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BIOS 1700 with Dr. Tanda Week 6

by: Hannah White

BIOS 1700 with Dr. Tanda Week 6 BIOS 1700

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Hannah White

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Cellular Respiration and Energy and Photosynthesis
Biological Sciences I: Molecules and Cells
Soichi Tanda
Class Notes
Science, Biology
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This 17 page Class Notes was uploaded by Hannah White on Wednesday October 5, 2016. The Class Notes belongs to BIOS 1700 at Ohio University taught by Soichi Tanda in Fall 2015. Since its upload, it has received 4 views. For similar materials see Biological Sciences I: Molecules and Cells in Biological Sciences at Ohio University.

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Date Created: 10/05/16
Monday, September 26, 2016 BIOS 1700 with Dr. Tanda Lecture 14 Chapter 6: Energy and Metabolism - How do we demonstrate that an enzyme can ind to a substrate? • β-galactosidase Experiment - A container is separated into two compartments by a selectively permeable membrane. - Part 1: • Radioactively labeled β-galactosidase (S) is added to compartment 1 and the movement of S is followed by measuring the radioactivity levels in the two compartments. - Over time, the level of radioactivity is the same in the two compartments - Part 2: • Radioactively labeled substrate is added to compartment 1 and the enzyme (E) is added to compartment 2. The movement of S is followed by measuring the level of radioactivity in the two compartments 1 Monday, September 26, 2016 - Over time, the level of radioactivity is greater in compartment 2 than in compartment 1. - Conclusion: • If the substrate diffuses from compartment to compartment 2, forms a couple with the enzyme and then is not released because the enzyme cannot catalyze the conversion of substrate to product. - E and S form a complex • Although enzyme-substrate association is very specific, chemically similar molecules can fool this specificity. • Enzymes not only bind to substrates but also other molecules such as inhibitors and activators • Inhibition: reversible and irreversible • β-galactosidase binding to IPTG (fake substrate) is an example of irreversible inhibition because the IPTG will never be released - Reversible Inhibition • “Fake” substrate can be released • Two types - Competitive • Enzyme has 1 active site which can bind to either a substrate or an inhibitor - Substrate and inhibitor compete to be able to bind to active site - Ratio of substrate to inhibitor MATTERS 2 Monday, September 26, 2016 - Noncompetitive • Enzyme has an active site and an inhibitor site - Substrate binds to active site - Inhibitor binds to inhibitor/allosteric site - Ratio of substrate to inhibitors DOESN’T matter - The number of inhibitors MATTERS 3 Monday, September 26, 2016 • Allosteric Regulation - Allosteric site can regulate the activity of an active site • If an inhibitor binds to the allosteric site and does not allow the substrate to attach (by changing active site shape) then it is NEGATIVE regulation - Means there is more inhibitors than substrates - This inhibits the active site - Conserves Energy • If an inhibitor binds to the allosteric site and allows the substrate to attach then it is POSITIVE regulation - More substrate than inhibitor - Activates active site 4 Monday, September 26, 2016 - Clicker Questions • The portion of an enzyme that binds specifically to the substrate is referred to as the ____ of the enzyme - Active site • Which of the following types of inhibitor permanently alters the enzyme it inhibits? - Irreversible inhibitor • Avery and his colleagues wanted to understand what biological molecule(s) convert(s) nonvirulent Streptococcus pneumoniae to a virulent one. So, they treated extract of the heat-killed virulent strain with various enzymes prior to mixing a nonvirulent strain. They used RNase, protease, and glycosidases (carbohydrate- digesting enzymes). In all cases, the nonvirulent bacteria became the virulent strain. From THIS result, we can conclude that ( ) is (are) the genetic material. Consider all possible molecules. - DNA and or Lipids 5 Monday, September 26, 2016 BIOS 1700 with Dr. Tanda Lectures 14 and 15 Chapter 7: Cellular Respiration - What keeps us going? Eating and breathing • - Conversion of energy in carbohydrates and other molecules into ATP REDOX reactions: reduction and oxidation • • Mitochondria is the key organelle C6H 1206+ 60 2= 6CO 2 + 6H 0 + Energy • Oxidation = the loss of an • electron - Loss energy • Reduction = the gain of an electron - Gain energy • If an oxidation happens Direct product from a chemical reaction then a reduction must happen and vise versa - Memorize the following: Indirect production via electrons • Electrons have energy • Follow the electron to follow the energy • Reducing agents: Molecules that give away their electrons - Electron donors - Reducing agents themselves will be oxidized in the redox reaction - Reducing agents have energy 1 Monday, September 26, 2016 • Oxidizing agents: Molecules that can receive electrons - Electron acceptors - Oxidizing agents themselves will be reduced in the redox reaction - Oxidizing agents have less or no energy • A redox reaction is one in which an oxidation and a reduction occurs - 4 stages of Cellular Respiration Glycolysis • • Pyruvate Oxidation • Citric Acid Cycle • Oxidative Phosphorylation - Phosphorylation is the chemical reaction needed to add phosphate groups • ADP into ATP - Electron Carriers • Contain high-energy electrons • Key carriers in cellular respiration are NADH and FADH 2 • Their reduced forms, NADH and FADH 2, have more electrons (or energy) than the oxidized forms, NAD and FAD. - NAD + H + 2e —> NADH (oxidized reaction) - FAD + 2H + 2e —> FADH 2 (oxidized reaction) - NADH —> NAD + H + 2e (reduced reaction) - FADH 2 —> FAD + 2H + 2e (reduced reaction) • The H and 2e are produced from chemical reactions 2 Monday, September 26, 2016 • The H and 2e also dump their energy somewhere else in the cycle • Protons move with the electrons - Electron movement = proton movement - Following the electrons = following the protons - If you lose a H then you lose energy - ATP • C6H 1206+ 60 2= 6CO 2 + 6H 0 • Reactants (G1) Products (G2) - G1 > G2 • — G ; gain of ATP; Energy produced - ATP is produced by substrate level phosphorylation (phosphorylation of ADP) and oxidative phosphorylation (using electron carriers NADH and FADH 2) • Oxidative phosphorylation produces a MAJORITY of ATP - Redox Reactions in Biological Systems • There is no complete electron transfer • All depends on the elements electronegativity • Carbon atoms in glucose are oxidized • Carbon has partially lost electrons and is oxidized because the oxygen atom is more electronegative than the carbon atom - Carbon is the reducing agent / electron donor Loses electrons • • Oxygen atoms are reduced - Oxygen has partially gained electrons and is reduced because the oxygen atom is more electronegative than the carbon atom. - Oxygen is the oxidizing agent / electron receiver • Gains electrons - Glycolysis: The first step of cellular respiration 3 Monday, September 26, 2016 • Occurs in the cytoplasm • Turns ONE glucose molecule into TWO pyruvate molecules • Uses energy Consumes 2 ATP molecules to make • glucose bigger by adding phosphate groups to it so it won’t leave the cytoplasm • Creates 4 ATP and 2 NADH • Net Gains: 2 ATP and 2 NADH • No oxygen is involved, which makes this an anaerobic reaction - Pyruvate Oxidation • Occurs in the matrix of the mitochondria • Energy in pyruvate is transferred into Acetyl- CoA • Produces NADH + H and CO 2 per pyruvate • Produced 2 NADH + 2 H and 2CO 2 per glucose molecule - Glucose produces two pyruvate so you have to multiply the products by 2 to get the total number per glucose molecule - Citric Acid Cycle • Occurs in the matrix of the mitochondria • Know that we begin with Acetyl-CoA (2 carbons) which is transformed into Citrate (6 carbons) and then we end with Oxaloacetate (4 carbons) • Produces 1 ATP, 3 NADH, 1 FADH 2, and 2 CO 2per Acetyl-CoA • For find the total productions per glucose multiply these by 2. 4 Monday, September 26, 2016 - 2 ATP, 6 NADH, 2 FADH 2 and 4 CO 2 - Oxidative Phosphorylation • Occurs in the inner membrane of the mitochondria • Electron carriers bring in energy to create a gradient of H+ - Potential energy • Electrons from electron carriers are discharged at O 2(the electron acceptor) producing H2O. - Oxygen is reduced when it becomes H 20. - Potential energy produces ATP from ADP and P • Electron Transport Chain - NADH enters Complex 1 and CoQ takes it to Complex 3. Then cytochrome C takes it to Complex 4 where it exits - FADH 2enters Complex 2 and CoQ takes it to Complex 3. Then cytochrome C takes it to Complex 4 where it exits • The end product is H 20 - 0 2+ 4H + 4e —> H 2O - As the electrons move they discharge the energy required to make ATP - Proton Transport • Builds a gradient of H+ or potential energy • Complexes 1, 3, and 4 are proton pumps, which pump H+ against its gradient 5 Monday, September 26, 2016 - This allows ATP Synthase to create ATP by using the potential energy of the H+ gradient - Clicker Questions • In eukaryotic cells, glycolysis occurs in: - The cytoplasm • The loss of an electron is referred to as ____; the gain of an electron is referred to as____ - Oxidation; reduction • In glycolysis, one glucose molecule produces - 2 pyruvate molecules 6 Wednesday, September 28, 2016 BIOS 1700 with Dr. Tanda Lecture 16 Chapter 7: Cellular Respiration - A gradient of protons creates potential energy that in turn runs ATP production - ATP Synthase • Two Subunits - F0 Subunit • Forms a channel that rotates as protons pass through it - Also known as a fan - F1 Subunit • Uses the rotational (kinetic) energy of 0to catalyze the synthesis of ATP - Then ATP is created - How was it tested that ATP synthase uses the proton gradient? Observation • Hypothesis: A gradient of H+ (potential energy) is used to produce ATP - Experiment: • Materials Needed: proton pump activated by a light bulb, ATP synthase, Liposome (to hold all the protons), H+ (protons) ADP, Pi • Light activates the proton pump which “pushes” H+ into the lysosome. As H+ leaves through ATP synthase, ADP + Pi are turned into ATP • Results: A gradient of H+ is used to produce ATP - When the light is off, no protons move 1 Wednesday, September 28, 2016 into the cell and the protons inside the cell move out of the cell to equalize concentrations on both sides. • This is why the graph decreases - How do we measure the numbers of protons inside the cell? • Take the pH - When the light is on, the pH decreases because there are more protons inside. This makes it more acidic - When the light is off, the pH increases because the protons move the equalize their concentrations. This makes it more basic - What Occurs Where? • Glycolysis: Cytosol • Pyruvate Oxidation: Matrix of the mitochondria • Citric Acid Cycle: Matrix of the mitochondria • Electron Transport Chain: Inner membrane of the mitochondria - Its A Numbers Game • Cellular respiration makes a total of 32 ATP molecules per molecule of glucose. - How is that broken down? (per glucose) • Glycolysis : 2 ATP, 2 NADH Pyruvate • Oxidation: 0 ATP, 2 NADH • Citric Acid Cycle: 2 ATP, 6 NADH, 2 FADH 2 - 1 NADH transports 5 H+ 2 Wednesday, September 28, 2016 - 1 FADH 2 transports 3 H+ • 2 H+ = 1ATP - Fermentation • Anabolic (no oxygen) metabolism - ATP produced when no oxygen is present - Two Types: • Lactic Acid Fermentation - Occurs in animals and bacteria - The citric acid cycle can’t occur which means pyruvate molecules accumulate in the cell - The cell comes up with a way to remove the pyruvate which allows glycolysis to continue • The cell wants glycolysis to continue because although it only makes a small amount of ATP, it still makes some - The cell uses NADH to convert pyruvate into lactic acid - This produces NAD+ which is used in glycolysis • Causes the muscle ache we get after working out • Ethanol Fermentation - Occurs in plants and fungi • Especially yeast - The citric acid cycle can’t occur which means pyruvate molecules accumulate in the cell 3 Wednesday, September 28, 2016 - The cell comes up with a way to remove the pyruvate which allows glycolysis to continue • The cell wants glycolysis to continue because although it only makes a small amount of ATP, it still makes some - Pyruvate is turned into Acetaldehyde and then NADH turns Acetaldehyde into ethanol - The NADH then turns to NAD+ and is used for glycolysis • Helps in making bread - Retrieving Energy from Lipids • This only occurs when there is no glucose present • There is fat in food • Digestion of fat in the small intestine Absorption of triacyglyercols in the small intestine • • Breakdown of triacyglyercols to glycerol and fatty acids in the cell • One fatty acid makes a lot of ATP - Why? • Because it has many C-C and C-H bonds which have high potential energy • 2 carbons in one fatty acid can produce 1 FADH 2, 1 NADH and 1 Acteyl-CoA - All of which produce ATP - How Do We Control Cellular Respiration? • Positive and Negative Feedback Regulations - Higher concentrations of ADP or NAD+ means the body needs to produce more ATP 4 Wednesday, September 28, 2016 • This is positive feedback because it activates cellular respiration - High concentrations of ATP or NADH or citrate means the body is able to begin saving glucose • This is negative feedback because it halts cellular respiration - Allosteric Regulation • Active Site: Binding site for substrate • Allosteric Site: Binding site for positive or negative regulator - If a positive regulator binds to the allosteric site then it stimulates the enzyme - If a negative regulator binds to the allosteric site then it stops the enzyme • The products shut down the pathways to conserve glucose Allosteric regulation *Negative regulation is more important* 5 Step 3 in Fig. 7.4 Wednesday, September 28, 2016 - Clicker Questions: • Under aerobic conditions, pyruvate can be broken down by what? - Fermentation • The electron transport chain uses energy from ____ and _____ to run ____ to create a gradient of H+ across the inner membrane of the mitochondria - NADH; FADH 2; proton pumps • In cellular respiration, glucose is oxidized to produce CO ,2H O2 and energy. In other words, carbon atoms in glucose “lose” electrons when they become CO 2 because ( ) of oxygen is greater than that of carbon. - Electronegativity 6


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