Biomolecules: Class 12 Chemistry · Chapter 10

Picture a plate of dal, rice and curd. The rice is mostly starch, the dal is rich in protein, and the curd brings milk sugar, fat and a crowd of helpful bacteria. Within hours your body has taken these large molecules apart and started to rebuild the pieces as its own: muscle, blood cells, and a fresh copy of your DNA each time a cell divides.

The molecules that living things build and use are called biomolecules (जैव-अणु). The big families are carbohydrates, proteins, nucleic acids and lipids, and smaller helpers such as vitamins, hormones and mineral ions keep the chemistry on track. No single one of these molecules is alive. Life is what thousands of their reactions add up to when they run together in water, at body temperature, each at the right moment, and the study of that chemistry is biochemistry.

This unit takes the families one at a time: what each is made of, how its units are joined, and how its structure explains its job. You will reuse ideas from earlier units along the way: aldehydes, ketones, amines and acids; optical activity and stereocentres (Unit 6); and activation energy from chemical kinetics.

10.1 Carbohydrates

The sugar in your tea, the starch in a chapati and the cellulose in a cotton shirt are all carbohydrates. Green plants make them from carbon dioxide and water using the energy of sunlight, and nearly every other organism, including you, lives on that supply. The small, sweet, water-soluble members of the family are called sugars, and the whole family is also known as the saccharides, from the Greek word for sugar.

The name carbohydrate is a leftover from early chemistry. Many of these compounds have formulas that fit $\mathrm{C}{\phantom{X}}_x(\mathrm{H}{\phantom{X}}_2\mathrm{O}){\phantom{X}}_y$: table sugar, $\mathrm{C}{\phantom{X}}_{12}\mathrm{H}{\phantom{X}}_{22}\mathrm{O}{\phantom{X}}_{11}$, can be written $\mathrm{C}{\phantom{X}}_{12}(\mathrm{H}{\phantom{X}}_2\mathrm{O}){\phantom{X}}_{11}$, as if it were carbon plus water. As a test, though, the formula fails in both directions, as the next example shows.

What carbohydrates really share is a set of functional groups. Chemically, a carbohydrate is a polyhydroxy aldehyde or a polyhydroxy ketone (optically active), or a larger molecule that breaks down into such units on hydrolysis; polyhydroxy just means carrying several –OH groups.

10.1.1 Classification of Carbohydrates

The most useful way to sort carbohydrates is to ask what hydrolysis does to them (Fig. 10.1). Boiled with a dilute acid, or treated with the right enzyme, a carbohydrate takes up water at the links between its sugar units, and the links break.

• Monosaccharides are the simplest sugars, the units from which everything else is built; hydrolysis cannot break them into anything smaller of the same kind. Glucose, galactose and the pentose ribose are examples, and only around twenty occur in nature.
• Oligosaccharides (Greek oligos, few) break into a small number of units, from two to ten. A disaccharide gives two, a trisaccharide three, and so on. The two-unit kind is by far the one you meet most, whether its halves match, as in trehalose (glucose + glucose, the sugar of insect blood), or differ, as in lactose (galactose + glucose).
• Polysaccharides are giant chains of hundreds or thousands of units. Because they are tasteless, they are sometimes called non-sugars; the starch in a potato, the cellulose of cotton and the gum that oozes from some trees are all polysaccharides.

A second, chemical test sorts carbohydrates by whether they act as reducing agents. Warm the sugar with Tollens' reagent, and a silver mirror forms; warm it with Fehling's solution, and a brick-red precipitate of copper(I) oxide appears. Sugars that give these results are reducing sugars (अपचायी शर्करा). Every monosaccharide passes, ketoses as well as aldoses.11Fructose has no –CHO group, yet it reduces both reagents: in their alkaline solution it rearranges, through an enediol, into aldoses. For bigger sugars the answer depends on how the units are joined (Section 10.1.3).

10.1.2 Monosaccharides

A monosaccharide is named by two features: its carbonyl group and its number of carbon atoms. An aldose carries an aldehyde group, $-\mathrm{C}\mathrm{H}\mathrm{O}$, at one end of the chain; a ketose carries a keto group, $>\mathrm{C}=\mathrm{O}$, usually on carbon 2. The carbon count gives triose (3 C), tetrose (4), pentose (5), hexose (6) and heptose (7), and the two ideas combine into one word: glucose is an aldohexose and fructose a ketohexose (Table 10.1).

10.1.2.1 Glucose

Glucose is the sugar your blood carries to every cell and the unit from which starch, glycogen and cellulose are built; counting the glucose locked up in those polymers, no organic building block is more plentiful on Earth. Ripe fruit and honey contain it free. Two of its old names recall its history: grape sugar, after its best-known source, and dextrose, because its solution turns plane-polarised light to the right.

Preparation. Both routes to glucose are hydrolyses. In the laboratory the starting material is cane sugar: warming its alcoholic solution with a little dilute mineral acid cleaves each sucrose molecule into one glucose and one fructose.

On a large scale the raw material is cheap starch from maize or cassava. It used to be cooked with dilute sulfuric acid in pressure vessels at about 393 K; most factories now let the enzymes amylase and glucoamylase do the cutting at lower temperatures.

Working out the structure. Before X-ray methods, chemists had to deduce structures from reactions, one question at a time (Fig. 10.2):

1. How many atoms of each kind? Combustion analysis and a molar-mass measurement settle it: $\mathrm{C}{\phantom{X}}_6\mathrm{H}{\phantom{X}}_{12}\mathrm{O}{\phantom{X}}_6$.
2. Is the carbon skeleton branched? Hydrogen iodide, given long enough, strips away every oxygen and leaves n-hexane, the unbranched alkane.
3. Is there a carbonyl group? Yes: towards hydroxylamine (forming an oxime) and hydrogen cyanide (adding to give a cyanohydrin) glucose behaves like an aldehyde or a ketone.
4. Aldehyde or ketone? Bromine water, too gentle to break C–C bonds, converts glucose into gluconic acid without losing a carbon. Only a –CHO group at the end of the chain can be oxidised like that.
5. How many –OH groups, and where? Acetic anhydride acetylates five of them, giving a pentaacetate. A carbon carrying two –OH groups would lose water, and the pentaacetate is stable, so each –OH has a carbon of its own.
6. What is at the far end? Nitric acid oxidises both glucose and gluconic acid to saccharic acid, which has a –COOH group at each end. The second one can only come from a primary alcohol group, $-\mathrm{C}\mathrm{H}{\phantom{X}}_2\mathrm{O}\mathrm{H}$, on C6.

Together the clues give the open-chain formula $\mathrm{O}\mathrm{H}\mathrm{C}-(\mathrm{C}\mathrm{H}\mathrm{O}\mathrm{H}){\phantom{X}}_4-\mathrm{C}\mathrm{H}{\phantom{X}}_2\mathrm{O}\mathrm{H}$ for an aldohexose. Yet that formula leaves something out. Carbons 2, 3, 4 and 5 are all stereocentres, so $2^4=16$ stereoisomers share it. Emil Fischer spent years working out which one is glucose (he received the 1902 Nobel Prize in Chemistry), and he drew the answer in a style still named after him, the Fischer projection: the chain runs straight down with C1 at the top, and at each stereocentre the H and the OH point left or right.

D and L. In the Fischer projection of natural glucose, the –OH on C5, the stereocentre farthest from the aldehyde group, points to the right (Fig. 10.3). The letter D records exactly this. The reference compound is glyceraldehyde, the simplest aldose, which has just one stereocentre. The enantiomer with its –OH on the right is D-glyceraldehyde and its mirror image is L-glyceraldehyde. A sugar, drawn with its most oxidised carbon at the top, is D if the –OH on its lowest stereocentre points the same way as in D-glyceraldehyde and L if it points the other way; the other stereocentres play no part in the label.

D and L describe configuration, the arrangement of groups in space. They say nothing about which way the compound turns plane-polarised light; that has to be measured and is shown separately as (+), dextrorotatory, or (−), laevorotatory. Natural glucose is D-(+)-glucose. D-glyceraldehyde happens to be (+) as well, but many D sugars are (−), fructose among them. Don't mix up capital D and L with the old lower-case d and l, which were just other symbols for (+) and (−).

Where the open chain fails. The open-chain formula explained most reactions, but a few facts would not fit it:

• Two standard aldehyde tests fail: Schiff's reagent stays colourless, and sodium hydrogensulfite, $\mathrm{N}\mathrm{a}\mathrm{H}\mathrm{S}\mathrm{O}{\phantom{X}}_3$, forms no addition compound.
• Acetylate glucose and the product ignores hydroxylamine, so whatever happened to the aldehyde group, the pentaacetate has none left.
• Glucose crystallises in two distinct forms, named α and β. They melt at different temperatures (about 146 °C and 150 °C) and turn polarised light by different amounts: their specific rotations are about +112° and +19°. One open-chain structure cannot explain two isomers.

The ring. The way out is a reaction from aldehyde chemistry: an alcohol adds to a $\mathrm{C}=\mathrm{O}$ group to give a hemiacetal. In glucose the alcohol and the aldehyde belong to the same molecule. The chain curls round until the –OH on C5 reaches C1; its oxygen bonds to C1, and the carbonyl oxygen becomes a new –OH (Fig. 10.4). The result is a six-membered ring of five carbons and one oxygen.

Ring closure makes C1 a new stereocentre, so it can happen in two ways. In the α form the new –OH on C1 points to the opposite side of the ring from the $\mathrm{C}\mathrm{H}{\phantom{X}}_2\mathrm{O}\mathrm{H}$ group on C5 (down, as usually drawn); in the β form it points to the same side (up). The two forms differ only at C1, now called the anomeric carbon, and a pair of isomers like this are anomers (ऐनोमर). In water, α, β and a trace of the open chain keep converting into one another until they reach equilibrium, at roughly 36 % α and 64 % β, with far less than 1 % open chain.

This explains all three puzzles. With so little open chain present at any moment, slow aldehyde tests such as Schiff's reagent hardly respond. The pentaacetate is locked as a ring, with an acetyl group on C1, so it cannot reopen into an aldehyde. And α and β are the two crystalline forms. Reactions that use up the open chain, such as oxidation by Tollens' reagent, still go to completion, because the equilibrium keeps making more of it.

Dissolve either pure crystal form in water and the rotation slowly drifts to the same final value, +52.7°, as the equilibrium mixture forms; this drift is called mutarotation. Try it in the Fig. 10.5 lab.

Drawn as a flat hexagon seen almost edge-on, with the ring oxygen at the back right and C1 on the right, the ring is a Haworth projection. A group on the right of the Fischer projection points down in the Haworth projection. Because the six-membered ring resembles the heterocycle pyran, $\mathrm{C}{\phantom{X}}_5\mathrm{H}{\phantom{X}}_6\mathrm{O}$, these ring forms are called pyranoses: α-D-glucopyranose and β-D-glucopyranose.

10.1.2.2 Fructose

Fructose, $\mathrm{C}{\phantom{X}}_6\mathrm{H}{\phantom{X}}_{12}\mathrm{O}{\phantom{X}}_6$, is an isomer of glucose with the same unbranched six-carbon chain. The difference is the carbonyl group: instead of an aldehyde at C1, fructose has a ketone at C2, flanked by a $\mathrm{C}\mathrm{H}{\phantom{X}}_2\mathrm{O}\mathrm{H}$ group (C1) and the rest of the chain, which makes it the most important ketohexose. Its configuration at C3, C4 and C5 matches glucose, so it is a D sugar, yet it is strongly laevorotatory: D-(−)-fructose.

Honey and many fruits contain free fructose, and every sucrose molecule contains one fructose unit. Weight for weight it tastes sweeter than table sugar, which is why food makers like it.

Ring closure works as for glucose, except that the C5 oxygen now attacks the keto carbon, C2 (the product is strictly a hemiketal). Counting from C2 round to C5 and back through the oxygen gives a five-membered ring of four carbons and one oxygen, the same ring as in the heterocycle furan, $\mathrm{C}{\phantom{X}}_4\mathrm{H}{\phantom{X}}_4\mathrm{O}$, hence the name furanose (Fig. 10.6). The anomeric carbon is C2, and again there are α and β anomers. Fructose can also form six-membered rings in water, but in sucrose it is always the furanose.

10.1.3 Disaccharides

Two monosaccharides can join when an –OH group on one reacts with an –OH group on the other and a molecule of water is lost. The two units end up bridged by an oxygen atom, C–O–C. This bridge is a glycosidic linkage (ग्लाइकोसाइडी बंध), and at least one of the carbons it joins is an anomeric carbon. Hydrolysis, by dilute acid or by an enzyme, adds the water back and frees the two monosaccharides.

Whether a disaccharide is a reducing sugar depends on its anomeric carbons. If one unit still has its anomeric carbon free, carrying an –OH, that ring can open to an aldehyde, so the sugar reduces Tollens' and Fehling's reagents. If both anomeric carbons are tied up in the linkage, neither ring can open and the sugar is non-reducing. Fig. 10.7 compares the three common disaccharides.

Sucrose, cane or beet sugar, is the sugar in your kitchen. Its glycosidic linkage joins C1 of an α-D-glucose unit to C2 of a β-D-fructose unit. These are the anomeric carbons of both units, so sucrose is a non-reducing sugar. Hydrolysis gives equal amounts of glucose and fructose (the equation in 10.1.2.1).

Sucrose turns plane-polarised light to the right (specific rotation +66.5°). Glucose is dextrorotatory too (+52.7°), but fructose is strongly laevorotatory (−92.4°). So as sucrose is hydrolysed, the rotation falls, passes through zero and ends up negative. Because the sign of rotation is inverted, the equimolar mixture of glucose and fructose is called invert sugar (अपवृत्त शर्करा). Honey is mostly invert sugar, made when bees add the enzyme invertase to nectar.

Maltose, malt sugar, is what amylase leaves behind when it chops up starch, in your mouth or in sprouting grain. Both of its units are α-D-glucose, linked α(1→4): the bridge runs from the anomeric C1 of one unit to C4 of the other. That leaves the second unit's C1 unattached, its ring free to open into an aldehyde, so maltose reduces Tollens' and Fehling's reagents.

Lactose is found only in milk. Its galactose unit, in the β form, uses its anomeric C1 to bond to C4 of a glucose unit (a β(1→4) link), and once again the glucose end is left with a free anomeric carbon: lactose is a reducing sugar too. Many adults make little lactase, the enzyme that splits lactose, so milk upsets their stomachs while curd does not: in curd, bacteria have already used up much of the lactose.

10.1.4 Polysaccharides

Nearly all the carbohydrate in the living world is polysaccharide. Organisms use these giant molecules for two purposes, as a compact store of fuel or as tough building material. Three of them are made of glucose alone, and they show how a small change in the linkage produces very different materials (Fig. 10.8).

Rice, wheat, bajra, potatoes and tapioca owe their food value mainly to starch, the fuel store of plants and the biggest source of carbohydrate in the human diet. It is a mixture of two polymers of α-D-glucose. Amylose, the smaller part (typically 15–25 %), is an unbranched chain of hundreds to thousands of units joined by α(1→4) linkages; it coils into a helix and dissolves in hot water. Amylopectin, the larger part, does not dissolve in water. Its chains use the same α(1→4) links but sprout a branch through an α(1→6) linkage every 20–30 units or so.

Cotton is almost pure cellulose, and wood is roughly half cellulose: it is the material of plant cell walls, and no organic compound is more plentiful among plants. Its chains are unbranched and built from β-D-glucose units joined by β(1→4) linkages. The β links keep each chain straight and flat, so neighbouring chains lie side by side and hydrogen-bond into strong, insoluble fibres.

Animals, yeasts and fungi store glucose as glycogen. Built like amylopectin but branched far more often, about every 8–12 units, it earns the nickname animal starch. Your liver and muscles hold most of it, and the brain a little. The branching is the point: every branch ends in a chain end, and when blood glucose drops, enzymes release glucose from hundreds of ends at the same time.

10.1.5 Importance of Carbohydrates

Carbohydrates are the main fuel in most diets. Digestion turns starch and sugars into glucose, and cells oxidise glucose to carbon dioxide and water, capturing the energy released. Plants put spare glucose away as starch and animals as glycogen, to be drawn on later.

As materials, carbohydrates are everywhere in daily life: the wood of a door, the cotton and rayon of your clothes, the paper of a notebook, the starch that stiffens a starched kurta, and the sugars that yeast ferments when bread rises. They also turn up as parts of bigger molecules. Ribose and deoxyribose form part of the backbones of RNA and DNA (Section 10.5), and short sugar chains attached to proteins and lipids at cell surfaces act as identity tags; your ABO blood group, for example, is set by a few sugar units on your red blood cells.

10.2 Proteins

In 1838 the Swedish chemist Jöns Berzelius suggested the name protein, from the Greek proteios, of first importance, and the name has stood up well. Muscle, skin, hair and nails are largely protein; so are the enzymes that digest your food, the haemoglobin that carries oxygen, the antibodies that fight infection and hormones such as insulin. No other class of biomolecule is as abundant in a cell or does as many different jobs. You need a steady supply to grow and to repair tissue, and dal, soya, paneer, eggs, nuts, fish and chicken are all good sources.

Every protein is a long chain built from α-amino acids (ऐमीनो अम्ल), so we begin with them.

10.2.1 Amino Acids

Boil any protein with acid for long enough and it falls apart into α-amino acids, compounds of general formula $\mathrm{H}{\phantom{X}}_2\mathrm{N}-\mathrm{C}\mathrm{H}(\mathrm{R})-\mathrm{C}\mathrm{O}\mathrm{O}\mathrm{H}$ in which the amino group and the carboxyl group sit on the same carbon, the α-carbon. (Move the amino group one carbon further from the carboxyl group and you have a β-amino acid, then γ, δ and so on, but these are not the building units of proteins.) The group R, the side chain, is what makes one amino acid different from another; some side chains carry a further functional group, such as –OH, –SH, a second –COOH or a second $-\mathrm{N}\mathrm{H}{\phantom{X}}_2$.

Nobody in a biochemistry lab calls alanine 2-aminopropanoic acid: amino acids keep the names given when they were discovered, which often recall a source or a property. Asparagine was first isolated from asparagus juice; cysteine takes its name from cystine, which was discovered in bladder stones (Greek kystis, bladder). To write long chains compactly, each one also has a three-letter symbol (Ala, Gly…) and a one-letter code (A, G…). Table 10.3 lists the twenty amino acids of proteins, grouped by the kind of side chain.

10.2.2 Classification of Amino Acids

Amino acids are sorted in two ways. The first counts acidic and basic groups. One amino group and one carboxyl group, as in alanine or serine, make an amino acid neutral. A side chain with an extra carboxyl group makes it acidic (aspartic acid and glutamic acid), and a side chain with an extra basic nitrogen group makes it basic (lysine, arginine and histidine).

The second sorting is about diet. Your body can make about half of the twenty from other compounds; these are non-essential amino acids, for example glycine, alanine and glutamic acid. The others cannot be made at all, or not fast enough, and must come from food. These are the essential amino acids (आवश्यक ऐमीनो अम्ल), such as valine, lysine and tryptophan. Ten are usually listed for growing children; adults make enough arginine, so for them the list is nine. Cereals are short of lysine and pulses are short of methionine, which is why dal eaten with rice provides better protein than either alone.

Properties. Put some crystals of glycine on a spatula and they behave nothing like an amine or a carboxylic acid. They are colourless, dissolve readily in water and only melt, with decomposition, at high temperatures, often above 200 °C: the behaviour of a salt. The reason is an acid–base reaction inside the molecule (Fig. 10.9). The carboxyl group passes a proton to the amino group of the same molecule, giving the ion $\mathrm{H}{\phantom{X}}_3\mathrm{N}{\phantom{X}}^{+}-\mathrm{C}\mathrm{H}(\mathrm{R})-\mathrm{C}\mathrm{O}\mathrm{O}{\phantom{X}}^{-}$ with one positive and one negative charge. Such a dipolar ion is a zwitterion (ज़्विटर आयन), from the German Zwitter, hybrid. It is neutral overall, but its charged ends attract neighbouring molecules strongly, as the ions in a salt crystal do.

A zwitterion is amphoteric: it reacts with acids and with bases. Add acid and the $-\mathrm{C}\mathrm{O}\mathrm{O}-$ end picks up a proton, leaving a cation; add base and the $-\mathrm{N}\mathrm{H}{\phantom{X}}_3{\phantom{X}}^{+}$ end loses one, leaving an anion. This is one reason proteins help to hold the pH of blood and cells steady. The Fig. 10.10 simulation treats the two charged ends as point charges, so you can see which end an approaching ion is drawn to.

Optical activity. In every α-amino acid except glycine, where R is just H, the α-carbon carries four different groups. It is therefore a stereocentre, and the amino acid is chiral and optically active. Each exists in D and L forms, assigned by comparison with glyceraldehyde as for sugars. Proteins are built almost entirely from the L forms: in a Fischer projection with –COOH at the top, the $-\mathrm{N}\mathrm{H}{\phantom{X}}_2$ of an L-amino acid points to the left.

10.2.3 Structure of Proteins

The peptide bond. Amino acids join by condensation. The carboxyl group of one reacts with the amino group of the next, a molecule of water is lost, and an amide link, $-\mathrm{C}\mathrm{O}-\mathrm{N}\mathrm{H}{\phantom{X}}^{-}$, forms (Fig. 10.11). In protein chemistry this amide link is called the peptide bond or peptide linkage (पेप्टाइड आबंध).

Two amino acids joined this way form a dipeptide, and the order matters. When alanine supplies the carboxyl group and glycine the amino group, the product, $\mathrm{H}{\phantom{X}}_2\mathrm{N}-\mathrm{C}\mathrm{H}(\mathrm{C}\mathrm{H}{\phantom{X}}_3)-\mathrm{C}\mathrm{O}$–$\mathrm{N}\mathrm{H}-\mathrm{C}\mathrm{H}{\phantom{X}}_2-\mathrm{C}\mathrm{O}\mathrm{O}\mathrm{H}$ or Ala-Gly, is alanylglycine, a different compound from glycylalanine (Gly-Ala). By convention a peptide is written from the end with the free amino group (the N-terminus) to the end with the free carboxyl group (the C-terminus). Names follow the count of residues: tripeptide (two peptide bonds), tetrapeptide, pentapeptide, hexapeptide and so on.

Beyond about ten residues we simply say polypeptide. Chemists usually keep the word protein for chains of a hundred or more residues (molar mass above roughly 10 000 g/mol), but the cut-off is loose: insulin has just 51 residues, split between two chains, and still counts as a protein because it folds into a definite working shape. Build some peptides of your own in the Fig. 10.12 builder.

Fibrous and globular proteins. Compare a strand of your hair with the white of an egg. Hair is made of a fibrous protein, keratin. Many long chains lie parallel, cross-linked by hydrogen bonds and by disulfide (S–S) bridges, so the material is tough and water cannot pull it apart. Egg white is mostly albumin, a globular protein. Each chain folds back on itself into a compact ball with water-attracting groups on the outside, so it dissolves.

Four levels of structure. A protein is described at four levels, each built on the one before (Fig. 10.13).

The primary structure is the sequence of amino acids in each polypeptide chain, read from the N-terminus. It is set by the gene for that protein, and it decides everything else. Change a single amino acid and you have a different protein. In sickle-cell anaemia, one glutamic acid in each β-chain of haemoglobin is replaced by valine, and red blood cells stiffen into sickle shapes.

The secondary structure is the regular local shape of the chain's backbone, held by hydrogen bonds between the $\mathrm{C}=\mathrm{O}$ of one peptide group and the N–H of another (Fig. 10.14). Two shapes are common. In the α-helix the chain twists into a right-handed coil; the $\mathrm{C}=\mathrm{O}$ of each residue is hydrogen-bonded to the N–H four residues further along, so these bonds run up the helix almost parallel to its axis and every backbone $\mathrm{C}=\mathrm{O}$ and N–H is used. In a β-pleated sheet, stretches of chain lie next to one another as almost fully extended zigzags. Each strand hydrogen-bonds sideways to its neighbours, and the zigzags line up into regular folds, like a paper fan.

The tertiary structure is the overall three-dimensional folding of a whole chain: its helices, sheets and loops packed together into a fibre or a globule. It is held by hydrogen bonds, disulfide bridges between cysteine side chains, attractions between oppositely charged side chains (salt bridges), and van der Waals forces between the many non-polar side chains, which cluster in the core, away from the water.

Many proteins are teams of several folded chains. Each chain is a subunit, and the way the subunits fit together is the quaternary structure; a protein with only one chain has none. Haemoglobin is the classic example: two α-chains and two β-chains, each folded around an iron-containing haem group, pack together into one oxygen-carrying unit.

10.2.4 Denaturation of Proteins

Crack an egg into a hot pan and the clear, runny white turns opaque and firm within seconds: its main protein, albumin, has been denatured. In a living cell each protein has one particular folded shape, its native state, held mostly by weak forces. Heat shakes the hydrogen bonds apart; a change of pH alters the charges on side chains and breaks salt bridges; alcohol, heavy-metal ions and concentrated salt solutions interfere too. The chain unravels, tangles with its neighbours and stops working. Only the covalent backbone survives: the peptide bonds, and so the primary structure, are untouched, while the secondary, tertiary and any quaternary structure are lost. This is denaturation (विकृतीकरण).

Kitchens are full of other examples. Squeeze lemon juice into hot milk and the acid makes the milk protein casein coagulate into paneer; when curd sets, bacteria do the same job slowly by turning lactose into lactic acid. A hair straightener works on the same principle, breaking hydrogen bonds in keratin so the hair can be reshaped. Most denaturation, like cooking an egg, cannot be undone.

10.3 Enzymes

Chew a piece of plain bread for a minute and it starts to taste sweet: amylase in your saliva is already splitting its starch into maltose. In a flask the same breakdown needs boiling acid, yet your body runs thousands of such reactions at about 37 °C, close to pH 7 and in water. The difference is made by enzymes (एंज़ाइम): biological catalysts that speed up reactions enormously and are not used up, so a small amount does a great deal of work. Nearly all enzymes are globular proteins (a few are RNA molecules).

Enzymes are highly specific. Each one usually acts on one compound, its substrate, or on a small family of similar compounds, and it catalyses one kind of reaction. Most are named by adding -ase to the name of the substrate or of the reaction. Maltase hydrolyses maltose; sucrase, also called invertase, hydrolyses sucrose; lactase acts on lactose and urease on urea. Enzymes that catalyse redox reactions, oxidising one substrate while reducing another, are called oxidoreductases.

10.3.1 Mechanism of Enzyme Action

Like any catalyst, an enzyme changes neither the overall energy change of a reaction nor its equilibrium position. It offers a different route with a lower activation energy (Fig. 10.15). First the substrate binds in a small pocket on the enzyme's surface, the active site, to form an enzyme–substrate complex. There, side chains hold the substrate in exactly the right orientation, strain the bonds that must break and pass protons on or take them away. Then the products leave and the enzyme is free for the next substrate molecule.

In 1894 Emil Fischer pictured the active site as a lock into which only the right key, the substrate, fits, which accounts for specificity. We now know that the fit is often induced: the enzyme changes shape a little as the substrate binds, closing around it like a hand around a ball. Because the active site depends on the folded shape of the protein, anything that denatures the enzyme, such as high temperature or the wrong pH, destroys its activity. Most human enzymes work best near 37 °C, but pepsin, which digests protein in the acidic stomach, works best near pH 2.

10.4 Vitamins

Sailors on long voyages once lost teeth and bled from the gums until it was noticed that lemons and limes prevented it. People who lived on polished rice developed weak, swollen legs and heart failure. Neither disease is caused by a germ. Each comes from the lack of a particular compound that the body needs in tiny amounts, a vitamin (विटामिन).

Vitamins are a chemically mixed bag (alcohols, amines, acids and ring compounds), so they are defined by their role rather than their structure: organic compounds that the body needs in tiny amounts but cannot make in sufficient quantity, and so must get from food. Each does a particular job, and a shortage shows up as a particular deficiency disease. Our own cells make a little vitamin D in skin exposed to sunlight, and gut bacteria supply some B vitamins and vitamin K; plants, by contrast, make nearly all of them, which is one reason fresh vegetables and fruit matter so much. Letters label them, A, B, C, D, E and K, and the B group divides further into ${\mathrm{B}}_1$, ${\mathrm{B}}_2$, ${\mathrm{B}}_6$, ${\mathrm{B}}_{12}$ and others.

Too much can harm, too. Fat-soluble vitamins build up in the body, and large doses of vitamins A and D are poisonous, so supplements are for a doctor to prescribe, not for guesswork; a varied diet supplies what most people need.

10.4.1 Classification of Vitamins

Vitamins are grouped by whether they dissolve in fat or in water, and the grouping predicts how the body handles them (Fig. 10.16).

• Fat-soluble: A, D, E and K. Insoluble in water, they travel with dietary fat into the body and are kept in reserve in the liver and in body fat, so a store can last for months, and so can an overdose.
• Water-soluble: the B group and C. These dissolve in blood plasma, and whatever is surplus is filtered out by the kidneys into the urine. Vitamin ${\mathrm{B}}_{12}$ is the exception, stockpiled in the liver for years; the rest have to be eaten regularly.

10.5 Nucleic Acids

In 1869 Friedrich Miescher, working in Tübingen, washed white blood cells off used surgical bandages and extracted from their nuclei a new substance, rich in phosphorus and acidic. We now call it a nucleic acid. There are two kinds, deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), and both are long chains of units called nucleotides, so they are also called polynucleotides.

Their most famous job is heredity, the passing of characteristics from one generation to the next. DNA, wound around proteins, makes up the chromosomes in the nucleus of every cell, and its sequence carries the instructions that make a child resemble its parents. How DNA is copied, read and controlled is the subject of Class 12 Biology, Chapter 5 (Molecular Basis of Inheritance). Here we look at the chemistry: what nucleic acids are made of and how the pieces are joined.

10.5.1 Chemical Composition of Nucleic Acids

Break a nucleic acid down completely with acid and you are left with just three kinds of molecule. One is phosphoric acid, $\mathrm{H}{\phantom{X}}_3\mathrm{P}\mathrm{O}{\phantom{X}}_4$. One is a five-carbon sugar: β-D-ribose if you started with RNA, β-D-2-deoxyribose if you started with DNA (deoxy because the –OH on C2 of ribose is replaced by H). The rest are flat, ring-shaped organic molecules rich in nitrogen, called bases.

Five bases occur in all. Adenine (A) and guanine (G) are purines, with two fused rings; cytosine (C), thymine (T) and uracil (U) are pyrimidines, with a single ring. Thymine turns up only in DNA and uracil only in RNA, while the other three are common to both (Table 10.6). A single methyl group is all that distinguishes thymine from uracil.

10.5.2 Structure of Nucleic Acids

Think of the repeating unit as built in two moves (Fig. 10.17). First a base bonds to the sugar at C1′; to keep the sugar's atoms apart from the base's own numbering, the sugar carbons get a prime (1′ to 5′). Base plus sugar is a nucleoside. Second, phosphoric acid forms an ester with the –OH on C5′, and the nucleoside becomes a nucleotide (न्यूक्लियोटाइड).

Nucleotides link into a chain through their phosphate groups. The phosphate on C5′ of one nucleotide forms a second ester bond with the –OH on C3′ of the nucleotide before it, so each phosphate bridges two sugars in a phosphodiester linkage. The result is a repeating backbone, sugar–phosphate–sugar–phosphate, with a base hanging from every sugar. The two ends differ: one has a free phosphate on C5′ (the 5′ end) and the other a free –OH on C3′ (the 3′ end). A sequence is therefore read in a direction, usually 5′ → 3′, and the order of bases along the chain is the primary structure of the nucleic acid.

Watson and Crick's 1953 model gave DNA its famous secondary structure: two strands, running in opposite directions, twisted round a shared axis into a double helix, with the backbones outside and the bases stacked inside (Fig. 10.18). Only certain pairs of bases fit between the backbones, and they are held by hydrogen bonds: adenine with thymine (two bonds) and guanine with cytosine (three). Each pair joins a two-ring purine to a one-ring pyrimidine, so every rung of the ladder has the same width. The two strands are therefore not identical but complementary: the sequence of one fixes the sequence of the other.

RNA is usually a single strand. Parts of it fold back on themselves wherever short stretches of bases can pair, forming hairpins and loops; in RNA, uracil pairs with adenine. Because the strand has no partner strand, RNA shows no fixed ratio between its bases. Cells make three main kinds of RNA:

• messenger RNA (mRNA) carries a copy of a gene's instructions from the DNA to the ribosomes;
• ribosomal RNA (rRNA) makes up most of the ribosome, the machine that joins amino acids into proteins;
• transfer RNA (tRNA) brings each amino acid to the ribosome and matches it to the instructions on the mRNA.

10.5.3 Biological Functions of Nucleic Acids

Every cell in your body carries the same DNA, a copy of a copy made at each of trillions of cell divisions. That faithful copying is what heredity rests on. Before a cell divides, the two strands of each DNA molecule part, every exposed base picks up its partner, and two identical double helices result, one for each daughter cell. Over many generations the same mechanism keeps a species recognisably itself.

Most of DNA's instructions are instructions for proteins, yet DNA never makes a protein itself. A gene's sequence is first copied into mRNA; at the ribosome, whose core is rRNA, tRNA molecules read the mRNA three bases at a time and deliver the matching amino acids, which are joined by peptide bonds. The details belong to biology, but the chemistry you have just met, base pairing and the peptide bond, is what makes them possible.

10.6 Hormones

Get a sudden fright and within seconds your heart races and your muscles receive extra fuel. Part of that response is carried not by nerves but by a chemical released into the blood. Such messengers are hormones (हॉर्मोन): molecules secreted by the endocrine glands (the pancreas, thyroid, adrenal glands and others) straight into the bloodstream, which delivers them all over the body; only target cells with the matching receptor respond. Tiny amounts are enough.

Chemically, hormones belong to three families:

A central job of hormones is to keep conditions in the body steady, and blood glucose is a good example (Fig. 10.19). After a meal, glucose floods into the blood and the pancreas releases insulin. Insulin lets muscle and fat cells take glucose in and makes the liver store it as glycogen, so the level falls back. Between meals, when the level drops, the pancreas releases glucagon, which makes the liver break down glycogen and release glucose. Pulling in opposite directions, the two hormones keep blood glucose within narrow limits; in diabetes this control fails.

Other hormones prepare the body for action or steer its development. Epinephrine and norepinephrine (adrenaline and noradrenaline) from the adrenal glands produce the fight-or-flight response to a sudden stimulus: a faster heartbeat and more glucose in the blood. Growth hormone and the sex hormones control growth and development.

Thyroxine, from the thyroid gland in the neck, is a derivative of the amino acid tyrosine that carries four iodine atoms; it sets the pace of the body's metabolism. Too little causes hypothyroidism, with tiredness, sluggishness and weight gain, and too much causes hyperthyroidism. A diet short of iodine starves the thyroid of raw material, so it becomes underactive and swells into a goitre.

Steroid hormones come from the adrenal glands and the gonads. The outer layer of each adrenal gland, the cortex, makes two kinds. One kind, typified by cortisol, raises blood glucose by making new glucose from other molecules, calms inflammation (which is why cortisone-type creams soothe rashes) and helps you weather physical stress. The other, typified by aldosterone, tells the kidneys how much sodium and water to hold back, and so helps set blood pressure. When the adrenal cortex is destroyed, both are lost and the result is Addison's disease: blood sugar runs low, muscles feel weak, and an illness or injury that others shrug off can become life-threatening. Daily replacement of both kinds of hormone keeps patients well.

At puberty the gonads (testes or ovaries) step up production of their own steroids. Testosterone drives the male changes, such as a deeper voice and facial hair. Estradiol drives the female changes and, with progesterone, runs the monthly cycle; progesterone's special task is to ready the lining of the uterus for a fertilised egg.