Enzymes and Vitamins Chapter 19 on/index.html

Catalysis by Enzymes Unlike inorganic chemistry - reactions in living organisms take place in a very narrow range of temperature and ph conditions Fireflies must produce light without raising the temperature beyond physiological limits Luciferinase, an enzyme found in firefly tails, yields light as a reaction product.

The Big Idea Enzymes catalyze reactions essential for life. Many of these life sustaining reactions may not occur in the absence of enzyme action under physiological conditions. Therefore, the critical nature of enzymes quickly becomes apparent

The enzyme lactate dehydrogenase acts upon the substrate L-lactate Substrate: A reactant in an enzyme-catalyzed reaction Enzyme: A protein or other molecule that acts as a catalyst for a biological reaction.

Enzymes have active sites that provide Specificity 1.A pocket in an enzyme with the specific shape and chemical makeup necessary to bind a substrate 2.The active site has an specific shape and chemical reactivity needed to catalyze the reaction 3.It holds one or more substrates in place by attractions to groups that line the pocket Link 4.Within the folds of an enzyme’s protein chain is the active site— the region where the reaction takes place

Specificity is a matter of fit 7 1.Because of the need to “fit” into a fold, active sites are very specific – and enzymes work on only one enantiomer 2.The enantiomer at the top fits the reaction site like a hand in a glove, but the enantiomer at the bottom does not. – The enzyme lactate dehydrogenase catalyzes the removal of hydrogen from L- lactate but not from D-lactate.

Turnover Number 8 Maximum number of substrate molecules acted upon per enzyme per unit time. Most enzymes turn over 10–1000 molecules per second.

Enzyme Cofactors The dehydrogenation of L- lactate shown requires a coenzyme which acts as an oxidizing agent  that makes the reaction possible. – (NAD+ accepts the H ; “donating electrons”, so it is reduced, this makes it an oxidizing agent – the L-lactate is oxidized)

What is a Cofactor? Cofactor: A nonprotein part of an enzyme essential to catalytic activity; often a metal ion or a coenzyme. Coenzyme: An organic molecule that acts as an enzyme cofactor. The functional groups in proteins are limited to those of the amino acid side chains. By combining with cofactors, enzymes acquire chemically reactive groups not available as side chains

Oxidoreductases 1.Catalyze redox reactions of substrates 2.Addition or removal of oxygen or hydrogen. 3.These enzymes require coenzymes that are reduced or oxidized as the substrate is oxidized or reduced.

Transferases Catalyze the transfer of a group from one molecule to another. Kinases transfer a phosphate group from ATP; producing to give ADP and a phosphorylated product.

Hydrolases Catalyze the breaking of bonds with addition of water. The digestion of carbohydrates and proteins by hydrolysis requires these enzymes.

Ligases Catalyze the bonding together of two substrates. These reactions are generally not require energy from ATP hydrolysis.

Isomerases Catalyze the rearrangement of atoms of a substrate in reactions that have but one substrate and one product.

Lyases Catalyze the addition of a molecules to a double bond or the reverse reaction in which a molecule is eliminated from a double bond.

Enzyme Classification Enzymes are divided into six main classes according to the general kind of reaction they catalyze. 1.Oxidoreductases: addition or removal of oxygen 2.Transferases: move a group 3.Hydrolases: Breaking by adding water 4.Ligases: Bonding together 5.Isomerases: rearrangement 6.Lyases: addition to a double bond or the reverse

Classification expanded

Nomenclature Enzymes have the family-name ending -ase. – (Exceptions occur for enzymes such as papain and trypsin, which are still referred to by older common names). Modern systematic names always have two parts: – the first identifies the substrate on which the enzyme operates – the second part is an enzyme subclass name Example: Pyruvate carboxylase is a ligase that acts on the substrate pyruvate to add a carboxyl group.

How Enzymes Work: Two Models lock-and-key model (Historical) The substrate is described as fitting into the active site as a key fits into a lock. Induced-fit: (Current Model) As an enzyme and substrate come together, their interaction induces changes in the shape of the active site, that results in exactly the right fit for catalysis of the reaction.

How Enzymes Work: Two Models Induced-fit: (Current Model) As an enzyme and substrate come together, their interaction induces changes in the shape of the active site, that results in exactly the right fit for catalysis of the reaction. Link

Link : nduced_fit/index.html Link nduced_fit/index.html Link people/giannini/flasha nimat/enzymes/chemic al%20interaction.swf people/giannini/flasha nimat/enzymes/chemic al%20interaction.swf Link names of enzymes Link /site/biology/activity5. asp?outline=no /site/biology/activity5. asp?outline=no

Hydrolysis of a peptide bond by chymotrypsin. Copyright © 2010 Pearson Education, Inc. a) The polypeptide enters the active site (b) Hydrogen transfer allows formation of a strained intermediate (c) The peptide bond is broken.

Enzymes act as catalysts because of their ability to: – Bring substrate(s) and catalytic sites together (proximity effect). – Hold substrate(s) at the exact distance and in the exact orientation necessary for reaction (orientation effect). – Provide acidic, basic, or other types of groups required for catalysis (catalytic effect). – Lower the energy barrier by inducing strain in bonds in the substrate molecule (energy effect). – Link : dex.html Link

Concentration & Enzyme Activity Rate of an enzyme catalyzed reaction is controlled by the amount of substrate and the overall efficiency of the enzyme. If the enzyme–substrate complex is rapidly converted to product, the rate at which enzyme and substrate combine to form the complex becomes the limiting factor. Enzyme and substrate molecules moving at random in solution can collide with each other no more often than about 10 8 collisions per (mole/liter) per second. One of the most efficient enzymes is catalase, this enzyme can break down H 2 O 2 at a rate of up to 10 7 catalytic events per second.

At Low Concentrations of substrate Not all enzyme is bound by substrate  the substrate and enzyme must first “find” each other in solution – Increasing S or E will impact the rate. Therefore, both E and S appear in the rate law The reaction cannot go any faster than the rate at which E and S come together Reaction rate is directly proportional to substrate concentration.

At Saturating conditions Enzyme is saturated with Substrate. Increasing [S] will not impact the rate. At saturated condition, the rate of the reaction is determined by the K cat That is – the rate of catalytic turnover

28 In the presence of excess substrate, the concentration of an enzyme can vary according to our metabolic needs. – This is why enzymes are considered metabolic regulators If the concentration of substrate does not become a limitation, the reaction rate varies directly with the enzyme concentration. The Michaelis-Menten equation (curve) can be converted to a linear form that matches the general formula y = mx+b.

Copyright © 2010 Pearson Education, Inc. Chapter Nineteen29 Effect of Temperature and pH on Enzyme Activity Enzyme catalytic activity is highly dependent on pH and temperature. Optimum conditions vary slightly for each enzyme but are generally near normal body temperature and the pH of the body fluid in which the enzyme functions. – Pepsin, which initiates protein digestion in the highly acidic environment of the stomach, has its optimum activity at pH 2. – Trypsin, which acts in the alkaline environment of the small intestine, has optimum activity at pH 8.

Copyright © 2010 Pearson Education, Inc. Chapter Nineteen30 (a) The rate increases with increasing temperature until the protein begins to denature; then the rate decreases rapidly. (b) The optimum activity for an enzyme occurs at the pH where it acts.

Enzyme Regulation: A variety of strategies are utilized to adjust the rates of enzyme-catalyzed reactions. Any process that starts or increases the action of an enzyme is an activation. Any process that slows or stops the action of an enzyme is an inhibition. Feedback and Allosteric Control are two strategies for enzyme regulation.

Feedback control: Regulation of an enzyme’s activity by the product of a reaction later in a pathway. If a product near the end of a metabolic pathway inhibits an enzyme that functions near the beginning of that pathway, then no energy is wasted making the ingredients for a plentiful substance. Allosteric control: An interaction in which the binding of a regulator at one site on a protein affects the protein’s ability to bind another molecule at a different site.

Copyright © 2010 Pearson Education, Inc. Chapter Nineteen33 Allosteric control can be either positive or negative. Binding a positive regulator changes the active sites so that the enzyme becomes a better catalyst and the rate accelerates. Binding a negative regulator changes the active sites so that the enzyme is a less effective catalyst and the rate slows down.

Copyright © 2010 Pearson Education, Inc. Chapter Nineteen34 Enzyme Regulation: Inhibition Enzyme inhibition can be reversible or irreversible. In reversible inhibition, the inhibitor can leave, restoring the enzyme to its uninhibited level of activity. In irreversible inhibition, the inhibitor remains permanently bound and the enzyme is permanently inhibited. The inhibition can also be competitive or noncompetitive, depending on whether the inhibitor binds to the active site or elsewhere.

Copyright © 2010 Pearson Education, Inc. Chapter Nineteen35

Copyright © 2010 Pearson Education, Inc. Chapter Nineteen36 A competitive inhibitor can eventually be overcome by higher substrate concentrations. With a noncompetitive inhibitor the maximum rate is lowered for all substrate concentrations.

Copyright © 2010 Pearson Education, Inc. Chapter Nineteen37 Hg +2 and Pb +2 ions are irreversible inhibitors that bond to the S atoms in cysteine residues. Organophosphorus insecticides such as parathion and malathion, and nerve gases like Sarin are irreversible inhibitors of the enzyme acetylcholinesterase.

Copyright © 2010 Pearson Education, Inc. Chapter Nineteen Enzyme Regulation: Covalent Modification and Genetic Control There are two general modes of enzyme regulation by covalent modification, removal of a covalently bonded portion of an enzyme, or addition of a group. Some enzymes are synthesized in inactive forms known as zymogens or proenzymes, activation requires a chemical reaction that splits off part of the molecule. Genetic (enzyme) control: Regulation of enzyme activity by hormonal control of the synthesis of enzymes is especially useful for enzymes needed only at certain times.

Copyright © 2010 Pearson Education, Inc. Chapter Nineteen39 Enzymes that cause blood clotting or digest proteins are examples of enzymes that must not be active at the time and place of their synthesis.

Copyright © 2010 Pearson Education, Inc. Chapter Nineteen40 Glycogen phosphorylase, the enzyme that initiates glycogen breakdown, is more active when phosphorylated. When glycogen stored in muscles must be hydrolyzed to glucose for quick energy, two serine residues are phosphorylated. The groups are removed once the need to break down glycogen for quick energy has passed.

Copyright © 2010 Pearson Education, Inc. Chapter Nineteen Vitamins Vitamin: An organic molecule, essential in trace amounts that must be obtained in the diet because it is not synthesized in the body. Scurvy, pellagra, and rickets are caused by deficiencies of vitamins. Vitamins are grouped by solubility into two classes: water-soluble and fat-soluble. Some vitamins are valuable as antioxidants.

Copyright © 2010 Pearson Education, Inc. Chapter Nineteen42 Water soluble vitamin C is biologically active without any change in structure, biotin is connected to enzymes by an amide bond at its carboxyl group but otherwise undergoes no structural change from dietary biotin.

Copyright © 2010 Pearson Education, Inc. Chapter Nineteen43 Other water-soluble vitamins incorporate into coenzymes.

Copyright © 2010 Pearson Education, Inc. Chapter Nineteen44 The fat-soluble vitamins A, D, E, and K are stored in the body’s fat deposits. Although the clinical effects of deficiencies of these vitamins are well documented, the molecular mechanisms by which they act are not nearly as well understood as those of the water- soluble vitamins. None has been identified as a coenzyme. The hazards of overdosing on fat-soluble vitamins are greater than those of the water-soluble vitamins because of their ability to accumulate in body fats. Excesses of the water-soluble vitamins are more likely to be excreted in the urine.

Copyright © 2010 Pearson Education, Inc. Chapter Nineteen45 An antioxidant is a substance that prevents oxidation. In the body, we need protection against active oxidizing agents that are by-products of normal metabolism. Our principal dietary antioxidants are vitamin C, vitamin E,  -carotene, and the mineral selenium. They work together to defuse the potentially harmful action of free radicals, highly reactive molecular fragments with unpaired electrons.

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