Biomolecules: Carbohydrates, Proteins, Vitamins & Nucleic Acids

1. Carbohydrates: Classification & Open-Chain Proofs

• Chemical Definition: Optically active polyhydroxy aldehydes or ketones, or substances that produce these units upon hydrolysis.
• Classification by Hydrolysis:
  • Monosaccharides: Cannot be hydrolysed into simpler sugars (e.g., glucose, fructose, galactose, ribose).
  • Oligosaccharides: Yield 2 to 10 monosaccharide units on hydrolysis (e.g., disaccharides like sucrose, maltose, lactose).
  • Polysaccharides: Non-sugars yielding hundreds to thousands of monosaccharide units (e.g., starch, cellulose, glycogen).
• Reducing vs Non-Reducing Sugars: Carbohydrates that reduce Fehling's solution and Tollens' reagent are reducing sugars. All monosaccharides (both aldoses and ketoses) and disaccharides with free hemiacetal carbons (maltose, lactose) are reducing sugars. Sucrose is non-reducing.
• Structural Proofs of Open-Chain D-Glucose:
  • Molecular formula is $\text{C}_6\text{H}_{12}\text{O}_6$.
  • Prolonged heating with $\text{HI} + \text{Red P}$ yields n-hexane, proving an unbranched 6-carbon backbone:

$$\text{CHO-(CHOH)}_4\text{-CH}_2\text{OH} \xrightarrow[\Delta]{\text{HI / Red P}} \text{CH}_3\text{-CH}_2\text{-CH}_2\text{-CH}_2\text{-CH}_2\text{-CH}_3$$

• Reaction with hydroxylamine ($\text{NH}_2\text{OH}$) forms an oxime, and addition of $\text{HCN}$ yields a cyanohydrin, confirming a carbonyl ($>\text{C}=\text{O}$) group.
• Mild oxidation with bromine water selectively converts glucose into the 6-carbon monocarboxylic acid gluconic acid, proving the carbonyl is an aldehyde ($-\text{CHO}$):

$$\text{CHO-(CHOH)}_4\text{-CH}_2\text{OH} \xrightarrow{\text{Br}_2 / \text{H}_2\text{O}} \text{COOH-(CHOH)}_4\text{-CH}_2\text{OH} \quad (\text{Gluconic acid})$$

• Acetylation with acetic anhydride forms glucose pentaacetate, proving the presence of five $-\text{OH}$ groups on separate carbon atoms.
• Oxidation with concentrated $\text{HNO}_3$ oxidises both the aldehyde and the primary alcohol to form the dicarboxylic acid saccharic acid, confirming a primary alcohol ($-\text{CH}_2\text{OH}$) at C-6.

2. Cyclic Glucose, Anomers & Mutarotation

• Limitations of Open-Chain Structure:
  • D-Glucose does not restore the pink colour of Schiff's reagent and fails to form a crystalline bisulphite adduct with $\text{NaHSO}_3$.
  • Glucose pentaacetate does not react with hydroxylamine, showing the absence of a free $-\text{CHO}$ group.
  • Glucose exists in two distinct crystalline forms: $\alpha$-form ($\text{m.p. } 419\text{ K}$, crystallized at $303\text{ K}$) and $\beta$-form ($\text{m.p. } 423\text{ K}$, crystallized at $371\text{ K}$).
• Cyclic Hemiacetal (Pyranose) Formation: Intramolecular nucleophilic addition of the $-\text{OH}$ group at C-5 to the C-1 carbonyl forms a six-membered pyranose ring.
• Anomers & Anomeric Carbon: The new chiral center created at C-1 is called the anomeric carbon. $\alpha$-D-Glucose has the anomeric $-\text{OH}$ pointing downward in Haworth projection; $\beta$-D-Glucose has it pointing upward.

• Mutarotation: When pure $\alpha$-D-glucose ($+112^\circ$) or pure $\beta$-D-glucose ($+19^\circ$) is dissolved in water, the optical rotation spontaneously changes over time until it reaches a stable equilibrium value of $+52.5^\circ$, establishing an equilibrium mixture containing $\approx 36\%\ \alpha$, $64\%\ \beta$, and $< 0.02\%$ open-chain aldehyde.

3. Disaccharides, Polysaccharides & Invert Sugar

• Glycosidic Linkage: The covalent oxide bond formed between two monosaccharide units through condensation with elimination of water.
• Key Disaccharides:
  • Sucrose ($\text{C}_{12}\text{H}_{22}\text{O}_{11}$): Composed of $\alpha$-D-glucopyranose and $\beta$-D-fructofuranose linked through $\text{C}1(\alpha) - \text{O} - \text{C}2(\beta)$. Non-reducing sugar. Hydrolysis inverts optical rotation from $+66.5^\circ$ to $-20^\circ$ (forming invert sugar):

$$\text{C}_{12}\text{H}_{22}\text{O}_{11} + \text{H}_2\text{O} \xrightarrow{\text{Invertase / } \text{H}^+} \text{D-(+)-Glucose } (+52.5^\circ) + \text{D-(-)-Fructose } (-92.4^\circ)$$

• Maltose: Two $\alpha$-D-glucose units joined by a $\text{C}1-\text{C}4$ glycosidic bond. Reducing sugar with a free hemiacetal at C-1.
• Lactose (Milk Sugar): $\beta$-D-galactose and $\beta$-D-glucose joined by a $\beta\text{-C}1-\text{C}4$ bond. Reducing sugar.
• Polysaccharides:
  • Starch: Plant storage polymer of $\alpha$-glucose consisting of water-soluble unbranched Amylose ($15-20\%$, linear $\alpha-\text{C}1-\text{C}4$ chains) and water-insoluble branched Amylopectin ($80-85\%$, linear $\alpha-\text{C}1-\text{C}4$ with $\alpha-\text{C}1-\text{C}6$ branch points every 24-30 units).
  • Cellulose: Structural polymer of plant cell walls composed exclusively of straight unbranched chains of $\beta$-D-glucose held together by $\beta-\text{C}1-\text{C}4$ glycosidic bonds.
  • Glycogen (Animal Starch): Major carbohydrate store in animals (liver, muscles); structurally resembles amylopectin but has tighter branching (every 8-12 glucose units).

4. Amino Acids: Zwitterions & Isoelectric Point

• Structure of $\alpha$-Amino Acids: Contain an amino group ($-\text{NH}_2$) and a carboxylic acid group ($-\text{COOH}$) attached to the same $\alpha$-carbon ($\text{R-CH(NH}_2)\text{-COOH}$).
• Stereochemistry: All naturally occurring $\alpha$-amino acids in proteins have the L-configuration (represented with $-\text{NH}_2$ on the left in Fischer projection) and are optically active, with the sole exception of Glycine ($\text{H}_2\text{N-CH}_2\text{-COOH}$).
• Classification by Reaction:
  • Neutral: Equal amino and carboxyl groups (e.g., Glycine, Alanine, Valine).
  • Acidic: Excess carboxyl groups (e.g., Aspartic acid, Glutamic acid).
  • Basic: Excess amino/guanidino groups (e.g., Lysine, Arginine, Histidine).
• Zwitterion & Amphoteric Nature: In aqueous solution, internal proton transfer from $-\text{COOH}$ to $-\text{NH}_2$ forms a dipolar zwitterion:

$$\text{R-CH(NH}_2)\text{-COOH} \rightleftharpoons \text{R-CH(NH}_3^+)\text{-COO}^- \quad (\text{Zwitterion})$$

• Isoelectric Point (pI): The specific $\text{pH}$ at which the amino acid carries no net electrical charge. At $\text{pH} = \text{pI}$, solubility is minimal, and the amino acid does not migrate toward either electrode in an electric field.

5. Proteins: Primary to Quaternary & Denaturation

• Peptide Bond ($-\text{CO-NH}-$): Amide linkage formed between the $\alpha\text{-COOH}$ of one amino acid and the $\alpha\text{-NH}_2$ of another with elimination of water. Resonance gives the $\text{C}-\text{N}$ bond partial double-bond character, making it planar and rigid.

• Four Levels of Protein Architecture:
  1. Primary ($1^\circ$): Linear sequence of amino acid residues connected by covalent peptide bonds.
  2. Secondary ($2^\circ$): Conformation of the polypeptide backbone stabilized by backbone hydrogen bonds.
     • $\alpha$-Helix: Right-handed coil stabilized by intramolecular H-bonds between $-\text{NH}$ of residue $n$ and $>\text{C}=\text{O}$ of residue $n+4$.
     • $\beta$-Pleated Sheet: Polypeptide chains extended side by side and held by intermolecular H-bonds.
  3. Tertiary ($3^\circ$): Overall 3D folding of secondary structures into Fibrous (water-insoluble, structural; keratin, myosin) or Globular (water-soluble, functional; insulin, albumin) shapes, stabilized by hydrogen bonds, disulphide linkages ($-\text{S}-\text{S}-$), electrostatic interactions, and van der Waals forces.
  4. Quaternary ($4^\circ$): Spatial arrangement of two or more individual polypeptide subunits (e.g., haemoglobin has 4 subunits: $2\alpha + 2\beta$).
• Protein Denaturation: Physical (heat) or chemical ($\text{pH}$, heavy metal ions) disruption of native higher-order conformation. Globules unfold and helices uncoil, resulting in loss of biological activity. Secondary, tertiary, and quaternary structures are destroyed, while the primary covalent sequence remains intact. Common examples: boiling an egg (coagulation of albumin) and curdling of milk.

6. Enzymes & Vitamin Deficiencies

• Enzymes: Highly specific biocatalysts that are predominantly globular proteins. They accelerate biochemical reactions by lowering activation energy without altering equilibrium constants.
• Vitamins Classification:
  • Fat-Soluble: Stored in liver and adipose tissue; not excreted in urine ($\text{Vitamins A, D, E, K}$).
  • Water-Soluble: Excreted in urine; must be supplied regularly in diet ($\text{B-complex}$ vitamins and $\text{Vitamin C}$). Exception: $\text{Vitamin B}_{12}$ is stored in the liver.

7. Nucleic Acids: Nucleotides, DNA vs RNA

• Chemical Components:
  • Pentose Sugar: $\beta\text{-D-2-deoxyribose}$ in DNA; $\beta\text{-D-ribose}$ in RNA (contains $-\text{OH}$ at C-2').
  • Heterocyclic Bases:
    • Purines (bicyclic): Adenine (A) and Guanine (G).
    • Pyrimidines (monocyclic): Cytosine (C) and Thymine (T) in DNA; Cytosine (C) and Uracil (U) in RNA.
• Nucleoside vs Nucleotide:
  • Nucleoside: Nitrogenous base linked to C-1' of the pentose sugar by a $\beta\text{-N-glycosidic}$ bond.
  • Nucleotide: Nucleoside esterified with phosphoric acid at the C-5' position of the sugar moiety.

• Phosphodiester Linkage: Polynucleotide chains run in a directional $5' \rightarrow 3'$ sense, formed by phosphodiester bridges linking the C-3' $-\text{OH}$ of one nucleotide sugar to the C-5' $-\text{OH}$ of the next.
• Watson-Crick Double Helix (DNA):
  • Two antiparallel polynucleotide strands wound around a central axis in a right-handed double helix.
  • Complementary hydrogen bonding:

    $$\text{Adenine} = \text{Thymine} \quad (\text{Two hydrogen bonds})$$

    $$\text{Guanine} \equiv \text{Cytosine} \quad (\text{Three hydrogen bonds})$$

• RNA Structure & Types: Single-stranded polynucleotide that can fold back on itself. Three functional classes: messenger RNA ($\text{mRNA}$), ribosomal RNA ($\text{rRNA}$), and transfer RNA ($\text{tRNA}$).
• DNA Fingerprinting: Information encoded in unique tandem-repeat base sequences in an individual's DNA; identical in all cells and impossible to alter by surgery. Used in forensics, paternity testing, and victim identification.