Triplets, introns and exons

A gene is a base sequence of DNA that codes for the amino acid sequence of a polypeptide (or for a functional RNA). Its position on a chromosome is its locus. Different versions of the same gene are alleles.

• Triplet — three bases code for one amino acid. With 4 bases, 4³ = 64 possible triplets code for only 20 amino acids.
• Degenerate — most amino acids have more than one triplet. A consequence: a base substitution often changes nothing (a silent mutation).
• Non-overlapping — each base is read once, in one triplet only.
• Universal — the same triplets code for the same amino acids in almost all organisms, which is what makes genetic engineering across species possible.
• Some triplets are stop codons, which terminate translation.

Eukaryotes vs prokaryotes: eukaryotic DNA is linear, associated with histones, and contains non-coding introns within genes (plus non-coding repeats between them). Prokaryotic DNA is circular, not associated with histones, and has no introns. Mitochondria and chloroplasts contain small, circular, histone-free DNA — evidence for endosymbiosis.

Genome = the complete set of genes in a cell. Proteome = the full range of proteins a cell can produce.

Transcription and translation

Transcription (in the nucleus):

• DNA helicase breaks the hydrogen bonds; the helix unwinds and exposes the bases.
• One strand acts as the template. Free RNA nucleotides align by complementary base pairing (U pairs with A).
• RNA polymerase joins them with phosphodiester bonds, forming pre-mRNA.
• Splicing: introns are removed and exons joined, producing mature mRNA, which leaves through a nuclear pore. (In prokaryotes there is no splicing — mRNA is produced directly.)

Translation (at the ribosome):

• The ribosome binds the mRNA and reads the first codon. A tRNA with the complementary anticodon, carrying a specific amino acid, binds.
• A second tRNA binds the next codon. A peptide bond forms between the two amino acids — this requires ATP.
• The ribosome moves along three bases at a time; the first tRNA leaves and is reloaded. The chain grows until a stop codon is reached, and the polypeptide is released.

Splicing means one gene can make several proteins — different combinations of exons can be joined. That is one reason the proteome is much larger than the genome.

Your turn — exons to amino acids

What a change of one base actually does

A gene mutation is a change in the base sequence of DNA. Mutations occur spontaneously during DNA replication, and their rate is increased by mutagenic agents (UV, ionising radiation, some chemicals).

• Substitution — one base is swapped. Because the code is degenerate, this may code for the same amino acid (silent, no effect). It may code for a different amino acid — which changes the primary structure, so the hydrogen/ionic/disulfide bonds form differently, so the tertiary structure changes, so an enzyme’s active site may no longer be complementary to its substrate. Or it may create a premature stop codon.
• Deletion or insertion — a base is lost or added, so every subsequent triplet is shifted: a frameshift. Almost every amino acid downstream is changed, and the protein is usually non-functional. This is far more likely to be damaging than a substitution.

Chromosome mutations arise from errors in meiosis: non-disjunction (chromosomes fail to separate) gives a gamete with one chromosome too many or too few — for example trisomy 21. Polyploidy (whole extra sets) is common in plants.

Why a deletion is worse

Meiosis and the sources of variation

Meiosis halves the chromosome number (diploid → haploid), so that fertilisation restores the diploid number. Two divisions produce four genetically different haploid cells.

• Meiosis I — homologous chromosomes pair up (forming bivalents) and are separated. This is the reduction division.
• Meiosis II — sister chromatids are separated, like mitosis.

Where the variation comes from:

• Crossing over (prophase I) — homologous chromosomes twist around each other at chiasmata and exchange equivalent sections. This creates new combinations of alleles on the same chromosome.
• Independent segregation (metaphase I) — each homologous pair lines up on the equator independently of every other pair, so the maternal and paternal chromosomes are shuffled. With n homologous pairs there are 2ⁿ possible combinations — in humans, 2²³ ≈ 8.4 million before crossing over is even considered.
• Random fertilisation — any gamete may fuse with any other, multiplying the variation again.

Mitosis vs meiosis, spotted on a diagram: if homologous chromosomes are paired at the equator (two rows), it is metaphase I of meiosis. A single row of chromosomes each with two chromatids is metaphase of mitosis (or metaphase II).

Your turn — independent segregation

Genetic diversity and types of selection

Genetic diversity is the number of different alleles in a population. It is reduced by genetic bottlenecks (a sharp fall in population size) and by the founder effect (a few individuals establish a new population), and by selective breeding.

Natural selection requires: variation caused by random mutation; a selection pressure; differential reproductive success; and the passing on of the advantageous allele, so its frequency in the population increases over generations.

• Directional selection — one extreme is favoured; the modal phenotype shifts. Classic example: antibiotic resistance. A random mutation confers resistance; the antibiotic is the selection pressure; resistant bacteria survive, reproduce and pass on the allele.
• Stabilising selection — the mean is favoured and both extremes are selected against, so variation is reduced. Example: human birth mass. Occurs when the environment is unchanging.
• Disruptive selection — both extremes are favoured over the mean, splitting the distribution into two peaks. It can be the first step towards sympatric speciation.

Write it carefully: individuals do not "become" resistant, and the antibiotic does not cause the mutation. The mutation already existed; the antibiotic merely selected for it.

Taxonomy, phylogeny and species

A species is a group of similar organisms that can breed together to produce fertile offspring. Each is given a binomial name: Genus species.

Phylogenetic classification arranges species into groups based on their evolutionary relationships and common ancestry. The taxonomic hierarchy is: domain, kingdom, phylum, class, order, family, genus, species — each group contained entirely within the one above, with no overlap.

Evidence used to build a phylogeny:

• DNA base sequences — the more similar the sequences, the more recently the species shared a common ancestor. This is the gold standard and has overturned many classifications based on appearance alone.
• Amino acid sequences in a common protein (e.g. cytochrome c) — a direct consequence of the DNA sequence.
• Immunological comparison — antibodies to one species’ protein will bind to another’s to a degree that reflects similarity; more precipitate = more closely related.

Careful: similar appearance does not mean close relation — convergent evolution produces similar features in unrelated species facing the same selection pressures (e.g. the streamlined body of a shark and a dolphin).

Courtship behaviour and quantifying variation

Because a species is defined by successful interbreeding, animals must be able to recognise a fertile member of their own species. Courtship behaviour does exactly that:

• It allows individuals to recognise members of their own species — so mating produces fertile offspring, not sterile hybrids.
• It identifies a mate capable of breeding (sexually mature, fertile, in season).
• It synchronises mating so that the gametes are released at the same time, and it forms a pair bond that helps raise the young.

Courtship is usually a stimulus-response chain: each action by one animal is the stimulus for the next action by the other. A wrong response breaks the chain — an unambiguous species check.

Quantifying variation: take a random sample that is large enough for chance to be smoothed out, calculate the mean, and use the standard deviation to describe the spread. If the mean ± SD ranges of two samples do not overlap, the difference is likely to be significant; heavy overlap means it may simply be chance. Variation may be genetic, environmental, or (usually) a combination of both.

The point of courtship

Measuring biodiversity properly

Species richness is simply the number of different species in a community. It says nothing about how many individuals of each there are — a wood with 100 oaks and 1 elm scores the same as one with 50 of each, which is obviously wrong.

A higher value of d means greater diversity: a diverse community is more stable, because more feeding relationships exist and no one species dominates.

Farming reduces diversity: monoculture, removal of hedgerows and woodland, over-grazing, pesticides and herbicides all destroy habitats and remove species. Conservation compromises include maintaining hedgerows, leaving field margins and using crop rotation. You should also be able to argue this in terms of genetic diversity within a species: measured by the proportion of polymorphic gene loci, or by comparing base or amino acid sequences.

Your turn — index of diversity

Reading a phylogeny

Where does it happen?

Tap a statement, then tap the process it describes.

Define the term

Tap an item on the left, then its partner on the right.

The big ideas to take away

That is the whole of AQA 3.4 Genetic information, variation and relationships between organisms. Press Finish to see your score.