Biomolecules: Class 11 Biology · Chapter 9

Scoop up a little soil from a flower bed and pick a spinach leaf growing in the same bed. One is alive and the other is not. Yet if both went to a laboratory for elemental analysis, the two reports would name much the same elements: carbon, hydrogen, oxygen, nitrogen, calcium, sodium and so on. Life has no private elements. Every element found in an organism also occurs in rocks, water and air.

What differs is the proportion. Carbon is nearly a fifth of your body's mass but only about 0.02 % of the Earth's crust, and hydrogen tells a similar story. Silicon, the crust's second most common element, is barely present in you (Fig. 9.1). Living matter is built mainly from compounds of carbon and hydrogen. This chapter is about those compounds. You will see how chemists extract them from a tissue and how small ones join into giant ones. Then you will meet one family of giants, the enzymes, which runs the chemistry of every cell. In Hindi the chapter is called जैव अणु (jaiv anu).

9.1 How to Analyse Chemical Composition?

Knowing the elements is only a start, because a cell is not a bag of loose atoms. Which compounds does a tissue hold? The first step towards an answer is a crude but powerful separation (Fig. 9.2). Put a few spinach leaves or a scrap of mutton in a mortar, add trichloroacetic acid ($\mathrm{C}\mathrm{l}{\phantom{X}}_3\mathrm{C}\mathrm{C}\mathrm{O}\mathrm{O}\mathrm{H}$) and work the pestle until only a thick paste is left. Then pour the paste onto cheesecloth or cotton held over a beaker. Two fractions result. The liquid that runs through, the filtrate, is called the acid-soluble pool; the solid caught on the cloth, the retentate, is the acid-insoluble fraction. The filtrate alone contains thousands of kinds of organic molecule.

How would you identify a single compound in such a mixture? Separate it, purify it, then analyse it. Methods such as chromatography pull the mixture apart step by step until one compound remains on its own, and instruments such as spectrometers then suggest its formula and the arrangement of its atoms; you will study these methods in later classes. We use the word biomolecule for every carbon compound that comes from a living tissue.

Inorganic matter calls for a harsher test, one that destroys the sample, and three weighings tell the story. Straight from the plant or animal, the sample gives its wet weight. Kept in an oven until no more water can be driven off, it gives its dry weight. Finally it is heated in a flame until every carbon compound has burnt away as carbon dioxide and water vapour. What remains is a pinch of grey ash, and the ash holds the inorganic elements, such as calcium, magnesium and potassium.

Inorganic substances also turn up in the acid-soluble fraction. Besides water itself there are cations such as $\mathrm{N}\mathrm{a}{\phantom{X}}^{+}$, $\mathrm{K}{\phantom{X}}^{+}$, $\mathrm{C}\mathrm{a}{\phantom{X}}^{2+}$ and $\mathrm{M}\mathrm{g}{\phantom{X}}^{2+}$, anions such as chloride, phosphate ($\mathrm{P}\mathrm{O}{\phantom{X}}_4{\phantom{X}}^{3-}$) and sulphate ($\mathrm{S}\mathrm{O}{\phantom{X}}_4{\phantom{X}}^{2-}$), and salts such as $\mathrm{N}\mathrm{a}\mathrm{C}\mathrm{l}$ and $\mathrm{C}\mathrm{a}\mathrm{C}\mathrm{O}{\phantom{X}}_3$. The two kinds of analysis complement each other: elemental analysis tells us which elements a tissue holds, and compound analysis tells us which molecules, organic and inorganic, carry them.

How should the organic molecules be sorted? A chemist might file them under their functional groups (alcohols, acids, amines and the like). A biologist files them by the part they play in the cell, which gives the families amino acids, fatty acids and other lipids, nitrogen bases with their nucleosides and nucleotides, and sugars. We meet them one family at a time.

Amino acids

Start from methane, $\mathrm{C}\mathrm{H}{\phantom{X}}_4$, and replace three of its hydrogens: one by an amino group ($\mathrm{N}\mathrm{H}{\phantom{X}}_2$), one by an acidic carboxyl group ($\mathrm{C}\mathrm{O}\mathrm{O}\mathrm{H}$) and one by a variable R group. The result is an amino acid. The central carbon, now carrying H, $\mathrm{N}\mathrm{H}{\phantom{X}}_2$, $\mathrm{C}\mathrm{O}\mathrm{O}\mathrm{H}$ and R, is the α-carbon, so these molecules are called α-amino acids; chemically they are substituted methanes (Fig. 9.3).

The R group decides which amino acid you have. Many R groups are chemically possible, but the proteins of living things are built from only 20 kinds of amino acid. In glycine the R group is a single hydrogen atom, in alanine a methyl group ($\mathrm{C}\mathrm{H}{\phantom{X}}_3$), in serine a hydroxymethyl group ($\mathrm{C}\mathrm{H}{\phantom{X}}_2\mathrm{O}\mathrm{H}$) and in cysteine a group carrying sulphur ($\mathrm{C}\mathrm{H}{\phantom{X}}_2\mathrm{S}\mathrm{H}$).

Since every amino acid has the same amino and carboxyl groups, most differences in behaviour come from R. Count the extra acidic or basic groups in R and they fall into three groups. Glutamic acid and aspartic acid are acidic, lysine and arginine are basic, and valine and leucine are neutral. Tyrosine, phenylalanine and tryptophan carry ring-shaped side chains and are the aromatic amino acids.

The amino and carboxyl groups are ionizable: they can gain or lose a proton, so an amino acid's charge depends on the pH around it (Fig. 9.4). In strongly acidic solution both groups hold protons and the molecule is a cation, $\mathrm{H}{\phantom{X}}_3\mathrm{N}{\phantom{X}}^{+}-\mathrm{C}\mathrm{H}\mathrm{R}-\mathrm{C}\mathrm{O}\mathrm{O}\mathrm{H}$. Near neutral pH the carboxyl group has lost its proton, giving $\mathrm{H}{\phantom{X}}_3\mathrm{N}{\phantom{X}}^{+}-\mathrm{C}\mathrm{H}\mathrm{R}-\mathrm{C}\mathrm{O}\mathrm{O}{\phantom{X}}^{-}$. This form carries one positive and one negative charge, so its net charge is zero: it is a zwitterion. In strongly basic solution the amino group gives up its extra proton too, leaving the anion $\mathrm{H}{\phantom{X}}_2\mathrm{N}-\mathrm{C}\mathrm{H}\mathrm{R}-\mathrm{C}\mathrm{O}\mathrm{O}{\phantom{X}}^{-}$.

Lipids

Lipids are the cell's greasy, water-insoluble molecules. The simplest are the fatty acids: a carboxyl group joined to a hydrocarbon R group. R ranges from a single carbon (a methyl group) up to a chain of 19 carbons, so a fatty acid has between 2 and 20 carbon atoms in all. Palmitic acid, plentiful in palm oil, has 16 carbons counting the carboxyl carbon; arachidonic acid has 20.

A chain with only single C–C bonds is saturated: it is straight and packs tightly against its neighbours. One or more C=C double bonds make a chain unsaturated, and in most natural fatty acids each double bond puts a kink in the chain (Fig. 9.5).

Glycerol is a three-carbon alcohol with an –OH group on every carbon: trihydroxypropane, $\mathrm{C}{\phantom{X}}_3\mathrm{H}{\phantom{X}}_8\mathrm{O}{\phantom{X}}_3$. Each –OH can react with the carboxyl group of a fatty acid to form an ester, releasing a molecule of water. Glycerol with one fatty acid attached is a monoglyceride, with two a diglyceride and with three a triglyceride. Triglycerides are what we call fats and oils, and the only difference between the two is the melting point.

Oils melt below room temperature and stay liquid; fats are solid. In a Delhi winter a bottle of coconut oil turns white and solid while the mustard oil next to it stays runny. Coconut oil is rich in saturated fatty acids, whose straight chains pack easily into a solid, whereas mustard oil is mostly unsaturated. Ghee and butter, also rich in saturated fats, set solid on a cool morning for the same reason.

Swap one fatty acid of a triglyceride for a phosphate group, and link a small organic group (often one containing nitrogen) to that phosphate: the result is a phospholipid. Lecithin, whose extra group is choline, is a common example. With a water-loving head and two water-avoiding tails, phospholipids have exactly the shape needed to build cell membranes. The brain and nerves are packed with lipids more elaborate still, and cholesterol, built from four fused rings rather than from fatty acids, is another lipid you will meet often.

Nitrogen bases, nucleosides and nucleotides

Rings built from both carbon and nitrogen atoms, heterocyclic rings, are the core of another family. Its five key members, the nitrogen bases, are adenine, guanine, cytosine, thymine and uracil. They seldom float free. Hook a base to a sugar and it becomes a nucleoside; attach a phosphate to that sugar by an ester link as well and you have a nucleotide (Fig. 9.11, drawn in Section 9.6). The names follow a regular pattern (Table 9.1). String nucleotides together, and nothing else, and you get DNA or RNA, the genetic material that stores and passes on hereditary information.

The last family is the sugars (carbohydrates). Their units are the monosaccharides: glucose ($\mathrm{C}{\phantom{X}}_6\mathrm{H}{\phantom{X}}_{12}\mathrm{O}{\phantom{X}}_6$), a six-carbon sugar or hexose that fuels most cells, and ribose ($\mathrm{C}{\phantom{X}}_5\mathrm{H}{\phantom{X}}_{10}\mathrm{O}{\phantom{X}}_5$), a five-carbon sugar or pentose found in RNA, are the commonest. Two monosaccharides joined together make a disaccharide, such as sucrose (cane sugar) or lactose (milk sugar). Long chains of them are the polysaccharides of Section 9.5.

9.2 Primary and Secondary Metabolites

Biomolecules number in the thousands, and since every one of them is made or used in the chemistry of life, its metabolism, biologists also call them metabolites. Two kinds are recognised. The primary metabolites are the amino acids, sugars, fatty acids, nucleotides and other families of Section 9.1. They turn up in every cell, animal or plant, and each has a known job in growth, energy supply or heredity.

Secondary metabolites are the specialities of plants, fungi and microbes (Fig. 9.6): the alkaloid of the opium poppy, the pigment of a beetroot, the scent of jasmine, the gum oozing from a babool tree, the latex of a rubber tree, an antibiotic made by a mould, the flavonoids of tea, the flavour of a spice. Thousands are known. For many of them nobody yet knows what they do for the organism that makes them. Some clearly help it survive, by colouring a flower for pollinators or by poisoning an animal that grazes on it, so they matter to its ecology. And many are valuable to people as medicines, dyes, flavours, perfumes and raw materials (Table 9.2).

9.3 Biomacromolecules

Weigh the molecules of the acid-soluble pool and a pattern appears: every one is small, with a molecular mass between 18 daltons (water) and roughly 800 Da. One dalton (Da) is one-twelfth of the mass of a carbon-12 atom, about the mass of a hydrogen atom.

The material caught on the cloth tells a different story. Only four classes of organic compound are found there, proteins, nucleic acids, polysaccharides and lipids, and three of the four are giants of 10 000 Da or more (Fig. 9.7). Size therefore splits biomolecules into two groups. Below about 1000 Da are the micromolecules, usually just called biomolecules, which make up the acid-soluble pool. The giants are macromolecules, also called biomacromolecules.

Lipids are the puzzle: their molecules never exceed about 800 Da, yet they end up with the giants. Picture a building made of loose bricks and thin plastic sheets being smashed. The bricks wash through a sieve, but the torn plastic curls into small closed bags that are caught with the rubble. In a cell the plastic sheets are the membranes, made largely of lipid. Grinding rips the cell membrane and the membranes of organelles into fragments, which seal themselves into tiny water-insoluble bags called vesicles, and the vesicles stay behind with the acid-insoluble material. So lipids join the macromolecular fraction because of how they are arranged, not because of their size; strictly speaking, lipids are not macromolecules.

Put the two fractions back together and you have the whole tissue: the small dissolved molecules, which roughly reflect what the cytoplasm contains, plus the macromolecules of the cytoplasm and the organelles. Rank everything by amount and the winner is not a biomolecule at all. Water is the most abundant chemical in every living organism (Fig. 9.8).

9.4 Proteins

Proteins are polypeptides: unbranched chains of amino acids. Neighbours in the chain are joined by a peptide bond. It forms when the carboxyl group of one amino acid reacts with the amino group of the next, and a molecule of water is removed (Fig. 9.9). Every chain therefore has a free amino group at one end and a free carboxyl group at the other.

Starch and cellulose, which you will meet next, repeat one kind of unit over and over; such a polymer is a homopolymer. A protein instead strings together up to 20 different kinds of amino acid (glycine, leucine, histidine, methionine and the rest) in a definite order, so it is a heteropolymer.

Your body can make some amino acids from other molecules; these are the non-essential amino acids. Others it cannot make, or cannot make fast enough, so they must come from food: these are the essential amino acids. That is why proteins in the diet matter. Digestion breaks them into amino acids, which supply the essential ones. 11Adults need nine essential amino acids, among them lysine, tryptophan, methionine and leucine.

A protein might be an enzyme in your saliva, a hormone in your blood, a pump or channel in a cell membrane, or an antibody that fights germs (Table 9.3). Two records are worth remembering. Collagen is the most abundant protein in the animal world. RuBisCO (ribulose bisphosphate carboxylase-oxygenase), the enzyme that fixes carbon dioxide in photosynthesis, tops the whole biosphere as the most plentiful protein of all.

9.5 Polysaccharides

Join hundreds or thousands of monosaccharides into a chain and you have a polysaccharide, the third kind of macromolecule in the insoluble fraction. Remarkably, three of the most important are built from the very same unit, glucose. Cellulose is the fibre of plant cell walls, which is why cotton and paper (made from the pulp of wood or bamboo) are almost pure cellulose. Starch is the plant's energy store, in a potato or a grain of rice, and glycogen is the animal equivalent, kept in liver and muscle. Each uses only one kind of monosaccharide, so each is a homopolymer. Not every polysaccharide is made of glucose: inulin, stored in dahlia tubers and chicory roots, is built from fructose.

Each link between sugars has a direction, so the two ends of a chain are different. One end, by convention drawn on the right, is the reducing end; the other, on the left, is the non-reducing end. Glycogen is heavily branched, and every branch finishes in its own non-reducing end, so a glycogen molecule has many non-reducing ends but only one reducing end (Fig. 9.10).

Shape matters too. Starch chains coil into helices, and iodine molecules ($\mathrm{I}{\phantom{X}}_2$) can slip inside the coil; the starch–iodine complex is blue (blue-black when concentrated). Cellulose chains lie straight and side by side, with no helix to hold iodine, so cellulose gives no blue colour. This difference is the basis of the iodine test for starch.

Sugars can also be chemically modified before they are strung together. Chitin, the tough material of arthropod exoskeletons (the shell of a prawn, the wing of a housefly), is made of an amino-sugar, and it also forms the cell walls of fungi. Glucosamine and N-acetylgalactosamine are other modified sugars found in such complex polysaccharides, and most of these, like cellulose, are homopolymers.

9.6 Nucleic Acids

Nucleic acids, or polynucleotides, complete the list. They, the polysaccharides and the polypeptides are the genuine giants of the insoluble fraction, its true macromolecules; lipids, remember, only travel with it.

Take a nucleotide apart and you get three chemically different pieces (Fig. 9.11): a ring-shaped nitrogenous base, a five-carbon pentose sugar and a phosphate group, derived from phosphoric acid. The bases are the five met in Section 9.1, and their ring skeletons sort them into two families. Adenine and guanine are built on the double-ring skeleton called purine, so they are substituted purines. Cytosine, thymine and uracil are built on the single-ring pyrimidine skeleton: they are substituted pyrimidines.

Two sugars are possible. Ribose carries an –OH group on its carbon 2′; 2′-deoxyribose has just a hydrogen there (deoxy means 'without oxygen'). The sugar names the nucleic acid: deoxyribose makes deoxyribonucleic acid (DNA) and ribose makes ribonucleic acid (RNA). The bases differ slightly too: DNA uses thymine and RNA uses uracil, while both use adenine, guanine and cytosine. In Class 12 you will see how these chains pair, copy themselves and carry information.

9.7 Structure of Proteins

A word like structure means different things in different sciences. Ask for the structure of washing soda and a chemist may simply write $\mathrm{N}\mathrm{a}{\phantom{X}}_2\mathrm{C}\mathrm{O}{\phantom{X}}_3$; ask about glucose and you may be shown a ring drawn flat on paper; a crystallographer would hand you a three-dimensional model. Biologists describing proteins use a ladder of four levels, each built on the one below (Fig. 9.12).

Level one, the primary structure, is simply the order of the amino acids, like a word spelt with a 20-letter alphabet. By convention it is written from the end with a free amino group, the N-terminal amino acid, to the end with a free carboxyl group, the C-terminal amino acid. Change one letter and the meaning may change: in sickle-cell anaemia, a single swapped amino acid in haemoglobin is enough to cause disease.

Level two, the secondary structure, describes the local shapes that short stretches of the chain adopt. Some stretches coil like a spring into a helix; others lie in flat zigzag strands side by side, or form loops. The coil found in proteins, the α-helix, is always right-handed, and the zigzag strands make β-pleated sheets. Hydrogen bonds between nearby parts of the backbone hold both in shape.

The whole chain, helices and sheets included, then folds back on itself into a compact three-dimensional shape. Think of a long earphone cable bunched into a knot in your pocket, except that a protein folds the same way every time. This overall fold is level three, the tertiary structure. Hydrogen bonds, ionic attractions, the clustering of water-avoiding side chains and covalent disulphide (S–S) bonds between cysteines hold it together. Most of what proteins do depends on this fold: unfold it, and an enzyme stops working.

Level four applies only to proteins built from more than one folded polypeptide, each called a subunit. The way the subunits fit together, whether in a row, a ring or a compact cluster, is the quaternary structure. Adult human haemoglobin (Hb) has four subunits: two identical α chains and two identical β chains (${\alpha }_2{\beta }_2$).

9.8 Enzymes

Nearly every reaction in a cell is speeded up by an enzyme. Almost all enzymes are proteins; a few are RNA molecules with catalytic power, called ribozymes.

Like any protein, an enzyme has a primary, secondary and tertiary structure. Picture the folded enzyme as a lumpy ball with dents in its surface. Most dents are just a result of folding, but one is special: the active site, a cleft whose shape and lining of chemical groups let one particular molecule, the substrate, settle into it. The reaction happens there, and it is through this site that the enzyme achieves its remarkable speed.

Heat separates enzymes most sharply from industrial catalysts. The iron catalyst that makes ammonia works at about 450 °C and very high pressure, and the platinum in a car's exhaust converter must be hot to work at all. Most enzymes, by contrast, start to fall apart above about 40 °C. Microbes of hot springs and deep-sea vents, the thermophiles, are the exception: their enzymes keep working at 80–90 °C. That heat stability makes them valuable tools; in Class 12 you will meet Taq polymerase, which copies DNA at 72 °C. The comparison below lists other differences.

9.8.1 Chemical Reactions

To see what an enzyme achieves, be clear first about what a reaction is. When a substance only changes shape or state, as when ice melts or water boils, no bonds within its molecules break: that is a physical change. When bonds break and new bonds form, so that new substances appear, the change is a chemical reaction. Mixing solutions of silver nitrate and common salt gives a white precipitate of silver chloride, an inorganic reaction.22$\mathrm{A}\mathrm{g}\mathrm{N}\mathrm{O}{\phantom{X}}_3+\mathrm{N}\mathrm{a}\mathrm{C}\mathrm{l}\stackrel{}{\to }\mathrm{A}\mathrm{g}\mathrm{C}\mathrm{l}\downarrow +\mathrm{N}\mathrm{a}\mathrm{N}\mathrm{O}{\phantom{X}}_3$ Splitting sucrose into glucose and fructose, which happens when you digest table sugar, is an organic one.

How fast a physical or chemical process goes is its rate: how much product appears in each unit of time ((9.1)). Give the rate a direction and biochemists call it a velocity.

Temperature affects the rate of almost every process. A handy rule of thumb: the rate roughly doubles for every 10 °C rise and halves for every 10 °C fall ((9.2)).

A catalyst can make a reaction run enormously faster, and enzymes are the champion catalysts. Carbon dioxide combining with water to give carbonic acid is a good example ((9.3)). On its own the reaction is very slow. The enzyme carbonic anhydrase, present in the cytoplasm of red blood cells, speeds it up about ten million times. One enzyme molecule can then turn out hundreds of thousands of molecules of carbonic acid every second.

A cell holds thousands of kinds of enzyme, each running its own reaction, and the reactions come in chains: the product of one enzyme is the substrate of the next. Such a sequence, with every step run by an enzyme (or by one enzyme complex), is a metabolic pathway. Glucose, for instance, becomes pyruvic acid through ten enzyme-catalysed reactions ((9.4)): you will follow them in Chapter 12, Respiration in Plants.

Where such a pathway ends depends on conditions, because one or two extra reactions can be bolted on at the end. A well-supplied cell with plenty of oxygen keeps the pyruvic acid for further oxidation. A sprinter's thigh muscle, short of oxygen, converts it into lactic acid. Yeast in rising bread dough turns it into ethanol and carbon dioxide.

9.8.2 How do Enzymes bring about such High Rates of Chemical Conversions?

Call the molecule an enzyme acts on the substrate (S) and what it becomes the product (P), so the reaction is $\mathrm{S}\stackrel{}{\to }\mathrm{P}$. Catalysis begins with a meeting. Substrate molecules diffuse about until one lands in the active site, and enzyme and substrate are then locked together for an instant as the enzyme–substrate complex, ES. No ES, no reaction: every catalysed conversion passes through this complex. In the enzyme's grip the substrate is distorted into a fleeting, high-energy arrangement, the transition state. Bonds finish breaking and forming, and the product drifts away.

Picture the journey from S to P as a walk over a mountain pass (Fig. 9.13). Height stands for potential energy, and distance along the path for the progress of the reaction. Stable molecules sit in the valleys; the unstable in-between arrangements lie up the slopes, with the transition state at the summit.

The valley at the end may be lower than the one at the start: then the reaction releases energy (it is exothermic) and needs no heating to keep going. But even a downhill journey begins with a climb. The height of the summit above the substrate's average energy is the activation energy, and every reaction, energy-releasing or energy-requiring, must pay it. An enzyme is like a tunnel cut low through the mountain. The start and finish valleys stay exactly where they were, so the energy released does not change, but the climb is far smaller, and many more molecules make it across each second.

9.8.3 Nature of Enzyme Action

Written as an equation, one round of catalysis reads as (9.5). Enzyme (E) and substrate (S) combine reversibly into the short-lived, highly reactive ES complex; ES turns into an enzyme–product complex, EP; and EP comes apart into product (P) and free enzyme. E appears unchanged at both ends: the enzyme is borrowed, not spent.

Seen as a moving picture, the catalytic cycle has four stages (Fig. 9.14):

1. Bind. A substrate molecule settles into the active site.
2. Fit. Its arrival makes the enzyme shift shape slightly and close snugly round it (the induced fit).
3. React. Gripped this closely, the substrate's bonds are broken by the active site, giving the enzyme–product complex.
4. Release. The products leave, and the empty enzyme can take the next substrate molecule round the same cycle.

Because the enzyme is recycled every time, a tiny amount of it can process a huge amount of substrate.

9.8.4 Factors Affecting Enzyme Activity

An enzyme works only while it keeps its folded shape, so whatever disturbs its tertiary structure alters its activity. Four influences matter most: temperature, pH, how much substrate is present, and chemicals that latch on to the enzyme and regulate it (Fig. 9.15).

Temperature and pH

Plot an enzyme's activity against temperature or against pH and you get a hill. Its summit marks the optimum temperature or optimum pH, and activity falls away on both sides, so each enzyme is useful over only a fairly narrow range. The two sides of the temperature hill are not alike, though. On the cold side the enzyme is merely slowed, switched off for the time being: warm it and it works again, which is one reason a refrigerator keeps food fresh. On the hot side heat unfolds the protein, a change called denaturation, and the loss is permanent.

An enzyme's optimum pH suits the place where it works. Pepsin, which digests protein in the acidic stomach, works best near pH 2. Trypsin, working in the alkaline small intestine, does best near pH 8, and salivary amylase prefers a pH close to neutral.

Concentration of substrate

Think of the enzyme molecules as the autorickshaws at a railway station and the substrate molecules as arriving passengers. While passengers are few, more arrivals mean more trips per minute. Once every rickshaw is busy, extra passengers simply queue, and the number of trips per minute stops rising. An enzyme behaves the same way when temperature and pH are held steady and substrate is added to a fixed amount of it. The velocity of the reaction climbs steeply, then more slowly, and finally levels off at a maximum velocity, $V_{max}$ (Fig. 9.15, last step). Enzyme molecules are far fewer than substrate molecules, so at high substrate concentration every active site is occupied: the enzyme is saturated.

The curve has one more landmark. The substrate concentration at which the velocity reaches half its maximum, $V_{max}\mathrm{/}2$, is called $K_m$. An enzyme with a small $K_m$ reaches half speed at a low substrate concentration, a sign that it binds its substrate strongly.33$K_m$ is the Michaelis constant, named after Leonor Michaelis, who with Maud Menten described this curve in 1913.

Inhibitors

Some chemicals can switch an enzyme down or off by attaching to it. Slowing or stopping an enzyme in this way is inhibition, and the chemical responsible is an inhibitor.

Some inhibitors work by impersonation. A competitive inhibitor is shaped so much like the real substrate that the active site accepts it, yet no reaction follows; while it sits in the site the genuine substrate is locked out, and the enzyme's output falls (Fig. 9.17). The classic case involves succinic dehydrogenase, the enzyme that acts on succinate. Malonate carries the same two charged carboxylate ends with one carbon fewer between them, and it inhibits the enzyme competitively (Table 9.7).

Because inhibitor and substrate compete for the same sites, flooding the enzyme with substrate crowds the inhibitor out and the activity recovers. Medicine uses the same trick against disease-causing bacteria (bacterial pathogens). Sulpha drugs, for instance, mimic a compound called PABA that bacteria need to make the vitamin folic acid, and so they jam the bacterial enzyme that uses it.

9.8.5 Classification and Nomenclature of Enzymes

Biochemists have characterised several thousand enzymes, and they sort most of them into six classes according to the kind of reaction catalysed (Table 9.8). Each class is divided into 4–13 subclasses, and every enzyme receives a code of four numbers. Salivary α-amylase, for example, is EC 3.2.1.1: class 3 (a hydrolase), then a subclass, a sub-subclass and a serial number.

9.8.6 Co-factors

Some enzymes are pure protein. Many others sit idle until a non-protein helper, a cofactor, joins them. For these enzymes the protein part on its own is called the apoenzyme; with its cofactor in place, the complete active enzyme is often called a holoenzyme. Cofactors come in three kinds (Fig. 9.18).

A prosthetic group is an organic cofactor that stays firmly attached to its apoenzyme; that permanence is its defining feature. Haem is the textbook case. It sits within the active site of catalase and peroxidase, two enzymes that destroy hydrogen peroxide (catalase splits it: $2\mathrm{H}{\phantom{X}}_2\mathrm{O}{\phantom{X}}_2\stackrel{}{\to }2\mathrm{H}{\phantom{X}}_2\mathrm{O}+\mathrm{O}{\phantom{X}}_2$).

Co-enzymes are organic as well, but only loosely and briefly attached: one joins an enzyme for the moment of catalysis and then leaves, often to help a quite different enzyme next. Many co-enzymes are made from vitamins, which is why we need vitamins in tiny amounts yet fall ill without them. Niacin, a B vitamin, is part of both NAD (nicotinamide adenine dinucleotide) and NADP.

Metal ions act as bridges. The ion is held by coordination bonds to side chains in the active site and forms one or more coordination bonds with the substrate too. Carboxypeptidase, a protein-digesting enzyme, depends on zinc in this way.

Strip the cofactor away and the apoenzyme can no longer catalyse its reaction, the clearest evidence that the cofactor is part of the catalytic machinery.