Biomolecules
Easy Overview
Biomolecules are the organic compounds that make up living organisms. Carbohydrates, proteins, nucleic acids, and lipids are the four major classes. They are the stuff of life — from the sugar in your blood to the DNA in your cells to the proteins that do almost everything inside you. Each class of biomolecule is built from simpler building blocks: monosaccharides for carbohydrates, amino acids for proteins, nucleotides for nucleic acids, and fatty acids for lipids. Carbohydrates are aldehydes or ketones with many hydroxyl groups, or compounds derived from them. They are classified as monosaccharides (simple sugars like glucose and fructose — cannot be hydrolyzed further), disaccharides (two monosaccharides linked — sucrose, maltose, lactose), and polysaccharides (long chains — starch, cellulose, glycogen). Glucose is the most important monosaccharide — it is the primary energy source for cells, and its level in blood is regulated by insulin. The structure of glucose was a triumph of early organic chemistry — Fischer determined its configuration, and Haworth proposed the cyclic (pyranose) form that dominates in solution. Proteins are polymers of α-amino acids linked by peptide bonds. The sequence of amino acids determines the protein's three-dimensional structure, which in turn determines its function. Proteins do everything: they catalyze reactions (enzymes), transport oxygen (hemoglobin), provide structure (collagen), fight infection (antibodies), and contract muscles (actin, myosin). The 20 standard amino acids all have the general structure H₂N-CHR-COOH (except proline), and they are classified by the properties of their R group (nonpolar, polar, acidic, basic). The peptide bond is a planar amide linkage with partial double-bond character due to resonance, which restricts rotation and influences protein folding. The secondary structure (α-helix and β-sheet) arises from hydrogen bonding patterns between backbone N-H and C=O groups.
Carbohydrates — classification and structure
Carbohydrates = polyhydroxy aldehydes or ketones with formula Cₙ(H₂O)ₘ. Classification: Monosaccharides (simple sugars, cannot be hydrolyzed) — n = 3-7. Trioses (C₃), tetroses (C₄), pentoses (C₅ — ribose, deoxyribose), hexoses (C₆ — glucose, fructose, galactose). Oligosaccharides — 2-10 monosaccharides linked. Disaccharides: sucrose (glucose + fructose), maltose (glucose + glucose), lactose (glucose + galactose). Polysaccharides — >10 units: starch (amylose + amylopectin, α-1,4 and α-1,6 links), glycogen (animal starch, highly branched), cellulose (β-1,4 links, structural component of plant cell walls). Glucose exists as open-chain (aldehyde) and cyclic (pyranose) forms. In solution, the cyclic hemiacetal form predominates (>99%). The anomeric carbon (C1) can have α-OH (axial, down) or β-OH (equatorial, up) configuration. Mutarotation: when glucose dissolves in water, the specific rotation changes from +112° (α-D-glucose) to +52.5° (equilibrium mixture of α and β anomers).
Glucose — structure and reactions
Glucose (C₆H₁₂O₆): occurrence — grapes, honey, blood. Open chain form (Fischer projection): aldehyde at C1, OH groups at C2, C3, C4, C5, CH₂OH at C6. The relative configurations of the chiral carbons were determined by Fischer. Absolute configuration: D-glucose has OH at C5 on the right in Fischer projection. D-glucose is the naturally occurring form. Reactions: (1) Oxidation with mild reagents (Tollens', Fehling's, Br₂ water) → gluconic acid (C1-COOH). This shows the presence of an aldehyde group. (2) Oxidation with conc. HNO₃ → saccharic acid (dicarboxylic acid — both C1 and C6 oxidized). (3) Reduction (NaBH₄, H₂/Ni) → sorbitol (glucitol, a sugar alcohol used as a sweetener). (4) Acetylation with (CH₃CO)₂O → glucose pentaacetate (shows 5 -OH groups). (5) Reaction with HCN → cyanohydrin (extension by one carbon — Kiliani-Fischer synthesis, used to determine sugar structures). (6) Osazone formation with phenylhydrazine (excess) → glucosazone (yellow crystals, characteristic shape under microscope — used to identify glucose from other sugars). The cyclic (pyranose) structure: glucose exists mainly as a six-membered ring (pyranose) with an oxygen bridge connecting C1 and C5, forming an intramolecular hemiacetal.
Disaccharides and polysaccharides
Disaccharides: two monosaccharides linked by a glycosidic bond. Sucrose (cane sugar, table sugar): α-D-glucopyranosyl-(1→2)-β-D-fructofuranoside. Both anomeric carbons are involved in the glycosidic bond → no free aldehyde/ketone → sucrose is a non-reducing sugar. Hydrolysis (invertase or dil. HCl) → glucose + fructose. The mixture is called invert sugar (sweeter than sucrose, used in confectionery). Maltose (malt sugar): α-D-glucopyranosyl-(1→4)-D-glucopyranose. One free anomeric carbon → reducing sugar. Lactose (milk sugar): β-D-galactopyranosyl-(1→4)-D-glucopyranose. Reducing sugar. People with lactase deficiency cannot hydrolyze lactose → lactose intolerance. Polysaccharides: Starch — mixture of amylose (linear α-1,4, water-soluble) and amylopectin (branched α-1,4 and α-1,6, water-insoluble). Iodine test: starch + I₂ → blue-black color (amylose helix traps I₂ molecules). Cellulose: β-1,4 linked D-glucose. Humans cannot digest cellulose (no β-glucosidase); ruminants can (via symbiotic bacteria). Cellulose is the most abundant organic polymer on Earth. Glycogen: animal storage polysaccharide, highly branched (α-1,4 and α-1,6), stored in liver and muscles.
Amino acids — structure and properties
α-Amino acids: general structure H₂N-CH(R)-COOH, where R varies. The α-carbon is chiral (except for glycine where R = H). All naturally occurring amino acids in proteins are L-amino acids (absolute configuration related to L-glyceraldehyde). The 20 standard amino acids classified by R group: (1) Nonpolar, hydrophobic: Gly, Ala, Val, Leu, Ile, Met, Phe, Trp, Pro. (2) Polar, uncharged: Ser, Thr, Cys, Tyr, Asn, Gln. (3) Acidic (negatively charged at pH 7): Asp, Glu. (4) Basic (positively charged at pH 7): Lys, Arg, His. Properties: Amino acids are zwitterions (dipolar ions) in the solid state and in solution at neutral pH: H₃N⁺-CHR-COO⁻. The isoelectric point (pI) is the pH at which the molecule has no net charge (equal positive and negative charges). At pI, the amino acid has minimum solubility in water. Amino acids are amphoteric — they can act as both acids and bases (buffers). The α-NH₂ group has pKa ~9-10, and the α-COOH has pKa ~2-3. For R groups with ionizable side chains, additional pKa values exist.
Proteins — structure and function
Proteins are polypeptides (chains of amino acids linked by peptide bonds). The peptide bond (amide bond) is formed by condensation between the α-COOH of one amino acid and α-NH₂ of another: H₂N-CHR-COOH + H₂N-CHR'-COOH → H₂N-CHR-CONH-CHR'-COOH + H₂O. The peptide bond has partial double-bond character (due to resonance: C=O ↔ C-O⁻) → it is planar, and rotation around the C-N bond is restricted. This planarity is crucial for protein folding. Primary structure: the linear sequence of amino acids in the polypeptide chain (determined by the gene). Secondary structure: local folding patterns maintained by hydrogen bonds between backbone N-H and C=O groups. α-helix — right-handed spiral, 3.6 amino acids per turn, stabilized by H-bonds between residue i and i+4. β-sheet — extended chain segments held by H-bonds between adjacent chains (parallel or antiparallel). Tertiary structure: the overall three-dimensional folding of a single polypeptide chain, stabilized by hydrophobic interactions, H-bonds, ionic bonds, and disulfide bridges (between Cys residues). Quaternary structure: the arrangement of multiple polypeptide subunits (e.g., hemoglobin is α₂β₂ tetramer). Denaturation: loss of native structure (heat, pH change, organic solvents) → loss of function. Renaturation (if not too severe) can restore both structure and function (Anfinsen's classic experiment on ribonuclease).
Nucleic acids — DNA and RNA
Nucleic acids are polymers of nucleotides. Each nucleotide = a nitrogenous base + pentose sugar + phosphate group. Pentose sugars: ribose (in RNA) and 2-deoxyribose (in DNA). Nitrogenous bases: Purines — adenine (A) and guanine (G); Pyrimidines — cytosine (C), thymine (T, in DNA only), uracil (U, in RNA only). Nucleoside = base + sugar (without phosphate). Nucleotide = nucleoside + phosphate (also called a nucleoside monophosphate). DNA structure (Watson-Crick, 1953): Two antiparallel polynucleotide chains wound in a right-handed double helix. Bases pair via hydrogen bonds: A=T (2 H-bonds) and G≡C (3 H-bonds). The sugar-phosphate backbone is on the outside, bases are stacked inside (hydrophobic stacking interactions). The two strands are complementary — if you know one strand's sequence, you know the other. RNA: single-stranded (but can form secondary structures), has ribose (not deoxyribose) and uracil (not thymine). Types: mRNA (messenger — carries genetic code from DNA to ribosomes), tRNA (transfer — brings amino acids to ribosomes), rRNA (ribosomal — structural component of ribosomes). The genetic code — triplets of nucleotides (codons) each specify one amino acid. There are 64 codons for 20 amino acids + 3 stop codons. The code is degenerate (multiple codons for same amino acid) and universal (same in almost all organisms).
Key Points
- •Carbohydrates: Cn(H₂O)m; monosaccharides → disaccharides → polysaccharides
- •Glucose: C₆H₁₂O₆; aldehyde + 5 OH groups; cyclic pyranose form in solution
- •Mutarotation: α-D-glucose (+112°) → β-D-glucose (+18.7°) → equilibrium (+52.5°)
- •Reducing sugars: free aldehyde/ketone → positive Tollens', Fehling's test
- •Sucrose: non-reducing (both anomeric carbons in glycosidic bond)
- •Starch + I₂ → blue-black (amylose helix); cellulose: β-1,4, indigestible by humans
- •Amino acids: zwitterions (H₃N⁺-CHR-COO⁻), amphoteric, L-configuration
- •pI = isoelectric point = pH where net charge = 0 (minimum solubility)
- •Peptide bond: planar (amide resonance), formed by condensation of α-COOH + α-NH₂
- •Protein structure: primary (sequence) → secondary (α-helix, β-sheet) → tertiary (3D fold) → quaternary (subunits)
- •Disulfide bridges (S-S between Cys residues) stabilize tertiary structure
- •DNA: double helix, A=T (2 H-bonds), G≡C (3 H-bonds), antiparallel strands
- •RNA: single strand, ribose + uracil; mRNA, tRNA, rRNA
- •Genetic code: 64 codons, degenerate, universal
Practice Questions
- What are carbohydrates? Classify them with examples. Distinguish between reducing and non-reducing sugars.
- Explain the structure of D-glucose using Fischer and Haworth projections. What is mutarotation?
- Write reactions: (a) Glucose + HNO₃ → (b) Glucose + (CH₃CO)₂O → (c) Glucose + C₆H₅NHNH₂ (excess) →
- Describe the peptide bond. Explain primary, secondary, tertiary, and quaternary structures of proteins.
- What are amino acids? Explain zwitterion formation, isoelectric point, and amphoteric nature.
- Describe the Watson-Crick model of DNA structure. Write the complementary strand for 5'-ATGC-3'.
- Distinguish between DNA and RNA. What are the different types of RNA and their functions?
- Explain the glycosidic linkage. Give examples of disaccharides containing α-1,4 and β-1,4 linkages.