In-Depth Notes on Amino Acid and Nitrogen Metabolism

I. Nitrogen Acquisition and Fate
A. Nitrogen Cycle
1. All organisms convert ammonia ($NH3$) into organic nitrogen (C-N compounds). 2. Dinitrogen gas ($N2$) is abundant but less accessible for many organisms to fix ammonia.
3. Biological nitrogen fixation rarely occurs; conversion from $NO3^-$ to $NH3$ is predominant, especially in plants and microbes.
4. Nitrogen limitation is critical for growth in many organisms.
5. Examining nitrogen economics helps understand nitrogen supply, demand, use, and maintenance.

II. Nitrogen Fixation
A. Sites of Nitrogen Fixation
1. Nitrogen-fixing crops like clover, soybeans, and alfalfa contain bacteria in root nodules that assist in fixation.
2. The triple bond in $N2$ has high energy (~940 kJ/mol), making it energetically challenging to reduce. B. Enzyme: Nitrogenase 1. Responsible for biological reduction of $N2$.
C. Haber-Bosch Process
1. Industrial replication of nitrogen fixation.

III. Biological Assimilation of Ammonia
A. Ammonia is toxic in excess and is assimilated into molecules such as:
1. Glutamate
2. Glutamine
3. Asparagine
4. Carbamoyl phosphate
B. Key Enzyme Activities
1. Glutamate dehydrogenase – converts $α-ketoglutarate$ to glutamate; the reaction direction varies based on environment.
2. Glutamine synthetase – generates active amide nitrogen with ATP hydrolysis.
3. Asparagine synthetase – similar role to glutamine synthetase.

IV. Nitrogen Economy and Protein Turnover
A. Nitrogen Economy
1. Cycle from inorganic nitrogen to organic nitrogen via ammonia ($NH_3$).
2. Study by Rudolf Schoenheimer (1930s) observed nitrogen metabolism in rats with 15N-labeled tyrosine; ~50% nitrogen was excreted and the rest was incorporated into proteins.
B. Protein Turnover
1. Continuous synthesis and degradation allow for regulation and replacement of damaged proteins.
2. Typical protein half-life in rats: 1-2 days.

V. Proteasome Functionality
A. The proteasome is an ATP-dependent non-lysosomal protease.
B. Targets only proteins tagged with ubiquitin, aiding proteolysis.
C. Ubiquitin ligase catalyzes attachment of ubiquitin to proteins for degradation.

VI. Cofactors and Coenzymes in Nitrogen Metabolism
A. Pyridoxal Phosphate (PLP)
1. Acts as a coenzyme for amino acid transformations.
2. Forms a Schiff base with substrates, facilitating reactions at specific carbons (α, β, and γ).
B. Tetrahydrofolate (THF)
1. Derives from folic acid; carries one-carbon units for bond formation.
2. Deficiency leads to cardiovascular issues and birth defects; active coenzyme generated via dihydrofolate reductase (DHFR).
C. Vitamin B12
1. Coenzymes include methylcobalamin and 5'-deoxyadenosylcobalamin.
2. Critical roles in metabolic processes; deficiency leads to pernicious anemia.

VII. Amino Acid Degradation and Biosynthesis
A. Transamination
1. Converts amino acids into corresponding α-keto acids via aminotransferases using PLP.
2. Important for central metabolism and ammonia assimilation.
B. Urea Cycle
1. Eliminates excess ammonia; urea contains carbon from carbamoyl phosphate and nitrogen from aspartate.
C. Biosynthetic and Degradative Pathways
1. Amino acids interconnected through metabolic pathways involving intermediates from glycolysis or the citric acid cycle.
2. Essential amino acids must be obtained from the diet.