Biomolecules

All living organisms, from unicellular bacteria to giant mammals and plants, are constructed from carbon-based organic compounds and inorganic minerals. To analyze chemical composition:

• Extraction with Trichloroacetic Acid ($ ext{Cl}_3 ext{C-COOH}$): A living tissue sample (vegetable, leaf, or animal liver) is ground thoroughly in trichloroacetic acid using a mortar and pestle to produce a thick slurry.
• Filtration: Straining the slurry through cheesecloth separates it into two distinct biochemical pools:
  • Acid-Soluble Pool (Filtrate): Contains thousands of low-molecular-weight compounds (molecular weights ranging between 18 and 800 Daltons). Termed biomicromolecules, this pool represents the soluble cytoplasmic matrix (monosaccharides, amino acids, nucleotides, organic acids).
  • Acid-Insoluble Pool (Retentate): Material retained on the filter; contains high-molecular-weight polymers (molecular weights $> 10,000$ Daltons). Termed biomacromolecules, this pool comprises three polymeric classes: proteins, polysaccharides, and nucleic acids.
• The Lipid Anomaly: Lipids have molecular weights rarely exceeding 800 Da (e.g., palmitic acid MW ~256 Da, lecithin MW ~734 Da) and are technically micromolecules. However, lipids are embedded in cell membranes. Homogenization disrupts membranes into insoluble fragments that spontaneously roll into water-insoluble vesicles (liposomes). Because these vesicular aggregates cannot pass through the cheesecloth, lipids are collected in the acid-insoluble retentate.
• Ash Analysis for Inorganic Elements: A small amount of living tissue is weighed (wet weight), dried to evaporate water (dry weight), and fully incinerated. All carbonaceous compounds burn off as gaseous $ ext{CO}_2$ and water vapor. The remaining non-combustible residue is the ash, containing inorganic elements: cations ($ ext{Ca}^{2+}, ext{Mg}^{2+}, ext{K}^+, ext{Na}^+$) and anions ($ ext{PO}_4^{3-}, ext{SO}_4^{2-}, ext{Cl}^-$).

Metabolites are cellular intermediates and products of metabolic reactions:

• Primary Metabolites: Compounds that possess direct, identifiable physiological functions essential for growth, development, and basic cellular metabolism (e.g., glucose, ribose, amino acids, fatty acids, purines, pyrimidines, ATP). Found universally across all living taxa.
• Secondary Metabolites: Diverse organic compounds synthesized primarily by plants, fungi, and microbes that are not directly required for primary vegetative growth. They serve ecological roles such as chemical defense against herbivores, allelopathy, attractants for pollinators, and medicinal agents:

Carbohydrates are organic compounds with the empirical formula $ ext{C}_n( ext{H}_2 ext{O})_n$, chemically defined as polyhydroxy aldehydes or polyhydroxy ketones and their polymeric derivatives:

• Monosaccharides: Simplest monomeric sugars that cannot be hydrolyzed into smaller carbohydrate units:
  • Based on Carbon Number: Trioses ($n=3$: Glyceraldehyde, Dihydroxyacetone), Tetroses ($n=4$: Erythrose), Pentoses ($n=5$: Ribose $ ext{C}_5 ext{H}_{10} ext{O}_5$, Deoxyribose $ ext{C}_5 ext{H}_{10} ext{O}_4$), Hexoses ($n=6$: Glucose, Fructose, Galactose), Heptoses ($n=7$: Sedoheptulose).
  • Aldoses vs Ketoses: Aldoses contain a terminal aldehyde group ($- ext{CHO}$, e.g., Glucose, Ribose, Galactose); Ketoses contain an internal ketone group ($> ext{C}= ext{O}$, e.g., Fructose, Ribulose).
• Disaccharides: Formed by condensation of two monosaccharides linked by a glycosidic bond:
  • Maltose (Malt Sugar): $lpha$-D-Glucose + $lpha$-D-Glucose joined by an $lpha-1,4$ glycosidic bond. Possesses a free anomeric C1 hemiacetal; reducing sugar.
  • Lactose (Milk Sugar): $eta$-D-Galactose + $eta$-D-Glucose joined by a $eta-1,4$ glycosidic bond. Possesses a free anomeric C1 hemiacetal; reducing sugar.
  • Sucrose (Cane / Table Sugar): $lpha$-D-Glucose + $eta$-D-Fructose joined by an $lpha-1,eta-2$ glycosidic linkage. Because both anomeric carbons (C1 of glucose and C2 of fructose) are tied up in the bond, it has no free carbonyl group; non-reducing sugar.

Long chains of monosaccharides joined by glycosidic bonds. They are non-reducing, insoluble or colloidal, and function in energy storage or structural support:

• Homopolysaccharides: Composed of a single repeating monosaccharide type:
  • Starch: Chief carbohydrate reserve in plants. Consists of two components:
    • Amylose (15–20%): Linear, unbranched chain of $lpha$-D-glucose linked by $lpha-1,4$ glycosidic bonds. Spontaneously coils into a right-handed helix that traps iodine molecules ($ ext{I}_2$) to give a diagnostic deep blue-black color.
    • Amylopectin (80–85%): Branched polymer; contains $lpha-1,4$ linear chains with $lpha-1,6$ branch points occurring every 24–30 glucose residues.
  • Glycogen (Animal Starch): Storage polysaccharide stored in animal liver and muscle fibers. Highly branched polymer of $lpha$-D-glucose with $lpha-1,6$ branch points every 8–12 residues. Gives a reddish-brown to violet color with iodine. Possesses a reducing right end and non-reducing left ends.
  • Cellulose: Structural component of plant cell walls; most abundant organic biomolecule on Earth. Straight, unbranched polymer of $eta$-D-glucose linked by $eta-1,4$ glycosidic bonds. Neighboring chains form tight parallel microfibrils stabilized by intra- and inter-molecular hydrogen bonds. Because it lacks helical coils, it cannot hold iodine and yields no color.
  • Inulin: Linear storage polymer of fructose linked by $eta-2,1$ bonds, found in roots of *Dahlia*; used clinically to determine glomerular filtration rate (GFR).
• Heteropolysaccharides: Composed of two or more different monosaccharide derivatives:
  • Chitin: Homopolymer of N-acetylglucosamine (NAG) linked by $eta-1,4$ bonds; forms the tough exoskeleton of arthropods and the cell walls of fungi. Second most abundant organic polymer.
  • Peptidoglycan (Murein): Alternating units of NAG and N-acetylmuramic acid (NAM) cross-linked by short peptide chains in bacterial cell walls.
  • Hyaluronic Acid: Repeating disaccharide units of D-glucuronic acid and NAG; lubricating component of synovial fluid and vitreous humor.

Lipids are heterogeneous water-insoluble organic biomolecules that dissolve readily in non-polar organic solvents (benzene, chloroform, ether). They are not polymers and exhibit high caloric energy density:

Organic carboxylic acids with a long hydrocarbon chain ($R- ext{COOH}$), where $R$ may range from 1 to over 29 carbon atoms:

• Saturated Fatty Acids: Contain no carbon-carbon double bonds ($ ext{C-C}$ single bonds only); have higher melting points and are solid at room temperature (e.g., Palmitic acid [16 carbons: $ ext{CH}_3( ext{CH}_2)_{14} ext{COOH}$], Stearic acid [18 carbons: $ ext{CH}_3( ext{CH}_2)_{16} ext{COOH}$]).
• Unsaturated Fatty Acids: Contain one or more carbon-carbon double bonds ($ ext{C=C}$); have lower melting points and remain liquid at room temperature (oils):
  • Monounsaturated (MUFA): One double bond (e.g., Oleic acid [18:1, $\Delta^9$]).
  • Polyunsaturated (PUFA): Two or more double bonds (e.g., Linoleic acid [18:2], Linolenic acid [18:3], Arachidonic acid [20 carbons, 4 double bonds: 20:4]).
  • Essential Fatty Acids: Linoleic acid and Linolenic acid cannot be synthesized de novo by the human body and must be acquired through diet.

Esters of the trihydric alcohol glycerol (propane-1,2,3-triol) with fatty acids:

• Mono-, Di-, and Triglycerides (Triacylglycerols): Formed by condensation of 1, 2, or 3 fatty acids with the hydroxyl groups of glycerol via covalent ester bonds ($-COO-$). Triglycerides serve as the body's chief long-term energy reserve stored in adipocytes.
• Fats vs Oils: Fats are rich in saturated fatty acids and have higher melting points (solid at room temperature); oils are rich in unsaturated fatty acids (e.g., gingelly oil) and remain liquid in cold weather.

Lipids containing phosphorus and polar groups, forming the structural foundation of biological membranes:

• Lecithin (Phosphatidylcholine): Composed of glycerol esterified to two fatty acids at C1 and C2, with the C3 hydroxyl attached to a phosphate group linked to the nitrogenous base choline.
• Amphipathic Nature: Phospholipids possess a polar, hydrophilic phosphate 'head' and two non-polar, hydrophobic fatty acid 'tails', enabling spontaneous bilayer assembly in aqueous environments.

Lipids lacking glycerol or fatty acid ester chains, characterized by a fused four-ring cyclopentanoperhydrophenanthrene (steroid) nucleus:

• Cholesterol: The principal sterol in animal cell membranes; modulates membrane fluidity, prevents hydrocarbon crystallization at low temperatures, and serves as the precursor for steroid hormones (testosterone, estrogen, progesterone, cortisol), vitamin D, and bile salts (glycocholate, taurocholate).

Amino acids are substituted methanes wherein the four valencies of the central $lpha$-carbon are occupied by: (1) An amino group ($- ext{NH}_2$), (2) A carboxyl group ($- ext{COOH}$), (3) A hydrogen atom ($- ext{H}$), and (4) A variable side-chain ($- ext{R}$ group):

• Classification based on R-Group:
  • Neutral / Non-polar / Aliphatic: Glycine ($ ext{R} = - ext{H}$, simplest, achiral/optically inactive), Alanine ($ ext{R} = - ext{CH}_3$), Valine ($ ext{R} = - ext{CH}( ext{CH}_3)_2$).
  • Acidic: Carry a carboxyl group in the side chain; Glutamic acid, Aspartic acid.
  • Basic: Carry an amino group in the side chain; Lysine, Arginine, Histidine.
  • Aromatic: Contain aromatic benzene rings; Phenylalanine, Tyrosine, Tryptophan.
  • Sulfur-containing: Cysteine (forms covalent disulfide bridges $- ext{S}- ext{S}-$), Methionine.
• Zwitterionic Nature: At physiological pH or the isoelectric point (pI), the carboxyl group ionizes to $- ext{COO}^-$ and the amino group protonates to $- ext{NH}_3^+$, forming a dipolar zwitterion with zero net electrical charge.

Proteins are linear heteropolymers formed by the condensation of $lpha$-amino acids. The $lpha$-carboxyl group of one amino acid reacts with the $lpha$-amino group of the next with the elimination of water, forming a covalent amide linkage: the peptide bond ($- ext{CO}- ext{NH}-$). Polypeptides have intrinsic polarity: a free amino group at the N-terminus (first residue) and a free carboxyl group at the C-terminus (last residue).

Nucleic acids (DNA and RNA) are linear biomacromolecules composed of repeating monomer units called nucleotides. Each nucleotide comprises three distinct components:

• Nitrogenous Bases:
  • Purines (Double-ring Heterocycles): 9-membered bicyclic rings with nitrogens at positions 1, 3, 7, and 9: Adenine (A) and Guanine (G).
  • Pyrimidines (Single-ring Heterocycles): 6-membered monocyclic rings with nitrogens at positions 1 and 3: Cytosine (C), Uracil (U) (RNA only), and Thymine (5-methyluracil, T) (DNA only).
• Pentose Sugar: $eta$-D-Ribose in RNA ($ ext{C}_5 ext{H}_{10} ext{O}_5$) and 2'-deoxy-$eta$-D-ribose in DNA ($ ext{C}_5 ext{H}_{10} ext{O}_4$, lacking an $- ext{OH}$ group at C2').
• Phosphate Group: Phosphoric acid ($ ext{H}_3 ext{PO}_4$) esterified to the 5'-hydroxyl group of the pentose sugar.

• Nucleoside: Nitrogenous base + Pentose sugar linked by an N-glycosidic bond between C1' of sugar and N9 of purine or N1 of pyrimidine (e.g., Adenosine, Deoxyadenosine, Guanosine, Cytidine, Thymidine, Uridine).
• Nucleotide: Nucleoside + Phosphate group joined by a phosphoester bond at the 5'-carbon of sugar (e.g., Adenylic acid / AMP, dAMP, ATP).
• Phosphodiester Linkage: Successive nucleotides in a polynucleotide chain are joined by $3'-5'$ phosphodiester bonds between the 3'-OH of one nucleotide's sugar and the 5'-phosphate group of the next nucleotide, imparting a directional polarity ($5' ext{-end} o 3' ext{-end}$).

Formulated in 1953 by James Watson and Francis Crick based on Rosalind Franklin and Maurice Wilkins' X-ray crystallography data:

• Two Antiparallel Helical Strands: DNA consists of two polynucleotide strands coiled around a central axis in a right-handed direction. One strand runs $5' o 3'$ and the complementary strand runs $3' o 5'$.
• Sugar-Phosphate Backbone: Alternating deoxyribose and phosphate groups form the external hydrophilic scaffolding; hydrophobic nitrogenous bases project inward toward the helical axis.
• Complementary Base Pairing: Specific purines always pair with pyrimidines through hydrogen bonding:
  • Adenine pairs with Thymine: via 2 hydrogen bonds ($A = T$).
  • Guanine pairs with Cytosine: via 3 hydrogen bonds ($G \equiv C$).
• Dimensions of B-DNA:
  • Pitch: Length of one complete helical turn is $3.4 ext{ nm}$ ($34 ext{ \AA}$).
  • Base Pairs per Turn: Exactly 10 base pairs per complete turn.
  • Distance between adjacent Base Pairs: $0.34 ext{ nm}$ ($3.4 ext{ \AA}$).
  • Diameter: Constant diameter of $2.0 ext{ nm}$ ($20 ext{ \AA}$) maintained by purine-pyrimidine pairing.
• Chargaff's Rules: For any double-stranded DNA: $[A] = [T]$ and $[G] = [C]$; $[A + G] = [T + C]$ (Purines equal Pyrimidines); $rac{[A+G]}{[T+C]} = 1.0$.

Enzymes are specialized biological catalysts. Almost all enzymes are globular proteins, with the notable exception of ribozymes (catalytic RNA molecules like 23S rRNA peptidyl transferase). Enzymes possess high catalytic power ($10^6 ext{–}10^{12}$ fold rate enhancement), extraordinary substrate specificity, and thermal sensitivity.

Reactant molecules must overcome an energetic barrier—the activation energy ($E_a$)—to reach an unstable transition state where bonds can break and reform:

• Enzyme-Substrate Complex ($ES$): The substrate ($S$) binds into a specific 3D cleft on the enzyme called the active site: $$ ext{E} + ext{S} ightleftharpoons ext{ES} o ext{EP} o ext{E} + ext{P}$$
• Transition State Stabilization: Binding induces conformational changes that stretch and weaken substrate bonds, aligning reactive groups. This drastically lowers the activation energy ($E_a$), allowing rapid conversion to products without altering the overall free energy change ($\Delta G$) or equilibrium constant ($K_{eq}$).

• Substrate Concentration ($[S]$): As $[S]$ increases, initial velocity ($v_0$) rises hyperbolically until all active sites are saturated at maximum velocity ($V_{\max}$). The Michaelis Constant ($K_m$) is the substrate concentration at which reaction rate is half maximal ($rac{1}{2}V_{\max}$). A low $K_m$ indicates high enzyme-substrate binding affinity.
• Temperature: Activity displays a bell-shaped curve. Reaction rate peaks at the optimum temperature (approx. 37°C in humans). Lower temperatures cause reversible inactivation; higher temperatures cause irreversible thermal denaturation of tertiary protein structure. ($Q_{10} pprox 2$).
• pH: Each enzyme has an optimum pH (Pepsin pH 1.5–2.0, Salivary amylase pH 6.8, Trypsin pH 8.0). Deviations alter ionization states of catalytic amino acid side chains.

• Competitive Inhibition: The inhibitor closely resembles the substrate's chemical structure and competes for binding at the active site:
  • Kinetics: $V_{\max}$ remains unchanged (can be achieved at high $[S]$); apparent $K_m$ increases.
  • Examples: Malonate competitively inhibits succinate dehydrogenase (resembling succinate); Sulfa drugs inhibit bacterial dihydropteroate synthase (mimicking PABA).
• Non-Competitive Inhibition: The inhibitor binds to an allosteric site distinct from the active site, inducing a conformational change that inactivates the catalytic site:
  • Kinetics: $V_{\max}$ is decreased; $K_m$ remains unchanged.
  • Examples: Cyanide ($ ext{CN}^-$) poisons cytochrome c oxidase in cellular respiration; Heavy metal poisoning ($ ext{Hg}^{2+}, ext{Pb}^{2+}$).

Enzymes are systematically divided into six major classes based on the reaction catalyzed:

1. Oxidoreductases / Dehydrogenases: Catalyze redox reactions ($ ext{S}_{ ext{red}} + ext{S}'_{ ext{ox}} ightleftharpoons ext{S}_{ ext{ox}} + ext{S}'_{ ext{red}}$), e.g., Alcohol dehydrogenase.
2. Transferases: Transfer specific functional groups (other than hydrogen) between substrates, e.g., Hexokinase transferring phosphate.
3. Hydrolases: Cleave ester, ether, peptide, or glycosidic bonds via hydrolysis, e.g., Pepsin, Amylase, Lipase.
4. Lyases: Catalyze elimination reactions removing groups non-hydrolytically, forming double bonds, e.g., Fumarase, Aldolase.
5. Isomerases: Catalyze interconversion of optical, geometric, or structural isomers, e.g., Triose phosphate isomerase.
6. Ligases (Synthetases): Catalyze joining of two molecules coupled with ATP cleavage, e.g., DNA ligase, Glutamine synthetase.

Many enzymes require non-protein chemical components called co-factors to achieve catalytic competence. A complete active enzyme is a Holoenzyme, consisting of the protein portion (Apoenzyme) and the co-factor: $ ext{Holoenzyme} = ext{Apoenzyme} + ext{Co-factor}$. Co-factors are classified into three types:

• Prosthetic Groups: Tightly and permanently bound organic moieties:
  • Example: Heme is the prosthetic group in catalase and peroxidase, which break down $ ext{H}_2 ext{O}_2$ into water and oxygen.
• Coenzymes: Loosely and transiently associated organic molecules, functioning as co-substrates; almost all are derivatives of water-soluble vitamins:
  • $ ext{NAD}^+$ and $ ext{NADP}^+$: Contain Niacin (Vitamin B3); act as electron carriers in redox reactions.
  • FAD and FMN: Contain Riboflavin (Vitamin B2).
  • Coenzyme A (CoA): Contains Pantothenic acid (Vitamin B5).
• Metal Ion Activators: Divalent or monovalent cations that form coordination bonds with active site residues and substrate:
  • $ ext{Zn}^{2+}$: Co-factor for Carbonic anhydrase (fastest enzyme) and Carboxypeptidase.
  • $ ext{Mg}^{2+}$: Co-factor for Hexokinase and all ATP-dependent phosphotransferases.
  • $ ext{Fe}^{2+} / ext{Fe}^{3+}$: Cytochromes and catalase.