A transcription unit is a segment of DNA that is transcribed into a single RNA molecule. It is defined by three key regions that together control when, where, and how much RNA is produced. The three regions are: the promoter (where transcription begins), the structural gene (what is transcribed), and the terminator (where transcription ends). Understanding the transcription unit is fundamental to understanding gene expression — how the information stored in DNA is converted into functional RNA and eventually protein. The concept applies to prokaryotes and eukaryotes, though with important differences in complexity.

The promoter is a DNA sequence that serves as the binding site for RNA polymerase and associated transcription factors, initiating transcription. It is located upstream (5') of the structural gene — towards the 5' end of the structural gene. Important characteristics: (1) The promoter is NOT transcribed into RNA (it provides a signal for where to start, but is not itself part of the transcript). (2) RNA polymerase binds to the promoter and identifies the template strand. (3) The promoter effectively defines which strand is the template (antisense) strand and which is the coding (sense) strand. (4) Prokaryotic promoters: contain conserved sequences called Pribnow box (−10 region: TATAAT) and −35 region (TTGACA). (5) Eukaryotic promoters: TATA box (~25 bp upstream of transcription start site), CAAT box (~75 bp upstream), GC box. Different promoter strengths determine the level of gene expression — strong promoters → high transcription rate → more mRNA → more protein.

The structural gene is the DNA sequence between the transcription start site and the transcription termination site that is actually transcribed into RNA. In prokaryotes: structural gene is often polycistronic (multiple genes in one transcript, forming an operon). In eukaryotes: typically monocistronic (one gene per mRNA). The structural gene has two strands with specific designations: Template strand (antisense strand, non-coding strand, Crick strand): read 3'→5' by RNA polymerase. The strand that RNA polymerase uses as a template. Coding strand (sense strand, non-template strand, Watson strand): has the same sequence as the mRNA (except T→U). The coding strand is the strand that is NOT used as template. Runs 5'→3' and matches the mRNA sequence. The coding strand was historically assumed to carry the code — though it is actually the template strand that is read. The distinction between template and coding strand is fundamental to understanding gene expression.

The terminator is a DNA sequence that signals the end of transcription. It is located downstream of the structural gene — towards the 3' end of the coding strand (or 3' end of the mRNA). In prokaryotes, two types of terminators: (1) Intrinsic (ρ-independent): GC-rich palindromic sequence followed by poly-T. The RNA forms a hairpin loop (stem-loop) from the GC palindrome → destabilises the elongation complex → transcription terminates. (2) ρ (rho)-dependent: requires the ρ (rho) protein — an ATPase that tracks along the newly made RNA. When RNA polymerase pauses (at a pause site), ρ catches up → dissociates the RNA polymerase from the template. In eukaryotes: termination involves polyadenylation signals (AAUAAA) and cleavage/polyadenylation of the 3' end. The terminator defines the 3' end of the RNA transcript.

This is one of the most frequently confused topics in molecular biology. Template strand: the strand of DNA that is read by RNA polymerase in the 3'→5' direction. Complementary to the RNA transcript (with the substitution of U for T). Also called: antisense strand, non-coding strand, Crick strand, minus strand. Coding strand: has the same sequence as the mRNA (5'→3'), with T instead of U. NOT read by RNA polymerase. Also called: sense strand, non-template strand, Watson strand, plus strand. Example: If DNA coding strand is 5'-ATGCATGC-3', the mRNA is 5'-AUGCAUGC-3' (same, U instead of T), and the template strand is 3'-TACGTACG-5' (complementary). The promoter defines which strand is template for that particular gene. Different genes on the same chromosome may use different strands as templates.

Prokaryotic transcription: single RNA polymerase (core enzyme: α₂ββ'ω + sigma factor = holoenzyme). Sigma factor (σ) recognises the promoter. After initiation, σ dissociates. Transcription and translation are coupled (simultaneous, as there is no nuclear membrane separating them). Primary transcript = functional mRNA (no introns in most prokaryotic genes). Eukaryotic transcription: three RNA polymerases. RNA Pol I (nucleolus): rRNA. RNA Pol II (nucleoplasm): mRNA precursors (hnRNA). RNA Pol III: tRNA and 5S rRNA. Primary transcript (hnRNA = heterogeneous nuclear RNA) requires processing: 5' capping (7-methylguanosine cap added), 3' polyadenylation (poly-A tail of 200+ A residues added), splicing (introns removed by spliceosome, exons joined). Processed mRNA exported to cytoplasm for translation.

Eukaryotic pre-mRNA undergoes extensive post-transcriptional processing before it can be translated: (1) 5' Capping: a 7-methylguanosine (m⁷G) cap is added to the 5' end of the primary transcript. Functions: protects mRNA from 5'→3' exonuclease degradation, helps ribosome bind mRNA, required for nuclear export. (2) 3' Polyadenylation: after a specific sequence (AAUAAA in mRNA), the pre-mRNA is cleaved and a poly(A) tail of 200-250 adenosine residues is added by poly(A) polymerase. Functions: protects mRNA from degradation, aids nuclear export, helps translation. (3) Splicing: introns (non-coding intervening sequences) are removed and exons (expressed sequences) are joined together. Carried out by the spliceosome — a complex of snRNPs (small nuclear ribonucleoproteins). Alternative splicing: same pre-mRNA can be spliced differently in different tissues → different proteins from the same gene.

Jacob and Monod (1961, Nobel Prize 1965) proposed the Operon model for gene regulation in prokaryotes based on their study of the lac operon in E. coli. An operon is a functional unit of DNA consisting of: structural genes (lacZ, lacY, lacA encoding β-galactosidase, permease, transacetylase), an operator (DNA sequence where repressor binds), a promoter (where RNA polymerase binds), and a regulator gene (separate gene encoding repressor protein). In the absence of lactose (inducer): repressor (synthesised by regulator gene) binds to operator → blocks RNA polymerase from transcribing structural genes → no enzyme synthesis. In the presence of lactose: lactose → allolactose (inducer) → binds repressor → repressor changes shape → dissociates from operator → RNA polymerase transcribes structural genes → enzymes synthesised to metabolise lactose. This is a negative regulatory system — the repressor turns the operon OFF. Positive regulation: activator protein needed to turn operon ON (e.g., CAP protein with cAMP in lac operon positive regulation).