Biomolecules

Carbohydrates (saccharides) are polyhydroxy compounds with general formula Cₙ(H₂O)ₘ. They are classified into monosaccharides (simple sugars), disaccharides (2 units), oligosaccharides (3–10), and polysaccharides (>10).

Monosaccharides: they are aldehydes or ketones with at least 2 —OH groups. They have the formula CₙH₂ₙOₙ.

• Aldoses: aldehyde carbonyl group (—CHO) at position 1. Examples: D-glucose (aldohexose), D-ribose (aldopentose).
• Ketoses: ketone carbonyl (>C=O) at position 2. Example: D-fructose (ketose).

Stereoisomerism: each asymmetric carbon atom (stereocenter) generates 2ⁿ isomers. D-glucose has 4 stereocenters (16 stereoisomers). The configuration of the last stereocenter (farthest from C=O) determines D-series (OH right in Fischer) or L-series (OH left). Almost all natural carbohydrates are D-series.

Cyclization and mutarotation: aldoses with 4+ C form cyclic hemiacetals by intramolecular addition of OH to C=O. D-glucose in water exists as a mixture of:

• α-D-glucopyranose (36%): anomeric OH in axial position (down in Haworth representation)
• β-D-glucopyranose (64%): anomeric OH in equatorial position (up)
• Open chain form (trace)

Mutarotation is the change in optical rotation until equilibrium, due to interconversion between α and β forms through the open-chain form.

Real-world applications: glucose is the main cellular energy source (glycolysis). Ribose is the sugar in RNA, deoxyribose in DNA. Artificial sweeteners (saccharin, aspartame) mimic the sweet taste of sugars.

The glycosidic bond forms by condensation between the anomeric OH (C1) of one monosaccharide and an —OH (or —NH) group of another molecule, with elimination of H₂O. The bond can be α or β depending on the anomeric configuration.

Disaccharides:

• Sucrose (table sugar): α-D-glucopyranosyl-(1→2)-β-D-fructofuranoside. α(1→2) bond between glucose and fructose. No free anomeric OH → non-reducing.
• Lactose (milk sugar): β-D-galactopyranosyl-(1→4)-D-glucopyranose. β(1→4) bond. Has a free anomeric OH on glucose → reducing. Lactose-intolerant individuals lack the enzyme lactase.
• Maltose (malt sugar): α-D-glucopyranosyl-(1→4)-D-glucopyranose. α(1→4) bond. Reducing.

Polysaccharides:

• Starch: mixture of amylose (linear, α(1→4) bonds) and amylopectin (branched, α(1→4) and α(1→6) bonds). It is the storage polymer of plants.
• Glycogen: highly branched amylopectin. Storage polymer of animals (liver, muscles).
• Cellulose: linear polymer of β-D-glucose with β(1→4) bonds. The β bonds give a rigid ribbon structure. Main component of plant cell wall. Mammals lack cellulase (enzyme that hydrolyzes β bonds) → cellulose is indigestible fiber.
• Chitin: polymer of N-acetylglucosamine with β(1→4) bonds. Component of arthropod exoskeleton.

Real-world applications: cellulose is the raw material for paper, rayon, and nitrocellulose. Starch is used as a food thickener and in bioethanol production. Chitin is used in medicine for absorbable sutures.

Lipids are hydrophobic biological molecules (soluble in organic solvents, insoluble in water). Main classes are:

Fatty acids: long-chain carboxylic acids (C12–C24). They are divided into:

• Saturated: no double bonds (e.g., palmitic acid C₁₆H₃₂O₂, stearic acid C₁₈H₃₆O₂). Solid at room temperature.
• Unsaturated: 1+ double bond (e.g., oleic acid C₁₈H₃₄O₂, cis-9). The cis double bond introduces a kink that prevents ordered packing → liquids at RT (oils).
• Essential: the body cannot synthesize them (linoleic and linolenic acids, omega-6 and omega-3).

Triglycerides: triesters of glycerol (glycerin, a triol) with 3 fatty acids. They are the main energy storage (9 kcal/g, double that of carbohydrates and proteins). Saponification: the reaction of triglycerides with strong base (NaOH) gives glycerol and fatty acid salts (soaps). Soaps are surfactants: the hydrophobic tail dissolves in grease, the ionic hydrophilic head in water, forming micelles.

Phospholipids: similar to triglycerides but with a phosphate group (and an amine/alcohol) at position 3 of glycerol. Phospholipids constitute the cell membrane bilayer: hydrophobic tails inward, hydrophilic heads outward (toward the aqueous environment).

Steroids: compounds with a 4-ring fused structure (3 six-membered + 1 five-membered). Cholesterol is the precursor of steroid hormones (testosterone, estrogens, cortisol) and vitamin D.

Real-world applications: excess saturated fat increases LDL (bad) cholesterol, cardiovascular risk. Unsaturated fats (olive oil) increase HDL (good) cholesterol. Trans fatty acids (industrial hydrogenated fats) are particularly harmful. Saponification is the soap-making process.

Proteins are polymers of α-amino acids (20 common, all L). Each amino acid has the general formula H₂N—CH(R)—COOH, with R (side chain) variable. The α carbon is chiral (except Glycine, R=H).

Amino acid classes:

• Polar charged +: Lysine (Lys), Arginine (Arg), Histidine (His) — basic
• Polar charged −: Aspartic acid (Asp), Glutamic acid (Glu) — acidic
• Polar neutral: Serine (Ser), Threonine (Thr), Asparagine (Asn), Glutamine (Gln)
• Nonpolar: Alanine (Ala), Valine (Val), Leucine (Leu), Isoleucine (Ile), Proline (Pro), Phenylalanine (Phe), Tryptophan (Trp), Methionine (Met)
• Special: Cysteine (Cys, forms disulfide bridges —S—S—)

Peptide bond: condensation between the —COOH group of one amino acid and the —NH₂ group of the next, with loss of H₂O, forming an amide bond (—CO—NH—). The C—N bond has partial double bond character (resonance), preventing rotation (≈ 40% double bond character, length 1.32 Å vs 1.47 Å for a simple C—N bond).

Protein structure:

• Primary (1°): linear sequence of amino acids, genetically determined.
• Secondary (2°): regular local arrangement, stabilized by H-bonds between C=O and N—H of the backbone. α-helix: 3.6 residues/turn, H-bonds between residue n and n+4. β-sheet: aligned parallel/antiparallel chains, H-bonds between adjacent chains.
• Tertiary (3°): global folding of the polypeptide chain, stabilized by hydrophobic interactions, H-bonds, ionic bonds, disulfide bridges (Cys—Cys).
• Quaternary (4°): association of multiple subunits (e.g., hemoglobin: 4 subunits, 2α + 2β).

Enzymes: biological protein catalysts, highly specific. The active site binds the substrate (lock-and-key or induced fit model). Enzymatic kinetics follows the Michaelis-Menten equation.

Real-world applications: protein denaturation (heat, pH, salts) destroys 2°–4° structures (e.g., cooking egg white). Drugs like aspirin inhibit enzymes (COX-1/COX-2) by blocking the active site. Recombinant proteins (insulin, monoclonal antibodies) are biotechnological products.

Nucleic acids (DNA and RNA) are polymers of nucleotides. Each nucleotide is composed of:

1. Nitrogenous base: purine (adenine A, guanine G) or pyrimidine (cytosine C, thymine T in DNA, uracil U in RNA)
2. Sugar: D-ribose (RNA) or 2-deoxy-D-ribose (DNA)
3. Phosphate group: bonded to C5' of the sugar via a phosphoester bond

DNA (deoxyribonucleic acid): double helix structure (Watson & Crick, 1953):

• Two antiparallel polynucleotide chains (5'→3' and 3'→5') helically wound.
• Nitrogenous bases inside, paired via hydrogen bonds: A=T (2 H bonds), G≡C (3 H bonds). Complementary base pairing is specific and geometrically explained (purine + pyrimidine = constant width).
• The backbone is sugar-phosphate, hydrophilic, on the outside.
• One complete turn: 10.5 base pairs, pitch 34 Å, diameter 20 Å.

RNA (ribonucleic acid): single strand, with ribose and U (uracil) instead of T. Types: mRNA (messenger, gene copy for protein synthesis), tRNA (transfer, amino acid/codon adapter), rRNA (ribosomal, component of the ribosome).

DNA replication: semi-conservative process. Each strand serves as a template for synthesis of the new complementary strand. DNA polymerase adds nucleotides in the 5'→3' direction, using dNTP (deoxynucleoside triphosphates).

Transcription and translation: transcription copies a gene into mRNA (RNA polymerase). Translation (protein synthesis) occurs on ribosomes: each codon (base triplet of mRNA) specifies an amino acid (via tRNA with complementary anticodon). The genetic code is degenerate (18 of the 20 amino acids are encoded by 2+ codons).