MICB 211 Chapter 7 Notes

Anabolism and its Diversity

Anabolism

-process where microorganisms take up nutrients and use energy to assimilate them into biomass

  • supports cellular maintenance, growth, reproduction

-synthesis of organic compounds that are retained in biomass

-conversion of simple organic compounds into complex organic macromolecules

-endergonic processes

  • requires ATP derived from catabolic metabolism

-involves electron transfer reactions

  • electron exchange between catabolic and anabolic metabolisms

Carbon Fixation and Assimilation

-carbon is largest elemental constituent of microorganisms

-derived from 2 main sources

  1. inorganic carbon (mostly CO2) for autotrophs

  2. organic carbon for heterotrophs

Carbon Fixation

  • uptake of CO2 and conversion into macromolecules that make up cells

  • fixation of carbon from CO2 into biomass is primary entry point of carbon from geological sources to the biosphere

Primary Biological Production

  • carbon fixation by autotrophs

-heterotrophs assimilate organic compounds

  • organic compounds derived from decayed biomass or excretion of waste products

Secondary Production

  • heterotrophic carbon assimilation

  • relies on carbon originally fixed by autotrophic primary producers

  • CO2 fixation requires endergonic reaction of C from its 4+ oxidation state in CO2 to lower oxidation states of carbon in organic macromolecules

-assimilation of carbon from organic compounds requires less energy

  • carbon is already in a redox state of 0 to -4

  • organisms that use organic substrates in catabolism also assimilate carbon from these same substrates for anabolic purposes

Autotrophic Carbon Fixation

Calvin Cycle

-biochemical pathways for fixation

-used by all oxygenic phototrophs

-responsible for fixation of most carbon that enters biosphere through primary production

-uses NADPH and ATP, ribulose biphosphate carboxylase (RubisCO) and phosphorribulokinase, series of intermediate compounds and enzymes to cyclically activate and reduce carbon from CO2 in its 4+ redox state to its 0 redox state in the form of sugar (fructose phosphate)

-produces fructose phosphate

  • 6 carbon compound

  • feeds into a suite of macromolecule biosynthetic pathways

-process requires 6 molecules of CO2, electrons from 12 NADPH molecules, energy from 18 molecules of ATP

RubisCO

  • enzyme that initiates Calvin cycle by binding to and activating CO2

  • kinetics respond strongly to CO2 concentrations

  • in non-light limiting environments

    • rate of CO2 turnover by RubisCO that limits rate of photosynthesis → responds to changes in CO2 concentrations

  • most abundant and important enzymes in biosphere since carbon fixation through oxygenic photosynthesis depends on this first step in Calvin cycle

Heterotrophic Carbon Fixation

-accomplished through extraction of intermediate carbon compounds produced through catabolic organic carbon breakdown

-ex: citrate and malate produced as intermediates in citric acid cycle can be converted to fatty acids and sugars downstream anabolic reactions

  • since these compounds are produced as intermediates in catabolic pathways

    • heterotrophic assimilation of carbon from pre-existing organic compounds comes at a comparatively

    • smaller energetic cost relative to the fixation of carbon from CO2

Nitrogen Fixation and Assimilation

-conversion of biologically inert N2 gas to biologically usable ammonia

-entry point for nitrogen from lithosphere (terrestrial part of planet) into biosphere (organic or living part of planet)

-high activation energy

  • strong triple bond on nitrogen atoms in N2 that needs to be broken before NH4 can be formed

-requires 8 ATP for fixation of 1 molecule of nitrogen (16 ATP for 1 molecule of N2)

-since N in ammonia has a lower redox state (-3) than in N2 (0)

  • a source of electrons (6 per N2 molecule) is also needed

-only known in bacteria and archaea

  • microorganisms support all of nitrogen needs in biosphere

-accomplished by nitrogenase enzyme

  • metal rish

  • contains iron (Fe), molybdenum (Mo) centered sub-units

  • oxygen sensitive

  • irreversibly inactivated with O2 exposure

-nitrogen-fixing oxygen photosynthetic organisms have special strategies to avoid exposure of nitrogenase to O2

  • some cyanobacteria fix nitrogen at night when photosynthetic activity ceases and stops O2 production

  • other cyanobacteria develop pigment free cells (heterocysts) that don’t absorb light → don’t photosynthesize or produce O2

    • heterocystic cells fix nitrogen instead

    • grow in filaments with pigmented cells exchanging photosynthetically fixed carbon with heterocysts in return for receiving fixed oxygen

-microorganisms that don’t fix N2 can assimilate both inorganic and organic forms of nitrogen

-ammonium NH4+ is readily assimilated by most bacteria and archaea

  • scarce in most oxygenated environments

-many aerobic bacteria and archaea also assimilate more oxidized nitrogen species including nitrate (NO3-) and nitrite (NO2-)

  • these oxidized forms of nitrogen are reduced before they can be incorporated into biomass as amino acids and other nitrogenous compounds

  • known as assimilatory nitrogen reduction

Phosphorus and Sulfur Assimilation

-phosphorus usually taken up as inorganic phosphate (PO43-) ion

  • scarce but most widely available form of phosphorus

-phosphorus is considered the limiting nutrient for biological production

  • relative to cellular quotas → phosphorus most scarce of macronutrient elements in surrounding environments

-rations of P:C and P:N in cellular biomass are higher than rations of P:C and P:N nutrients in environment

-for a given availability of P

  • process of nitrogen fixation will provide N needed to match P:N ratio in biomass

-carbon fixation will proceed in turn until available P is used up

-most biological molecules contain P in form of PO43- ion

  • doesn’t need to be reduced or oxidized following uptake

-environmental phosphate concentrations are low and PO43- needs to be taken up against a strong concentration gradient

-active transport systems help overcome the energetic barrier due to strong concentration gradients

  • active transport commonly used in PO43- uptake from environment

-sulfur is widely available in most environments as sulfate (SO42-) anion

-sulfate can be taken up and assimilated into sulfate lipids

-many key biological sulfur compounds require sulfur in more reduced state

  • sulfur from sulfate is reduced through addition of 8 electrons to sulfide before it gets used in synthesis of sulfur containing amino acids and vitamins

-assimilatory sulfate reduction is an energy consuming process

  • in anoxic environments, however, when sulfide is produced through dissimilatory sulfate reduction → can be directly assimilated with little to no energetic cost

Molecular Biosynthesis

-both autotrophs and heterotrophs use energy derived from catabolic pathways and a suite of inorganic and organic nutrients to synthesize some simple molecules that are used to form macromolecular compounds that make up cells

-simple molecules derived from intermediates in

  • carbon fixation pathways (Calvin cycle) for autotrophs

  • respiration pathways (glycolysis or citric acid cycle) for heterotrophs

-first step is normally synthesis of simple sugars

  • used to form more complex molecules

-polysaccharides made through endergonic conversion of simple sugars into glycogen or peptidoglycan

-a wide range of both lipid molecules and amino acids can be synthesized from intermediate and products of glycolysis and citric acid cycle

-amino acids are building blocks of proteins

  • import process in biosynthesis of amino acids and proteins is endergonic amination of sugar and organic acid precursors

-subsequent joining of amino acids to build proteins is endergonic

  • requires energy from cell

-nucleic acids derived from sugars, amino acids, phosphate

  • endergonic conversion reactions

-any biochemical pathways serve dual functions in both catabolism and anabolism

  • amphibolic pathways

Electron Balance

-incorporation of elements and molecules into biomass requires reduction or oxidation

  • overall oxidation state of cellular biomass is not the same as average oxidation state of elements and molecules taken up as nutrients

-cells need to take up or secret compounds that are either more reduced or oxidized than average redox state of overall biomass

-electron deficits created by anabolism of compounds that are more oxidized than average biomass can be overcomed by using electrons derived from oxidation of primary electron donor in catabolism

-electron excesses can develop

  • nutrients are taken up that are more reduced than average biomass

  • common in heterotrophy

-electron balance must be maintained through catabolic and anabolic metabolisms

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