Gene Expression and Regulation

Gene Expression and Regulation

Gene Expression and Regulation

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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.

Central Dogma of Molecular Biology simplified diagram

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).

Eukaryotic transcription initiation complex

⭐ 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.

Eukaryotic RNA processing and translation

Gene Regulation - Who's the Boss?

  • Prokaryotes: Primarily at transcription.
    • Operon Model: Coordinated gene clusters.
      FeatureLac Operon (Catabolic)Trp Operon (Anabolic)
      TypeInducible (Default OFF)Repressible (Default ON)
      Inducer/Corep.Allolactose (inducer)Tryptophan (co-repressor)
      RepressorActive alone; inactivated by inducerInactive 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.

Eukaryotic Gene Expression and Regulation

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.

Practice Questions: Gene Expression and Regulation

Test your understanding with these related questions

Which of the following statements is NOT applicable to bacterial genomes?

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Flashcards: Gene Expression and Regulation

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_____ is a technique to record ion current flow through a single protein channel.

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_____ is a technique to record ion current flow through a single protein channel.

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