28.4 Transcription of DNA

Transcription and RNA

RNA transcription is the process of copying a DNA sequence into RNA. It's the first step in gene expression, where genetic information flows from DNA → RNA → protein (the central dogma of molecular biology). Every protein your cells make starts with transcription, so this process sits at the heart of how genes actually get used.

Three major types of RNA come out of transcription, each with a distinct job:

• mRNA (messenger RNA) carries the genetic instructions from a gene to the ribosome, where proteins are built.
• rRNA (ribosomal RNA) forms the structural and catalytic core of ribosomes themselves.
• tRNA (transfer RNA) acts as an adapter, delivering the correct amino acid to match each codon during translation.

Stages of Transcription

Transcription happens in three stages: initiation, elongation, and termination. In eukaryotes it takes place in the nucleus; in prokaryotes it occurs in the cytoplasm.

1. Initiation

RNA polymerase binds to a promoter sequence located upstream of the gene. In eukaryotes, common promoter elements include the TATA box and CAAT box; in prokaryotes, the key consensus sequences sit at the -10 and -35 positions. Transcription factors help RNA polymerase recognize and bind these sequences. Once bound, the enzyme unwinds a short stretch of the DNA double helix to expose the template strand.

2. Elongation

RNA polymerase reads the template strand (3'→5') and synthesizes a complementary RNA strand in the 5'→3' direction. Ribonucleotides are added one at a time based on base-pairing rules:

• A on DNA pairs with U in RNA
• T on DNA pairs with A in RNA
• G pairs with C (and vice versa)

Notice the key difference from DNA replication: RNA uses uracil (U) instead of thymine (T). The growing RNA strand is sometimes called the coding strand because its sequence matches the non-template DNA strand (except with U replacing T).

3. Termination

Transcription ends when RNA polymerase encounters a termination signal in the DNA. The newly synthesized RNA is released, and the polymerase dissociates from the template. In prokaryotes, termination can be intrinsic (a hairpin loop forms in the RNA) or rho-dependent (the rho protein helps release the transcript). In eukaryotes, termination is coupled to cleavage and polyadenylation of the transcript.

Types of RNA and Their Functions

Messenger RNA (mRNA) is the direct readout of a gene. Its sequence is read in sets of three nucleotides called codons, each specifying a particular amino acid (or a stop signal). In eukaryotes, the primary transcript (pre-mRNA) undergoes processing before it can be translated.

Ribosomal RNA (rRNA) makes up most of the ribosome's mass. It isn't just structural scaffolding; rRNA is the actual catalyst (a ribozyme) that forms peptide bonds between amino acids during translation.

Transfer RNA (tRNA) is a small, cloverleaf-shaped molecule. One end carries a specific amino acid, while a three-base anticodon on the opposite loop pairs with the complementary mRNA codon. This is how the correct amino acid gets matched to each codon during protein synthesis.

Exons, Introns, and mRNA Processing

Eukaryotic genes are not continuous stretches of coding sequence. They contain exons (the segments that code for amino acids) interrupted by introns (non-coding sequences that do not appear in the final protein).

Transcription initially produces pre-mRNA, which includes both exons and introns. Before this transcript can leave the nucleus and be translated, it undergoes several processing steps:

1. 5' capping adds a modified guanine nucleotide to the 5' end, which protects the mRNA and helps ribosomes recognize it.
2. 3' polyadenylation adds a poly-A tail (a string of adenine nucleotides) to the 3' end, which stabilizes the mRNA and aids in export from the nucleus.
3. Splicing removes the introns and joins the remaining exons together. This is carried out by the spliceosome, a large complex made of small nuclear RNAs (snRNAs) and proteins.

One particularly important consequence of splicing is alternative splicing: by including or excluding certain exons, a single gene can produce multiple distinct mRNA variants. Each variant can encode a different protein isoform. This is a major source of protein diversity in eukaryotes, since the roughly 20,000 human genes can generate far more than 20,000 different proteins.

After processing, the mature mRNA consists only of exons (plus the 5' cap and poly-A tail) and is exported to the cytoplasm for translation.