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This 8 page Class Notes was uploaded by Renee Lehner on Wednesday September 9, 2015. The Class Notes belongs to BIOL 200 at University of Washington taught by Mark Cooper in Fall. Since its upload, it has received 11 views. For similar materials see /class/192316/biol-200-university-of-washington in Biology at University of Washington.
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Date Created: 09/09/15
I Metabolism Lecture Outline 5 and 6 Cells make and use ATP as a source of energy to drive endothermic endergonic reactions Synthesis and use is a dynamic process A Energy is needed to fuel many different processes in the cell 1 Since ATP cannot cross membrane organisms must rely on other sources of energy to Jutl i ATP 39 39 39 39 r39 or light phototrophs 2 In the case of nonphotosynthetic organisms these energy sources are reduced organic molecules such as sugar carbohydrates proteins and fats The energy stored in these molecules is in their covalent bonds B Components of Metabolism l Metabolism is the sum total of all chemical reactions occurring in cell 2 Catabolism are chemical reactions that are degradative ie breaking down in function Catabolic reactions are generally regarded as carbon consuming and energy generating 3 Anabolism chemical reactions that are building in function ie carbon generating and require an expenditure of energy Anabolic reactions are also known as biosynthetic reactions Metabolism must accomplish 3 tasks Generate metabolic energy Most often think of chemical energy e g ATP but there are other chemical energy sources cell need and use Cells also need to generate energy in the form of electrochemical energy or proton motive force see below 2 Synthesize l2 molecules called essential precursor molecules If is from these molecules that all other molecules are made 3 Generate a source of reducing power Cells need a source of electrons or electronsprotons to carry out certain oxidiationreduction redox reactions D Redox reactions accomplish the conversion from energy source to usable energy ATP Electrons are the most important source of energy in cells 2 ATP holds a lot ofpotential energy a The phosphate groups in the ATP molecule are negatively charged b These negative charges repel each other and thus hold a lot of potential energy c When end phosphate hydrolyzed covalent bond broken have production of inorganic phosphate Pi ADP and the release energy 3 Other highenergy phosphate compounds include phosphoenol pyruvate PEP and l 3 dibisphosphoglycerate Both have a higher energy of hydrolysis than ATP 4 Another form of energy needed by all cells is electrochemical energy or proton motive force 5 Energy is required to make ATP from ADP and Pi a The energy to make ATP comes from harnessing the energy in the bonds of usedstored carbohydrates proteins and fats or by transferring a highenergy phosphate group from PEP for example to ADP to make ATP ATP made in this manner is called substrate level phosphorylation b Energy is harnessed via oxidationreduction redox reactions 1 In a redox reaction one compound loses an electron reducing agent or reductant and another compound gains an electron oxidizing agent or oxidant Redox reactions may also involve a shifting of electrons 2 The electron donor becomes oxidized and the electron acceptor becomes reduced In biological systems redox reactions frequently involve the transfer of a pair of electrons or a pair of electrons and protons Reduced compounds have a high potential energy and act as electron donors to reduce molecules that can receive that energy This is how energy is slowly stepped down and harnessed for use in the synthesis of ATP 7 Can measure the reduction potential of atoms or molecules ie tendency to retain or give up its electronsprotons electrically in reference to hydrogen gas Can organize these oxidationreduction pairs into an electron tower a Electrons or electrons and protons can ow down electron tower b A molecule maybe a reductant or an oxidant depending on what molecule it is interaction with c Some OR pairs can only accept electrons others can accept a pair of electronsprotons d A certain amount of energy is release as electron or electrons ow down electron tower Amount of energy released is difference in reduction potential of OR pair involved Since electrons or electrons and protons cannot exist on their own they must be associated with a carrier molecule Four important carrier molecules are nicotinamide adenine dinuleotide or NAD NADVNADH the phosphorylated derivative of NAD NADP NADPNADPH avin mononucleotide FMN and avin adenine dinucleotide or FAD FADFADH Protons can associate with water to form hydrodrium ion H30 3 V 4 V 6 V 8 V E The oxidation of glucose releases energy The most straightforward way to oxidize glucose is to burn it in the presence of oxygen C5H1205 602 gt 6C0 6H20 energy 2 Glucose is a reduced organic molecule with a high potential energy that serves as the electron donor 3 Oxygen is the oxidized molecule that acts as the terminal electron acceptor 4 CO is the fully oxidized form of glucose and water is the product of the reduction of oxygen 5 This reaction releases 686 kcal of energy as heat 6 Key to cells metabolizing glucose is to carry out OR reactions between two molecules that differ sufficiently in their OR potential to generate enough energy to make ATP but not so much that most of the energy is given off as heat 11 The 3 types of metabolisms carried out by organisms as a group aerobic anaerobic respiration and fermentation What are the 3 central pathways of metabolism used by all organisms III Glycolysis Begins the Oxidation of Glucose A The Glycolytic Reactions and Their Yields 1 Glycolysis involves 10 enzymecatalyzed reactions that occur in the cytoplasm of nearly 3911 all cells Why is the g1 if pathway 39J Jan r39 39 pathway 2 Initially an input of energy is required to energize glucose ie raise the potential energy of glucose a ATP is used to phosphorylate glucose to glucose6phosphate b An enzyme rearranges this molecule into fructose6phosphate c ATP is used again to add another phosphate forming fructose 16bisphosphate 3 The next set of reactions yield an energy payoff a Fructose 16bisphosphate is split into two 3carbon compounds b One of these compounds called glyceraldehyde phosphate is converted to 13 bisphosphoglycerate and in the process reduces 2 NAD molecules to yield 2 NADH molecules c The energy released during the oxidation of glyceraldehyde 3phosphate fuels the addition of another inorganic phosphate to the reactant therefore 13 bisphosphoglycerate contains two phosphate groups and a large potential energy d In the next reaction an enzyme removes a phosphate from 13 bisphosphoglycerate and uses it to phosphorylate ADP forming ATP The resulting intermediate is called 3phosphoglycerate e This method of ATP synthesis is called substratelevel phosphorylation f After a twostep enzymatic conversion to phosphoenolpyruvate another substrate level phosphorylation event occurs and ATP is generated g The product of glycolysis is pyruvic acid or salt of acid pyruvate 4 Glycolysis results in production of a 2 NADH molecules oxidation of glyceraldehyde phosphate b 4 total ATP molecules via substrate level phosphorylation for a net yield of 2 ATP s c 612 essential precursor molecules d Where are glycolytic enzymes found eukaryotes and prokaryotes IV The Krebs Citric Acid Cycle Completes the Oxidation of Glucose A What is the fate of the pyruvate generated by glycolysis 1 Before pyruvate can be metabolized by Krebs cycle enzymes it must be converted to Acetyl CoA a b c d Kre This step is considered a linking step between glycolysis and the Krebs cycle Your textbook refers to this as the pyruvate processing step Step result in the reduction NAD to NADH and a molecule of carbon dioxide is given off Keep in mind that have two acetyl CoA produced per glucose acetyl CoA is one of the essential precursor molecules bs Cycle Pathway is known as the Citric Acid Cycle or the Tricarboxylic Acid Cycle TCA cycle Is this pathway an amphibolic pathway a b Cycle enzymes are found in cytoplasm of bacteria and in mitochondrial matrix in nonphotosynthetic eukaryotes Acetyl CoA condense with an intermediate in Krebs cycle called oxalacetate to form intermediate citric acid citric acid undergoes 4 OR reactions that result in production of NADH 3 and FADH 1 and 1 ATP by substrate level phosphorylation for every Acetyl CoA metabolized Three intermediates of cycle are essential precursor molecules Where are Krebs cycle enzymes found in prokaryotes and eukaryotes 3 Remain two precusor molecules are made inPentose Phosphate Pathway This pathway also produces reduing power in form of NADPH NADPH is used primary when reducing power needed for biosynthetic reaction and not for energy generation V Electron Transport Chain ETC Chemiosmosis and ATP Synthesis A Composition of the ETC 1 The electron transport chain is a series of increasingly oxidized molecules in the inner mitochondrial membrane that accept electrons from electron carriers and pass them to oxygen in case of aerobic respiration In bacteria ETC is integral to cytoplasmic membrane 2 Four of the ETC components are proteins a These proteins all contain chemical groups such as avin ironsulfur heme or copper where the reductionoxidation reactions take place b They are all anchored to the inner mitochondrial membrane In bacteria they are anchored to cytoplasmic membrane 3 One of the components is a lipidsoluble coenzyme called ubiquinone Q a Unlike the protein components of the ETC Q can move through the membrane b This ability to move allows it to shuttle electrons from one protein complex to the other 4 The electron carriers NADH and FADH donate electrons to the ETC a The ETC components are organized from least oxidized to most oxidized b NADH donates electrons to a avin containing protein at the top of the chain c FADH donates electrons to an ironsulfur complex that donates them to Q effectively skipping a step in the ETC d Oxygen is highly oxidized and is the nal electron acceptor in many cell types B The Chemiosmotic HypothesisiHow does the ETC harness energy for ATP production 1 Peter Mitchell hypothesized that the ETC indirectly provides energy for ATP production a Mitchell suggested that the ETC uses the energy from reductionoxidation reactions to fuel the pumping of protons up a concentration gradient from the matrix to the inner membrane space b This would create an electrochemical gradient proton motive force across membrane c A protein in the inner membrane then uses the protonmotive force to synthesize ATP d This hypothesized link between the ETC and ATP synthesis is called the chemiosmotic hypothesis C Organization of the ETCiHow does it pass electrons and pump protons 1 Three of the four large protein complexes of the ETC are proton pumps a In complexes I and IV the protons presumably pass directly through the complex of electron carriers b In complex III Q shuttles protons as well as electrons When it donates the electrons to complex IV it releases the protons into the intermembrane space Fig 612 2 The other protein complex cytochrome c and Q shuttle the electrons from one complex to the other Fig 612 D How does ATP synthase use the protonmotive force to generate ATP E Oxidative Phosphorylation l Oxidative phosphorylation is the formation of ATP by ATP synthase that is fueled by the protonmotive force generated by the ETC 2 Aerobic respiration occurs when oxygen is the nal electron acceptor during oxidative phosphorylation 3 theoretically it is possible to make 3 ATPs for every NADH oxidized through ETC and 2 for every FADH oxidized through ETC 4 If all glucose goes into make ATP what is the net yield of ATPs made during aerobic respiration 5 What is the net yield generated by eukaryotes and why the difference with prokaryotes V Anaerobic respiration l A metabolic process in which an inorganic molecule other than oxygen serves as the terminal electron acceptor e g nitrate or sulfate 2 A unique form of metabolism carried out by certain bacterial species VI Fermentation l A metabolic process in which an organic molecule in most case synthesized by organism serves as the terminal electron acceptor 2 Bacterial fermentors do not have an ETC eukaryotic cells that carry out fermenation ie muscle cells maintain their mitochondria In this situation the only source of ATP is substratelevel phosphorylation during glycolysis 3 All ATP made is by substrate level phosphorylation that is made in glycolysis 4 Examples the lactic acid bacteria and the yeast Sacchromyces cerevisiae This means that they cannot accept electrons from NADH 5 Muscle cells when deprived of oxygen rigorous exercise carry out lactic acid fermentation Why is this to the advantage of cells VI Chemolithrophic bacteria 1 Obtain their energy from reduced inorganic molecules and carbon from C02 2 Example the hydrogen bacteria and time permitting the deepsea vent organisms like ia VIII Regulation Many type of regulation exist that govern gene expression and proteinenzyme function Three common these are competitive inhibition covalent modification of a protein and use of allosteric proteins controls How does competitive inhibition of an enzyme differ from allosteric control of an enzyme A The Regulation of Glycolysis 1 How do high concentrations of ATP regulate glycolysis a allosteric control feedback inhibition 2 Regulation of the glycolytic pathway by ATP allows the cell to conserve glucose when ATP is plentiful B The Krebs cycle is regulated at several key steps 1 The enzyme complex that converts pyruvate to acetyl CoA is regulated a This complex is phosphorylated when levels of ATP are high 99057 f Phosphorylation inhibits this enzyme complex High levels of NADH also inhibit the activity of this complex High levels of acetyl coenzyme A CoA also inhibit this complex Because NADH and acetyl CoA are products of the enzyme pathway in which this complex participates inhibition by them is called feedback inhibition This type of regulation slows the rate of the pathway when the products of that pathway build up in the cell This is an energy conservation mechanism On the other hand high levels of AMP NAD and CoA enhance the activity level of this enzyme complex High levels of ATP also regulate the enzyme that catalyzes the formation of citrate from oxaloacetate and acetyl CoA Regulation of both glycolysis and the Krebs cycle allows cells to carefully match the rate at which they use glucose to their energy requirements Prokaryotic and Eukaryotic Cell Structure and Function Lecture Outline 4 I Prokaryotes Eukaryotes and the three domains of life Analysis of cell structure by electron microscopy revealed two types of cellular architecture prokaryotes and eukaryotes B How were the 3 cellular domains of life established and what are these domains C What general features can be used to distinguish between prokaryotes and eukaryotes II Prokaryotic cell structure Cell Wall i Peptidoglycan unique to Bacteria ii What is the signi cance of peptidoglycan both structurally and medically iii How does the cell wall of Archaea differ from that of Bacteria iv Role of MreB in determining cell shape What eukaryotic protein does this protein share homology with B Flagellum i How does structure differ from that of eukaryotes ii How is movement generated and what is source of engery required for movement in prokaryotes and eukaryotes C Genome and plasmids i How does the genome of eukaryotes differ in structure ii What are plasmids and how do they differ from the genome of organisms D Ribosome s i What is the composition of the 70S ribosome ii How do eukaryotic ribosome s differ iii How do the Archaea ribosomes differ from those of Bacteria III Eukaryotic cell Structure Nucleus i nuclear envelope nuclear lamina ii chromatin heterochromatin euchromatin iii nucleolus B The below 3 structure makeup the endomembrane system of eukaryotes C Ribosomes and rough ER i What types of proteins are made on rough ER D Golgi Apparatus i What role does this structure play in protein localization E Smooth Endoplasmic Reticulum i What functions are carried out in this structure F Peroxisomes F9 Lysosomes Mitochondria i What is the origin of this structure ii What functional role does structure have Will return to structure in metabolism lecture Cytoskeleton i What roles does the cytoskeleton have ii Actin intermediate laments and microtubules What roles do each of these structures have and how are they distinguished iii How do microtubules and microf11aments differ
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