Chapter 13 Notes – Regulation of Gene Expression & Mutations

13.1 Prokaryotic Regulation

• Bacterial metabolic economy

  • Cells synthesize enzymes only when needed; saves energy & resources.

• Operon model (François Jacob & Jacques Monod, 1961)

  • Definition – group of structural + regulatory genes functioning as one transcriptional unit.

  • Regulatory gene

    • Located outside the operon.

    • Encodes a repressor protein that toggles operon activity.

  • Promoter (P)

    • Short DNA segment where RNA-polymerase initially binds.

  • Operator (O)

    • Short DNA sequence where an active repressor can attach.

  • Structural genes

    • 1–several contiguous encoding enzymes of a specific metabolic pathway.

    • Transcribed simultaneously as one polycistronic mRNA.

trp Operon (repressible; anabolic pathway)

• Regulatory gene makes an inactive repressor (apo-repressor).

• Tryptophan absent → repressor cannot bind O → operon ON (positive feedback) → enzymes for Trp biosynthesis synthesized.

• Tryptophan present → Trp acts as corepressor → binds repressor, activates it → repressor-Trp complex binds O → operon OFF (negative feedback).

lac Operon (inducible; catabolic pathway)

• Regulatory gene makes an active repressor by default.

• Lactose absent → repressor binds O → operon OFF.

• Lactose present → lactose binds repressor, inactivates it → RNA-polymerase binds P → transcribes β-galactosidase, permease, transacetylase.

Catabolite repression (CAP-cAMP layer)

• E. coli preferentially uses glucose.

• Glucose ↓ → cell cAMP ↑ → cAMP binds CAP (catabolite activator protein) → CAP-cAMP binds near P → enhances RNA-pol affinity → lac operon maximally ON.

• Glucose ↑ → cAMP low → CAP inactive → only basal transcription even if lactose present.

13.2 Eukaryotic Regulation (5 hierarchical levels)

Nuclear controls

1. Chromatin structure

   • DNA + histone octamer (8 proteins) = nucleosome ("beads-on-a-string").

   • Level of coiling governs accessibility:

     • Euchromatin – loose, transcriptionally active.

     • Heterochromatin – dense, inactive.

   • Epigenetic inheritance

     • Heritable changes without altering DNA sequence (e.g., histone modification, DNA methylation).

     • Impacts growth, aging, cancer, & explains atypical inheritance patterns.

2. Transcriptional control

   • Requires transcription factors (TFs) that assist RNA-pol II.

   • Activators bind enhancer DNA; looping brings enhancer close to promoter.

   • TFs are constitutive in cells but often require post-translational activation.

3. Post-transcriptional control

   • Acts on primary mRNA (pre-mRNA).

     • Alternative intron excision & exon splicing generate isoforms.

     • Regulates nuclear export speed; influences protein yield.

   • Example: Calcitonin gene → thyroid vs. hypothalamus splice variants produce different peptide hormones.

   • Small RNA (sRNA) pathways

     • Non-coding regions produce ≈ 21–24 nt RNAs.

     • miRNA – pairs imperfectly with mRNA → translation silencing/degradation.

     • siRNA – perfect base-pair → mRNA cleavage; forms RISC complex.

     • Collectively termed RNA interference (RNAi).

Cytoplasmic controls

4. Translational control

   • Factors influencing initiation & mRNA longevity:

     • Integrity of 5′ cap.

     • Length of 3′ poly-A tail.

5. Post-translational control

   • Regulates protein activation & half-life.

   • Proteases inside proteasomes/lysosomes perform targeted degradation.

   • Proteins may require chemical modifications (phosphorylation, cleavage) to become active.

13.3 Gene Mutations

• Definition – permanent nucleotide sequence change in DNA.

• Range of effects

  • No impact ⇢ complete loss of protein function.

• Categories by cell type

  • Germ-line → heritable.

  • Somatic → confined to body tissues.

Causes of mutations

• Spontaneous

  • Intrinsic chemical changes cause mispairing.

  • Movement of transposons ("jumping genes").

  • Replication errors; DNA-pol proofreading keeps error rate ≈ $1\times10^{-9}$ per base.

• Induced

  • Exposure to mutagens (radiation, organic chemicals). Many are also carcinogens.

  • Environmental sources: certain foods, tobacco smoke, etc.

• Detection – Ames test uses Salmonella his⁻ strains to quantify mutagenicity.

Molecular consequences

• Point mutation (base substitution)

  • Single-nucleotide change alters one codon.

  • Outcomes: silent, missense (reduced/non-functional protein), or nonsense.

• Frameshift mutation (insertion/deletion of 1–2 bases)

  • Shifts reading frame → usually non-functional protein.

  • Illustration:

  • Normal: THE CAT ATE THE RAT

  • Deletion: THE ATA TET HER AT

  • Insertion: THE CCA TAT ETH ERA T

• Human examples

  • Sickle-cell disease – point mutation in β-globin gene.

  • PKU – faulty phenylalanine hydroxylase; phenylalanine accumulates, causing intellectual disability.

  • Androgen insensitivity – non-functional androgen receptor; XY individuals develop female traits.

Mutations & cancer

• Cancer arises via accumulating mutations.

• Key gene classes

  • Proto-oncogenes – normal cell-division stimulators.

  • Mutation → oncogenes (constitutively active).

  • Tumor suppressor genes – brakes on the cell cycle.

• Oncogene activation + loss of tumor suppressor → uncontrolled proliferation & tumor formation.