Revision sheet: Gene Expression and RNA Processing

Molecular Biology: Gene Expression & RNA

1. 📌 Essentials

• Transcription: DNA to RNA synthesis by RNA polymerase.
• RNA processing: Capping, polyadenylation, splicing (removal of introns).
• Translation: mRNA decoding into amino acid chains by ribosomes.
• Promoter sequences: Bacterial (-10, -35); Eukaryotic (TATA box).
• RNA types: mRNA, tRNA, rRNA, snRNA, regulatory RNAs.
• Genetic code: 64 codons, AUG start, UAA/UAG/UGA stop.
• RNA modifications: 5′ cap, 3′ poly-A tail, sp.
• RNA's catalytic role: Ribozymes, self-replication- Gene structure: Exons (coding), introns (noncoding).
• Key differences: Prokaryotic vs eukaryotic transcription and processing.

2. 🧩 Key Structures & Components

• RNA polymerase — enzyme synthesizing RNA from DNA template.
• Promoters — DNA sequences signaling initiation (-10, -35 in bacteria; TATA in eukaryotes).
• snRNPs — small nuclear ribonucleoproteins involved in splicing.
• Ribosome — molecular machine translating mRNA; has A, P, E sites.
• tRNA — adaptor molecules matching codons to amino acids.
• mRNA — messenger RNA carrying genetic info.
• Spliceosome — complex of snRNPs executing splicing.
• Ubiquitin-proteasome system — degrades proteins tagged with ubiquitin.
• RNA modifications — 5′ cap, 3′ poly-A tail, exon junction complexes.
• Genetic code — codon table translating nucleotide triplets into amino acids.

3. 🔬 Functions, Mechanisms & Relationships

• Transcription initiation:
  • Bacteria: sigma factor binds -10/-35 promoter.
  • Eukaryotes: TFIID binds TATA box, recruits RNA polymerase II.
• Elongation:
  • RNA polymerase moves 3′-to-5′ on DNA, synthesizes RNA 5′-to-3′.
• Termination:
  • Bacteria: specific terminator sequences.
  • Eukaryotes: cleavage and polyadenylation signals.
• RNA processing:
  • 5′ capping stabilizes mRNA and aids translation.
  • Poly-A tail enhances stability and export.
  • Splicing removes introns, joins exons.
• Translation:
  • Initiation involves eIFs and initiator tRNA binding start codon.
  • Ribosome moves along mRNA, decoding codons.
  • Polyribosomes produce multiple proteins simultaneously.
• Protein regulation:
  • Post-translational modifications modulate activity.
  • Proteasome degrades ubiquitinated proteins.
• RNA's catalytic activity:
  • Ribozymes catalyze reactions, supporting RNA world hypothesis.
• Gene expression hierarchy:
  • DNA → Transcription → RNA processing → Export → Translation → Protein.

4. Comparative Table: Prokaryotic vs Eukaryotic Transcription

Item	Prokaryotes	Eukaryotes	Notes / Differences
Promoter sequences	-10 and -35 regions	TATA box (~25-30 bp upstream)	Eukaryotes require general transcription factors
RNA polymerase	Single type	Multiple types (I, II, III)	Different polymerases for different RNAs
Initiation factors	Sigma factor guides RNA polymerase	TFIID, TFIIB, TFIIF, TFIIH, etc.	Complex assembly in eukaryotes
Transcription site	Cytoplasm	Nucleus	Eukaryotic transcription occurs in nucleus
Processing of RNA	Minimal	Extensive (capping, splicing, poly-A)	Eukaryotic mRNA is processed before export

5. 🗂️ Hierarchical Diagram

Gene Expression System
 ├─ DNA
 │    ├─ Promoter
 │    ├─ Exons
 │    └─ Introns
 ├─ Transcription
 │    ├─ Initiation
 │    ├─ Elongation
 │    └─ Termination
 ├─ RNA Processing
 │    ├─ Capping
 │    ├─ Splicing
 │    └─ Polyadenylation
 ├─ Export
 │    └─ Nuclear pore complex
 └─ Translation
      ├─ Ribosome assembly
      ├─ Codon decoding
      └─ Protein synthesis

6. ⚠️ High-Yield Pitfalls & Confusions

• Confusing promoter sequences: -10/-35 (bacteria) vs TATA box (eukaryotes).
• Mistaking introns for exons; introns are noncoding.
• Overlooking RNA modifications: capping and poly-A tail are crucial for stability.
• Assuming all RNA is translated; some RNAs (e.g., miRNA) are regulatory.
• Confusing initiation factors in eukaryotes with bacterial sigma factors.
• Believing splicing occurs after transcription; it is co-transcriptional.
• Misidentifying stop codons: UAA, UAG, UGA.
• Overlooking RNA's catalytic role in early evolution.
• Assuming proteasome degrades all proteins indiscriminately; it targets ubiquitinated proteins.

7. ✅ Final Exam Checklist

• Understand the core steps of transcription in prokaryotes and eukaryotes.
• Recognize key promoter elements and their binding proteins.
• Describe RNA polymerase structure and function.
• Explain RNA processing steps: capping, splicing, polyadenylation.
• Identify snRNPs and their role in splicing.
• Know the genetic code: codons, start/stop signals, degeneracy.
• Describe translation initiation, elongation, and termination.
• Understand ribosome structure and function.
• Recognize post-translational modifications and their effects.
• Comprehend protein degradation via proteasome and ubiquitin.
• Appreciate RNA's catalytic roles and evolutionary significance.
• Differentiate prokaryotic and eukaryotic transcription mechanisms.
• Be familiar with nuclear export signals and processes.
• Know alternative splicing and its contribution to proteomic diversity.
• Recall RNA modifications essential for stability and translation.
• Understand the hierarchical organization of gene expression.

End of Revision Sheet