Lesson 1_1P91_Students PDF

E N E R GY , ENZYMES & M E TA B O L I S M Dr. Szuroczki Chapter 6 Dr. Szuroczki c0-ordinates Week 4 – 6 Email: [email protected] Please email me any questions you may have! A bit about myself... A little about me Key Concepts 1. Energy and Chemical Reactions 2. Enzymes 3. Overv...

E N E R GY , ENZYMES & M E TA B O L I S M Dr. Szuroczki Chapter 6 Dr. Szuroczki c0-ordinates Week 4 – 6 Email: [email protected] Please email me any questions you may have! A bit about myself... A little about me Key Concepts 1. Energy and Chemical Reactions 2. Enzymes 3. Overview of Metabolism 4. Recycling of Organic Molecules 1. Energy & Chemical Reactions Chemical reaction: the process in which one or more substances are changed into other substances Chemical reactions occur when atoms combine with or dissociate from other atoms 4H  C CH (methane) = Chemical bonds are energy relationships involving 4 the electrons of reacting atoms interactions among Matter and energy Matter: anything that occupies space and has mass and has 3 states: Solid: definite shape and volume Liquid: definite volume; shape of container Gaseous: neither a definite shape nor volume Matter may be changed: Physically: Changes do not alter the basic nature of a substance Examples include changes in the state of matter (solid, liquid, or gas) Chemically: Changes alter the chemical composition of a substance Matter and energy Energy: the ability to do work Has no mass and does not take up space Kinetic energy: energy is doing work Potential energy: energy is inactive or stored Forms of energy: Chemical energy is stored in chemical bonds of substances Electrical energy results from movement of charged particles Mechanical energy is energy directly involved in moving matter Radiant energy travels in waves; energy of the electromagnetic spectrum Energy and Chemical Reactions Two forms: Kinetic Energy: associated with movement Potential Energy: energy held by an object becau of its position relative to other objects Types of Energy That Are Important in Biology Thermodynamics Thermodynamics: study of energy interconversions (energy being converted from one form to another) First Law of Thermodynamics “Law of conservation of energy” Energy cannot be created or destroyed, but Glu Sta from one type to another can be transformed cos ATP ATP (chemical energy = heat) rch e ATP ATP ATP ATP Thermodynamics Second Law of Thermodynamics Transfer of energy from one form to another increases the entropy (degree of disorder) of a system As entropy increases, less energy is available for organisms to use to promote change or do work (unusable energy) Change in free energy determines direction of chemical reactions Total energy = Usable energy + Unusable energy Energy transformations involve an increase in entropy (disorder that cannot be harnessed to do work) Free energy (G) = amount of energy available to do work Also called Gibbs free Change in free energy determines direction of chemical reactions H = enthalpy or total energy G = free energy or amount of energy for work S = entropy or unusable energy T = absolute temperature in Kelvin (K) G H  TS Gibbs free energy is used to predict whether a chemical process is spontaneous or non- spontaneous Spontaneous reactions Occur without input of additional energy (will) proceed naturally You may have to provide some activation energy; the rest will proceed without the need of a continuous input of an external source of energy E.g., Combustion Non-spontaneous reactions A continuous energy input is necessary for the reaction to proceed E.g., Photosynthesis: a process in which plants use to make glucose Photosynthesis requires energy (in the form of sunlight) to drive chemical reactions At night when it’s dark, photosynthesis does not work! Spontaneous vs. non- spontaneous Is bread making a spontaneous or non-spontaneous reaction? 1. Yeast + flour = fermentation: Spontaneous or NON-spontaneous? 2. For bread to bake it needs to go into the over @ 450 C for 45 min : Spontaneous or NON- How to tell? G H  TS Key factor is the free energy change – if ΔG is negative, then process is spontaneous Exergonic = spontaneous ΔG < 0 (negative free energy change) Energy is released by reaction Endergonic = not spontaneous ΔG > 0 (positive free energy change) Requires addition of energy to drive reaction Hydrolysis of ATP: Spontaneous or NON- spontaneous? ΔG= −7.3kcal/mole Exergonic = spontaneous: ΔG < 0 (negative free energy change) Endergonic = not spontaneous: ΔG > 0 (positive free energy change) Reaction favors formation of products The energy liberated is used to drive a variety of cellular processes  most molecules in body are either “glued” or “cut” via water Cells use ATP hydrolysis to drive reactions An endergonic reaction can be coupled to an exergonic reaction so that the two reaction overall is thermodynamically favored! ATP is the major 'energy' molecule produced by metabolism: it’s “dispatched” to wherever a non-spontaneous reaction needs to occurs within the cell The reactions will be spontaneous if the net free energy change for both processes is negative ATP drives endergonic reactions Glucose  Phosphate2- Glucose  6  phosphate 2  H2O ΔG = + 3.3Kcal/mole (endergonic) + ATP 4-  H2O ADP2-  Pi2- ΔG = − 7.3Kcal/mole (exergonic) = Glucose  ATP 4  Glucose  6  phosphate 2  ADP 2 ΔG = − 4.0Kcal/mole (exergonic) Coupled reaction = spontaneous! Cells use ATP hydrolysis to drive reactions In the couple reaction a phosphate is directly transferred from ATP to glucose – phosphorylation Typical cell uses millions of A TP molecules per second to drive endergonic processes Breakdown of food releases energy that allows cells to make more A TP from ADP Examples of Proteins That Use A T P for Energy Many Proteins Bind ATP and Use That ATP as a Source of Energy Each ATP undergoes 10,000 cycles of hydrolysis and resynthesis every day! Particular amino acid sequences in proteins function as A TP-binding sites On average, 20% of all proteins bind A TP Likely an underestimate because there may be other types of ATP-binding sites This illustrates the enormous importance of A T P as an energy source 2. Enzymes A spontaneous reaction is not necessarily a fast reaction Catalyst: an agent that speeds up the rate of a chemical reaction without being consumed during the reaction Enzymes: protein catalysts in living cells Ribozymes: RNA molecules with catalytic properties Enzymes Enzymes Act as biological catalysts Increase the rate of chemical reactions Bind to substrates at an active site to catalyze reactions Can be recognized by their –ase suffix Hydrolase Oxidase Hydrolase Enzymes that facilitate the cleavage of bonds in molecules with the addition of the elements of water Activation energy Initial input of energy to start reaction Allows molecules to get close enough to cause bond rearrangement Can now achieve transition state where bonds are stretched Common ways to overcome activation energy: 1. Large amounts of heat 2. Using enzymes to lower activation energy How enzymes lower activation energy Straining bonds in reactants to make it easier to achieve transition state Positioning reactants together to facilitate bonding Enzymes bring reactants together, so they don't have to expend energy moving about until they collide at random Other enzyme terminology Active site: location where reaction takes place Substrates: reactants that bind to active site Enzyme substrate complex: formed when enzyme and substrate bind Substrate binding Enzymes have a high specificity for their substrate Lock and key metaphor for substrate and enzyme binding – only the right key (substrate) will fit in the lock (enzyme) Induced fit phenomenon: interaction also involves conformational changes Enzyme reactions Affinity: Degree of attraction between an enzyme and its substrate Saturation: Plateau where nearly all active sites are Vmax  occupied byvelocity of reaction near maximal rate substrate Enzyme reactions MichaelisKconstant, M Substrate concentration where velocity is half maximal value OR half of the active sites are occupied at one time Substrate concentration required for the chemical reaction to occur HigK enzyme needs higher substrate concentration M h Inversely related to affinity between enzyme and Enzyme Inhibitors Are molecules that interact with enzymes (temporary or permanent) in some way and reduce the rate of an enzyme- catalyzed reaction or prevent enzymes to work in a normal manner 1. Competitive inhibition: Inhibitor molecules binds to active site Inhibits ability of substrate to bind = Km needs to increase as more substrate needed Enzyme Inhibitors 2. Noncompetitive inhibition: lowers Vmax without affecting Km Inhibitor binds to allosteric site (another spot on the enzyme), not active site Causes a shape change in the enzyme Other requirements for enzymes Prosthetic groups: small molecules permanently attached to the enzyme and aids in enzyme function Cofactor: usually inorganic ion that temporarily binds to enzyme to promote a chemical reaction Coenzyme: organic molecule that participates in reaction but is left unchanged afterward Enzymes are affected by environment Most enzymes function maximally in a narrow range of temperature and pH Enzymes Review Video 3. Overview of Metabolism Chemical reactions occur in metabolic pathways Each step is coordinated by a specific enzyme Overview of Metabolism 1. Anabolic pathways: Synthesis cellular components Endergonic (must be coupled to exergonic reactions) 2. Catabolic pathways: Breakdown cellular components Exergonic How to build large molecules: Anabolic Synthesis (“to make”) Building bigger molecules from smaller molecules (e.g. dehydration reactions) Building cells and bodies + ATP Example Amino Protei Acids n Proteins are synthesized by bonding amino acids (e.g. dehydration reaction) Catabolic reactions Breakdown of reactants (e.g., hydrolysis reactions) Used for recycling building blocks Used for energy to drive endergonic reactions Energy stored in intermediates such as NADH and ATP (which releases the energy needed for metabolic processes in all cells throughout the body) Two ways to make ATP Substrate-level phosphorylation: Enzyme directly transfers phosphate from one molecule to another molecule Chemiosmosis: Energy stored in an electrochemical gradient is used to make A T P from A D P and Pi Cellular respiration = Metabolism! (Chemiosmosis) Cellular respiration and ETC Electron carriers, also called electron shuttles, are small organic molecules that play key roles in cellular respiration (or anabolic processes) Their name is a good description of their job: they pick up electrons from one molecule and drop them off with another NAD+ and FAD “pick up” electrons become NADH and FADH2 Return to original form once electrons have been “dropped off” How are electrons shuttled? Redox reactions! The reactions in which NAD+ and FAD gain or lose electrons are examples of a class of reactions called redox reactions Name come from: “oxidation-reduction reactions” Cellular respiration involves many reactions in which electrons are passed from one molecule to another Oxidation – removal of electrons Reduction – addition of electrons Ae  B A  Be   A is oxidized, B is reduced Regulation of metabolic pathways Needed for the cell to regulate materials: Catabolic pathways are regulated so that organic molecules are broken down ONLY AFTER they’re no longer needed or when the cell needs energy Anabolic pathways – ensures a cell synthesizes molecules when needed Regulation of metabolic pathways 1. Gene regulation: Turn genes on or off that encode for the creation of enzymes 2. Cellular regulation: Cell-signaling pathways like hormones (i.e., targeted on and off switch via chemical messenger) 3. Biochemical regulation: Feedback inhibition: product of pathway inhibits early steps to prevent over accumulation of product. Can also alter a pathway by regulating the slowest step in the reaction (rate-limiting step) 4. Recycling of organic molecules Most large molecules exist for a relatively short period of time Half-life – time it takes for 50% of the molecules to be broken down and recycled All living organisms must efficiently use and recycle organic molecules (saves energy) For example: expression of genome allows cells to respond to changes in their environment RNA and proteins made when needed Broken down when they are not Proteasome A large complex that breaks down proteins using protease enzymes Proteases cleave bonds between amino acids Ubiquitin tags target proteins to the proteasome to be broken down and recycled Ubiquitin tagging allows the cell to: Degrade improperly folded proteins Lysosomes Lysosomes contain hydrolases to break down proteins, carbohydrates, nucleic acids, and lipids Digest substances taken up by endocytosis Autophagy: recycling worn out organelles using an autophagosome Review Video: ATP!