Gene Expression I: The Genetic Code and Transcription – Study Notes

Chapter 18: Gene Expression I – The Genetic Code and Transcription

Directional Flow of Genetic Information

The central dogma of molecular biology describes the flow of genetic information within a cell. This process involves the transfer of information from DNA to RNA and then to protein, with some exceptions.

• Replication: DNA is copied to produce identical DNA molecules.

• Transcription: DNA is used as a template to synthesize RNA.

• Translation: RNA directs the synthesis of proteins.

• Reverse Transcription: In some viruses, RNA is reverse-transcribed to DNA.

• RNA Replication: Some viruses replicate their RNA genomes directly.

Example: Retroviruses use reverse transcription to convert their RNA genome into DNA.

Transcription Factors in Eukaryotic Gene Transcription

Transcription factors are essential proteins that regulate the transcription of nuclear genes by facilitating the binding of RNA polymerase to DNA.

• General Transcription Factors (TFs): Required for the transcription of all nuclear genes; the process begins with the binding of TFIID to the promoter.

• Preinitiation Complex: A large assembly of proteins, including RNA polymerase and multiple TFs, forms at the promoter to initiate transcription.

• Protein-Protein Interactions: Transcription factors interact with each other, making their coordinated action crucial for gene expression.

Example: TFIID recognizes the TATA box in the promoter region and recruits other TFs and RNA polymerase II.

Messenger RNA (mRNA) Processing in Eukaryotes

Eukaryotic mRNA undergoes several processing steps before it is translated into protein. These modifications are necessary for mRNA stability, export, and translation.

• 5' Capping: Addition of a 7-methylguanosine cap to the 5' end of the mRNA.

• Poly(A) Tail Addition: Addition of a long stretch of adenines (poly(A) tail) to the 3' end.

• Removal of Introns: Non-coding sequences (introns) are removed from the pre-mRNA.

Example: The mature mRNA in eukaryotes contains only exons, with a 5' cap and a poly(A) tail.

Transcription and Translation in Prokaryotes vs. Eukaryotes

There are key differences in how transcription and translation occur in prokaryotic and eukaryotic cells.

• Prokaryotes: Transcription and translation are coupled; mRNA is translated as soon as it is synthesized.

• Eukaryotes: Transcription occurs in the nucleus; mRNA must be processed and exported to the cytoplasm for translation.

• Heterogeneous Nuclear RNA (hnRNA): Refers to the initial, unprocessed RNA transcripts in the nucleus.

Example: Eukaryotic mRNA processing includes splicing, capping, and polyadenylation, which do not occur in prokaryotes.

Eukaryotic Transcripts: Pre-mRNA and mRNA

Pre-mRNA is the initial transcript produced from DNA, containing both exons and introns. It undergoes processing to become mature mRNA.

• Pre-mRNA: Contains both coding (exons) and non-coding (introns) sequences.

• Processing: Involves splicing out introns and adding 5' caps and 3' poly(A) tails.

• RNA Polymerase II: Synthesizes pre-mRNA and has a carboxy-terminal domain (CTD) that coordinates processing events.

Example: The mature mRNA is exported to the cytoplasm for translation.

5' Cap and 3' Poly(A) Tail

These modifications are critical for mRNA stability, export, and translation initiation.

• 5' Cap: A 7-methylguanosine is added to the 5' end via a 5'-5' triphosphate linkage.

• Functions: Protects mRNA from degradation, assists in ribosome binding for translation initiation.

• Poly(A) Tail: Added to the 3' end by poly(A) polymerase; typically 50–250 adenines.

• Functions: Enhances mRNA stability, aids in export from the nucleus, and assists in translation.

Example: The presence of a 5' cap and poly(A) tail distinguishes mature eukaryotic mRNA from other RNA species.

Splicing and Removal of Introns

Introns are removed from pre-mRNA by a process called splicing, which is essential for producing functional mRNA.

• Splice Sites: Conserved sequences at the 5' and 3' ends of introns guide the splicing machinery.

• Spliceosome: A large complex of small nuclear ribonucleoproteins (snRNPs) assembles on the pre-mRNA to catalyze splicing.

• Lariat Structure: During splicing, the intron forms a loop (lariat) before being excised.

• Exon Junction Complex: Proteins deposited at exon-exon boundaries facilitate mRNA export.

• Clinical Relevance: Splicing errors can lead to inherited diseases due to production of abnormal proteins.

Example: The human β-globin gene contains two introns that must be correctly spliced for proper hemoglobin production.

Comparison Table: Prokaryotic vs. Eukaryotic mRNA Processing

Feature	Prokaryotes	Eukaryotes
Location of Transcription	Cytoplasm	Nucleus
mRNA Processing	None	5' capping, poly(A) tail, splicing
Introns	Absent	Present (removed by splicing)
Translation	Coupled with transcription	Occurs after export to cytoplasm

Key Equations and Sequences

• Polyadenylation Signal: The consensus sequence for poly(A) addition is AAUAAA.

• Splice Site Consensus: 5' splice site: GU; 3' splice site: AG.

• General Transcription Reaction:

$\text{DNA} \xrightarrow{\text{Transcription}} \text{RNA} \xrightarrow{\text{Translation}} \text{Protein}$

$\text{Pre-mRNA} \xrightarrow{\text{Splicing}} \text{mRNA}$

Additional info: The notes above expand on the original slides and text, providing definitions, examples, and a comparison table for clarity and completeness.