nitrogen metabolism Flashcards
Conversion of ammonia to nitrates
Nitrification (via reduction)
- ammonia is oxidized
Process by which nitrates and nitrites are broken down to molecular nitrogen
Denitrification
- broken down to release nitrogen gas back into the atmosphere
the process of turning nitrogen gas from the air (N₂) into ammonia (NH₃) or ammonium ions (NH₄⁺) that plants can use
Nitrogen Fixation
- Reduction of N2 to NH3
- Plants and animals cannot carry out nitrogen fixation
As plants and animals can’t do this on their own. How does special bacteria handle this process.
These bacteria often live in partnership with plants, forming small bumps (called nodules) on the roots of plants like beans, peas, and other legumes.
The bacteria use nitrogenase to convert nitrogen gas into a usable form. It adds six electrons to nitrogen gas = ammonium ions.
Ammonium ions are an essential form of nitrogen that plants can absorb and use to grow.
Why is ammonia important in nitrogen fixation
Ammonia (NH₃) is one of the main ways nitrogen becomes available for living things.
It’s the only natural source of nitrogen in the biosphere, apart from nitrates (another usable form of nitrogen).
How do living things use ammonia?
Ammonia can turn into ammonium ions (NH₄⁺), which plants use as a building block to make important compounds like proteins and DNA.
Ammonia in fertilizer
Scientists can make ammonia in factories by combining nitrogen (from the air) and hydrogen.
This ammonia is used to create synthetic fertilizers, which often include nitrates to help plants grow better.
how does the enzyme nitrogenase helps convert nitrogen gas (N₂) from the air into ammonia (NH₃)
- Binding Nitrogen Gas:
The enzyme nitrogenase attaches to a nitrogen gas molecule (N≡N) from the air. - Step-by-Step Reduction:
The nitrogen gas molecule is reduced (changed) by adding hydrogen atoms in three stages.
This happens with the help of a helper molecule (called a reducing agent, like ferredoxin), which supplies the hydrogen atoms.
Each step adds 2 hydrogen atoms until the nitrogen is fully converted. - Final Product:
Once fully reduced, the nitrogen molecule turns into ammonia (NH₃).
Two molecules of ammonia are released, and the enzyme is freed to start the process again with a new nitrogen gas molecule.
how nitrogenase works to convert nitrogen gas (N₂) into ammonia (NH₃) with the help of several protein
Ferredoxin: Supplies electrons to the system.
Dinitrogenase reductase:
- iron–sulfur (Fe–S) protein
- Transfers electrons from ferredoxin to dinitrogenase. This step requires energy from ATP.
Dinitrogenase:
- iron–molybdenum (Fe–Mo) protein
- Uses the electrons to reduce nitrogen gas (N₂) into ammonia (NH₃).
Nitrogenase Reaction
The half-reaction of reduction:
6 electrons are needed to turn nitrogen gas (N₂) into ammonia (NH₃).
2 electrons are used to turn hydrogen ions (H⁺) into hydrogen gas (H₂).
The half-reaction of oxidation:
The source of electrons (needed for these reductions) depends on the organism. Different organisms use different substances to supply the electrons.
Process by which the final product of a series of reactions inhibits the first reaction in the series
Feedback Inhibition in Nitrogen Metabolism
in Feedback Inhibition in Nitrogen Metabolism, what happens if there is a high level of amino acids or nucleotides
the cell saves energy by not making these compounds through a feedback inhibition mechanism
- Helps save energy as biosynthetic pathways for many nitrogen containing compounds are long and complex
[It’s a way for cells to turn off a process when they already have enough of a product, like amino acids or nucleotides.
If there’s a lot of these compounds, the final product signals the first step of the reaction chain to stop making more.
This saves the cell energy because making nitrogen-containing compounds involves long and complicated processes.]
Transfer of amino groups from one molecule to another
Transamination
- it is when an amino group (a part of an amino acid) is moved from one molecule to another to help make different amino acids.
what does amidation of glutamate gives
glutamine
- glutamine is made by adding another group to glutamate, a process called amidation.
Glutamate is formed by reductive amination of
a-ketoglutarate and NH4
- Glutamate is made by adding an amino group (NH₄⁺) to a molecule called α-ketoglutarate. This is called reductive amination.
what are the different families of amino acids based on biosynthetic pathways
index card
How is glutamate formed?
Glutamate is formed by combining α-ketoglutarate and ammonium (NH₄⁺) in a reaction catalyzed by glutamate dehydrogenase (GDH) using NADPH.
What role does glutamate play in amino acid biosynthesis?
Glutamate is a major donor of amino groups in many reactions, while α-ketoglutarate acts as the acceptor.
How is glutamine made from glutamate?
Glutamate undergoes amidation to form glutamine, a reaction catalyzed by glutamate synthase (GS) and requiring ATP.
When do GDH and GS reactions occur together?
When nitrogen is abundant, both GDH and GS reactions occur.
What happens when nitrogen is limited?
Only the GS reaction occurs to conserve nitrogen.
How is glutamate replenished?
By the reductive amination of α-ketoglutarate, catalyzed by the enzyme glutamate:oxoglutarate aminotransferase (GOGAT).
Relationship between Amino Acid Metabolism and the Citric Acid Cycle
ppt
it is the biologically active form of vitamin B6 and plays a critical role in reactions involving amino acids.
Pyridoxal Phosphate (PyrP)
- transamination: transfer the amino group from one molecule to another
- decarboxylation: removing a carbon dioxide group
What type of bond does PyrP form with an amino acid during transamination?
An imine (Schiff base).
What are the products of the transamination reaction involving PyrP?
An α-keto acid and pyridoxamine phosphate.
- all transamination reactions with PyrP are reversible
What is the precursor molecule for serine?
3-phosphoglycerate.
Which molecule donates nitrogen to 3-phosphoglycerate in the biosynthesis of serine?
Glutamate
What is the intermediate formed during serine biosynthesis?
3-phosphoserine
- this is formed by removing the phosphate grp thru hydrolysis
