Chapter 6 and 7 (through Feb. 10)
Chapter 6 and 7 (through Feb. 10) Bio 1510
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This 8 page Class Notes was uploaded by Michelle Notetaker on Friday February 12, 2016. The Class Notes belongs to Bio 1510 at Wayne State University taught by Dr. Nataliya Turchyn in Summer 2015. Since its upload, it has received 48 views. For similar materials see Basic Life Mechanisms in Biology at Wayne State University.
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Date Created: 02/12/16
Chapter 6: Energy and Metabolism Where Do We Get Energy From? o All of our energy is from the sun (solar energy) Physically humans can’t use energy from the sun but plants can o Energy is stored in CH bonds of glucose o Energy is then released from CH bonds We release high energy electrons when we break down the glucose from plants o The energy from electrons is then used indirectly to make ATP ATP is chemical energy used by all living organisms o Photosynthetic organisms use both solar energy and ATP o Nonphotosynthetic organisms ONLY use ATP o ATP is used for cellular functions o ORGANISMS CAN’T SURVIVE WITHOUT ATP! What Supplies “Energy” for ATP o Cation = more protons than electrons o Anion = more electrons than protons o When something loses electrons it lowers its energy and electrons will be closer to the nucleus o If it gains electrons, then it will have a higher level of energy o REDOX reactions involve electrons being reduced or oxidized If something is oxidized, then something must be reduced Endergonic vs. Exergonic Reactions o Endergonic reactions require input of energy to proceed (ex. Photosynthesis) “ender” = inward “gonic” = energy Carbon dioxide + water glucose + oxygen (sunlight is needed for this reaction Carbon dioxide and water are reactants Glucose and oxygen are the products Products have more energy than reactants Glucose has MORE energy than carbon dioxide o Exergonic reactions release energy (ex. Cellular respiration) “exer” = outward Glucose + oxygen carbon dioxide + water + ATP Glucose and oxygen are reactants Carbon dioxide and water are products ATP is NOT a product Reactants have more energy than products Roles of Enzymes in Chemical Reactions o Enzymes lower the activation energy (E )a– minimum energy required to start a chemical reaction o Enzymes speed up reactions by lowering the activation energy allowing products to be made much faster o Activation energy = energy of activation o You need activation to start any reaction whether its endo or exergonic How Do Enzymes Work? o Substrate = A molecule upon which an enzyme acts o Each enzyme has its own substrate o The names of many enzymes end in –ase o Their names can tell us about their functions Usually named for their substances Dnase is an enzyme that breaks down DNA; it hydrolyzes bonds between deoxynucleotides Rnas is an enzyme that breaks down RNA between ribonucleotides; it hydrolyzes bonds between ribonucleotides Nucleases are enzymes that break down nucleic acids by hydrolyzing phosphodiester bonds between nucleotides o Sucrose breaks down sucrose (disaccharide) into glucose and fructose Glucose and fructose are held together by glycosidic bonds Sucrose binds with the active site of sucrose You need hydrolysis to break sucrose Glycosidic bond between glucose and fructose is straight It eventually becomes bent It makes it easier for water to separate glucose from fructose Sucrose can then bind with another sucrose substrate o Enzymes are not consumed in chemical reactions; they are REUSED o Many enzymes are proteins Nucleases are proteins even though they break down nucleic acids Some Catalysts are RNAs o Ribozymes – RNA molecules that catalyze chemical reactions o One of the ribosomal rRNA of the large ribosomal subunit is ribozyme that catalyzes the formation of peptide bonds between amino acids o It is needed for translation (RNA to protein) Factors that Control Enzymes o Temperature Most human enzymes have optimal temperature between 3540 degrees Celsius Specifically 37 degrees Celsius Many of our enzymes are proteins and elevated temperatures cause denatured proteins which make it nonfunctional Thermophilic bacteria like high temperatures Bacteria that live in hot springs have enzymes that operate at 70 degrees Celsius or higher o pH most human enzymes work best at pH 7 which is a neutral environment [H ]=[OH] Pepsin in the stomach works best at pH 2 which is an acidic environment because of the hydrochloric acid [H ]>[OH] Digestive enzymes of lysosomes work best at pH 5 which is a weak acid Trypsin in the small intestine works best at pH 8 which is a weak base [OH]>[H ] + Pepsin and trypsin are proteins themselves that break down proteins Proteases are enzymes that break down proteins by hydrolyzing peptide bonds Factors that Control Enzymes o Inhibitors stop enzymes from working Competitive inhibitor interferes with active site of enzyme so substrate can’t bind It competes with substrates for the enzymes active site C.I. can be overcome by increasing the amount of substrate Noncompetitive inhibitor does not compete with substrate for enzyme’s active site Allosteric inhibitor changes the shape of the enzyme so it can’t bind to the substrate, altering its active site The allosteric site is a site where noncompetitive inhibitor binds to the enzyme Since the active site is altered the substrate can’t bind to the active site preventing a chemical reaction from occurring NC can be overcome by preventing the binding of noncompetitive inhibitor to the enzyme’s allosteric side o Activators help enzymes work better It causes substrate to bind better with the active site Cofactors Inorganic metal ions (iron, zinc, and copper) Organic nonprotein molecules (coenzymes) o Vitamins (B6 and B12) Modified nucleotides (NAD, NADP, and FAD) What is Metabolism? o A total of all chemical reactions carried out in an organism o Anabolic reactions create large molecules from smaller molecules They require energy to happen Photosynthesis Endergonic reactions o Catabolic reactions create smaller molecules from larger ones Release energy Cellular respiration Exergonic reactions Biochemical Pathway o Includes multiple chemical reactions that occur at the same area and the product of one enzyme serves as the substrate for another enzyme o Ex. Glycolysis Positive vs. Negative Feedback o Positive feedback is a process in which final (end) product increases its own production (ex. Release of oxytocin during childbirth) Oxytocin is a hormone that stimulates the contraction of the uterus During labor oxytocin increases its own production by leading to more contractions and further movement of the baby into the birth canal The end product is an activator on the allosteric site o Negative Feedback is a process in which final (end) product inhibits its own production (ex. High concentration of ATP inhibits the production of more ATP) Also known as feedback inhibition It inhibits its own production by inhibiting the enzyme acting early in the pathway End product is a noncompetitive inhibitor Many Biochemical Pathways Need ATP to Work o ATP consists of 5C sugar (ribose), nitrogenous base (adenine), 3 phosphate group (negatively charged) Makes the bonds unstable Each phosphate contain lots of energy When they break they release energy How Does ATP Work? o ATP hydrolysis o Inorganic phosphate can bind to a target molecule and make it phosphorylated Gained energy o ADP hydrolysis use water to make AMP o ATP>ADP>AMP ATP has the most phosphate groups therefore has the most energy Chapter 7: How Cells Harvest Energy Introduction o Cellular Respiration Glucose and oxygen are reactants Carbon dioxide and water are products Cellular respiration is catabolic Exergonic reaction Reactants have more energy than products Glucose is oxidized to carbon dioxide Oxygen is reduced to water Why Do We Need to Eat Plants? o Glycolysis Sugar breaking apart It occurs in the cytoplasm It can happen in the presence or absence of oxygen When oxygen is absent glycogen is followed by fermentation Glucose is broken down into 2 pyruvate (3C sugar) that happens ONLY if oxygen is presence o Pyruvate Oxidation 2 molecules of pyruvate is converted into AcetylCoA (coenzyme A) Occurs in the mitochondrial matrix o Krebs Cycle Occurs in the mitochondrial matrix o Electron Transport Chain (ETC) Is in the inner mitochondrial membrane How to Make ATP? o Substratelevel phosphorylation is a way of making ATP during glycolysis and the Krebs cycle by the enzymatic transfer of phosphate group from a phosphorylated organic substrate directly to ADP o We need ADP, phosphate, and enzyme to make ATP o Kinase transfers phosphate group of one molecule to another o PEP (phosphoenolpyruvate) + ADP pyruvate + ATP (exergonic reaction) ATP Synthase o Oxidative phosphorylation produces the largest amount of ATP and occurs in the inner mitochondrial membrane ATP synthase phosphorylates ADP to form ATP, using energy from a proton (H ) gradient ATP synthase is a transmembrane protein that only enzyme that oxidative phosphorylation needs Found in the inner mitochondrial membrane of eukaryotes and in the plasma membrane of prokaryotes o Some protists don’t have mitochondria but they have ATP synthase so they can still produce ATP How Does ATP Synthase Work? o Proton gradient is created by proton (H ) pumps o Hydrogen pumps = Proton pumps Hydrogen pumps need high energy electrons to function They always pump hydrogen ions from the mitochondrial matrix (where we have less of them) to the intermembrane space (where we have most of them) up (against) their concentration gradients using active transport We have more hydrogen ions in the intermembrane space than the mitochondrial matrix They always pump hydrogen ions from the mitochondrial matrix to the intermembrane space They pump up their concentration using active transport They use energy from electrons to work They create the proton gradient = to an equal distribution of hydrogen ions across the inner mitochondrial membrane (eukaryotes) In protists and bacteria it creates a proton gradient across the plasma membrane o The force of protons diffusing through ATP synthase is used to produce ATP (chemical energy) chemiosmosis o The proton gradient is needed for ATP synthase to work o Hydrogen ions rush through ATP synthase from their intermembrane space to the mitochondrial matrix DOWN their concentration gradients using passive transport (facilitated diffusion) o As hydrogen ions rush through ATP synthase, it physically rotates and combines ADP with inorganic phosphate to make ATP (chemiosmosis) Electron Transport Chain (ETC) o Proton pumps are part of ETC o 3 types of hydrogen pumps NADH dehydrogenase bc com1lex cytochrome oxidase complex o Electrons come from Glycolysis (cytoplasm) Pyruvate oxidation (mitochondrial matrix) Krebs Cycle (mitochondrial matrix) Electron Shuttles: NAD and FAD o NAD (nicotinamide adenine dinucleotide) o FAD (Flavin adenine dinucleotide) o Dehydrogenase are enzymes that transfer hydrogen atoms from 1 molecule to another o Each hydrogen atom = 1 electron and 1 proton o Energy rich molecule has 2 electrons and 2 protons o NAD (coenzyme) and 2 electrons and 1 hydrogen is reduced to NADH o FAD + 2H is reduced to FADH 2 o NADH carries 1 proton o FADH ca2ries 2 protons o NADH and FADH are reduced forms of NAD and FAD + + 2 o NAD and FAD are oxidized forms of NADH and FADH 2 Electron Transport Chain (ETC) o NADH donates electrons to NADH dehydrogenase o Electrons are then taken into ubiquinone (Q = FADH ) an2 delivers it to bc 1 complex o bc complex passes its electrons to cytochrome C and delivers its electrons to 1 cytochrome oxidase complex then reduced into water o FADH is2only produced in the Krebs Cycle because there are no enzymes in other places o Cytochrome oxidase complex cytochrome C which then donates its electrons and water is reduced o ETC: 3 hydrogen pumps and 2 mobile electron carries (Q and cytochrome C) o As electrons move from one molecule to another in the electron transport chain, they lose energy o ETC and chemiosmosis are needed for oxidative phosphorylation to happen Glycolysis o Converts 1 glucose (6C) to 2 pyruvate (3C) o Occurs in the cytoplasm o Net production of 2 ATP molecules (4 ATP produced – 2 ATP consumed = 2 ATP) by substratelevel phosphorylation + o 2 NADH produced by the reduction of 2 NAD o Glycolysis for the most part is an EXERGONIC process The Beginning of Glycolysis o You start with glucose and hexokinase is needed to convert into glucose into glucose 6phosphate Hexokinase transfers phosphate from ATP to C6 of glucose o Glucose6 phosphate has a phosphate group attached to it Phosphoglucose isomerase moves atoms around o Fructose 6phosphate Phosphofructokinase transfers phosphate from ATP to C1 of fructose 6 phosphate o Fructose 1,6biphosphate Dihydroxyacetone phosphate G3P (isomerase is needed) o Isomer same number of elements, atoms, but different arrangement in space o Glucose + 2 ATP = 2 G3P + 2 ADP (endergonic reaction) The Middle of Glycolysis o Glyceraldehyde 3phosphate dehydrogenase removes 2H atoms (2 protons and 2 + electrons) from G3P and transfers 1 proton and 2 electrons to NAD This makes 2 BPG o Phosphoglycerate kinase transfers phosphate from BPG to ADP, forming ATP which creates 2 3PG + o 2G3P + 2NAD + 2P + 2ADP 2 3PG + 2NADH + 2H + 2ATP (exergonic reaction) The End of Glycolysis o 3PG 2PG PEP o Pyruvate kinase transfers phosphate from PEP to ADP, forming ATP o 2 3PG + 2ADP = 2 PYRUVATE + 2 ATP + 2 WATER o Glucose + 2ATP + 2NAD 2 pyruvate + 2ATP +2NADH + 2H + 2 Water o 2 ATP produced so it’s exergonic
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