⚗️Biological Chemistry II Unit 10 – Nitrogen Metabolism

Key Concepts and Definitions

• Nitrogen is an essential element for life found in amino acids, nucleic acids, and other biomolecules
• Amino acids are the building blocks of proteins and contain an amino group ($-NH_2$) and a carboxyl group ($-COOH$)
• Nucleic acids (DNA and RNA) contain nitrogenous bases (adenine, guanine, cytosine, thymine, and uracil) that store and transmit genetic information
• Nitrogen fixation converts atmospheric nitrogen ($N_2$) into biologically usable forms such as ammonia ($NH_3$)
  • Biological nitrogen fixation is carried out by certain bacteria and archaea using the enzyme nitrogenase
• Assimilation incorporates fixed nitrogen into organic compounds like amino acids and nucleotides
• Transamination transfers an amino group from one molecule to another, often involving the cofactor pyridoxal phosphate (PLP)
• Deamination removes an amino group from an amino acid, releasing ammonia or transferring the group to another molecule
• Urea cycle is a series of biochemical reactions that convert toxic ammonia to urea for excretion

Nitrogen's Role in Biological Systems

• Nitrogen is a crucial component of proteins, which perform various functions in living organisms (enzymes, structural proteins, hormones, and antibodies)
• Nucleic acids (DNA and RNA) contain nitrogen in their nitrogenous bases, enabling the storage and transmission of genetic information
• Nitrogen is present in essential biomolecules such as ATP, NAD+, NADP+, and coenzyme A, which participate in energy transfer and metabolic reactions
• Chlorophyll, the primary pigment in photosynthesis, contains nitrogen in its structure
• Nitrogen is a key element in neurotransmitters (dopamine, serotonin, and norepinephrine) that regulate various physiological processes
• Nitrogen-containing compounds like urea, uric acid, and ammonia are involved in nitrogen excretion and waste management
• Nitrogen is essential for the synthesis of complex biomolecules (porphyrins, heme, and creatine) that have critical roles in biological processes

Nitrogen Fixation and Assimilation

• Atmospheric nitrogen ($N_2$) is converted into biologically usable forms through nitrogen fixation
  • Abiotic nitrogen fixation occurs through lightning, industrial processes (Haber-Bosch process), and combustion
  • Biological nitrogen fixation is carried out by diazotrophs, including bacteria (Rhizobium) and archaea
• Nitrogenase, a complex metalloenzyme, catalyzes the reduction of $N_2$ to $NH_3$ in biological nitrogen fixation
  • The enzyme consists of two components: dinitrogenase reductase (Fe protein) and dinitrogenase (MoFe protein)
  • The reaction requires a significant energy input in the form of ATP and reduced electron carriers (ferredoxin or flavodoxin)
• Fixed nitrogen in the form of $NH_3$ or $NH_4^+$ is assimilated into organic compounds through various pathways
  • Glutamate dehydrogenase (GDH) catalyzes the reductive amination of $\alpha$-ketoglutarate to form glutamate
  • Glutamine synthetase (GS) and glutamate synthase (GOGAT) work together to incorporate $NH_4^+$ into glutamine and glutamate
• Transaminases transfer the amino group from glutamate to other $\alpha$-ketoacids, forming various amino acids
• Amino acids serve as nitrogen donors for the synthesis of other nitrogenous compounds (nucleotides, chlorophyll, and secondary metabolites)

Amino Acid Metabolism

• Amino acids are the building blocks of proteins and can be classified as essential (obtained from diet) or non-essential (synthesized by the body)
• Transamination reactions, catalyzed by aminotransferases, transfer amino groups between amino acids and $\alpha$-ketoacids
  • Pyridoxal phosphate (PLP) serves as a cofactor in these reactions, forming a Schiff base intermediate with the amino acid
• Deamination removes the amino group from amino acids, either releasing ammonia or transferring the group to another molecule
  • Oxidative deamination, catalyzed by glutamate dehydrogenase, converts glutamate to $\alpha$-ketoglutarate and releases $NH_4^+$
• Amino acid catabolism involves the removal of the amino group and the oxidation of the carbon skeleton for energy production or glucose synthesis
  • Glucogenic amino acids (alanine and aspartate) can be converted into glucose precursors
  • Ketogenic amino acids (leucine and lysine) can be converted into ketone bodies or fatty acids
• Amino acid biosynthesis pathways are tightly regulated to maintain homeostasis
  • Feedback inhibition controls the activity of key enzymes in the biosynthetic pathways
  • Transcriptional regulation modulates the expression of genes encoding enzymes involved in amino acid metabolism

Protein Synthesis and Degradation

• Protein synthesis (translation) occurs on ribosomes and involves the decoding of mRNA to produce a specific sequence of amino acids
  • Aminoacyl-tRNA synthetases attach amino acids to their cognate tRNAs, ensuring the accuracy of protein synthesis
  • The ribosome catalyzes the formation of peptide bonds between amino acids, following the genetic code
• Protein folding occurs during and after translation, allowing the polypeptide chain to assume its functional three-dimensional structure
  • Chaperones (Hsp70 and Hsp60) assist in the folding process and prevent aggregation
  • Post-translational modifications (phosphorylation, glycosylation, and disulfide bond formation) can modulate protein function and stability
• Protein degradation is essential for maintaining cellular homeostasis and removing damaged or misfolded proteins
  • The ubiquitin-proteasome system selectively targets proteins for degradation by tagging them with ubiquitin molecules
  • Lysosomes, containing various hydrolytic enzymes, break down proteins and other cellular components through autophagy
• Protein turnover, the balance between synthesis and degradation, is regulated by hormones, growth factors, and cellular signaling pathways
  • Insulin promotes protein synthesis and inhibits degradation, while glucocorticoids have the opposite effect
• Nitrogen balance, the difference between nitrogen intake and loss, is an indicator of overall protein metabolism in the body

Nitrogen Excretion and the Urea Cycle

• Nitrogen excretion is the process of removing nitrogenous waste products from the body to maintain homeostasis
  • Ammonia ($NH_3$) is toxic and must be converted into less harmful compounds before excretion
  • Different organisms use various strategies for nitrogen excretion (ammonia, urea, or uric acid) depending on their environment and physiology
• The urea cycle is a series of biochemical reactions that convert ammonia to urea in the liver
  • The cycle involves five enzymes: carbamoyl phosphate synthetase I (CPS1), ornithine transcarbamylase (OTC), argininosuccinate synthetase (ASS), argininosuccinate lyase (ASL), and arginase
  • The cycle begins with the formation of carbamoyl phosphate from $NH_4^+$, $HCO_3^-$, and ATP by CPS1
  • Citrulline is formed by the condensation of carbamoyl phosphate with ornithine, catalyzed by OTC
  • Aspartate is added to citrulline to form argininosuccinate, which is then cleaved into arginine and fumarate by ASL
  • Arginase cleaves arginine to release urea and regenerate ornithine
• Urea is a water-soluble compound that is excreted in urine, allowing the efficient removal of nitrogenous waste
• The urea cycle is regulated by substrate availability and allosteric control of key enzymes (CPS1 and OTC)
  • N-acetylglutamate (NAG), synthesized from glutamate and acetyl-CoA, is an essential activator of CPS1

Metabolic Disorders and Clinical Relevance

• Inborn errors of metabolism can disrupt nitrogen metabolism, leading to various clinical manifestations
  • Phenylketonuria (PKU) is caused by a deficiency in phenylalanine hydroxylase, leading to the accumulation of phenylalanine and its toxic metabolites
  • Maple syrup urine disease (MSUD) results from a defect in the branched-chain $\alpha$-ketoacid dehydrogenase complex, causing the accumulation of branched-chain amino acids and their $\alpha$-ketoacids
• Urea cycle disorders arise from deficiencies in any of the five enzymes involved in the cycle
  • Ornithine transcarbamylase deficiency (OTCD) is the most common urea cycle disorder, characterized by hyperammonemia and neurological symptoms
  • Treatment for urea cycle disorders includes dietary protein restriction, amino acid supplementation, and medications (sodium benzoate and phenylbutyrate) to remove excess nitrogen
• Nitrogen balance is an important consideration in clinical nutrition
  • Positive nitrogen balance (nitrogen intake > nitrogen loss) is essential for growth, pregnancy, and recovery from illness or injury
  • Negative nitrogen balance (nitrogen loss > nitrogen intake) can occur during starvation, severe illness, or prolonged stress
• Nutritional support in clinical settings aims to maintain nitrogen balance and prevent muscle wasting
  • Enteral nutrition provides nutrients through a feeding tube into the gastrointestinal tract
  • Parenteral nutrition delivers nutrients intravenously when enteral feeding is not possible or sufficient

Lab Techniques and Experimental Methods

• Kjeldahl method is used to determine the total nitrogen content in a sample
  • The sample is digested with sulfuric acid and a catalyst (copper sulfate) to convert organic nitrogen to ammonium sulfate
  • The ammonia is then distilled and titrated with a standard acid solution to quantify the nitrogen content
• Amino acid analyzers use ion-exchange chromatography to separate and quantify individual amino acids in a sample
  • The sample is hydrolyzed to break down proteins into their constituent amino acids
  • The amino acids are derivatized with ninhydrin to form colored complexes that can be detected spectrophotometrically
• High-performance liquid chromatography (HPLC) is used to separate and analyze amino acids and other nitrogen-containing compounds
  • Reverse-phase HPLC employs a non-polar stationary phase and a polar mobile phase to separate compounds based on their hydrophobicity
  • Pre-column derivatization with fluorescent tags (o-phthalaldehyde or phenylisothiocyanate) enhances the detection sensitivity
• Mass spectrometry (MS) is a powerful tool for identifying and quantifying nitrogen-containing compounds
  • Electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI) are commonly used ionization techniques for biomolecules
  • Tandem mass spectrometry (MS/MS) enables the fragmentation of ions and provides structural information for peptide sequencing and protein identification
• Isotopic labeling techniques are used to study nitrogen metabolism and trace the fate of nitrogen atoms in biological systems
  • Stable isotopes ($^{15}N$) can be incorporated into amino acids, nucleic acids, or other compounds to monitor their synthesis, turnover, and degradation
  • Radioactive isotopes ($^{13}N$ and $^{14}C$) are used in metabolic labeling experiments, but their short half-lives limit their applications
• Enzyme assays are employed to measure the activity of enzymes involved in nitrogen metabolism
  • Coupled enzyme assays indirectly measure the activity of the target enzyme by monitoring the formation or consumption of a product or cofactor in a secondary reaction
  • Spectrophotometric assays detect changes in absorbance due to the formation or depletion of a chromogenic substrate or product
• Recombinant DNA technology allows the expression and purification of enzymes involved in nitrogen metabolism for functional and structural studies
  • Genes encoding enzymes of interest are cloned into expression vectors and transformed into suitable host cells (E. coli or yeast)
  • Affinity chromatography (His-tag or GST-tag) is used to purify the recombinant enzymes for biochemical characterization and crystallization