630 Microbiology for Teachers

Nutrition and Metabolism

Nutrition

The following substances are required for growth of some or all microbes:

• Macronutrients:
  • carbon (C) is obtained from carbon dioxide (lithotrophs and phototrophs) or from organic compounds (organotrophs)
  • hydrogen (H) is obtained from the environment via hydrogenase or from organic compounds
  • oxygen (O) is obtained from the atmosphere as well as from inorganic and organic compounds which are readily available in the environment
  • nitrogen (N) is obtained from nitrogen fixation, nitrate reduction or nitrogen-containing organic compounds
• Minor macronutrients are obtained primarily from inorganic sources:
  • phosphorus (P) is a component of lipids, nucleic acids and coenzymes
  • sulfur (S) is used in two amino acids and can be an energy source
  • potassium (K) issued to activate certain enzymes and to prevent dehydration (via binding to acidic proteins) by Halobacteria
  • magnesium (Mg) is used to stabilize ribosomes as well as to bind ATP to enzymes, and is a component of chlorophyll
  • calcium (Ca) is used to stabilize outer membrane in Gram negative bacteria
  • sodium (Na) is a salt component and is used by some for ATP generation
  • iron (Fe) is a component of cytochromes and ferredoxin
• Micronutrients:
  • cobalt (Co) is used in the formation of vitamin B12
  • zinc (Zn) is a structural and activating component ins many enzymes, including those needed for RNA and DNA synthesis
  • molybdenum (Mo) is a component of nitrogenase
  • copper (Cu) is a component of some respiratory enzymes
  • manganese (Mn) activates some enzymes; energy source when oxidized
  • nickel (Ni) is important for the function of hydrogenase
  • tungsten (W) and selenium (Se) are part of formate dehydrogenase
• Vitamins are organic compounds that generally function as coenzymes
• Environmental factors
  • temperature
    • psychrophiles ... grow at temperatures up to 20C
    • mesophiles ... grow at temperatures of 20-40C
    • thermophiles ... grow at temperatures above 50C
  • pH - most prefer pH 5-8, but some thrive at pH 3 and others at pH 10
  • salt - some microbes are halophiles (require high salt concentration)
  • oxygen
    • aerobes require oxygen at atmospheric (or near-atmospheric) levels
    • microaerophiles require oxygen at ~ one-tenth atmospheric levels
    • facultative aerobes grow well in the absence of oxygen, but can tolerate oxygen and will grow in its presence
    • anaerobes cannot tolerate oxygen and will not grow in its presence
  • water availability - adequate water is required for metabolism

Metabolism

Metabolism is the sum total of all the chemical reactions (generally catalyzed by enzymes) used by living cells.

• General Considerations
  • Types of metabolism
    • catabolism - degradation of chemical compounds via oxidation, which yields energy and reducing power (both "from" electrons)
    • anabolism - biosynthesis of chemical compounds used by cells for metabolism and/or growth; generally uses both energy and reducing power
  • Classification according to metabolism
    • organotroph - chemotrophic organism that obtains both its energy and its carbon from organic compounds
    • autotroph - organism that does not depend upon other organisms for either energy or carbon (for which it uses CO₂)
      • phototroph - organism which obtains its energy from light
      • lithotroph - organism which obtains its energy from inorganic compounds
  • Redox reactions - reduction and oxidation always occur together
    • oxidation - removal of electrons from the reducing agent (reductant) which acts as an electron donor during a redox reaction and is oxidized as a result
    • reduction - addition of electrons to the oxidizing agent (oxidant) which acts as an electron acceptor during a redox reaction and is reduced as a result
  • Assimilative vs. dissimilative metabolism
    • assimilative - metabolism in which small amounts of a molecule (just enough to satisfy growth requirements) are incorporated into the organism
    • dissimilative - metabolism (associated with anaerobic respiration) in which large amounts of molecules outside the cell are used as electron acceptors
• Catabolism
  • Organotrophy - mode of life in which organisms extract chemical bond energy from organic compounds by removal of electrons (oxidation) and use it to generate ATP and NAD(P)H (reducing power) ... then use these as carbon-containing building blocks for generating the organic molecules they need
    • fermentation - anaerobic catabolism in which electron donor and electron acceptor are both organic molecules (ETS is not used)
    • aerobic respiration - utilizes the TCA cycle, the electron transport system (ETS), proton gradients, ATP synthase, and oxygen as final electron acceptor
    • anaerobic respiration - dissimilative catabolism that involves the ETS and which uses a molecule other than oxygen the final electron acceptor
  • Lithotrophy
    • mode of life in which organisms capture chemical bond energy from inorganic compounds to generate ATP and NAD(P)H (reducing power) ... then use them to reduce carbon dioxide to form organic compounds
    • most lithotrophs are aerobic oxidizing bacteria
      • electrons are captured by enzymatic oxidation of reduced forms of inorganic molecules, leading to formation of NADH, which transfers the electrons to the
      • ETS, which generates a proton gradient by pumping protons from the inner surface of the cytoplasmic membrane ... thus allowing ATP synthase to generate ATP as the proton gradient collapses when the protons move back across the membrane
      • carbon dioxide fixation generally occurs via Calvin cycle
  • Phototrophy - mode of life in which organisms utilize photosynthesis to capture light energy to generate ATP and reducing power, then use them to reduce carbon dioxide so they can form organic compounds
    • light reactions - capture and conversion of light (photon) energy into chemical energy by membrane/protein-associated molecules, leading to formation of ATP and NADPH (reducing power)
    • dark reactions - utilize energy stored as ATP and reducing power stored as NADPH to convert carbon dioxide into organic compounds at the oxidation level of carbohydrate, generally using one of these pathways:
      • Calvin cycle (reductive pentose cycle) is used by cyanobacteria and purple bacteria
      • reverse (reductive) TCA cycle is used by green bacteria
• Anabolism - if not available in the environment, organic compounds must be synthesized by the cell
  • Carbohydrates (for polysaccharides, nucleic acids, CO₂ fixation, vitamins)
    • hexoses are synthesized via gluconeogenesis:
      • after conversion of oxalacetate to form phosphoenolpyruvate hexoses can be synthesized by "reversing" glycolysis
      • after glucose is coupled with uridine diphosphate (UDP), it can be used to synthesize structural or storage polysaccharides
    • pentoses are synthesized via the pentose phosphate shunt
      • hexose is cleaved to form pentose (ribulose-5-phosphate) plus carbon dioxide, which can be used in the Calvin cycle or for ribose synthesis
      • ribulose-5-phosphate is converted to ribose, which can be oxidized to form deoxyribose (both of which are used in synthesis of nucleotides and vitamins such as NAD)
  • Amino acids (for proteins, purines and pyrimidines)
    • two major aspects:
      • synthesis of the carbon skeleton from metabolic intermediates
      • attachment of an amino group
        • glutamate dehydrogenase adds an amino group to a-ketoglutarate directly, thus generating glutamate
        • other amino acids are generated from different carbon skeletons via transamination using glutamate as the source of the amino group
    • families of amino acids based on precursor source:
      • alpha-ketoglutarate amination leads to glutamate, which is a precursor to glutamine, proline and arginine
      • oxalacetate transamination leads to aspartate, which is a precursor to asparagine, lysine, methionine, threonine and isoleucine
      • pyruvate transamination generates alanine, a precursor of valine and leucine
      • 3-phosphoglyceraldehyde transamination leads to serine, which is a precursor to serine and glycine
      • phosphoenolpyruvate and erythrose-4-phosphate combine to form chorismate, which is the precursor of the aromatic amino acids tryptophan, phenylalanine and tyrosine
      • phosphoribosylpyrophosphate is a precursor to histidine
  • Purines and pyrimidines (for RNA, DNA, ATP, NAD)
    • purines (adenine, guanine) are synthesized via complex sequence of reactions in which components are donated by aspartate, glutamate, glycine, carbon dioxide and formate (from folic acid)
    • pyrimidines (cytosine, thymine, uracil) are synthesized from aspartate, carbon dioxide and ammonia (also via several reactions in a sequence)
  • Fatty acids (for lipids)
    • fatty acids are generated by fatty acid synthetase from successive addition of acetate groups donated by acetyl-CoA
    • glycerol is derived from dihydroxyacetone phosphate (in glycolysis) and is subsequently esterified by fatty acids to form mono-, di- or triglycerides (diglycerides may then be modified by addition of phosphate, amino, or other groups to better suit them for their functions in membranes, etc.)