lecture 19- nitrogen and the boring billion

What collective term is used for nitrogen-fixing bacteria such as cyanobacteria and rhizobia?

Diazotrophs

Which specific bacteria form symbiotic relationships within plant root nodules to fix N₂?

Rhizobia

Identify three examples of diazotrophs from the source material excluding rhizobia and cyanobacteria.

Green-sulfur bacteria, purple-sulfur bacteria, and Frankia (or Azotobacteraceae).

In the nitrogen cycle, which process involves the conversion of N₂ into ammonia by specialized bacteria using nitrogenase?

Biological fixation

How does atmospheric fixation contribute to the nitrogen cycle?

Lightning energy breaks N₂ bonds, allowing reaction with oxygen to form nitrogen oxides that fall with rain.

What is the name of the industrial process used to create synthetic nitrogen fertilizers?

Haber-Bosch process

Define the process of nitrification.

The transformation of ammonia in the soil into nitrites and then nitrates by specific bacteria.

Which genus of bacteria is responsible for converting ammonia (NH₃) into nitrites (NO₂^-)?

Nitrosomonas

Which genus of bacteria is responsible for converting nitrites (NO₂^-) into nitrates (NO₃^-)?

Nitrobacter

The process by which plants absorb nitrates or ammonium to build proteins and DNA is called _.

Assimilation

What occurs during the process of ammonification?

Decomposers break down organic matter from dead organisms or waste and convert it back into ammonium.

Under what environmental condition does denitrification typically occur?

Oxygen-poor (anaerobic) environments

What is the gaseous end product of the denitrification process?

Nitrogen gas

Why is N₂ gas considered chemically inert and stable?

It possesses a triple bond and a symmetrical charge distribution across identical atoms.

What are the three key subunits that compose the nitrogenase enzyme?

NifD, NifH, and NifK

What is the specific stoichiometry of the three subunits in the nitrogenase complex?

D₂K₂H_i

Which nitrogenase subunit contains the ATP binding site and a single 4Fe-4S cluster?

The H subunit (NifH)

The Mo-Fe protein of nitrogenase is formed by which two subunits?

D (NifD) and K (NifK)

What is the chemical composition of the P-cluster found in the Mo-Fe protein?

8Fe-7S

What is the chemical composition of the M-cluster found in the Mo-Fe protein?

Mo-7Fe-9S-C-homocitrate

Provide the balanced chemical equation for biological nitrogen fixation by nitrogenase.

N₂ + 8H⁺ + 8e^- + 16ATP → 2NH₃ + H₂ + 16ADP + 16Pi

Which molecule acts as the electron donor for the nitrogenase reaction?

Reduced ferredoxin

How many molecules of ATP are hydrolysed for every single molecule of N₂ fixed by nitrogenase?

16

Why are nitrogenase co-factors described as being extremely sensitive to O₂?

Oxygen causes a cycle of limitation or inactivation of the enzyme.

In the nitrogenase mechanism, what event triggers the association of NifH with NifK and NifD?

Reduction of the NifH dimer by ferredoxin and subsequent ATP binding.

Describe the sequence of electron transfer within the nitrogenase complex after the conformational change.

P → M then F → P

How many electrons must the M-cluster accumulate before N₂ can bind?

4

In the nitrogenase mechanism, what event causes the complex to dissociate?

The release of ADP and Pi following ATP hydrolysis.

What is the 'Janus state' in the context of the nitrogenase mechanism?

A state where 2H can become H₂ and be productively exchanged for N₂

Under what condition is the forward reaction (productive NH₃ evolution) favoured over backsliding in nitrogenase?

A high N₂/H₂ ratio

How did the evolution of land plants contribute to rising atmospheric O₂ levels during the 'Boring Billion'?

It allowed massive CO₂ burial in the form of nitrogen-free cellulose.

What specialized cells did cyanobacteria evolve to protect nitrogen fixation from rising O₂ levels?

Heterocysts

How did nitrifying bacteria act as a sink for O₂ produced by cyanobacteria?

They used O₂ to oxidise ammonia into nitrite and nitrates

What are the two primary Krebs cycle intermediates used for the amination reactions that generate amino acids?

alpha-ketoglutarate and oxaloacetate

Which enzyme carries out the amination of alpha-ketoglutarate to form glutamate?

Glutamate dehydrogenase

Which intermediate is formed by the elimination of water during the amination of Krebs cycle intermediates?

Schiff base intermediate

What molecule provides the reducing power to convert a Schiff base into an amino acid?

NADPH

Which enzyme facilitates the amination of glutamate to produce glutamine?

Glutamine synthetase

Describe the activation step in the synthesis of glutamine from glutamate.

Glutamate is activated by ATP to form an acyl-phosphate intermediate.

What is the function of glutamine synthase (GOGAT) in nitrogen metabolism?

It transfers an amino group from glutamine to alpha-ketoglutarate to form two molecules of glutamate.

Term: Transamination

A reaction that transfers amino groups from one molecule (often glutamine or glutamate) to different amino acids.

What metabolic intermediate serves as the precursor for all 20 amino acids via conversion to PEP?

Oxaloacetate

How many of the 20 standard amino acids are classified as 'essential' for humans?

9

List the nine essential amino acids that humans must obtain through their diet.

Histidine, Isoleucine, Leucine, Lysine, Methionine, Phenylalanine, Threonine, Tryptophan, and Valine.

According to the metabolic pathway diagram, which amino acid is derived from Ribose-5-phosphate (R5P)?

Histidine

Which amino acid is directly produced from 3-phosphoglycerate (3PG)?

Serine

Which three amino acids are derived from the precursor Erythrose 4-phosphate (E4P)?

Phenylalanine, tyrosine, and tryptophan

Which four amino acids are derived directly from pyruvate?

Alanine, valine, isoleucine, and leucine

Besides glutamate, which three amino acids are derived from alpha-ketoglutarate?

Glutamine, proline, and arginine

Besides aspartate, which four amino acids are derived from oxaloacetate?

Asparagine, methionine, threonine, and lysine