21.5 Amino Acid & Nitrogen Metabolism + Protein Structure

Transamination and Deamination

Amino acid metabolism centers on the management of the α-amino group. Transamination, catalyzed by aminotransferases (transaminases) using the cofactor pyridoxal phosphate (PLP, vitamin B6), transfers the α-amino group from an amino acid to an α-ketoacid, producing a new amino acid and a new α-ketoacid. The most clinically relevant are ALT (alanine → pyruvate; liver-specific marker of hepatocellular injury) and AST (aspartate → oxaloacetate; found in liver, heart, muscle). The universal amino-group acceptor is α-ketoglutarate, forming glutamate. Oxidative deamination of glutamate by glutamate dehydrogenase (matrix, NAD+/NADP+-linked, activated by ADP, inhibited by GTP) releases free ammonia (NH4+), which enters the urea cycle.

Urea Cycle

The urea cycle in the liver converts toxic ammonia to urea for renal excretion, the principal route of nitrogen disposal in humans. The five enzymatic steps span mitochondria and cytosol:

1. Carbamoyl phosphate synthetase I (CPS-I) — mitochondrial; NH4+ + CO2 + 2 ATP → carbamoyl phosphate; N-acetylglutamate (NAG) is an obligate activator. NAG is synthesized from acetyl-CoA and glutamate, signaling amino acid abundance.
2. Ornithine transcarbamylase — carbamoyl phosphate + ornithine → citrulline (mitochondrial → cytosolic exit).
3. Argininosuccinate synthetase — citrulline + aspartate + ATP → argininosuccinate.
4. Argininosuccinate lyase → arginine + fumarate.
5. Arginase → urea + ornithine (ornithine re-enters mitochondria).

Urea cycle disorders (e.g., OTC deficiency, X-linked, most common) cause hyperammonemia, cerebral edema, lethargy, vomiting, and protein aversion; treatment limits protein, uses nitrogen scavengers (benzoate, phenylbutyrate) and citrulline/arginine supplementation.

One-Carbon Metabolism and Specialized Products

Folate and vitamin B12 (cobalamin) underpin one-carbon (C1) metabolism, the network that synthesizes purines, thymidylate (dTMP), and remethylates homocysteine to methionine (via methionine synthase, B12-dependent). Tetrahydrofolate (THF) carries one-carbon units at three oxidation levels (methylene, methenyl, formyl). S-adenosylmethionine (SAM), synthesized from methionine + ATP, is the universal methyl donor for DNA, RNA, proteins, lipids, and catecholamines. Elevated homocysteine results from folate, B12, or B6 deficiency and is associated with vascular disease and neural tube defects; folate supplementation prenatally reduces neural tube defect risk.

Heme synthesis occurs in all cells (mostly bone marrow erythroblasts and liver) across mitochondria and cytosol. The committed step is δ-aminolevulinic acid (ALA) synthase (mitochondrial, PLP-dependent, feedback-inhibited by heme). ALA dehydratase (zinc-dependent) → porphobilinogen → uroporphyrinogen → coproporphyrinogen → protoporphyrin IX, which ferrochelatase metalates with Fe2+ to form heme. Lead poisoning inhibits ALA dehydratase and ferrochelatase, causing microcytic anemia and elevated ALA and coproporphyrin. Porphyrias (e.g., acute intermittent porphyria, porphobilinogen deaminase deficiency) cause neurovisceral attacks and photosensitivity depending on the affected step.

Protein Structure: Levels and Forces

Protein function derives from structure, organized in four hierarchical levels:

• Primary structure — the linear amino acid sequence, encoded by the gene, joined by peptide bonds (planar, partial double-bond character, trans configuration).
• Secondary structure — local folding stabilized by backbone hydrogen bonds: α-helix (3.6 residues/turn, R-groups outward), β-sheet (parallel or antiparallel strands), β-turns, and loops. The peptide bond itself is rigid; only the N-Cα and Cα-C bonds rotate, defining the Ramachandran allowed regions.
• Tertiary structure — the overall three-dimensional fold of a single polypeptide, stabilized by hydrophobic packing (the dominant driving force, the hydrophobic effect), hydrogen bonds, ionic interactions (salt bridges), and disulfide bonds (cystine, oxidized cysteine, in the ER).
• Quaternary structure — arrangement of multiple polypeptide subunits (e.g., hemoglobin's α2β2 tetramer, immunoglobulin's 4-chain structure); stabilized by the same non-covalent forces.

Protein folding is largely spontaneous in vivo but assisted by chaperones (Hsp60/GroEL, Hsp70) that prevent misfolding and aggregation. Misfolded proteins underlie many diseases — prion diseases, Alzheimer's (Aβ, tau), cystic fibrosis (CFTRΔF508 folding defect), α1-antitrypsin deficiency.

Hemoglobin, Myoglobin, and Collagen

Myoglobin is a single-subunit, 153-residue muscle protein storing O2; its O2-binding curve is hyperbolic (no cooperativity). Hemoglobin is an α2β2 tetramer; its O2-binding curve is sigmoidal due to cooperative binding — binding of O2 to one subunit shifts that subunit from the T (tense, low-affinity) to R (relaxed, high-affinity) state, favoring the R state in adjacent subunits. 2,3-BPG binds the central cavity of deoxy-Hb, stabilizing T state and reducing affinity (right shift). Low pH and high CO2 (Bohr effect) reduce Hb affinity, promoting O2 unloading in tissues. The PA-CAT Bulletin of Information, rev. 20240815, links oxygen binding to protein structure within Metabolism/Proteins.

Collagen, the most abundant protein in mammals, is a triple helix of three left-handed polyproline-II chains (Gly-X-Y repeat, where X often Pro, Y often hydroxyproline). Glycine at every third residue (smallest side chain) fits the helix core. Vitamin C is required for proline/lysine hydroxylation by prolyl/lysyl hydroxylases; deficiency (scurvy) produces weak collagen, bleeding gums, and poor wound healing. Extracellular processing by procollagen peptidases and lysyl oxidase (copper-dependent) cross-links mature collagen fibers.

Tying this to a representative PA-CAT sample-item skill: given an enzyme with a high Km and a noncompetitive inhibitor, the correct interpretation is that the enzyme has low substrate affinity and that Vmax decreases while Km is unchanged — a direct application of Michaelis-Menten concepts from Section 21.1. This integration of enzyme kinetics, metabolism, and protein structure is exactly what the PA-CAT Biochemistry (5%) content tests.