1.3.1 Cellular respiration supplies ATP

What cellular respiration is

1. Cellular respiration is the series of enzyme-controlled reactions that breaks glucose down inside a cell so the energy held in its bonds can be transferred to ATP.
2. It is a universal process, which means it goes on in every living cell of every living organism, from a single bacterium to an oak tree to you.
3. It also runs continuously, day and night, awake and asleep, from the moment a cell is formed until the moment it dies.
4. A cell keeps no useful reserve of ready energy, so if respiration paused for even a short time the cell would have nothing left to power its reactions.
5. The breakdown is not one single reaction but a chain of many small steps, and each step has its own enzyme controlling it.
6. Splitting the job into small steps lets the energy leave the glucose in small, usable amounts instead of all at once, which would damage the cell.
7. Because enzymes run every step, the rate of respiration rises with temperature up to an optimum and falls away if the enzymes are denatured.
8. Glucose is the main respiratory substrate, which is the name for the molecule that gets broken down.
9. An animal cell receives glucose from digested food carried to it in the blood, while a plant cell makes its own glucose by photosynthesis and then respires it.
10. Respiration is a chemical process happening inside cells, so it is a different thing from breathing, which simply moves air in and out of the lungs.

How ATP stores and releases energy

1. ATP stands for adenosine triphosphate, and the name describes the molecule: an adenine base, a ribose sugar and a chain of three phosphate groups.
2. Energy transferred by respiration is used to attach a third phosphate group onto ADP, which stands for adenosine diphosphate, and this builds a molecule of ATP.
3. Building ATP can be written as $ADP+P_i\to ATP$, where $P_i$ stands for an inorganic phosphate group.
4. When a process in the cell needs energy, the bond holding that third phosphate group is broken instead, giving $ATP\to ADP+P_i$.
5. Breaking that bond releases the stored energy at the exact place in the cell where the work is being done.
6. The ADP and the phosphate group are not thrown away; they stay in the cell and are joined together again by the next round of respiration.
7. A single ATP molecule is therefore spent and rebuilt over and over, so a cell needs a fast rate of respiration rather than a large store of ATP.
8. ATP is called the cell's energy currency because every process that needs energy is paid for in ATP, whatever fuel the energy originally came from.
9. Glucose cannot power a reaction directly, because one glucose molecule holds far more energy than any single reaction needs, and ATP breaks that store into small packets.

What cells spend ATP on

1. Muscle contraction is powered by ATP, so every movement an animal makes depends on a supply of it.
2. Synthesis of large molecules from smaller ones needs ATP, because joining subunits together does not happen on its own.
   1. Amino acids are joined into proteins, glucose molecules are joined into starch or glycogen, and nucleotides are joined into DNA.
3. Active transport needs ATP, because moving a substance against its concentration gradient can only happen if energy is supplied.
4. Cell division needs ATP to copy the DNA and to pull the chromosomes to opposite ends of the cell.
5. Transmission of nerve impulses needs ATP to pump ions back across the membrane after each impulse has passed.
6. In mammals and birds, part of the energy transferred by respiration warms the body and helps hold the internal temperature steady.

Respiration as an exothermic reaction

1. An exothermic reaction transfers energy out to its surroundings, so the surroundings end up warmer than they started.
2. The bonds in glucose hold more energy than the bonds in the products of respiration, so there is a surplus every time a glucose molecule is broken down.
3. Only part of that surplus is captured in ATP, and the rest leaves the cell as heat, which makes respiration exothermic.
4. Because respiration never stops, this heat is being released all the time, in every cell of every organism.
5. A tissue that respires quickly releases heat quickly, so it warms up more than a tissue that is resting.
6. Contracting muscles respire faster during exercise, which is why you feel hot after sprinting for a bus.
7. A large number of respiring organisms packed together warms its surroundings noticeably, which is why the middle of a compost heap or a bag of damp grass cuttings feels hot.
8. In a mammal or bird, this steady release of heat is what makes a constant internal body temperature possible even when the air outside is cold.
9. A plant releases heat from respiration too, but it has no way of holding its temperature steady, so that heat is simply lost to the air around it.

1.3.2 Aerobic and anaerobic respiration

Aerobic respiration

1. Aerobic respiration is respiration that uses oxygen, and it is the pathway a cell uses whenever enough oxygen is reaching it.
2. The substrate is glucose, and because oxygen is available the glucose is broken down completely.
3. Complete breakdown means every carbon atom in the glucose ends up in carbon dioxide and every hydrogen atom ends up in water, so none of the chemical energy is left locked in a leftover molecule.
4. The word equation is glucose + oxygen $\to$ carbon dioxide + water.
5. The balanced symbol equation is $C_6{H}_{12}{O}_6+6O_2\to 6C{O}_2+6H_{2}O$.
6. Check the balancing by counting atoms: there are $6$ carbon, $12$ hydrogen and $18$ oxygen atoms on each side of the arrow.
7. The first steps take place in the cytoplasm, and the reactions that need oxygen are completed inside the mitochondria.
8. A cell with a heavy demand for ATP, such as a muscle fibre or a liver cell, is therefore packed with mitochondria.
9. Because the glucose is used up completely, aerobic respiration gives a large yield of ATP, roughly thirty molecules of ATP from each molecule of glucose.
10. Oxygen has to be delivered continuously by the blood, so the maximum rate of aerobic respiration is set by how fast the heart and lungs can supply it.

Anaerobic respiration in animal cells

1. Anaerobic respiration is respiration without oxygen, and an animal cell switches to it when oxygen is being used faster than the blood can deliver it.
2. The clearest example is a muscle during vigorous exercise, when the heart and lungs cannot keep up with the demand of the working fibres.
3. The substrate is still glucose, but without oxygen the glucose is broken down only incompletely.
4. The word equation is glucose $\to$ lactic acid.
5. All of these reactions happen in the cytoplasm, because the stages that use the mitochondria cannot run without oxygen.
6. The yield of ATP is small, only about two molecules of ATP per molecule of glucose, which is roughly fifteen times less than the aerobic pathway gives.
7. The yield is small because lactic acid still holds a great deal of unreleased chemical energy in its bonds.
8. The advantage of the pathway is speed, because it supplies ATP quickly enough to keep a muscle contracting during a short burst of hard effort.
9. The disadvantage is that lactic acid builds up in the muscle and the blood, causing muscle fatigue and pain, so the pathway can only be used for a short time.
10. The lactic acid is later broken down once oxygen is available again, which is why heavy breathing continues after the exercise has stopped.

Anaerobic respiration in plant and fungal cells

1. In plant cells and in fungi such as yeast, anaerobic respiration follows a different route and is called fermentation.
2. The conditions are the same, which is an absence of oxygen, and the substrate is again glucose broken down incompletely.
3. The word equation is glucose $\to$ ethanol + carbon dioxide.
4. These reactions also take place entirely in the cytoplasm, and the yield is the same small amount of about two molecules of ATP per glucose.
5. The energy that is not transferred stays locked in the bonds of the ethanol, which is why ethanol burns so readily.
6. Plant roots ferment when the soil becomes waterlogged, because water fills the air spaces and no oxygen can reach them.
7. Yeast ferments whenever it is sealed away from air, which is what makes it useful for making bread and for brewing.

Comparing the pathways

1. Conditions
   1. Aerobic respiration needs a supply of oxygen, while both forms of anaerobic respiration run only when oxygen is absent or in short supply.
2. Substrate
   1. All three pathways start with glucose, so the substrate is not what makes them different.
3. Extent of breakdown
   1. Aerobic respiration breaks the glucose down completely, whereas anaerobic respiration leaves an energy-rich product behind.
4. Products
   1. Aerobic respiration gives carbon dioxide and water, an animal cell respiring anaerobically gives lactic acid, and a plant or yeast cell gives ethanol and carbon dioxide.
5. Site in the cell
   1. Aerobic respiration begins in the cytoplasm and is completed in the mitochondria, while anaerobic respiration is confined to the cytoplasm.
6. Relative yield of ATP
   1. Aerobic respiration gives roughly thirty ATP per glucose and anaerobic respiration only about two, so the aerobic pathway is around fifteen times more productive.
7. A cell will always use the aerobic pathway when it can, because using glucose anaerobically wastes most of the energy the molecule holds.

1.3.3 Sugars and carbohydrates

Monomers and polymers

1. A monomer is a small molecule that can be joined to many others of the same kind, and a polymer is the long chain that results.
2. Cells build almost every large molecule this way, because it needs only a small set of subunits and one joining reaction to make an enormous variety of products.
3. A carbohydrate is a molecule made of carbon, hydrogen and oxygen only, and its monomers are simple sugars.
4. Glucose, the commonest of those sugars, has the formula $C_6{H}_{12}{O}_6$, so its ratio of carbon to hydrogen to oxygen is $1:2:1$.
5. Every carbohydrate keeps roughly that ratio, which is why carbohydrates hold so much oxygen compared with the other groups of biological molecule.
6. The same joining reaction builds a carbohydrate from sugars, and the reverse reaction takes it apart again when the cell needs the sugars back.

Sugars as the monomers of carbohydrates

1. A monosaccharide is a single sugar unit, and it is the monomer from which every carbohydrate is assembled.
2. Glucose, fructose and galactose are the monosaccharides you need to recognise, and all three share the formula $C_6{H}_{12}{O}_6$.
3. They share a formula but not a shape, because their atoms are arranged differently, so they taste different and enzymes treat them differently.
4. Glucose and galactose form six-sided rings while fructose forms a five-sided ring.
5. A plant cell makes its own glucose by photosynthesis, while an animal cell receives glucose from digested food carried in the blood.
6. A disaccharide is made when two monosaccharides are joined together.
7. Maltose is glucose joined to glucose, sucrose is glucose joined to fructose, and lactose is glucose joined to galactose.
8. Sucrose is the sugar a plant moves around in its phloem, and lactose is the sugar in milk.
9. Both monosaccharides and disaccharides are soluble in water and taste sweet, which is what everyday use of the word sugar refers to.

Building and breaking carbohydrates

1. A condensation reaction joins two sugars together and releases one molecule of water as the new bond forms.
2. The water comes from the two sugars themselves, because a hydrogen atom is taken from one and a hydroxyl group from the other.
3. Building a long chain means repeating that reaction, so joining $n$ monomers into one polymer releases $n-1$ molecules of water.
4. The reactions are controlled by enzymes and driven by energy from ATP, which is why a growing cell needs a fast supply of it.
5. Hydrolysis is the reverse reaction, in which a molecule of water is added at each bond to break the chain back into its monomers.
6. Hydrolysis is what happens when a carbohydrase enzyme digests a carbohydrate, so amylase hydrolyses starch and maltase hydrolyses maltose.
7. Hydrolysis is essential because a polymer is far too large to cross a cell membrane, while a single sugar is small enough to be absorbed.
8. Taken together, the two reactions let a cell store glucose safely when it is plentiful and release it again the moment it is needed.

The three polysaccharides

1. A polysaccharide is a carbohydrate polymer of many monosaccharides joined in a long chain.
2. Starch is the polysaccharide a plant uses to store glucose, and it is built from glucose monomers alone.
3. Its chains are coiled, and some of them branch, which packs a very large number of glucose units into a small space inside a cell.
4. Starch is insoluble, so it does not dissolve in the cytoplasm and does not draw water into the cell by osmosis the way stored glucose would.
5. A plant lays down starch in its leaves during the day and in storage organs such as potato tubers and seeds for the longer term.
6. Glycogen is the equivalent store in animals and fungi, and it is also built from glucose monomers alone.
7. Its chains are much more highly branched than those of starch, which means many chain ends are exposed at once.
8. Every exposed end is a place an enzyme can start hydrolysing, so glycogen can be broken back down to glucose very quickly when demand rises.
9. That matters because an animal can move suddenly and needs glucose released within seconds, which is why glycogen is stored in the liver and muscles.
10. Cellulose is not a store at all; it is a structural polysaccharide, and it too is built from glucose.
11. Its glucose units are joined so that the chains stay straight rather than coiling, and neighbouring chains are then cross-linked to one another.
12. Bundles of cross-linked chains form strong fibres that are laid down in layers to make the cell wall of a plant cell.
13. Those fibres are what let a plant cell resist the outward pressure of the water inside it without bursting, and what makes celery stringy and wood strong.
14. All three are made from the same monomer, so it is the arrangement of the chains, not the subunit, that decides what each polysaccharide can do.

1.3.4 Amino acids and proteins

Amino acids as the monomers of proteins

1. An amino acid is the monomer from which every protein is built, and a protein is the polymer that results from joining them.
2. Amino acids contain carbon, hydrogen, oxygen and nitrogen, and a few of them contain sulfur as well.
3. Nitrogen is what sets proteins apart from carbohydrates and lipids, which contain no nitrogen at all.
4. There are about twenty different amino acids available to a cell, and each one has a different side group attached to the same basic structure.
5. Because the basic structure is the same in every amino acid, any one of them can be joined to any other, in any order.
6. The sequence, meaning the order in which the amino acids are joined, is different for every different protein.
7. A short chain is called a polypeptide, and a protein is one or more of those chains folded into its finished shape.
8. Even a small protein of a hundred amino acids can be assembled in an almost unimaginable number of different orders, which is why one set of twenty monomers can build every protein a body needs.
9. A plant makes all its own amino acids by combining sugars with nitrates taken up from the soil, while an animal has to obtain most of its from protein in food.

Building and breaking proteins

1. Amino acids are joined by condensation reactions, and each new bond releases one molecule of water.
2. Joining $n$ amino acids into a single chain therefore forms $n-1$ bonds and releases $n-1$ molecules of water.
3. The joining happens on the ribosomes, and the energy needed for it comes from ATP supplied by respiration.
4. Hydrolysis breaks a protein back down, adding one molecule of water at each bond to release the individual amino acids again.
5. Protease enzymes hydrolyse the protein in food during digestion, because a whole protein molecule is far too large to be absorbed.
6. The amino acids released are absorbed into the blood and delivered to cells, which then join them together in a completely new order to build the proteins that body needs.
7. A protein eaten in a meal is therefore not used as it is; it is taken apart into its monomers and those monomers are reassembled.
8. Amino acids cannot be stored, so any that are surplus to requirements are broken down in the liver rather than kept for later.
9. Proteins in the body are also being hydrolysed and rebuilt all the time, which is why a steady supply of amino acids is needed even in an adult who is no longer growing.

Folding gives each protein its shape

1. Once the chain has been assembled it does not stay stretched out; it folds into a particular three-dimensional shape.
2. The folded shape is held in place by bonds between different parts of the same chain, formed wherever two side groups come close enough to attract one another.
3. Which side groups end up close together depends entirely on the sequence, so the sequence determines the shape.
4. A different sequence brings different side groups together, folds into a different shape, and therefore produces a protein that does a different job.
5. Most proteins work by binding to another molecule, and binding only happens when the two shapes are complementary, which means they fit together.
6. An enzyme is a protein whose folded shape leaves a pocket called the active site, and only a substrate with a matching shape will fit into it.
7. The same principle explains why an antibody binds to one pathogen and not another, and why a receptor in a cell membrane responds to one hormone only.
8. Structural proteins are shaped for strength instead of binding, which is how collagen makes tendons tough and keratin makes hair and nails hard.
9. Carrier proteins in a cell membrane are folded so that a channel runs right through them, which is what lets particular substances pass into and out of the cell.

What happens when a protein loses its shape

1. Denaturation is the permanent change in a protein's folded shape that happens when the bonds holding the fold together are broken.
2. A high temperature breaks those bonds because the chain vibrates so strongly that the weak attractions between side groups cannot hold.
3. An extreme pH breaks them because it changes the charge on the side groups, so groups that were attracting each other no longer do.
4. Once the fold is lost the chain takes up a different shape, and the binding site it used to carry no longer fits the molecule it was built for.
5. The sequence of amino acids is not affected, because the bonds joining the amino acids into a chain are much stronger than the ones holding the fold.
6. Denaturation is not reversible, so a denatured protein cannot be cooled or neutralised back into working order.
7. You see it happen every time an egg is fried, because the clear runny protein in the white turns solid and white as it denatures and does not turn back.

1.3.5 Fatty acids and lipids

The two building blocks of a lipid

1. A lipid is built from two different kinds of subunit, which makes it unlike a carbohydrate or a protein.
2. Glycerol is the small three-carbon molecule that acts as the backbone, and there is exactly one of it in every lipid molecule.
3. A fatty acid is a long chain of carbon and hydrogen atoms with an acid group at one end, and three of them are attached to each glycerol.
4. The ratio of subunits is therefore $1:3$, one glycerol to three fatty acids, and a lipid built this way is called a triglyceride.
5. Because there are two kinds of subunit rather than one repeating monomer, a lipid is not a polymer in the way that starch and a protein are.
6. A lipid molecule is also a fixed size, since it always contains four subunits, whereas a polymer chain can be any length.
7. Lipids contain carbon, hydrogen and oxygen like carbohydrates, but the long fatty acid chains hold a far smaller proportion of oxygen.
8. Less oxygen means more carbon to hydrogen bonds per molecule, and that is exactly why a lipid releases so much more energy per gram than a carbohydrate.
9. The three fatty acids attached to one glycerol do not have to be identical, which is one reason different lipids have different properties.

Building and breaking lipids

1. Each fatty acid is attached to the glycerol by a condensation reaction, and each of those reactions releases one molecule of water.
2. Since three fatty acids are attached to each glycerol, building one lipid molecule releases three molecules of water.
3. The reactions are controlled by enzymes and need energy from ATP, in the same way that building any large molecule does.
4. Hydrolysis reverses the process, adding one molecule of water at each of the three bonds to release the glycerol and the three fatty acids.
5. Lipase is the enzyme that hydrolyses lipids, and it does this in the small intestine so that the products are small enough to be absorbed.
6. Once absorbed, the fatty acids and glycerol are rejoined to build the particular lipids that body needs, including the lipids of its cell membranes.
7. A cell also hydrolyses its own stored lipid whenever it needs the energy, releasing fatty acids that can be respired.
8. This is why a body that has used up its stored carbohydrate begins to lose stored fat instead.

What cells use lipids for

1. A lipid is a concentrated energy store, releasing roughly twice as much energy per gram as a carbohydrate does.
2. That matters for an animal that has to carry its store around, because the same amount of energy can be stored in half the mass.
3. Lipids are also insoluble in water, so a large store can sit in a cell without dragging water in by osmosis.
4. A layer of fat under the skin gives thermal insulation, because fat conducts heat poorly and so slows the rate at which heat is lost.
5. Fat packed around organs such as the kidneys and the heart acts as protection, cushioning them against knocks.
6. Lipids form part of every cell membrane, which is why even a cell that stores no fat at all still has to make them.
7. Plant seeds store lipid rather than starch when they need a compact energy reserve, which is why sunflower and rapeseed are pressed for oil.

Saturated and unsaturated fatty acids

1. The three fatty acids attached to the glycerol can be saturated or unsaturated, and this changes the properties of the whole lipid.
2. A saturated fatty acid has no carbon to carbon double bonds in its chain, so every carbon holds as many hydrogen atoms as it can.
3. With no double bonds the chain stays straight, so neighbouring molecules pack closely together and attract one another strongly.
4. Close packing means more energy is needed to separate the molecules, so lipids rich in saturated fatty acids are usually solid fats at room temperature.
5. An unsaturated fatty acid has one or more carbon to carbon double bonds, written as $C=C$.
6. Each double bond puts a kink in the chain, which stops the molecules packing neatly and weakens the attraction between them.
7. Loose packing means less energy is needed to separate them, so lipids rich in unsaturated fatty acids are usually liquid oils at room temperature.
8. Saturated fatty acids come mainly from animal sources such as butter, cheese, lard and fatty meat.
9. Unsaturated fatty acids come mainly from plant and fish sources such as olive oil, sunflower oil, nuts and oily fish.
10. Both kinds are still lipids, so both release about the same amount of energy per gram when they are respired.