Metabolism: Energy and Reactions

Chapter 7: Metabolism

• Free energy during a reaction is referred to as ∆G0'.
• Reactions with –∆G0' release are exergonic reactions; reactants are higher than products.
• Reactions with +∆ G0' require energy and are endergonic; reactants are lower than products.
• Reducing power is the ability to donate electrons during electron transfer reactions (redox reactions).
• Redox reactions include two half reactions.
  • An electron donor transfers electrons (oxidized).
  • An electron acceptor adds electrons (reduced).
• ATP provides free energy, powering transporters against their concentration gradient.
• Molecules like NADH, NADPH, and FADH2 provide reducing power by storing high-energy electrons used to reduce other molecules in metabolic pathways.
• Catabolic pathways are exergonic cellular processes that generate free energy, which gets conserved by making energy-rich molecules
• Anabolic pathways are endergonic cellular processes in which cellular synthesis requires energy, which is derived from ATP hydrolysis.
• Reactants become product in catabolic reactions.
  • ADP + Pi transforms to ATP in such reactions.
• Precursors to cellular material proceed via anabolism.
  • ATP becomes ADP + Pi in such reactions.
• Metabolic classifications can be based on a microbe's energy and reducing power sources:
  • Energy can be obtained from light (photo-) or chemical compounds (chemo-).
  • Reducing power may come from organic (organo-) or inorganic (litho-) sources.
  • Microbes can be autotrophs (carbon fixers/producers) or heterotrophs (consumers).
• NADH are coenzymes that allow interaction between different electron donors and acceptors.
• NADH carries electrons from glycolysis to the citric acid cycle, then to the electron transport chain.
• ATP (Adenosine Triphosphate) is the most important energy-rich phosphate compound, containing two high-energy phosphate bonds.
• ATP is generated through substrate-level phosphorylation, where an energy-rich substrate bond is directly hydrolyzed to drive ATP formation (e.g., hydrolysis of phosphoenolpyruvate).
• Oxidative phosphorylation uses the movement of electrons to generate a proton-motive force (electrochemical gradient) to synthesize ATP.
• Photophosphorylation uses light to form a proton motive force.
• NADH is generated when NAD+ is oxidized, becoming the reduced form NADH.
• The citric acid cycle provides a source of electrons.
• A higher position on a redox tower indicates greater reducing power; a substrate can reduce anything below it.
  • Better donors are at the top, and better acceptors are at the bottom.
  • Start to finish on the tower indicates how much energy is yielded.
  • Plants serve as an example.
• Respiration involves electron transfer from reduced electron donors to external electron acceptors.
  • It requires an external electron acceptor and generates ATP by oxidative phosphorylation from electron transport (proton motive force).
  • It can be anaerobic or aerobic, generates high ATP, and uses the Electron Transport Chain.
  • Byproducts include CO2, H2O, and energy.
  • Efficient in most eukaryotes and many prokaryotes.
• Fermentation doesn't require an external electron acceptor and is always anaerobic.
  • ATP is generated primarily by substrate-level phosphorylation.
  • Byproducts: lactic acid or ethanol
  • Yields low ATP (2 ATP per glucose).
• There's no Electron Transport Chain in fermentation.
• Found in bacteria and yeast.
• Important metabolic pathway inputs and outputs:
  • Glycolysis inputs: Glucose, 2 ATP, and 2 NAD+.
  • Glycolysis outcomes: 2 ATP, 2 NADH, and 2 pyruvate per glucose.
  • Fermentation inputs: Pyruvate and NADH.
  • Fermentation outcomes: Pyruvate is reduced, accepting electrons from NADH.
  • Citric Acid Cycle inputs: Acetyl-CoA, NAD+, FAD, and ADP.
  • Citric Acid Cycle outcomes: Pyruvate is oxidized to CO2, 3 CO2, 4 NADH, 1 FADH2, and 1 ATP per oxidized pyruvate.
• An electron transport chain generates a proton-motive force using electrons donated by carriers such as NADH and FADH2 undergoing oxidation-reduction (redox) reactions.
• The position in the electron chain is determined by standard reduction potential.
  • Electrons transfer from NADH or FADH2, which are at the top with better donors, to O2, which is at the bottom with better acceptors.
• Anaerobic respiration utilizes alternate terminal electron acceptors such as nitrate, sulfate, or fumarate.
  • Organisms would benefit from Aerobic Respiration rather than Fermentation
• Metabolic "modularity" allows cells to switch between different electron acceptors based on availability in the environment.
• Nitrogen, needed for proteins, nucleic acids, and other organics, comes from “fixed” nitrogen (ammonia, NH3, or nitrate, NO3-).
• Prokaryotes can conduct nitrogen fixation, forming ammonia (NH3) from gaseous dinitrogen (N2) at the cost of 16 ATP.
• Nitrogen fixation, catalyzed by nitrogenase complex is inhibited by oxygen, causing it to shut down.

Chapter 8: Metabolic Diversity

• Aerobic respiration requires oxygen, occurs in the mitochondria, produces about 37 ATP per glucose, generates a final byproduct of CO2 and H2O, and exhibits high efficiency.
• Anaerobic respiration doesn't require oxygen, happens in the cytoplasm, produces about 2 ATP per glucose, has a final byproduct of lactic acid or ethanol + CO2 and shows low efficiency.
• Aerobic respiration generates more energy.
• Assimilative processes incorporate inorganic nutrients into cells, consuming energy (ATP and reducing power) to acquire nutrients for biosynthesis through assimilative reduction reactions.
• Most important assimilative process is CO2 fixation.
• Carbon, nitrogen, and sulfur metabolism are examples of Assimilative processes.
• Dissimilative processes conserve energy; electron acceptors are reduced and excreted.
• Dissimilative reductions are part of anaerobic respiration.
• Sulfur reductions are examples of Dissimilative processes.
• Mixotrophy defines organisms on the plane of being able to both auto and heterotrophic.
  • These organisms can either make cheeseburgers or buy their own cheeseburgers.
• Oxygenic photosynthesis uses water as an electron donor and releases O2 as a byproduct of energy and carbon from carbon dioxide (CO2).
• Anoxygenic photosynthesis uses other electron donors and doesn't produce O2, but gets the energy and carbon from carbon dioxide (CO2).
• The main difference between Oxygenic and Anoxygenic photosynthesis is that the former produce oxygen, while the latter uses different sources.
• Anoxygenic photosynthesis cycles electrons without an external source, foregoing water addition.
• Sulfur oxidation energy source from reduced sulfur compounds (H2S, Sº, S2O3, SO32-) with oxygen as the final acceptor.
  • Type of trophy: Chemolithotroph.
• Iron oxidation oxidizes Ferrous (Fe2+) iron with oxygen as final receptor.
  • Type of trophy: Chemolithotroph.
• Both sulfur and iron oxidation are aerobic.
• Nitrification is a two-step aerobic process.
  • Ammonia Oxidation (Ammonium to Nitrite)
    • Inputs: NH4+ + O2.
    • Outputs: NO2 + H2O + Energy (ATP).
  • Nitrite Oxidation (Nitrite to Nitrate)
    • Inputs: NO2 + O2.
    • Outputs: NO3-+ Energy (ATP).
• Nitrate reduction is characterized by the following:
  • Process happens with nitrate as an input, as well as organic/inorganic electron donor.
  • Reduction outputs N2 (nitrogen gas) or NO2 (nitrite) + energy; nitrate plays a essential role.
• Sulfate Reduction is Characterized by the following:
  • The process input is SO42- (sulfate) and organic/inorganic electron donor + ATP.
  • Reduction outputs H2S (hydrogen sulfide) with the sulfate playing a key role, as well as an energy byproduct.
• Anaerobic conditions are required for both nitrate and sulfate reduction.
• End products will be gaseous.
• In the order of nitrogen compounds 1-2, NADH + H goes in and NO3¯ comes out; 2 H+ + NO3¯ is reduced to produce NO2 + H2O.
• Microbes with alternate metabolisms are found in both aerobic and anaerobic places.

Lecture 9: Ecological Diversity

• Metabolic diversity, ecological diversity, and phylogenetic diversity describe types of diversity supporting growth.
  • Metabolic diversity is defined in terms of cellular processes.
  • Ecological diversity is defined in terms of microbial interactions.
  • Phylogenetic diversity is defined by evolutionary relationships.
• Photosynthesis includes light and dark reactions.
  • Sunlight is captured for the light reactions to produce ATP and NADH.
  • Energy converts Carbon Dioxide into glucose during Dark reactions.
• Ecological role of cyanobacteria
  • First oxygen-evolving phototrophs.
  • Five major morphological types: Unicellular, Colonial, Filamentous, Filamentous heterocystous, Filamentous branching.
  • They make oxygen for us, fix nitrogen as necessary to make DNA and protein.
• Key cyanobacteria and their processes:
  • Prochlorococcus, Synechococcus, Trichodesmium, Anabaena.
    • Synechococcus, Prochlorococcus are important for productivity in the oceans.
    • Make up almost all of marine photosynthesis and almost half of all nitrogen in ocean.
• Diazotrophs are nitrogen fixers that fix N gas into ammonia (NH3), which can be assimilated.
  • Fixation demands ATP and nitrogenase, which are required in Bacteria, and Archaea.
  • Horizontal gene transfer occurs when fixation is found.

Lecture 10: Ecological Diversity (cont.)

• Denitrifiers grow: respiration of nitrogen (NO3, NO2¯) yields NO, N2O, & N2 through aerobic facultative respiration
• Nitrifiers form chemolithotrophically by organic compounds: ammonia & nitrites, and grow by aerobic/autotrophic means
• Syntrophy – one is producing what the other one needs.
  • Microbes work together to carry out transformations that neither can accomplish alone
  • Microbe metabolic interations can be complementary metabolisms by which one microbe supplies the needs for another.
• Metabolic strategies can be complementary such as.
  • Nitrifying bacteria/archaea, that are themselves
  • Ammonia oxidizing bacteria or archaea supply the nitrite for nitrite oxidizers
• Nitrifiers and denitrifiers:
  • Nitrification with coupled denitrifiers use nitrification to supply nitrate for coupled nitrification-denitrification.
  • This coupling of interactions provides most of the nitrate in poor nitrogen environments to denitrifiers
• Fermenters, denitrifiers, sulfate reducers supply reduced carbon (methanogen).
• Sulfate reducers generate reduces sulfide
• Iron reducers, Fe3 & Fe2 cycle reduced ferrous & oxidize ferric.
• Changes from Oxic (oxidation env’s.) to Anoxic (reduction env’s) determine the interaction location.
  • Anoxia consists reactions including Nitrification, Iron Oxidation, and Sulfur Oxidation
  • Reduction/Oxidation
  • Reduction location consisting of:
    • Nitrification, Iron Oxidation, and Sulfur Oxidation
    • Denitrification, Iron Reduction, Sulfur Reduction, Fermentation, and Methanogenesis
• Winogradsky column is a container to fill with mud, water, and nutrients to measure microbial growth in time
• Metabolic needs/products of microbes
• (B.O.) lifestyle, predation by periplasmic predators (attacks gram -) not (+)
• Msc but definitely important:
  • N.S.I - aerobes
  • F.S.D - anaerobes

Chapter 10- Quorum Sensing

• Autoinducer (AI) is a messenger for cell- to extracellular signal molecules
• Bacteria autoinducers will increase number and their density.
• 3 Quorum sensing parts: AI “I” enzyme, AI ligand, autoinducer R receptor
• AHL = gram -
• Peptides = gram +
• How can “languages” from both inter-specific and intra-specific:
  • Communication within species, w/ specific communication in taxa
  • Ex. Pseudocommunicating w/ different communication
• Why is it good for bacteria to coordinate their activity?
• Why wait until there are a high density of neighbors?
• Defense, formation, virulence from quorum sensing
• Dense predation= efficient/effective and conservation benefit
• Biofilm, high coordination in community and organism consistent.
• Virulence is operons that are opportunistic pathogens describe the squid symbiotic and why (host) quorum matters.

Chapter 11- Biofilms

• What a biofilm is and what its 3 components are: matrix: living/ inert surface that hosts components of a biofilm: the microorganisms, slime, surface on top of/ inert material.

• 4 features that a biofilm contains are:

• Must exhibit self-organization

• Biofilms is insulated by conditions/perturbations

• Toxins that contain antibiotics through water-proof coating/impervious to elements

• Can contain horizontal transfer if can be exploited by some organisms

• The communality should exhibit responses to environmental shifts than solitary ones, with biofilm expression of regulation affected

• Patterns of recognition affect the expression

• biofilm step process of formation: multiple staging through reversible attachment.

• cells will adhere to the surface.

• After approaching closer to the surface, bacteria can be selective/resistant toward bacteria.

• Microbes in bacteria secrete polysaccharide to link cells in a semi-stick/complex material with the surface.

• After adherence microbes are stuck and are permanent, but remain open for other species.

• Mature (adhered/organized) layers of cells produce proteins/lipases to breakdown for cell motor regulation.

• Signal transduction through mature biofilm.

• Why is it significant?

• Matrix w/ cells, sugars, protein DNA and role helps cells with surfaces, protection and can share each other to create colonies

Why can’t chemical/antibiotic attacks from resistance: slimy barrier/layer for internal organisms as well. Explain what (non) wettable means. Why advantages to living in biofilm: water-imperviousness to antibiotics