Per disputationem veritatem quaerimusDNA, genes and chromosomes
DNA packaging into chromosomes 3.4.1
- Diploid (2n): two complete chromosome sets, one from each parent, as homologous pairs (human somatic cells). Haploid (n): one complete set (gametes, produced by meiosis).
- A human somatic cell has 23 pairs of homologous chromosomes (46 total) — 22 pairs of autosomes, plus one pair of sex chromosomes (XX female, XY male).
- Chromosome number equals DNA molecule number only in G1/G0 of the cell cycle; from S phase to anaphase, every chromosome is temporarily two sister chromatids (two DNA molecules) joined at a centromere.
- A chromosome is DNA complexed with histone proteins (in eukaryotes) to form chromatin — DNA winds around histone cores, and this coiling is itself further coiled and condensed to package a very long DNA molecule into a structure that fits inside the nucleus.
- Each chromatid contains one long, linear, double-stranded DNA molecule — the double helix itself is not further modified by packaging, only wound up more and more tightly around and between histone proteins.
Genes, loci and gene products 3.4.1
- Gene: a DNA sequence coding for a specific polypeptide or functional RNA. Allele: one alternative version of a gene, differing in base sequence at one or more points. Locus: the fixed position a gene occupies on a chromosome.
- Genome: an organism's complete genetic material. Proteome: its complete set of expressed proteins — the two are not in a fixed one-to-one relationship, since not all DNA codes for protein and different cell types express different subsets of an identical genome.
- Homologous chromosomes carry the same genes at the same loci, but not necessarily the same alleles at each locus — one homologue (maternal) may carry a different allele from the other (paternal) at a given gene.
- A gene can encode either a polypeptide (via mRNA and translation) or a functional RNA molecule directly (e.g. tRNA or rRNA, which are never translated at all) — 'coding DNA' does not mean 'codes for protein' in every case.
- The genetic code is a triplet code (three DNA bases specify one amino acid), is degenerate (most amino acids are specified by more than one triplet — e.g. both GCT and GCC code for alanine), is non-overlapping (each base is read as part of exactly one triplet), and is nearly universal across almost all known organisms.
- A single gene's pre-mRNA can itself be spliced differently in different tissues (alternative splicing), so the genome stays constant across almost all of an organism's cells while the proteome varies with cell type, developmental stage and environmental conditions.
Gene organisation in the genome 3.4.1
- Exon: a coding (or untranslated-region-carrying) sequence within a gene that is retained in mature mRNA. Intron: a non-coding sequence within a gene that is removed from the RNA transcript during splicing.
- A eukaryotic gene is not one uninterrupted coding sequence — it comprises exons interspersed with introns, plus non-coding repeat sequences elsewhere in the genome.
- Introns remain physically present in the genomic DNA at all times; they are removed only from the RNA transcript, during splicing, on the way to producing mature mRNA — the DNA sequence itself is never edited.
- Exons are not necessarily entirely protein-coding either: an exon can include untranslated regions (before the start codon or after the stop codon) alongside its protein-coding portion.
- Non-coding DNA more broadly includes regulatory sequences that control whether and how much a gene is transcribed, in addition to introns — 'non-coding' does not mean 'functionless'.
DNA in prokaryotes, mitochondria and chloroplasts 3.4.1
- Bacterial DNA is a single circular chromosome, free in the cytoplasm — no nuclear envelope encloses it, and it is not wound around histone proteins as eukaryotic nuclear DNA is (though other DNA-binding proteins are present).
- Mitochondria and, in plants, chloroplasts each carry their own small circular genome, structurally resembling bacterial DNA rather than eukaryotic nuclear DNA — strong evidence for the endosymbiotic theory that both organelles evolved from free-living prokaryotes.
- Mitochondrial (and chloroplast) DNA is inherited separately from nuclear DNA — in most animals, mitochondrial DNA is inherited maternally only (via the egg cell, since sperm contribute negligible cytoplasm), so a mitochondrial mutation carried by a mother reaches every one of her children regardless of their sex, while a mutation carried only by a father reaches none of his children.
Worked examples
Worked example 3.4.1 · 6 marks
A cell in G1 of the cell cycle contains 46 chromosomes.
State the number of DNA molecules present in this cell
(i) in G1, and (ii) at the end of S phase / during G2. (iii) Briefly explain what happens to both the chromosome number and the DNA molecule number as the cell passes through anaphase of mitosis.
Show worked solution
(i) In G1, each of the 46 chromosomes is a single DNA molecule, so 46 DNA molecules are present. (ii) By the end of S phase, every chromosome has been replicated into two sister chromatids joined at a centromere, so each of the 46 chromosomes now consists of two DNA molecules: 46 chromosomes, DNA molecules. (iii) In anaphase, each centromere divides and sister chromatids separate; each separated chromatid immediately becomes an individual chromosome.
Chromosome number doubles, transiently, to 92, while the number of DNA molecules stays at 92.
Mark scheme · 6 marks
- States 46 DNA molecules in G1 1 mark
- States 46 chromosomes remain at end of S phase / G2 1 mark
- Calculates 92 DNA molecules at end of S phase / G2 1 mark
- States chromosome number doubles to 92 in anaphase 1 mark
- States DNA molecule number stays at 92 through anaphase 1 mark
- Explains separation redefines what counts as one chromosome, without creating or destroying DNA 1 mark
Do not count matching words alone — ask whether your answer actually makes the same claim.
Worked example 3.4.1 · 5 marks
A bacterial cell and a human liver cell are compared.
Both contain DNA coding for broadly similar core metabolic enzymes.
Explain two structural differences between how DNA is organised in each cell, and explain why a human cell's DNA needs to be organised this way while a bacterial cell's does not.
Show worked solution
In the bacterial cell, DNA is short, circular, and free in the cytoplasm, not associated with protein.
In the human liver cell, nuclear DNA is very long and linear, and is associated with histone proteins, together forming chromosomes, within a nucleus.
The human cell needs this packaging because a eukaryotic genome is vastly longer — without histone winding and coiling, DNA of this length could not fit within the nucleus or keep specific genes individually locatable.
The bacterial cell's short, circular DNA has no equivalent requirement.
Mark scheme · 5 marks
- States bacterial DNA is short, circular, and not associated with protein 1 mark
- States human DNA is long, linear, and associated with histones, forming chromosomes 1 mark
- Explains the human genome's much greater length requires this packaging to fit in the nucleus 1 mark
- Explains packaging keeps specific genes individually locatable/accessible 1 mark
- States the bacterial genome's shorter length needs no equivalent packaging 1 mark
Do not count matching words alone — ask whether your answer actually makes the same claim.
DNA and protein synthesis
DNA and transcription 3.4.2
- Transcription: RNA polymerase binds DNA at a specific site → the double helix unwinds locally → the enzyme reads the template strand 3′ to 5′, synthesising a complementary, single-stranded pre-mRNA transcript 5′ to 3′ by base pairing against it (using free RNA nucleotides, with U pairing with A since RNA has no thymine) → phosphodiester bonds join the new RNA nucleotides together as they are added.
- Only one of the two DNA strands — the template strand — is actually read and transcribed at a given gene; the other (coding) strand has the same base sequence as the resulting mRNA (with U in place of T), which is often how it is presented for convenience even though it is not physically copied.
- RNA polymerase moving along the template strand while synthesising RNA in the opposite direction (5′ to 3′, against a 3′-to-5′ template read) is exactly analogous to how DNA polymerase reads a template strand during DNA replication — the same antiparallel logic applies to both processes.
- In prokaryotes, which lack a nucleus, transcription usually produces mRNA that is used directly for translation, without the splicing step eukaryotic pre-mRNA requires.
RNA splicing and translation 3.4.2
- Alternative splicing: the same pre-mRNA transcript, from an identical gene, spliced to retain a different combination of exons in different tissues, producing different mature mRNAs and therefore different protein products from a single gene.
- Splicing: introns are removed from pre-mRNA and the remaining exons are joined together, producing mature mRNA — which then leaves the nucleus through a nuclear pore into the cytoplasm.
- Translation: mRNA binds a ribosome → each tRNA (charged with a specific amino acid, using ATP) carries an anticodon complementary to one mRNA codon, so successive tRNAs deliver amino acids in the order the codons specify → as each anticodon pairs with its codon, the ribosome catalyses a peptide bond forming by condensation between the incoming amino acid and the growing polypeptide chain, and moves to the next codon (5′ to 3′ along the mRNA) → a stop codon, recognised by no tRNA, halts translation and releases the completed polypeptide.
- The genetic code's near-universality across almost all organisms is evidence for a shared evolutionary origin, since there is no chemical necessity linking any particular codon to any particular amino acid — it is also the practical basis for cross-species genetic engineering, since a gene transferred into an unrelated organism is translated using the same codon assignments.
- Alternative splicing is why a cell's proteome cannot be predicted from its genome, or even from one gene's DNA sequence alone, without also knowing which splicing pattern that particular cell applies.
- A tRNA molecule is itself folded RNA, held in its characteristic cloverleaf shape partly by internal complementary base pairing within its own sequence — not just a simple linear strand.
Worked examples
Worked example 3.4.2 · 5 marks
A gene's coding DNA sequence is 1200 base pairs long, but the mature mRNA transcript produced from it is only 720 nucleotides long (excluding any additional non-coding regions at either end).
Explain this difference in length, and state what a molecule of tRNA would be doing at the ribosome once this mRNA is being translated.
Show worked solution
The difference arises from splicing.
The gene's DNA (and initial pre-mRNA) contains alternating exons and introns; during RNA processing, introns are removed and exons joined to produce the shorter mature mRNA.
The 1200 bp includes intron sequences never appearing in the 720-nucleotide transcript.
During translation, each tRNA carries a specific amino acid at one end and an anticodon at the other; the anticodon base-pairs with a complementary codon on the mRNA at the ribosome, delivering the correct amino acid in sequence.
Mark scheme · 5 marks
- States the difference arises from splicing 1 mark
- States introns are removed and exons joined to form mature mRNA 1 mark
- Links the 1200 bp figure to including intron sequences absent from the 720-nucleotide transcript 1 mark
- States tRNA carries a specific amino acid and has an anticodon 1 mark
- Explains the anticodon base-pairs with a complementary mRNA codon, delivering the correct amino acid 1 mark
Do not count matching words alone — ask whether your answer actually makes the same claim.
Worked example 3.4.2 · 4 marks
Part of the template strand of a DNA gene reads 3′-TACGGCATT-5′.
(a) State the corresponding sequence of the mRNA transcribed from this template strand, including the 5′/3′ orientation.
(b) Explain why RNA polymerase, not DNA polymerase, is responsible for producing this transcript.
Show worked solution
(a) mRNA is synthesised complementary to the template strand, using uracil in place of thymine, running antiparallel: 5′-AUGCCGUAA-3′.
(b) RNA polymerase joins RNA nucleotides (ribose, uracil) using a DNA template, producing mRNA; DNA polymerase joins DNA nucleotides during DNA replication, copying DNA to produce more DNA.
Since transcription's product is RNA, only RNA polymerase can carry it out.
Mark scheme · 4 marks
- States the correct complementary sequence 5′-AUGCCGUAA-3′ 1 mark
- States the correct 5′/3′ orientation 1 mark
- States RNA polymerase joins RNA nucleotides using a DNA template 1 mark
- Explains DNA polymerase instead produces DNA, not RNA, so cannot carry out transcription 1 mark
Do not count matching words alone — ask whether your answer actually makes the same claim.
Genetic diversity: mutation and meiosis
Mutation and the reference sequence 3.4.3
- Gene mutation: a change to the base sequence of DNA.
- Mutations can arise spontaneously during DNA replication (errors in base pairing), and mutagenic agents (e.g. certain chemicals, ionising radiation, UV light) increase the rate at which they occur.
- Working from a short reference DNA sequence through transcription and translation to a resulting polypeptide gives a fixed baseline against which the effect of any particular mutation can be directly compared — exactly the approach used throughout the following sections.
Substitution mutations 3.4.3
- Substitution mutation: one DNA base is replaced by a different base — the reading frame is never affected, since the total number of bases is unchanged.
- Synonymous (silent) substitution: the altered codon still specifies the same amino acid — possible because the genetic code is degenerate — so the resulting protein is unchanged.
- Missense substitution: the altered codon specifies a different amino acid — the resulting protein has one changed residue, which may or may not affect its function.
- Nonsense substitution: the altered codon becomes a premature stop codon — translation halts early, producing a truncated (shortened) polypeptide, almost always non-functional.
- All three substitution outcomes affect only ONE triplet (and so at most one amino acid) — substitution never shifts the reading frame of any other triplet, unlike an insertion or deletion.
- Whether a substitution is synonymous, missense or nonsense depends entirely on which specific bases are involved and where in the triplet the change falls — there is no way to predict the outcome from 'a substitution occurred' alone, without knowing the actual sequence change.
Insertion and deletion mutations 3.4.3
- Frameshift mutation: an insertion or deletion of a number of bases that is NOT a multiple of three, shifting the reading frame from that point onward and altering essentially every downstream triplet — unlike a substitution, which affects only one.
- Insertion or deletion of one or two bases shifts the reading frame from that point onward, regrouping every downstream triplet — changing the amino acid sequence from that point on, and often altering or removing the position of the stop codon.
- Insertion or deletion of a number of bases that IS a multiple of three (e.g. deleting a whole codon) does NOT shift the reading frame — it simply adds or removes one or more complete amino acids, leaving the rest of the sequence's reading frame, and so the rest of the protein, unaffected.
- The distinction between 'a multiple of three' and 'not a multiple of three' is the single most important fact in this section: it is not insertion/deletion itself that causes widespread damage, but specifically a frameshift, and only a non-multiple-of-three change causes one.
- A frameshift's damage compounds with every base read afterward, since the ribosome has no way of 'knowing' the reading frame has shifted — it simply continues grouping bases into triplets from the altered point onward, producing an essentially unrelated amino acid sequence for the rest of the protein.
- Because a frameshift changes so much of the downstream sequence at once, it is far more likely to seriously disrupt protein function than a single substitution — though, as with substitutions, the actual functional consequence still depends on exactly where in the gene the frameshift occurs.
Chromosome mutations: inversion, duplication and translocation 3.4.3
- Inversion: a segment of a chromosome is reversed in order and orientation. Duplication: a segment of a chromosome is copied, so an extra copy is present. Translocation: segments are exchanged (reciprocally) between two non-homologous chromosomes.
- These are larger-scale rearrangements of whole DNA segments (potentially containing many genes), distinct from the single- or few-base changes covered by substitution and insertion/deletion mutations.
- The functional effect of any of these three rearrangements depends heavily on exactly where the breakpoints fall: a breakpoint landing within a gene's coding sequence or its regulatory region can disrupt that gene directly, while a breakpoint falling between genes may leave every affected gene's own sequence, and so its protein product, completely unchanged.
- Duplication can also alter gene dosage — having an extra functional copy of a gene can itself change how much of its product is made, independent of whether the gene's own sequence changed at all.
- As with point mutations, the outcome is never automatic: a rearrangement's effect depends on the specific segment involved and precisely where its breakpoints fall, not on the type of rearrangement alone.
How mutations affect protein structure and function 3.4.3
- The causal chain from a DNA-level change to a functional consequence runs: altered base sequence → possibly a different amino acid sequence → possibly different R-group interactions — hydrogen bonds, ionic interactions, disulfide bridges, hydrophobic interactions → possibly altered tertiary (or quaternary) folding and shape → possibly altered protein function (e.g. an active site or binding site changing shape).
- Each 'possibly' in that chain is genuine, not just cautious phrasing: a mutation need not change function at all — whether it does depends on the specific position and nature of the change, exactly as established for substitution, insertion/deletion and chromosome mutations individually.
- A changed R group in a position NOT involved in any stabilising interaction, or not near the active site, may have negligible effect on overall folding or function — while an equivalent change at a genuinely critical position can be catastrophic for function, even though both are 'one amino acid changed' in exactly the same formal sense.
Mutation as a source of genetic diversity 3.4.3
- Mutation creates entirely new alleles — it is the ONE process (of mutation, meiosis and random fertilisation) able to add an allele not previously present anywhere in a population's gene pool at all; meiosis and fertilisation can only reshuffle alleles a gene pool already contains.
- Most mutations that have any effect are neutral or harmful rather than beneficial, since a change to an already-functional protein is statistically more likely to impair it than to improve it — this does not make mutation unimportant, since natural selection can only act on variation that already exists and cannot itself create a new allele.
- Over a large population across many generations, even a low per-mutation chance of a beneficial outcome supplies a steady trickle of occasionally advantageous alleles, which selection can then increase in frequency (see Natural selection and adaptation).
- Errors introducing a new mutation can arise spontaneously during DNA replication itself, and external mutagens increase the rate at which they occur, exactly as established for gene mutations generally.
Meiosis, crossing over and independent segregation 3.4.3
- Independent segregation: each homologous pair's maternal and paternal chromosome is distributed to gametes independently of how every other pair segregates.
- Crossing over: the reciprocal exchange of corresponding DNA segments between non-sister chromatids of a homologous pair, at chiasmata during prophase I of meiosis.
- Meiosis: one round of DNA replication, followed by two nuclear divisions (meiosis I separates homologous chromosomes, meiosis II separates sister chromatids, with no further DNA replication in between) — producing four haploid cells from one diploid parent cell.
- Independent segregation alone gives possible chromosome combinations in a gamete, where is the haploid chromosome number ( for humans).
- Meiosis reshuffles EXISTING alleles into new combinations; it does not create any new allele itself — that distinction from mutation is the key thing to keep straight when explaining sources of genetic diversity.
- Crossing over recombines alleles that were originally linked together on the same chromosome, multiplying the number of possible gamete combinations far beyond the figure that independent segregation alone would give — the two mechanisms compound rather than substitute for each other.
- Because meiosis I separates homologous chromosomes (each still as two sister chromatids) and only meiosis II separates the sister chromatids themselves, chromosome number halves specifically at meiosis I, not meiosis II — meiosis II is mechanically similar to mitosis (separating sister chromatids) but starting from a haploid, not diploid, cell.
Non-disjunction and fertilisation 3.4.3
- Non-disjunction: the failure of homologous chromosomes (in meiosis I) or sister chromatids (in meiosis II) to separate properly, producing gametes with an abnormal chromosome number.
- Non-disjunction in meiosis I produces some gametes with one extra chromosome () and some with one missing (), rather than the normal — the same abnormal outcome can also arise from non-disjunction occurring instead in meiosis II.
- Random fertilisation: the random union of any one of a huge number of genetically different possible gametes from one parent with any one of a similarly huge number from the other — for independent segregation alone, this squares the combinations again ().
- Non-disjunction is a genuine error in the mechanics of meiosis, not a normal source of diversity in the same sense as independent segregation or crossing over — its products typically have serious functional consequences (e.g. Down syndrome, trisomy 21, results from non-disjunction affecting chromosome 21).
- Random fertilisation compounds with, rather than replaces, the diversity already generated by independent segregation and crossing over during gamete formation in both parents — together, mutation, meiosis (independent segregation and crossing over) and random fertilisation are the three distinct sources of genetic diversity within a sexually reproducing species.
Worked examples
Worked example 3.4.3 · 4 marks
A gene's coding sequence includes the base triplet TGG, which is later found in a mutated individual to have changed to TGA.
In the genetic code being used, TGG codes for the amino acid tryptophan, while TGA is a stop codon.
Identify the type of mutation shown here, and explain why this particular substitution is likely to have a much more serious effect on the resulting protein than a substitution that changed TGG to, say, TGT (which also codes for a different amino acid, cysteine).
Show worked solution
This is a substitution mutation — specifically a nonsense mutation, since TGA is a stop codon.
This is far more serious than the TGG→TGT missense mutation because a stop codon appearing partway through causes translation to terminate prematurely — the polypeptide is truncated, missing every amino acid that should have followed.
A missense mutation only changes one amino acid within an otherwise complete, full-length polypeptide.
Mark scheme · 4 marks
- Identifies a substitution mutation 1 mark
- Identifies it specifically as a nonsense mutation (new triplet is a stop codon) 1 mark
- Explains a premature stop codon truncates the polypeptide, losing everything downstream 1 mark
- Contrasts this with a missense mutation only changing one amino acid in a full-length protein 1 mark
Do not count matching words alone — ask whether your answer actually makes the same claim.
Worked example 3.4.3 · 5 marks
A diploid organism with 8 chromosomes (4 homologous pairs) undergoes meiosis, but non-disjunction occurs during meiosis I in one pair of homologous chromosomes.
(a) State the chromosome number of the resulting gametes.
(b) If one of these gametes is fertilised by a normal gamete from the other parent, state the chromosome number of the resulting zygote, and name the type of condition this would produce.
Show worked solution
(a) Non-disjunction means both homologous chromosomes from one pair move to the same pole, producing two gametes with 5 chromosomes and two gametes with 3 chromosomes.
(b) A 5-chromosome gamete fertilised by a normal 4-chromosome gamete gives a zygote with chromosomes — trisomy (one extra) — the same general mechanism that produces trisomy 21 (Down syndrome) in humans.
Mark scheme · 5 marks
- States two gametes with 5 chromosomes result 1 mark
- States two gametes with 3 chromosomes result 1 mark
- Calculates the zygote has 9 chromosomes 1 mark
- Names the condition as trisomy 1 mark
- Links this to the same mechanism producing trisomy 21 in humans 1 mark
Do not count matching words alone — ask whether your answer actually makes the same claim.
Worked example 3.4.3 · 5 marks
A species of plant has 4 pairs of homologous chromosomes.
Calculate the number of genetically distinct chromosome combinations possible in its gametes as a result of independent segregation alone, and the number of distinct combinations possible from the fusion of two of its gametes at fertilisation.
Explain why the true number of genetically distinct gametes an individual plant could produce is actually far higher than the first value calculated.
Show worked solution
With : combinations per gamete from independent segregation alone.
At fertilisation:
Crossing over during prophase I additionally recombines alleles within each chromosome at chiasmata, so gametes differ in the particular combination of alleles along each chromosome too, not just which whole chromosome is inherited — the true number of genetically distinct gametes is far higher than 16.
Mark scheme · 5 marks
- Calculates combinations per gamete 2 marks
- Calculates combinations at fertilisation 1 mark
- States crossing over recombines alleles within chromosomes 1 mark
- Explains this makes the true gamete diversity far exceed the whole-chromosome-segregation figure of 16 1 mark
Do not count matching words alone — ask whether your answer actually makes the same claim.
Genetic diversity and adaptation
Natural selection and adaptation 3.4.4
- Directional selection: selection favouring one extreme of a range of phenotypes, shifting the population mean toward that extreme over generations — exemplified by antibiotic resistance in bacteria.
- Stabilising selection: selection favouring phenotypes near the middle of a range and acting against both extremes, keeping the population mean stable over generations — exemplified by human birth weight.
- Principles of natural selection: random mutation can produce a new allele → in a particular environment, that allele may benefit its possessor, increasing their reproductive success → the advantageous allele is inherited by members of the next generation → over many generations, the allele's frequency increases in the population.
- Genetic diversity (the number of different alleles present in a population) is what makes natural selection possible at all — selection can only act on variation that already exists within a population, never generate it from nothing.
- Directional selection shifts a population toward one extreme when that extreme is newly favoured — in antibiotic resistance, bacteria already carrying a resistance allele (present in the population before the antibiotic was ever applied) survive and reproduce while susceptible bacteria are killed, so the resistant allele's frequency rises sharply across subsequent generations.
- Stabilising selection instead favours the existing middle of a range and acts against both extremes — in human birth weight, babies of very low or very high birth weight have historically had lower survival rates than babies of an intermediate weight, keeping the population's typical birth weight stable over time rather than shifting it in either direction.
- The adaptations natural selection produces may be anatomical (structural), physiological (functional/biochemical), or behavioural — all three categories count as genuine adaptations, not just visible physical structures.
- Required practical 6 (aseptic technique investigating the effect of antimicrobial substances on microbial growth) is the practical context this subtopic is usually assessed alongside, directly connected to the antibiotic-resistance example of directional selection.
Worked examples
Worked example 3.4.4 · 5 marks
In a population of insects, individuals with a rare new mutant allele are slightly better camouflaged against a recently changed background colour than individuals with the more common allele.
Explain, as a step-by-step sequence, how this single new mutation could lead to a change in allele frequency in the population over many generations, and name the type of selection this describes if the population's coloration is now gradually shifting entirely toward the new, better-camouflaged phenotype.
Show worked solution
The new allele arises by random mutation.
Carriers are better camouflaged, giving a survival advantage and greater reproductive success.
Being heritable, the allele is passed to a greater-than-average share of offspring.
Over many generations, this repeated pattern raises the allele's frequency in the gene pool steadily.
Since the whole population is shifting toward one extreme, this is directional selection.
Mark scheme · 5 marks
- States the allele arises by random mutation 1 mark
- States carriers have a survival/reproductive advantage from better camouflage 1 mark
- States the allele is heritable, passed to more offspring 1 mark
- States repeated generations of this pattern raise the allele's frequency 1 mark
- Names directional selection, justified by the shift toward one extreme 1 mark
Do not count matching words alone — ask whether your answer actually makes the same claim.
Worked example 3.4.4 · 4 marks
In a large human population, birth weight is measured and found to follow a roughly normal (bell-shaped) distribution.
Babies born at either extreme — significantly underweight or significantly overweight — are found to have a higher mortality rate than babies born close to the population average.
Explain what effect this pattern of survival would be expected to have on the distribution of birth weight in the population over successive generations, and name this type of selection.
Show worked solution
Because both extremes have reduced survival, alleles associated with either extreme are selected against, while intermediate-birth-weight alleles are favoured.
Over successive generations, this narrows the distribution around the mean, without the mean itself necessarily shifting.
This is stabilising selection: favouring the intermediate phenotype and acting against both extremes.
Mark scheme · 4 marks
- States alleles at both extremes are selected against 1 mark
- States intermediate-associated alleles are favoured 1 mark
- Explains this narrows the distribution over generations 1 mark
- Names stabilising selection 1 mark
Do not count matching words alone — ask whether your answer actually makes the same claim.
Species and taxonomy
Taxonomic hierarchy and the species concept 3.4.5
- Taxonomic hierarchy, broadest to most specific: domain, kingdom, phylum, class, order, family, genus, species — each level (taxon) is nested entirely within the one above it, and taxa at the same rank never overlap.
- Biological species concept: a species is a group of organisms able to interbreed naturally and produce fertile offspring.
- This definition applies directly only to sexually reproducing organisms — it does not straightforwardly apply to asexually reproducing organisms, for which alternative species concepts are needed.
- Courtship behaviour, where it occurs, supports species recognition between potential mates — part of why courtship displays themselves can be a meaningful piece of evidence when assessing whether two populations belong to the same species.
Binomial nomenclature 3.4.5
- A binomial name has two parts: the genus name (capitalised) and the specific epithet (lowercase) — together, both words form the full species name, e.g. Homo sapiens.
- Binomial names are italicised in print, or each word underlined separately when handwritten — a formatting convention worth getting right, since it is specifically examined.
- Binomial nomenclature avoids the ambiguity of different common names being used for the same organism, or the same common name being applied to different organisms, across different languages and regions — a single, internationally standardised name resolves this.
Phylogenetic trees and evidence for relatedness 3.4.5
- Convergent evolution: unrelated or only distantly related species independently evolving similar features under similar selection pressures — can produce misleading morphological similarity with no recent shared ancestor behind it.
- A phylogenetic tree represents evolutionary ancestry directly: taxa sharing a more recent common ancestor with each other than with a third taxon are shown branching from a more recent shared node — branch lengths on a simple tree diagram are not necessarily a literal time scale.
- Evidence for classification and phylogeny includes morphological and embryological similarity, but the most reliable evidence at fine scales is molecular: comparing DNA base sequences, or the amino acid sequence of a homologous protein, on the principle that fewer differences generally indicate a more recent common ancestor.
- Molecular evidence is specifically what distinguishes genuine relatedness from convergent evolution — two unrelated species that merely LOOK similar due to convergent evolution will still show large molecular sequence differences, revealing the lack of a recent shared ancestor that morphology alone could not.
- The three-domain system (Bacteria, Archaea, Eukarya) is the clearest historical example of molecular evidence substantially revising a classification previously based on morphology: all prokaryotes were once grouped together on the basis of their shared, structurally simple cell type, but once ribosomal RNA sequence and membrane lipid chemistry could be compared, it became clear this group actually contained two lineages (Bacteria and Archaea) whose molecular differences were comparable in scale to those separating either from Eukarya — despite looking similar under a microscope.
- Immunological comparison (antibody cross-reactivity between species) is a further, less direct line of evidence: a stronger cross-reaction between the antibodies/proteins of two species generally indicates a closer evolutionary relationship, though it is a proxy for underlying molecular similarity rather than a direct sequence comparison.
Worked examples
Worked example 3.4.5 · 4 marks
Two populations of a fish species, isolated on opposite sides of a newly formed land barrier, are found many generations later to be unable to produce fertile offspring when specimens from each population are experimentally crossed.
(a) State what this observation demonstrates about the two populations' current taxonomic classification.
(b) State the correct binomial format for naming a newly identified species discovered in one of these populations, using the genus name Percalates as an example.
Show worked solution
(a) The two populations are now separate species — the biological definition of species requires the ability to interbreed and produce fertile offspring, which this cross fails to meet.
(b) The binomial is genus name (capitalised) followed by species name (lower case), conventionally italicised: e.g.
Percalates novaemaculata.
Mark scheme · 4 marks
- States the two populations are now classified as separate species 1 mark
- Justifies this via the biological species definition (fertile offspring) 1 mark
- States the binomial format: capitalised genus + lower-case species name 1 mark
- Gives a correctly formatted example (e.g. italicised) 1 mark
Do not count matching words alone — ask whether your answer actually makes the same claim.
Worked example 3.4.5 · 5 marks
A phylogenetic tree, based on DNA sequence comparison, shows species A and species B sharing a more recent common ancestor with each other than either does with species C.
A student argues that, since species A and C look more physically similar to each other than A and B do, the tree must be wrong.
Evaluate this argument.
Show worked solution
The argument is not well founded.
A DNA-sequence-based tree reflects genetic relatedness directly and need not agree with physical similarity.
Convergent evolution can produce superficially similar (analogous) features in distantly related species facing similar pressures, while closely related species can look different if adapted to different niches.
DNA comparison is generally more reliable precisely because it is not subject to this convergence — the student's argument would need independent genetic evidence, not appearance alone.
Mark scheme · 5 marks
- States the argument is not well founded 1 mark
- States DNA-based trees reflect genetic relatedness, not physical appearance 1 mark
- Explains convergent evolution can produce similar features in distantly related species 1 mark
- States closely related species can look different if adapted to different niches 1 mark
- Concludes DNA comparison is more reliable than appearance for judging relatedness 1 mark
Do not count matching words alone — ask whether your answer actually makes the same claim.
Biodiversity within a community
Biodiversity within a community 3.4.6
- Species richness: the number of different species present in a community, taking no account of how many individuals belong to each.
- Index of diversity (): a single value combining species richness and evenness (how evenly individuals are distributed across those species) into one measure of a community's diversity.
- Biodiversity is measured at three levels: species diversity within a habitat (both richness and evenness), genetic diversity within a species, and habitat/ecosystem diversity across a wider region.
- AQA's index of diversity: , where is the total number of organisms of all species in the sample and is the total number of organisms of each individual species.
- Species richness alone is not an adequate measure of diversity on its own, since it completely ignores evenness — a habitat with 10 species, one of which makes up 91% of all individuals, is intuitively less diverse than a habitat with the same 10 species roughly evenly represented, even though both have identical species richness.
- This is the specific formula AQA requires — it is NOT the same as the more general 'Simpson's Index of Diversity' (, bounded between 0 and 1) sometimes taught elsewhere: AQA's has no fixed upper bound and grows larger as diversity increases, so a habitat with is straightforwardly more diverse than one with , but there is no single 'maximum possible' value to compare either against.
- A community dominated by one species contributes a large term from that one species to the denominator, shrinking sharply — the same underlying evenness-sensitivity as any diversity index, just expressed through a different algebraic form.
Worked examples
Worked example 3.4.6 · 6 marks
Habitat A contains 5 species with 20 individuals of each (100 individuals in total).
Habitat B contains the same 5 species and the same total of 100 individuals, but 80 individuals belong to just one species, with the remaining 20 individuals shared equally among the other four species (5 each).
Using AQA's index of diversity formula, calculate for each habitat and comment on what the comparison shows.
Show worked solution
Habitat A: each species contributes:
Habitat B: dominant species contributes:
others contribute:
Both habitats have identical species richness, yet A's index is far higher, because A's individuals are evenly distributed while B is dominated by one species — the index captures evenness as well as richness.
Mark scheme · 6 marks
- Calculates for Habitat A 1 mark
- Calculates for Habitat A 1 mark
- Calculates for Habitat B 1 mark
- Calculates for Habitat B 1 mark
- States both habitats have identical species richness 1 mark
- Explains the difference in reflects evenness, not richness 1 mark
Do not count matching words alone — ask whether your answer actually makes the same claim.
Worked example 3.4.6 · 4 marks
A nature reserve records 12 different bird species with a combined total of 340 individuals.
A nearby farmland site of similar size records only 6 bird species, but with a combined total of only 90 individuals.
A student concludes that the reserve is definitely more biodiverse because it has both more species and more individuals.
Evaluate this reasoning.
Show worked solution
Species richness alone (12 against 6) genuinely is higher at the reserve.
However, the reasoning conflates richness with overall biodiversity — total individual count is not part of what the index of diversity measures.
What matters beyond richness is evenness.
Properly comparing biodiversity requires examining the distribution of individuals across species, ideally by calculating each site's index of diversity, not species and individual counts alone.
Mark scheme · 4 marks
- Acknowledges richness alone is genuinely higher at the reserve 1 mark
- States total individual count is not part of what the index measures 1 mark
- Identifies evenness as the missing factor 1 mark
- States a proper comparison requires calculating the index of diversity from the actual distribution 1 mark
Do not count matching words alone — ask whether your answer actually makes the same claim.
Investigating diversity
Investigating diversity 3.4.7
- Genetic similarity methods, most to least direct: DNA base sequence comparison (most reliable — reads inherited sequence directly) > protein/amino-acid sequence comparison > immunological method (antiserum cross-reaction strength, an indirect proxy that can miss differences the other two methods would catch).
- A greater number of sequence differences generally indicates a more distant common ancestor, but the rate at which differences accumulate is not constant across every gene or lineage — genes under strong stabilising selection change more slowly than genes under weaker selective constraint.
- Converting an observed sequence difference into an actual divergence time therefore needs that mutation rate to be calibrated independently (e.g. against fossil evidence), rather than simply assumed to be constant across all genes and lineages.
- Quadrat positions in a field survey must be chosen randomly rather than by subjective judgement of what 'looks representative', which would introduce observer bias into the sample.
- A species-area curve (cumulative species found plotted against sampled area) rises steeply while still finding new species and flattens once further sampled area adds few or no new species — that plateau signals a sample size large enough to represent a habitat's true diversity reliably.
- Quantitative investigations of variation within a species (e.g. a measurable characteristic like height or leaf length) involve collecting data from random samples, then calculating a mean and standard deviation of that data — the standard deviation shows how spread out the values are around the mean, so two samples can share an identical mean while differing sharply in standard deviation.
Worked examples
Worked example 3.4.7 · 4 marks
A biologist wants to investigate whether two populations of the same plant species, growing in different fields, show genetic differences.
State two different types of data that could be collected to investigate this, and explain why comparing the DNA base sequence directly is considered more reliable than comparing only observable (phenotypic) characteristics.
Show worked solution
(1) Comparing the frequency of observable/measurable characteristics between random samples; (2) comparing DNA base sequence (or mRNA sequence, or amino acid sequence) directly.
DNA comparison is more reliable because observable characteristics are influenced by both genetic and environmental factors — genetically identical plants can look different in different environments, and genetically different plants can converge on similar appearance — making inferred genetic difference from appearance alone potentially misleading.
Mark scheme · 4 marks
- States comparing observable/measurable characteristics as one approach 1 mark
- States comparing DNA (or mRNA/protein) sequence directly as the other approach 1 mark
- Explains observable characteristics are influenced by environment as well as genotype 1 mark
- Explains this makes appearance alone an unreliable proxy for genetic difference 1 mark
Do not count matching words alone — ask whether your answer actually makes the same claim.
Worked example 3.4.7 · 4 marks
A researcher measures the height of 50 randomly sampled plants from population X and 50 randomly sampled plants from population Y.
Population X has a mean height of 34 cm with a large standard deviation; population Y has a mean height of 31 cm with a very small standard deviation.
Explain what the standard deviation values indicate about each population's variation, and explain why comparing means alone, without also considering standard deviation, could be misleading.
Show worked solution
Standard deviation measures how spread out individual values are around the mean.
X's large standard deviation indicates considerable variation around 34 cm; Y's very small standard deviation indicates values clustered tightly around 31 cm.
Comparing means alone could be misleading because it gives no information about how much the two populations' actual ranges overlap — given X's large spread, many individual X plants could be shorter than many Y plants despite X's higher mean.
Mark scheme · 4 marks
- States standard deviation measures spread of values around the mean 1 mark
- States X shows considerable variation, Y shows tight clustering 1 mark
- Explains means alone give no information about overlap between the two distributions 1 mark
- Explains X's spread could mean some X plants are shorter than many Y plants despite the higher mean 1 mark
Do not count matching words alone — ask whether your answer actually makes the same claim.