Microbial Metabolism

Microbial Metabolism

1. A. Basic Concepts of Metabolism

   • 1. Definitions
     • -Metabolism:The process of catabolism and anabolism - Catabolism: The process by which living organism obtains energy and raw materials from nutrients CATS EAT AND USE FOOD FOR ENERGY - Anabolism: The process by which energy and raw materials are used to build macromolecules and cellular structures (biosynthesis) ANTS TINY AND BUILD
   • 2.Reduction & Oxidation
     • a) An atom is REDUCED when is undergoes a chemical reaction in which it - Gains electrons - By bonding to a less electronegative atom - And often this occurs when the atom becomes bonded to a hydrogen b) An atom is OXIDIZED when it undergoes a chemical reaction in which it - Losses electrons - By bonding to a more electronegative atom - And often this occurs when the atoms become bonded to an oxygen c) In metabolic pathways, we are often concerned with CARBON d) REDUCED forms of Carbon carry a great deal of potential chemical energy in their bonds (hydrocarbons, methane,fats,carbohydrates, alcohols) e) OXIDIZED forms of Carbon carry very little potential chemical energy in their bonds (ketones, aldehydes, carboxylic acids, carbon dioxide f) R & O always occur together. The thing that gets reduced is the electron acceptor the thing that gets oxidized is the electron donor  (DO, AR)
   • 3. Enzymatic Pathways for Metabolism
     • a) Step-wise in which raw materials are rearranged, often one at a time, until the formation of the final product takes place b) Each step requires its own enzyme c) The sequence of steps from raw to final end products is called an enzymatic pathway (or metabolic pathway)
   • 4. Cofactors for Redox Reactions
     • a) Enzymes that catalyze redox reactions typically require a cofactor to shuttle electrons from one part of the metabolic pathway to another part.
     • b) There are two main cofactors: NAD and FAD, they are small organic molecules in which part of the structure can either be reduced( accept) or oxidized(donate)
     • NAD(ox)+H+Pair of Electrons--> NADH(reduced)
       • NAD is accepting a pair of electrons and becomes reduced turing into NADH If NADH were to donate its electrons it would become oxidized and turn into NAD
     • FAD(ox)+H+Pair of Electrons--> FADH(reduced)
   • 5. ATP: "A currency of energy" for many cellular reactions"
     • a)ATP is a nucleotide with three phosphate groups linked together in a small chain b)The last phosphate in the chain can be removed by hydrolysis where ATP becomes ADP (This is energetically favorable with a G of -7.5kcal/mol ATP+H2O--> ADP+Phosphate+ Energy(7.5 kcal/mol) c)ATP hydrolysis is used as an energy source in many biological reactions that require energy (e.g. active transport in sodium potassium pumps) d) During catabolism, energy released from oxidation of carbon is captured and used to synthesize ATP from ADP and phosphate
     • C6H12O6 + 6O2--> 6CO2+ 6H2O+ ENERGY
     • ADP+ Phosphate+ Energy--> ATP +H2O

2. B. Glycolytic Pathways

   • 1. Features of a Glycolytic Pathway
     • a) Partial oxidation of glucose to form pyruvic acid b) A small amount of ATP is made c) A small amount of NAD is reduced to NADH
   • 2. 4 major glycolytic pathways found in different bacteria
     • a) Embden-Meyerhoff Parnas pathway
       • Glucose--> 2 Glyceraldhyde-->Pyretic Acid, NADH, ATP
     • b) Pentose phosphate pathway
       • Glucose--> Phosphglutonate-->5-C, 4-C, 7-C, 3-C, 6-C--> Pyretic Acid, NADH, ATP
     • c)Enther-Doudoroff pathway
       • Glucose--> Phosphoglutonate-->Glyceraldehyde+Pyrivic Acid--> Pyrivic Acid, ATP, NADH
     • d) Phosplhoketolase pathway
       • Glucose--> Phosophogluctonate--> 5C Intermediate, CO2--> CoA Glyceraldhyde-->Pyrivic Acid NADH ATP

3. C. Fermentation

   • 1. Features of Fermentation
     • a) Pyretic acid is reduced to form reduced organic acids or alcohols.
     • b)The final electron acceptor is a reduced derivative of pyruvic acid
     • c) NADH is oxidized to form to form NAD: Essential for continued operation of the glycolytic pathways
     • d) O2 is not required
     • e) No additional ATP are made
     • f) Gasses (CO2 and/or H2) may be released
   • 2. Fermentation pathways are useful as tools in biochemical identification
   • 3. Also used in industry: Synthesis of certain organic compounds.
   • 4. Examples of Fermentation Pathways
     • a) Lactic Acid Fermentation: Found in bacteria; e.g. Streptococcus cremoris, Lactobacillus acidophilus
     • b) Mixed Acid Fermentation: e.g. E. coli, Basis of the methyl red test
     • c) 2,3-Butanediol Fermentation: e.g. Enterobacter aerogenes or E. cloacae, Basis of the Voges-Proskauer reaction
     • d) Important Endproducts
       • Ethanol via Saccharomyces cerevesiae
       • Propanoic Acid via Propionibacterium
       • Acetone, buteraldehyde, and butanol via Clostridium Acetobutylicum

4. D. Respiration

   • 1. Features of Respiration
     • a) Pyrivic acid is oxidized completely to CO2 b) The final electron acceptor is usually an inorganic substance c) NADH is oxidized to form NAD: Essential for continued operation of the glycolytic pathways d) O2 may or may not be required (AEROBIC: O2 is the final e- acceptor) (ANAEROBIC: A substance, usually inorganic, other than O2 is the accepts (eg nitrate, nitrite, sulfate) e) A lot of additional ATP are made (up to 36 per glucose molecule)
   • 2. Stages of Respiration
     • a) Preliminary reactions and the Krebs Cycle (TCA or Citric Acid Cycle b) Respiratory electron transport

5. E. Photosynthesis

   • a) Light-Dependent Photosynthesis
     • -Light energy is harvested by photosynthetic pigments and then transferred to special reaction center chlorophyll molecules -The light energy is used to strip electrons from an electron donor (the electron donor goes from a reduced to an oxidized state) -The electrons are shuttled through a series of electron carriers from high to low energy states -During this process ATP is formed -In the cyclic pathway of electron transport, electrons are returned to the ETC - In the non-cyclic pathway the electrons are used to reduce NAD (or NADP) to NADH or (NADPH)
   • b) Light-Independent Photosynthesis
     • -ATP and NADH (NADPH) from the light dependent reactions are used to reduce CO2 to form organic carbon compounds (carbon fixation) -The reduced organic carbon is usually converted into glucose or other carbohydrates
   • 2. Oxygenic photosynthesis
     • a) Cyanobacteria (blue-green algaeO and eukaryotic chloroplasts b) Electron do not is H2O: Oxidized to form O2 c) Two photosystems: PSII and PSI d) Major Function is to produce NADPH and ATP for the carbon fixation pathways
   • 3. Anoxygenic photosynthesis
     • a) Found in:  - Green sulfur bacteria (Chlorobium) - Green non-sulfur bacteria (Chloroflexus) - Purple sulfur bacteria (Chromatium) - Purple non-sulfur bacteria (Rhodobacter) b) Electron donors vary: - H2S or S0 in the green and purple sulfur bacteria - H2 or organic compounds in the green and purple non-sulfur bacteria c) Only ONE photosystem - In green bacteria, the photosystem is similar to PSI -In purple bacteria the photosystem is similar to PSII d) PRIMARY function is ATP production, chiefly via cyclic photophosphorylation

6. F. Chemolithotrophy

   • 1. Features of Chemolithotrophy
     • a) Electrons are removed from a reduced inorganic electron donor b) The electrons are passed through a membrane bound electron transport pathway, often coupled by the synthesis of ATP and NADH c) The electrons are ultimately passed to a final electron acceptor d) ATP and NADH may be used to convert CO2 to carbohydrate
   • 2. Examples of Electron Donors
     • a) Ammonia (NH4)-->Nitrite (NO2) in Nitrosomonas b) Nitrite (NO2)--> Nitrate (NO3) in Nitrobacter c) Hydrogen sulfide (H2S)--> Sulfur (S0) in Thiobacillus and Beggiatoa d) Sulfur (S0)--> Sulfate(SO4) in Thiobacillus e) Hydrogen(H2)--> Water (H2O) in Alcaligenes
   • 3. Examples of Electron Acceptirs
     • a) Oxygen--> Water in many organisms b)Carbon Dioxide (CO2--> Methane( CH4) in the methanogenic bacteria/ archaea

7. G. Nitrogen Cycle

   • 1. Mineralization
     • -Organic nitrogen (mostly amino acids)--> NH4 (All organisms)
   • 2. Nitrification
     • Oxidized: NH4-->NO2 (Nitrosomonas) NO2-->NO3 (Nitrobacteria)
   • 3. Dentrification
     • Reduction: NO3-->N2O N2O-->N2 (several species, Pseudomonas and Bacillus)
   • 4.Assimilatroy Nitrate Reduction
     • NO3--> Organic Nitrogen (Many microbial species and plants)
   • 5. N2 Fixation
     • N2--> NH4 Free Living nitrogen fixers (Azotobacter and Aospirillum) Symbiotic nitrogen fixers (Rhizobium and Bradyrhizobium, Cyanobacteria attached to the cordgrass plant Spartina in salt marshes