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Chapter 6 and 7 (through Feb. 10)

by: Michelle Notetaker

Chapter 6 and 7 (through Feb. 10) Bio 1510

Marketplace > Wayne State University > Biology > Bio 1510 > Chapter 6 and 7 through Feb 10
Michelle Notetaker
GPA 3.4

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About this Document

Chapter 6 and a portion of 7 notes from this week's lecture.
Basic Life Mechanisms
Dr. Nataliya Turchyn
Class Notes
Wayne State University, Turchyn, BIO 1510, notes, chapter 6, chapter 7
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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.


Reviews for Chapter 6 and 7 (through Feb. 10)


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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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