Chapter 06 Lecture Outline - Biology PDF

Chapter 06 Lecture Outline See separate PowerPoint slides for all figures and tables pre-inserted into PowerPoint without...

Chapter 06 Lecture Outline See separate PowerPoint slides for all figures and tables pre-inserted into PowerPoint without notes. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.  Chapter 6 Energy, Enzymes, and Metabolism Key Concepts: Energy and Chemical Reactions Enzymes and Ribozymes Overview of Metabolism Recycling of Organic Molecules 2  Energy and Chemical Reactions Energy = ability to promote change or do work Two forms  Kinetic Energy – associated with movement  Potential Energy – due to structure or location Chemical energy, the energy in molecular bonds, is a form of potential energy 3  Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. (a) Kinetic energy (b) Potential energy a: © moodboard/Corbis RF; b: © amanaimages/Corbis RF 4 Laws of Thermodynamics First Law of Thermodynamics  “Law of conservation of energy”  Energy cannot be created or destroyed, but can be transformed from one type to another 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 5  Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Highly ordered 6  Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Increase in entropy Highly ordered More disordered 7 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 energy 8  H = G + TS 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) 9 Spontaneous reactions Occur without input of additional energy Not necessarily fast, can be slow  Breakdown of sucrose to CO2 and H2O is spontaneous, but will take a long time for sugar in a sugar bowl to break down Key factor is the free energy change – if ΔG is negative, then process is exergonic and spontaneous 10  ΔG = Δ H – T Δ S Exergonic = spontaneous  ΔG0 (positive free energy change)  Requires addition of energy to drive reaction 11  Hydrolysis of ATP Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Adenine (A) NH2 N N Phosphate groups H ΔG = -7.3 kcal/mole O– O– O– N N H2C O P O ~ P O ~ P O– O O O O Reaction favors H H Ribose H H formation of products OH OH Adenosine triphosphate (ATP) H2O Hydrolysis NH2 of ATP The energy liberated is used to drive a variety N N H N N H2C O O– P O ~ O– P OH + HO O– P O– of cellular processes O O O O H H H H OH OH Adenosine diphosphate (ADP) Phosphate (Pi) 12 Cells use ATP hydrolysis to drive reactions An endergonic reaction can be coupled to an exergonic reaction The reactions will be spontaneous if the net free energy change for both processes is negative 13 Glucose + Phosphate → Glucose-6-phosphate + H2O ΔG = +3.3 Kcal/mole (endergonic) ATP + H2O → ADP + Pi ΔG = -7.3 Kcal/mole (exergonic) Coupled reaction: Glucose + ATP → Glucose-6-phosphate + ADP ΔG = - 4.0 Kcal/mole (exergonic) = spontaneous 14  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 ATP-binding sites We can predict whether a newly discovered protein uses ATP or not On average, 20% of all proteins bind ATP Likely an underestimate because there may be other types of ATP-binding sites This illustrates the enormous importance of ATP as an energy source  Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. The energy to synthesize ATP comes from chemical reactions that are exergonic. Energy input (endergonic) Synthesis ADP + Pi Hydrolysis ATP + H2O Energy release (exergonic) ATP hydrolysis provides the energy to drive cellular processes that are endergonic.  Enzymes and Ribozymes 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 17 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  Large amounts of heat  Using enzymes to lower activation energy 18  Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. ATP Reactant molecules Glucose Enzyme Transition state Activation energy (EA) without enzyme Activation energy (EA) Free energy (G) with enzyme Reactants Change in free energy (G) Products Progress of an exergonic reaction 19 How enzymes lower activation energy Straining bonds in reactants to make it easier to achieve transition state Positioning reactants together to facilitate bonding Changing local environment  Direct participation through very temporary bonding 20 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 21 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Glucose ATP Active site Hexokinase 1 Substrates (ATP and glucose) bind to the enzyme (hexokinase). 22  Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. ADP Glucose-6- Glucose phosphate ATP Active site Enzyme-substrate complex Hexokinase 1 Substrates (ATP and 2 Enzyme undergoes conformational 3 Substrates are 4 Products (ADP and glucose) bind to the change that binds the substrates more converted to products. glucose-6-phosphate) enzyme (hexokinase). tightly. This induced fit strains are released. Enzyme chemical bonds within the substrates is ready to be reused. and/or brings them closer together. 23 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 24 Enzyme reactions Saturation  Plateau where nearly all active sites are occupied by substrate  Vmax = velocity of reaction near maximal rate Michaelis constant, KM  Substrate concentration where velocity is half maximal value  High KM enzyme needs higher substrate concentration  Inversely related to affinity between enzyme and substrate 25  Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Vmax D C (product/second) Vmax 2 Velocity B Tube A B C D Amount of 1 g 1 g 1 g 1 g enzyme Incubation 60 sec 60 sec 60 sec 60 sec time A Substrate Low Moderate High Very concentration high 0 KM [Substrate] Reaction velocity in the absence of inhibitors 26 Inhibition Competitive inhibition  Molecule binds to active site  Inhibits ability of substrate to bind  Apparent KM increases – more substrate needed Noncompetitive inhibition  Lowers Vmax without affecting Km  Inhibitor binds to allosteric site, not active site 27  Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Vmax (product/second) Velocity Plus competitive inhibitor Substrate Enzyme Inhibitor 0 KM KM with inhibitor [Substrate] Competitive inhibition Vmax (product/second) V max with inhibitor Velocity Plus noncompetitive inhibitor Enzyme Allosteric site Substrate Inhibitor 0 KM [Substrate] Noncompetitive inhibition 28 Other requirements for enzymes Prosthetic groups – small molecules permanently attached to the enzyme Cofactor – usually inorganic ion that temporarily binds to enzyme Coenzyme – organic molecule that participates in reaction but is left unchanged afterward 29 Enzymes are affected by environment Most enzymes function maximally in a narrow range of temperature and pH Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. High chemical reaction Rate of a 0 0 10 20 30 40 50 60 Temperature (ºC) 30  Overview of Metabolism Chemical reactions occur in metabolic pathways Each step is coordinated by a specific enzyme Catabolic pathways  Breakdown cellular components  Exergonic Anabolic pathways  Synthesiscellular components  Endergonic  Must be coupled to exergonic reaction 31  Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Enzyme 1 Enzyme 2 Enzyme 3 PO42— PO42— PO42— OH OH OH OH OH OH PO42— PO42— PO42— Initial substrate Intermediate 1 Intermediate 2 Final product 32 Catabolic reactions Breakdown of reactants Used for recycling building blocks Used for energy to drive endergonic reactions  Energy stored in intermediates such as ATP, NADH 33 Two ways to make ATP 1. Substrate-level phosphorylation  Enzyme directly transfers phosphate from one molecule to another molecule 2. Chemiosmosis  Energy stored in an electrochemical gradient is used to make ATP from ADP and Pi 34 Redox reaction Electron removed from one molecule is added to another Oxidation – removal of electrons Reduction – addition of electrons Ae + B → A + Be - - A is oxidized, B is reduced 35 NADH Electrons removed by oxidation of organic molecules are used to create energy intermediates like NADH NAD+ Nicotinamide adenine dinucleotide NADH useful in two ways:  Releases a lot of energy when oxidized that can be used to make ATP  Can donate electrons during synthesis reactions to energize them 36  Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. H O C Nicotinamide NH2 + 2e– + H+ N+ O CH2 O P O– H H H H O OH OH NH2 O P O– N O CH2 N H N N H Nicotinamide H H Adenine adenine H H dinucleotide OH OH (NAD)+ 37  Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. The 2 electrons and H+ can be added to this ring, which now has 2 double bonds instead of 3. H O O Reduction H H C C Nicotinamide NH2 + 2e– + H+ NH2 Oxidation N + N Two electrons are released O CH2 during the oxidation of the O CH2 O P O– H H nicotinamide ring. O P O– H H H H H H O O OH OH NH2 OH OH NH2 O P O– O P O– N N O CH2 N O CH2 N H H N N H N N Nicotinamide H H Adenine adenine NADH H H H H H H dinucleotide (an electron OH OH (NAD)+ carrier) OH OH 38 Anabolic reactions Biosynthetic reactions Make large macromolecules or smaller molecules not available from food Require energy inputs from intermediates (NADH or ATP) to drive reactions 39 Regulation of metabolic pathways Gene regulation  Turn genes on or off Cellular regulation  Cell-signaling pathways like hormones Biochemical regulation  Feedback inhibition – product of pathway inhibits early steps to prevent over accumulation of product 40  Feedback Inhibition Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Initial substrate Intermediate 1 Intermediate 2 Final product Active site Enzyme 1 Enzyme 2 Allosteric site Enzyme 3 Conformational Feedback Inhibition: change If the concentration of the final product becomes high, it will bind to enzyme 1 and cause a conformational change that inhibits the enzyme’s ability to convert the initial substrate into intermediate 1. Final product 41  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 42  Expression of genome allows cells to respond to changes in their environment  RNA and proteins made when needed  Broken down when they are not mRNA degradation important  Conserve energy by degrading mRNAs for proteins no longer required  Remove faulty copies of mRNA 43 mRNA degradation Exonucleases – enzymes cleave off nucleotides from end Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Exosome – Multiprotein complex uses exonucleases Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 44  Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Cap mRNA A A AA AAA A 3´ 5´ Poly A tail 45  Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Cap mRNA A A A AA AA A 3´ 5´ Poly A tail Poly A tail is shortened. A 3´ 5´ 5´ cap is removed. A 3´ 5´ Nucleotides RNA is degraded in are recycled. the 5´ to 3´ direction Exonuclease via an exonuclease. A 3´ 46  Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Cap mRNA A A A AA AA A 3´ 5´ Poly A tail Poly A tail is shortened. A 3´ 5´ RNA is degraded in the 3´ to 5´ direction via the exosome. 5´ Nucleotides are recycled. Exosome 47  Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Cap mRNA A A A A AA A A 3´ 5´ Poly A tail Poly A tail is shortened. A 3´ 5´ RNA is degraded in 5´ cap is removed. the 3´ to 5´ direction A via the exosome. 3´ 5´ Nucleotides RNA is degraded in 5´ are recycled. the 5´ to 3´ direction Exonuclease via an exonuclease. A Nucleotides 3´ Exosome are recycled. (a) 5´ 3´ degradation by exonuclease (b) 3´ 5´ degradation by exosome © Liu, Q., Greimann, J.C., and Lima, C.D., (2006). Reconstitution, activities, and structure of the eukaryotic exosome. Cell, 127, 1223-1237. Graphic generated using DeLano, W.L. (2002). The PyMOL Molecular Graphics System (San Carlos, CA, USA, DeLano Scientific) 48 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  rapidly degrade proteins to respond to changing cell conditions 49  Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Cap 1 2 3 4 Core proteasome (4 rings) Cap (a) Structure of the eukaryotic proteasome 50  Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Ubiquitin 1 String of ubiquitins Target are attached protein to a target protein. 2 Protein with attached ubiquitins is directed to the proteasome. 3 Protein is unfolded by enzymes in the cap and injected into the core proteasome. Ubiquitin is released back into the cytosol. 4 Protein is degraded to small peptides and amino acids. 5 Small peptides and amino acids are recycled back to the cytosol. 51 (b) Steps of protein degradation in eukaryotic cells 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 52  Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Autophagosome Outer membrane Inner membrane Lysosome Organelle 2 Double membrane Autophagosome fuses with a 3 completely encloses 1 Membrane tubule begins lysosome. Contents are degraded to enclose an organelle. an organelle to form and recycled back to the cytosol. an autophagosome. 53