Transcription, Splicing, and Translation: Mechanisms and Regulation

Transcription, Splicing, and Translation

The Central Dogma

The central dogma of molecular biology describes the flow of genetic information within a biological system. It states that DNA is transcribed into RNA, which is then translated into protein.

• Transcription: Synthesis of RNA from a DNA template.

• Translation: Synthesis of proteins from an mRNA template.

Nonstandard Codons

Some codons can code for amino acids differently in certain organisms or organelles, but the genetic code is largely universal.

Transcription and Splicing

RNA Polymerase Holoenzyme

RNA polymerase is the enzyme responsible for synthesizing RNA from a DNA template. In eukaryotes, there are three main types:

• RNA Polymerase I: Synthesizes rRNA

• RNA Polymerase II: Synthesizes mRNA ("typical genes")

• RNA Polymerase III: Synthesizes tRNA and 5S rRNA

Transcription Initiation

• Promoter: DNA sequence where RNA polymerase binds to initiate transcription.

• Synthase: Enzyme that catalyzes the synthesis of a compound.

• Initiation (in prokaryotes): Involves recognition of the promoter and formation of the transcription initiation complex.

Prokaryotic Initiation

• TATA box: Conserved DNA sequence found in promoters, important for transcription initiation.

• Start site: The location where transcription begins.

Eukaryotic Promoters

• The distance between the TATA box and the transcription site is usually 25-30 nucleotides.

• Promoters contain enhancers and repressors that regulate gene expression.

Synthase 5' to 3'

RNA is synthesized in the 5' to 3' direction.

Prokaryotic Termination

• Often involves inverted repeats that form hairpin structures in the RNA, causing termination.

Eukaryotic Termination

• Recognition of termination sequences (e.g., AAUAAA) signals the end of transcription.

RNA Processing

Cleavage of pre-mRNA

As RNA polymerase continues transcription, the pre-mRNA is cleaved and processed.

snRNAs (Small Nuclear RNAs)

• U1, U2, U4, U5, U6: Components of the spliceosome, which removes introns from pre-mRNA.

Capping and Polyadenylation

• Capping machinery: Adds a 5' methylguanosine cap to the mRNA.

• Polyadenylation machinery: Adds a poly-A tail to the 3' end of the mRNA.

Eukaryotic RNA Processing

• RNA is processed before leaving the nucleus.

• 5' cap and 3' poly-A tail are added.

• Splicing removes introns.

• RNA is exported to the cytoplasm for translation.

Spliceosome

• RNA pol II transcribes RNA.

• U2 is a key spliceosome element.

Translation

Translation Steps

• Initiation: Assembly of the translation initiation complex.

• Elongation: Addition of amino acids to the growing polypeptide chain.

• Termination: Release of the completed polypeptide.

Eukaryotic Translation Initiation

• Ribosome binds the 5' cap of mRNA.

• Scans for the start codon (AUG).

• Initiation factors assist throughout the process.

• Translation starts at the start codon and proceeds until a stop codon is reached.

Direction of Synthesis

• Proteins are synthesized from the N-terminus to the C-terminus.

Elongation

• GTP is required for the release of amino acids by the ribosome.

Termination

• Eukaryotes have one release factor.

• Prokaryotes have multiple release factors (E. coli has 3).

Prokaryotic vs. Eukaryotic Translation

• Prokaryotes do not add a 5' cap to mRNA.

• No scanning for the start codon; initiation occurs at the Ribosome Binding Site (RBS) or Shine-Dalgarno Sequence.

Polycistronic RNA

• Prokaryotic ribosomes can translate polycistronic mRNA (multiple proteins from one mRNA).

• Eukaryotic ribosomes typically translate monocistronic mRNA (one protein per mRNA).

• Chloroplasts and mitochondria have their own ribosomes and may use polycistronic mRNA.

Genetic Code Universality

Most organisms use the same genetic code, with only minor differences in some cases (e.g., mitochondria).

Table: Comparison of Prokaryotic and Eukaryotic Transcription/Translation

Feature	Prokaryotes	Eukaryotes
RNA Polymerases	One main type	Three types (I, II, III)
mRNA Processing	None	5' cap, splicing, poly-A tail
Translation Initiation	RBS/Shine-Dalgarno	5' cap scanning
Polycistronic mRNA	Common	Rare
Release Factors	Multiple (e.g., 3 in E. coli)	One

Example: In E. coli, translation initiation occurs at the Shine-Dalgarno sequence, while in humans, the ribosome binds to the 5' cap and scans for the start codon.

Additional info: The notes above have been expanded with academic context to clarify the mechanisms and differences between prokaryotic and eukaryotic gene expression.