Transcription, RNA Processing, and Translation: Study Notes

Transcription, RNA Processing, and Translation

Overview of Transcription

Transcription is the process by which RNA polymerases synthesize an RNA copy of the instructions stored in DNA. This process is fundamental to gene expression and occurs in both prokaryotic and eukaryotic cells.

• RNA polymerases use ribonucleoside triphosphates (NTPs) to build RNA.

• They match complementary bases to one strand of DNA, known as the template strand.

• The non-template (coding) strand matches the sequence of the mRNA, except that uracil (U) replaces thymine (T).

Mechanism of Transcription

RNA polymerases perform template-directed synthesis in the 5' to 3' direction. Unlike DNA polymerases, RNA polymerases do not require a primer to begin transcription.

• Bacteria have one RNA polymerase, while eukaryotes have at least three distinct types.

Initiation of Transcription in Bacteria

Initiation is the first phase of transcription. In bacteria, RNA polymerase cannot initiate transcription on its own and requires a sigma protein to bind first. Together, they form a holoenzyme.

• Sigma protein recognizes promoter sites where transcription begins.

• Promoters are specific DNA sequences upstream of the transcription start site.

• The TATA box (TATAAT sequence) and the -35 box (TTGACA sequence) are key promoter elements.

Events Inside the Holoenzyme

Transcription begins when the sigma part of the holoenzyme binds to the promoter. The orientation of the promoter determines which DNA strand is used as the template and the direction of RNA polymerase movement.

• RNA polymerase opens the DNA double helix, creating a transcription bubble.

• The template strand is threaded through the active site, and incoming NTPs pair with complementary DNA bases.

Elongation and Termination in Bacteria

During elongation, RNA polymerase reads the DNA template and adds nucleotides to the 3' end of the RNA. Termination occurs when RNA polymerase transcribes a termination signal, which codes for RNA that forms a hairpin structure, causing the polymerase to separate from the RNA transcript.

• Hairpin structure in RNA leads to termination.

Transcription in Eukaryotes

Eukaryotic transcription differs from bacterial transcription in several ways:

• Three distinct RNA polymerases (I, II, III).

• Larger and more diverse promoters, including the TATA box.

• General transcription factors recognize promoters instead of sigma proteins.

• Termination involves a poly(A) signal and cleavage of the RNA downstream.

• Transcription occurs in the nucleus, while translation occurs in the cytoplasm.

RNA Processing in Eukaryotes

Primary Transcript and RNA Processing

In bacteria, transcription produces fully functional RNAs. In eukaryotes, the initial product is an immature primary transcript (pre-mRNA) that must undergo processing before translation.

• RNA processing includes splicing, capping, and addition of a poly(A) tail.

Discovery of Split Eukaryotic Genes

Protein-coding genes in eukaryotes contain noncoding DNA. Experiments showed that stretches of DNA are not present in mature mRNA, revealing the existence of introns (noncoding regions) and exons (coding regions).

• Introns are removed during RNA processing.

• Exons remain in the final mRNA.

RNA Splicing

Splicing removes introns from primary RNA transcripts. This process is catalyzed by small nuclear ribonucleoproteins (snRNPs), which form a complex called the spliceosome.

• Splicing allows different mRNAs and proteins to be produced from a single gene (alternative splicing).

• Four steps to splicing:

  1. snRNPs bind to exon–intron and intron–exon boundaries and to an A near the end of the intron.

  2. Other snRNPs join to form the spliceosome.

  3. The intron forms a lariat structure (stem plus loop).

  4. The lariat is cut out, exons are linked, and the intron is degraded.

Adding Caps and Tails to Transcripts

Pre-mRNAs are processed by two additional events:

• 5' cap: A modified guanine nucleotide that enables ribosomes to bind and protects the RNA from degradation.

• Poly(A) tail: 100–250 adenine nucleotides added after cleavage at the 3' end, needed for translation and protection from degradation.

• After splicing and addition of the cap and tail, the product is a mature mRNA.

• Mature mRNAs contain untranslated regions (UTRs) at both ends.

Summary Table: Comparison of Transcription in Bacteria and Eukaryotes

Feature	Bacteria	Eukaryotes
RNA Polymerases	One	Three (I, II, III)
Promoter Elements	TATA box, -35 box	TATA box, diverse elements
Initiation Factors	Sigma protein	General transcription factors
Termination Signal	Hairpin structure	Poly(A) signal and cleavage
Location	Cytoplasm	Nucleus (transcription), Cytoplasm (translation)
RNA Processing	None	Splicing, capping, poly(A) tail