Biochemistry

15.1Carbohydrates and their functions

Life needs energy. Green plants capture the energy of sunlight and store it as chemical energy in carbohydrates, proteins and lipids. Animals eat these compounds to get energy and to build their bodies. So a balanced diet contains carbohydrates, proteins and lipids, together with vitamins, minerals and fiber. This unit also studies the nucleic acids (DNA and RNA), which store and pass on genetic information in every living cell.

What carbohydrates are

Carbohydrates are the most abundant class of organic compounds in nature. They are made of only three elements: carbon, hydrogen and oxygen. Each carbon atom is bonded to at least one oxygen atom.

Carbohydrates

Polyhydroxy aldehydes or polyhydroxy ketones, or compounds that give these on hydrolysis. Every simple carbohydrate contains several hydroxyl ($-\mathrm{OH}$) groups and one aldehyde ($-\mathrm{CHO}$) or keto ($\mathrm{C}=\mathrm{O}$) group.

Most carbohydrates fit the general formula below. It looks like carbon joined to water, which is where the name 'carbo-hydrate' (hydrate of carbon) comes from.

How plants make carbohydrates

Plants make glucose from carbon dioxide and water by photosynthesis. Chlorophyll absorbs the energy of sunlight to drive the reaction. Plants then join glucose units to make starch (their food store) and cellulose (the material of their cell walls).

Functions of carbohydrates

• Energy: they are the body's main and quickest source of energy. Glucose is oxidised in cells in respiration to release energy.
• Structure and support: cellulose forms plant cell walls. Ribose and deoxyribose are part of RNA, DNA and ATP.
• Growth and development: they supply energy and carbon skeletons for making other molecules in a growing organism.
• Storage: starch (in plants) and glycogen (in animals) are compact, branched molecules. They can be stored in large amounts, and they are quickly hydrolysed to glucose, which cells absorb and use for energy.

15.1.2Classification of carbohydratesOften examined

Carbohydrates are classified by what happens when they are hydrolysed (split by water in the presence of an acid or an enzyme). The number of simple sugar units obtained from one molecule decides the class.

15.1.2MonosaccharidesOften examined

Monosaccharides

The simplest carbohydrates. They cannot be hydrolysed into smaller sugars. General formula $(\mathrm{CH}{}_2\mathrm{O}{)}_n$, where $n$ is 3 to 6.

Naming by number of carbon atoms

Aldoses and ketoses

A monosaccharide with an aldehyde group ($-\mathrm{CHO}$, always on carbon 1) is an aldose. One with a keto group ($\mathrm{C}=\mathrm{O}$, usually on carbon 2) is a ketose. The two names are combined: glucose is an aldohexose and fructose is a ketohexose.

Glucose and fructose both have the molecular formula $\mathrm{C}{}_6\mathrm{H}{}_{12}\mathrm{O}{}_6$, so they are isomers. Glucose is a pentahydroxy aldehyde (five $-\mathrm{OH}$ groups and one $-\mathrm{CHO}$). Fructose is a pentahydroxy ketone (five $-\mathrm{OH}$ groups and one $\mathrm{C}=\mathrm{O}$). Their open-chain structures are drawn below as Fischer projections: the carbon chain runs down the page, carbon 1 is at the top, and each crossing point is a carbon atom.

Cyclic (ring) forms

In water, glucose exists mostly as a six-membered ring. The $-\mathrm{OH}$ group on C-5 adds to the $\mathrm{C}=\mathrm{O}$ of C-1, and the ring closes through an oxygen atom. C-1 now carries a new $-\mathrm{OH}$ group, which can point in two directions. This gives two forms, $\alpha$ and $\beta$. In solution the $\alpha$ form, the $\beta$ form and a very small amount of the open chain are in equilibrium.

Fructose forms a five-membered ring: the $-\mathrm{OH}$ on C-5 adds to the keto group on C-2.

Properties of monosaccharides

• White crystalline solids.
• Soluble in water, because their many $-\mathrm{OH}$ groups form hydrogen bonds with water molecules.
• Sweet in taste.
• Cannot be hydrolysed into simpler sugars.
• Reducing sugars: their free aldehyde group (or a keto group next to an $-\mathrm{OH}$) reduces Tollens' reagent and Fehling's solution.
• Optically active: they contain chiral carbon atoms, so they rotate the plane of plane-polarised light. Sugars that rotate it to the right (clockwise) are dextrorotatory. Glucose is dextrorotatory, which is why it is also called dextrose.

15.1.2D and L forms of sugarsOften examined

Most sugars have chiral carbon atoms, so each sugar can exist as two mirror-image forms (enantiomers). The two forms are called D and L. The letter tells us the arrangement (configuration) of the groups around the chiral carbon that is **farthest from the $\mathrm{C}=\mathrm{O}$ group**. For glucose this is C-5, the second-last carbon.

The reference compound: glyceraldehyde

Glyceraldehyde, $\mathrm{CH}{}_2\mathrm{OH}-\mathrm{CHOH}-\mathrm{CHO}$, is the simplest sugar with a chiral carbon. In its Fischer projection (with $\mathrm{CHO}$ at the top), the $-\mathrm{OH}$ on the chiral carbon is on the right in D-glyceraldehyde and on the left in L-glyceraldehyde.

How to decide D or L

Comparison of D-glucose and L-glucose

Why D and L matter in living things

Enzymes and the carrier proteins that take glucose into cells are made of L-amino acids, so they are chiral too. Their binding sites fit only one mirror-image form, just as a right hand fits only a right-hand glove. Human enzymes such as hexokinase (the first enzyme of glucose respiration) and the glucose transporters are shaped for D-glucose. L-glucose does not fit their active sites, so it is hardly absorbed and cannot be used for energy, even though it tastes sweet. This is why nearly all natural sugars are D sugars, while the amino acids in proteins are L.

15.1.2Oligosaccharides and disaccharidesOften examined

Oligosaccharides

Carbohydrates that give 2 to 10 monosaccharide molecules on hydrolysis. The prefixes di-, tri-, tetra- and so on give the number of units: a disaccharide gives 2, a trisaccharide gives 3.

Oligosaccharides are white crystalline solids. They taste sweet and dissolve in water.

The glycosidic bond

Two monosaccharides join when an $-\mathrm{OH}$ group of one reacts with an $-\mathrm{OH}$ group of the other and a molecule of water is removed (a condensation reaction). The $\mathrm{C}-\mathrm{O}-\mathrm{C}$ link formed is called a glycosidic bond (glycosidic linkage). Hydrolysis breaks this bond again: it needs water plus an acid catalyst or an enzyme.

Hydrolysis of the three common disaccharides

15.1.2PolysaccharidesOften examined

Polysaccharides

Carbohydrates that give hundreds to thousands of monosaccharide units on hydrolysis. Most are polymers of glucose with the general formula (\ce{C6H10O5})_n.

• Amorphous (non-crystalline) solids.
• Tasteless (not sweet).
• Insoluble in water, because the molecules are very large. Starch forms a colloid in hot water.
• Non-reducing: a huge molecule has only one free reducing end.

15.1.3Carbohydrates and health conditions

The body breaks down digestible carbohydrates into simple sugars, which are absorbed into the bloodstream. The type and amount of carbohydrate we eat therefore affect our health.

• Heart disease: foods high in simple (added) sugars, especially fructose in sweet drinks, raise blood triglyceride levels. This increases the risk of cardiovascular disease.
• Blood sugar and diabetes: simple sugars are absorbed quickly and raise blood glucose sharply. Monitoring carbohydrate intake is essential for controlling blood sugar. Years of excess intake, together with obesity, raise the risk of type 2 diabetes.
• Weight gain: extra glucose that is not needed for energy is turned into fat. So too many simple carbohydrates and high-calorie foods lead to weight gain and obesity.
• Cholesterol: a high-fiber diet, including whole grains, lowers blood cholesterol and reduces the risk of cardiovascular disease.
• Digestion: fiber-rich carbohydrates feed beneficial gut bacteria and keep the digestive system healthy.
• Teeth: bacteria in the mouth ferment sugars into acids that dissolve tooth enamel and cause tooth decay.

Dietary fiber

Dietary fiber is the part of plant food (mainly cellulose and related polysaccharides) that our enzymes cannot digest. It is not a source of energy, but it is essential for health.

• Insoluble fiber (wheat bran, vegetables, fruit skins) absorbs water and adds bulk to food waste, so it moves easily through the intestine. This prevents constipation and lowers the risk of gut disorders.
• Soluble fiber (oats, pulses, apples) forms a gel. It binds bile acids and cholesterol and removes them, which lowers 'bad' LDL cholesterol. It also slows the absorption of sugar, which helps control blood glucose.
• Fiber is food for helpful gut bacteria, and it makes a meal more filling, which helps control body weight.

15.1.4Nutritional importance of carbohydratesOften examined

Carbohydrates have five main jobs in the human body: energy production, energy storage, building macromolecules, sparing protein, and supporting fat metabolism.

1. Energy production

Digested carbohydrates supply glucose, which every cell can use for energy. In respiration glucose is oxidised to carbon dioxide and water. The brain and red blood cells depend almost entirely on glucose.

This is the book's value: 1 g of glucose provides 15.6\,\mathrm{kJ}. Food tables round carbohydrates to about 17\,\mathrm{kJ\,g^{-1}} (4 kcal per gram).

2. Energy storage

Extra glucose is converted to glycogen, the storage form of carbohydrate in animals. Hundreds of grams of glycogen are stored in the liver and muscles, and are broken down to glucose when quick energy is needed, for example during intense physical activity. When the glycogen stores are full, extra glucose is converted into fat and stored in fat cells.

3. Building macromolecules

Some glucose is converted into ribose and deoxyribose, which are building blocks of RNA, DNA and ATP. Sugars are also attached to proteins and lipids to make glycoproteins and glycolipids.

4. Protein sparing

When enough carbohydrate is eaten, the body does not need to burn protein for energy. Proteins are then 'spared' for their main jobs: building and repairing tissues and making enzymes and hormones.

5. Supporting fat metabolism and other pathways

Carbohydrates are needed for the complete breakdown of fats. Intermediate compounds from carbohydrate breakdown are also used to make other molecules, such as some amino acids and fatty acids.

6. Fiber for digestion

Fiber (an indigestible carbohydrate) promotes good digestion by preventing constipation and lowers the risk of gut disorders. It also helps lower LDL ('bad') cholesterol and so the risk of heart disease.

15.1.5Glycogen: a store houseOften examined

Glycogen is the stored form of glucose in animals and humans. It is a very large polysaccharide made of many \alpha-glucose units joined by \alpha(1\to4) links, with \alpha(1\to6) branches about every 8 to 12 units. It is often called 'animal starch' because its structure is like amylopectin, but it is even more branched.

Where it is stored and how it is used

• Liver glycogen (about 100 g in an adult) keeps the blood glucose level steady between meals and overnight.
• Muscle glycogen (about 400 g) is used by the muscle itself to supply energy for contraction.
• Glycogenesis: after a meal, excess glucose is converted to glycogen. The hormone insulin promotes this.
• Glycogenolysis: when the body needs energy and glucose is short, glycogen is broken back into glucose, which is respired to give energy in the form of ATP. The hormones glucagon and adrenaline promote this.

Why animals keep large glycogen deposits for muscular activity

• Fast release: the many branch ends let many enzyme molecules work at once, so glucose is supplied within seconds, for example when running or lifting.
• Works without oxygen: glucose from glycogen can be broken down anaerobically (without oxygen) during sudden hard exercise, when the blood cannot bring oxygen fast enough. Fat can only be used with oxygen.
• Stored where it is needed: muscle glycogen sits inside the muscle cells, ready for use.
• Compact and insoluble: it does not dissolve, so it does not upset the water balance (osmotic balance) of the cell, as a large amount of free glucose would.

15.1.6Complex carbohydrates for joint lubrication

The ends of the bones in the elbow and knee are covered by smooth cartilage, and the joint is filled with a slippery synovial fluid. Three carbohydrate-based substances keep these joints healthy and flexible.

GAGs carry many negative charges (from carboxylate and sulphate groups). These attract water and push the chains apart, forming a slippery, springy gel. This gel lubricates the joint so bones slide smoothly, and cushions it against pressure. GAGs are the most abundant heteropolysaccharides in the body.

15.2Proteins and amino acidsOften examined

Proteins

Nitrogenous, high molecular mass polymers of amino acids. All proteins give amino acids on complete hydrolysis. They contain C, H, O and N, and most also contain S.

Proteins do almost every job in a cell: they speed up reactions (enzymes), carry substances (haemoglobin), build structures (collagen, keratin), fight infection (antibodies) and send messages (insulin). Their building blocks are amino acids.

Structure of an amino acid

An **\alpha-amino acid** has an amino group (\ce{-NH2}) and a carboxyl group (\ce{-COOH}) attached to the same carbon atom, called the \alpha-carbon. This carbon also carries a hydrogen atom and a side chain \ce{R}. About 20 different amino acids are found in proteins, and they differ only in their \ce{R} group.

In every amino acid except glycine, the \alpha-carbon is attached to four different groups, so it is chiral. The amino acids found in proteins are all the L form.

Zwitterions

An amino acid contains an acidic group (\ce{-COOH}) and a basic group (\ce{-NH2}) in the same molecule. The acid group gives a proton to the basic group, forming a zwitterion (dipolar ion) with a positive and a negative end. This is why amino acids are crystalline solids with high melting points and dissolve in water.

Essential and non-essential amino acids

15.2Peptide bond and polypeptidesOften examined

Amino acids join by a condensation reaction: the \ce{-COOH} group of one amino acid reacts with the \ce{-NH2} group of the next, and a molecule of water is removed. The amide link formed, \ce{-CO-NH-}, is called a peptide bond.

• 2 amino acids give a dipeptide, 3 give a tripeptide, and many give a polypeptide.
• The product still has a free \ce{-NH2} at one end (the N-terminal) and a free \ce{-COOH} at the other (the C-terminal), so more amino acids can be added.
• A protein is made of one or more long polypeptide chains, usually more than about 50 amino acids, with molar masses from about 10\,000 to over 1\,000\,000\,\mathrm{g\,mol^{-1}}.
• The repeating \ce{-NH-CHR-CO-} units form the backbone of the chain; the \ce{R} groups stick out from it.

Peptide bonds are broken by hydrolysis: by boiling with dilute acid in the laboratory, or by digestive enzymes (pepsin, trypsin) in the body. This releases the amino acids again.

15.2.1Classification of proteins and levels of structureOften examined

Proteins are classified in four ways. The relationship between structure and function is close: the three-dimensional shape of a protein decides its function.

Structure-based classification: four levels

a) Primary structure

The sequence of amino acids in a polypeptide chain, joined by peptide bonds (strong covalent bonds). The sequence is set by the gene (DNA) that codes for the protein. Example: insulin, with 51 amino acids in a fixed order.

b) Secondary structure

The regular coiling or zig-zag folding of the polypeptide backbone, held by hydrogen bonds between the \ce{C=O} of one peptide bond and the \ce{N-H} of another. Two common forms: the **\alpha-helix (a right-handed spiral, as in keratin of hair and wool) and the \beta-pleated sheet** (chains lying side by side in a zig-zag, as in silk). The book gives collagen as an example; collagen is a triple helix of three chains.

c) Tertiary structure

The complete three-dimensional folding of one whole polypeptide chain. It is held by bonds between the \ce{R} groups: hydrogen bonds, ionic bonds (salt bridges) between \ce{-NH3+} and \ce{-COO-} groups, disulfide bridges (\ce{-S-S-}) between cysteine units, and hydrophobic interactions between non-polar side chains. Example: myoglobin, the oxygen store of muscle.

d) Quaternary structure

The arrangement of two or more folded polypeptide chains (subunits) into one working protein. The subunits are held by the same kinds of bonds: hydrogen bonds, salt bridges and disulfide bonds. Example: haemoglobin, with four chains.

15.2.2Classification of proteins based on constitution

1. Simple proteins

Proteins that give only amino acids on complete hydrolysis. Examples: albumins (egg white, blood), globulins, collagens.

2. Conjugated (compound) proteins

A simple protein part (apoprotein) joined to a non-protein part called the prosthetic group.

3. Derived proteins

Products formed when simple or conjugated proteins are partly hydrolysed by acids, bases or enzymes. Examples: proteoses, peptones and peptides (formed during digestion).

15.2.3Classification of proteins based on shapeOften examined

Fibrous proteins are made of long, elongated polypeptide chains that lie side by side to form fibres or sheets. Globular proteins fold into a compact, roughly spherical (globe-like) shape.

15.2.4Classification of proteins on the basis of function

15.2.5Structure-function relationship of proteins

The sequence of amino acids (primary structure) decides how the chain coils (secondary), folds (tertiary) and packs with other chains (quaternary). This final shape decides the function: an enzyme's active site, an antibody's binding site and haemoglobin's oxygen pockets all depend on exact folding.

• Primary: insulin works only with its correct sequence of 51 amino acids.
• Secondary: the triple helix of collagen makes it strong like a rope, which suits tendons and skin.
• Tertiary: myoglobin folds to form a pocket that holds a haem group, which stores oxygen in muscle.
• Quaternary: haemoglobin's four subunits work together, so it loads oxygen in the lungs and unloads it in the tissues efficiently.

15.2.4Haemoglobin: the oxygen carrierOften examined

Haemoglobin (Hb, also spelt hemoglobin) is the red, iron-containing protein inside red blood cells. It is a globular, conjugated (haemoprotein) transport protein with quaternary structure. Each red blood cell contains about 270 million haemoglobin molecules.

Structure

• Four polypeptide (globin) chains: **two \alpha chains (141 amino acids each) and two \beta chains** (146 amino acids each). Molar mass about 64\,500\,\mathrm{g\,mol^{-1}}.
• Each chain holds one haem group: a flat porphyrin ring with an iron(II) ion, \ce{Fe^2+}, at its centre.
• Each \ce{Fe^2+} binds one \ce{O2} molecule reversibly, so one haemoglobin molecule carries up to four \ce{O2} molecules.

Function

\ce{Hb(O2)4} is oxyhaemoglobin (bright red). High oxygen in the lungs pushes the equilibrium right; low oxygen in the tissues pushes it left, releasing oxygen.

• Carries oxygen from the lungs to all tissues. This is its main function.
• Carries some carbon dioxide from the tissues back to the lungs (as carbaminohaemoglobin).
• Buffers the blood: it picks up \ce{H+} ions released in the tissues, helping to keep blood pH steady.
• Loading and unloading are cooperative: when one subunit binds oxygen, the others change shape slightly and bind oxygen more easily, so haemoglobin loads fully in the lungs and unloads readily in active tissues.

15.2.6Key roles of proteins in maintaining body functionOften examined

Proteins are essential macromolecules for the structure, function and regulation of the body's tissues and organs. We must eat enough protein to supply the amino acids, the building blocks of life. Good dietary sources are meat, poultry, fish, eggs, dairy products, legumes (pulses), nuts and seeds.

Roles of proteins in the body

• Growth and protoplasm: proteins are a major part of protoplasm, the living material of all cells, and are needed for growth and repair of tissues.
• Structure: collagen and elastin support tissues, tendons, ligaments and skin; keratin forms hair and nails.
• Catalysis: enzymes speed up the reactions of digestion, metabolism and the synthesis of molecules.
• Regulation: insulin and growth hormone act as chemical messengers for metabolism, growth and development.
• Transport: haemoglobin carries oxygen in blood; membrane proteins move nutrients, ions and molecules across cell membranes.
• Movement: actin and myosin cause muscle contraction and locomotion.
• Defence: antibodies identify and neutralise bacteria and viruses.
• Signalling: receptor proteins on cell surfaces respond to signalling molecules.
• Control of enzymes: some proteins act as enzyme inhibitors.
• Storage: ferritin stores iron and casein stores amino acids and calcium, ensuring a steady supply.

Nutritional importance of proteins

• Supply essential amino acids, which the body cannot make.
• Needed in larger amounts by growing children, pregnant and breast-feeding women, and people recovering from injury.
• Provide energy (about 17\,\mathrm{kJ\,g^{-1}}, 4 kcal per gram) when carbohydrate and fat are short.
• Blood proteins such as albumin keep water inside blood vessels. Severe protein deficiency causes swelling (oedema) and the disease kwashiorkor in children.
• Animal proteins contain all essential amino acids (complete proteins). Most plant proteins lack one or more, so mixing foods such as cereals and pulses gives a complete supply.

15.2.7Fibrous proteins for structure and support

Fibrous proteins are specialised structural proteins. They work like building blocks, giving strength to different parts of living things.

Hair and silk compared: keratin in hair is mostly \alpha-helix. The coils can stretch and spring back, so wet hair can be stretched. The disulfide bridges make hair and nails tough. Silk fibroin is made of \beta-sheets that are already fully extended, so silk is very strong but hardly stretches.

Fibrin and blood clotting: when a blood vessel is cut, a chain of enzyme reactions converts the soluble protein fibrinogen into insoluble fibrin threads. Calcium ions (\ce{Ca^2+}) are needed at several steps of this chain, so calcium is a requirement for blood coagulation.

The book also mentions insulin here: besides controlling blood sugar, insulin signals cells to absorb amino acids. Doctors use insulin to treat certain types of diabetes (see 15.8).

15.3Precipitation of milk proteins

Milk contains about 3.5% protein: mainly casein (about 80%) and whey proteins (about 20%). Casein is a phosphoprotein. Its molecules gather into tiny clusters called micelles, which stay spread through the milk.

15.4EnzymesOften examined

The word enzyme comes from Greek: 'en' means in and 'zyme' means yeast, because enzymes were first studied in yeast.

Enzymes

Biocatalysts: complex protein molecules, made by living cells, that change (usually increase) the rate of metabolic reactions in living bodies without being used up. They are very specific in action and sensitive to temperature and pH.

Characteristics of enzymes

• Protein nature: almost all enzymes are globular proteins, so heat, strong acids and bases and heavy metal ions denature them.
• Efficiency: they are extremely fast. One enzyme molecule can convert thousands to millions of substrate molecules every second.
• Specificity: each enzyme acts on one substrate or a small group of similar substrates. For example, urease acts only on urea and maltase only on maltose.
• Small amounts: because they are not used up, a tiny amount of enzyme is enough.
• Sensitivity: each works best at an optimum temperature and an optimum pH.
• No change in equilibrium: like all catalysts, they speed up the forward and reverse reactions equally; they do not change \Delta H or the final equilibrium position.
• Regulation: their activity can be switched up by activators or down by inhibitors.

Parts of an enzyme

• Active site: a small pocket or groove on the enzyme's surface, formed by a few amino acid side chains. The substrate binds here and the reaction happens here.
• Cofactor: some enzymes need a non-protein helper to work. It may be a metal ion (for example \ce{Zn^2+} in carbonic anhydrase, \ce{Mg^2+}) or an organic molecule called a coenzyme (often made from a vitamin).
• The protein part alone is the apoenzyme. Apoenzyme + cofactor = holoenzyme (the active enzyme).

Enzymes are usually named by adding -ase to the name of the substrate or the reaction: maltase (maltose), lactase (lactose), lipase (lipids), protease (proteins), dehydrogenase (removes hydrogen).

15.4.1Role of enzymes as a biocatalystOften examined

Metabolism is the whole set of chemical reactions in a living organism that keep it alive. These reactions let organisms grow, reproduce, maintain their structures and respond to their surroundings. Metabolism has two types of process.

Every step of metabolism is catalysed by an enzyme. The molecule an enzyme acts on is its substrate; the molecules formed are the products.

How does an enzyme work

The substrate (S) binds to the active site of the enzyme (E) to form a temporary enzyme–substrate complex (ES). The substrate is changed into product while it is held in the complex. The complex then breaks up to release the product (P) and the unchanged enzyme, which is free to bind another substrate molecule.

How enzymes lower the activation energy

The activation energy E_a is the minimum energy colliding molecules need to react. Enzymes do not add energy. Instead, they provide a new reaction pathway through the ES complex that has a much lower activation energy, so many more molecules can react at body temperature.

• Holding reactants together: the active site holds the reacting molecules close together and in the correct orientation, so they do not need a lucky collision.
• Straining bonds: binding bends or stretches bonds in the substrate, making them easier to break.
• Helpful chemical groups: side chains in the active site can donate or accept \ce{H+} ions, or form temporary bonds, which makes bond breaking easier.
• Suitable surroundings: the active site provides a microenvironment (for example, free of water) that favours the reaction.

Enzymes in the digestion of food

Digestion is a series of enzyme-catalysed hydrolysis reactions that break large food molecules into small ones that can be absorbed into the blood. Without enzymes, hydrolysis of starch at 37^\circ\mathrm{C} would take years; in the laboratory it needs boiling with acid.

15.4.1Lock and key and induced fit modelsOften examined

Lock and key model (Emil Fischer, 1894)

The active site has a fixed, rigid shape that is exactly complementary to the shape of the substrate, just as only one key fits a particular lock. The substrate (key) fits into the active site (lock) to form the ES complex; the products then leave and the enzyme is unchanged. This model explains why enzymes are specific.

Limitation: it treats the enzyme as rigid. It cannot explain why some enzymes act on several similar substrates, or why the enzyme's shape changes when a substrate binds.

Induced fit model (Daniel Koshland, 1958)

The active site is flexible. It is not an exact fit at first. When the substrate binds, the active site changes shape (is 'moulded') and closes tightly around it, like a glove taking the shape of a hand. This close fit also strains the substrate's bonds, which helps the reaction. After the products leave, the enzyme returns to its original shape. The induced fit model is more widely accepted than the lock and key model.

15.4.2Factors affecting enzyme activityOften examined

Enzymes are very sensitive to their surroundings. Anything that changes the shape of the enzyme (especially its active site) or changes how often enzyme and substrate meet changes the rate of the reaction. The main factors are temperature, substrate concentration, pH, enzyme concentration, and inhibitors or activators.

1. Temperature

• Low temperature: molecules move slowly and collide rarely, so the rate is low. The enzyme is inactive but not damaged; warming it up restores activity. This is why food keeps longer in a fridge.
• Rising temperature: molecules gain kinetic energy, collide more often and more of the collisions have energy above E_a. The rate roughly doubles for every 10^\circ\mathrm{C} rise.
• Optimum temperature: the temperature at which the enzyme works fastest. It is about 37^\circ\mathrm{C} for human (animal) enzymes; the book quotes about 60^\circ\mathrm{C} for a plant enzyme. Each enzyme has its own value.
• Above the optimum: the atoms of the enzyme vibrate so strongly that the weak bonds (hydrogen bonds, ionic bonds) holding its folded globular shape break. The active site loses its shape, the substrate no longer fits, and the rate falls sharply. This is denaturation, and it is usually permanent.

Denaturation

The loss of the specific three-dimensional shape of a protein (secondary, tertiary and quaternary structure) caused by heat, extreme pH, heavy metal ions or some chemicals. The peptide bonds (primary structure) stay intact, but the protein loses its biological activity. Example: the white of a boiled egg.

2. Substrate concentration

When there are enough free enzyme molecules, adding more substrate increases the rate, because more ES complexes form. If the amount of enzyme is fixed, a point is reached where all the active sites are occupied. The enzyme is then saturated, so extra substrate cannot find a free active site and the rate stays constant at its maximum (V_{\max}). The book calls this saturation the 'active site state'. Only adding more enzyme can raise the rate further.

3. pH

Each enzyme works fastest within a narrow range of pH called its optimum pH. A small change of pH either slows or stops the enzyme. The reason is that pH changes the charges on the acidic and basic side chains (\ce{-COOH}/\ce{-COO-} and \ce{-NH2}/\ce{-NH3+}) in the active site and in the ionic bonds that hold the enzyme's shape. The substrate then binds less well, and at extreme pH the enzyme is denatured.

4. Enzyme concentration

When substrate is present in excess, the rate is directly proportional to the enzyme concentration, because doubling the enzyme doubles the number of active sites available.

5. Inhibitors and activators

Inhibitors slow down or stop enzyme action (see 15.4.3). Activators increase enzyme activity; for example, chloride ions activate salivary amylase, and many enzymes need metal ions such as \ce{Mg^2+} or \ce{Zn^2+} as cofactors.

How these factors affect reactions in the human body

• High fever: a body temperature above about 40^\circ\mathrm{C} can begin to denature important enzymes, which is why very high fever is dangerous.
• Hypothermia: a low body temperature slows all enzyme reactions, so metabolism slows down.
• Stomach and intestine: pepsin works in the acid of the stomach (pH 2) but stops working in the small intestine (pH 8), where trypsin takes over. Salivary amylase stops working once food reaches the acidic stomach.
• Poisons and drugs: heavy metals, nerve gases and many medicines act as enzyme inhibitors.

15.4.3Role of inhibitors in enzyme-catalysed reactionsOften examined

Enzyme inhibitor

A substance that binds to an enzyme and decreases or stops its activity.

Inhibitors play a key role in regulating enzyme-catalysed reactions. Cells use them to switch metabolic pathways on and off (for example, the final product of a pathway often inhibits the first enzyme). Many drugs and poisons also work as enzyme inhibitors. Inhibitors are grouped by how firmly they bind.

• Reversible inhibitors bind by weak non-covalent bonds and can leave the enzyme again: competitive and non-competitive inhibitors.
• Irreversible inhibitors form strong covalent bonds with the enzyme and destroy its activity permanently.

Competitive inhibitors

A competitive inhibitor has a shape similar to the substrate. It competes with the substrate for the active site. When it binds, the substrate cannot bind, but the inhibitor is not converted into product. Because the two molecules compete, adding more substrate pushes the inhibitor out, so the inhibition can be overcome and the same maximum rate is still reached.

Example: malonic acid. The enzyme succinate dehydrogenase removes two hydrogen atoms from succinic acid to form fumaric acid. Malonic acid has a very similar structure (one \ce{CH2} group fewer), so it binds to the active site of succinate dehydrogenase. But it cannot be dehydrogenated (it has no \ce{-CH2-CH2-} unit to turn into \ce{-CH=CH-}), so no product forms and the enzyme is blocked.

Medical example: in methanol poisoning, the patient is given ethanol. Ethanol competes with methanol for the active site of the enzyme alcohol dehydrogenase, so less methanol is turned into poisonous methanal.

Non-competitive inhibitors

A non-competitive inhibitor does not compete for the active site. It binds to another site on the enzyme (an allosteric site) and changes the shape of the enzyme and its active site. The substrate may still bind, but it cannot be converted to product properly. Adding more substrate does not remove the inhibitor, so the maximum rate is lowered.

Example: heavy metal ions such as mercury (\ce{Hg^2+}), lead (\ce{Pb^2+}) and silver (\ce{Ag+}) bind to the thiol (\ce{-SH}) groups of cysteine side chains in the enzyme and change its shape and activity.

Irreversible inhibitors

An irreversible inhibitor reacts with an amino acid side chain in (or near) the active site and forms a covalent bond. The bond does not break under normal conditions, so the active site is permanently blocked or changed. Adding substrate cannot reverse it; activity returns only when the cell makes new enzyme molecules.

15.5LipidsOften examined

Butter, cooking oil, the wax on a leaf and the cholesterol in blood look very different, but they share one property: none of them dissolves in water. This single property is what puts them in one class, the lipids.

Lipids

Naturally occurring, heterogeneous (mixed) groups of organic compounds of animal and plant origin that are insoluble in water but soluble in organic solvents such as ether, chloroform and benzene. They include fats, oils, waxes, some hormones and some membrane components.

Lipids are insoluble in water because their molecules are made mostly of long non-polar hydrocarbon chains or rings. These cannot form hydrogen bonds with water. Like dissolves like, so lipids dissolve in non-polar organic solvents.

Functions of lipids in brief

• Energy store: fats store more than twice as much energy per gram as carbohydrates.
• Membranes: phospholipids and cholesterol are the main constituents of cell membranes.
• Chemical messengers: steroid hormones and prostaglandins carry signals in the body.
• Protection and insulation: waxes waterproof leaves and feathers; fat under the skin keeps the body warm and cushions organs.

15.5.1Classification of lipidsOften examined

Lipids are a mixed group, so the book classifies them in four different ways. Each way answers a different question: what the molecule is built from, what its chemical make-up is, what job it does, and what it looks like at room temperature.

The first classification is based on structure and function. It gives five classes.

1. Triglycerides (fats and oils)

Fats and oils are made from two kinds of molecules: glycerol (a trihydric alcohol, propane-1,2,3-triol) and three fatty acid molecules. Each \ce{-OH} group of glycerol forms an ester with the \ce{-COOH} group of one fatty acid, and one molecule of water is removed for each ester bond. Because the product contains three fatty acid units, it is called a triglyceride (triacylglycerol).

\ce{R} is a long hydrocarbon chain. The three \ce{R} groups may be the same or different.

Fatty acids are long-chain carboxylic acids with 12 to 22 carbon atoms (usually an even number) and a \ce{-COOH} group at one end. They are the building blocks of most lipids. Examples: palmitic acid \ce{C15H31COOH}, stearic acid \ce{C17H35COOH}, oleic acid \ce{C17H33COOH} and linoleic acid \ce{C17H31COOH}.

Triglycerides are found in oils, butter and adipose tissue (fat tissue). If the fatty acids are saturated, they form fats, which are solid at room temperature (butter, ghee). If they are unsaturated, they form oils, which are liquid at room temperature (olive oil, sunflower oil, cotton seed oil).

2. Phospholipids

Phospholipids are esters of glycerol with two fatty acids and one phosphate group (\ce{PO4^3-}), which is usually joined to a small nitrogen-containing group such as choline. The phosphate end is charged and polar, so it is hydrophilic (water-loving). The two fatty acid chains are non-polar and hydrophobic (water-hating).

They are an integral part of cell membranes. The bilayer lets fat-soluble substances pass but blocks ions and large polar molecules, so it controls what enters and leaves the cell.

3. Steroids

Steroids are lipids whose molecules contain four fused rings of carbon atoms: three six-membered rings and one five-membered ring. They are not esters and contain no fatty acids. They act as structural components of cell membranes and are the precursors of various hormones. Examples: cholesterol, testosterone, oestrogen.

4. Waxes

Waxes are esters of a long-chain fatty acid with a long-chain alcohol (not glycerol). They are very water-repellent, so they act as a protective cover for plants and animals, for example the shiny coating on leaves and fruit and the waterproofing of feathers. Examples: lanolin (wool fat), beeswax, carnauba wax, whale oil (spermaceti).

5. Isoprenoids or terpenes

Lipids built from isoprene units (five-carbon units, \ce{C5H8}, 2-methylbuta-1,3-diene) are called terpenes or isoprenoids. They have various functions: pigments in plants (carotenoids such as the orange colour of carrots), electron carriers in cellular respiration (ubiquinone), and flavours and smells. Examples: pinene, camphor, menthol, chlorophyll (its side chain), vitamin A.

15.5.2Classification of lipids based on chemical structureOften examined

On the basis of chemical structure, lipids are classified into three groups.

15.5.3Classification of lipids on the basis of function

15.5.4Classification of lipids on the basis of physical characteristicsOften examined

On the basis of physical characteristics, glycerides (triglycerides) are classified by the kind of fatty acid they contain.

Saturated glycerides (fats)

Glycerides whose fatty acids contain only single bonds between carbon atoms (general formula of the acid \ce{C_nH_{2n+1}COOH}). They are solids at room temperature. Foods rich in them: butter, cheese, ghee, lard, some fatty meats.

Unsaturated glycerides (oils)

Glycerides whose fatty acids contain at least one \ce{C=C} double bond. They are liquids at room temperature. Foods rich in them: nuts, avocado, and vegetable oils such as canola oil and olive oil.

Oils are converted into solid fats (vegetable ghee, margarine) by hydrogenation: hydrogen is added across the \ce{C=C} bonds using a nickel catalyst.

15.5.5Nutritional and biological importance of lipidsOften examined

Lipids play three important biochemical roles:

1. Storehouse of metabolic energy (triglycerides).
2. Components of membranes (phospholipids, glycolipids, cholesterol).
3. Messengers (prostaglandins and steroid hormones).

Nutritional importance

• Concentrated energy: saturated, unsaturated and trans fats all provide about 9\,\mathrm{kcal} (37\,\mathrm{kJ}) per gram, compared with about 4\,\mathrm{kcal} (17\,\mathrm{kJ}) per gram for carbohydrates and proteins. Fat molecules contain much less oxygen, so there is more carbon and hydrogen to oxidise per gram.
• Fat-soluble vitamins: fats are needed to absorb the fat-soluble vitamins A, D, E and K from food.
• Essential fatty acids: some fatty acids (omega-3 and omega-6) cannot be made by the body and must come from the diet.
• Fats are high in calories but do not necessarily cause weight gain if the total energy intake is controlled.

Biological importance

• Insulation: fat under the skin reduces heat loss; it is especially thick in animals of cold regions.
• Protection: fat around the kidneys and heart cushions them against shock.
• Nerves: the myelin sheath around nerve fibres is rich in lipids and insulates the nerve impulses.
• Hormones: cholesterol is the starting material for sex hormones, adrenal hormones and vitamin D.
• Metabolic water: oxidation of fat produces water, which is important for desert animals such as the camel.

15.5.6, 15.5.7Essential and non-essential lipids

Essential lipids

Lipids that are not produced by the body and must enter the body through food.

Non-essential lipids

Lipids that the body can synthesise itself, so they are not required in the diet.

Essential lipids

The most important essential lipids are the polyunsaturated fatty acids (PUFA), found as polyunsaturated fats: omega-6 (e.g. linoleic acid) and omega-3 (e.g. linolenic acid) fats. They are needed for making hormones, for cell membrane structure, and for brain and vision health, and they can help lower blood cholesterol levels.

• Omega-6 sources: vegetable oils and nuts.
• Omega-3 sources: flax seeds, walnuts and fatty fish.

Non-essential lipids

Monounsaturated fats (one \ce{C=C}, e.g. oleic acid) are not required in the diet because the body can make them. They reduce the risk of cardiovascular disease. Sources: olive oil, peanuts, avocado.

Saturated fats, trans fats and cholesterol are also present in the diet and raise the 'bad' (LDL) cholesterol level in blood. Trans fats come from processed and fried foods, and cholesterol comes from fatty animal foods.

15.6Cholesterol as a hormone precursor

Cholesterol is a steroid lipid, \ce{C27H46O}, made in the liver and also taken in from animal foods. It is a building block of hormones: our bodies use it to produce several important steroid hormones. These hormones act like messengers, delivering signals to different parts of the body.

• Sex hormones: oestrogen (estrogen) and testosterone. They control the development of secondary sexual characteristics and the regulation of the reproductive system.
• Adrenal hormones: cortisol (controls glucose metabolism and stress) and aldosterone (controls salt and water balance).
• Vitamin D is made from a cholesterol derivative in the skin in sunlight.
• Bile salts, made from cholesterol in the liver, help digest fats.

The steroid hormones keep the four-ring skeleton of cholesterol; only the groups attached to the rings and the side chain change.

15.7Amino acids as hormone components

Some hormones consist of amino acids linked together by peptide bonds. They are called peptide hormones (or protein hormones). They also act as messengers, but they do different tasks from the steroid hormones made from cholesterol, and they work differently: being large and water-soluble, they cannot pass through the cell membrane, so they bind to receptor proteins on the cell surface.

Some other hormones are made from a single amino acid. For example, adrenaline and the thyroid hormone thyroxine are made from tyrosine.

15.8InsulinOften examined

Insulin is a protein (peptide) hormone produced by the \beta-cells of the pancreas. It consists of two polypeptide chains: the A (alpha) chain of 21 amino acids and the B (beta) chain of 30 amino acids, 51 amino acids in all. The two chains are connected by disulfide bridges. Its molar mass is 5808\,\mathrm{g\,mol^{-1}}.

How insulin regulates blood glucose

Diabetes mellitus

Insulin deficiency leads to diabetes mellitus: a disorder in which the body does not produce enough insulin, or does not respond normally to it, so the blood glucose level stays abnormally high. Type 1 diabetes (no insulin made) is treated with insulin injections; type 2 (cells resist insulin) is controlled by diet, exercise and medicines.

15.9Fat as the energy store for hibernation

Hibernation is a long, deep sleep through the winter that occurs in many species, including bears, reptiles and amphibians. Under favourable conditions (summer and autumn) the animal eats a lot and its body accumulates large amounts of fat. During the cold months:

• breathing becomes very slow and the heart rate falls;
• body temperature drops, depending on the surrounding temperature;
• metabolism slows down and the animal becomes much less active, usually hidden in a cave or burrow;
• the stored fat is oxidised to meet its energy needs, and its oxidation also releases metabolic water.

Fat is the ideal store for this because it gives about twice as much energy per gram as glycogen and is stored without water.

15.10Nucleic acidsOften examined

A fertilised egg is a single cell, yet it grows into a person with legs, hands, a heart and kidneys. The instructions for building all these are stored in chemical form in molecules called nucleic acids. They were first found in the nucleus of cells and are acidic because of their phosphate groups, hence the name.

Nucleic acids

Naturally occurring biomolecules that serve as the primary information-carrying molecules in cells. They are long polymers of nucleotides and are present in every living cell and in viruses.

There are two types of nucleic acids:

1. Deoxyribonucleic acid (DNA): stores the genetic information; found mainly in the nucleus.
2. Ribonucleic acid (RNA): uses the information to make proteins; found mainly in the cytoplasm.

15.10.1Structural components of DNA and RNAOften examined

DNA and RNA are large polymeric molecules. Their monomers are called nucleotides. Four types of nucleotide build a DNA strand; they differ only in the base attached to carbon number 1 of the pentose sugar.

Components of a nucleotide

Each nucleotide consists of three components: a pentose sugar, a nitrogenous base and a phosphate group.

1. Pentose sugar (five-carbon sugar)

In RNA the sugar is ribose, \ce{C5H10O5}. In DNA it is deoxyribose, \ce{C5H10O4}. 'Deoxy' means 'without oxygen': in deoxyribose, the hydroxyl group at carbon 2 of ribose is replaced by a hydrogen atom. The carbons of the sugar are numbered 1′ to 5′ (read 'one prime').

2. Nitrogenous bases

Four different nitrogenous bases are found in DNA: adenine (A), guanine (G), cytosine (C) and thymine (T). In RNA, thymine is replaced by uracil (U). The bases are of two kinds:

• Purines: adenine and guanine. They have a double ring (a six-membered ring fused to a five-membered ring) containing nitrogen atoms.
• Pyrimidines: cytosine, thymine and uracil. They have a single six-membered ring containing two nitrogen atoms.

3. Phosphate unit

The phosphate group is linked to C-5′ of the deoxyribose sugar in DNA and of the ribose sugar in RNA. It carries negative charge, which makes nucleic acids acidic.

Sugar + base = nucleoside. Nucleoside + phosphate = nucleotide. The book's drawings of a DNA nucleotide and an RNA nucleotide are shown below.

Joining nucleotides: the phosphodiester bond

The phosphate on C-5′ of one nucleotide forms an ester bond with the \ce{-OH} on C-3′ of the next nucleotide, and water is removed. Each phosphate is therefore joined by two ester bonds, one to each sugar, so the link is called a phosphodiester bond. Repeating this makes a long sugar–phosphate backbone with a base attached to every sugar. One end of the chain has a free 5′ phosphate (the 5′ end) and the other a free 3′ \ce{-OH} (the 3′ end).

15.10.2Difference between RNA and DNAOften examined

DNA can store and transmit all the genetic information needed to build an organism. For instance, in human beings the single fertilised egg cell carries the information for making legs, hands, head, liver, heart, kidneys and every other part. DNA is found primarily in the cell nucleus.

The double-helix structure of DNA was discovered by James Watson and Francis Crick in 1953, using X-ray photographs taken by Rosalind Franklin. Watson, Crick and Maurice Wilkins were awarded the 1962 Nobel Prize. The discovery started the field of molecular biology. Cancer research also involves extensive study of nucleic acids.

15.10.3Structure of DNAOften examined

DNA exists as a double helix: two strands spiral around each other like a twisted ladder.

• The sides of the ladder are the two sugar–phosphate backbones, on the outside.
• The rungs are pairs of bases, on the inside. The bases of the two strands are joined by hydrogen bonds.
• Base pairing is complementary: adenine always pairs with thymine by two hydrogen bonds (A = T), and guanine always pairs with cytosine by three hydrogen bonds (G ≡ C). A purine always pairs with a pyrimidine, so every rung has the same width.
• The two strands are antiparallel: one runs 5'\to3' and the other 3'\to5'.
• One complete turn of the helix contains about 10 base pairs (about 3.4\,\mathrm{nm}); the helix is about 2\,\mathrm{nm} wide.

How DNA stores genetic information

The information is stored in the sequence of bases along one strand, just as a sentence stores meaning in its sequence of letters. The DNA 'alphabet' has four letters (A, T, G, C). A section of DNA that carries the information for making one protein (or one RNA) is called a gene. Every group of three bases (a triplet or codon) stands for one amino acid, so the order of bases in a gene fixes the order of amino acids in a protein.

Replication: passing information to the next generation

DNA is self-replicating. Before a cell divides, the hydrogen bonds between the two strands break and the strands unzip. Each strand acts as a template: free nucleotides pair with it (A with T, G with C) and are joined together by the enzyme DNA polymerase. Two identical DNA molecules are formed, each with one old and one new strand (semi-conservative replication). So each daughter cell carries an exact copy of the genetic code, and the organism can pass it on to its offspring.

15.10.4Structure of ribonucleic acid (RNA)Often examined

RNA exists as a single strand of ribonucleotides (sugar ribose; bases A, G, C and U). It is made from DNA to carry the genetic information, and it controls the synthesis of new proteins by receiving, reading, decoding and using the information from DNA. The strand can fold back on itself where its bases pair (A with U, G with C), forming loops (Fig 15.6).

Types of RNA

From gene to protein

So the RNA sequence (the transcript) directly decides the amino acid sequence of the protein. A change in a single base of the gene can change one amino acid and may stop the protein from working.

In summary: DNA stores the information (replication copies it), mRNA carries it (transcription), and tRNA and rRNA use it to build the protein (translation).

15.11Minerals of biological significanceOften examined

Minerals are inorganic nutrients (elements, usually taken in as their ions) that the body needs to support life. They are as necessary for life as oxygen. They are found in food in both organic and inorganic forms. Only about 5% of the human body mass is made of minerals, but they are essential for every mental and physical process: they are constituents of teeth, bones, tissues, blood, muscles and nerve tissue, and they are the most important factor in maintaining physiological processes.

Types of nutrients: macro and micro

Sources of important minerals (15.11.1)

15.11.2Role of important minerals in nutritionOften examined

Iron

• Iron (\ce{Fe^2+}) is part of haemoglobin, the protein in red blood cells that carries oxygen from the lungs to every part of the body. It is also part of myoglobin, which carries and stores oxygen in muscle tissue.
• It helps maintain healthy blood, is essential for the development and growth of the brain in children, and is needed for the normal generation and function of cells and some hormones.
• Deficiency: low iron means too little haemoglobin, so the red blood cells cannot carry enough oxygen. This is iron-deficiency anaemia, causing extreme tiredness (fatigue), dizziness and lightheadedness. It is most common in children, in women who are pregnant or menstruating, and in people on kidney dialysis.

Calcium

• Calcium is one of the most abundant minerals in the body. About 99% of it is stored in bones and teeth (as calcium phosphate); the remaining 1% is in blood, muscle and other tissues.
• \ce{Ca^2+} ions are essential for blood coagulation (clotting), for muscle contraction, for regulating normal heart rhythm and for nerve function.
• Calcium absorption depends on vitamin D. Vitamin D deficiency lowers the ionised calcium in blood and tissues and causes rickets (soft, bent bones in children), osteomalacia (soft bones in adults) and osteoporosis (weak, brittle bones).

Phosphorus

• Phosphorus (as phosphate) plays a key role in the structure of bones and teeth and of cell membranes (phospholipids).
• It is part of DNA, RNA and ATP; ATP is the body's main energy carrier.
• It activates enzymes (by phosphorylation) and helps maintain the blood's pH (phosphate buffer).
• It is needed for the proper functioning of nerves and muscles, including the heart.
• Deficiency (rare) causes weak bones and teeth, bone pain, muscle weakness and loss of appetite.

Zinc

• Zinc is the most important trace element in humans; the body contains about 2\,\mathrm{g} of it.
• It supports the immune system; low zinc levels increase the risk of infections such as pneumonia.
• It is needed for the production of proteins and DNA (it is a cofactor of many enzymes), promotes wound healing, and influences child growth and development.
• It maintains healthy skin and plays a role in prostate health and testosterone levels.

Formula sheet

Key terms

Carbohydrates

Polyhydroxy aldehydes or ketones, or compounds that give them on hydrolysis; general formula \mathrm{C}_x(\mathrm{H_2O})_y.

Monosaccharide

A simple sugar that cannot be hydrolysed into smaller sugars, (\ce{CH2O})_n with 3 to 6 carbons; e.g. glucose, fructose, ribose.

Oligosaccharide

A carbohydrate that gives 2 to 10 monosaccharide units on hydrolysis; e.g. sucrose, maltose, lactose (disaccharides).

Polysaccharide

A carbohydrate that gives hundreds to thousands of monosaccharide units on hydrolysis; e.g. starch, glycogen, cellulose.

Aldose / ketose

A monosaccharide with an aldehyde group (\ce{-CHO}) / a keto group (\ce{C=O}).

D and L sugars

Mirror-image forms of a sugar; D if the \ce{-OH} on the chiral carbon farthest from \ce{C=O} is on the right in the Fischer projection, L if on the left.

Glycosidic bond

The \ce{C-O-C} link between two sugar units, formed by condensation (loss of water).

Glycogen

The highly branched storage polysaccharide of \alpha-glucose in the liver and muscles of animals.

Dietary fiber

Indigestible plant carbohydrate (mainly cellulose) that aids digestion and lowers cholesterol.

Glycosaminoglycans (GAGs)

Long unbranched polysaccharides containing amino sugars that lubricate and cushion joints.

Proteins

Complex nitrogenous macromolecules that give amino acids on complete hydrolysis.

Amino acid

A compound containing an amino (\ce{-NH2}) group and a carboxyl (\ce{-COOH}) group; the monomer of proteins.

Essential amino acid

An amino acid the body cannot make, which must come from food; e.g. lysine.

Peptide bond

The amide link \ce{-CO-NH-} between two amino acids, formed with loss of water.

Primary structure

The sequence of amino acids in a polypeptide chain.

Denaturation

Loss of the three-dimensional shape of a protein (not its peptide bonds) by heat, pH or chemicals, with loss of function.

Fibrous / globular protein

Long insoluble structural protein (keratin) / compact soluble functional protein (haemoglobin, enzymes).

Haemoglobin

The iron-containing globular protein of red blood cells that carries oxygen; four chains, each with a haem group containing \ce{Fe^2+}.

Enzyme

A biocatalyst: a globular protein that speeds up a specific metabolic reaction by lowering its activation energy.

Active site

The pocket on an enzyme where the substrate binds and reacts.

Substrate

The molecule on which an enzyme acts.

Optimum temperature / pH

The temperature / pH at which an enzyme works fastest (about 37^\circ\mathrm{C} and pH 7 for most human enzymes).

Lock and key model

Fischer's model: a rigid active site exactly complementary to the substrate.

Induced fit model

Koshland's model: the flexible active site changes shape to fit the substrate.

Competitive inhibitor

An inhibitor resembling the substrate that competes for the active site; overcome by more substrate.

Non-competitive inhibitor

An inhibitor that binds elsewhere on the enzyme and changes its shape; not overcome by more substrate.

Irreversible inhibitor

An inhibitor that bonds covalently to the enzyme and destroys its activity permanently; e.g. nerve gas, aspirin.

Lipids

Naturally occurring heterogeneous organic compounds, insoluble in water and soluble in organic solvents.

Triglyceride

An ester of glycerol with three fatty acids (fats and oils).

Phospholipid

An ester of glycerol with two fatty acids and a phosphate group; forms cell membranes.

Steroid

A lipid with four fused carbon rings (three six-membered, one five-membered); e.g. cholesterol.

Wax

An ester of a long-chain fatty acid with a long-chain alcohol; a protective coating.

Terpenes

Lipids built from five-carbon isoprene units; e.g. menthol, carotenoids.

Saturated / unsaturated glyceride

Glyceride with only \ce{C-C} single bonds (solid fat) / with at least one \ce{C=C} (liquid oil).

Essential lipids

Lipids the body cannot make and must obtain from food; e.g. omega-3 and omega-6 fatty acids.

Insulin

Protein hormone of the pancreas (51 amino acids in two chains) that lowers blood glucose.

Nucleic acids

Information-carrying biomolecules (DNA and RNA), polymers of nucleotides.

Nucleotide

The monomer of nucleic acids: a pentose sugar, a nitrogenous base and a phosphate group.

Purines / pyrimidines

Double-ring bases (adenine, guanine) / single-ring bases (cytosine, thymine, uracil).

Double helix

Two antiparallel DNA strands twisted round each other and held by hydrogen bonds between complementary bases (A = T, G ≡ C).

Gene

A section of DNA whose base sequence carries the information for one protein.

Transcription / translation

Copying of a DNA gene into mRNA / decoding of mRNA into a protein at the ribosome.

Minerals

Inorganic nutrients essential for body structure and physiological processes.

Macro / trace minerals

Minerals needed in large amounts (Ca, P, Mg, S) / in small amounts (Fe, Zn, Cu, I).

Iron-deficiency anaemia

Condition of too little haemoglobin due to lack of iron, causing fatigue and dizziness.

FBISE 2026 questions

Questions from the FBISE HSSC-II 2026 (1st Annual) papers that belong to this unit, answered the way an examiner expects.

Exam focus

1. Classify carbohydrates (mono-, oligo-, polysaccharides) with examples. (short)
   Asked in 2026 (Set D); also a long question in the book.
   Go to answer
2. Structural difference between D- and L-glucose and its biological effect. (short)
   Asked in 2026 (old syllabus); learn the C-5 rule and the Fischer drawing.
   Go to answer
3. Factors affecting enzyme activity, with temperature and pH graphs. (long)
   Asked in 2026 (Set B, MCQ and Q.2); draw both graphs and mark the optimum.
   Go to answer
4. Competitive, non-competitive and irreversible inhibition with examples. (long)
   Inhibition appears every year; irreversible inhibitors were asked in 2026.
   Go to answer
5. Classify lipids (simple, compound, derived) with one example of each. (short)
   Asked in 2026 (Set B, Q.2 (xi)).
   Go to answer
6. Three differences between DNA and RNA. (short)
   Asked in 2026 (old syllabus); sugar, base, strands.
   Go to answer
7. Structure of DNA and RNA related to storage and transfer of information. (long)
   Covers four SLOs: double helix, base pairing, transcription, translation.
   Go to answer
8. Lock and key and induced fit models; how enzymes lower activation energy. (short)
   Standard 3-mark questions with a diagram.
   Go to answer
9. Levels of protein structure and fibrous vs globular proteins. (short)
   Frequent short questions; learn one example of each level.
   Go to answer
10. Function and structure of haemoglobin; role of iron. (short)
    Asked as an MCQ in 2026 (Set D) and in the book exercise.
    Go to answer
11. Triglycerides: formation, structure, saturated vs unsaturated. (short)
    Concept assessment and short question v; draw the ester structure.
    Go to answer
12. Role of iron, calcium, phosphorus and zinc in nutrition. (long)
    Long question vi; learn one role and one deficiency disease for each.
    Go to answer