Chapter 6 and 7 Lecture Notes
Chapter 6 and 7 Lecture Notes 10120
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This 8 page Class Notes was uploaded by Hannah Kennedy on Saturday February 27, 2016. The Class Notes belongs to 10120 at Kent State University taught by Professor Grampa in Spring 2016. Since its upload, it has received 68 views. For similar materials see Biological Foundations Honors in Biological Sciences at Kent State University.
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Date Created: 02/27/16
Copyright ©: Hannah Kennedy, Kent State University 1 Chapter 7 Lecture Notes 1. Energy sources a. Autotroph = an organism able to build all the complex organic molecules that it requires as its own food source, using only simple inorganic compounds i. Ex = plants, algae, and bacteria b. Heterotroph = an organism that can’t derive energy from photosynthesis or inorganic chemicals so it must feed on other plants and animals and obtain chemical energy by degrading their organic molecules i. Ex = humans 1. We take in glucose and make ATP 2. Harvesting Energy a. Overall balanced redox reaction for the harvesting of energy i. C 6 O12+66O 2 6C2 + 6H2O + ATP 1. Start with 1 molecule of glucose, 6 molecules of oxygen, ending with 6 molecules of carbon dioxide, 6 molecules of water, and ATP b. 2 reactions that harvest energy i. Glycolysis = process that occurs in the cytoplasm and that converts glucose into 3 carbon molecules of pyruvate; as glucose is oxidized (losing electrons) to carbon dioxide, cells transfer electrons temporarily to electron carriers and eventually to oxygen (aerobic respiration) 1. For each molecule of glucose the cell makes 2 ATP 2. Purpose: to make energy (ATP) ii. Krebs cycle = series of 9 reactions that occur in the mitochondrial matrix that take in acetylCoA and oxidizes it to transfer electrons and protons to NADH and FADH , 2 thus driving proton pumps that generate ATP c. 2 important electron carriers + i. NAD ii. FAD 1. These are “temporary electron shuttles that hold onto electrons and then used them to make ATP 3. Cellular Oxidation a. The foods that we consume and digest as broken bonds occurs through a series of oxidation reacti+ns b. NAD = nicotinamide adenosine dinucleotide = common cofactor used for redox reactions i. 2 forms 1. Oxidized form: NAD (lost electrons) 2. Reduced form: NADH (gained electrons) a. NAD will receive 2 electrons and 1 proton to become NADH and during this transfer some energy is captured to form ATP and some is lost as heat ii. When electrons are transferred, protons are transferred to maintain balance 1. H = proton; because it is positive it contains no electrons and only 1 protons remains 4. Glycolysis = the anaerobic breakdown of glucose (happens in cytoplasm) a. Net yield is 2 molecules of pyruvate and 2 molecules of ATP b. Net reaction of glycolysis: Copyright ©: Hannah Kennedy, Kent State University 2 i. C H O + 2ADP + 2P + 2NAD 2pyruvate + 2ATP + 2NADH + 2H +2H O + 6 12 6 i 2 Stage of glycolysis What is happening End result of glycolysis stage Priming reactions = 5 reactions total glucose is made into rearrangement of glucose and uses 2 molecules of ATP glyceraldehyde 3phosphate aka addition of 2 phosphates that G3P prepares glucose to be cleaved + Cleavage = G3P is split into 2 NAD receives 2 electrons phosphate is added to G3P and molecules of 1,3 and 1 protons while G3P is biphosphoglycerate is made biphosphoglycerate (BPG) oxidized (BPG) Oxidation and ATP formation = 4 reactions BPG is converted into pyruvate the phosphates can be added to ADP to form ATP 5. Recycling of NADH a. Cells don’t have a high concentration of NAD (used to deliver electrons to the electron transport chain) so NADH needs to be converted back to it to continue glycolysis (happens 2 ways) i. Aerobic respiration = process in which the final electron acceptor is oxygen; occurs in the mitochondria of eukaryotic cells when oxygen is present ii. Fermentation = process in which oxygen is unavailable so organic molecules accept the electrons instead b. At the end of glycolysis, pyruvate is oxidized to acetyl CoA via the Krebs cycle 6. Oxidation of pyruvate a. Energy is extracted from pyruvate in the mitochondria (involves a multienzyme complex) i. Pyruvate is decarboxylated and a carboxyl group is cleaved to CO 2 ii. The remaining acetyl group is attached to coenzyme A to form acetylCoA iii. NAD is reduced to NADH iv. AcetylCoA now enters Krebs cycle b. Overall reaction of oxidation of pyruvate: + + i. Pyruvate + NAD + CoA acetylCoA + NADH + CO + H 2 7. Krebs cycle = 9 steps which use acetylCoA to produce ATP a. NAD is reduced to NADH b. FAD is reduced to FADH 2 i. FAD = Flavin adenine dinucleotide c. What goes in: 1 acetylCoA d. What comes out: 2 CO and21 ATP 8. Electron transport chain = component the consists of a series of transmembrane proteins in the inner mitochondrial membrane that uses the electrons gained by NAD and FAD in glycolysis and the Krebs cycle to pump electrons from the mitochondrial matrix into the intermembrane space a. Each transmembrane protein acts as a proton pump to pump hydrogen ions into the intermembrane space of the mitochondrion b. Energy to pump protons against their gradient comes from the electrons i. Electrons gradually lose energy as this occurs c. Each electron carrier is only able to interact with adjacent carriers d. ATP synthase carries electrons from the intermembrane space back to the matrix Copyright ©: Hannah Kennedy, Kent State University 3 Electron transport chain Description Intermediate/proton pump component st NADH dehydrogenase complex 1 protein of the chain Proton pump accepts H and 2 electrons from NADH Ubiquinone within the membrane Intermediate transfers electrons from the NADH dehydrogenase complex nd to the 2 protein (cytochrome bc1 complex) oxidized FADH 2o FAD Cytochrome bc c1mplex 2 protein of the chain Proton pump accepts electrons from ubiquinone passes the accepted electrons to cytochrome c Cytochrome c within the plasma membrane Intermediate transfers electrons to the 3 complex (cytochrome oxidase complex) Cytochrome oxidase complex accepts 1 electron at a time Proton pump from cytochrome c passes electrons 4 at a time to oxygen e. Chemiosmosis = a process facilitated by ATP synthase in which the protons that were pumped into the intermembrane space flow back across the inner mitochondrial membrane i. pass through channels that couple their passage with ATP synthesis ii. ATP synthase = used to generate ATP (made of 2 portions); makes 100 ATP per molecule per second 1. F 0omplex = component that is embedded within the inner mitochondrial membrane and acts like a rotor; contains a proton channel a. As protons move through this it rotates i. Proton movement: protons move from the intermembrane space into the matrix 2. F complex = component that is attached to the F complex by a stale and 1 0 that has enzymatic activity a. the stalk rotate as the F complex rotates which changes the 0 conformation of the catalytic head of the F c1 plex iii. once 3 protons move through the channel, 1 ATP is made 9. Yield of Aerobic Respiration a. Glycolysis = 2 ATP b. Krebs cycle = 2 ATP c. Oxidative phosphorylation = 2 ATP d. Total = 36 ATP per glucose molecule Copyright ©: Hannah Kennedy, Kent State University 1 Chapter 6 1. Energy = the capacity to do work, 2 types a. Potential energy = the stored energy an object can use to do work b. Kinetic energy = energy of motion; energy currently being used by an object c. Energy can be found in different forms such as heat, sound, light, and electricity i. Biological energy is obtained from the sun which autotrophs use for photosynthesis d. Breaking bonds (i.e. C—H bonds) requires a lot of energy i. Ex = storing fatty acids in our fat reserves and using them when energy is limited because we get energy from their broken C—H bonds e. Redox reactions = oxidationreaction reactions = when bonds are broken or formed; when electrons are transferred from one atom to another i. Oxidation = when an atom loses an electron ii. Reduction = when an atom gains an electron 1. Oxidation and reduction always occur together a. Mnemonic: OIL RIG When a reaction is When a reaction is a an oxidation (O in is a reduction (R in rig) oil) electrons are electrons are gained overall lost overall 2. Thermodynamics a. First law of thermodynamics = states that energy can’t be created or destroyed; that energy can only change from one form to another i. ex: phase changes, rearranging bonds (ATP) b. second law of thermodynamics = states that the disorder in the universe = entropy and it is continuously increasing i. the less organized energy is the more stable (i.e. its easier for bricks to collapse then it is for them to stay upright and stacked) 3. Chemical Reactions a. Free energy = G = energy available to do work in any stem i. Can be positive or negative b. Endergonic reactions = (“enter”gonic) = reactions that require an input of energy; positive G i. This is not a spontaneous reaction because energy needs to effortfully put in ii. Occurs when it is beneficial 1. Ex = when a cell puts in ATP for active transport for the movement of molecules (i.e. there is a good end pay off to putting in the energy and the effort) Copyright ©: Hannah Kennedy, Kent State University 2 c. Exergonic reactions = “exit” gonic) = reactions that release excess free energy as heat; negative G i. This is spontaneous reaction because energy is easily liberated ii. Ex = breaking of phosphate bonds in ATP 4. ATP = adenosine triphosphate; energy currency of the cell; used for endergonic reactions a. Adenosine = adenine and ribose b. Naming system: i. Adenosine + 1 phosphate = adenosine monophosphate (AMP) ii. Adenosine + 2 phosphate = adenosine diphosphate (ADP) iii. Adenosine + 3 phosphate = adenosine triphosphate (ATP) c. The phosphate bonds are high energy covalent bonds that are very easily broken i. Within these bonds there are a lot of strain and tension due to the negative charges on phosphate being so close to each other 1. This strain makes them easily breakable ii. When broken energy is released and used to power other things in the cell (i.e. muscle contraction, sodiumpotassium pump) d. ATP is easily replenishable and therefore cells don’t have a lot of ATP build up; they break the bonds, use the energy, and replace it. 5. Activation energy = the amount of energy needed to initiate a chemical reaction; can be minimized by a catalyst; known as “the hurdle the reaction needs to overcome” a. The lower the activation energy, the more stable the reaction b. Catalysts decrease the activation energy by stressing existing bonds (i.e. rearranging them) and making them easier to break; the reaction is more likely to occur because of this c. Transition state = the more stable phase in the reaction; the stage in between the making and breaking of bonds 6. Enzymes = biological catalysts (usually proteins) that increase the rate of a reaction by decreasing activation energy; they are not changed or consumed a. Each enzyme catalyzes only 1 or a few reaction i. Advantage: gives the cell tight and specific control over what it is doing at any particular time ii. Why we don’t want a multipurpose enzyme: the cell has no backup plan and no control over what the enzyme is doing b. The location of the enzyme (i.e. the cytoplasm, plasma membrane, and organelles) is determines by what the mission is of that enzyme i. Ex: Location Function/Mission Organelles: lysosomes and peroxisomes When enzymes are found here they are in a protected by a phospholipid bilayer in the lysosome or peroxisome to help break Copyright ©: Hannah Kennedy, Kent State University 3 harmful things down Plasma membrane Enzymes here are involved as transmembrane proteins Cytoplasm Enzymes here catalyze reactions with polar molecules and make sure reactants and products don’t enter the cell; they are also involved in facilitated diffusion here by helping nonpolar substances through the bilayer; ex = brush border enzymes c. Substrates = starting materials d. Products = substances formed during the reactions e. Active site = the specific part of the enzyme where the substrate(s) will bind and the reaction will take place i. The bond is temporary and forms an enzymesubstrate complex ii. Enzymes can change the shape of the active site while the substrates are bound and conform the sit to fit the shape of the substrates 1. At this point the substrates are in close range to the enzyme and the enzyme can stress bonds, allowing the reaction to take place more quickly f. Multienzyme complexes = complexes that occur when several enzymes are bound to each other to form a larger molecule and each enzyme catalyzes sequential reactions of a pathway; “relay race” g. 2 things that allow reactions to happen easier i. When the shape of the substrate is more similar to the active site the more likely the reaction will be to occur; “lock and key theory” ii. The affinity the substrate has for the active site (if the substrate is negative then the active site should be positive) 1. The higher the affinity the tighter the bonding strength between the substrate and the active site 7. Factors affecting enzymes Factor name Effect on enzyme Additional info Temperature The higher the Optimum temp = the temperature the faster the temperature at which our rate of the reaction until enzymes function the best; optimum temperature is anything higher than this reached; molecules move can cause them to lose more with heat and the function and denature (i.e. motion from this stresses a fever); 98.6°F bonds pH Enzymes have an optimum Exceptions to the 68 rule: pH (68) at which they can pepsin (stomach enzyme function because enzymes that prefers its optimum are sensitive to the pH at 2.5) and trypsin Copyright ©: Hannah Kennedy, Kent State University 4 concentration of hydrogen (enzyme that helps digest ions proteins that prefers a basic pH) Inhibitors = binds to and works to prevent the In noncompetitive deactivates an enzyme “turns making of too much of inhibition the substrate no something longer fits into the it off”; can do this in 2 ways 1. Competitive prevents the enzyme from allosteric site; this is made inhibition = functioning possible by tertiary and inhibitions in which quaternary protein the inhibitor and the structure shifting so that enzymes cant fit substrate bind for the same active site; reversible 2. Noncompetitive inhibition = inhibition in which inhibitor binds to a different site than the substrate = allosteric site and changes the shape of the active site Activators = binds to and Allows the enzyme to Binding of a molecule to activates an enzyme “turns it function the allosteric site can also on”; 2 kinds activate an enzyme 1. Cofactors = additional chemicals that are required for a reaction to occur; assist the enzyme in speeding up the reaction by manipulating electrons and attracting them away from covalent bonds to weaken them (ex = Zn and Mn); obtained in diet 2. Coenzymes = type of cofactor that are non protein organic (containingcarbon) Copyright ©: Hannah Kennedy, Kent State University 5 molecules (ex = vitamins and modified nucleotides) 8. Metabolism = the sum of all chemical reactions occurring in the organism; metabolism = anabolism + catabolism a. Anabolism = chemical reactions that use energy to synthesize molecules; bonds are formed (dehydration synthesis) b. Catabolism = chemical reaction that break down molecules and release energy; bonds are broken (hydrolysis) 9. Biochemical pathways = series of reactions taking place in sequence; “relay race” a. Each step of a biochemical pathway requires a unique enzyme and typically happen in one area of the cell b. Negative feedback inhibition = regulation of a biochemical pathway by controlling the activity of the first step of the pathways i. This is possible because the end product becomes the allosteric inhibitor of the first enzyme
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