Week 2: Lecture/Reading Notes 3 & 4
Week 2: Lecture/Reading Notes 3 & 4 Bio Sci 152
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This 14 page Class Notes was uploaded by KelseyH on Friday September 18, 2015. The Class Notes belongs to Bio Sci 152 at University of Wisconsin - Milwaukee taught by Dr. Daad Saffarini, Dr. Erica Young, Dr. Jane Witten in Fall 2015. Since its upload, it has received 77 views. For similar materials see Foundations of Biological Sciences II in Biological Sciences at University of Wisconsin - Milwaukee.
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Date Created: 09/18/15
Biological Sciences 11 B10 SCI 152 9915 Reading Covered in These Notes 2nd edition pages 106116 119121 1 edition pages 100111 113118 Last Lecture Notes Cell Structure and Function Lecture 3 Outline The Prokaryotes Metabolic Diversity The Prokaryotes Metabolic Diversity 1 Collection and Storage of Chemical Energy a ATP and Coenzymes i ATP Energy ii Redox Reactions iii NADH amp ATP b Carbohydrate Catabolism with Oxygen i Glycolysis ii Citric Acid Cycle iii Oxidative Phosphorylation iv Chemiosmosis c Carbohydrate Catabolism without Oxygen d Photosynthesis Chemical Reaction i Light Energy Absorption ii Photochemical Change Collection and Storage of Chemical Energy ATP and Coenzymes Energy is gathered in the bonds of molecules when the chemical bonds are broken the energy that was stored up is then released 1Page Biological Sciences 11 B10 SCI 152 9915 Five principles of metabolic pathways 1 Chemical transformation happens in a set of prompt and independent reactions which create a metabolic pathway Reactions call for precise enzymes All organisms have similar metabolic pathways Eukaryotes have compartmental metabolic pathways 91 Enzymes control the metabolic pathways 0 Exergonic reactions release energy reaction normally doesn t require energy and is spontaneous o Endergonic reactions require energy to be performed and absorb energy reaction is not spontaneous These two reactions are regularly performed at the same time and place Cells use adenosine triphosphate ATP as energy to power their cell processes and chemical reactions 0 Molecules like reactions can also be coupled o A commonly coupled pair are coenzymes ATP and nicotinamide adenine dinucleotide NADH 0 ATP is formed from adenosine diphosphate ADP and hydrogen phosphate Pi 0 Energy from exergonic reactions is gathered in bonds when ATP is created I ATP can be hydrolyzed broken down in different locations around the cell releasing free energy for other reactions Processes that require free energy 0 Active transport 0 Condensation reactions 0 Motor proteins 2Page Biological Sciences 11 B10 SCI 152 9915 ATP molecule is built from a nitrogen containing base adenine bonded to ribose which is bonded to a series of three phosphate groups Phosphate Groups Adenine HI OH Hydrolysis reaction produces free energy 0 ATP H2O ADP Pi free energy exergonic reaction 0 The energy released comes from the P 0 bond breaking Redox Reactions The act of transferring electrons is also a way to transfer energy 0 When one substance transfers one of more electrons to another substance energy is transferred this reaction is referred to as a redox reaction or reduction oxidation reaction 0 An atom ion or molecule gain one or more electrons is a reduction o The loss of one or more electrons is a oxidation 0 Reduction and Oxidation ALWAYS happen together o Molecules are oxidizing agents and reducing agents 3Page Biological Sciences 11 B10 SCI 152 9915 0 Hydrogen atoms are transferred along with electrons in reactions H H e39 0 Example Molecule becomes oxidized when hydrogen atoms are lost 0 More reducedmore energy stored in covalent bonds Coenzyme nicotinamide adenine dinucleotide gNAD is used by cells as an electron carrier in redox reactions 0 Nicotinamide adenine dinucleotide has two chemical forms 0 NAD is oxidized I Oxidation reaction NADH H 12 02 gt NADJr H2O Oxygen is extremely electronegative and accepts electrons from reduced NADH Oxygen acts as oxidizing agent Highly exergonic releasing energy 0 NADH is reduced I Reduction reaction NADJr H 2e39 gt NADH NADJr reduction is remarkably endergonic electrons do not stay with NADH transfer of a proton H and two electrons released by coupled oxidation reaction 0 Oxidation of NADH releases more energy than ATP hydrolysis o NADJr is an electron carrier 0 Other carriers I Flavin adenine dinucleotide FAD glucose metabolism I Nicotinamide adenine dinucleotide phosphate NADP used in photosynthesis NADH amp ATP NADH oxidation and ATP production are coupled these are key coenzymes 4Pag Biological Sciences 11 B10 SCI 152 9915 0 Catabolism releases energy by oxidation 0 ATP provides energy to processes that need energy anabolism Carbohydrate Catabolism with Oxygen Cellular respiration series of metabolic reactions used by cells to collect energy from food Chemical energy released from full oxidation of glucose to CO2 Glucose 602 gt 6CO2 6H2O energy 686 kcal per mole of glucose See g 66 EnergyReleasing Metabolism Pathways 2nd edition page 109 1 edition page 107 g 69 Catabolism of glucose under aerobic conditions with oxygen goes through three connected biochemical pathways 1 Glycolysis six carbon monosaccharide glucose converts into two three carbon molecules of pyruvate 2 Pvruvate oxidation two three carbon molecules of pyruvate are oxidized to two two carbon molecules of acetyl CoA and two molecules of C02 3 Citric acid cvcle two two carbon molecules of acetyl CoA are oxidized to molecules of C02 Glycolysis o Takes place in the c osol o Glycolysis has two stages 0 Energyinvesting reactions consuming energy from ATP 0 Energv harvesting reactions producing ATP and NADH o idation reduction at the end of glycolysis is an exergonic reaction that traps energy forming NADH by the reduction of NADJr o Substratelevel phosphorvlation at the end of glycolysis is an exergonic reaction transfers a phosphate from a substrate to ADP which then forms ATP 5Pase Biological Sciences 11 B10 SCI 152 9915 Following glycolysis 1 glucose gt 2 pyruvate 2 ATP 2 NADH o Pyruvate gets oxidized forming acetate and C02 o Acetate binds with Coenzyme A producing acetyl CoA which can then move on to the citric acid cycle Citric Acid Cycle Once the 2 pyruvate are converted to 2 acetyl CoA groups they then enter the mitochondrion where they go through a series of reactions 0 The cycle functions twice once for each pyruvate that enters the cycle The following reactants generate the following products from the citric acid cycle 0 2 acetyl CoA gt 4 C02 6 NADH 2 FADH 2 ATP Oxidative Phosphorylation Electrons generated from the oxidation of NADH are used to move protons H across the inner mitochondrial membrane making a ow gradient across the membrane 0 Proteins called the electron transport proteins allow electrons to move protons H across the inner mitochondrial membrane to the inner membrane space 0 The electrons aid protons H to connect and bind with 02 to form H20 Reactants and products 0 6NADHH ZHUHIOz 26ATPEhO Chemiosmosis See g 69 Electron Transport and ATP Synthesis in Mitochondria 2nd edition page 112 1 edition page 109 g 612 6Page Biological Sciences 11 B10 SCI 152 9915 The gradient produced from the electron transport proteins yields a higher concentration of protons on one side of the semipermeable membrane and a lower concentration on the other 0 Chemiosmosis is the movement of these ions across that barrier o 90 of ATP in aerobic respiration is created from chemiosmosis oxidative phosphorylation ATP svnthase are molecular motor enzymes that use potential energy and function as an H channel 0 The H ions that travel through the channel meet ADP and Pi at binding sites on the ATP synthase and form ATP Carbohydrate Catabolism without Oxygen Anaerobic respiration operates in the absence of oxygen 0 Without oxygen ATP is created through fermentation a metabolic reaction that converts glucose to acid or alcohol 0 Fermentation is used by bacteria and veast o Fermentation that produces lactic acid can also take place in oxygg deprived muscle cells 0 Fermentation oxidizes glucose in glycolysis and just like aerobic respiration ends with 2 pyruvate 0 After 2 pyruvate are made fermentation can go one of two ways 0 Two types of fermentation 1 Lactic acid fermentation 1 glucose 2 ADP 2 Pi gt 2 lactic acid 2 ATP I End product is lactic acid 7Pase Biological Sciences 11 B10 SCI 152 9915 2 Alcoholic fermentation 1 glucose 2 ADP 2 Pi gt 2 ethanol 2 CO2 2 ATP I End product is ethyl alcohol o For all types of fermentation the end product is only 2 ATP the 2 ATP generated from glycolysis Photosynthesis Chemical Reaction Light Energy Absorption Photosynthesis uses is used by autotrophs to convert light energy into useable chemical energy for the organism o Photosynthesis 6 C02 6 H20 1 glucose C6H1206 6 02 Photosynthesis uses two pathways 1 Light reactions the pathway that uses light energy and converts it into chemical energy in the form of ATP a The electron carrier in this reaction is NADPH similar to NADH but with an extra phosphate group 2 Carbonfixation reactions this pathway uses the NADPH and ATP created in the light reaction and adds it to CO2 to form carbohydrates Light is a form of radiant energy or electromagnetic radiation that is transmitted in wavelengths 0 Short wavelengths have more energy than long wavelengths o The longer the wavelengths the less energy it possesses o The shorter the wavelength the more energy it possesses 0 Light wavelengths are measure and placed on an electromagnetic spectrum which details the complete range of wavelengths of all radiation 8Page Biological Sciences 11 B10 SCI 152 9915 0 This include in order from longest little energy to shortest greater energy wavelength I Radio Microwaves Infrared Visible Ultraviolet X ray Gamma ray Cosmic rays 0 Ligm also travels in groups of particles bundles of light energy known as photons o Organisms that use photosynthesis take in photons in order to collect my to fuel their metabolic processes 0 There are three outcomes when a pho comes in contact with a molecule 1 Photon is scattered or re ected from bouncing off the molecule 2 Photon is transmitted by going through the molecule 3 Photon is absorbed by the molecule which grants the molecule energy Plants are able to absorb wavelengths through their colored pigments 0 Plants can absorb white light which contains all colors and wavelengths of visible light and re ects back to us the color that cannot be absorbed o This is why most plants appear green to us all colors are absorbed except green 0 Chlorophvll is a pigment that can absorb red and blue light and re ects green Photochemical Change A Dhotosvstem is an extensive multi protein complex that extends over the thylakoid membrane in the chloroplasts this complex contains antenna systems and reaction center 0 Antenna systems or ght harvesting complei are the pigments in photosynthetic organisms that absorb energy 9Page Biological Sciences 11 B10 SCI 152 9915 lolPagc Biological Sciences 11 B10 SCI 152 91115 Reading Covered in These Notes 2nd edition pages 389390 394396 1 edition pages 371383 Last Lecture Notes Outline The Prokaryotes Metabolic Diversity Lecture Notes 4 Outline The Prokaryotes Metabolic Diversity Ecology The Prokaryotes Metabolic Diversity Ecology 1 Prokaryotic Diversity Ancient Origins a Euryarchaeotes b Archaea Lineage 2 Ecological Communities a Prokaryote Metabolic Pathways b Element Cycling Prokaryotic Diversity Ancient Origins Euryarchaeotes Methanogens are a species of euryarchaeota that generate methane CH4 from reduced CO2 0 80 90 of the methane that is in the atmosphere originated in methanogens o 2 billion tons of methane is released by methanogens per year 0 1 3 of the methane comes from the guts of ruminants animals that take up nutrients from digesting plant based food through fermentation in their compartmented stomach o The methane produced adds up and increases the amount of methane in earth s atmosphere by 1 each year Extreme halophiles salt lovers take residence in ONLY really salty enviornments 0 These archaea have pink carotenoid pigments 1Page Biological Sciences 11 B10 SCI 152 91115 0 The bright pink color makes them easy to spot 0 Extreme halophiles live in the Dead Sea and in brines o Colonies of extreme halophiles can be seen on pickled fish 0 EH use photosynthesis to capture light energy and convert it into ATP without chlorophyll 0 They do this by using a retinal pigment called microbial rhodonsin and protein Thermoplasma archaea that live in coal deposits 0 No cell wall 0 Acidophilic o Thermophilic 0 1000000 bp genome Archaea Lineages Achaea that are not well recognized are korarchaeotes and thaumarchaeotes o Thaumarchaeotes have a part in the nitrogen cycle 0 Oxidation of ammonia Nanoarchaeota were found in a hydrothermal deep sea vent o Organism is parasitic and lives on the cells of I gnicoccus crenarchaeote Ecological Communities Prokaryote Metabolic Pathways Bacteria and archaea are more diverse metabolically that eukaryotes 2Page Biological Sciences 11 B10 SCI 152 91115 Oxygen is poisonous to some prokaryotes these organisms survive only by anaerobic metabolism o Obligate anaerobes are organisms that are harmed by oxvgen o Facultative anaerobes can go back and forth using both aerobic and anaerobic metabolism 0 Aerotolerant anaerobes are organisms that are not sensitive to oxygen but can t use aerobic respiration o Obligate aerobes cannot live without the presence of oxygen and conduct cellular respiration Photoautotrophs are organisms that can use photosynthesis use CO2 as a carbon source and light as an energy source 0 Examples cyanobacteria proteobacteria Photoheterotrophs are organisms that ingest organic compounds made by other organisms to take in carbon atoms and also use light as their energy source Chemoautotrophs use oxidization of inorganic substances as an energy source and use CO2 as their carbon source 0 Examples archaea Chemoheterotrophs gather both their energy and carbon fix from complex organic compounds synthesized by other organisms 0 Examples of chemoheterotrophs can be found in every domain Both chemoautotrophs and chemoheterotrophs fall under the category chemolithotrophs organisms that get their energy from oxidation of reduced inorganic compounds and use CO2 as their source of carbon Element Cycling Prokaryote metabolic processes move many elements through the ecosystem BIPa Biological Sciences 11 B10 SCI 152 91115 0 A lot of prokaryotes are decomposers which ingest decomposing organic material and cycle back inorganic substances into the environment o Fungi plays a part in recycling carbon back into the atmosphere as CO2 Nitrogen and sulfur are used as electron acceptors in prokaryotes o Denitrifiers dispense nitrogen into the environment as nitrogen gas N2 o 2 N0339 me 12 H gt N2 6 H20 0 Nitrogen fixers convert the N2in the atmosphere into ammonia that can be used by other nitrogen fixers and other organisms 0 N2 6 H gt 2 NH3 o Nitrifiers are chemoautotrophic bacteria that oxidize ammonia into nitrate 0 Examples Nitrosomonas and Nitrosococcus convert ammonia NH3 into nitrite ions NOz39 4Pagg
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