BIOL 302 Lecture 2 Outline of Last Lecture II. What is a cell?A. Unity and diversity of cellsB. How to observe/study cellsC. Classification of cells III. Prokaryotes , EukaryotesA.Cytoplasm vs. cytosolB.Endosymbiotic theoryC.Cytoskeleton IV. Chemical components of cellsA. Organic compoundsB. AtomsC. Molecules in cells Outline of Current Lecture V. Chemical ReactionA. Laws of Thermodynamics B. Enzymatic CatalysisC. Prosthetic groups, coenzymes and co-factorsVI. Regulation of Enzyme ActivityA.Feedback Inhibition & Allosteric regulationB.Enzyme inhibitors VII. Free Energy of MoleculesA. Activated carrier moleculesB. HydrolysisCurrent LectureAll living things must create and maintain order in a universe that is tending toward greater disorder… These notes represent a detailed interpretation of the professor’s lecture. GradeBuddy is best used as a supplement to your own notes, not as a substitute.•To create this order, living organisms must carry out a never-ending stream of chemical reactions •The sum of these reactions is referred to as metabolism (all chemical rations that occur in a cell) •Two sub-classes: 1- anabolic (building up) 2-catabolic (breaking down) •These reactions are very complex, but highly regulated and efficient •Each cell can be viewed as a tiny chemical factory, performing millions of reactions every second Chemical reactions in cells are organized in pathways …•in a chemical reaction, a reactant (substrate) is changed into a product •in any given pathway, the chemical reactions are connected where the product of the first is the reaction is the reactant (substrate) for the next •in cells chemical reactions are catalyzed by enzymes (biological catalysts), allowing them to be highly regulated •A fundamental task of proteins is to act as enzymes—catalysts that increase the rate of virtually all the chemical reactions within cells.Although some RNAs are capable of catalyzing some reactions, most biological reactions are catalyzed by proteins. •In the absence of enzymatic catalysis, most biochemical reactions are so slow that they would not occur under the mild conditions of temperature and pressure that are compatible with life. •Enzymes accelerate the rates of such reactions by over a million-fold, so reactions that would take years in the absence of catalysis can occur in fractions of seconds if catalyzed by the appropriate enzyme. •Cells contain thousands of different enzymes, and their activities determine which of the manypossible chemical reactions actually take place within the cell. The Catalytic Activity of Enzymes… •Like all other catalysts, enzymes are characterized by two fundamental properties: 1- they increase the rate of chemical reactions without themselves being consumed or permanently altered by the reaction. 2- they increase reaction rates without altering the chemical equilibrium between reactants and products.Laws of Thermodynamics •The chemical equilibrium between S and P is determined by the laws of thermodynamics •Second Law of Thermodynamics: the universal tendency of things to become disordered •Any isolated system will change spontaneously towards the greatest degree of disorder. Cells have to work around the second law to maintain their complex and organized structure Cells generate order at the expense of order in the universe- First Law of Thermodynamics: energy can be transferred or transformed from one form to another, but it cannot be created or destroyed •The effect of the enzyme on a reaction is best illustrated by the energy changes that occur during the conversion of S to P •The equilibrium of the reaction is determined by the final energy states of S and P, which are unaffected by enzymatic catalysis. •In order for the reaction to proceed, the substrate must be converted to a higher energy state, called the transition state. •The energy required to reach the transition state (the activation energy) acts as a barrier to theprogress of the reaction, limiting the rate of the reaction. •Enzymes act by reducing the activation energy, thereby increasing the rate of reaction. •The catalytic activity of enzymes involves the binding of their substrates to form an enzyme-substrate complex (ES). •The substrate binds to a specific region of the enzyme, called the active site. •While bound to the active site, the substrate is converted into the product of the reaction, which is then released from the enzyme. Mechanisms of Enzymatic Catalysis …•The binding of a substrate to the active site of an enzyme is a very specific interaction. •Active sites are clefts or grooves on the surface of an enzyme, usually composed of amino acids from different parts of the polypeptide chain that are brought together in the tertiary structure of the folded protein.•Substrates initially bind to the active site by noncovalent interactions (hydrogen bonds, ionic bonds, and hydrophobic interactions).Once a substrate is bound to the active site of an enzyme, multiple mechanisms can accelerate its conversion to the product. •Enzymes also accelerate reactions by altering the conformation of their substrates. •Lock-and-key model: the substrate fits precisely into the active site •In many cases, however, the configurations of both the enzyme and substrate are modified by substrate binding—a process called induced fit. •Here, the conformation of the substrate is altered so that it more closely resembles that of the transition state. •In addition to bringing multiple substrates together and distorting the conformation of substrates to approach the transition state, many enzymes participate directly in the catalytic process. •Specific amino acid side chains in the active site may react with the substrate and form bonds with reaction intermediates. •The acidic and basic amino acids are often involved in these catalytic mechanisms. Example: chymotrypsin (a member of a family of enzymes that digest proteins by catalyzing the hydrolysisof peptide bonds) Prosthetic Groups, Coenzymes, and Co-factors …•Prosthetic groups are small molecules bound to proteins that play critical functional roles. –Example, the oxygen carried by hemoglobin is bound to heme, a prosthetic group of these proteins. In many cases metal ions (such as zinc or iron) are bound to enzymes and play central roles in the catalytic process. •Other low-molecular-weight organic molecules, called coenzymes,