1.2.1 Structure of DNA

DNA stores the genetic information of a cell

1. DNA stands for deoxyribonucleic acid, and it is the chemical that stores the genetic information of a living organism.
2. In an animal or plant cell, almost all of the DNA is held inside the nucleus, packaged into thread-like structures called chromosomes.
3. The information is stored as a chemical code written along the length of the molecule.
4. The cell reads that code to build proteins, and the proteins it builds decide what the cell is able to do.
5. Every body cell of an organism contains the same DNA, so the same complete set of instructions is available in each one.

DNA is a polymer built from nucleotides

1. A polymer is a long molecule made by joining many small repeating units, called monomers, into a chain.
2. The monomer of DNA is a nucleotide, so DNA is described as a polymer of nucleotides.
3. Each nucleotide is made of three parts joined together: a sugar, a phosphate group and one base.
4. The sugar and the phosphate group are identical in every nucleotide, which is what makes them the repeating part of the chain.
5. The base is the only part that varies, and there are four bases to choose from: $A$, $C$, $G$ and $T$.
6. Nucleotides join into a chain when the sugar of one nucleotide bonds to the phosphate group of the next.
7. This alternating run of sugars and phosphate groups is the sugar-phosphate backbone, and it forms the outside edge of the strand.
8. One base is attached to each sugar along the backbone, and every base points sideways, off the edge of the chain.
9. A single strand of DNA is therefore a backbone with a row of bases hanging from it, and the order of those bases is the coded information.

Two strands twist together into a double helix

1. A complete DNA molecule is made of two strands, not one.
2. The two strands lie alongside each other with their backbones on the outside and their bases pointing inwards, towards the other strand.
3. Each base on one strand lines up with a base on the other strand, and the two joined bases are called a base pair.
4. The base pairs act as the rungs of a ladder, holding the two backbones a fixed distance apart along the whole length of the molecule.
5. The bonds holding each base pair together are weak, so the two strands can be separated when the cell needs to read or copy the code, then joined again afterwards.
6. The two strands are also twisted around each other into a spiral, and this two-stranded spiral shape is the double helix.
7. The two strands run in opposite directions to each other, which is why a flat diagram of DNA shows one strand drawn the other way up.
8. Winding the molecule into a helix keeps a very long chain compact enough to fit inside a nucleus and holds the bases protected in the middle.

1.2.2 Nucleotides and complementary bases

There are four different nucleotides

1. All four nucleotides in DNA share the same sugar and the same phosphate group.
2. The one part that differs between them is the base attached to the sugar.
3. The four bases are adenine ($A$), thymine ($T$), cytosine ($C$) and guanine ($G$).
4. Because there are four possible bases, there are exactly four different nucleotides, and DNA is built from those four alone.
5. A strand of DNA is a chain of these four nucleotides in a particular order, and that order is what carries the coded information.
6. A single gene can be thousands of nucleotides long, so the number of possible orders is enormous, which is how a four-letter alphabet codes for every protein an organism makes.

Bases join in fixed complementary pairs

1. The bases on the two strands are not paired at random, they follow a fixed rule called complementary base pairing.
2. Adenine always pairs with thymine, written as the pair $A$ and $T$.
3. Cytosine always pairs with guanine, written as the pair $C$ and $G$.
4. Each base pair is held together by weak hydrogen bonds that form across the middle of the molecule.
5. One hydrogen bond on its own is easily broken, but a DNA molecule contains millions of them, so together they hold the two strands firmly.
6. Every pair contains one larger base and one smaller base, so each rung of the ladder is the same width and the helix keeps a constant shape along its length.
7. A pairing such as $A$ with $G$ never happens, because the shapes of those two bases do not fit together across the gap.

One strand sets the sequence of the other

1. Because the pairing rule is fixed, knowing the base order of one strand tells you the base order of the other.
2. To work out the partner strand, replace every $A$ with $T$, every $T$ with $A$, every $C$ with $G$ and every $G$ with $C$.
3. The two strands are called complementary because each is the matching partner of the other, not an identical copy of it.
4. This also means the amount of $A$ in a DNA molecule always equals the amount of $T$, and the amount of $C$ always equals the amount of $G$.
5. When the hydrogen bonds break and the strands separate, each exposed strand can act as a template, because the pairing rule leaves only one possible partner for each base.
6. Fixed pairing is therefore what lets the base sequence be rebuilt without error whenever the molecule is copied or read.

1.2.3 Protein synthesis

Protein synthesis happens in two stages

1. A gene is a section of DNA that carries the code for one protein, and that code is simply the order of the bases along the gene.
2. Protein synthesis is the process that turns that coded order into an actual protein molecule.
3. The DNA itself never leaves the nucleus, because the molecule is far too large to pass out through the pores in the nuclear membrane.
4. Proteins are assembled at ribosomes out in the cytoplasm, so a copy of the gene has to be carried from the nucleus to the ribosome.
5. That need for a copy is why the process is split into two stages: transcription in the nucleus, then translation in the cytoplasm.
6. Only the genes a cell currently needs are used, which is why a muscle cell and a liver cell carry identical DNA but build very different sets of proteins.

Transcription copies the gene into mRNA

1. Transcription begins when the DNA unzips along the length of the gene that is being used.
2. The weak hydrogen bonds between the base pairs break, the two strands come apart, and the bases of the gene are left exposed.
3. The enzyme RNA polymerase attaches at the start of the gene and moves along one of the exposed strands, which acts as the template.
4. Free RNA nucleotides floating in the nucleus line up against the template strand by complementary base pairing, so the copy matches the gene base for base.
5. RNA carries the base uracil ($U$) in place of thymine, so a $T$ appears as a $U$ in the copy while $A$, $C$ and $G$ stay the same.
6. RNA polymerase joins the lined-up nucleotides into one continuous strand of messenger RNA (mRNA).
7. When the end of the gene is reached the mRNA is released, and the two DNA strands pair up again so the gene is left undamaged.
8. The mRNA is short and single-stranded, so unlike the DNA it is small enough to pass out through a nuclear pore into the cytoplasm.

Translation builds the protein at a ribosome

1. Out in the cytoplasm the mRNA attaches to a ribosome, which grips the strand between its two halves.
2. The ribosome reads the mRNA in groups of three bases at a time, working steadily from one end of the strand to the other.
3. Transfer RNA (tRNA) molecules in the cytoplasm collect amino acids and carry them to the ribosome.
4. Each tRNA carries one particular amino acid and can only slot into the ribosome opposite the group of three mRNA bases that matches it.
5. The ribosome joins each delivered amino acid onto the end of the growing chain, then moves on to the next group of three bases.
6. The empty tRNA leaves the ribosome, picks up another amino acid of the same type and is used again.
7. Because the tRNA molecules can only bind where they match, the amino acids are joined in exactly the order set out by the mRNA.
8. When the ribosome reaches a stop signal at the end of the mRNA, the finished chain of amino acids is released.
9. The released chain then folds up into a particular three-dimensional shape, and the folded chain is the finished protein.

1.2.4 DNA structure and the proteins made

Three bases code for one amino acid

1. The bases along a gene are read in groups of three, and each group of three is called a triplet.
2. Every triplet stands for one amino acid, and this rule is known as the triplet code.
3. The triplets are read in order from one end of the gene to the other, so the order of the triplets fixes the order in which the amino acids are joined.
4. Reading in threes gives $4\times 4\times 4=64$ possible triplets, which is comfortably more than the $20$ amino acids used to build proteins.
5. Reading in pairs would give only $4\times 4=16$ combinations, which is too few, and that is why the code works in threes rather than twos.
6. Because there are more triplets than amino acids, several different triplets can stand for the same amino acid.
7. A few triplets code for no amino acid at all and act as a stop signal, marking the end of the chain.
8. The number of amino acids in a protein is therefore the number of coding bases in the gene divided by three.

Amino acid order sets shape, and shape sets function

1. The amino acids are joined into a long chain in the exact order the gene specifies.
2. There are $20$ different amino acids, and each has its own chemical properties, so different parts of the chain attract or repel each other.
3. Those attractions pull the chain into a folded, three-dimensional shape.
4. The same order of amino acids always produces the same pattern of attractions, so the chain always folds into the same shape.
5. A protein can only do its job if it has the correct shape, so the shape of a protein determines its function.
6. An enzyme works because the folding leaves a pocket whose shape matches the molecule it acts on.
7. A structural protein such as collagen works because its chains fold into long, strong fibres that hold tissues together.
8. A hormone such as insulin works because its shape fits the receptor on the cells it acts on.
9. Antibodies and the carrier proteins in a cell membrane work in the same way, each with a shape suited to the one job it does.

A change in the bases can change the protein

1. A mutation is a change in the base sequence of DNA, and because the bases are the code, changing them can change the message.
2. If one base is swapped for another, only the triplet containing it changes, so at most one amino acid in the chain is replaced.
3. If a base is removed instead, every base after it shifts along, so all the triplets from that point on are grouped differently and most of the remaining amino acids change.
4. A different amino acid brings different attractions into the chain, so the chain can fold into a different shape.
5. Once the shape is wrong, the protein works less well or stops working altogether.
6. In an enzyme, a change to the shape of the pocket can mean the molecule it normally acts on no longer fits, so that reaction is no longer speeded up.
7. In a structural protein, a change to the shape can weaken the fibre it forms, so the tissue it supports is weaker.
8. Many changes to the bases have no effect at all, either because the new triplet codes for the same amino acid or because the change falls in DNA that does not code for a protein.
9. A change can also fall in a part of the DNA that switches a gene on or off, in which case the protein itself is normal but the amount of it produced changes.

1.2.5 Investigating enzymatic reactions

Measuring the rate of an enzyme-controlled reaction

1. An enzyme investigation is followed either by measuring how quickly the substrate disappears or by measuring how quickly a product appears.
2. For amylase, the substrate is starch, and starch is detected with iodine solution, which turns blue-black when starch is present and stays orange-brown when it is not.
3. The moment the iodine first stays orange-brown is the end point, because all the starch has by then been broken down into sugars.
4. For catalase, the substrate is hydrogen peroxide and one product is oxygen gas, so the reaction is followed by collecting the gas given off: $2{\mathrm{H}}_2{\mathrm{O}}_2\to 2{\mathrm{H}}_2\mathrm{O}+{\mathrm{O}}_2$.
5. When the measurement is a time taken for the reaction to finish, the rate is the reciprocal of that time, $rate=\frac{1}{t}$.
6. Multiplying by a constant such as $1000$ gives easier numbers to plot, $rate=\frac{1000}{t}$, and does not change the shape of the graph.
7. When the measurement is a volume of gas, the rate is the volume divided by the time, $rate=\frac{V}{t}$, in $\mathrm{c}{\mathrm{m}}^3{\mathrm{s}}^{-1}$.
8. A shorter time therefore means a faster rate, so a graph of time against temperature and a graph of rate against temperature are opposite shapes.
9. The value of the independent variable that gives the highest rate is the optimum.

Setting up a fair test of temperature and pH

1. The factor you deliberately change is the independent variable, and the thing you measure is the dependent variable.
2. Everything else that could affect the rate is a control variable and must be kept the same, otherwise you cannot tell which factor caused the change.
3. The control variables in an enzyme investigation are the concentration and volume of the enzyme, the concentration and volume of the substrate, and whichever of temperature and pH you are not changing.
4. Temperature is controlled with a water bath, which holds the tubes steady at a set value far better than leaving them on the bench.
5. pH is controlled with a buffer solution, which resists changes in pH as the reaction proceeds.
6. The enzyme and the substrate are left in the water bath in separate tubes before they are mixed, so that the reaction starts at the temperature being tested.
7. Each value of the independent variable is repeated at least three times and a mean is calculated, which reduces the effect of random error.
8. A reading that sits well away from the others is an anomaly, and it is left out of the mean and, where possible, repeated rather than simply ignored.

Reading the results and improving the method

1. A graph of rate against temperature rises to a peak at the optimum and then falls away steeply, so the curve is not symmetrical.
2. The steep fall after the peak is caused by denaturation, in which the enzyme loses its folded shape and the substrate can no longer bind.
3. Denaturation is not reversed by cooling the mixture down again, so a tube taken above the optimum stays slow for the rest of the run.
4. Read the optimum from the peak of the curve rather than from the highest point you happened to test, because the true optimum can lie between two of your temperatures.
5. Judging the colour change by eye is a source of error, because different people call the end point at slightly different moments.
6. Sampling every $30\mathrm{s}$ means the true end point lies somewhere inside the last interval, so taking samples every $10\mathrm{s}$ improves the precision.
7. A colorimeter removes the personal judgement altogether, because it measures the colour of the mixture as a number.
8. Testing more values close to the peak gives a better estimate of the optimum than spreading the same number of readings across a wide range.

1.2.6 Mechanism of enzyme action

Enzymes are the biological catalysts of metabolism

1. Every chemical reaction needs a certain amount of energy before it will start, and at body temperature most reactions in a cell would run far too slowly to keep the organism alive.
2. A catalyst speeds a reaction up by lowering the energy needed to start it, and it is not used up, so the same molecule works over and over again.
3. An enzyme is a protein that acts as a biological catalyst, which means it is a catalyst made by and working inside a living organism.
4. Metabolism is the whole set of chemical reactions taking place in a cell, and almost every one of them is controlled by its own enzyme.
5. Enzymes let a cell run those reactions quickly at about $37{}^{\circ }\mathrm{C}$, instead of needing the high temperatures a chemist would use to force the same reaction along.
6. Some enzymes catalyse breaking-down reactions, splitting one large molecule into smaller ones, as happens when a sugar such as maltose is broken into glucose.
7. Others catalyse building-up reactions, joining small molecules into a larger one, as happens when glucose molecules are joined to make starch in a plant cell.
8. Because enzymes are proteins, they are themselves built by protein synthesis, so the genes a cell uses decide which reactions that cell can carry out.

The substrate binds to the active site

1. Every enzyme has a pocket in its surface called the active site, which is formed by the way its chain of amino acids folds up.
2. The molecule an enzyme acts on is called its substrate.
3. Enzyme and substrate molecules move about randomly in solution, so a reaction can only begin when the two collide.
4. If the substrate hits the active site the right way round, it binds and forms an enzyme-substrate complex.
5. Holding the substrate in the active site puts strain on its bonds, and in a building-up reaction it holds two substrate molecules side by side in exactly the right position.
6. Either way, less energy is needed for the reaction to happen, which is how the enzyme speeds it up.
7. The reaction takes place while the substrate is held, turning it into the products.
8. The products have a different shape from the substrate, so they no longer fit the active site and are released into the solution.
9. The enzyme itself is left completely unchanged, so its active site is free at once to bind another substrate molecule.
10. This is why a cell needs only a small quantity of each enzyme, since one molecule can catalyse the same reaction thousands of times.

Specificity comes from the shape of the active site

1. The lock and key hypothesis explains enzyme action by treating the active site as a lock and the substrate as the only key that fits it.
2. The shape of the active site is complementary to the shape of the substrate, meaning the two match each other the way a hand matches a glove.
3. Only a substrate with the matching shape can bind, so each enzyme catalyses just one reaction, and this is called specificity.
4. A molecule of the wrong shape cannot enter the active site, so no complex forms and the enzyme has no effect on it.
5. Amylase breaks starch down into sugars, and it has no effect on protein or fat.
6. Protease breaks protein down into amino acids by splitting the bonds between them.
7. Lipase breaks lipids down into fatty acids and glycerol.
8. Because every reaction has its own enzyme, a cell controls which reactions run simply by controlling which enzymes it makes and where it puts them.

Temperature, pH and concentration change the rate

1. Raising the temperature gives the enzyme and substrate molecules more kinetic energy, so they move faster, collide more often and collide harder.
2. More successful collisions with the active site means more enzyme-substrate complexes form each second, so the rate rises.
3. Above the optimum temperature the enzyme vibrates so strongly that the bonds holding its folded shape break, and the active site changes shape.
4. The enzyme is then denatured, the substrate no longer fits, and the rate falls steeply and does not recover when the mixture is cooled again.
5. Most human enzymes have an optimum close to $37{}^{\circ }\mathrm{C}$ and are denatured above roughly $50$ to $60{}^{\circ }\mathrm{C}$.
6. Moving the pH away from the optimum changes the charges on the amino acids that hold the active site in shape, so the site is distorted and eventually denatured.
7. A pH graph therefore has a peak at the optimum with the rate falling away on both the acidic and the alkaline side.
8. Different enzymes have different optimum pH values to suit where they work, so amylase in the mouth works best near pH $7$ while pepsin in the acidic stomach works best at about pH $2$.
9. Increasing the substrate concentration increases the rate, because collisions between substrate molecules and active sites become more frequent.
10. Once every active site is occupied the rate levels off, because the number of enzyme molecules has become the limiting factor and extra substrate has to wait.
11. Increasing the enzyme concentration increases the rate, because there are more active sites available for the substrate to collide with.
12. If the substrate then runs short the rate levels off again, because the substrate has become the limiting factor instead.