# Gene Expression and Regulation
The central dogma describes information flow: DNA → RNA → Protein. AP Biology (Units 6–7) requires detailed understanding of replication, transcription, translation, and how gene expression is regulated in prokaryotes and eukaryotes.
1. DNA Replication
- Semi-conservative: each new molecule has one old strand + one new strand
- Helicase: unwinds and separates strands
- Primase: lays RNA primers
- DNA polymerase III: adds nucleotides 5'→3' (leading strand continuous, lagging strand in Okazaki fragments)
- DNA ligase: joins Okazaki fragments
- Proofreading: DNA polymerase checks for errors ( error rate → after proofreading)
2. Transcription
- RNA polymerase binds to promoter (TATA box in eukaryotes)
- In eukaryotes: transcription factors help RNA polymerase bind
- RNA polymerase reads template strand 3'→5', synthesises mRNA 5'→3'
- Base pairing: A→U, T→A, C→G, G→C
- Terminates at terminator sequence
Post-transcriptional Modification (Eukaryotes)
- 5' cap (modified GTP): protects from degradation, aids ribosome binding
- 3' poly-A tail (~200 A's): protects from degradation, aids export
- RNA splicing: introns removed by spliceosomes; exons joined
- Alternative splicing: different exon combinations → different proteins from one gene
3. Translation
- Initiation: small ribosomal subunit + mRNA + initiator tRNA (Met/AUG) + large subunit
- Elongation: tRNA anticodon matches mRNA codon at A site; peptide bond forms; ribosome translocates
- Termination: stop codon (UAA, UAG, UGA) → release factor → polypeptide released
The Genetic Code
- Triplet: 3 bases = 1 codon = 1 amino acid
- Degenerate: multiple codons for most amino acids (61 sense + 3 stop = 64 total)
- Universal: same code in nearly all organisms
- Non-overlapping: each base read once
4. Gene Regulation in Prokaryotes
The Lac Operon (E. coli)
Structure: Promoter — Operator — lacZ — lacY — lacA
Without lactose (glucose present):
- Repressor protein (from lacI gene) binds the operator
- RNA polymerase cannot transcribe the structural genes → genes OFF
With lactose (no glucose):
- Allolactose (lactose metabolite) binds repressor → repressor releases operator
- RNA polymerase can now transcribe lacZ, lacY, lacA → genes ON
- CAP (catabolite activator protein) + cAMP bind upstream → enhance transcription when glucose is absent
The Trp Operon (Repressible)
- When tryptophan is abundant: trp binds the repressor, activating it → repressor binds operator → genes OFF
- When tryptophan is scarce: repressor inactive → genes ON → trp synthesis enzymes produced
5. Gene Regulation in Eukaryotes
Regulation occurs at multiple levels:
| Level | Mechanism |
|---|---|
| Chromatin | DNA methylation (silences); histone acetylation (activates); chromatin remodelling |
| Transcriptional | Transcription factors, enhancers, silencers, mediator proteins |
| Post-transcriptional | Alternative splicing, mRNA stability, microRNA (siRNA, miRNA) |
| Translational | mRNA degradation rate, initiation factors |
| Post-translational | Protein folding, phosphorylation, ubiquitination (targeting for proteasome degradation) |
6. Mutations
| Type | Effect |
|---|---|
| Silent (synonymous) | No amino acid change (degenerate code) |
| Missense | Different amino acid; may or may not affect function |
| Nonsense | Creates premature stop codon → truncated, non-functional protein |
| Frameshift (insertion/deletion) | Shifts reading frame → all downstream amino acids wrong |
Worked Example
Question: Explain how the lac operon is regulated in the presence and absence of lactose. (4 points)
Solution:
Without lactose: The lac repressor (produced by the lacI gene) binds to the operator sequence, physically blocking RNA polymerase from transcribing the structural genes (lacZ, lacY, lacA). The operon is OFF and no lactose-metabolising enzymes are produced.
With lactose (and no glucose): Lactose is converted to allolactose, which binds to the repressor protein and causes a conformational change that prevents the repressor from binding the operator. The operator is now free, allowing RNA polymerase to transcribe the structural genes. Additionally, low glucose levels increase cAMP, which binds CAP (catabolite activator protein). The cAMP-CAP complex binds upstream of the promoter and enhances RNA polymerase binding, maximising transcription.
Practice Questions
- Compare the roles of DNA polymerase and RNA polymerase. (3 points)
- Explain why a frameshift mutation is generally more harmful than a point substitution. (3 points)
- Describe three post-transcriptional modifications in eukaryotes. (3 points)
- Compare regulation of the lac operon (inducible) and trp operon (repressible). (4 points)
Answers
- DNA polymerase synthesises new DNA during replication; reads 3'→5' and builds 5'→3'; requires a primer; has proofreading ability. RNA polymerase synthesises RNA during transcription; reads 3'→5' and builds 5'→3'; does NOT require a primer; no proofreading. Both add nucleotides by complementary base pairing.
Want to check your answers and get step-by-step solutions?
Summary
- Replication: semi-conservative; helicase, primase, DNA polymerase III, ligase.
- Transcription: RNA polymerase + promoter → mRNA; eukaryotes: capping, poly-A tail, splicing.
- Translation: ribosome reads mRNA codons → tRNA delivers amino acids → polypeptide.
- Prokaryotic regulation: operons (lac = inducible, trp = repressible).
- Eukaryotic regulation: chromatin modification, transcription factors, alternative splicing, miRNA, post-translational.
- Mutations: silent, missense, nonsense, frameshift — frameshifts most severe.