Eukaryotic Gene Expression and Protein Synthesis Mechanisms
Gene Regulation and Transcription
Bacteria: Default genes are ON; sigma factors recognize promoters; termination is rho-dependent or rho-independent. Eukaryotes: Default genes are OFF because DNA is wrapped in nucleosomes/chromatin.
- Pol II: Transcribes protein genes and many regulatory ncRNAs.
- PIC Assembly: TFIID recognizes TATA/Inr; PIC consists of Pol II + TFIIA/B/D/E/F/H.
- TFIIH: Opens DNA using ATP and phosphorylates Pol II CTD.
- CTD Phosphorylation: Coordinates initiation, elongation, RNA processing, and termination.
Chromatin and Epigenetic Control
Gene regulation determines cell identity. Regulation occurs at transcription, RNA processing, mRNA stability, translation, and post-translational modification.
- Enhancers: Act far from promoters via DNA looping; architectural proteins bend DNA.
- Combinatorial Control: Multiple TFs regulate one gene.
- Chromatin States: Euchromatin (open/active) vs. Heterochromatin (condensed/silent).
- Histone Modifications: Methylation and acetylation of histone tails regulate compaction. H3K9me recruits HP1 for constitutive heterochromatin; H3K27me mediates facultative heterochromatin via PRC2.
- Remodeling: HATs add acetyl groups (decompacting chromatin); HDACs remove them. Chromatin remodelers (SWI/SNF) use ATP to reposition nucleosomes.
mRNA Processing and Splicing
Eukaryotic mRNAs require a 5′ cap, splicing, and a poly-A tail. Processing is co-transcriptional, coordinated by Pol II CTD phosphorylation.
- 5′ Cap: 7-methylguanosine linked by 5′→5′ triphosphate; protects mRNA and promotes export.
- Splicing: Introns are removed by the spliceosome (U1/U2/U4/U5/U6 snRNPs) via two transesterification reactions.
- Polyadenylation: Endonuclease cleaves the transcript; poly-A polymerase adds residues template-independently.
Mobile Genetic Elements
DNA transposons use a cut/paste mechanism, while retrotransposons use copy/paste via an RNA intermediate and reverse transcriptase (RT). LINEs encode RT/endonuclease, while SINEs hijack LINE proteins.
Translation and Protein Synthesis
The genetic code is degenerate, with 61 sense codons and 3 stop codons. tRNAs form cloverleaf structures; wobble pairing at the third codon position allows fewer tRNAs to decode multiple codons.
- Aminoacyl-tRNA Synthetases: Charge tRNAs with the correct amino acid using ATP.
- Ribosome: Composed of rRNA and protein; small subunit decodes, large subunit catalyzes peptide bonds.
- Initiation: Bacteria use the Shine-Dalgarno sequence; eukaryotes use the 5′ cap and scan for AUG.
- Elongation: EF-Tu-GTP delivers aa-tRNA to the A site; EF-G-GTP drives translocation.
- Termination: Release factors (RFs) recognize stop codons; class I RFs mimic tRNA.
Protein Folding and Degradation
Chaperones like HSP70 and HSP60 (GroEL/ES) prevent aggregation. Proteins marked with K48 polyubiquitin chains by E3 ligases are degraded by the proteasome.