Types of RNA and the process of Transcription

The Three Major Types of RNA in Bacteria

In a bacterial cell, three distinct kinds of RNA work together to build a protein. Messenger RNA (mRNA) provides the actual template — the sequence of codons that will be read. Transfer RNA (tRNA) brings the correct amino acids to the growing protein chain and reads the genetic code on the mRNA. Ribosomal RNA (rRNA) plays both a structural and a catalytic role inside the ribosome during translation. All three are essential; none can be skipped.

Transcription in Bacteria — One Enzyme Does It All

Bacteria have a single DNA-dependent RNA polymerase that catalyses the transcription of all three types of RNA. This enzyme uses nucleoside triphosphates as substrates and polymerises RNA in a template-dependent fashion, following the rule of complementarity (A pairs with U, T pairs with A, C pairs with G, G pairs with C).

The process has three stages:

• Initiation: RNA polymerase binds to a specific DNA sequence called the promoter and begins transcription.
• Elongation: The enzyme somehow helps open the DNA helix and continues adding nucleotides. Only a short stretch of newly made RNA remains bound to the enzyme at any time.
• Termination: When the polymerase reaches a terminator region on the DNA, the nascent RNA falls off, and the RNA polymerase itself detaches. Transcription stops.

How the Same Enzyme Does Three Different Jobs

Here is an intriguing puzzle: RNA polymerase can only catalyse elongation by itself. How then does it manage initiation and termination? The answer lies in two transient helper factors.

• Initiation factor (σ, sigma): This factor associates with RNA polymerase temporarily, changing its specificity so that it recognises the promoter and starts transcription.
• Termination factor (ρ, rho): This factor associates with the polymerase later, altering its specificity so that it recognises the terminator and stops transcription.

Without these factors, the core enzyme can only elongate — it cannot start or stop on its own.

Coupled Transcription and Translation in Bacteria

Because bacteria have no nucleus, transcription and translation occur in the same compartment (the cytosol). Moreover, bacterial mRNA does not require any processing to become active. As a result, translation can begin on the mRNA even before the full mRNA molecule has been transcribed. This means transcription and translation are coupled in bacteria — a ribosome can start reading the 5' end of the mRNA while the 3' end is still being synthesised.

The Extra Complexities in Eukaryotes

Eukaryotic cells face two major additional complexities that bacteria do not.

First complexity — multiple RNA polymerases with division of labour. The nucleus contains at least three distinct RNA polymerases (organelles like mitochondria have their own separate RNA polymerase).

• RNA polymerase I transcribes the genes for ribosomal RNAs (28S, 18S, and 5.8S rRNAs).
• RNA polymerase II transcribes the precursor of mRNA, which is called heterogeneous nuclear RNA (hnRNA).
• RNA polymerase III transcribes tRNA, 5S rRNA, and small nuclear RNAs (snRNAs).

Second complexity — the primary transcript must be processed. The initial RNA transcript (hnRNA) contains both exons (coding sequences) and introns (non-coding intervening sequences). This primary transcript is non-functional. It must undergo three processing steps before it becomes mature mRNA.

1. Splicing: The introns are removed, and the exons are joined together in a defined order.
2. Capping: An unusual nucleotide — methyl guanosine triphosphate — is added to the 5' end of the hnRNA.
3. Tailing: Adenylate residues (200–300 of them) are added to the 3' end in a template-independent manner.

Only after this full processing is the hnRNA called mRNA. It is then transported out of the nucleus into the cytoplasm for translation.

Why These Complexities Matter

The split-gene arrangement (exons interrupted by introns) is probably an ancient feature of the genome. The presence of introns is reminiscent of antiquity, and the process of splicing represents the dominance of an RNA world in early evolution. In recent times, the understanding of RNA and RNA-dependent processes in living systems has assumed much greater importance.

The Genetic Code — A Triplet Code

During replication and transcription, one nucleic acid is copied to form another nucleic acid, so complementarity makes these processes easy to understand. But translation requires transferring information from a polymer of nucleotides to a polymer of amino acids. No complementarity exists between nucleotides and amino acids, nor could any be drawn theoretically. Yet evidence strongly supported the idea that changes in nucleic acids (genetic material) caused changes in amino acids in proteins. This led to the proposition of a genetic code that could direct the sequence of amino acids during protein synthesis.

The Triplet Hypothesis

It was George Gamow, a physicist, who argued that since there are only four bases and they must code for 20 amino acids, the code must be a combination of bases. He proposed that the code should be made up of three nucleotides — a triplet. This was a bold proposition because a permutation combination of four cubed (4 × 4 × 4) would generate 64 codons — many more than the 20 needed.

Deciphering the Code

Providing proof that the codon was a triplet was a daunting task. The chemical method developed by Har Gobind Khorana was instrumental in synthesising RNA molecules with defined combinations of bases (homopolymers and copolymers). Marshall Nirenberg's cell-free system for protein synthesis finally helped decipher the code. Severo Ochoa's enzyme (polynucleotide phosphorylase) was also helpful in polymerising RNA with defined sequences in a template-independent manner (enzymatic synthesis of RNA). The final result was a checkerboard for the genetic code.

Salient Features of the Genetic Code

1. The codon is triplet. 61 codons code for amino acids, and 3 codons do not code for any amino acid — they function as stop codons.
2. The code is degenerate. Some amino acids are coded by more than one codon.
3. The code is read in a contiguous fashion. There are no punctuations between codons. …