Transcription in Prokaryotes & Eukaryotes

NCERT grounding

NCERT Class XII Biology, Chapter 5 (Molecular Basis of Inheritance), Section 5.5 defines the process directly: "The process of copying genetic information from one strand of the DNA into RNA is termed as transcription." The text stresses that the principle of complementarity governs transcription, "except the adenosine complements now forms base pair with uracil instead of thymine." Crucially, unlike replication — where the total DNA of an organism gets duplicated — in transcription only a segment of DNA and only one of the strands is copied into RNA.

That single sentence forces three downstream ideas the syllabus then develops: the need to demarcate the region to be transcribed (the transcription unit), the need to choose one strand (template versus coding strand), and the need for a machine to read it (DNA-dependent RNA polymerase). Sections 5.5.1 to 5.5.3 cover the transcription unit, the relationship between transcription unit and gene, and the contrasting machinery of bacteria and eukaryotes. The NIOS supplement (Chapter 23, Section 23.7.3) reinforces the same sequence of steps and the role of the sigma and rho factors.

"Why both the strands are not copied during transcription has the simple answer. First, if both strands act as a template, they would code for RNA molecule with different sequences... Second, the two RNA molecules if produced simultaneously would be complementary to each other, hence would form a double stranded RNA." — NCERT Class XII Biology, Section 5.5

How transcription works

Transcription is RNA synthesis on a DNA template. The enzyme responsible is DNA-dependent RNA polymerase: it reads a DNA strand and polymerises ribonucleotides into a complementary RNA chain. Like DNA-dependent DNA polymerase in replication, RNA polymerase catalyses polymerisation only in the 5'→3' direction, and it uses nucleoside triphosphates both as substrates and as the energy source for the reaction. It also facilitates the local opening of the DNA helix — a useful NEET fact, since NEET 2020 asked which enzyme opens the DNA helix during transcription, and the answer is RNA polymerase itself, not a separate helicase.

Because RNA polymerase moves only 5'→3', the strand it actually copies must run 3'→5'. That strand is the template strand. The other strand, which is not copied, runs 5'→3' and is displaced during transcription. By NCERT's convention this displaced, non-coding strand is — somewhat counter-intuitively — called the coding strand, because its base sequence is identical to the RNA transcript except that thymine occupies the positions where the RNA has uracil. All reference points of a transcription unit are written with respect to the coding strand.

Transcription unfolds in three steps. The enzyme cannot perform all three on its own — a recurring NEET point. RNA polymerase by itself is capable only of elongation; it associates transiently with accessory factors to initiate and to terminate.

The base-pairing logic is identical to replication, with one substitution. Where DNA replication would place a thymine opposite adenine, transcription places a uracil. So a template strand reading 3'-ATGC-5' is transcribed into RNA reading 5'-UACG-3'. The coding strand of that same region reads 5'-TACG-3' — note it matches the RNA exactly, with T standing in for U. This is why the fastest way to write an mRNA sequence in an exam is to copy the coding strand and swap every T for a U.

The transcription unit and the gene

A transcription unit in DNA is defined primarily by three regions: a promoter, the structural gene and a terminator. The promoter and terminator flank the structural gene. The promoter sits towards the 5' end — described as upstream, with the reference made to the polarity of the coding strand — and provides the binding site for RNA polymerase. It is the presence of the promoter that defines which strand is template and which is coding: NCERT notes that by switching the positions of promoter and terminator, the definitions of coding and template strands would be reversed. The terminator lies towards the 3' end (downstream) and usually defines the end of transcription. Additional regulatory sequences may lie further upstream or downstream of the promoter.

A gene is the functional unit of inheritance. Defining a cistron as a segment of DNA coding for a polypeptide, the structural gene of a transcription unit can be monocistronic — mostly in eukaryotes — or polycistronic — mostly in bacteria. In eukaryotes the monocistronic structural genes have interrupted coding sequences: the genes are split. The expressed sequences that appear in the mature RNA are exons; the intervening sequences that do not appear in the mature RNA are introns. This split-gene arrangement is absent in bacteria and is the structural basis of the eukaryotic processing machinery discussed below.

Prokaryotes versus eukaryotes

In bacteria there are three major types of RNA — mRNA, tRNA and rRNA — and all three are needed to synthesise a protein: mRNA provides the template, tRNA brings amino acids and reads the genetic code, and rRNAs play structural and catalytic roles in translation. A single DNA-dependent RNA polymerase catalyses transcription of all three RNA types. This enzyme binds the promoter and initiates transcription, uses nucleoside triphosphates as substrate, polymerises in a template-dependent fashion following complementarity, facilitates opening of the helix, and continues elongation until it reaches the terminator — at which point the nascent RNA falls off along with the polymerase.

The bacterial enzyme is only capable of catalysing elongation. It associates transiently with the initiation factor sigma (σ) and the termination factor rho (ρ); association with these factors alters the specificity of the polymerase to either initiate or terminate. Because the bacterial mRNA needs no processing to become active, and because transcription and translation take place in the same compartment — there is no separation of cytosol and nucleus in bacteria — translation can begin well before the mRNA is fully transcribed. Transcription and translation are therefore said to be coupled in bacteria.

Eukaryotes add two complexities. First, there are at least three RNA polymerases in the nucleus (in addition to the organellar polymerase), with a clear division of labour. Second, the primary transcripts contain both exons and introns and are non-functional; they must be processed before use. These two facts together explain why eukaryotic transcription cannot be coupled to translation.

The division of labour among the eukaryotic polymerases is examined almost every year, so it is worth memorising precisely. RNA polymerase I transcribes the ribosomal RNAs 28S, 18S and 5.8S. RNA polymerase II transcribes the precursor of mRNA — the heterogeneous nuclear RNA (hnRNA). RNA polymerase III is responsible for tRNA, 5S rRNA and the small nuclear RNAs (snRNAs). A clean mnemonic: the numbers go up with the size of the product — Pol I makes the big rRNAs, Pol II makes the message, Pol III makes the small RNAs.

Processing of hnRNA into mature mRNA

Because eukaryotic genes are split, the primary transcript made by RNA Pol II — hnRNA — contains both exons and introns and is non-functional as made. Three processing events convert it into a translatable mRNA. Splicing removes the introns and joins the exons in a defined order. Capping adds an unusual nucleotide — methyl guanosine triphosphate — to the 5' end of the hnRNA. Tailing adds 200–300 adenylate residues (the poly-A tail) to the 3' end, in a template-independent manner. It is the fully processed hnRNA, now called mRNA, that is transported out of the nucleus for translation.

NCERT closes the section by noting the evolutionary significance: split genes probably represent an ancient feature of the genome, and the process of splicing "represents the dominance of RNA-world." For NEET, the exam-relevant takeaway is structural — spliceosomes (the splicing machinery) are absent in bacteria, which is why NEET 2017 could ask in which cells spliceosomes are not found, with bacteria as the answer.

Worked examples

Common confusion & NEET traps

Transcription questions punish three specific confusions: the template/coding strand naming, the mismatch between which strand is copied and which polarity it has, and the identity of the three eukaryotic polymerases. The callouts below isolate each.