Gene Expression and Regulation

Basics & Central Dogma - Code of Life

• DNA: Double helix. Bases: Adenine (A), Guanine (G), Cytosine (C), Thymine (T). A=T, G≡C.
• RNA: Single-stranded. Bases: A, G, C, Uracil (U).
• Central Dogma: DNA $\xrightarrow{\text{Replication}}$ DNA $\xrightarrow{\text{Transcription}}$ RNA $\xrightarrow{\text{Translation}}$ Protein.
  • Reverse Transcription: RNA → DNA (retroviruses).
• Genetic Code: Triplet codons (3 bases = 1 Amino Acid).
  • 64 codons: 61 sense (for AAs), 3 stop (UAA, UAG, UGA). 📌 U Are Away, U Are Gone, U Go Away.
  • Start codon: AUG (Methionine).
  • Properties: Degenerate, unambiguous, universal (mostly), non-overlapping.

⭐ Degeneracy of the genetic code (multiple codons for one amino acid) acts as a mutation buffer.

Transcription - Scribing the Message

• Process: DNA template → complementary RNA. Enzyme: RNA Polymerase.
• Prokaryotes: Single RNA Pol. Holoenzyme (σ factor for promoter recognition).
• Eukaryotes:
  • RNA Pol I: rRNA (28S, 18S, 5.8S). Located in Nucleolus.
  • RNA Pol II: mRNA, snRNA, miRNA. Nucleoplasm. (📌 Most Sensitive to α-amanitin)
  • RNA Pol III: tRNA, 5S rRNA, U6 snRNA. Nucleoplasm.
• Key Steps:
  • Initiation: RNA Pol & General Transcription Factors (GTFs) bind promoter (e.g., TATA box ~-25 bp, CAAT box ~-75 bp). Forms initiation complex.
  • Elongation: RNA synthesis in 5'→3' direction. Template strand read 3'→5'.
  • Termination: Specific termination sequences signal release of RNA.
• Regulation: Enhancers (↑ rate, can be distant), Silencers (↓ rate).

⭐ Rifampicin inhibits prokaryotic DNA-dependent RNA polymerase (β subunit), crucial for TB treatment.

RNA Processing & Translation - Message to Protein

• RNA Processing (Eukaryotic Nucleus): Key modifications to pre-mRNA.
  • 5' Capping: Addition of $m^7G$ (7-methylguanosine) cap; aids ribosome binding, protects mRNA from degradation.
  • 3' Polyadenylation: Addition of poly-A tail (multiple adenine residues) to 3' end; enhances stability, facilitates nuclear export.
  • Splicing: Removal of introns (non-coding regions) and joining of exons (coding regions) by spliceosome complex (snRNPs + proteins). Alternative splicing can produce multiple protein isoforms from a single gene.
• Translation (Cytoplasmic Ribosomes): Synthesis of protein from mRNA template.
  • Genetic Code: Sequence of mRNA codons (triplets of nucleotides) determines amino acid sequence. AUG is the start codon (Methionine); UAA, UAG, UGA are stop codons. 📌 Mnemonic for Stop Codons: U Are Away (UAA), U Go Away (UGA), U Are Gone (UAG).
  • Key Players:
    • mRNA: Carries genetic code.
    • tRNA: Adaptor molecule with anticodon (pairs with mRNA codon) and attached amino acid.
    • Ribosomes: Composed of rRNA and proteins; site of protein synthesis (A, P, E sites).
  • Steps: Initiation (assembly of ribosomal subunits, mRNA, initiator tRNA), Elongation (codon recognition, peptide bond formation, translocation), Termination (recognition of stop codon, release of polypeptide).

⭐ Wobble hypothesis: The base at the 5' end of the tRNA anticodon can form non-standard base pairs with the base at the 3rd position of the mRNA codon. This allows a single tRNA to recognize multiple codons for the same amino acid, reducing the number of tRNAs needed.

Gene Regulation - Who's the Boss?

• Prokaryotes: Primarily at transcription.
  • Operon Model: Coordinated gene clusters.

    Feature	Lac Operon (Catabolic)	Trp Operon (Anabolic)
    Type	Inducible (Default OFF)	Repressible (Default ON)
    Inducer/Corep.	Allolactose (inducer)	Tryptophan (co-repressor)
    Repressor	Active alone; inactivated by inducer	Inactive alone; activated by co-repressor

  • Positive Control: e.g., CAP-cAMP in Lac operon.
• Eukaryotes: Complex, multi-level control.
  • Chromatin Remodeling: Histone Acetylation (↑ expression), Methylation (variable). 📌 HATs are HAppy (Active).
  • Transcriptional: Transcription Factors (TFs), enhancers (↑), silencers (↓).
  • Post-transcriptional: RNA processing (splicing, cap, tail), transport.
  • Translational: miRNAs, siRNAs (RNAi) degrade/block mRNA.
  • Post-translational: Folding, cleavage, modifications (e.g., phosphorylation).

⭐ Many eukaryotic genes are controlled by multiple enhancers and silencers, allowing for fine-tuned regulation in response to various signals.

High‑Yield Points - ⚡ Biggest Takeaways

• Lac operon exemplifies prokaryotic gene induction; Trp operon shows repression.
• Eukaryotic gene expression is controlled by transcription factors, enhancers/silencers, and chromatin structure.
• RNA Polymerase II is crucial for mRNA synthesis in eukaryotes.
• Post-transcriptional modifications include 5' capping, poly-A tail, and splicing of introns.
• The genetic code is degenerate, non-overlapping, and nearly universal.
• DNA methylation typically silences genes; histone acetylation often activates transcription.
• MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression post-transcriptionally.