Biomolecules

Historically defined as hydrates of carbon with the empirical formula C_x(H₂O)_y, carbohydrates are chemically defined as optically active polyhydroxy aldehydes, polyhydroxy ketones, or substances that produce such units upon aqueous hydrolysis. Exceptions to the empirical formula include rhamnose (C₆H₁₂O₅) and deoxyribose (C₅H₁₀O₄), which do not fit C_x(H₂O)_y but are carbohydrates, whereas acetic acid (C₂H₄O₂) and formaldehyde (CH₂O) fit the formula but are not carbohydrates.

• Monosaccharides: Simplest carbohydrates that cannot be hydrolyzed further into smaller polyhydroxy units (e.g., glucose, fructose, ribose). Classified by carbon number and carbonyl functional group (aldotriose, aldohexose, ketohexose).
• Oligosaccharides: Carbohydrates that yield 2 to 10 monosaccharide units upon hydrolysis. Subdivided into disaccharides (sucrose, maltose, lactose), trisaccharides (raffinose), and tetrasaccharides (stachyose).
• Polysaccharides: High-molecular-weight polymers yielding hundreds to thousands of monosaccharide units on complete hydrolysis (e.g., starch, cellulose, glycogen). They are non-sugars (insoluble, amorphous, tasteless).
• Reducing vs. Non-Reducing Sugars: Carbohydrates containing free hemiacetal or hemiketal groups reduce Fehling's solution, Tollens' reagent, and Benedict's solution (all monosaccharides, maltose, lactose). Sugars with engaged anomeric carbons that lack free carbonyl potential are non-reducing (sucrose).

The stereochemical configuration of monosaccharides is assigned relative to the reference standard glyceraldehyde. In a standard Fischer projection with the most oxidized carbon (C-1) oriented at the top, the configuration is determined by the spatial orientation of the hydroxyl (–OH) group on the penultimate chiral carbon (the highest-numbered stereocenter, C-5 in hexoses):

• D-Series: The –OH group at the penultimate carbon (C-5 in glucose) lies on the right-hand side of the Fischer projection. Naturally occurring glucose is D-(+)-glucose.
• L-Series: The –OH group at the penultimate carbon lies on the left-hand side. D and L are non-superimposable mirror images (enantiomers).
• Critical Note: The capital letters 'D' and 'L' denote absolute spatial configuration and have no correlation with the sign of optical rotation, which is experimentally designated as (+) for dextrorotatory and (−) for levorotatory.

The acyclic Fischer structure of D-glucose as an aldohexose, HOCH₂–(CHOH)₄–CHO, was proven through systematic chemical transformations:

Despite explaining many properties, the open-chain aldehyde structure fails to explain critical experimental observations:

1. Glucose does not restore pink color to Schiff's reagent, nor does it form a bisulfite addition compound with sodium hydrogen sulfite (NaHSO₃).
2. Glucose pentaacetate does not react with hydroxylamine (NH₂OH), confirming the absence of a free –CHO group in the acetate derivative.
3. Glucose exists in two distinct crystalline diastereomeric forms: α-D-glucose (m.p. 419 K, [α]_D = +112°) obtained by crystallization from concentrated ethanol, and β-D-glucose (m.p. 423 K, [α]_D = +19°) obtained by crystallization from hot concentrated pyridine.

To resolve these anomalies, Tollens proposed that glucose forms an intramolecular cyclic hemiacetal via nucleophilic addition of the C-5 hydroxyl group to the C-1 carbonyl group. This produces a six-membered oxygen-containing heterocyclic ring resembling pyran, known as a glucopyranose ring.

• Anomeric Carbon (C-1): The cyclization converts the achiral carbonyl carbon C-1 into a new chiral stereocenter.
• α and β Anomers: In Haworth projections:
  • α-D-(+)-Glucopyranose: The anomeric C-1 –OH group points downwards (trans to the terminal –CH₂OH group at C-5).
  • β-D-(+)-Glucopyranose: The anomeric C-1 –OH group points upwards (cis to the terminal –CH₂OH group at C-5). In chair conformation, all bulky substituents (–OH and –CH₂OH) occupy equatorial positions, making β-D-glucose thermodynamically more stable.
• Mutarotation: When either pure α-D-glucose ([α]_D = +112°) or pure β-D-glucose ([α]_D = +19°) is dissolved in water, its specific rotation spontaneously shifts over time until reaching a stable equilibrium value of +52.7°. This phenomenon, termed mutarotation, occurs via reversible ring-opening into the transient acyclic aldehyde (<0.02%), establishing an equilibrium mixture containing ~36% α-anomer and ~64% β-anomer.

D-(−)-Fructose is a ketohexose with the molecular formula C₆H₁₂O₆. It contains a ketone group at C-2 and five hydroxyl groups [HOCH₂–CO–(CHOH)₃–CH₂OH]. It cyclizes via intramolecular hemiketal formation between the C-2 ketone and C-5 –OH group to form a five-membered furanose ring (α-D-fructofuranose and β-D-fructofuranose).

Monosaccharide units in oligosaccharides and polysaccharides are linked together through an oxide bridge formed by condensation between the anomeric carbon hemiacetal/hemiketal hydroxyl of one sugar and an alcoholic hydroxyl group of another sugar, accompanied by the loss of a water molecule. This specific ether linkage is termed a glycosidic linkage (or glycosidic bond).

Sucrose is naturally dextrorotatory with a specific rotation of [α]_D = +66.5°. When hydrolyzed with dilute mineral acid (HCl) or by the enzyme invertase, it cleaves into an equimolar mixture of D-(+)-glucose and D-(−)-fructose:

Because the magnitude of levorotation of D-(−)-fructose (−92.4°) is significantly greater than the dextrorotation of D-(+)-glucose (+52.7°), the resulting equimolar hydrolysate exhibits a net negative specific rotation:

Since the optical sign inverts from dextro (+) to levo (−), the hydrolysis reaction is termed the inversion of cane sugar, and the resulting sweet syrup is known as Invert Sugar (found abundantly in honey).

• Starch (Amylum): Main dietary carbohydrate storage in plants. Consists of two structural components:
  • Amylose (15–20%): Water-soluble fraction. Linear unbranched polymer of 200–1000 α-D-glucopyranose units linked solely by α-1 → 4 glycosidic bonds. Adopts a helical coil conformation that traps molecular iodine (I₂) inside the core to produce an intense deep-blue complex.
  • Amylopectin (80–85%): Water-insoluble fraction. Highly branched polymer of several thousand α-D-glucose units. Main backbone consists of α-1 → 4 linkages, with branch points formed by α-1 → 6 glycosidic linkages occurring every 24 to 30 glucose residues. Gives a red-violet or purplish color with iodine.
• Cellulose: Predominant structural polysaccharide of plant cell walls and the most abundant organic biomolecule on Earth. Exclusively composed of linear unbranched chains of β-D-glucopyranose units linked by β-1 → 4 glycosidic linkages.
  • Linear Ribbon Architecture: Because of the β-linkage, adjacent glucose rings flip 180° relative to each other, forming rigid flat ribbons stabilized by extensive intra- and intermolecular hydrogen bonding. Bundles of these chains assemble into insoluble microfibrils with high tensile strength.
  • Human Digestibility: Humans cannot utilize cellulose as food because the human gastrointestinal tract lacks the enzyme cellulase (β-glucosidase) necessary to hydrolyze β-1 → 4 glycosidic bonds. It serves as dietary fiber (roughage).
• Glycogen (Animal Starch): Storage polysaccharide stored in mammalian liver and muscle tissues. Structurally resembles amylopectin but is much more densely branched, with α-1 → 6 branch points occurring every 8 to 12 glucose units. When energy is needed, enzymes break down glycogen from the abundant terminal ends into glucose (glycogenolysis).

Amino acids are bifunctional organic compounds containing both an amino group (–NH₂) and a carboxylic acid group (–COOH). In α-amino acids, both functional groups are bonded to the same central carbon atom (α-carbon), represented by the general formula:

• Optical Activity & L-Configuration: With the exception of glycine (where R = H, making the α-carbon achiral), all naturally occurring amino acids contain at least one asymmetric carbon and are optically active. Natural amino acids isolated from proteins belong exclusively to the L-stereochemical series (in Fischer projection with –COOH on top, the –NH₂ group lies on the left).
• Nutritional Classification:
  • Essential Amino Acids (10): Cannot be synthesized endogenously by human metabolic pathways and must be supplied through dietary intake: Valine, Leucine, Isoleucine, Phenylalanine, Tryptophan, Methionine, Threonine, Lysine, Histidine, Arginine (Mnemonic: PVT TIM HaLL).
  • Non-Essential Amino Acids (10): Readily synthesized in the human body from carbohydrate intermediates and transamination reactions: Glycine, Alanine, Serine, Cysteine, Aspartate, Asparagine, Glutamate, Glutamine, Tyrosine, Proline.
• Acid-Base Classification:
  • Neutral: Equal numbers of –NH₂ and –COOH groups (e.g., Glycine, Alanine, Valine).
  • Acidic: More –COOH groups than –NH₂ groups (e.g., Aspartic acid, Glutamic acid).
  • Basic: More –NH₂ groups than –COOH groups (e.g., Lysine, Arginine, Histidine).

In aqueous solution, amino acids undergo an internal acid-base neutralization. The acidic carboxyl group (–COOH, pK_a ≈ 2) donates a proton to the basic amino group (–NH₂, pK_a ≈ 9), generating a dipolar internal ionic species called a Zwitterion (German for "hybrid ion"):

Because of this salt-like dipolar structure, amino acids behave as high-melting crystalline solids (m.p. > 250°C with decomposition), possess high dipole moments, and dissolve readily in polar solvents (water) while being insoluble in non-polar organic solvents (benzene, ether). Zwitterions are amphoteric:

• In acidic medium (low pH): The –COO⁻ group accepts a proton, converting the zwitterion into a cation [H₃N⁺–CH(R)–COOH] that migrates toward the cathode in an electric field.
• In basic medium (high pH): The –NH₃⁺ group loses a proton, converting the zwitterion into an anion [H₂N–CH(R)–COO⁻] that migrates toward the anode.

The isoelectric point (pI) is the precise pH of the aqueous medium at which the amino acid carries no net electrical charge (the concentration of dipolar zwitterion is maximal, and [cation] = [anion]). At its pI, an amino acid does not migrate toward either electrode during electrophoresis.

For example, in glycine, pK_a1 (–COOH) = 2.34 and pK_a2 (–NH₃⁺) = 9.60; thus, pI = (2.34 + 9.60)/2 = 5.97. At pH < pI, the species is positively charged and migrates to the cathode; at pH > pI, it is negatively charged and migrates to the anode. At the isoelectric point, water solubility and buffering capacity reach their minimum values.

When α-amino acids are heated with an alcoholic solution of ninhydrin (indane-1,2,3-trione hydrate), oxidative deamination and decarboxylation occur, releasing ammonia, carbon dioxide, and an aldehyde. The reduced hydrindantin couples with unreduced ninhydrin and ammonia to form an intensely colored blue-violet chromophore known as Ruhemann's purple (λ_max ≈ 570 nm).

Proteins are high-molecular-weight polymers composed of α-amino acids linked linearly through peptide bonds (or peptide linkages). A peptide bond is an amide bond (–CO–NH–) formed between the α-carboxyl group of one amino acid and the α-amino group of another, with elimination of a water molecule:

• Resonance & Planarity: Delocalization of the nitrogen lone pair into the carbonyl group gives the C–N bond approximately 40% double-bond character (bond length 1.32 Å, intermediate between single C–N 1.47 Å and double C=N 1.28 Å). This restricts free rotation around the C–N axis, locking the six atoms of the peptide unit (C_α, C, O, N, H, C_α) into a rigid, planar geometry in the trans configuration.
• Distinction between Peptides and Proteins: Chains with ≤ 10 residues are oligopeptides; 10 to 100 residues are polypeptides. Polymers containing > 100 amino acid residues with molecular mass exceeding 10,000 u are classified as proteins (Exception: Insulin consists of 51 amino acids with a molecular mass of 5,733 u, but is classified as a protein due to its well-defined tertiary architecture).

• Primary (1°) Structure: The specific linear sequence of amino acids linked together by covalent peptide bonds along the polypeptide backbone. Primary structure is genetically encoded and dictates all higher-order folding. Even a single alteration in sequence can produce severe pathological consequences (e.g., in sickle-cell anemia, normal hemoglobin HbA is altered to HbS due to the substitution of a single glutamic acid residue by valine at position 6 of the β-globin chain).
• Secondary (2°) Structure: Local conformational folding of the polypeptide backbone stabilized exclusively by hydrogen bonds between the carbonyl oxygen (>C=O) of one peptide bond and the amide hydrogen (–NH–) of another:
  • α-Helix: The polypeptide backbone twists into a right-handed coil. Every –NH– group of residue n forms an intramolecular hydrogen bond with the >C=O group of residue n + 4. Pitch is 5.4 Å, with 3.6 amino acid residues per turn. All amino acid side chains (R groups) project outward from the helix cylinder.
  • β-Pleated Sheet: Polypeptide chains lie fully extended alongside one another and are interconnected by intermolecular hydrogen bonds between adjacent chains. Sheets may be parallel (all chains run N→C in the same direction) or antiparallel (adjacent chains run in alternating directions, as in silk fibroin).
• Tertiary (3°) Structure: Overall three-dimensional spatial conformation achieved by the folding and supercoiling of secondary structural domains into a compact globular or fibrous unit. Stabilized by five types of interactions:
  1. Disulfide Bridges (–S–S–): Covalent cross-links between the thiol groups of two cysteine residues.
  2. Electrostatic Attractions (Salt Bridges): Ionic bonds between positively charged side chains (e.g., –NH₃⁺ of Lys) and negatively charged side chains (–COO⁻ of Asp).
  3. Hydrogen Bonding: Between polar side chains (e.g., –OH of Ser or Tyr and carbonyls).
  4. Hydrophobic Interactions: Non-polar hydrocarbon side chains cluster together inside the interior core away from aqueous solvent.
  5. Van der Waals Dispersions: Weak attractions between closely packed aliphatic groups.
• Quaternary (4°) Structure: The spatial assembly and non-covalent association of two or more independent polypeptide chains (called subunits or protomers) into a functional multimeric protein complex. Example: Adult Hemoglobin (HbA) is an α₂β₂ tetramer composed of two identical α-chains (141 residues each) and two identical β-chains (146 residues each).

When a native protein in its unique biological conformation is exposed to physical changes (heating, UV radiation) or chemical perturbations (extremes of pH, concentrated urea, detergents, heavy metal ions like Hg²⁺, Pb²⁺), the non-covalent bonds stabilizing its secondary, tertiary, and quaternary structures are ruptured. The globule uncoils, helical domains unfold, and the protein precipitates, suffering a complete loss of biological activity. This irreversible transformation is termed denaturation.

Nucleic acids are high-molecular-weight biopolymers (polynucleotides) responsible for storing, transmitting, and translating genetic information. Complete chemical hydrolysis of nucleic acids yields three fundamental components:

• Pentose Sugars:
  • β-D-2-Deoxyribose in Deoxyribonucleic Acid (DNA): Lacks an oxygen atom at C-2' (contains –H instead of –OH).
  • β-D-Ribose in Ribonucleic Acid (RNA): Possesses a hydroxyl group (–OH) at both C-2' and C-3'.
• Nitrogenous Bases: Heterocyclic aromatic amines classified into two categories:
  • Purines (Bicyclic): Adenine (A) and Guanine (G), present in both DNA and RNA.
  • Pyrimidines (Monocyclic): Cytosine (C) present in both; Thymine (T / 5-methyluracil) present exclusively in DNA; Uracil (U) present exclusively in RNA.
• Phosphoric Acid: H₃PO₄, which forms ester linkages connecting adjacent pentose sugars.

In a polynucleotide chain, nucleotides are linked linearly by 3',5'-phosphodiester linkages: the phosphate group attached to the 5'-carbon of one pentose sugar forms a phosphoester bond with the 3'-hydroxyl group of the pentose sugar of the adjacent nucleotide. The backbone consists of alternating sugar and phosphate groups, with the nitrogenous bases attached to C-1' projecting perpendicularly inward. The chain possesses a distinct polarity, with a free 5'-phosphate group at one end (5'-terminus) and a free 3'-hydroxyl group at the other (3'-terminus).

In 1953, James Watson and Francis Crick elucidated the secondary structure of double-stranded B-DNA based on Rosalind Franklin's X-ray diffraction data:

1. Antiparallel Strands: DNA consists of two helical polynucleotide chains coiled around a common central axis in a right-handed spiral. The strands run in opposite polarities (one runs 5'→3', while the complementary strand runs 3'→5').
2. Complementary Base Pairing: The nitrogenous bases project into the core of the helix. A purine on one strand always pairs with a specific pyrimidine on the opposite strand via specific hydrogen bonds:
   • Adenine pairs with Thymine (A = T): Joined by two hydrogen bonds.
   • Guanine pairs with Cytosine (G ≡ C): Joined by three hydrogen bonds. Because G≡C pairs feature three H-bonds, DNA molecules with higher GC content exhibit higher thermal denaturation temperatures (T_m).
3. Geometric Dimensions:
   • Diameter of the double helix = 20 Å (2.0 nm).
   • Pitch (length of one complete 360° helical turn) = 34 Å (3.4 nm).
   • Base pairs per turn = 10 base pairs.
   • Distance between adjacent base pairs = 34 Å / 10 = 3.4 Å (0.34 nm).
4. Chargaff's Rules: In any double-stranded DNA molecule:
   • The total molar amount of purines equals the total molar amount of pyrimidines: [A] + [G] = [T] + [C].
   • The ratio of adenine to thymine is unity: [A] / [T] = 1; and guanine to cytosine is unity: [G] / [C] = 1.
   • Note: The base ratio ([A]+[T]) / ([G]+[C]) varies from species to species but is constant within an organism. Chargaff's rules do not apply to single-stranded RNA.

Unlike DNA, RNA is typically single-stranded and contains D-ribose and uracil instead of thymine. Three primary classes execute protein biosynthesis:

• Messenger RNA (mRNA): Transcribes genetic instructions from genomic DNA in the nucleus and carries triplet codons to the cytoplasmic ribosomes.
• Transfer RNA (tRNA): Small adaptor molecules (~75–90 nucleotides) adopting a cloverleaf secondary structure. Each tRNA carries a specific amino acid esterified at its 3'-CCA terminal and recognizes corresponding mRNA codons via its anticodon loop.
• Ribosomal RNA (rRNA): Major structural and catalytic component of ribosomes, catalyzing peptide bond formation via peptidyl transferase ribozyme activity.

Enzymes are specialized biocatalysts produced by living cells that accelerate biochemical reactions by factors of 10⁶ to 10¹². With the exception of ribozymes (catalytic RNA), all enzymes are globular proteins.

• Mechanism of Action: Enzymes accelerate reaction rates strictly by lowering the activation energy (E_a) of the chemical transition state without altering the overall thermodynamic free energy change (ΔG) or equilibrium constant (K_eq). For example, the activation energy for the hydrolysis of sucrose is 107 kJ/mol uncatalyzed, which drops to only 36 kJ/mol in the presence of the enzyme invertase.
• Substrate Specificity: Enzymes display extraordinary substrate and stereochemical specificity. Emil Fischer's Lock and Key model and Daniel Koshland's Induced Fit model describe how active site crevices bind complementary substrate transition states. For instance, urease hydrolyzes urea exclusively and has zero effect on methylurea.
• Cofactors & Coenzymes: Many enzymes require non-protein cofactors for catalytic activity:
  • Prosthetic groups: Tightly and permanently bound organic moieties (e.g., heme in catalase and peroxidase).
  • Coenzymes: Loosely bound transient organic carriers, often derived from water-soluble vitamins (e.g., NAD⁺ and NADP⁺ derived from niacin; FAD derived from riboflavin; Thiamine pyrophosphate / TPP).
  • Metal Activators: Coordination metal ions (e.g., Zn²⁺ in carbonic anhydrase and carboxypeptidase; Mg²⁺ in kinases).

Vitamins are essential organic micronutrients required in trace quantities in the human diet to maintain normal physiological growth, metabolic vitality, and cellular homeostasis, which cannot be synthesized in adequate quantities by human tissues.

Hormones are intercellular chemical messengers synthesized by ductless endocrine glands and secreted directly into the bloodstream to coordinate physiological activities in specific target organs. Structurally, hormones fall into three major chemical classes:

• Steroid Hormones: Derivatives of cyclopentanoperhydrophenanthrene (sterane core):
  • Glucocorticoids (Cortisol, Cortisone): Secreted by adrenal cortex; regulate carbohydrate and protein metabolism and suppress inflammation.
  • Mineralocorticoids (Aldosterone): Regulate electrolyte excretion and water balance in renal tubules.
  • Sex Hormones: Androgens (Testosterone) controlling male secondary sexual characteristics; Estrogens (Estradiol) and Progestins (Progesterone) regulating female reproductive cycles and pregnancy.
• Peptide & Protein Hormones:
  • Insulin (51 amino acids): Secreted by β-cells of the Islets of Langerhans in the pancreas; lowers blood glucose by accelerating glycogenesis. Deficiency causes diabetes mellitus.
  • Glucagon (29 amino acids): Secreted by α-cells of the pancreas; acts antagonistically to insulin by stimulating glycogenolysis in the liver.
  • Oxytocin & Vasopressin (ADH): Nonapeptides released by the posterior pituitary, regulating uterine contractions and renal water reabsorption, respectively.
• Amine Derivatives:
  • Epinephrine (Adrenaline) & Norepinephrine: Derived from tyrosine, secreted by the adrenal medulla to mediate rapid "fight or flight" responses.
  • Thyroxine (T₄) & Triiodothyronine (T₃): Iodinated tyrosine derivatives secreted by the thyroid gland; regulate basal metabolic rate (BMR). Deficiency leads to hypothyroidism and enlargement of the thyroid gland (endemic goiter).