Nitrogen part 1 : The cycle and Toxicity Flashcards
Nitrogen in the air (3)
-All lifeforms require nitrogen compounds like proteins and nucleic acids
-Air which is 78% nitrogen gas (N2) us the major reservoir of nitrogen
-Most organisms cannot use nitrogen in this form, with only a few prokaryotes being able to fix and utilize N2
The nitrogen cycle (4)
1) Nitrogen fixation: N2 -> NH3
2). Nitrification: NH3 -> NO3-
3). Denitrification -> NO3- -> N2
4). Decay: Amino and nucleic acids -> NH3
Breakdown of atmospheric nitrogen (3)
-The breakdown of the N2 molecule requires the input of a substantial amount of energy
Nitrogen (N2) can be fixed by:
-Energy from lightning strikes (atmospheric)
-Bacteria and Archaea (biological)
Atmospheric Nitrogen fixation
Energy from lightning breaks down atmospheric N2, which then binds to oxygen forming NO and NO2. These dissolve in the rain forming nitrates (NO3-) that are carried to earth.
Biological nitrogen fixation (4)
-The ability to fix nitrogen is only found in certain bacteria and archaea
-Some live in symbiotic relationships with the legume family
-Some establish symbiotic relationships with animals like termites and shipworms
-Some nitrogen fixing bacteria called cyanobacteria live feely in soil and aquatic environments
Nitrogenase system (4)
-How nitrogen fixers fix nitrogen
-Takes 16 mol of ATP for 1 mol of N2
-Metabolic processes in nitrogen fixers produce ferredoxin and flavodoxin which transfer electrons to nitrogen reductase.
-Nitrogen reductase donates its electrons to nitrogenase which catalyzes the reaction turning N2 +8protons +8electrons into 2 NH3 and 2 H2
Nitrogenase and oxygen
-The nitrogenase system is extremely sensitive to oxygen and needs to be protected from it. To do this most nitrogen fixing bacteria produce an enzyme called hydrogenase, which binds oxygen to hydrogen forming water and preventing the oxygen from messing with the nitrogen fixing.
Harber Bosch process
Under great amounts of pressure, at temperatures of 600C, and with the use of a catalyst, atmospheric nitrogen can be fixed! This is known as industrial fixation and is used to create fertilizer
Nitrification (3)
-Ammonium (NH4) can be used directly by plants however most of it is converted into nitrates by nitrifying bacteria
-This process happens in 2 steps:
1) Bacteria from genus Nitrosomonas oxidize ammonium into nitrites
2NH4 + 3O2 -> 2NO2- + 4H+ 2H2O
2). Bacteria from genus nitrobacter oxidize nitrites into nitrates
2NO2- + O2 -> 2NO3-
Decay
The proteins made by plants enter and pass through food web, some getting used and some getting in amino and nucleic acids and some being directly secreted as urine. When an animal excretes these (or dies) decomposing bacteria and fungi break these down into ammonia
Denitrification (6)
-Breaks down nitrates into nitrogen gas, replenishing the supply in the atmosphere.
-Done by anaerobic bacteria who use nitrates instead of oxygen for respiration
- Nitrate reductase A converts Nitrates into nitrite (NO3- –> NO2-)
2). Nitrite reductase convers Nitrite into nitrogen oxide (NO2 -> NO)
- NO reductase reduces Nitrogen Oxide into nitrous oxide (NO - N2O)
4). N2O reductase converts Nitrous oxide into Nitrogen gas (N2O -> N2)
Amino Acids (3)
-Nitrogen is used to from amino acids witch are required for energy metabolism, and protein synthesis.
-There are 22 amino acids called the standard amino acids that are required for protein synthesis in all organisms
-Some of these standard acids (10) are essential, meaning they cannot be synthesized and need to be taken in fully formed from food sources
What makes up an amino acid (5)
- A carboxyl group
-and alpha amino group
- A central carbon
-A hydrogen atom
-A unique side chain (R group)
Essential Amino Acids (10)
- Valine
-Leucine
-Methionine
-Isoleucine
-Phenylalanine
-Tyrosine
-Tryptophan
-Threonine
- Lysine
-Histidine
Amino group donators (2)
Asparagine and Glutamine
Amino group acceptors (2)
Aspartate and glutamate
Ammonia vs Ammonium (3)
-Ammonia is a weak base
-in terms of physiology, 97-99% of ammonia exists in its ionic form NH4+ aka ammonium
-1-3% of ammonia exists in is gas form NH3 which is small, uncharged, and toxic
Toxicity of Ammonia (7)
It fucks with
-energy metabolism by reducing the H+ concentration gradient used in ATP synthesis, as it binds to the protons to from NH4
-Intracellular pH
-K+ transport systems because they are of similar size to K+
-Amino Acid metabolism by stopping new acids from forming
-Intracellular charges by changing the structure of proteins therefore their charges
-its also a neurotoxin (Mammalian Hepatic Encephalopathy)
-And its membrane permeable
Ammonia trapping
If Ammonia crosses a membrane from a low pH zone (little H+) to a high pH zone (lots of H+) it starts to bind to the extra protons forming NH4. Because NH4 cannot cross back over the membrane it becomes trapped. An example of this is the mitochondria, where NH3 enters the matrix (innermost part of the powerhouse) through an ATP synthase (pump) where it then crosses into the intermembrane space, accumulating as NH4 and killing the mitochondria
Mammalian Hepatic Encephalopathy theories (2)
-Excess glutamate neurotransmission hypothesis
-Astrocyte swelling hypothesis
Excess glutamate neurotransmission hypothesis (4)
-3 parts, the pre-synaptic neuron, the post-synaptic neuron and the astrocyte
-Ammonia activates the NMDA receptor (normally activated by glutamate) on the post-synaptic cell
-Ammonia also inhibits the Na dependent glutamate re-uptake, preventing the glutamate from being recycled into the astrocyte
-The increased NMDA receptor activity caused by excess glutamate and ammonia causes a massive and uncontrolled amount of calcium to enter the post-synaptic neuron, leading to the death of the cell
Astrocyte swelling hypothesis (4)
-Excess NH3 from liver problems enters the astrocyte from the blood
-The ammonia activates the glutamate synthase within the astrocyte, causing it to produce more glutamate than it can give back to the pre-synaptic cell
-the accumulated glutamate is now concentrated, causing water to enter the astrocyte via osmosis
-The astrocyte swells, leading to cell death, similar to how Alzheimer’s functions
