-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 is largest elemental constituent of microorganisms
-derived from 2 main sources
inorganic carbon (mostly CO2) for autotrophs
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
-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
-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
-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 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
-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
-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