HookThe bear that spent a century disguised as a raccoon
For more than a century, zoologists could not agree what the giant panda was. It ate bamboo like a raccoon, had a skull and teeth some read as raccoon-like, and even a strange extra 'thumb' — yet it lumbered like a bear. The great naturalists filed it one way, their rivals filed it another, and the textbooks kept changing their minds. The argument was not settled by another look at the bones. In 1985 the geneticist Stephen O'Brien compared the panda's DNA and its proteins against those of bears and raccoons, and the molecules were decisive: the panda sits firmly among the bears, having branched off around nineteen million years ago. Anatomy had bickered for a hundred years; a genetic comparison ended it in a single study.
That is the shape of the whole of section 3.4. Life stores its information as a sequence of DNA bases, reads that sequence into proteins, and copies it imperfectly — and every imperfection, reshuffled by meiosis and multiplied by random fertilisation, is raw material. Natural selection then edits the raw material into adaptation, and the differences that accumulate let us define species and reconstruct how they are related. You will learn how the triplet code works, how a gene becomes a protein, where new variation comes from, how selection shapes populations, how we classify a species, and — with real arithmetic — how to measure the diversity of an entire community.
ModelThe triplet code and how a genome is packaged
A gene is a base sequence of DNA that codes for the amino acid sequence of a polypeptide, or for a functional length of RNA. Its position on a chromosome is its locus. The code is read in triplets: three DNA bases (a codon, once written on mRNA) specify one amino acid. Three features are examinable and each earns a mark by name. The code is a triplet code — three bases per amino acid; it is degenerate — most amino acids have more than one triplet, because four bases give 4×4×4 = 64 triplets for only 20 amino acids; it is non-overlapping — each base is read once, in a single triplet; and it is universal — the same triplet codes the same amino acid in almost every organism, which is precisely why the panda's genes can be compared with a bear's at all.
Packaging differs between cell types, and the differences are marked. In a eukaryote the DNA is long, linear and wound around histone proteins to form chromosomes; the coding sequences (exons) are interrupted by non-coding sequences (introns), with further non-coding repeats between genes. In a prokaryote the DNA is shorter, circular and not associated with histones, and it contains no introns. The DNA inside mitochondria and chloroplasts is circular and histone-free too — a clue to their bacterial ancestry. A pair of homologous chromosomes carry the same genes at the same loci, but possibly different alleles — versions of a gene that differ in base sequence.
A length of mature mRNA is 300 nucleotides long and includes one stop codon. What is the longest polypeptide it can encode? Every amino acid is specified by three bases, so there are 300 ÷ 3 = 100 triplets; one is a stop signal coding for no amino acid, leaving at most 99 amino acids. The trap runs the other way too: a 99-amino-acid protein needs at least 99 × 3 = 297 coding bases plus a stop — and, in a eukaryotic gene, extra bases again for the introns that are spliced out before this mRNA ever exists.
MechanismFrom gene to protein: transcription and translation
In transcription, the enzyme RNA polymerase binds and unwinds the DNA, and one strand acts as the template (antisense) strand. Free RNA nucleotides pair with the exposed template bases — adenine with uracil, since RNA carries uracil in place of thymine, and guanine with cytosine — and RNA polymerase joins them into messenger RNA (mRNA). In a eukaryote the first product is pre-mRNA; splicing then removes the introns and joins the exons to make mature mRNA. A prokaryote has no introns, so its mRNA needs no splicing.
In translation, the mRNA leaves the nucleus and attaches to a ribosome. Transfer RNA (tRNA) molecules, each carrying a specific amino acid and bearing a three-base anticodon, pair their anticodon with the complementary mRNA codon. The ribosome moves codon by codon, catalysing a peptide bond between adjacent amino acids, with ATP supplying the energy; at a stop codon the finished polypeptide is released. Because the code is degenerate, a substitution in the third base of a triplet frequently changes nothing — a fact that matters the moment we turn to mutation.
Transcribe and translate a short gene. A DNA template strand reads 3'–TAC GGA AAT–5'. Pairing each base (A–U, T–A, G–C, C–G) builds the mRNA 5'–AUG CCU UUA–3'. The matching tRNA anticodons are therefore 3'–UAC GGA AAU–5'. AUG is the start codon, so three DNA triplets give three mRNA codons and a chain of three amino acids — the one-to-one bookkeeping that base-sequence questions reward. Change the middle base of that first triplet and you change the amino acid; change the third base of many triplets and, because the code is degenerate, often nothing happens at all.
MechanismWhere variation comes from: mutation and meiosis
A gene mutation is a change in the base sequence of DNA. A substitution swaps one base for another and, thanks to the degenerate code, may be silent (no change to the amino acid), missense (one amino acid changed), or nonsense (a premature stop). Deletion and insertion are more destructive: they shift the reading frame so that every triplet downstream is misread — a frameshift. Mutations arise spontaneously during DNA replication, and their rate is raised by mutagens such as ultraviolet light, X-rays and certain chemicals.
Sexual reproduction adds variety without any new mutation, through meiosis and random fertilisation. Meiosis is two divisions that halve the chromosome number to make haploid gametes, and two events shuffle the alleles. Independent segregation lines up each homologous pair and separates it independently of every other pair; crossing over lets homologous chromosomes exchange sections, recombining alleles along a chromosome. Then random fertilisation of any gamete by any other multiplies the variety yet again.
How much variety can meiosis and fertilisation create? With a human haploid number of 23, each homologous pair can line up two ways at metaphase, so independent segregation alone gives \(2^{23} = 8\,388\,608\) — over eight million genetically different gametes, before crossing over adds any more. Random fertilisation then pairs any one gamete with any of a partner's, giving \(2^{23} \times 2^{23} \approx 7.0 \times 10^{13}\) possible zygotes from a single couple. That is why siblings differ, and why sexual reproduction generates variation far faster than mutation alone.
CaseNatural selection and the shapes of adaptation
Genetic diversity — the number of different alleles in a population — is the raw material of evolution: the more alleles present, the more a population can respond when conditions change. A selection pressure, such as a predator, a drought or an antibiotic, means some alleles confer better survival and reproduction, so the individuals carrying them leave more offspring and the allele frequency shifts over generations. This is natural selection, and it comes in patterns. Directional selection favours one extreme and shifts the mean — antibiotic resistance in bacteria is the classic case. Stabilising selection favours the middle and trims both extremes, reducing variation — human birth mass sits near an optimum, with very small and very large babies historically at higher risk.
Adaptations — features raised in frequency by selection — come in three kinds the examiner expects you to name. Anatomical adaptations are structures, like the thick blubber of a seal; physiological adaptations are working processes, like an enzyme that breaks down an antibiotic; behavioural adaptations are actions, like a woodlouse sheltering under damp bark by day. Diversity can also be lost. A genetic bottleneck or founder effect strips alleles from a population — the cheetah, squeezed through a near-extinction, is now so genetically uniform that unrelated individuals will accept skin grafts from one another. Selective breeding narrows a gene pool in exactly the same way, only on purpose.
CaseTesting antimicrobials with aseptic technique — Required practical 6
Antibiotic resistance is natural selection you can culture on a plate, and Required practical 6 measures how well a substance kills microbes — using aseptic technique so that only your chosen microbe grows. You sterilise the inoculating loop in a Bunsen flame, work in the rising air current close to the flame, flame the neck of every bottle, and lift the Petri dish lid only at a shallow angle, just enough to work. A known volume of bacterial culture is spread over sterile agar to make an even lawn; paper discs soaked in different antimicrobials — or in different concentrations of one — are placed on the surface; and the dish is taped (but not sealed all the way round, which would favour anaerobic pathogens), stored inverted and incubated at no more than 25°C in a school laboratory to avoid culturing organisms that thrive at body temperature.
Each effective disc leaves a zone of inhibition — a clear ring where microbes cannot grow — and its size measures potency. The independent variable is the type or concentration of antimicrobial; the dependent variable is the size of the zone; and you must control the volume and age of the culture, the depth of the agar, the disc diameter, the temperature and the incubation time so the comparison is fair. The reliable measurement is the zone's area, not its diameter: measure the diameter across two or three axes and average, because zones are rarely perfect circles, and remember that area scales with the square of the radius, so a small error in diameter is magnified.
Two antibiotics are tested against the same lawn of bacteria. Disc A leaves a clear zone 18 mm across; disc B a zone 12 mm across. How much better is A?
Convert each diameter to a zone area with \(A = \pi r^2\). Disc A has radius 9 mm, so \(A = \pi \times 9^2 = 254\ \text{mm}^2\). Disc B has radius 6 mm, so \(A = \pi \times 6^2 = 113\ \text{mm}^2\).
By area, A is not 1.5 times better (the ratio of the diameters) but \(254 \div 113 = 2.25\) times better, because a zone's area grows with the square of its radius. Always compare areas, average two or three diameters per zone, and keep the agar, culture volume and temperature identical — otherwise the difference you record is not the antibiotic's doing.
ModelWhat counts as a species, and how we sort them
A species is a group of organisms that can breed together to produce fertile offspring — the reason a horse and a donkey are separate species, since their offspring, the mule, is sterile. Species are named by the binomial system: genus then species, as in Homo sapiens, always latinised. Members of a species must be able to find and recognise a mate, which is the work of courtship behaviour. Courtship lets an animal recognise its own species (so gametes are not wasted on a doomed hybrid), identify a mate that is sexually mature and receptive, stimulate the release of gametes, form a pair bond, and synchronise mating — and the more elaborate the display, the more reliably it separates one species from a close relative.
Classification arranges species into a nested hierarchy — domain, kingdom, phylum, class, order, family, genus, species — with no overlap between groups. Modern classification is phylogenetic: it groups organisms by evolutionary relationship, so the arrangement is meant to mirror the actual tree of descent. The broadest level, the three domains — Bacteria, Archaea and Eukarya — was proposed by Carl Woese in the 1970s from differences in ribosomal RNA, molecular evidence overturning a classification that had rested on appearance alone, exactly as it did for the panda.
DataMeasuring a community: the index of diversity
Counting how many species live somewhere — species richness — misses something important: a wood with one dominant tree and a scatter of rarities is less diverse than a wood in which every species is common, even if both list the same number of species. An index of diversity fixes this by weighting abundance as well as richness. AQA uses
\[ D = \frac{N(N-1)}{\sum n(n-1)} \]
where \(N\) is the total number of organisms of all species and \(n\) is the number of each individual species. A larger \(D\) means greater diversity, and greater diversity generally means a more stable community — one better able to withstand a disease or a hard winter.
This is why the spread of monoculture farming matters. Clearing hedgerows to plant a single crop replaces a mixed community with a near-single-species one; the index collapses, and with it the food web that depended on the hedge. Conservation and food production pull against each other here, and the diversity index is how the argument is quantified rather than merely asserted.
Two woodlands each hold 35 ground-flora plants across four species. Wood X has 20, 8, 5 and 2 individuals; Wood Y has 30, 3, 1 and 1. Same richness, same total \(N\) — so are they equally diverse?
For both, \(N(N-1) = 35 \times 34 = 1190\).
Wood X: \(\sum n(n-1) = (20\times19)+(8\times7)+(5\times4)+(2\times1) = 458\), giving \(D = 1190 \div 458 = 2.6\).
Wood Y: \(\sum n(n-1) = (30\times29)+(3\times2)+0+0 = 876\), giving \(D = 1190 \div 876 = 1.4\).
Wood X is nearly twice as diverse, even though both woods hold the same number of species and the same number of plants — because X's individuals are spread evenly while Y is dominated by one species. Quote \(D\) as a bare number; it has no units.
MechanismComparing organisms: from appearance to DNA
Biologists once judged relationships by observable characteristics — count the petals, measure the skull — but appearances mislead: they are shaped by the environment as well as by genes, and two unrelated species can converge on the same look. So we now compare the molecules themselves. The strongest evidence is the base sequence of DNA, supported by the base sequence of mRNA and the amino acid sequence of proteins: the more similar two species' sequences, the more recently they shared a common ancestor. Because the genetic code is universal, these comparisons work across the whole tree of life — which is exactly how the panda was finally placed among the bears.
The same tools measure diversity within a species. Genetic diversity can be quantified as the proportion of genes that are polymorphic (have more than one allele in the population) or the proportion of loci at which a typical individual is heterozygous. For observable variation you take a representative sample, measure a characteristic, and describe it with a mean and a standard deviation — the latter telling you how spread out the values are about the mean. Two populations can share a mean yet differ sharply in their standard deviation, and that spread is itself part of their diversity.
VocabularyKey terms the mark scheme pays for
TrapsMisconceptions that cost marks
ExamWhat examiners want
Definitions here are marked to the word. A species is not 'animals that look alike' but organisms that breed to give fertile offspring; the genetic code earns marks only when you name it as triplet, degenerate and non-overlapping, and you should say why degeneracy matters — that a substitution is often silent. Keep the confusable pairs straight: exon and intron, codon and anticodon, gene and allele. Muddling them is the commonest way marks leak away in this section.
At least 10% of the marks on the paper are mathematical, and much of that quota lives here. Practise the diversity index until the \(N(N-1)\) over \(\sum n(n-1)\) structure is automatic, show the substitution, and quote \(D\) as a unitless number. For variation from meiosis, the \(2^n\) rule and its combination with random fertilisation is a standard calculation; in required practical 6, convert zone diameters to areas with \(\pi r^2\) and control the obvious variables.
The six-mark 'explain how a population becomes adapted' answer is a chain, and AQA awards the higher levels to a logical, connected line of reasoning: existing genetic variation arising from mutation, a named selection pressure, differential survival and reproduction, a rise in the frequency of the advantageous allele, and repetition over many generations. Anchor any evaluation in evidence — molecular sequence data outrank appearance because they are not swayed by the environment — and you will reach the top band. This is prime synoptic material, so expect to connect it to DNA structure, enzymes and biodiversity rather than recall it in isolation.