(a)(i) Describe the synthetic theory of evolution. (10 marks) (a)(ii) Describe common types of mimicry in insects with suitable…

(a)

(i) Synthetic theory of evolution

The synthetic theory (modern synthesis, or Neo-Darwinism) was built between about 1918 and 1950 by uniting Darwin's natural selection with Mendelian genetics, population genetics, systematics and palaeontology. Its mathematical base came from R.A. Fisher, J.B.S. Haldane and Sewall Wright; its main architects were Theodosius Dobzhansky (Genetics and the Origin of Species, 1937), Julian Huxley (who named it in Evolution: The Modern Synthesis, 1942), Ernst Mayr (Systematics and the Origin of Species, 1942), G.G. Simpson (Tempo and Mode in Evolution, 1944) and G.L. Stebbins (plants, 1950).

Its main propositions are:

• Evolution is a change in allele frequencies in the gene pool of a population over generations; the population, not the individual, is the unit that evolves.
• Genetic variation arises from gene and chromosomal mutation and is reshuffled by recombination during meiosis and fertilisation; variation is random with respect to need, correcting the Lamarckian and blending-inheritance errors of Darwin's time.
• Natural selection is differential reproduction of genotypes; it is the main directing force that produces adaptation.
• Genetic drift (random change, strongest in small populations, including founder and bottleneck effects) and gene flow (migration) also change allele frequencies.
• Hardy–Weinberg equilibrium (p² + 2pq + q² = 1) is the null model: frequencies stay constant only without mutation, selection, drift, migration and non-random mating, so deviations reveal evolution.
• Reproductive isolation (pre- and post-zygotic mechanisms) allows populations to diverge into new species, usually after geographic separation (allopatric speciation); species are groups of interbreeding natural populations (Mayr's biological species concept).
• Macroevolution is the accumulation of these microevolutionary processes over long periods, consistent with the fossil record (Simpson).

The theory has since been extended by molecular evidence (DNA and protein sequence phylogenies, the neutral theory), kin selection and evolutionary developmental biology, but it remains the framework of evolutionary biology.

(ii) Common types of mimicry in insects

Mimicry is a close resemblance of one organism (the mimic) to another organism or object (the model) that deceives a third, the signal receiver, usually a predator, and so benefits the mimic.

• Batesian mimicry (H.W. Bates, 1862, Amazon butterflies): a palatable, harmless mimic resembles an unpalatable or dangerous model. In India, the female of the common Mormon (Papilio polytes) has forms mimicking the distasteful common rose (Pachliopta aristolochiae) and crimson rose (Pachliopta hector); the female danaid eggfly (Hypolimnas misippus) mimics the plain tiger (Danaus chrysippus); hoverflies (Syrphidae) mimic wasps and bees. It works best when mimics are rarer than models, and it favours female-limited polymorphic mimicry controlled by a "supergene" (doublesex in P. polytes).
• Müllerian mimicry (Fritz Müller, 1878): two or more unpalatable species share the same warning pattern, so predators learn to avoid all of them faster and each species loses fewer individuals. Examples are the Neotropical Heliconius erato and H. melpomene, which converge on the same local colour patterns, and in India the tigers and crows (Danaus, Tirumala, Euploea), which form mimicry rings with many species; stinging bees and wasps sharing black-and-yellow bands are another case.
• Aggressive mimicry: a predator or parasite resembles something harmless or attractive to approach its prey. Female Photuris fireflies copy the flash code of female Photinus to lure and eat Photinus males; the orchid mantis (Hymenopus coronatus) resembles a flower and attracts pollinators.
• Automimicry (self-mimicry): mimicry within a species or of the animal's own body. Palatable monarch butterflies (Danaus plexippus) reared on non-toxic milkweed are protected because they resemble their toxic conspecifics; the "false head" of hairstreak butterflies (Lycaenidae), with hindwing tails and eyespots, directs attacks away from the real head.
• Protective resemblance (masquerade): insects resemble inedible objects, such as the orange oakleaf butterfly (Kallima inachus) of the Himalaya and north-east India looking like a dead leaf, stick insects (Phasmida) resembling twigs, and some caterpillars resembling bird droppings.

These examples show how predator learning and natural selection shape colour pattern evolution.

(b) Chain elongation during protein synthesis in prokaryotes

After initiation, the 70S ribosome (30S + 50S) sits on the mRNA with fMet-tRNAᶠᴹᵉᵗ in the P site and the second codon in the empty A site. Elongation then adds one amino acid per cycle, about 15–20 amino acids per second in Escherichia coli, in three steps.

1. Binding of aminoacyl-tRNA (decoding): the aminoacyl-tRNA specified by the A-site codon arrives as a ternary complex with elongation factor EF-Tu and GTP. When the anticodon pairs correctly with the codon, the 16S rRNA bases (A1492, A1493, G530) sense the geometry of the minor groove, inducing GTP hydrolysis by EF-Tu; EF-Tu·GDP leaves, and the tRNA swings fully into the A site (accommodation). Incorrect tRNAs are rejected before and after GTP hydrolysis (kinetic proofreading), keeping the error rate to about 1 in 10⁴. EF-Ts regenerates EF-Tu·GTP by exchanging GDP for GTP.
2. Peptide bond formation (transpeptidation): the peptidyl transferase centre of the 50S subunit, formed by 23S rRNA (so the ribosome is a ribozyme), positions the α-amino group of the A-site aminoacyl-tRNA to attack the ester bond linking the peptide to the P-site tRNA. The peptide is transferred to the A-site tRNA, lengthening it by one residue at the C-terminus, and a deacylated tRNA is left in the P site. No extra energy is needed, as the aminoacyl ester bond provides it.
3. Translocation: the tRNAs first move into hybrid states (A/P and P/E). EF-G·GTP binds (it mimics the shape of the EF-Tu–tRNA complex), and GTP hydrolysis drives movement of the ribosome by exactly one codon (three nucleotides) towards the 3′ end: the peptidyl-tRNA moves from the A to the P site, the deacylated tRNA moves to the E site and leaves, and the A site is empty for the next aminoacyl-tRNA.

The cycle repeats, costing two GTP per peptide bond (plus two ATP equivalents used earlier to charge the tRNA), and the growing chain leaves the ribosome through the exit tunnel in the 50S subunit, where it may start folding. When a stop codon (UAA, UAG, UGA) reaches the A site, release factors RF1 or RF2 cause hydrolysis of the peptide from the tRNA, RF3·GTP removes them, and ribosome recycling factor with EF-G separates the subunits. In prokaryotes transcription and translation are coupled, and several ribosomes translate one mRNA as a polysome.

Many antibiotics act on elongation: tetracycline blocks aminoacyl-tRNA binding to the A site; streptomycin causes misreading; chloramphenicol and linezolid inhibit peptidyl transferase; erythromycin blocks the exit tunnel; fusidic acid holds EF-G on the ribosome; kirromycin traps EF-Tu; and puromycin, resembling aminoacyl-tRNA, causes premature chain release.

(c) Mechanism of ribozyme action and technological applications

Ribozymes are RNA molecules with catalytic activity, discovered by Thomas Cech (self-splicing group I intron of Tetrahymena, 1982) and Sidney Altman (RNA component of RNase P, 1983), who shared the 1989 Nobel Prize in Chemistry.

Mechanism: RNA folds into precise three-dimensional structures that create an active site. Catalysis uses metal ions (mainly Mg²⁺) that position substrates, activate nucleophiles and stabilise negative charge in the transition state, together with nucleobases (often G and A) acting as general acids and bases. Most ribozymes catalyse phosphoryl transfer at phosphodiester bonds:

• Self-cleaving ribozymes (hammerhead, hairpin, hepatitis delta virus, glmS): the 2′-OH next to the cleavage site attacks the adjacent phosphorus (in-line attack), producing a 2′,3′-cyclic phosphate and a 5′-OH end. The hammerhead has three helical stems around a conserved catalytic core; it cleaves after the sequence NUH, so a target can be chosen by designing the flanking arms to base-pair with it.
• Group I introns: the 3′-OH of a free guanosine attacks the 5′ splice site; the freed exon 3′-OH then attacks the 3′ splice site, joining the exons (two transesterifications).
• Group II introns: the 2′-OH of a bulged adenosine within the intron attacks the 5′ splice site, forming a lariat, as in the spliceosome, whose catalytic core (U2/U6 snRNA) is itself a ribozyme.
• RNase P: its RNA cleaves the 5′ leader from precursor tRNAs by hydrolysis.
• The ribosome: the 23S (or 28S) rRNA peptidyl transferase centre forms peptide bonds, with no protein near the active site.

Technological applications:

• Gene knockdown: designed hammerhead and hairpin ribozymes cleave specific mRNAs (catalytically and repeatedly, unlike antisense oligonucleotides, and by a mechanism different from RNA interference). They were tested in clinical trials against HIV (anti-*tat*/*rev* ribozymes in gene-modified blood stem cells) and against angiogenesis in cancer (Angiozyme, targeting VEGF receptor-1), though none has yet been approved.
• Precise RNA processing: self-cleaving ribozymes placed at the ends of transcripts generate exact 5′ and 3′ ends, used to produce guide RNAs for CRISPR from a single transcript, viral RNA genomes in reverse genetics, and RNA for structural studies.
• Synthetic biology and sensing: aptazymes (ribozymes joined to aptamers) and natural riboswitch–ribozymes such as glmS switch gene expression on or off in response to small molecules, and are used as biosensors and regulatable switches in gene therapy vectors.
• In vitro evolution: SELEX has produced ribozymes that ligate RNA, copy RNA templates (RNA polymerase ribozymes) and make DNA-cleaving "DNAzymes", used in diagnostics.

Ribozymes also give strong support to the RNA-world hypothesis, that early life used RNA both to store information and to catalyse reactions.