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Bio 160 Week 6 Notes

by: Alex

Bio 160 Week 6 Notes Bio 160

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These notes cover the role and function of enzymes as well as the HUGE topic of cellular respiration. Drawn images help to understand how they work. Step by step description of glycolysis, the citr...
Biological Sciences I
Class Notes
Biology, bio160, symula, Enzymes, glycolysis, citricacidcycle, ETC, electrontransportchain, cellularrespiration
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This 15 page Class Notes was uploaded by Alex on Tuesday October 4, 2016. The Class Notes belongs to Bio 160 at University of Mississippi taught by SYMULA, REBECCA E in Fall 2016. Since its upload, it has received 62 views. For similar materials see Biological Sciences I in Biology at University of Mississippi.


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Date Created: 10/04/16
Bio- enzymes role in cellular respiration See handout given in class Endergonic and exergonic reactions can be “coupled” Get energy from one to do another Catalysts increase the rate of reaction Adding a catalyst will enable a reaction to happen much quicker Catalysts don’t change G, it just decreases the time between the reactants and products G is the free energy Catalysts do not cause a reaction to occur It lowers the activation energy needed to start the reaction Activation energy Reactan Transition state G Products Activation energy overcomes an energy barrier Transition state- the point after the activation energy is put in when it is unstable and more likely to go through the reaction Enzymes are proteins that reduce activation energy by binding specific reactants The shape helps determine its function Active site- where the reactants bind to the enzyme Substrate- when the reactants are bound to the enzyme Nonsubstrate- a shape that won’t fit in the enzyme The enzymes force the molecules to come together to form something new putting the two molecules together and allowing the reaction to occur Enzyme names end in “-ase” (kinase, amylase, lactase, etc) Enzymes can alter substrates Puts molecules in an orientation Puts physical strain on them Can put a chemical charge to the molecule Isn’t forcing it, but gives it a boost for the reaction to occur (activation energy) Enzyme shape change exposes the active site When the substrates bind, the enzyme changes shape to form the shape of the substrates Is called induced fit Helps overcome the activation energy needed to do the reaction The substrates change, but the enzyme doesn’t Once the enzyme is finished with the substrates, it releases the product and returns to its former shape Cofactor- usually an ion but more generally a nonprotein molecule that are often used for oxidation/reduction reactions (nonpermanent) Coenzymes- small organic molecules (contains carbon) that carry small charged parts. (nonpermanent) Prosthetic groups- covalently bonded to the enzyme (permanent). Need to know each other types of molecules, examples of them, and what they do (definitely on test) Chart included at the bottom Substrate concentration affects reaction rate Maximum Reaction with Reaction without enzyme enzyme Enzymes can be inhibited (turned off) Toxins can covalently bond to the enzyme and then the enzyme is no longer of use because it changes the shape of the enzyme Irreversible inhibitors- toxins are examples. Permanent damage to an enzyme Two different ways enzymes are inhibited: You can add more things for the active site so the substrate has to compete for the active site (competitive inhibition) Noncompetitive inhibition- a molecule that binds to the enzyme to change the shape of the enzyme to prevent the substrate binding to the active site (allosteric inhibition) Allosteric reaction- when a reaction changes the shape of an enzyme Allosteric enzymes can be activated or inactivated An allosteric enzyme needs an activator to get it started, it has a longer activation rate After the activator binds, the slope of energy is vertical until the maximum rate (look back at the graph at the bottom of page 2) When an allosteric inhibitor binds, the active site shape is changed and there is no product Enzymes work in a metabolic pathways in the cell When you start with one substrate and it goes through small, many steps to get to the final product Each step will produce an intermediate Enzymatic reactions are regulated by negative feedback Feedback inhibition = negative feedback Shutting off the process, the final end product will shut off its own pathway When there are high levels of ATP, the ATP goes back to shut it off to not waste cell energy Cells capture energy stored in covalent bonds Extract energy from the environment to do work Need enzymes to explain how to produce energy All energy ultimately comes from the sun Photosynthesis produces glucose (not ATP) Plants use glucose to make other things: nucleic acids proteins etc and then produces energy When oxygen is present, most organisms will do cellular respiration Organisms without oxygen will do fermentation Plants capture energy to put into covalent bonds that can be broken to create energy Cells can transfer energy in different ways Use the energy of something else to fuel another reaction Gradients, ATP phosphate transfer, redox reactions, oxidation and reduction; can all be used to fuel another reaction Redox reaction- the movement of electrons Transfer elections- one compound will be reduced while the other is oxidized. This is a “coupled” term (like hypertonic and hypotonic. Comparative words) LEO and GER Loss of Electrons is Oxidation Gain of Electrons is Reduction This is a HUGE energy transfer Oxidation reduces the energy held by carbon When Methane (CH ) l4oses an H, that means that Methane is oxidized (taking off an electron) Methane can release energy every time it loses a hydrogen to a reaction and becomes more oxidized until it becomes carbon dioxide Glucose can be oxidized because of all the hydrogens that can be transferred (can release a lot of energy) Taking a hydrogen is the equivalent of taking 2 electrons and one proton. The one proton and electron from the atom itself, and then the molecule taking the H will also take another electron to stabilize Nad+ is a coenzyme that carries elections The molecule MUST transfer the electron to something else. The electron cannot float around NAD+ can collect hydrogens to produce NADH (reduced) NADH can lose its electron to something else- another redox reaction Each electron transfer has a big G (-52.4 Kcal/mol) For comparison, ATP= -7.3 kcal/mol How energy is harvested depends on O 2 Cellular respiration- oxygen is present Fermentation- oxygen is not present The difference between these will be expressed in later notes! Must know name, function, and group they belong in Prosthetic groups Heme Binds ions, O2, and electrons FAD Carries electrons/protons Retinal Converts light energy Inorganic Cofactors Iron (Fe2+or Fe ) Oxidation/reduction Copper (Cu or Cu ) 2+ Oxidation/reduction 2+ Zinc (Zn ) Stabilizes DNA binding structure Coenzymes - Biotin Carries-COO Coenzyme A Carries-CO-CH 3 NAD Carries electrons/protons ATP Provides/extracts energy Bio- cellular respiration NAD+ is an electron carrier NADH is when you add a proton and 2 electrons to NAD+ from another molecule NAD+ accepts a hydrogen atom (1 proton and 1 electron) and takes another electron to stabilize the + charge and make it neutral NAD+ is made by a redox reaction Cellular locations of energy pathways differ Eukaryotes use mitochondria Prokaryotes use folds in plasma membrane Cellular respiration occurs in 3 steps Glycolysis Citric acid cycle Oxidative phosphorylation Glycolysis is the start of processing glucose Aerobic – needs oxygen Anaerobic – does not need oxygen “lysis”- to break apart End product of glycolysis is 2 pyruvates You need to invest some ATP to end up with more ATP Energy investing- when you use energy to invest in the process Collecting the energy created- harvesting energy Glycolysis can happen whether or not oxygen is present glycolysis has energy-investing and energy harvesting reactions highly suggest looking up a picture of glycolysis at the end of the energy investing reactions, you have two molecules Starts with 1 molecule of glucose 2 G3P for each glucose molecule- energy investing stage product Each of the G3P will be used to do start the energy harvesting stage Know what kind of enzyme does what Kinases transfer a phosphate from ATP to the molecule Isomerases make the molecule into an isomer When we add phosphates to molecules, we energize them Invest 2 ATP and end with 2 pyruvates and 4 ATP Energy-investing reactions use specific enzymes and ATP Energy-investing reactions rearrange and break up glucose Energy-harvesting reactions yield NADH and ATP Take 1 G3P molecule Results in pyruvate First time we use NAD+ Reducing G3P, there are two phosphates Add them to A to make ADP (A---sugar----P-P) This process makes 2 ATP molecules from one G3P (4 with 2 G3Ps) and 1 NADH (2 with 2 G3Ps) Doesn’t make much energy Glycolysis invests and releases energy Glycolysis produces 2 molecules of pyruvate to start glucose processing Anaerobic process- doesn’t need oxygen End with 4 ATP and 2 NADH and 2 pyruvates Glycolysis occurs in the cytoplasm Pyruvate moves from the cytosol and is converted to Acetyl CoA in the mitochondria Pyruvate moves into the mitochondria matrix Carbon dioxide is taken off, NAD+ + H (from pyruvate taking off CO2) and becomes NADH Coenzyme A chaperones molecule, becomes acetyl CoA Fully oxidized carbon atoms- the first step of cellular respiration to do this End 2 NADH, 2 CO2, and 2 Acetyl CoA Overall 4 NADH so far Citric acid cycle Kregs cycle=citric acid cycle The citric acid cycle completely oxidizes glucose Highly suggest pulling up a picture of cycle We oxydize the carbons and get as many hydrogens off it as possible do not have to memorize the steps, molecules, or enzymes in process Acetyl CoA goes in and oxidizes to NAD+, NAD+ gets reduced to NADH Acetyl CoA becomes Oxaloacetate Citrate=citric acid We will also be producing CO2 because we are oxidizing carbon Phosphate in bottom of circle breaks off to make GTP Oxidation happens all on right side of the figure Oxaloacetate is made out of the pyruvate, making a circle Two functions: oxidize carbon and regenerate the beginning of the cycle Overall get 2 CO2, 1 H2O, 3 NADH, and 1 FADH2 The citric acid cycle completely oxidizes the carbons of glucose Adding an H to NAD+ is an endergonic reaction Goes in- 1 acteyl CoA, water, NAD+, FAD, GTP Comes out 2CO2, 3 NADH, FADH2, 1 ATP How many for one glucose? Double bc 2 pyruvates are produced from 1 molecule of glucose Bio- ATP formation Know chart about enzymes in book, probably not going to be FAD since there is conflicting definitions The citric acid cycle completely oxidizes glucose The citric acid cycle uses specific enzymes and recycles oxaloacetate The citric acid cycle produces ATP and many coenzyme electron carriers Glycolysis: 4 ATP (net 2) and 2 NADH Pyruvate oxidation: 2 NADH Citric acid cycle: 2 ATP, 6 NADH, 2 FADH2 ATP can be made by enzyme phosphate transfer Pyruvate kinase binds pyruvate and ADP and transfers the phosphate from the phosphoenol Pyruvate to make ATP- substrate level phosphorylation ADP + substrate = ATP ATP is also made by oxidative phosphorylation Electron Transport Chain Endergonic combined with exergonic- coupled reaction Series of redox reactions create energy Osmosis when the electron is caught by the O to make water 2 Uses energy from a gradient to go through processes The respiratory chain is in the mitochondrial inner membrane Cristae- between the folds of the membrane in mitochondria Use the matrix and space between the folds Matrix- cytoplasm of the inside of mitochondria Intermembrane space- the space between inner and outer membrane Has 2 membranes The respiratory chain transfers electrons and releases energy Proteins embedded in membrane will accept an electron from a carrier or another protein and pass it onto another protein Releases more and more energy each time it goes through a protein NADH give to a protein and protein becomes reduced and NADH is oxidized and becomes NAD+ Series of redox reactions FADH 2tarts later in the chain than the NADH (specifically the smaller peripheral acceptor protein in the membrane also the second protein in the chain) She will ask on the test why O 2s needed in cellular respiration The electron can’t stay in the proteins or bounce around in the cell and so O 2 takes the electron from the last protein and creates water It does NOT HELP US BREATHE. It will be the last electron acceptor. Will be on this test AND FINAL Oxygen is the final electron acceptor When NADH transfers electrons to the protein (start the chain) it releases a proton into the matrix. The energy transferred from electron jumping from protein, the protein has enough energy to pump the proton to the other side of the membrane This generates a proton gradient- the outside of membrane is very positive, and inside is very negative Electron can’t stay in the proteins and so O 2ccepts it to keep it from bouncing around the cell FADH 2ransfers to the smaller protein and then goes through last two big proteins (the same as NADH except 1 less protein) Proton diffusion is coupled to ATP synthesis ATP synthase Proton motive force- protons have a charged gradient. To reach equilibrium they will go across the membrane. Moving through ATP synthase, the proton creates energy. This energy fuels the ATP synthase to create ATP Oxidative phosphorylation makes a ton of ATP Molecule count Glycolysis: 4 ATP (net 2) and 2 NADH Pyruvate oxidation: 2 NADH Citric acid cycle: 2 ATP, 6 NADH, 2 FADH 2 Oxidative phosphorylation : 28-38 ATP This is for each molecule of glucose Example of cellular respiration with…snickers 30g of sugar in snickers = 3.2 *10^24 molecules of ATP! Other macromolecules are used in glycolysis or the citric acid cycle Polysaccharides- glucose Lipids- fatty acids; glycerol Proteins-amino acids These are the molecules that come in and what we convert them to process them Anabolism and recycling Amino acids come in at many places Fats- glycerol gets converted to a G3P to go in glycolysis (don’t have to go through energy investment stage of glycolysis ) and fatty acids go right into citric acid cycle after theyre converted to Acetyl CoA If you need amino acids etc, you can convert steps of the process and go back to the original amino acid, etc. Fermentation happens without oxygen Alcoholic fermentation- yeast, etc produce ethanol- plants and fungus etc They use it to generate electron carriers Lactic acid fermentation is in animal cells Goes through glycolysis but converts pyruvate into lactic acid and it produces a small amount of ATP Respiration yields more ATP than Fermentation Fermentation- when you work out a lot and your muscles begin to burn. This is a BACKUP Bio- photosynthesis and finishing CR Cellular respiration is regulated Glycolysis and cellular respiration produces a lot of ATP and intermediates. Option to store, or build macromolecules instead of making ATP If we have enough ATP, we can shut off the process and create macromolecules or lipids Negative feedback regulates cellular processes When you produce one end product, the product can turn around and turn off the process in which it was made Ex: enzyme turns molecule C into molecule F. enzyme turns molecule F into molecule G. Molecule G can then go back and turn off the enzyme that turns molecule C into molecule F Allosteric regulation-the regulation of a protein by binding an effector molecule at a site other than the enzyme's active site Allosteric activation- when a molecule is attached to an enzyme and activates it, opening up the active site so the enzyme can work Allosteric inhibition- when a molecule is attached to an enzyme and deactivates it, closing the active site so the enzyme cannot work Citrate is produced in the first step of the citric acid cycle Starts with Acetyl Coa and binds to Oxaloacetate and then a citrate to make citric acid You produce twice as much citrate with one molecule of glucose. Citrate can be easily converted to isocitrate Citrate has several impacts on respiration Formation of isocitrate Increase fatty acid metabolism, will make break down Acetyl CoA instead of sending it into the citric acid cycle Negative feedback- citrate turns Acetyl CoA into a fatty acid and lowers the production of citrate At high concentrations, citrate will leave the mitochondria and work in the cytosol. Citrate and ATP inhibit PFK PFK= phosphofructokinase This is the specific enzyme that will be shut down if you’ve eaten too much sugar PFK is the enzyme we regulate glycolysis with (energy investing side of glycolysis) Citrate is an allosteric inhibitor to PFK. Negative feedback with an allosteric inhibitor ATP and NADH inhibit conversion of isocitrate NAD+ and ADP activate isocitrate dehydrogenase NADH and ATP inhibit isocitrate dehydrogenase They slow their own production, but once they get converted back to the previous form, they react accordingly For example, if there are a lot of NADH/ATP, the isocitrate dehydrogenase will be inhibited. Once the amount of NADH/ATP decreases and becomes NAD+/ADP, then they will reactivate the enzyme to build more NADH/ATP Electron transport chain If a protein receptor is malfunctioning and it cant give away its electron, it backs up the whole process. Therefore, if the last is malfunctioning, the ones before it are backed up while if its only the first, then only the first is effected but the rest are doing nothing Looking at the table, we can see that the levels of Glucose and Pyruvate are normal and so we can conclude that there is nothing wrong with the glycolysis. Since the ETC deals directly with the NAD+ and NADH values, we can say that there is something wrong with the ETC. But, we cannot say which of the acceptor proteins is malfunctioning without further information. An example is if the FAD and FADH2 levels are normal, we can conclude that it is only the first acceptor protein that is malfunctioning. If they are not normal, we can infer that the second or third may also be malfunctioning but not specifically the first This is a concept that WILL be on the test. I suggest studying this concept in detail. Metabolite Average Patient Level (µM) Normal levels (µM) Glucose 99 100 Pyruvate 27 25 NAD+ 10 75 NADH 400 50 Plants and photosynthesis play an essential role in our atmosphere Converts energy and carbon into usable form Primary producers vs consumers Take energy from the environment and convert inorganic molecules into organic- plants Carbon fixation- takes CO2 and uses it to make sugars Most photosynthesis occurs in bacteria Cellular respiration occurs in plants too Takes CO2 and makes it into macromolecules to make something we can use When there’s a lot of CO2 in the air, its an insulator, or it traps in heat If there is no sun, the CO2 keeps it cool (prevents change in temperature) Plants need CO2, water and light. 6CO2 + 6H20 + light C6H12O6 +6O2 Evapotranspiration- when water is evaporated through the leaves’ stomata G is super high and positive and so takes a lot of energy (from the sun- photons) This energy is going to excite electrons Photosynthesis takes place in the leaves and maybe even the stem The roots DO NOT have chloroplasts and therefore do not undergo photosynthesis Leaves have pores in them called stomata that open and close to allow CO2 to come in and H2O to come out (evaporation) The roots soak up water and will be drawn out of the plant Gas exchange- the exchange of CO2 for H2O


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