Chemistry of Biomolecules: Proteins and Amino Acids

Practice vocabulary flashcards outlining protein structure, amino acid categories, nutritional classification, metabolic catabolism, and specialized derivatives synthesized from amino acids.

Proteins

Organic macromolecules with a backbone formed by the polymerization of amino acids (polypeptides) that constitute over $50\%$ of the dry weight of cells and serve as the instruments through which genetic information is expressed.

Proteous

The Greek word meaning 'primary' from which the term 'protein' is derived.

Peptide Bond Formation

A condensation reaction linking amino acids with the loss of one water ($H_2O$) molecule, where the $-OH$ is contributed from the carboxyl terminal of one amino acid and the $-H$ is removed from the nitrogen terminal of the other.

Chirality of Standard Amino Acids

The property of $19$ of the $20$ standard amino acids having an asymmetric (chiral) $\alpha$-carbon atom, occurring exclusively as L-stereoisomers in proteins.

Glycine

The smallest standard amino acid, which is uniquely achiral because it has a second hydrogen atom attached to its $\alpha$-carbon.

4-Hydroxyproline and 5-Hydroxylysine

Uncommon amino acid residues created by the post-incorporation modification of proline and lysine residues, respectively.

Methyllysine

An uncommon modified amino acid residue that serves as a constituent of myosin, a contractile protein found in muscle.

$\gamma$-Carboxyglutamate

An uncommon amino acid residue found in the blood-clotting protein prothrombin and in other proteins that bind $Ca^{2+}$ as part of their biological function.

Desmosine

A modified derivative of four lysine (Lys) residues found in the fibrous protein elastin.

Essential Amino Acids

Ten amino acids that must be obtained from the diet, remembered by the mnemonic 'VITTAL LyMPH': Val, Ile, Thr, Trp, Arg, Leu, Lys, Met, Phe, and His.

Semi-Essential Amino Acids

Arginine (Arg) and Histidine (His); synthesized in sufficient amounts by healthy adults, but require dietary supplementation during childhood growth, sickness, convalescence, and pregnancy.

Enzymes

Highly specialized proteins possessing catalytic activity that catalyze nearly all chemical reactions of organic biomolecules in the cell (e.g., phosphatases, hydrolases).

Transport Proteins

Proteins that move substances between body locations; examples include hemoglobin ($O_2$ and $CO_2$), lipoproteins (plasma lipids), albumin (aldosterone and testosterone), sex hormone-binding protein, and cortisol-binding protein.

Contractile (Motile) Proteins

Proteins that confer the ability to contract, change shape, and move to cells and organisms; exemplified by actin and myosin in skeletal muscle.

Structural Proteins

Proteins functioning as supporting cables that provide strength and protection; includes collagen (connective tissue, cartilage, bone, eyeball), elastin (ligaments, large arteries, vocal cords), and keratin (nails, hair, feathers).

Defense Proteins

Proteins that defend organisms against foreign invasion or injury; includes antibodies produced by lymphocytes (WBCs) that recognize and hydrolyze invading bacteria, viruses, or foreign proteins.

Regulatory Proteins

Proteins involved in regulating cellular activity, such as protein and amino acid-derived hormones including insulin, ADH, ACTH, catecholamines, and thyroid hormones.

Storage Proteins

Proteins dedicated to storing essential chemical species within cells, such as myoglobin (oxygen in muscle), ferritin (iron), and ceruloplasmin (copper).

Globular Proteins

Proteins composed of compactly folded and coiled polypeptides forming a globular (ovoid) shape that are usually soluble in aqueous media (e.g., insulin, blood proteins, nearly all enzymes, antibodies, receptors).

Fibrous Proteins

Proteins composed of polypeptide chains extended along one axis that coil in a spiral/helix, cross-linked by covalent or hydrogen bonds; they are insoluble in aqueous systems and highly resistant to enzyme digestion (e.g., collagen, keratin, elastin, myosin, actin).

Simple Proteins

Proteins that contain only standard amino acids in their structure (e.g., insulin, anti-diuretic hormone [ADH], ACTH).

Conjugate (Complex) Proteins

Proteins that contain an additional non-amino acid component in their structure, such as heme, coenzymes, lipids, or carbohydrates.

Prosthetic Group

The non-amino acid portion of a complex or conjugated protein.

Apoprotein

The protein portion alone of a conjugated or complex protein, without its prosthetic group.

Proline

A nonpolar aliphatic amino acid whose cyclic imino group is held in a rigid conformation that reduces the flexibility of polypeptide regions in which it is found.

Cystine

A covalently linked dimeric amino acid formed when two cysteine residues are oxidized to establish a disulfide bond.

Histidine

A positively charged (basic) amino acid with an ionizable side chain of near neutrality, enabling it to facilitate enzyme-catalyzed reactions by acting as a proton donor and acceptor.

Acidic Amino Acids

Aspartic acid and glutamic acid; amino acids that act as proton donors, are negatively charged at physiologic pH, and form ionic or electrostatic bonds with positively charged molecules.

Ketogenic Amino Acids

Amino acids whose carbon skeletons are catabolized to acetyl CoA or acetoacetyl CoA.

Glucogenic Amino Acids

Amino acids whose carbon skeletons are catabolized to pyruvate, $\alpha$-ketoglutarate, succinyl CoA, fumarate, or oxaloacetate.

Purely Ketogenic Amino Acids

Leucine and lysine; the only two standard amino acids that yield solely ketogenic precursors upon degradation.

Both Ketogenic and Glucogenic Amino Acids

The five amino acids that give rise to both glucose and fatty acid precursors upon degradation: isoleucine, phenylalanine, tryptophan, threonine, and tyrosine.

Creatine Phosphate

A high-energy reservoir compound in muscle synthesized from glycine, arginine, and a methyl group from SAM; it reversibly donates a phosphate to ADP to regenerate ATP via creatine kinase (CK).

Creatinine

The metabolic waste product formed from the spontaneous, non-enzymatic cyclization of unstable creatine phosphate, which is subsequently excreted in urine.

S-Adenosylmethionine (SAM)

The principal methyl group donor in one-carbon metabolism, synthesized from methionine and ATP by methionine adenosyl transferase; notable for being a high-energy compound that contains no phosphate.

Histamine

A potent vasodilator and mediator of gastric acid secretion produced by the decarboxylation of histidine via the PLP-dependent enzyme histidine decarboxylase, released by mast cells in response to allergic reactions or trauma.

Serotonin (5-Hydroxytryptamine)

A biogenic amine synthesized from tryptophan that stimulates smooth muscle contraction, mediates pain perception, regulates sleep, temperature, and blood pressure, and is concentrated mostly in the intestinal mucosa.

Melatonin

A neurohormone synthesized in the pineal body through the N-acetylation and subsequent O-methylation of serotonin; it regulates circadian rhythm and acts as a non-enzymatic free radical scavenger.

Melanin

A protective biological pigment found in the eye, hair, and skin that shields cells from UV radiation, provides antioxidant defense, protects neural cells from toxins, and assists in inner ear sound conduction.

Catecholamines

Biologically active amines synthesized from tyrosine—comprising dopamine, norepinephrine, and epinephrine—that act as neurotransmitters in neural tissues and as adrenal hormones in the circulation.

$\gamma$-Aminobutyrate (GABA)

The primary inhibitory neurotransmitter of the CNS gray matter, synthesized by the decarboxylation of L-glutamate via the PLP-dependent enzyme L-glutamate decarboxylase.

Glutathione (GSH)

A protective tripeptide synthesized sequentially from glutamate, cysteine, and glycine that detoxifies toxic peroxides produced during normal aerobic metabolism.