Biomolecules: NEET notes

1. What counts as a carbohydrate

NCERT §10.1–10.1.2

• Living things are built from lifeless atoms and molecules; biochemistry studies the chemistry going on inside them. The large biomolecules are carbohydrates, proteins, nucleic acids and lipids, helped by small ones such as vitamins and mineral salts.
• Carbohydrates are made mostly by plants. Many fit the formula Cx(H₂O)y, which is why they were once thought of as 'hydrates of carbon': glucose, C₆H₁₂O₆, can be written C₆(H₂O)₆.
• The formula is not a test. Acetic acid, CH₃COOH, fits it as C₂(H₂O)₂ yet is not a carbohydrate, and rhamnose, C₆H₁₂O₅, is a carbohydrate that does not fit it.
• The chemical definition: carbohydrates are optically active polyhydroxy aldehydes or ketones, or compounds that give such units when hydrolysed. The sweet ones are called sugars; household sugar is sucrose and milk sugar is lactose. Another name is saccharides, from the Greek sakcharon, sugar.
• Grouping by hydrolysis. A monosaccharide cannot be hydrolysed into a simpler polyhydroxy aldehyde or ketone; about 20 occur in nature, among them glucose, fructose and ribose.
• An oligosaccharide gives two to ten monosaccharide units on hydrolysis (disaccharides, trisaccharides and so on). Disaccharides are the commonest: sucrose gives one glucose and one fructose, maltose gives two glucose.
• A polysaccharide gives a large number of units: starch, cellulose, glycogen and gums. They do not taste sweet and are called non-sugars.
• Sugars that reduce Fehling's solution and Tollens' reagent are reducing sugars. Every monosaccharide, aldose or ketose, is a reducing sugar.
• Naming monosaccharides (Table 10.1): an aldehyde group makes it an aldose, a keto group a ketose, and the carbon count is built in. Three to seven carbons give triose, tetrose, pentose, hexose and heptose, so glucose is an aldohexose and fructose a ketohexose.

2. Glucose: how it is made and the open-chain evidence

NCERT §10.1.2.1

• Glucose occurs free in sweet fruits, honey and ripe grapes, and in combined form in larger carbohydrates.
• From sucrose: boiling cane sugar with dilute HCl or H₂SO₄ in alcoholic solution gives equal amounts of glucose and fructose; one sucrose plus one water yields one of each hexose.
• From starch (the commercial route): boiling with dilute H₂SO₄ at 393 K under 2–3 atm pressure. (C₆H₁₀O₅)n + nH₂O → nC₆H₁₂O₆.
• Glucose, also called dextrose, is an aldohexose and the monomer of starch and cellulose. NCERT calls it probably the most abundant organic compound on earth.
• Evidence 1 and 2: the molecular formula is C₆H₁₂O₆, and long heating with HI gives n-hexane, so the six carbons form an unbranched chain.
• Evidence 3: glucose forms an oxime with hydroxylamine and adds HCN to give a cyanohydrin, so it has a carbonyl group, >C=O.
• Evidence 4: a mild oxidant, bromine water, turns it into gluconic acid, a six-carbon carboxylic acid. Only an aldehyde is oxidised so easily, so the carbonyl is –CHO.
• Evidence 5: acetic anhydride gives glucose pentaacetate, so there are five –OH groups. The pentaacetate is stable, so the five –OH groups sit on different carbons.
• Evidence 6: nitric acid oxidises both glucose and gluconic acid to saccharic acid, a dicarboxylic acid. The second –COOH comes from a primary alcohol, –CH₂OH, at C6.
• Result: OHC–(CHOH)₄–CH₂OH. Fischer later fixed where each –OH points (structure I); gluconic acid (II) and saccharic acid (III) keep that arrangement.

3. D and L: relative configuration

NCERT §10.1.2.1

• The full name is D-(+)-glucose. D describes configuration; (+) says it is dextrorotatory. D and L tell you nothing about the sign of rotation, and they are not the same as the small letters d and l.
• D or L relates a compound's configuration to a reference whose configuration is known. For sugars the reference is glyceraldehyde, which has one asymmetric carbon and two enantiomers.
• (+)-Glyceraldehyde is D: drawn in the standard way, its –OH is on the right. (–)-Glyceraldehyde is L, with –OH on the left.
• Compounds that can be chemically correlated with D-(+)-glyceraldehyde are D; those correlated with the L-(–) isomer are L.
• For a monosaccharide, only the lowest asymmetric carbon is compared, with the most oxidised carbon (–CHO here) written at the top. In glucose that carbon (C5) has –OH on the right, so glucose is D. The other asymmetric carbons are ignored for this purpose.
• Fructose is D as well but laevorotatory, D-(–)-fructose: proof that D does not mean (+).

4. Ring forms of glucose and fructose

NCERT §10.1.2.1–10.1.2.2

• Facts the open chain cannot explain: glucose gives no Schiff's test and no hydrogensulphite addition product with NaHSO₃, and its pentaacetate does not react with hydroxylamine, so no free –CHO is present.
• Glucose also crystallises in two forms. The α-form (m.p. 419 K) comes from a concentrated solution at 303 K; the β-form (m.p. 423 K) from a hot saturated aqueous solution at 371 K.
• Explanation: the –OH on C5 adds to the –CHO group, closing a six-membered ring as a cyclic hemiacetal. With no free –CHO, the aldehyde tests fail.
• Ring closure makes C1 a new asymmetric centre, so there are two cyclic forms that differ only in the –OH on C1. C1 is the anomeric carbon and the two forms, α and β, are anomers. Both cyclic forms stay in equilibrium with the open chain.
• A six-membered ring of five carbons and one oxygen is named pyranose, after pyran. The Haworth formula draws it as a flat hexagon with groups above and below.
• Fructose is a ketohexose, C₆H₁₂O₆, with its keto group at C2 and six carbons in an unbranched chain. It comes with glucose from hydrolysis of sucrose and is found in fruits, honey and vegetables; pure, it is used as a sweetener.
• In fructose the C5 –OH adds to the C2 keto group, closing a five-membered ring of four carbons and one oxygen: a furanose, after furan. It too has α and β anomers.

5. Disaccharides and the glycosidic link

NCERT §10.1.3

• Two monosaccharides join by losing a water molecule, leaving an oxide bridge between them. A link between sugar units through oxygen is a glycosidic linkage. Dilute acid or enzymes hydrolyse it back.
• If both reducing groups (the aldehydic or ketonic carbons) are used up in the link, the disaccharide is non-reducing. If one stays free it is reducing.
• Sucrose: C1 of α-D-glucose joined to C2 of β-D-fructose. Both reducing carbons are in the bond, so sucrose is a non-reducing sugar.
• Sucrose is dextrorotatory. Its hydrolysis gives equal moles of D-(+)-glucose (+52.5°) and D-(–)-fructose (–92.4°). Fructose's laevorotation is the larger, so the mixture is laevorotatory.
• The sign of rotation flips from (+) to (–) on hydrolysis; the product is called invert sugar.
• Maltose: two α-D-glucose units, C1 of one joined to C4 of the other. The second unit's C1 can open to a free aldehyde in solution, so maltose is reducing.
• Lactose (milk sugar): β-D-galactose and β-D-glucose linked from C1 of galactose to C4 of glucose. The glucose unit's C1 can give a free aldehyde, so lactose is reducing.

6. Polysaccharides and why carbohydrates matter

NCERT §10.1.4–10.1.5

• Polysaccharides are long chains of monosaccharide units held by glycosidic linkages. They are the carbohydrates met most often in nature and serve mainly for food storage or structure.
• Starch, the main storage polysaccharide of plants and the chief dietary source for people, is a polymer of α-glucose found richly in cereals, roots, tubers and some vegetables. It has two parts.
• Amylose, about 15–20% of starch, dissolves in water. It is an unbranched chain of 200–1000 α-D-(+)-glucose units joined C1–C4.
• Amylopectin, about 80–85% of starch, is insoluble in water. Its chains are joined C1–C4 and it branches through C1–C6 links.
• Cellulose is found only in plants, is the most abundant organic substance in the plant kingdom and makes up much of plant cell walls. It is an unbranched chain of β-D-glucose units joined C1 to C4.
• Starch and cellulose are both glucose polymers linked C1–C4. The difference is the anomer: α-glucose in starch, β-glucose in cellulose.
• Glycogen is how animals store carbohydrate, hence 'animal starch'. It resembles amylopectin but is more highly branched, occurs in liver, muscles and brain (and in yeast and fungi), and enzymes break it down to glucose when the body needs it.
• Uses: carbohydrates are a large part of food, and honey has long served Vaids in ayurveda as instant energy. Cellulose makes the cell walls of bacteria and plants, and reaches us as wood for furniture and cotton for clothes. Textiles, paper, lacquers and breweries use carbohydrates as raw material.
• D-ribose and 2-deoxy-D-ribose, both aldopentoses, are the sugars of nucleic acids. Carbohydrates also occur bound to proteins and lipids.

7. Amino acids

NCERT §10.2–10.2.2

• Proteins are the most abundant biomolecules in living systems. Milk, cheese, pulses, peanuts, fish and meat are rich sources. The name comes from Greek proteios, of prime importance. Every protein is a polymer of α-amino acids.
• Amino acids carry –NH₂ and –COOH. By where the amino group sits relative to the carboxyl they are α, β, γ, δ and so on; protein hydrolysis gives only α-amino acids, R–CH(NH₂)–COOH, where R is the side chain.
• They have trivial names and three-letter (sometimes one-letter) symbols. Glycine (Gly, G) is named for its sweet taste (Greek glykos) and tyrosine (Tyr, Y) for cheese (Greek tyros). Table 10.2 lists twenty.
• Side chains from Table 10.2: glycine H; alanine –CH₃; serine HO–CH₂–; cysteine HS–CH₂–; lysine H₂N–(CH₂)₄–; aspartic acid HOOC–CH₂–; phenylalanine C₆H₅–CH₂–.
• Classification by charge-bearing groups: equal numbers of amino and carboxyl groups make a neutral amino acid, more amino groups a basic one (lysine, arginine), more carboxyl groups an acidic one (aspartic, glutamic acid).
• Non-essential amino acids can be made in the body; essential ones cannot and must come from food. The ten essential ones in Table 10.2 are valine, leucine, isoleucine, arginine, lysine, threonine, methionine, phenylalanine, tryptophan and histidine.
• Amino acids are colourless, crystalline, water-soluble solids with high melting points, behaving more like salts than like simple amines or acids.
• Reason: in water the –COOH gives up a proton and the –NH₂ takes one, forming a dipolar zwitter ion, H₃N⁺–CHR–COO⁻. It is neutral overall but carries both charges, and it reacts with acids and bases alike: it is amphoteric.
• Every naturally occurring α-amino acid except glycine (R = H) has an asymmetric α-carbon and is optically active. Both D and L forms exist, but most natural ones are L, drawn with –NH₂ on the left.

8. Peptides and the four levels of protein structure

NCERT §10.2.3

• A peptide bond is an amide, –CO–NH–, formed when the carboxyl group of one amino acid joins the amino group of another with loss of water. Glycine's –COOH with alanine's –NH₂ gives the dipeptide glycylalanine.
• Three amino acids joined by two peptide bonds make a tripeptide; then tetra-, penta-, hexapeptide. More than ten amino acids make a polypeptide.
• A polypeptide with over a hundred residues and molecular mass above 10,000 u is called a protein. The line is not sharp: insulin, with only 51 amino acids, counts as a protein because it has a definite protein-like shape.
• By shape. Fibrous proteins: parallel chains held by hydrogen and disulphide bonds form fibres, generally insoluble in water, e.g. keratin (hair, wool, silk) and myosin (muscles). Globular proteins: chains coil into a sphere and usually dissolve in water, e.g. insulin and albumins.
• Primary structure: the exact sequence of amino acids in each chain. Change the sequence and you have a different protein.
• Secondary structure: the shape of the backbone, held by hydrogen bonds between the C=O and –NH– groups of peptide bonds. Two kinds occur: α-helix and β-pleated sheet.
• α-Helix: the chain twists into a right-handed screw so that each residue's –NH is hydrogen-bonded to a C=O on the next turn, making the most hydrogen bonds possible.
• β-Pleated sheet: chains stretched almost fully lie side by side, held by hydrogen bonds between chains; the folds look like pleated drapery.
• Tertiary structure: the overall folding of the chain beyond the secondary structure, giving the fibrous or globular shape. Hydrogen bonds, disulphide linkages, van der Waals forces and electrostatic attraction stabilise 2° and 3° structure.
• Quaternary structure: the arrangement in space of two or more chains (sub-units) in one protein. Haemoglobin is NCERT's example.

9. Denaturation and enzymes

NCERT §10.2.4–10.3

• A native protein is one in its natural three-dimensional shape with its biological activity. A physical change (temperature) or chemical change (pH) disturbs its hydrogen bonds, globules unfold, helices uncoil, and the activity is lost: denaturation.
• In denaturation the secondary and tertiary structures are destroyed but the primary structure, the sequence held by peptide bonds, survives.
• Everyday cases: egg white setting on boiling, and milk curdling when its bacteria make lactic acid.
• Enzymes are biocatalysts that let the body's reactions run under mild conditions. Almost all are globular proteins, and each is highly specific to one reaction and one substrate.
• Names usually come from the substrate plus -ase: maltase hydrolyses maltose, C₁₂H₂₂O₁₁ + H₂O → 2C₆H₁₂O₆ (glucose). Some come from the reaction: oxidoreductases catalyse oxidation of one substrate with reduction of another.
• Enzymes are needed only in small amounts and, like chemical catalysts, lower the activation energy. NCERT's example: acid hydrolysis of sucrose has Ea 6.22 kJ mol⁻¹, hydrolysis by sucrase only 2.15 kJ mol⁻¹.

10. Vitamins

NCERT §10.4–10.4.1

• Vitamins are organic compounds needed in small amounts in the diet for specific biological functions, growth and health; lacking one causes a specific disease. They come from many chemical classes, so they cannot be defined by structure.
• Our bodies cannot make most of them, though plants make nearly all and gut bacteria make some. They are named A, B, C, D and so on, with sub-groups such as B₁, B₂, B₆, B₁₂. Too much is also harmful, so vitamin pills need a doctor's advice.
• The old name 'vitamine' (vital + amine) came from the first ones found having amino groups; most do not, so the 'e' was dropped.
• Fat-soluble vitamins A, D, E and K dissolve in fats and oils but not in water, and are stored in the liver and adipose tissue.
• Water-soluble vitamins, the B group and C, are excreted in urine and cannot be stored (B₁₂ is the exception), so they must be eaten regularly.
• Table 10.3, deficiency diseases: A, xerophthalmia (hardening of the cornea) and night blindness; B₁ (thiamine), beri beri; B₂ (riboflavin), cheilosis, digestive disorders and burning skin; B₆ (pyridoxine), convulsions; B₁₂, pernicious anaemia.
• Continued: C (ascorbic acid), scurvy with bleeding gums; D, rickets in children and osteomalacia in adults; E, fragile red blood cells and muscular weakness; K, increased blood clotting time.
• Sources: A from fish liver oil, carrots, butter, milk; C from citrus fruits, amla and green leafy vegetables; D from sunlight exposure, fish and egg yolk; E from vegetable oils such as wheat germ and sunflower oil; K from green leafy vegetables; B₁₂ from meat, fish, egg and curd.

11. Nucleic acids

NCERT §10.5–10.5.3

• Heredity is carried by chromosomes in the cell nucleus, made of proteins and nucleic acids. The two nucleic acids are DNA (deoxyribonucleic acid) and RNA (ribonucleic acid). Both are long chains of nucleotides, so they are also called polynucleotides.
• Complete hydrolysis gives three things: a pentose sugar, phosphoric acid and nitrogen-containing heterocyclic bases. The sugar is β-D-2-deoxyribose in DNA and β-D-ribose in RNA.
• Bases: DNA's four are A (adenine), G (guanine), C (cytosine) and T (thymine). RNA shares A, G and C but carries U (uracil) where DNA has T.
• A nucleoside is a base joined to C1′ of the sugar; the primes keep sugar carbons apart from base atoms. A nucleotide is a nucleoside with phosphoric acid on C5′ of the sugar.
• Nucleotides join through phosphodiester links between the 5′ and 3′ carbons of neighbouring sugars, so the backbone alternates sugar and phosphate with a base on each sugar.
• Primary structure is the sequence of nucleotides. Watson and Crick proposed DNA's secondary structure: two strands wound as a double helix, held by hydrogen bonds between bases.
• Pairing is specific: adenine with thymine, cytosine with guanine. So the two strands are complementary, not identical.
• RNA is a single-stranded helix that sometimes folds back on itself. Its three types are messenger (m-RNA), ribosomal (r-RNA) and transfer (t-RNA).
• DNA is the chemical basis of heredity. It copies itself during cell division so each daughter cell gets identical DNA, and it keeps a species' identity over millions of years. It carries the message for each protein, which the RNAs then build.
• DNA fingerprinting uses the base sequence, unique to a person and the same in every cell: in forensics, for paternity, to identify accident victims by comparing with parents or children, and to study racial groups and evolution.

12. Hormones

NCERT §10.6

• Hormones are intercellular messengers made by endocrine glands and released straight into the blood, which carries them to where they act.
• Chemically they fall into three kinds: steroids (estrogens, androgens), polypeptides (insulin, endorphins) and amino acid derivatives (epinephrine, norepinephrine).
• They keep body activities in balance. Insulin is released when blood glucose rises fast; glucagon raises blood glucose. Together they hold it in a narrow range.
• Responses to outside stimuli run through epinephrine and norepinephrine; growth and sex hormones steer growth and development.
• Thyroxine, from the thyroid, is an iodinated derivative of the amino acid tyrosine. Too little causes hypothyroidism (lethargy, obesity); too much, hyperthyroidism. Low dietary iodine can cause hypothyroidism and an enlarged thyroid, now largely prevented by adding sodium iodide to table salt.
• Steroid hormones come from the adrenal cortex and the gonads. Glucocorticoids control carbohydrate metabolism, modulate inflammation and act in stress; mineralocorticoids control how much water and salt the kidney excretes.
• A failing adrenal cortex can cause Addison's disease (hypoglycemia, weakness, poor tolerance of stress), fatal unless treated with glucocorticoids and mineralocorticoids.
• Gonad hormones drive secondary sex characters. Testosterone is the main male hormone (deep voice, facial hair, build); estradiol the main female one, also helping control the menstrual cycle; progesterone prepares the uterus to receive a fertilised egg.

Must-know facts

1. Carbohydrates: optically active polyhydroxy aldehydes or ketones, or compounds that hydrolyse to them. Cx(H₂O)y is not a test: acetic acid fits, rhamnose (C₆H₁₂O₅) does not.
2. Mono (no hydrolysis; about 20 in nature), oligo (2–10 units), poly (many units; non-sugars).
3. All monosaccharides, aldoses and ketoses, are reducing sugars.
4. Glucose from starch: dilute H₂SO₄, 393 K, 2–3 atm. From sucrose: dilute HCl or H₂SO₄ in alcoholic solution, equal glucose and fructose.
5. Glucose evidence: HI → n-hexane (straight chain); oxime + cyanohydrin (C=O); Br₂ water → gluconic acid (–CHO); pentaacetate (5 –OH); HNO₃ → saccharic acid (1° alcohol).
6. D/L compares the lowest asymmetric carbon with glyceraldehyde; –OH on the right = D. It says nothing about (+) or (–): D-(–)-fructose.
7. Glucose has no free –CHO: no Schiff's test, no NaHSO₃ adduct, pentaacetate ignores NH₂OH. C5–OH closes a six-membered pyranose ring.
8. α-glucose m.p. 419 K (crystallised at 303 K); β-glucose m.p. 423 K (crystallised at 371 K). They are anomers, differing at C1.
9. Fructose: ketohexose, keto at C2; C5–OH closes a five-membered furanose ring; D-(–).
10. Sucrose: α-glucose C1 – β-fructose C2, non-reducing. Hydrolysis gives invert sugar because fructose (–92.4°) outweighs glucose (+52.5°).
11. Maltose: α-glucose C1–C4 α-glucose, reducing. Lactose: β-galactose C1–C4 β-glucose, reducing.
12. Starch = amylose (15–20%, soluble, unbranched, 200–1000 units, C1–C4) + amylopectin (80–85%, insoluble, branched C1–C6). Cellulose: β-glucose C1–C4, unbranched. Glycogen: like amylopectin, more branched.
13. Proteins hydrolyse to α-amino acids only. Zwitter ion H₃N⁺–CHR–COO⁻ explains high m.p., water solubility and amphoteric behaviour.
14. Glycine is the one optically inactive natural α-amino acid. Natural ones are mostly L.
15. Ten essential amino acids: Val, Leu, Ile, Arg, Lys, Thr, Met, Phe, Trp, His.
16. Peptide bond –CO–NH–; >10 amino acids = polypeptide; >100 residues and >10,000 u = protein; insulin has 51.
17. Fibrous (keratin, myosin; insoluble) versus globular (insulin, albumins; soluble).
18. 1° sequence; 2° α-helix (right-handed, intrachain H-bonds C=O···H–N) and β-pleated sheet (interchain H-bonds); 3° overall folding; 4° sub-unit arrangement.
19. Denaturation (heat, pH) destroys 2° and 3° structure; 1° stays. Boiled egg, curdled milk.
20. Enzymes: mostly globular proteins, specific, named with -ase; sucrose hydrolysis Ea 6.22 kJ mol⁻¹ with acid, 2.15 with sucrase.
21. Fat-soluble A, D, E, K (stored); water-soluble B group and C (not stored, except B₁₂).
22. A: xerophthalmia, night blindness. B₁: beri beri. B₂: cheilosis. B₆: convulsions. B₁₂: pernicious anaemia. C: scurvy. D: rickets, osteomalacia. E: fragile RBCs. K: longer clotting time.
23. Nucleoside = base + sugar (at C1′); nucleotide = nucleoside + phosphate (at C5′); chain links 5′–3′ phosphodiester.
24. DNA: 2-deoxyribose, A G C T, double helix, A–T and C–G. RNA: ribose, A G C U, single strand; m-, r-, t-RNA.
25. Hormones: steroids (estrogens, androgens), polypeptides (insulin, endorphins), amino acid derivatives (epinephrine, norepinephrine; thyroxine from tyrosine).

Common traps

Formulas

Key terms

Carbohydrate

Optically active polyhydroxy aldehyde or ketone, or a compound that hydrolyses to one.

Reducing sugar

A sugar that reduces Fehling's solution and Tollens' reagent.

Aldose / ketose

Monosaccharide with an aldehyde / keto group.

Anomers

Cyclic forms of a sugar that differ only at the anomeric carbon (C1 in glucose).

Pyranose / furanose

Six-membered / five-membered sugar ring containing one oxygen.

Glycosidic linkage

Oxygen bridge between two sugar units, formed with loss of water.

Invert sugar

The laevorotatory glucose–fructose mixture from hydrolysing dextrorotatory sucrose.

Zwitter ion

Dipolar form of an amino acid, H₃N⁺–CHR–COO⁻, neutral overall.

Essential amino acid

One the body cannot make, so it must come from the diet.

Peptide bond

The amide link –CO–NH– between amino acids.

Denaturation

Loss of 2° and 3° structure and of activity on heating or pH change; 1° structure kept.

Enzyme

A biocatalyst, almost always a globular protein, specific to its reaction and substrate.

Nucleotide

Base + pentose sugar + phosphate (at C5′).

Complementary strands

DNA strands whose bases pair A with T and C with G.

Hormone

An intercellular messenger released by an endocrine gland into the blood.