Biomolecules revision notes

• Complementary Base Pairing Rule: In the DNA double helix, the two strands are complementary. Adenine (A) always forms hydrogen bonds with Thymine (T), and Cytosine (C) always forms hydrogen bonds with Guanine (G).
• Amino Acid Classification Rule: Amino acids are neutral if amino and carboxyl groups are equal. More amino groups = basic; more carboxyl groups = acidic.
• Essential vs Non-Essential Amino Acids: Amino acids synthesized in the body are non-essential. Those that cannot be synthesized and must be obtained through diet are essential amino acids.

Carbohydrates are classified by their behavior on hydrolysis:

1. Monosaccharides: Cannot be hydrolysed further (e.g., glucose, fructose, ribose). ~20 occur in nature.
2. Oligosaccharides: Yield 2 to 10 monosaccharide units. Disaccharides are most common.
3. Polysaccharides: Yield large numbers of monosaccharide units. They are non-sugars (e.g., starch, cellulose, glycogen, gums).

Monosaccharides: Glucose & Fructose

• Glucose ($C_6H_{12}O_6$): An aldohexose, also known as dextrose. Monomer of starch and cellulose.

• Cyclic Structure of Glucose: Forms a 6-membered hemiacetal ring (pyranose) involving C1 aldehyde and C5 –OH. Exists in equilibrium with open-chain structure.
• Fructose ($C_6H_{12}O_6$): A ketohexose, naturally found in fruits and honey. D-(-)-fructose exists in a 5-membered cyclic hemiacetal ring (furanose) by the addition of C5 –OH to the C2 ketone group.

Disaccharides & Polysaccharides

JEE Tip You MUST memorize the exact linkages and monomers for the following polymers.

• Sucrose: Non-reducing. Hydrolysis gives $\alpha$-D-glucose + $\beta$-D-fructose. Linkage is between C1 of $\alpha$-glucose and C2 of $\beta$-fructose.
• Maltose: Reducing. Composed of two $\alpha$-D-glucose units. Linkage is C1 of one glucose to C4 of the other.
• Lactose (Milk Sugar): Reducing. Composed of $\beta$-D-galactose and $\beta$-D-glucose. Linkage is C1 of galactose to C4 of glucose.

• Cellulose: Most abundant organic substance in the plant kingdom (cell wall). Straight chain polymer of $\beta$-D-glucose units. Linkage: C1–C4.
• Glycogen: Animal starch. Structure similar to amylopectin but more highly branched. Found in liver, muscles, brain, yeast, and fungi.

Amino Acids

Amino acids contain amino (–$NH_2$) and carboxyl (–COOH) groups. Only $\alpha$-amino acids are obtained on protein hydrolysis. Nomenclature is often trivial (e.g., Glycine = sweet, Tyrosine = from cheese).

The 20 Natural Amino Acids & Symbols

• Neutral (Aliphatic): Glycine (Gly, G), Alanine (Ala, A), Valine* (Val, V), Leucine* (Leu, L), Isoleucine* (Ile, I).
• Hydroxyl-containing: Serine (Ser, S), Threonine* (Thr, T), Tyrosine (Tyr, Y).
• Sulfur-containing: Cysteine (Cys, C), Methionine* (Met, M).
• Acidic & Amides: Aspartic acid (Asp, D), Glutamic acid (Glu, E), Asparagine (Asn, N), Glutamine (Gln, Q).
• Basic: Lysine* (Lys, K), Arginine* (Arg, R), Histidine* (His, H).
• Aromatic: Phenylalanine* (Phe, F), Tryptophan* (Trp, W), Tyrosine (Tyr, Y).
• Cyclic (Imino acid): Proline (Pro, P). (Asterisk * denotes Essential Amino Acids. JEE Tip Essential amino acids are NOT synthesized in the body, hence essential in the diet!)

Protein Structure Levels

1. Primary (1°): Specific sequence of amino acids. Determines the unique identity of the protein.
2. Secondary (2°): Shape of the long polypeptide chain.
   • $\alpha$-Helix: Right-handed screw, stabilized by H-bonds between –NH and >C=O of adjacent turns.
   • $\beta$-Pleated Sheet: Peptide chains stretched and laid side-by-side, held by intermolecular H-bonds.
3. Tertiary (3°): Overall 3D folding (fibrous or globular molecular shapes). Stabilized by H-bonds, disulfide linkages, van der Waals, and electrostatic forces.
4. Quaternary (4°): Spatial arrangement of two or more polypeptide sub-units relative to each other.

Fibrous vs Globular Proteins

• Fibrous: Parallel polypeptide chains held by H-bonds and disulfide bonds. Insoluble in water. Examples: Keratin (hair, wool, silk), Myosin (muscles).
• Globular: Polypeptides coil into a spherical shape. Soluble in water. Examples: Insulin, albumins.

Enzymes

Globular proteins acting as biological catalysts. Ending in "-ase" (e.g., maltase for maltose hydrolysis). They act by heavily reducing activation energy. E.g., Acid hydrolysis of sucrose $E_a = 6.22$ kJ/mol, but with enzyme sucrase $E_a = 2.15$ kJ/mol. Oxidoreductases catalyze simultaneous oxidation/reduction.

Vitamins

JEE Tip Extremely high yield table for matching type MCQs. Memorize all sources and diseases.

1. Fat Soluble Vitamins (A, D, E, K)

Stored in liver and adipose tissues.

Vitamin A

Fish liver oil, carrots, butter, milk. Deficiency: Xerophthalmia (hardening of cornea), Night blindness.

Vitamin D

Exposure to sunlight, fish, egg yolk. Deficiency: Rickets (bone deformities in children), Osteomalacia (soft bones/joint pain in adults).

Vitamin E

Wheat germ oil, sunflower oil. Deficiency: Increased fragility of RBCs, muscular weakness.

Vitamin K

Green leafy vegetables. Deficiency: Increased blood clotting time.

2. Water Soluble Vitamins (B-group, C)

Excreted in urine, cannot be stored (except B12).

Vitamin B1 (Thiamine)

Yeast, milk, cereals. Deficiency: Beri beri (loss of appetite, retarded growth).

Vitamin B2 (Riboflavin)

Milk, egg white, liver. Deficiency: Cheilosis (fissuring at corners of mouth and lips), burning sensation of skin.

Vitamin B6 (Pyridoxine)

Yeast, milk, egg yolk. Deficiency: Convulsions.

Vitamin B12

Meat, fish, egg, curd. Deficiency: Pernicious anaemia (RBC deficient in haemoglobin).

Vitamin C (Ascorbic acid)

Citrus fruits, amla, green leafy veg. Deficiency: Scurvy (bleeding gums).

Nucleic Acids (DNA & RNA)

• Chromosomes are made of proteins and nucleic acids (polynucleotides). Complete hydrolysis yields pentose sugar, phosphoric acid, and nitrogen bases.
• Sugars: $\beta$-D-2-deoxyribose (in DNA) and $\beta$-D-ribose (in RNA).

• Structure: DNA exists as a double-stranded helix (Watson & Crick model) held by complementary H-bonds. RNA exists as a single-stranded helix (which can fold back on itself).
• RNA Types: mRNA (messenger), rRNA (ribosomal), tRNA (transfer) carry out protein synthesis based on DNA messages.
• DNA Fingerprinting: Uses unique base sequences for criminal identification, paternity, identifying dead bodies, and racial group tracing.

Hormones

Produced by endocrine glands, poured directly into blood.

• Chemical Classes: Steroids (estrogens, androgens), Polypeptides (insulin, endorphins), Amino acid derivatives (epinephrine, norepinephrine).

(Crucial Glucose Preparations & Reactions):

1. Preparation from Sucrose:
   • $C_{12}H_{22}O_{11} + H_2O \xrightarrow{H^+} C_6H_{12}O_6 \text{ (Glucose)} + C_6H_{12}O_6 \text{ (Fructose)}$ (Boiled with dilute $HCl$ or $H_2SO_4$ in alcoholic solution).
2. Preparation from Starch (Commercial):
   • $(C_6H_{10}O_5)_n + nH_2O \xrightarrow[2-3 \text{ atm}]{393\text{ K}, H^+} n C_6H_{12}O_6$ (Boiling with dilute $H_2SO_4$ at 393 K under 2-3 atm pressure).
3. Reduction: $Glucose + HI \xrightarrow{\Delta} n-hexane$.
4. Carbonyl Addition:
   • $Glucose + NH_2OH \rightarrow Glucose\ oxime$.
   • $Glucose + HCN \rightarrow Glucose\ cyanohydrin$.
5. Oxidation:
   • $Glucose + Br_2/H_2O \rightarrow Gluconic\ acid$.
   • $Glucose + HNO_3 \rightarrow Saccharic\ acid$ (Gluconic acid also oxidizes to this).
6. Acetylation: $Glucose + (CH_3CO)_2O \rightarrow Glucose\ pentaacetate$.

• Carbohydrate Formula Anomaly: Acetic acid ($CH_3COOH$) fits the $C_x(H_2O)_y$ formula (as $C_2(H_2O)_2$) but is NOT a carbohydrate. Conversely, Rhamnose ($C_6H_{12}O_5$) IS a carbohydrate but DOES NOT fit the hydrate formula.
• Schiff's Test & Hydrogen Sulfite Anomaly: Despite having a structural aldehyde group, glucose fails to give Schiff’s test and does not form the addition product with $NaHSO_3$.
• Hydroxylamine Reaction Anomaly: Glucose reacts with $NH_2OH$, but glucose pentaacetate DOES NOT. This anomaly proved the absence of a free –CHO group in the cyclic form.
• Protein Size/Definition Exception: By standard definition, a polypeptide is only called a protein if it has >100 amino acids and a molecular mass >10,000 u. However, Insulin is the exception, as it contains only 51 amino acids but is classified as a protein due to its well-defined conformation.
• Glycine Optical Anomaly: All naturally occurring $\alpha$-amino acids are optically active EXCEPT Glycine, which is optically inactive because its R-group is a simple hydrogen atom.
• Amino Acid Physical Property Anomaly: Amino acids behave unlike simple amines or carboxylic acids. Due to zwitterion formation, their melting points and solubility in water are exceptionally higher than corresponding halo acids.
• Vitamin B12 Anomaly: B-group vitamins are water-soluble and excreted in urine, meaning they cannot be stored. Vitamin B12 is the only exception; it is water-soluble but is stored in the human body.
• Sucrose Optical Rotation Anomaly (Inversion): Sucrose itself is dextrorotatory (+), but its hydrolysis products form a net laevorotatory (-) mixture, hence known as "invert sugar".
• RNA Base Anomaly: DNA contains Adenine, Guanine, Cytosine, and Thymine. In RNA, Thymine is an anomaly as it is entirely absent and replaced by Uracil.
• Stereochemical Frequency Anomaly: In nature, the vast majority of naturally occurring carbohydrates exist in the D-configuration, whereas the vast majority of naturally occurring amino acids exist in the L-configuration.

• Glucose reactions: Deductions from HI, Br2 water, and HNO3 oxidations are highly tested.
• Glycosidic Linkage matching: Knowing exactly which carbons link in Maltose, Lactose, and Sucrose, and the $\alpha$ or $\beta$ nature of the bond.
• Isoelectric point & Zwitterion chemistry: Amino acid migration in electric fields.
• Vitamin Table: Match-the-following questions mapping vitamin name, letter, and deficiency disease (especially B1, B2, B6, B12, and C).
• DNA/RNA Base pairs: Pyrimidine vs Purine structures and complementary H-bonding pairs.