Stages and General Mechanism
Transcription takes place within a locally unwound region of DNA. The enzyme RNA polymerase independently unwinds the helix ahead of itself and rewinds it behind. Information reading always occurs from the structural part of the gene, with the coding strand serving as the template.
The entire process is divided into three basic stages:
- Initiation — assembly of the enzyme complex and protein factors at regulatory regions of DNA. It is here that the primary control of synthesis takes place, determining tissue specificity and differentiation processes.
- Elongation — direct extension of the polynucleotide chain of the newly forming RNA molecule.
- Termination — the enzyme reaches the termination site, stops synthesis, and detaches the complex from the DNA template.
Features of Transcription in Bacteria (Prokaryotes)
Bacteria manage with just a single variety of RNA polymerase (consisting of five subunits), which synthesizes all types of RNA: messenger (mRNA), transfer (tRNA), and ribosomal (rRNA).
Key role in initiating synthesis is played by sigma factor. It helps the enzyme recognize the promoter — the gene's starting region. The prokaryotic promoter has two conserved sequences:
- At the -35 bp position (base pairs from the start) — the sigma factor binding site (TTGACA sequence).
- At the -10 bp position — the Pribnow box (TATAAT). RNA polymerase binds to it, and strand unwinding begins here. The region is rich in A=T pairs connected by only two hydrogen bonds, which greatly facilitates DNA separation.
As soon as synthesis is initiated, the sigma factor detaches. A key feature of prokaryotes is that the processes are not separated. Translation (protein synthesis) begins at the 5' end of the new RNA even before transcription is fully completed.
Eukaryotic Transcription
In eukaryotes, transcription occurs exclusively in the cell nucleus. The reading unit is the transcripton, consisting of a regulatory region (not transcribed) and a coding region.
Special proteins—transcription factors—are required for the process, and the enzymatic apparatus is represented by three major nuclear polymerases (consisting of 8–12 subunits and having a larger mass compared to bacterial ones):
- RNA polymerase I — synthesizes ribosomal RNAs (rRNA).
- RNA polymerase II — produces messenger RNAs (mRNA) and small nuclear RNAs (snRNA).
- RNA polymerase III — is responsible for transfer RNAs (tRNA), 5S rRNA, and certain types of snRNA.
(Separate polymerases also exist in mitochondria and chloroplasts).
Eukaryotic promoters include the TATA box (Hogness box, position -25), which performs an auxiliary role, and the CCAAT box (position -75), which is critical for initiation.
Additionally, the activity of RNA polymerase II is controlled by long-range regulatory elements: enhancers (upregulate) and silencers (downregulate). They serve as binding sites for regulatory proteins and can influence a gene from a huge distance. Unlike in bacteria, the primary eukaryotic transcript is unstable and undergoes mandatory modification (processing) before exiting into the cytoplasm.
Briefly: answers to topical questions
What steps are included in the processing of the primary transcript in eukaryotes?
Primary transcript (pre-mRNA) processing in eukaryotes includes three main stages:
- Capping — addition of 7-methylguanosine to the 5' end of the transcript; provides protection and participates in the initiation of translation.
- Polyadenylation — addition of a poly-A tail to the 3' end; ensures molecule stability.
- Splicing — excision of introns and joining of exons; spliceosomes are involved.
To remember which RNAs are synthesized by the three eukaryotic polymerases (I, II, III), use the mnemonic R-M-T: I — Ribosomal (rRNA), II — Messenger (mRNA), III — Transfer (tRNA).
Class and exam questions
What is the difference between transcription in prokaryotes and eukaryotes?
Prokaryotes operate with a single RNA polymerase, and transcription and protein synthesis occur simultaneously. Eukaryotes have three types of nuclear polymerases, and the processes are separated: transcription takes place in the nucleus, while translation occurs in the cytoplasm.
What role does the sigma factor play?
This is a component of prokaryotic RNA polymerase necessary for promoter recognition (around the -35 bp region). After RNA synthesis begins, it detaches from the enzyme complex.
Why are enhancers and silencers needed?
These are long-range regulatory elements in eukaryotes. By binding to regulatory proteins, enhancers enhance transcription, whereas silencers suppress it, even when located thousands of base pairs away from the promoter.
Why does DNA unwind specifically at the Pribnow box region?
This region (-10 bp) is rich in adenine-thymine (A=T) pairs. They are connected by only two hydrogen bonds (as opposed to three in G≡C pairs), making it much easier to separate the strands here.
What else to study on this topic
- Detailed Structure of the Eukaryotic Transcripton
- Primary Transcript Processing and mRNA Maturation
- Functions and Classification of Transcription Factors
- Mechanisms of Tissue-Specific Gene Regulation
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