Organic Compounds, Macromolecules, and Cellular Energetics

Vis vitalis

The hypothetical vital force previously believed to be unique to living organisms and essential for the synthesis of organic substances, an idea disproved in $1828$ by Friedrich Wöhler when he synthesized urea from inorganic starting materials.

Organic Compounds

All chemical compounds containing carbon, with the specific exceptions of carbon monoxide ($CO$), carbon dioxide ($CO_2$), carbonic acid ($H_2CO_3$), and its carbonate salts.

Small Organic Molecules

Cellular organic molecules containing up to $30$ carbon atoms with a relative molecular mass between $100$ and $1000$, typically existing freely in the cytosol as monomers or metabolic intermediates.

Biopolymers

High-molecular-weight biological macromolecules ($M_r$ ranging from $10\,000$ to $1\,000\,000$) formed by the covalent condensation of repeating monomeric subunits.

Chiral Carbon Atom

An asymmetric carbon atom bonded to four chemically distinct atoms or groups, giving rise to two non-superimposable mirror-image forms ($L$- and $D$-stereoisomers).

Phenylethylamine (PEA)

A low-molecular-weight monoamine alkaloid synthesized from the amino acid $L$-phenylalanine, known as the 'love hormone', which accelerates heart rate, elevates energy levels, and is naturally present in chocolate.

Monosaccharides

Low-molecular carbohydrates with the general empirical formula $C_n(H_2O)_n$ (where $n = 3\text{--}8$) that possess a single carbonyl group (aldehyde or ketone) and one or more hydroxyl groups.

Glycosidic Hydroxyl Group

The reactive hydroxyl group formed at the newly asymmetric $C1$ carbon atom when an open-chain monosaccharide cyclizes into a ring structure, enabling the formation of a glycosidic bond.

Reducing Sugars

Sugars containing a free aldehyde group that can reduce copper(II) hydroxide ($Cu(OH)_2$) upon heating to yield a characteristic brick-red precipitate of copper(I) oxide ($Cu_2O$).

Fatty Acids

Amphipathic lipid components consisting of a polar, hydrophilic carboxyl group head ($-COOH$) and a nonpolar, hydrophobic hydrocarbon tail.

Triglycerides (Neutral Fats)

Esters formed from one glycerol molecule joined to three fatty acid molecules, functioning as concentrated energy stores yielding $38.9\,kJ$ of energy per gram.

Phospholipids

Amphipathic membrane lipids consisting of a glycerol or sphingosine backbone linked to two hydrophobic fatty acid chains and a hydrophilic phosphate head group.

Steroids

Lipid compounds composed of a characteristic four-ring fused carbon core with appended functional groups, including cholesterol and steroid hormones (e.g., estrogen, testosterone, cortisol, aldosterone).

Glycemic Index (GI)

A numerical scale measuring how rapidly and significantly a specific food elevates blood glucose concentration compared to pure reference glucose (assigned a value of $100$).

Amphoteric Nature of Amino Acids

The capacity of an amino acid to exhibit both acidic and basic behaviors in solution depending on $pH$, mediated by its basic amino group ($-NH_2$) and acidic carboxyl group ($-COOH$).

Disulfide Bridge

A strong covalent bond formed by the oxidation of two sulfhydryl ($-SH$) groups belonging to separate cysteine residues, stabilizing protein tertiary and quaternary structures.

Peptide Bond

A covalent amide linkage ($-CO-NH-$) established between the carboxyl group of one amino acid and the amino group of an adjacent amino acid with the release of water ($H_2O$).

Nucleoside

A biochemical structural unit composed exclusively of a nitrogenous base covalently joined to the $C1'$ carbon of a pentose sugar via an $N$-glycosidic bond.

Macroergic (High-Energy) Bonds

Chemical bonds whose enzymatic hydrolysis releases a large amount of biologically usable free energy ($\Delta G' = 30\text{--}70\,kJ\,mol^{-1}$), commonly symbolized by a tilde ($\sim$).

Adenosine Triphosphate (ATP)

The universal cellular energy shuttle, comprised of the purine adenine, ribose, and three phosphate residues connected by one standard phosphoester bond and two macroergic phosphoanhydride bonds.

Nicotinamide Adenine Dinucleotide (NAD)

A dinucleotide coenzyme consisting of an $AMP$ moiety bonded via its phosphate to nicotinamide mononucleotide (derived from vitamin $PP$/niacin), functioning as an electron and hydrogen carrier.

Flavin Adenine Dinucleotide (FAD)

A redox coenzyme composed of riboflavin (vitamin $B_2$) linked to $ADP$, which can be reversibly reduced to $FADH_2$ by accepting two hydrogen atoms.

Aperiodic Heteropolymers

Biopolymers constructed from non-repeating sequences of diverse monomer units, enabling them to store, carry, and express biological information (e.g., nucleic acids and proteins).

Native Conformation

The unique, biologically functional three-dimensional spatial configuration adopted by a polypeptide chain upon synthesis and proper folding.

Alpha-Helix ($\alpha$-helix)

A helical secondary protein structure maintained by intramolecular hydrogen bonds formed between the $NH$ group of one peptide unit and the $CO$ group of another located three amino acid residues away.

Protein Denaturation

The disruption of a protein's secondary, tertiary, and quaternary structural levels with the destruction of noncovalent stabilizing bonds, leading to the loss of biological function.

Activation Energy ($E_a$)

The initial energetic threshold that reactant molecules must overcome to attain the high-energy transition state required for a chemical reaction to occur.

Apoenzyme

The high-molecular-weight protein component of a conjugated two-component enzyme that requires the addition of a non-protein cofactor or coenzyme to achieve catalytic capability.

Michaelis Constant ($K_m$)

The substrate concentration at which an enzyme catalyzes a reaction at half of its maximal velocity ($V_{max}/2$); a low $K_m$ signifies high substrate affinity.

Competitive Inhibition

Reversible enzyme inhibition occurring when an inhibitor structurally resembles the normal substrate and competes directly with it for occupancy of the active catalytic site.

Allosteric Regulation

The control of enzyme velocity resulting from the reversible binding of regulatory effector molecules to an allosteric site located outside the active catalytic domain.

Chargaff's Rules

The quantitative base ratios found in double-stranded DNA where the molar abundance of adenine equals thymine ($A = T$), guanine equals cytosine ($G = C$), and purines equal pyrimidines ($A + G = T + C$).

DNA Melting Temperature ($T_m$)

The temperature at which half of the helical structure of double-stranded DNA is denatured into single strands, increasing proportionally with the number of $G\text{--}C$ base pairs.

Nucleic Acid Hybridization