Enzymes: Unit 3 Cellular Energetics PDF

Unit 3: Cellular Energetics Topic 3.1 Enzyme Structure Topic 3.2 Enzyme Catalysis  Got Milk? Lactose intolerance happens when your small intestine does not make enough of a digestive enzyme called lactase. Lactase breaks down the lactose in food so your body can absorb i...

Unit 3: Cellular Energetics Topic 3.1 Enzyme Structure Topic 3.2 Enzyme Catalysis  Got Milk? Lactose intolerance happens when your small intestine does not make enough of a digestive enzyme called lactase. Lactase breaks down the lactose in food so your body can absorb it.  Naming conventions ▪ Enzymes named for reaction they catalyze ◆ sucrase breaks down sucrose ◆ carbohydrase break down carbohydrates ◆ DNA polymerase builds DNA ▪ adds nucleotides to DNA strand ◆ pepsin breaks down proteins (polypeptides) ◆ trypsin break down proteins Enzymes ▪ Biological catalysts ◆ proteins ◆ facilitate chemical reactions ▪ increase rate of reaction without being consumed ▪ reduce activation energy ▪ don’t change free energy (ΔG) released or required ◆ required for most biological reactions ◆ highly specific ▪ thousands of different enzymes in cells  Enzyme vocabulary substrate ▪ reactant which binds to enzyme ▪ enzyme-substrate complex: temporary association product ▪end result of reaction active site ▪ enzyme’s catalytic site; substrate fits into active site products substrate active site enzyme Enzyme Structrure For an enzyme-mediated chemical reaction to occur, the shape and charge of the substrate must be compatible with the active site of the enzyme. Enzymes are very specific and ONLY work with certain substrates Induced fit model ▪ More accurate model of enzyme action ◆ 3-D structure of enzyme fits substrate ◆ substrate binding cause enzyme to change shape leading to a tighter fit ▪ “conformational change” ▪ bring chemical groups in position to catalyze reaction  Properties of enzymes ▪ Reaction specific ◆ each enzyme works with a specific substrate ▪ chemical fit between active site & substrate H bonds & ionic bonds ▪ Not consumed in reaction ◆ single enzyme molecule can catalyze thousands or more reactions per second ▪ enzymes unaffected by the reaction ▪ Affected by cellular conditions ◆ any condition that affects protein structure ▪ temperature, pH  The structure and function of enzymes contribute to the Enzymes affect the regulation of biological processes: rate of biological Enzymes are biological catalysts that facilitate chemical reactions in cells by lowering the reactions activation energy. Chemical Reaction With and Without Enzyme Present Reactions are catalyzed (happen faster) with enzymes present. This line is higher because more energy is required for the reaction without the enzyme. This line is lower because less energy is required for the reaction to occur with the enzyme. Activation energy: the amount of energy it takes to get a reaction started (like buying a ticket to a movie) Enzymes LOWER the activation energy, the reaction requires less energy (like a discount or sale on the ticket)  Enzymes Lower the Activation Energy Enzymes generally lower activation energy by reducing the energy needed for reactants to come together and react. For example: Enzymes bring reactants together, so they don’t have to expend energy moving about until they collide at random. Enzymes bind both reactant molecules (called the substrate), tightly and specifically, at a site on the enzyme molecule called the active site By binding reactants at the active site, enzymes also position reactants correctly. This allows the molecules to interact with less energy. Enzymes may also allow reactions to occur by different pathways that have lower activation energy.  How does it work? ◆ ▪ ◆ ▪  Unit 3: Cellular Energetics Topic 3.3 Environmental Impacts Of Enzyme Function ENE-1: The highly complex organization of living systems requires constant input of energy and the exchange of macromolecules.  Enzymes speed up metabolic reactions by lowering energy barriers A catalyst is a chemical agent that speeds up a reaction without being consumed by the reaction An enzyme is a catalytic protein Hydrolysis of sucrose by the enzyme sucrase is an example of an enzyme- catalyzed reaction  How Enzymes Lower the EA Barrier Enzymes catalyze reactions by lowering the EA barrier Enzymes do not affect the change in free energy (∆G); instead, they speed up reactions that would occur eventually Enzyme-substrate complex stabilizes the transition state  Catalysis in the Enzyme’s Active Site In an enzymatic reaction, the substrate binds to the active site of the enzyme The active site can lower an EA barrier by Orienting substrates correctly Straining substrate bonds Providing a favorable microenvironment Figure 8.15-1 1 Substrates enter active site. 2 Substrates are held in active site by weak interactions. Substrates Enzyme-substrate complex Active site Enzyme Figure 8.15-2 1 Substrates enter active site. 2 Substrates are held in active site by weak interactions. Substrates Enzyme-substrate complex 3 Active site can lower EA and speed up a reaction. Active site Enzyme 4 Substrates are converted to products. Figure 8.15-3 1 Substrates enter active site. 2 Substrates are held in active site by weak interactions. Substrates Enzyme-substrate complex 3 Active site can lower EA and speed up a reaction. 6 Active site is available for two new substrate molecules. Enzyme 5 Products are 4 Substrates are released. converted to products. Products LE 8-17 Substrates enter active site; enzyme changes shape so its active site Substrates held in embraces the substrates (induced fit). active site by weak interactions, such as hydrogen bonds and ionic bonds. Active site (and R groups of its amino acids) can lower EA Substrates and speed up a reaction by Enzyme-substrate acting as a template for complex substrate orientation, stressing the substrates and stabilizing the transition state, providing a favorable Active microenvironment, site is participating directly in the available catalytic reaction. for two new substrate molecules. Enzyme Products are Substrates are released. converted into products. Products Factors Affecting Enzyme Function ▪ Enzyme concentration ▪ Substrate concentration ▪ Temperature ▪ pH ▪ Inhibitors Enzyme concentration Fixed substrate concentration as ↑ [enzyme] = ↑ reaction rate more enzymes = more frequently collide with substrate reaction rate levels off substrate becomes limiting factor [enzyme] = [substrate] All active sites are occupied All the substrates have been converted to products. Adding more enzyme does not increase rate of reaction. Substrate concentration Fixed enzyme concentration as ↑ [substrate] = ↑ reaction rate more substrate = more frequently collide with enzyme reaction rate levels off all enzymes have active site engaged enzyme is saturated, becomes limiting factor [enzyme] = [substrate] All active sites are occupied maximum rate of reaction. Adding more substrate does not increase rate of reaction.  Initial Velocity The reaction rate of an enzymatic reaction is always fastest at the beginning of the reaction when there is the greatest concentration of substrate. Why? Higher frequency of substrate binding to enzyme’s active site The reaction decreases over time because product to substrate ratio increases Rate of reaction can be measured by: ✓Product formation ✓Disappearance of substrate Calculating Rate of Reaction Rate of reaction in a chemical reaction is determined by the formation of product in a unit of time Rate = slope Example: What is the unit? M/sec Optimal Temperature Higher environmental temperatures increase the speed of movement of molecules in a solution, increasing the frequency of collisions between enzymes and substrates and therefore increasing the rate of reaction. Optimal pH Different enzymes function in different environments most human enzymes = pH 6-8 depends on localized conditions pepsin (stomach) = pH 2-3 Amylase (Saliva) = pH 7 trypsin (small intestines) = pH 8 Optimal pH Environmental pH can alter the efficiency of enzyme activity, including through disruption of hydrogen bonds that provide enzyme structure. Why does pH matter to enzymes? 1. Disrupt local folding of the amino acid chain: fewer hydrogen bonds in ɑ-helices and ẞ- sheets are formed. 2. Change protein conformation (2° structure) 3. Disrupt R-group interactions: changing number of possible hydrogen bonds in the environment 4. Change protein conformation (3° structure) 5. Changes function of protein (denatured)  Shape of the active site changes as a result of bonds within the enzyme Environmental breaking Impacts on Enzyme Function Change to the molecular structure of a component in an enzymatic system may result in a change of the function or efficiency of the system— Denaturation of an enzyme occurs when the protein structure is disrupted, eliminating the ability to catalyze reactions.  Environmental Impacts on Enzyme Function Environmental temperatures and pH outside the optimal range for a given enzyme will cause changes to its structure, altering the efficiency with which it catalyzes reactions.  Environmental Impacts on Enzyme Function In some cases, enzyme denaturation is reversible, allowing the enzyme to regain activity Denatured proteins have much lower activity or may become completely nonfunctional. ✓ Can denatured proteins be used as a negative control in the experiment? Enzyme Inhibitors 1. Competitive inhibitors bind to the active site of an enzyme, competing with the substrate 2. Noncompetitive inhibitors bind to another part of an enzyme, causing the enzyme to change shape and making the active site less effective ✓Examples of inhibitors include toxins, poisons, pesticides, and antibiotics Competitive Inhibitor Competitive inhibitor molecules can bind reversibly or irreversibly to the active site of the enzyme. Increase [substrate] can reduce inhibition Ex. Methotrexate inhibits cell division, competes for the active site binding for folic acid enzyme, used for chemotherapy. Competitive inhibitor & substrate “compete” for binding to the active site Noncompetitive Inhibitor Noncompetitive inhibitor: binds to another part of an enzyme called the allosteric site changing the activity of the enzyme. enzyme changes shape active site is nonfunctional, no longer binds substrate allosteric inhibitor binds to allosteric site Increase [substrate] does not reduce inhibition Ex. Pennicillium inhibits bacteria’s Noncompetitive inhibitor binds directly to allosteric site cell wall formation Figure 8.17 (a) Normal binding (b) Competitive inhibition (c) Noncompetitive inhibition Substrate Active site Competitive inhibitor Enzyme Noncompetitive inhibitor  Unit 3: Cellular Energetics Topic 3.4 Cellular Energy ENE-1: The highly complex organization of living systems requires constant input of energy and the exchange of macromolecules.  ENE-1.H: Describe the role of energy in living Cellular Energy organisms. All living systems require constant input of energy Cellular Respiration  Figure 8.8 Adenine Phosphate groups Ribose (a) The structure of ATP ATP + H2O → ADP + Pi Adenosine triphosphate (ATP) G = -7.3 kcal/mol Energy Inorganic Adenosine diphosphate (ADP) phosphate (b) The hydrolysis of ATP Photosynthesis  The Regeneration of ATP ATP is synthesized and hydrolyzed in a cyclic fashion ATP synthesis ATP hydrolysis requires energy releases energy The synthesis of ATP from ADP + Pi is endergonic and is powered by exergonic reaction. The hydrolysis of ATP to ADP + Pi is exergonic, and energy released is used to power endergonic function such as muscle contraction *Pi inorganic phosphate Energy Coupling Cells manage energy resources to do work by energy coupling: using an exergonic process to drive an endergonic one ATP powers cellular work by coupling exergonic reactions to endergonic reactions A cell does three main kinds of work: ✓ Mechanical ✓ Transport ✓ Chemical To do work, cells manage energy resources by energy coupling, the use of an exergonic process to drive an endergonic one  ENE-1.H: Describe the role of energy in living Cellular Energy organisms. Energy-related pathways in biological systems are sequential to allow for a more controlled and efficient transfer of energy. A product of a reaction in a metabolic pathway is generally the reactant for the subsequent step in the pathway. The sequential reactions allow for a more controlled and efficient transfer of energy. Apply Your Knowledge More about enzymes Some enzymes need helpers to do their job Cofactor: ions that promotes substrate and enzyme binding. They can either bind to the substrate or bind to the enzyme. Examples: zinc ion and copper ion Coenzyme: organic molecule that helps the enzyme. Some vitamins are coenzymes or precursors of coenzyme. Examples: vitamin C, niacin (B3) Inhibitors can also substitute these factors to reduce enzyme activity (some by changing the enzyme’s conformation.) Progress Check #4 Apply Your Knowledge Apply Your Knowledge This is an example of a positive control. Apply Your Knowledge