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 (PO₄^3-) 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 PO₄^3- ion

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

-environmental phosphate concentrations are low and PO₄^3- 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 PO₄^3- uptake from environment

-sulfur is widely available in most environments as sulfate (SO₄^2-) 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