Nitrogen Metabolism: An Overview

Nitrogen Metabolism Overview

• Nitrogen is abundant in living systems after carbon, hydrogen, and oxygen
• It is primarily found in amino acids and nucleotides.

Nitrogen's Role

• This chapter focuses on nitrogen metabolism, excluding amino acid catabolism, which is covered in Chapter 18
• Amino acids and nucleotides serve as precursors for proteins and nucleic acids, respectively
• They also contribute to neurotransmitters, metabolic cofactors, and various other biologically important molecules

Nitrogen Availability

• Nitrogen availability can be a limiting growth parameter within particular environments.
• Atmospheric N2 is inert, requiring conversion to ammonia or nitrate for biological use.
• Enzymatic processes, mainly in microorganisms, convert different molecular forms
• Reactive nitrogen global inventory comprises these enzymatic conversions

Oxygen and Regulation

• Oxygen and nitrogen metabolism are linked
• Oxidation and reduction of nitrogen forms in the biosphere often involve oxygen
• Regulation is critical to conserve this limited resource and balance amino acid and nucleotide supplies efficiently.
• Metabolic flux in these pathways is lower than in carbohydrate or lipid biosynthesis.
• Most amino acids and nucleotides are synthesized as needed, rather than stored.

Central Role of Glutamate and Glutamine

• Nitrogen enters biological systems through glutamate and glutamine.
• High concentrations of glutamate and glutamine in many tissues contribute to the electrochemical environment within cells
• The role of these two amino acids is a universal characteristic of nitrogen metabolism
• This is an example of the shared evolutionary history of organisms.

Biosynthesis Characteristics

• Amino acid and nucleotide biosynthesis are endergonic and reductive, requiring energy from ATP and reductants like NADPH.

Pathway Interconnections

• The biosynthetic pathways are interconnected and discussing them together is efficient
• Both amino acids and nucleotides contain nitrogen, with shared intermediates
• Amino acids, or parts of amino acids, get incorporated into purines and pyrimidines
• A purine ring also gets incorporated into the amino acid histidine.
• The pathways share common chemistry, involving reactions that transfer nitrogen or one-carbon groups.

Study Strategies

• Biochemical pathways can be better understood by focusing on metabolic principles, key intermediates/precursors and common reaction types
• Chemical transformations can offer rewards for study
• Metals like molybdenum, selenium, and vanadium are prominently used in these biological systems.
• Practical knowledge of these pathways is beneficial for students in human or veterinary medicine, as many genetic diseases and pharmaceuticals relate to amino acid and nucleotide metabolism.

Nitrogen Source

• Biosynthetic pathways for nucleotides and amino acids both require nitrogen
• Soluble nitrogen compounds are limited in natural environments
• Organisms use ammonia, amino acids, and nucleotides economically
• Available amino acids, purines, and pyrimidines are salvaged and reused through turnover of proteins and nucleic acids.

Nitrogen Cycling

• The nitrogen cycle is more accurately a complex web of interconversions
• N2 makes four-fifths of Earth's atmopshere with conversion to usable forms of nitrogen is called nitrogen fixation
• N2 reduction to NH3 or NH4+ provides the molecular basis for discussion and is completed by nitrogen-fixing bacteria and archaea
• A central role in making N2 available makes the single reaction of the conversion of N2 to NH3 synonymous with nitrogen fixation
• Independent Salvaging and reusing biologically available nitrogen describes biosphere metabolic processes
• Bacteria and archaea conduct the most key reactions

Detailed Reactions

• Section 22.2 describes reduction of nitrogen in detail
• Bacteria oxidize ammonia to derive energy
• Nitrification consists of Ammonia to nitrite (NO2-) and ultimately to nitrate (NO3-)
• Replacement of atmospheric N2 must occur for maintenance of steady-state concentration for organisms in the three domains of life
• Denitrification converts nitrate and nitrite to N2 under anaerobic conditions
• Specialized microorganisms perform denitrification
• NO3- / NO2- are ultimate electron acceptors
• ATP is synthesized to generate a transmembrane proton gradient
• Microorganisms that exist in anoxic environments containing nitrate include:
  • Soils
  • Marine sediments
  • Eutrophic marine zones
• Bacteria oxidize anaerobic ammonia = anammox
• Ammonia + nitrite -> N2 is preformed by anammox with 50-70% NH3/N2 conversation, with waste treatment solutions, going undetected into 1980s
• Air breathers overlook bacteria and archaea in anaerobic zones, with contributions to carbon and nitrogen balances on Earth

Energy Production and Versatility

• Energy for maintaining living system relies on proton gradients
• Proton release on the membrane side generates the transmembrane proton gradient, electrons derive from a reduced substrate into membrane carriers and throughout electron transfers to a final electron acceptor
• Anabolic environments such as marine/freshwater are extraordinarily diverse and versatile
• Redox pair can be an energy source per specialized group
• Lithotrophic chematrophs' hydrogenase reduces NAD+ to using inorganic sources
• Electons generate ATP synthesis gradients from e-accepters using NADH electrons
• Strict anaerobes known as methanogens extract energy, reduce CO2 -> methane, and maintain specialized cofactors

Nitrogen Use

• Nitrogen used in biosphere depends on specilaized bacteria
• Nitrifying bacteria oxidize ammonia to nitrites
• Some bacteria oxidize nitrite products to nitrates
• Nitrate is used as a nitrite e-acceptor for bacteria and archaea
• Denitrification is performed from ntrates and nitrites to mitrogen via fixed nitrogen
• Ammonia polltution can be found in sewage, animal waste/byproduct of oil and fertilizer manfucaturing
• Treating waste relies on convertng bacteria from waste to nitrogen, organic carbon, and oxygen

Anaerobis Oxidation

• Few research articles suggest aerobic ammonia oxidation
• Anammox has a waste-treatment process
• Plactomycyes have been isolated by a team of micribiologist
• Unveiling the anammox process includes hydrazine (N2H4)
• Highly reactive molecule with rocket fuel properties

Compartmentalization

• Anammox bacteria solves problems through anammoxosome organelle with ladderanes lipids
• Fused Ladderane cyclobutanes form a barrier with difficut synthesis and high bond angles
• Ammonia/Hydroxylamine converted to hydrazine /H2O via hydrazine hydrolase in reactions

Cell Structure

• External protons of anammoxosome produces hydroxylamine
• All enzymes embedded in the membrane
• Cyclobutane stacking forms hydrophobic membrane structures
• Sequestration from anammox produced in reactions
• Bacterial cells do not contain compartments (no membrane nucleus is primary for eukaryotes/bacteria)
• Planctomycetes contain a nucleus
• DNA in the membrane with anammox reactions and trace origins in nuclear evoluation
• Reducing ammonia costs conventional denitrification/aeration
• Fixed atmospheric nitrogen and reduced amonia from alternative nitrate fates
• Vascular plants/algae/microorganisms generate assimilated ntirate by a reductive process, N2 by pass/first by nitrate to nitrite, then nitrite by nitrite reductase to NH4 - catalyzed six e- transfer via nitrite reductase

Regulation Cont.

• Mo- containing cofactors play active roles
• A pair of electons from NADH cysteine FAD
• Cytachrome reduced substrates
• Fe-4s plants in chloroplasts, then Six e- from ferredoxin
• 4Fe-4S center through siroheme for NO3 reduction
• Nonphotosynthetic microbes have distinct NADPH reducing
• Fixed nigrogen nees boost with global balances of life in the biosphere, with nitrogen based fertilzers, non-farming releases

Nitrogenase Complex

• Fixed nitrogen's availability may have limited primordial biosphere size and requires nitrogen fixation
• Only bacterial/archaeon perform nitrogen fixation today
• Diazotrophs include cyanobacteria (soil/fresh)and methanogenic archaea (anaerobes in methane H2, CO2) as well as azotobacter/symbiont legumes
• Most important product is ammonia (from nitrogen fixation) usable for all w/alterations
• Reduction of nitrogen to ammoinia by exergonic rxns for stable nitrogen tripple bonds
• The Haber Process makes ammonia industrially using high heat/pressure
• ATP binding hydrosis provides necessary action energy for biological Nitrogen, is fixed
• N2/H+ -> NH4 / ADP by Nitrogenase Complex components in reductase dinitrogenase
• Reductase Fe-4s redox dimers are oxidized and have atp/adp bids
• Dinitrogenase protein transfers electrons to cofactors

Protein Structure

• P + cluser share fe/s atom to make center novel fe-mo to have atoms
• Heteroatoms help with fe ligands and homocitrate (with N atoms)
• Nitrogenase has forms- vanadium or fe-fe
• Genes that nitrogen and require separate enzymes are less efficient and have additional rxns
• vinelandil has capacity to catalyze the reducing co-> ethylene
• Highly reduced form - high electrons for reduction of Ns to production and help mechanisms with understoon biologial role
• Reductase transfers e- and subunits
• Immediate reduce source and reducing depends species

Activation Energy of Dinitrogenase

• Binding ATP aids with protein that decreases activaiton energy of nitrogen fixation for N2 half rxn
• Atp hydroysis changes reductase conformation to create signals with Gtp- proteins with binding and results in structure
• Transfer is then facillitated between enzymes

Instability of Dinitrogenase

• Nitrogen complex is unstable
• Air inactivates for life in second with halflife for air
• Bacteria copes (free living type represses and anaerobics)
• Species uncouple oxygen and atp to rid it self as they enters
• Symbiotic legumes are oxygen labile nodules for bacteria to tap into abundant citrate
• The oxygen is from soy proetin that has high levels that block fixation with oxygen transfer bacteria electron systems
• Bacterial symbions have soil enrichment

Regulation of Nitrogen Fixation

• Energetically costly to fix due to ATP demands
• High atp has expression
• Nitrogenase has algins and covalent reaction that responds when n03
• Nitrogen is highly important because industrial neede so large andexpensive production and needs high trans and new bacteria

Glutamate/Glutamine assimilation

• Most nitrogen-containing bimolecules assimilatied into amino acids and aminos
• Glutamate/glutamine provide critical entry by catalyzing role in catabolism and amino acids oxidation.
• Amino acid assimilation pathway is glutamate/ glutamine -> aminotransferase rxns -> others

Glutamine/Glutamate Regulation

• Concentration regulation is used for solute for cytiosl and medium by pathways
• Two rxns assimilate with glutamate requires one rxns net of glutamate at end
• Glutamine enzyme takes place in two steps and uses bound - glutamy phosphate as int.

Glutamate Synthesis

• Bacteria/Plants need ketoglutarate in reactions to glutamate molecules for free to aminos blood to reactions with one step rxns
  • ketagluteraste, H require and a rxn to reach significatn amount