Biomolecules

NCERT defines carbohydrates as optically active polyhydroxy aldehydes or ketones, or compounds that give these on hydrolysis. Most fit C_x(H₂O)_y, the origin of the old name 'hydrates of carbon', but the formula is not the definition: acetic acid C₂H₄O₂ fits it and is not a carbohydrate, while rhamnose C₆H₁₂O₅ is one and does not. Carbohydrates are also called saccharides; the sweet, water-soluble ones such as glucose and sucrose are sugars.

Two classifications matter. By hydrolysis: monosaccharides cannot be hydrolysed to anything simpler (glucose, fructose, ribose; about 20 are known); oligosaccharides give two to ten units, the important case being disaccharides such as sucrose, maltose and lactose; polysaccharides give a large number of units (starch, cellulose, glycogen), are not sweet and are called non-sugars.

By reducing behaviour: a reducing sugar reduces Fehling's solution and Tollens' reagent because it has a free aldehyde or ketone group (a free hemiacetal in the ring form). All monosaccharides are reducing. Among disaccharides, maltose and lactose are reducing while sucrose is not, because both its carbonyl carbons are tied up in the glycosidic bond.

Monosaccharides are classified by the carbonyl group (aldose or ketose) and by carbon count (triose to heptose). Glucose is an aldohexose, fructose a ketohexose, ribose an aldopentose.

Preparation of glucose. From sucrose: boil with dilute HCl or H₂SO₄ in alcoholic solution to get glucose and fructose. From starch, the commercial method: boil with dilute H₂SO₄ at 393 K under 2–3 atm.

Evidence for the open-chain structure. Learn it as a numbered list; the examiner ticks each point. (1) Molecular formula C₆H₁₂O₆. (2) Prolonged heating with HI gives n-hexane, so all six carbons are in a straight chain. (3) It forms an oxime with hydroxylamine and a cyanohydrin with HCN, so a carbonyl group is present. (4) Bromine water, a mild oxidant, oxidises it to gluconic acid, a six-carbon monocarboxylic acid, so the carbonyl is an aldehyde. (5) Acetic anhydride gives a stable pentaacetate, so five –OH groups are present on five different carbons. (6) Glucose and gluconic acid are both oxidised by nitric acid to saccharic acid, a dicarboxylic acid, showing a primary alcoholic –CH₂OH group.

Fischer fixed the spatial arrangement. Glucose is D-(+)-glucose: (+) because it is dextrorotatory, D because the –OH on the lowest asymmetric carbon (C5) is on the right in the Fischer projection, as in (+)-glyceraldehyde. D and L say nothing about the sign of rotation.

The open chain cannot explain three facts, and 'two reactions of glucose not explained by its open-chain structure' is a favourite 2-mark question. (1) Despite the aldehyde group, glucose does not give the 2,4-DNP test or Schiff's test and does not form the hydrogensulphite addition product with NaHSO₃. (2) The pentaacetate of glucose does not react with hydroxylamine, so it has no free –CHO group. (3) Glucose exists in two crystalline forms: the α-form crystallises from a concentrated solution at 303 K (melting point 419 K) and the β-form from a hot saturated aqueous solution at 371 K (melting point 423 K).

The explanation: the –OH on C5 adds across the C1 aldehyde to form a six-membered cyclic hemiacetal. C1 becomes a new asymmetric carbon, the anomeric carbon, so two ring forms exist differing only in the configuration at C1: α-D-glucose (C1 –OH below the ring in the Haworth projection) and β-D-glucose (C1 –OH above). Such a pair is called anomers. The ring has five carbons and one oxygen like pyran, so the forms are α-D-(+)-glucopyranose and β-D-(+)-glucopyranose. In solution the anomers are in equilibrium through a little open-chain form, which is why glucose still reduces Fehling's solution yet fails tests needing a stable free aldehyde.

Fructose, C₆H₁₂O₆, is a ketohexose found with glucose in fruit and honey and as one half of sucrose. Its carbonyl is a ketone at C2, with –CH₂OH groups at both ends. It has the D-configuration because the –OH on the lowest asymmetric carbon (C5) is on the right in the Fischer projection, yet it is laevorotatory, so it is written D-(−)-fructose. This is the standard example that D/L (configuration) and (+)/(−) (direction of rotation) are independent labels.

Like glucose, fructose forms cyclic hemiketals. The –OH on C5 adds to the C2 ketone, and the ring has four carbons and one oxygen, five-membered like furan. So the cyclic forms are furanose forms, α-D-(−)-fructofuranose and β-D-(−)-fructofuranose, differing at the anomeric carbon, C2. In the Haworth drawing C2 carries both the anomeric –OH and the C1 –CH₂OH. Fructose is a reducing sugar although it is a ketose, because its α-hydroxy ketone is oxidised in the alkaline medium of Fehling's and Tollens' tests.

A disaccharide is two monosaccharide units joined by an oxide linkage formed by loss of water between two –OH groups; this is the glycosidic linkage. Dilute acid or an enzyme hydrolyses it back to the monosaccharides.

Sucrose (cane sugar) gives one D-(+)-glucose and one D-(−)-fructose. The glycosidic bond joins C1 of α-D-glucose to C2 of β-D-fructose. Both reducing groups are used, so sucrose is non-reducing. Sucrose is dextrorotatory, but the hydrolysis mixture is laevorotatory because the laevorotation of fructose (−92.4°) exceeds the dextrorotation of glucose (+52.5°). The sign inverts, so the product is called invert sugar and the enzyme invertase (sucrase).

Maltose gives two α-D-glucose molecules; C1 of one unit is linked to C4 of the other. C1 of the second unit is free and can open to the aldehyde in solution, so maltose is reducing.

Lactose (milk sugar) gives β-D-galactose and β-D-glucose; C1 of galactose is linked to C4 of glucose. The C1 of the glucose unit is free, so lactose is reducing.

Put the three products and three linkages in one table; this is the most repeated 1- and 2-mark material in the chapter.

Polysaccharides are long chains of monosaccharides joined by glycosidic linkages, the storage and structural materials of living things.

Starch is the main storage polysaccharide of plants and our chief dietary carbohydrate (cereals, potatoes, pulses). It is a polymer of α-glucose with two components. Amylose, 15–20 per cent, is water-soluble, a long unbranched chain of 200–1000 α-D-(+)-glucose units held by C1–C4 glycosidic linkages. Amylopectin, 80–85 per cent, is water-insoluble and branched: C1–C4 linkages build the chain and C1–C6 linkages attach the branches.

Cellulose is the most abundant organic substance in the plant kingdom and the chief material of plant cell walls. It is a straight-chain polysaccharide of β-D-glucose units joined by C1–C4 glycosidic linkages. That one letter, β instead of α, is 'the basic structural difference between starch and cellulose' and is why we digest starch but not cellulose.

Glycogen is the stored carbohydrate of animals, hence 'animal starch'. It occurs in the liver, muscles and brain, and in yeast and fungi. Its structure resembles amylopectin but is even more branched. When the body needs glucose, enzymes break glycogen down to glucose.

This short section is asked as 'write two main functions of carbohydrates in plants' or 'state two functions of carbohydrates'. Know the list and pick what the question wants.

• Carbohydrates form the major portion of our food; the starch of cereals, pulses and potatoes is our main energy source, and honey (mostly glucose and fructose) has been used for centuries as an instant source of energy.
• Storage: plants store carbohydrate as starch and animals as glycogen, both broken down to glucose when energy is needed.
• Structure: cellulose builds the cell walls of plants and bacteria; wood is mostly cellulose and cotton is nearly pure cellulose, the raw material for paper and rayon.
• Carbohydrates are needed for the biosynthesis of fats and proteins.
• Two pentoses, D-ribose and 2-deoxy-D-ribose, are constituents of RNA and DNA.
• Plants make carbohydrates by photosynthesis, so they carry the energy of sunlight into every food chain.

The two functions 'in plants' the examiner expects are starch as the stored form of food and cellulose as the structural material of the cell wall.

Proteins are the most abundant biomolecules in living systems; the name comes from the Greek proteios, 'of prime importance'. Chemically they are polymers of α-amino acids.

An amino acid has an amino group and a carboxyl group. In the α-amino acids of proteins the –NH₂ sits on the α-carbon, next to –COOH, giving R–CH(NH₂)–COOH. Twenty amino acids occur in proteins, differing only in R, each with a trivial name and three-letter and one-letter codes, e.g. glycine (Gly, G, R = H) and alanine (Ala, A, R = CH₃).

Classification. By the relative number of amino and carboxyl groups: neutral when equal (glycine, alanine), acidic when carboxyl groups are more (aspartic acid, glutamic acid), basic when amino groups are more (lysine, arginine). By origin: essential amino acids cannot be synthesised in the body and must come from the diet (valine, leucine, isoleucine, phenylalanine, tryptophan, methionine, threonine, lysine, histidine, arginine); non-essential ones are made in the body (glycine, alanine, serine and others).

Properties. Amino acids are colourless, crystalline, water-soluble, high-melting solids that behave like salts. In aqueous solution the –COOH loses a proton and the –NH₂ accepts it, giving the dipolar zwitter ion H₃N⁺–CHR–COO⁻. This makes them amphoteric: –COO⁻ accepts a proton from acids, –NH₃⁺ donates one to bases. Except glycine, all α-amino acids are optically active because the α-carbon is asymmetric; natural ones have the L-configuration, drawn with –NH₂ on the left.

Amino acids link through the peptide bond, an amide –CO–NH– formed when the –COOH of one amino acid condenses with the –NH₂ of the next, losing water. Glycine and alanine give the dipeptide glycylalanine, Gly-Ala. Two amino acids make a dipeptide, three a tripeptide, many a polypeptide. A polypeptide with more than a hundred amino acid residues and a molecular mass above 10,000 u is called a protein.

By shape, proteins are fibrous or globular. In fibrous proteins the chains run parallel, held by hydrogen and disulphide bonds; they are water-insoluble: keratin (hair, wool, silk) and myosin (muscle). In globular proteins the chains coil into a spherical shape; they are usually water-soluble: insulin and albumins.

Four levels of structure. Primary: the sequence of amino acids; any change gives a different protein. Secondary: the local shape of the chain, held by hydrogen bonds between –C=O and –N–H of peptide bonds; the α-helix is a right-handed screw in which the –NH of each residue is hydrogen-bonded to the C=O of the adjacent turn, and the β-pleated sheet has chains stretched nearly to full length and laid side by side, held by intermolecular hydrogen bonds. Tertiary: the overall folding of the chain (further folding of the secondary structure) giving the fibrous or globular shape, stabilised by hydrogen bonds, disulphide linkages, van der Waals and electrostatic forces. Quaternary: for proteins of two or more polypeptide chains, the spatial arrangement of the subunits with respect to one another.

A protein found in a biological system with its own unique three-dimensional structure and biological activity is a native protein. When a native protein is subjected to a physical change such as temperature or a chemical change such as pH, the hydrogen bonds are disturbed, the globules unfold and the helix uncoils, and the protein loses its biological activity. This is denaturation.

The key marking point is what changes. Denaturation destroys the secondary and tertiary structures but leaves the primary structure intact: the amino acid sequence and the peptide bonds survive, only the folding is lost. Since the folding fits an enzyme to its substrate, a denatured enzyme is inactive.

Two NCERT examples appear in the paper. Boiling an egg coagulates the egg white: the soluble globular albumin unfolds into an insoluble fibrous mass, and the water in the egg is absorbed by the coagulated protein through hydrogen bonding. Milk curdles when lactobacillus bacteria produce lactic acid, which lowers the pH and denatures the milk protein.

Contrast with hydrolysis if a question hints at it: hydrolysis breaks the peptide bonds and destroys the primary structure; denaturation does not.

Enzymes are biological catalysts. Almost all are globular proteins, and each is specific for one reaction or one type of reaction. Reactions that would need high temperature and strong acid in the laboratory run in the body at about 310 K and near-neutral pH because an enzyme is present. Enzymes are named after the compound they act on or the reaction they catalyse, usually ending in -ase: maltase hydrolyses maltose to glucose, and an enzyme that oxidises one substrate while reducing another is an oxidoreductase.

Mechanism. Like any catalyst, an enzyme lowers the activation energy of the reaction. Quote NCERT's figures: the activation energy for the acid hydrolysis of sucrose is 6.22 kJ mol⁻¹, but only 2.15 kJ mol⁻¹ when the hydrolysis is catalysed by the enzyme sucrase. The enzyme binds the substrate at its active site and provides an alternative path through a lower-energy transition state.

Because enzymes are proteins, denaturation applies: heat, extreme pH or heavy-metal ions unfold them and stop the catalysis. Diseases due to a missing enzyme are asked occasionally; phenylketonuria (lack of phenylalanine hydroxylase) and albinism (lack of tyrosinase) are the usual examples.

Vitamins are organic compounds required in the diet in small amounts to perform specific biological functions for the normal maintenance of optimum growth and health. Most cannot be made by the body (vitamin D, formed in the skin in sunlight, is the exception NCERT flags), and both deficiency and excess cause disease. They are named A, B, C, D and so on, with the B group split into B₁, B₂, B₆, B₁₂ and others.

Classification is by solubility. Fat-soluble vitamins A, D, E and K are stored in the liver and adipose tissue. Water-soluble vitamins, the B group and C, must be supplied regularly in the diet because they are readily excreted in urine and cannot be stored, except vitamin B₁₂, which is stored in the liver.

The table to reproduce: A (fish liver oil, carrots, butter, milk) – xerophthalmia and night blindness. B₁ thiamine (yeast, milk, green vegetables, cereals) – beri beri. B₂ riboflavin (milk, egg white, liver, kidney) – cheilosis, digestive disorders, burning sensation of the skin. B₆ pyridoxine (yeast, milk, egg yolk, cereals, grams) – convulsions. B₁₂ (meat, fish, egg, curd) – pernicious anaemia, red blood cells deficient in haemoglobin. C ascorbic acid (citrus fruits, amla, green leafy vegetables) – scurvy, bleeding gums. D (sunlight, fish, egg yolk) – rickets in children, osteomalacia in adults. E (vegetable oils such as wheat-germ and sunflower oil) – increased fragility of red blood cells and muscular weakness. K (green leafy vegetables) – increased blood clotting time; K is the vitamin responsible for coagulation of blood.

Every cell nucleus has chromosomes made of proteins and nucleic acids. The nucleic acids carry heredity, and there are two: deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). Both are long-chain polymers of nucleotides, also called polynucleotides.

Composition. Complete hydrolysis of DNA or RNA gives 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; the difference is the –OH at C2, present in ribose and absent in deoxyribose. Purines, with two fused rings, are adenine (A) and guanine (G); pyrimidines, with one ring, are cytosine (C), thymine (T) and uracil (U). DNA contains A, G, C and T; RNA contains A, G, C and U. So thymine is found only in DNA, uracil only in RNA, and A, G, C are common to both.

Nucleoside and nucleotide. A base attached to C1' of the pentose is a nucleoside (sugar + base). A phosphoric acid unit joined at the 5'-OH of the sugar of a nucleoside gives a nucleotide (sugar + base + phosphate). Nucleotides join through phosphodiester linkages between the 5' carbon of one sugar and the 3' carbon of the next, so the backbone is sugar–phosphate–sugar–phosphate with a base on each sugar.

The primary structure of a nucleic acid is the sequence of nucleotides, the order of bases along the chain, which carries the genetic information.

The secondary structure of DNA is the double helix proposed by James Watson and Francis Crick in 1953. Two polynucleotide strands wind round each other in a right-handed helix, sugar–phosphate backbones outside and bases inside, held by hydrogen bonds between pairs of bases. The pairing is fixed: adenine with thymine through two hydrogen bonds (A=T) and guanine with cytosine through three (G≡C). So the two strands are not identical but complementary: wherever one has A the other has T, wherever one has G the other has C.

RNA is single-stranded. It sometimes folds back on itself so that complementary bases within one strand pair, but there is no rule linking the amounts of its bases; that is why hydrolysis of RNA gives no fixed ratio among A, G, C and U, while in DNA A equals T and G equals C. The three types are messenger RNA (m-RNA), ribosomal RNA (r-RNA) and transfer RNA (t-RNA), each with a different role in reading the DNA message and building proteins.

The two important functions of nucleic acids, which NCERT exercise 10.21 asks for, are heredity and protein synthesis.

DNA is the reserve of genetic information. It is the chemical basis of heredity and carries the information for the characteristics of an organism from one generation to the next. When a cell divides, the double helix unwinds and each strand acts as a template for a new complementary strand, so two identical DNA molecules result. This is replication, and it works only because the strands are complementary.

Protein synthesis. DNA does not make proteins directly. A message copied from a segment of DNA is carried by messenger RNA from the nucleus to the ribosome (transcription). At the ribosome, made largely of ribosomal RNA, the message is read three bases at a time and transfer RNA brings the amino acid matching each triplet; the amino acids are joined in that order (translation). So the base sequence of DNA fixes the amino acid sequence of every protein, and hence the enzymes and chemistry of the cell.

A sentence that earns marks: DNA is the same in every cell and stays constant through life, while RNA is made as needed and broken down after use.

Hormones are molecules that act as intermolecular messengers. They are produced by the endocrine glands and released directly into the blood stream, which carries them to the site of action. They control growth, metabolism, reproduction and the response to stress. The syllabus asks only an elementary idea, no structures.

By chemical nature there are three kinds. Steroids: estrogens, androgens, and the adrenal cortex hormones cortisol and aldosterone. Polypeptides: insulin and endorphins. Amino-acid derivatives: epinephrine, norepinephrine and thyroxine.

Insulin is a polypeptide made by the β-cells of the pancreas and released in response to a rapid rise in blood glucose; it lowers blood glucose, while glucagon raises it, and together they keep it steady. Epinephrine and norepinephrine mediate the response to external stimuli. Thyroxine, from the thyroid gland, is an iodinated derivative of tyrosine; too little iodine in the diet leads to hypothyroidism and enlargement of the thyroid gland (goitre), which is why table salt is iodised with sodium iodide.

Among steroids, the adrenal cortex makes glucocorticoids such as cortisol, which control carbohydrate metabolism, modulate inflammation and take part in the stress response, and mineralocorticoids such as aldosterone, which control the excretion of water and salt by the kidney. Sex hormones: testosterone (androgen, testes) governs male secondary characteristics; estradiol (estrogen, ovaries) governs female characteristics and the menstrual cycle; progesterone prepares the uterus for implantation of the fertilised egg.