Biomolecules revision notes for JEE

Key Concepts & Definitions

Biochemistry:: The domain of science that studies the chemical processes within living systems, which are composed of non-living atoms and molecules.
Carbohydrates:: Chemically defined as optically active polyhydroxy aldehydes or ketones, or compounds which produce such units upon hydrolysis.
Sugars & Saccharides:: Carbohydrates that are sweet in taste are called sugars (e.g., sucrose in homes, lactose in milk). The term "saccharide" comes from the Greek word sakcharon, meaning sugar.
Reducing Sugars:: Carbohydrates that contain free aldehydic or ketonic groups and can reduce Fehling’s solution and Tollens’ reagent.JEE TIPAll monosaccharides (aldoses and ketoses) and most disaccharides (like maltose and lactose) are reducing sugars.
Non-reducing Sugars:: Carbohydrates in which the reducing groups (aldehydic or ketonic) are bonded in the glycosidic linkage (e.g., sucrose).
Anomers:: Cyclic stereoisomers (like α\alphaα-form and β\betaβ-form of glucose) that differ only in the configuration of the hydroxyl group at C1 (the anomeric carbon).
Glycosidic Linkage:: An oxide linkage formed by the loss of a water molecule, joining two monosaccharide units through an oxygen atom.
Invert Sugar:: The equimolar mixture of glucose and fructose obtained by the hydrolysis of sucrose. It is named so because hydrolysis brings about a change in the sign of optical rotation from dextro (+) to laevo (-). The laevorotation of D-(-)-fructose (-92.4°) overpowers the dextrorotation of D-(+)-glucose (+52.5°).
Proteins:: Polymers of α\alphaα-amino acids linked by peptide bonds. They are the fundamental basis of structure and function in life. (Derived from Greek proteios, meaning "primary").
Zwitter Ion:: A neutral dipolar ion formed in aqueous solutions when the carboxyl group of an amino acid loses a proton and the amino group accepts it.JEE TIPThis gives amino acids amphoteric behavior and higher melting points/solubility than corresponding halo acids.
Peptide Linkage:: An amide bond (–CO–NH–) formed between the –COOH group of one amino acid and the –NH2 group of another, with the elimination of water.
Denaturation of Proteins:: The loss of biological activity of a native protein due to physical (temperature) or chemical (pH) changes.JEE TIPDuring denaturation, 2° and 3° structures are destroyed, but the 1° (primary) structure remains intact.
Enzymes:: Globular proteins that act as biocatalysts, lowering activation energy in specific biochemical reactions.
Vitamins:: Organic compounds required in small amounts in the diet to perform specific biological functions for normal growth and health. The term originally "Vitamine" (vital + amine) dropped the 'e' when it was discovered most do not contain amino groups.
Nucleoside vs Nucleotide:: A nucleoside is a base attached to the 1' position of a sugar. A nucleotide is a nucleoside linked to phosphoric acid at the 5'-position.
Hormones:: Intercellular messengers produced by endocrine glands, transported directly via the blood stream.

Important Rules, Laws & Principles

D and L Nomenclature Rule: 'D' and 'L' notations indicate the relative configuration of a stereoisomer with respect to glyceraldehyde. It has NO relation to optical activity (d/l or +/-).
- If the –OH group on the lowest asymmetric carbon atom is on the right side, it is assigned D-configuration.
- If it is on the left side, it gets L-configuration.JEE TIPMost naturally occurring carbohydrates have D-configuration, whereas most naturally occurring amino acids have L-configuration.
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

Carbohydrates are classified by their behavior on hydrolysis:

Monosaccharides: Cannot be hydrolysed further (e.g., glucose, fructose, ribose). ~20 occur in nature.
Oligosaccharides: Yield 2 to 10 monosaccharide units. Disaccharides are most common.
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.
Physical Constants of Glucose Anomers:
- $\alpha$ -form: Melting point 419 K. Obtained by crystallization from a concentrated solution of glucose at 303 K.
- $\beta$ -form: Melting point 423 K. Obtained by crystallization from a hot and saturated aqueous solution at 371 K.
Glucose Open Chain Evidences:
- Molecular formula: $C_6H_{12}O_6$ .
- Heating with HI $\rightarrow$ n-hexane (Proves 6 carbons in a straight chain).
- Reacts with $NH_2OH$ $\rightarrow$ oxime & with HCN $\rightarrow$ cyanohydrin (Proves presence of carbonyl group).
- Oxidation with $Br_2$ water (mild) $\rightarrow$ gluconic acid (Proves carbonyl is an aldehyde).
- Acetylation with acetic anhydride $\rightarrow$ glucose pentaacetate (Proves presence of 5 –OH groups on different carbons).
- Oxidation with $HNO_3$ (strong) $\rightarrow$ saccharic acid (dicarboxylic acid) from both glucose and gluconic acid (Proves presence of primary alcoholic –OH).
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.
Starch: Main storage in plants. Polymer of $\alpha$ $α$ -glucose. Two components:
- Amylose (15-20%): Water-soluble, long unbranched chain of 200-1000 $\alpha$ -D-glucose units. Linkage: C1–C4.
- Amylopectin (80-85%): Water-insoluble, branched chain. Linear linkage: C1–C4. Branching linkage: C1–C6.
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.

Proteins & Amino Acids

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

Primary (1°): Specific sequence of amino acids. Determines the unique identity of the protein.
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.
Tertiary (3°): Overall 3D folding (fibrous or globular molecular shapes). Stabilized by H-bonds, disulfide linkages, van der Waals, and electrostatic forces.
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 & Vitamins

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.

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.
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 & Hormones

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).
Bases:
- DNA: Adenine (A), Guanine (G), Cytosine (C), Thymine (T).
- RNA: Adenine (A), Guanine (G), Cytosine (C), Uracil (U).JEE TIPUracil replaces Thymine in RNA.
Detailed Linkages:
- Nucleoside: Base attaches to the 1' position of the sugar.
- Nucleotide: Phosphoric acid links to the 5' position.
- Polynucleotide: Nucleotides join via phosphodiester linkages specifically between the 5' and 3' carbon atoms of adjacent pentose sugars.
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).
Specific Hormones & Roles:
- Insulin/Glucagon: Insulin regulates/lowers blood glucose; glucagon increases it.
- Epinephrine/Norepinephrine: Mediate responses to external stimuli.
- Thyroxine: Iodinated derivative of Tyrosine (thyroid gland). Low levels $\rightarrow$ Hypothyroidism (obesity, lethargy, endemic goitre). Controlled by "Iodised" salt.
- Glucocorticoids/Mineralocorticoids: Secreted by adrenal cortex. Control carbohydrate metabolism and water/salt excretion. Deficiency causes Addison's disease (hypoglycemia, weakness).
- Sex Hormones: Testosterone (male), Estradiol (female secondary traits/menstrual cycle), Progesterone (prepares uterus for fertilized egg).

Reactions & Mechanisms

(Crucial Glucose Preparations & Reactions):

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).
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).
Reduction: $Glucose + HI \xrightarrow{\Delta} n-hexane$ .
Carbonyl Addition:
- $Glucose + NH_2OH \rightarrow Glucose\ oxime$ .
- $Glucose + HCN \rightarrow Glucose\ cyanohydrin$ .
Oxidation:
- $Glucose + Br_2/H_2O \rightarrow Gluconic\ acid$ .
- $Glucose + HNO_3 \rightarrow Saccharic\ acid$ (Gluconic acid also oxidizes to this).
Acetylation: $Glucose + (CH_3CO)_2O \rightarrow Glucose\ pentaacetate$ .

⚠️ EXCEPTIONS & ANOMALIES

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.

Previous Year JEE Topics

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.

Memory Aids & JEE Traps

JEE TIPMisconception: D- means a compound is dextrorotatory (+) and L- means it is laevorotatory (-). Correct Understanding: D/L nomenclature has zero relation to the sign of optical rotation (+/-) or d/l notation. It only dictates relative spatial configuration compared to glyceraldehyde.
JEE TIPMisconception: All disaccharides are non-reducing sugars because they are polymers. Correct Understanding: Sucrose is non-reducing because both reducing centers (C1 of glucose, C2 of fructose) are locked in the bond. Maltose and Lactose ARE reducing because they have one free hemiacetal anomeric carbon.
JEE TIPMisconception: Denaturation of a protein breaks peptide bonds and destroys its primary structure. Correct Understanding: Denaturation (like boiling an egg) only unfolds and destroys 2° and 3° structures. The 1° primary structure (peptide bonds) remains perfectly intact.
JEE TIPMisconception: $\alpha$ -D-glucose and $\beta$ -D-glucose are optical isomers (enantiomers) of each other. Correct Understanding: They are anomers (a subclass of diastereomers). They differ in stereochemistry only at C-1 (the anomeric carbon).
JEE TIPMisconception: Amylose is the highly branched, water-insoluble portion that makes up most of starch. Correct Understanding: Amylose is linear (C1-C4), water-soluble, and minor (15-20%). Amylopectin is the branched (C1-C4 & C1-C6), water-insoluble, and major component (80-85%).
JEE TIPMisconception: Essential amino acids are the ones synthesized continuously by the body because they are essential for survival. Correct Understanding: It is the exact opposite. They are "essential" in your diet precisely because the body CANNOT synthesize them.
JEE TIPMisconception: A nucleoside is just a different name for a nucleotide. Correct Understanding: A Nucleoside = Base + Sugar. A Nucleotide = Base + Sugar + Phosphate group.
JEE TIPMisconception: Cellulose is a polymer of $\alpha$ -D-glucose. Correct Understanding: Cellulose is composed exclusively of $\beta$ -D-glucose units joined by C1-C4 glycosidic linkages.
JEE TIPMisconception: Glucose pentaacetate will form an oxime with $NH_2OH$ because it is a derivative of glucose. Correct Understanding: Glucose pentaacetate does not react with $NH_2OH$ , which is the primary chemical proof that the -CHO group is NOT free, confirming the cyclic hemiacetal structure.
JEE TIPMisconception: DNA and RNA use the exact same four heterocyclic bases. Correct Understanding: RNA contains Uracil instead of Thymine. (DNA = A, T, C, G; RNA = A, U, C, G).