Biomolecules: Carbohydrates, Amino Acids, Nucleic Acids

1. Carbohydrates — Classification and Structure

Carbohydrates are polyhydroxy aldehydes or ketones with general formula Cn(H₂O)n. Classified as:

Monosaccharides (cannot be hydrolyzed further): Aldoses contain -CHO (glucose, mannose, galactose); ketoses contain C=O (fructose). Carbon count: triose (C₃), tetrose (C₄), pentose (C₅, ribose), hexose (C₆, glucose/fructose).

Open-chain D-Glucose (aldohexose with 4 chiral centers):

Glucose (C₆H₁₂O₆): Open-chain is an aldohexose with 4 chiral centers. In solution, exists predominantly as cyclic hemiacetal — pyranose ring (6-membered). The C₁-OH can be axial ($\alpha$-D-glucose) or equatorial ($\beta$-D-glucose). These are anomers (differ only at the anomeric carbon C₁). Mutarotation: fresh solution of either anomer equilibrates to a mixture ($\alpha$ 36%, $\beta$ 64%, trace open-chain) with specific rotation settling at +52.7 degrees.

Fructose (C₆H₁₂O₆): A ketohexose. Forms a furanose ring (5-membered) via intramolecular hemiketal. Anomeric carbon is C₂. Gives positive Tollens' and Fehling's tests despite being a ketone (tautomerizes to glucose/mannose in base via enediol intermediate).

Disaccharides: Sucrose = glucose + fructose (C₁-$\alpha$ to C₂-$\beta$ glycosidic bond, both anomeric carbons locked, NON-reducing).
Maltose = glucose + glucose (C₁-$\alpha$ to C₄, one free anomeric C, reducing).
Lactose = galactose + glucose (C₁-$\beta$ to C₄, reducing).

Polysaccharides: Starch = amylose (unbranched, $\alpha$-1,4) + amylopectin (branched, $\alpha$-1,4 + $\alpha$-1,6).
Cellulose = $\beta$-1,4 linked glucose (humans cannot digest — lack $\beta$-glycosidase).
Glycogen = animal starch (highly branched, $\alpha$-1,4 + $\alpha$-1,6).

2. Amino Acids, Peptides, and Proteins

Amino acids: Alpha-amino acids have NH₂ and COOH on the same carbon. All naturally occurring ones are L-configuration (S at $\alpha$-C, except cysteine which is R due to priority change with -CH₂SH).

Key amino acid structures:

Glycine (simplest amino acid, achiral)

L-Alanine (simplest chiral amino acid)

Zwitterion: At physiological pH, amino acids exist as H₃N+-CHR-COO- (internal salt). Isoelectric point (pI): pH at which net charge = 0. For neutral amino acids: pI = (pKa₁ + pKa₂)/2. At pH < pI: cation (migrates to cathode). At pH > pI: anion (migrates to anode).

Classification: Acidic (Asp, Glu — extra COOH, low pI ~3), Basic (Lys, Arg, His — extra NH₂, high pI ~10), Neutral (Gly, Ala, Val, Leu etc.), Aromatic (Phe, Tyr, Trp). Essential amino acids cannot be synthesized by the body (Val, Leu, Ile, Phe, Trp, Met, Thr, Lys + His, Arg for children).

Peptide bond: Formed by condensation of -COOH of one amino acid with -NH₂ of another. Partial double bond character (C-N rotation restricted, planar). Written N-terminus to C-terminus.

Protein structure: Primary (amino acid sequence), Secondary ($\alpha$-helix — H-bonds within same chain, $\beta$-sheet — H-bonds between chains), Tertiary (3D folding — hydrophobic interactions, disulfide bonds, ionic bonds), Quaternary (multi-subunit assembly, e.g., hemoglobin has 4 subunits).

Enzymes: Biological catalysts (proteins). Highly specific (lock-and-key model). Lower activation energy without being consumed. Named with -ase suffix (urease, lipase). Denatured by heat, pH extremes, heavy metals.

3. Nucleic Acids

Nucleoside = base + sugar (no phosphate). Nucleotide = base + sugar + phosphate.

DNA: Deoxyribose sugar, bases = A, G, C, T (thymine). Double helix with antiparallel strands. Base pairing: A=T (2 H-bonds), G triple-bond C (3 H-bonds). Chargaff's rule: %A = %T, %G = %C.

RNA: Ribose sugar (has 2'-OH), bases = A, G, C, U (uracil replaces thymine). Usually single-stranded. Types: mRNA (messenger), tRNA (transfer, cloverleaf), rRNA (ribosomal).

Key nucleobases:

Adenine (purine base, present in both DNA and RNA)

Uracil (pyrimidine base, replaces thymine in RNA)

4. Vitamins and Hormones

Water-soluble vitamins: B-complex (B₁ thiamine, B₂ riboflavin, B₆ pyridoxine, B₁₂ cobalamin, niacin, folic acid, biotin, pantothenic acid) and C (ascorbic acid). Cannot be stored in body — daily intake needed.

Fat-soluble vitamins: A (retinol — night vision), D (calciferol — calcium absorption), E (tocopherol — antioxidant), K (phylloquinone — blood clotting). Stored in liver/fat tissues.

Hormones: Chemical messengers. Insulin (peptide, lowers blood glucose), adrenaline (amino acid derivative, fight-or-flight), testosterone/estrogen (steroids, sex hormones), thyroxine (iodinated amino acid, metabolism).

The key problem-solving concept is recognizing structural features (reducing vs non-reducing sugars, anomeric carbon, glycosidic linkage type) and applying Chargaff's rules for nucleic acid calculations.