Biochem Exam 4
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Why must atmostpheric nitrogen be “fixed”
Atmospheric N₂ is very stable and relatively inert because of its strong triple bond. Most organisms cannot use N₂ directly, so it must be converted into more reactive nitrogen compounds.
What is nitrogen fixation
Nitrogen fixation is the conversion of atmospheric N₂ into biologically or chemically usable nitrogen forms such as NH₃, NO₂⁻, or NO₃⁻.
What percentage of the atmosphere is nitrogen gas
About 78% of Earth’s atmosphere is N2
What makes N₂ difficult to use chemically?
N₂ contains a very strong triple bond, making it difficult to break apart and therefore chemically inert under ordinary conditions.
What industrial process fixes nitrogen
The Haber process fixes atmospheric nitrogen by reacting N₂ with H₂ to produce ammonia, NH₃.
What are the major conditions of the Haber process?
The Haber process requires hydrogen gas, high temperature, and very high pressure to drive formation of ammonia.
What is the main product of the Haber process?
The main product is ammonia (NH₃), which is widely used to manufacture fertilizers.
Why is the Haber process important agriculturally?
It produces ammonia that can be converted into nitrogen-containing fertilizers, supplying plants with nitrogen needed for growth.
Can nitrogen fixation also occur naturally without organisms?
Yes. Lightning provides enough energy to break N₂ apart and promote reactions with oxygen, producing oxidized nitrogen compounds.
What nitrogen compound can form from lightning-driven fixation?
Lightning can ultimately contribute to formation of nitrate (NO₃⁻) and related nitrogen oxides that enter soils and water.
What role does O₂ play in lightning-based nitrogen fixation?
Oxygen reacts with nitrogen-derived intermediates formed by lightning, helping generate oxidized nitrogen compounds such as nitrate.
What is nitrification?
Nitrification is the biological oxidation of reduced nitrogen, especially ammonia/ammonium, toward nitrite and then nitrate.
what is the general direction of nitrification?
in simplified form: NH₃/NH₄⁺ → NO₂⁻ → NO₃⁻.
Is nitrification the same as nitrogen fixation?
No. Nitrogen fixation starts with atmospheric N₂, whereas nitrification converts already-fixed reduced nitrogen into more oxidized forms.
How can bacteria help plants obtain nitrogen?
Certain bacteria living in or near plant roots can perform biological nitrogen fixation, converting atmospheric N₂ into ammonia (NH₃).
What are nitrogen-fixing bacteria called?
They are often called diazotrophs. These organisms possess the enzymes needed to reduce N₂ to ammonia.
Where are nitrogen fixing bacteria found in some plants?
In many legumes, nitrogen-fixing bacteria live in specialized structures called root nodules.
What is a root nodule?
A root nodule is a specialized swelling on a plant root that contains nitrogen-fixing bacteria and provides an environment where nitrogen fixation can occur.
Why is ammonia useful to plants?
Ammonia can be incorporated into organic molecules and used to synthesize amino acids, nucleotides, and other nitrogen-containing compounds.
Why can't plants just use atmospheric N₂ directly?
The N≡N triple bond is extremely stable, so plants generally cannot break it themselves. They depend on fixed nitrogen from soil, fertilizers, or nitrogen-fixing microorganisms.
What type of relationship can exist between plants and nitrogen-fixing bacteria?
It can be a symbiotic relationship: the bacteria provide usable nitrogen to the plant, while the plant provides carbon compounds and a protected environment to the bacteria.
What enzyme complex carries out biological nitrogen fixation?
Biological nitrogen fixation is performed by the nitrogenase complex in nitrogen-fixing organisms called diazotrophs.
What is the purpose of nitrogenase?
Nitrogenase converts extremely stable atmospheric N₂ into ammonia (NH₃), a form of nitrogen that can be incorporated into biomolecules.
Why is N₂ difficult to reduce?
N₂ contains a very strong N≡N triple bond with a bond energy of about 930 kJ/mol, so breaking and reducing it requires overcoming a very high activation-energy barrier.
Is nitrogen fixation thermodynamically unfavorable?
No it has a negative ΔG°′, meaning the overall reaction is thermodynamically favorable, but it proceeds very slowly without nitrogenase because the activation energy is extremely high.
Why does nitrogenase use ATP if the overall reaction is exergonic?
ATP is needed to help drive electron transfer and conformational changes in the nitrogenase complex, allowing the reaction to overcome its large kinetic barrier.
What are the two major protein components of nitrogenase?
The complex contains dinitrogenase reductase and dinitrogenase.
What is dinitrogenase reductase?
Dinitrogenase reductase, also called the Fe protein, is a homodimer containing a [4Fe–4S] cluster. It transfers electrons to dinitrogenase and couples this transfer to ATP hydrolysis.
What is dinitrogenase?
Dinitrogenase, also called the MoFe protein, is the component where N₂ is actually reduced to NH₃.
What metal centers are found in dinitrogenase?
it contains the P-cluster and the FeMo cofactor, which participate in electron transfer and N₂ reduction.
What is the FeMo cofactor?
The iron-molybdenum cofactor is the specialized metal cluster at the active site where atmospheric N₂ binds and is progressively reduced.
What is the general direction of electron flow?
Electrons move from an external electron donor → dinitrogenase reductase (Fe protein) → dinitrogenase (MoFe protein) → N₂.
What role does the [4Fe–4S] cluster play?
The [4Fe–4S] cluster in dinitrogenase reductase acts as a redox center that carries electrons toward the MoFe protein.
What role does ATP hydrolysis play?
ATP binding and hydrolysis cause conformational changes in the Fe protein that promote electron transfer to dinitrogenase.
Where is N₂ converted to NH₃?
N₂ is reduced at the FeMo cofactor of dinitrogenase.
What happens to the electrons once they reach the FeMo cofactor?
They are delivered stepwise to N₂ together with protons, progressively reducing N₂ until NH₃ is produced.
Is H₂ also produced during nitrogen fixation?
Yes. Nitrogenase also reduces some protons to H₂, so hydrogen gas is an obligatory side product of the biological reaction.
What molecule provides electrons for nitrogen fixation?
Pyruvate is used as an electron source. Its electrons are transferred through ferredoxin to the nitrogenase complex.
What is ferredoxin?
Ferredoxin is a small iron-sulfur electron carrier that transfers electrons from metabolism to dinitrogenase reductase.
What is the first nitrogenase protein to receive electrons?
Dinitrogenase reductase, also called the Fe protein, receives electrons from ferredoxin.
How does dinitrogenase reductase transfer electrons?
It transfers electrons one at a time to dinitrogenase.
How many total electrons are transferred during one complete nitrogen-fixation cycle?
A total of 8 electrons are transferred.
Why are 8 electrons needed if N₂ → 2 NH₃ requires only 6 electrons?
6 electrons reduce N₂ to 2 NH₃, while another 2 electrons reduce 2 H⁺ to H₂.
How much ATP is required per electron transferred?
Each electron-transfer step requires 2 ATP.
How much ATP is required total for nitrogen fixation?
8 electrons × 2 ATP/electron = 16 ATP total.
Why is nitrogen fixation so energy-intensive?
The N≡N triple bond is extremely stable, so nitrogenase needs substantial energy to drive the electron transfers necessary for reduction.
What does ATP binding and hydrolysis do in the nitrogenase complex?
ATP binding/hydrolysis changes the conformation of dinitrogenase reductase and brings its [4Fe–4S] cluster closer to the P-cluster, allowing electron transfer.
What is the electron pathway through the nitrogenase complex?
Pyruvate → ferredoxin → dinitrogenase reductase → [4Fe–4S] cluster → P-cluster → FeMo cofactor → N₂.
What does dinitrogenase do?
Dinitrogenase is the MoFe protein that contains the catalytic centers where N₂ is reduced.
What two important metal centers are in dinitrogenase?
The P-cluster transfers electrons internally, while the FeMo cofactor is the active site where N₂ reduction occurs.
Where is N₂ actually reduced to NH₃?
At the FeMo cofactor of dinitrogenase.
How many electrons are needed to reduce N₂ to ammonia?
6 electrons reduce one N₂ molecule to 2 NH₃.
What other reaction occurs during nitrogen fixation?
2 H⁺ + 2 e⁻ → H₂, so hydrogen gas is produced as a side product.
Why is oxygen dangerous to nitrogenase?
The [4Fe–4S] clusters and FeMo cofactor are easily oxidized by O₂, which inactivates the nitrogenase complex.
Why must nitrogen-fixing organisms protect nitrogenase from oxygen?
Nitrogenase depends on reduced iron-sulfur centers. Exposure to oxygen damages these centers and prevents electron transfer and N₂ fixation.