10.3 Proteins, Amino Acids, and Peptides

Amino acid chemistry and the essential list

This topic is 13% of Chemistry. The official bullets are amino-acid catabolic and anabolic pathways, structure/properties/function, and food sources plus digestion. Peptide hormones as endocrine signals belong to the Hormones chapter; here the peptide is a substrate, a chain, or a dietary protein.

Quick Answer: Twenty standard amino acids, nine essential. Nitrogen leaves as urea after transamination (PLP) and the urea cycle (CPS-I + NAG). Leu and Lys are purely ketogenic. Pepsin then pancreatic endopeptidases digest dietary protein. Structure runs primary → secondary → tertiary → quaternary.

Every standard amino acid has an α-carbon, an α-amino group, an α-carboxylate, and an R group. At physiologic pH the α-carboxyl is deprotonated and the α-amino is protonated (zwitterion). The isoelectric point (pI) is the pH at which net charge is zero. Electrophoresis and ion-exchange chromatography sort amino acids by charge; a high-yield example is hemoglobin S (Glu6Val) changing charge and causing the sickle migration pattern.

Only glycine is achiral. The rest are L-α-amino acids in proteins. R groups set chemistry:

Essential amino acids cannot be synthesized in sufficient amount: His, Ile, Leu, Lys, Met, Phe, Thr, Trp, Val (PVT TIM HaLL). Arginine is semi-essential in children and whenever the urea cycle is draining it. Tyrosine is made from phenylalanine (phenylalanine hydroxylase + BH4); cysteine sulfur comes from methionine (transsulfuration). In PKU, tyrosine becomes essential. Kwashiorkor is protein deficiency with some calories (edema, fatty liver from apoB failure); marasmus is total energy deficiency (wasting without edema). Complete proteins (egg, milk, meat, soy) supply the essential set; many grains are lysine-poor and many legumes are methionine-poor — the complementarity story.

Glucogenic versus ketogenic. Catabolism to pyruvate or TCA intermediates can make net glucose. Catabolism only to acetyl-CoA or acetoacetate cannot. Leucine and lysine are purely ketogenic. Ile, Phe, Thr, Trp, Tyr are both. The rest are glucogenic. Alanine is the muscle-to-liver glucose carrier (Cahill cycle).

Digestion of dietary protein

Stomach chief cells secrete pepsinogen. HCl (parietal cell) and autocatalysis activate pepsin, an aspartic endopeptidase with optimum pH ~2 that prefers aromatic and acidic residues. Pepsin is denatured in the duodenum when bicarbonate raises pH.

Duodenal enteropeptidase (enterokinase) cleaves trypsinogen to trypsin. Trypsin then activates more trypsinogen plus chymotrypsinogen, proelastase, and procarboxypeptidases A/B. That cascade is why a small amount of enteropeptidase failure (or a trypsin inhibitor such as in acute pancreatitis pathophysiology) wrecks all downstream zymogens.

Free amino acids and di-/tripeptides are absorbed. Several Na+-dependent apical transporters split by amino-acid class. Hartnup disease (neutral amino-acid transporter, including tryptophan) can mimic pellagra. Cystinuria (dibasic transporter: Cys, Orn, Lys, Arg — COLA) produces hexagonal cystine stones. Those are digestion/absorption lesions, not urea-cycle lesions.

Pancreatic trypsin inhibitor (SPINK1) and the fact that zymogens are stored inactive are why the pancreas does not digest itself on a quiet day.

Nitrogen disposal: transamination, glutamate dehydrogenase, urea cycle

Aminotransferases move the α-amino group to α-ketoglutarate, producing glutamate plus an α-ketoacid. The cofactor is pyridoxal phosphate (PLP, vitamin B6), covalently bound via a Schiff base to a lysine, then to the substrate. ALT (alanine aminotransferase): alanine ⇌ pyruvate. AST (aspartate aminotransferase): aspartate ⇌ oxaloacetate. AST also feeds the urea cycle because aspartate donates the second nitrogen at argininosuccinate synthase. Both enzymes leak into plasma after hepatocyte injury; AST also lives in muscle and mitochondria, which is why the AST/ALT pattern is not liver-only.

Glutamate dehydrogenase (liver mitochondria) oxidatively deaminates glutamate to α-ketoglutarate + NH4+, using NAD+ or NADP+. GTP inhibits; ADP activates — a nitrogen valve tied to energy charge. Glutamine synthetase mops ammonia in muscle and brain (glutamate + NH4+ + ATP → glutamine). Glutaminase in liver periportal hepatocytes and in kidney (acid-base) releases NH4+ again. Brain is vulnerable to ammonia because glutamine accumulation in astrocytes swells cells and because glutamate/GABA neurotransmission is disturbed — the chemistry behind hyperammonemic encephalopathy, including in a chiropractic-college biochemistry item.

Urea cycle, recited with regulation

Urea is made in periportal hepatocytes. Two nitrogens: one from ammonia (via carbamoyl phosphate), one from aspartate. Carbon comes from CO2/HCO3−.

| Enzyme | Compartment | Reaction | Cofactors / notes | |---|---|---| | N-acetylglutamate synthase | Mitochondria | Glutamate + acetyl-CoA → NAG | Activated by arginine | | CPS-I | Mitochondria | NH4+ + HCO3− + 2 ATP → carbamoyl phosphate | Rate-limiting; absolute requirement for NAG | | OTC | Mitochondria | Carbamoyl phosphate + ornithine → citrulline | X-linked; most common cycle defect | | Argininosuccinate synthase | Cytosol | Citrulline + aspartate + ATP → argininosuccinate | Citrullinemia type I | | Argininosuccinate lyase | Cytosol | → arginine + fumarate | Fumarate links to TCA (aspartate-argininosuccinate shunt) | | Arginase | Cytosol | Arginine + H2O → urea + ornithine | Ornithine returns to mitochondria via ORNT1 |

N-acetylglutamate is the hormonal-metabolic switch: more protein / more arginine / more glutamate → more NAG → CPS-I on. Fasting still needs the cycle because muscle proteolysis continues; carbohydrate feeding with little protein lowers the amino-nitrogen load. Each urea costs 4 ATP equivalents (2 ATP at CPS-I; ATP to AMP at argininosuccinate synthase).

CPS-II is a different enzyme in cytosol pyrimidine synthesis (CAD complex) and uses glutamine, not ammonia, and is not NAG-activated. That distinction writes the orotic-acid item:

• OTC deficiency: carbamoyl phosphate leaks to cytosol → CPS-II-independent overflow into pyrimidine synthesis → orotic acid up, citrulline down, ammonia up, no megaloblastic anemia required. X-linked; male neonates present in crisis; female mosaics vary.
• CPS-I or NAGS deficiency: ammonia up, orotic acid not up, citrulline down.
• Argininosuccinate synthase deficiency: citrulline very high.
• Arginase deficiency: arginine high; spastic diplegia can dominate over neonatal hyperammonemia.

Treatment logic (physiology, not a prescription pad): limit protein, supply glucose to stop proteolysis, give phenylbutyrate/benzoate to siphon nitrogen, give citrulline or arginine to refill cycle intermediates distal to a block, and in NAGS deficiency the analog carglumic acid activates CPS-I.

Worked lab split. Neonate, lethargy, high ammonia, low citrulline. If urine orotate is high, name OTC. If orotate is low/normal, name CPS-I/NAGS. If citrulline is sky-high, you are past OTC. That algorithm is worth more than memorizing every rare allele.

Selected catabolic pathways that write items

Branched-chain amino acids (Val, Ile, Leu) are transaminated in muscle, then the branched-chain α-ketoacid dehydrogenase (same TPP/lipoamide/CoA/FAD/NAD architecture as PDH) oxidatively decarboxylates them. Maple syrup urine disease is that dehydrogenase. Leucine is the purely ketogenic branched-chain; valine is glucogenic; isoleucine is both.

Phenylalanine hydroxylase (BH4) → tyrosine. PKU: phenylalanine and phenylketones rise; tyrosine falls; hypomyelination and hypopigmentation (tyrosine is the melanin precursor). Dihydropteridine reductase defects mimic PKU but do not respond to dietary Phe restriction alone because BH4 is also needed for neurotransmitter hydroxylases.

Alkaptonuria: homogentisate oxidase; homogentisic acid oxidizes to a dark pigment in urine and deposits in cartilage (ochronosis) — a connective-tissue chemistry hook. Albinism: tyrosinase. Homocystinuria (classic cystathionine β-synthase, PLP): methionine and homocysteine high, cysteine low; thrombosis, lens dislocation, marfanoid habitus. Methionine synthase (methyl-B12, 5-methyl-THF) is the other homocysteine disposal route and is the folate trap connection.

Creatine is made from Gly + Arg + SAM; creatine kinase makes phosphocreatine. NO synthase uses arginine. Those are amino-acid anabolic side paths, not urea-cycle steps.

Protein structure and folding

A peptide bond is an amide between the α-carboxyl of one residue and the α-amino of the next. It is planar and usually trans because of partial double-bond character; rotation is around φ and ψ (Ramachandran). The chain has an N-terminus and a C-terminus. Primary structure is the covalent sequence, including disulfide bonds as covalent cross-links (still counted with primary/post-translational covalent structure).

Secondary structure: local hydrogen bonds between backbone C=O and N-H. α-helix (3.6 residues/turn, H-bonds i to i+4; Pro is a breaker). β-sheet (parallel or antiparallel). β-turns. Collagen is a left-handed polyproline type II helix packed as a right-handed triple helix with Gly-X-Y (X often Pro, Y often hydroxyproline). Vitamin C is required for prolyl and lysyl hydroxylases; without hydroxylation, triple helices are unstable (scurvy). That is protein chemistry, not a vitamin-chapter monopoly.

Tertiary structure: the fold of one polypeptide — hydrophobic core, salt bridges, H-bonds, disulfides (extracellular), van der Waals. Quaternary structure: more than one subunit (hemoglobin α2β2, PFK-1 tetramer, aspartate transcarbamoylase). Myoglobin is tertiary only. Denaturation (urea, guanidinium, SDS, heat, pH) unfolds without breaking peptide bonds; renaturation of ribonuclease (Anfinsen) showed sequence can determine fold. Chaperones (Hsp70, chaperonins) and the proteasome handle the failures. Prion disease is a β-sheet-rich conformer templating the same sequence — structure, not a virus (viruses and prions as microbes are Microbiology).

Motifs versus domains: a helix-turn-helix is a motif; a kinase domain is a independently folding module. Post-translational modifications change function without changing the gene: phosphorylation (Ser/Thr/Tyr), γ-carboxylation of clotting factors (vitamin K), N-glycosylation (ER, Asn-X-Ser/Thr), acetylation, ubiquitination.

Worked structure item. Insulin is two chains linked by disulfides, cut from proinsulin (C-peptide stays in the granule and is a secretion marker). The disulfides are covalent; the active hormone still has a defined tertiary fold. Hemoglobin’s T→R shift is quaternary regulation by O2, H+, 2,3-BPG, and CO2 — protein chemistry meeting respiratory physiology.

/practice/nbce-part1Practice questions with detailed explanations