Supplemental instruction For Dr. Wright’s Bio 7/27 Class Microbial Metabolism Supplemental instruction Fall 2010 For Dr. Wright’s Bio 7/27 Class Designed by Pyeongsug Kim ©2010 sibio@att.net

Metabolism: try the practice questions Metabolism: try the practice questions. Also, we talked about aerobic respiration, anaerobic respiration, and fermentation. Compare and contrast them as follows: Which types of organisms (obligate aerobes, anaerobes, facultative anaerobes, aerotolerant organisms): Utilize glycolysis (and which can’t) Utilize the Krebs cycle (and which can’t) Utilize an electron transport chain/oxidative phosphorylation (and which can’t) Can use a fermentation pathway (and which can’t) Which p[athway produces the most ATP? Which produces the least? Name an electron carrier used in each pathway (for one pathway, there is only one choice)

Designed by Pyeongsug Kim, ©2009 Metabolism : All body’s process that transform energy. Designed by Pyeongsug Kim, ©2009

Designed by Pyeongsug Kim, ©2010 www.science-i.com Picture from http://www.eosremediation.com/support/bioremediation.html Designed by Pyeongsug Kim, ©2010 www.science-i.com

Designed by Pyeongsug Kim, ©2010 www.science-i.com Microbial metabolism -Chemical reaction used for biosynthetic and energy-harvesting process. -to live and reproduce. -Components of metabolic pathways Energy sources ~ Sunlight, Organic or inorganic materials Enzymes ~ Biological catalyst ~ to facilitate the pathways ATP ~ The energy currency of a cell Electron donor ~ e- from energy source Electron carrier Electron acceptor Designed by Pyeongsug Kim, ©2010 www.science-i.com

Designed by Pyeongsug Kim, ©2010 www.science-i.com Chemical reactions in Metabolism: Anabolism A + B + energy  C Form larger molecules; require energy. Reactants Product  + energy Catabolism C  A + B + energy Breaking down into smaller molecules; release energy. Reactant Products  + energy Designed by Pyeongsug Kim, ©2010 www.science-i.com 6 6

Designed by Pyeongsug Kim, ©2010 www.science-i.com Metabolic pathway - A series of sequential chemical reactions. Initial compounds  intermediates  end products - Linear, Branched, Cyclical(eg. TCA Cycle) Picture from Dr.Wright Bio27 class slide Designed by Pyeongsug Kim, ©2010 www.science-i.com

Designed by Pyeongsug Kim, ©2010 www.science-i.com For metabolic process, each chemical reaction in a metabolic pathway needs specific ________. enzyme _______ -Biological catalysts speed up chemical reaction by … lowering activation energy -specific; proteins -sensitive to environmental conditions pH, Temperature, Enzymes Picture from Dr.Wright Bio6 class slide Designed by Pyeongsug Kim, ©2010 www.science-i.com

Designed by Pyeongsug Kim, ©2010 www.science-i.com Energy source or Electron donor - The compounds that are oxidized to release ATP. We inhale oxygen to generate ATP. ________ -donated by the energy source. -transferred to another compound (electron carrier eg. NAD+, FAD2+). Electrons Microorganisms oxidize carbohydrates(eg. glucose) as their primary source of energy. Picture from: http://i.telegraph.co.uk/telegraph/multimedia/archive/01031/news-graphics-2007_1031495a.jpg http://www.biojobblog.com/tags/microbes/ Designed by Pyeongsug Kim, ©2010 www.science-i.com

Designed by Pyeongsug Kim, ©2010 www.science-i.com Energy(or electron) Carriers - NAD+, NADP+, & FAD “Oxydized form” - participate ultimately in ATP synthesis - When electrons are carried… NADH, NADPH, FADH2  “Reduced forms” or “Reducing power” Oxydized form Reduced form Electron carrier Electron © Pyeongsug Kim ___________ generate a proton motive force which can drive ATP synthesis used in Biosynthesis (eg. Pentose Phosphate Pathway, Photosynthesis) NAD+, FAD NADP+ Terminal electron acceptor Aerobes – O2 Anaerobes – Inorganic molecules other than O2 Fermenters – Organic molecules Designed by Pyeongsug Kim, ©2010 www.science-i.com

Designed by Pyeongsug Kim, ©2010 www.science-i.com Precursor metabolites - metabolic intermediates (links) in anabolic and catabolic pathway. e.g. pyruvates, Glucose 6-phosphate, Acetyl-CoA, … - Used to generate ATP (catabolic) - Used to synthesize subunits of macromolecules (anabolic) Picture from: http://i.telegraph.co.uk/telegraph/multimedia/archive/01031/news-graphics-2007_1031495a.jpg Designed by Pyeongsug Kim, ©2010 www.science-i.com

Designed by Pyeongsug Kim, ©2010 www.science-i.com Three key metabolic pathways 1) Glycolysis -produce pyruvates. -produce reducing power. -produce 6 precursor metabolites -2 ATPs are produced. 2) Krebs cycle(TCA Cycle) -require transition step(3carbons  2carbons) = pyruvates(3C)  acetyl-CoA(2C) -produce 2 precursor metabolites 3) Respiration or ETC -oxydative phospholylation -Uses reducing power -Terminal electron acceptor(TEA) : oxygen, nitrate, carbon dioxide or other inorganic molecule, pyruvate  regenerate electron carriers. (NADH  NAD+, FADH2 FAD) -Lots of APTs!!! Picture from Dr.Wright Bio27 class slide Designed by Pyeongsug Kim, ©2010 www.science-i.com

Designed by Pyeongsug Kim, ©2010 www.science-i.com Glycolysis -Occur in _________________. -Glucose needs to be traped!  Glucose 6-phosphate 1C6H12O6  2 ________ + 2 ____ + 2 _______ 1glucose + 2NAD + 2ADP + 2Pi  2 pyruvates + 2NADH + (2H+)+ 2 ATP - Oxygen required? (Yes / No) Cytoplasm(Cytosol) - produce ____________. - NAD  NADH (reduced / oxidized). 2 pyruvic acids Pyruvates ATP NADH *All cells undergo glycolysis!!!. -used in aerobic, anaerobic, & fermentation. Designed by Pyeongsug Kim, ©2010 www.science-i.com

Designed by Pyeongsug Kim, ©2010 www.science-i.com Pentose phosphate pathway :alteranated glycolysis - commonly used to make 5-carbon sugars. -NAPDH(reducing power) produced for biosynthesis -Produce 2 precursors Mostly 5C-phosphate used synthesis of nucleotide (nucleic acids) 4C-phosphate used synthesis of amino acids -But, no ATP Designed by Pyeongsug Kim, ©2010 www.science-i.com

Designed by Pyeongsug Kim, ©2010 www.science-i.com After glycolysis… In presence of oxygen - Pyruvic acids enter ___________ in eukaryotes.  converted to __________ there.  Kerbs Cycle(TCA)! mitochondria Acetyl-CoA Copyright © The McGraw-Hill Companies, Inc. Kerbs Cycle(TCA) Aerobic, anaerobic respiration (but not fermentation) -Circular pathway -Completes the oxidation of glucose Produce…. Reducing power –NADH, FADH2 2 ATPs & 2 precursors. Designed by Pyeongsug Kim, ©2010 www.science-i.com

Designed by Pyeongsug Kim, ©2010 www.science-i.com Citric acid cycle = Tricarboxylic acid(TCA) cycle =Krebs cycle Where does Kerbs Cycle(TCA) occur? In Eukaryotic cell… Mitochondria In Prokaryotic cell… Cytoplasm Designed by Pyeongsug Kim, ©2010 www.science-i.com

Designed by Pyeongsug Kim, ©2009 Glycolysis and Krebs cycle In respiring cells. Glycolysis - in all organisms. - aerobic respiration, anaerobic respiration, fermentation - produce pyruvates, ATPs. - reducing power: NADH Krebs(TCA) cycle - aerobic respiration, anaerobic respiration - Convert pyruvate to acetyl-CoA - more ATPs than glycolysis - reducing powers: NADH, FADH2 Designed by Pyeongsug Kim, ©2009

Designed by Pyeongsug Kim, ©2010 www.science-i.com NADH, FADH2 -RNA coenzyme (derived from Vitamin) - ________________ -Used to temporarily store energy within the cell electron carrier NAD    NADH (Reduced/Oxidized) : at Glycolysis, Krebs cycle  NADH    NAD (Reduced/Oxidized)  : at ETC ( Electron Transport Chain )  Carried to ETC *The more reduced  =  the more energy it holds. Reduced coenzymes carry high-energy electrons to proton pumps where ATP is then made( ETC). Designed by Pyeongsug Kim, ©2010 www.science-i.com

Designed by Pyeongsug Kim, ©2010 www.science-i.com Respiration -Oxydative phosphorylation or ETC -used reducing powers(NADH, FADH2) made in glycolysis and TCA. -ETC(electron transport chain) ~ proton motive force by proton pumps  drive ATP synthase to produce ATP. Aerobic respiration - oxygen as a TEA -aerobes, facultative anaerobes(under O2 presence) -Most efficient at generating ATP Anaerobic respiration - inorganic molecule (not O2) as a TEA : NO3- (nitrate), (e.g., CO2, S, SO4-, NO3- or NO2-) -different electron carriers - Methanogens, sulfur bacteria, … Designed by Pyeongsug Kim, ©2010 www.science-i.com

Designed by Pyeongsug Kim, ©2010 www.science-i.com Electron transport chains(oxidative-phospholyration) -Redox reactions; transfer electrons from an electron donor to an electron acceptor. -NADH, FADH2 (proton motive force) is used to synthesize ATP. In aerobic respiration Electron carriers ~ NADH, FADH2 Final electron acceptors ~ O2 (Oxygen!) In anerobic respiration Alternative electron carriers Final electron acceptors ~ inorganic molecules(not O2)  NO3- (nitrate), (e.g., CO2, S, SO4-, NO3- or NO2-) Eukaryotes -In inner mitochondrial membrane Prokaryotes -In plasma membrane Designed by Pyeongsug Kim, ©2010 www.science-i.com

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Designed by Pyeongsug Kim, ©2010 www.science-i.com Cellular aerobic respiration (4 step) Glycolysis  (The transition step)  Krebs cycle (Citric Acid Cycle)  The electron transport system Final electron acceptor - oxygen Designed by Pyeongsug Kim, ©2010 www.science-i.com

Designed by Pyeongsug Kim, ©2010 www.science-i.com Cellular anerobic respiration (4 step) Glycolysis  (The transition step)  Krebs cycle (Citric Acid Cycle)  The electron transport system Final electron acceptor – inorganic molecule (not oxygen!) Designed by Pyeongsug Kim, ©2010 www.science-i.com

Designed by Pyeongsug Kim, ©2010 www.science-i.com In Eukaryotic cells… Designed by Pyeongsug Kim, ©2010 www.science-i.com

Designed by Pyeongsug Kim, ©2010 www.science-i.com Picture from http://faculty.irsc.edu/FACULTY/TFischer/micro%20resources.htm Designed by Pyeongsug Kim, ©2010 www.science-i.com

Designed by Pyeongsug Kim, ©2010 www.science-i.com Fermentation - Neither aerobic or anaerobic respiration - incomplete oxidation of a carbohydrate - Organic molecule(eg.pyruvate) as TEA!! - facultative anaerobes (under lack of O2 or inorganic molecule ) obligate fermenters (never use O2) - use Glycolysis and additional step. - Only 2 ATPs - NO TCA(Krebs) Cycle! NO ETC! Lactic Acid Fermenation - Food Spoilage - Food Production Yogurt from Milk Pickles, Kimchi Alcohol Fermentation -end product ~ alcohol,CO2 Alcoholic Beverages, Bread… Designed by Pyeongsug Kim, ©2010 www.science-i.com

Designed by Pyeongsug Kim, ©2009 Obligate fermenters - organic molecule as TEA - get their ATP from glycolysis - lactic acid bacteria, aerotolerants Different organisms can ferment different sugars. Commercially useful useful in identification Picture from Dr.Wright Bio27 class slide, http://www.sciencedaily.com/releases/2006/10/061017091752.htm# Designed by Pyeongsug Kim, ©2009

Designed by Pyeongsug Kim, ©2009 Identification of fermenter - Different organisms can ferment different sugars. Picture from http://www.mc.maricopa.edu/~johnson/labtools/Dbiochem/kiaa.jpg http://web.clark.edu/tkibota/240/Unknowns/PR_Carb.htm Designed by Pyeongsug Kim, ©2009

Designed by Pyeongsug Kim, ©2009 Prokaryotes: whole process occurs in cytoplasm. Since don’t have organelles(mitochondria). Eukaryotes: Oxidative decarboxylation of pyruvate (pyruvate  Acetyl-CoA) is required in process of getting into the mitochondrion (where Krebs cycle occurs) Picture from http://www.nslc.wustl.edu/courses/Bio2960/labs/04Microscopy/index.html Designed by Pyeongsug Kim, ©2009

Designed by Pyeongsug Kim, ©2009 Electron transport chain -for aerobes; aerobic respiration. - Oxidative phosphorylation : NADH, FADH2 (proton motive force) is used to synthesize ATP. Eukaryotes -In inner mitochondrial membrane Prokaryotes -In plasma membrane Picture from Dr. Wright Bio27 class slides Designed by Pyeongsug Kim, ©2009

Designed by Pyeongsug Kim, ©2010 www.science-i.com Aerobic respiration - terminal electron acceptor is ______. ( most / least) efficient at generating ATP -Obligate aerobes, Facultative anerobes(if O2 presence) Anaerobic respiration - terminal electron acceptor is ____________ (e.g., CO2, S, SO4-, NO3- or NO2-, But Oxygen(O2)) ( less / most ) efficient than aerobic respiration -Methanogens, sulfur bacteria, … Fermentation - terminal electron acceptor _____________. (e.g. pyruvate) - Do not use Krebs cycle (most / least) efficient at generating ATP -Facultative anerobes(if O2 absent) E.Coli oxygen inorganic molecule organic molecule Designed by Pyeongsug Kim, ©2010 www.science-i.com

Designed by Pyeongsug Kim, ©2010 www.science-i.com Aerobic respiration is the most efficient at generating ATP. Fermentation is the least efficient at generating ATP. Designed by Pyeongsug Kim, ©2010 www.science-i.com

Designed by Pyeongsug Kim, ©2010 www.science-i.com Phototrophs - Photosynthetic(Energy from sunlight) - Produce sugars(glucose)  consumed by chemoorganotrophs. -Photosynthesis Chemical energy is used to reduce CO2 to sugar (CH2O) Carbon Fixation - recycling of carbon in the environment. - Oxygenic phototrophs Green Plants, Algae, Cyanobacteria - Anoxygenic phototrophs Archaea, Green bacteria, Purple bacteria -Primary producers Picture from Dr.Wright Bio27 class slide, http://www.thedailygreen.com/healthy-eating/eat-safe/xtreme-eating-awards-50060309 Designed by Pyeongsug Kim, ©2010 www.science-i.com

Designed by Pyeongsug Kim, ©2010 www.science-i.com Lithotrophs -“Rock-Eaters” - Energy(Electron donor) source from inorganic molecules. H2, H2S, Fe2+, NH4+ -Use CO2 for carbon (autotrophs) (usually) - Methanogens Lithotrophs(archaea) at hydrothermal vents Iron oxidizing bacteria some nitrogen fixers Picture from http://www.nature.com/nature/journal/v417/n6885/full/417137a.html Designed by Pyeongsug Kim, ©2010 www.science-i.com

Designed by Pyeongsug Kim, ©2010 www.science-i.com Chemoorganotrophs(heterotrophs) - generate energy by degrading organic compounds. -Consumers, decomposers. We are chemooranotrophs. We are eating organic compounds (made by phototrophs) to generate ATP. Picture from Dr.Wright Bio27 class slide, http://www.thedailygreen.com/healthy-eating/eat-safe/xtreme-eating-awards-50060309 Designed by Pyeongsug Kim, ©2010 www.science-i.com