy Energy + + 2H 2H NAD+  FAD (flavin adenine dinucleotide) FAD is reduced to FADH2. It can transfer two electrons to another molecule. FAD + 2H FADH2  FAD + 2H FADH2 FADH2 Energy Energy + + 2H 2H FAD  NADP+ (Nicotinamide Adenine Dinucleotide Phosphate) NADP+ + 2H NADPH + H+ NADP+ is similar to NAD+ in that it can carry two electrons, one of them in a hydrogen atom, the other one comes from a hydrogen that is released as a hydrogen ion. Electrons carried by NADPH in photosynthesis are ultimately used to reduce CO2 to carbohydrate.  NADP + 2H NADPH + + H+ NADPH + H+ Energy Energy + + 2H 2H NADP+