(a) Describe the requirement of proteins for the initiation of transcription in an eukaryote. 10 (b) What is modern concept of…

(a) Protein requirements for the initiation of transcription in eukaryotes

Initiation by RNA polymerase II needs the polymerase and a set of general transcription factors (GTFs) assembling on the core promoter (TATA box, initiator, DPE).

• TFIID: its TBP subunit binds the TATA box and bends the DNA, and its TAFs recognise other promoter elements.
• TFIIA stabilises TFIID on the DNA, and TFIIB binds TFIID and the BRE and fixes the start site.
• TFIIF brings RNA polymerase II to the promoter.
• TFIIE joins and recruits TFIIH, which unwinds the DNA with its ATP-dependent helicase and, through its kinase CDK7, phosphorylates the C-terminal domain of the polymerase (Ser5), releasing it from the promoter.

These form the pre-initiation complex. Sequence-specific activators bound to enhancers, the Mediator complex and chromatin remodellers and histone acetyltransferases make the promoter accessible and raise the rate of initiation.

(b) Modern concept of gene and test of allelism

In the modern view the gene is a segment of DNA that is transcribed into a functional product (a polypeptide or RNA), together with its regulatory sequences. Genes are often split into exons and introns, can overlap, give several proteins by alternative splicing, and include genes for rRNA, tRNA and other non-coding RNAs. Benzer divided the classical gene into the cistron (unit of function), muton (unit of mutation) and recon (unit of recombination).

Test of allelism (complementation test): two recessive mutants with similar phenotype are crossed, or combined in trans. If the offspring show the mutant phenotype, the mutations are alleles of the same gene; if they are wild-type, the mutations are in different genes that complement each other. Example: two mutations with white-like eyes in Drosophila give mutant F₁ when allelic and wild-type F₁ when they affect different genes. Benzer used it on rII mutants of phage T4 in E. coli K12(λ): mixed infection gave lysis only when the mutations were in different cistrons (rIIA and rIIB).

(c) Mimicry and its types

Mimicry is the resemblance of an organism (the mimic) in colour, form or behaviour to another organism (the model) or to an object, which gives the mimic protection or another advantage. Its types are:

• Batesian mimicry: a palatable, harmless species resembles an unpalatable or harmful model, so predators avoid it. The female of the common mormon butterfly (Papilio polytes) has forms that mimic the unpalatable common rose (Pachliopta aristolochiae). Henry Bates described it in Amazonian butterflies.
• Müllerian mimicry: two or more unpalatable species resemble each other, so that predators learn the common warning pattern faster and each species loses fewer individuals; for example the plain tiger (Danaus chrysippus) and the common crow (Euploea core), or several species of Heliconius.
• Aggressive (Peckhamian) mimicry: a predator or parasite resembles a harmless or attractive object to approach its prey; examples are the angler fish with its lure, and fireflies of the genus Photuris imitating the flash signals of other fireflies to attract and eat them.
• Automimicry: palatable individuals of a species resemble unpalatable members of the same species and so share their protection. False eyespots, which divert an attack away from the head, are a related deflective device.

(d) Molecular techniques in animal taxonomy

Molecular data give objective characters that complement morphology, especially for cryptic species, juveniles and fragmentary material.

• DNA barcoding: sequencing about 650 bp of the mitochondrial cytochrome c oxidase subunit I (COI) gene to identify species and discover cryptic ones.
• DNA sequencing of other genes, such as 16S rRNA, cytochrome b and nuclear 18S and 28S rDNA, for phylogenetic trees at different depths.
• DNA–DNA hybridisation and protein and allozyme electrophoresis to estimate genetic distance.
• PCR-based markers: RFLP, RAPD, AFLP, microsatellites and SNPs for population structure, hybridisation and relationships of close species.
• Genomics: whole mitochondrial and nuclear genomes give high-resolution phylogenies.

Molecular clocks also date divergence and test the monophyly of groups, but the data should be combined with morphology (integrative taxonomy).

(e) Cladistics and the international code of nomenclature

Cladistics (Willi Hennig's phylogenetic systematics) classifies organisms by recency of common ancestry, using shared derived characters (synapomorphies) to group a common ancestor and all its descendants (monophyletic clades), shown as a cladogram. Shared ancestral characters (symplesiomorphies) are not used, and paraphyletic groups are rejected.

The International Code of Zoological Nomenclature (ICZN) governs animal names. Its main rules are:

• binomial nomenclature, a genus name with a capital and a species epithet in lower case, in italics (Panthera tigris);
• the principle of priority: the oldest available name, from Linnaeus's Systema Naturae, 10th edition (1758), is valid;
• type specimens: a holotype (or lectotype, neotype) fixes the application of a species name, and family names are based on a type genus;
• homonyms are not allowed, so the junior homonym is replaced;
• the family-group endings: -idae for family, -inae for subfamily, -oidea for superfamily;
• names must be published in a permanent, available form with Latin or Latinised forms.

The Code is administered by the International Commission on Zoological Nomenclature.