Gene Expression and Regulation — AP Biology
1. DNA Replication ★★☆☆☆ ⏱ 5 min
DNA replication relies on a coordinated set of enzymes that work at the replication fork, the site where the double helix is unwound. Key enzymes have specialized roles:
- **Helicase**: Unwinds the double helix and breaks hydrogen bonds between complementary base pairs
- **Single-strand binding proteins (SSBPs)**: Stabilize separated strands to prevent reannealing
- **Topoisomerase**: Relieves supercoiling strain ahead of the replication fork
- **Primase**: Synthesizes a short RNA primer to initiate DNA synthesis, as DNA polymerases cannot start from scratch
- **DNA polymerase III**: Main prokaryotic synthesis enzyme, adds nucleotides in the $5' \rightarrow 3'$ direction, proofreads mismatches
- **DNA polymerase I**: Replaces RNA primers with DNA nucleotides
- **Ligase**: Seals gaps between Okazaki fragments on the lagging strand
Due to the fixed $5' \rightarrow 3'$ synthesis direction, DNA synthesis is continuous on the leading strand (toward the replication fork) and discontinuous on the lagging strand, which is made of short segments called Okazaki fragments.
Exam tip: Always label 5' and 3' ends when writing nucleic acid sequences on the exam, you will lose points for missing labels.
2. Transcription and Translation (The Central Dogma) ★★★☆☆ ⏱ 6 min
Transcription and translation are the two core steps of the central dogma of molecular biology (DNA $\rightarrow$ RNA $\rightarrow$ Protein), converting genetic information stored in DNA into functional proteins.
Transcription occurs in three steps: initiation (RNA polymerase binds to the promoter sequence), elongation (RNA is synthesized $5' \rightarrow 3'$ from the $3' \rightarrow 5'$ DNA template), and termination (RNA polymerase releases the completed transcript at a terminator sequence). Eukaryotic pre-mRNA undergoes three processing steps before export to the cytoplasm:
- Addition of a 5' modified guanine cap to protect mRNA from degradation and aid ribosome binding
- Addition of a 3' poly-A tail to stabilize mRNA and facilitate nuclear export
- Splicing: The spliceosome removes non-coding introns and joins coding exons. Alternative splicing produces multiple distinct mRNA isoforms from one gene, increasing proteome diversity.
Translation relies on three key components: mRNA (carries 3-nucleotide codons), tRNA (carries amino acids and has complementary anticodons), and ribosomes (made of rRNA and protein, with A (incoming tRNA), P (growing polypeptide), and E (exit) binding sites). Key steps are initiation (starts at the AUG start codon for methionine), elongation (peptide bonds form between amino acids), and termination (stops at a UAA, UAG, or UGA stop codon when a release factor binds).
3. Prokaryotic Gene Regulation: Operons ★★★☆☆ ⏱ 3 min
All operons share a common structure: a promoter (RNA polymerase binding site), an operator (binding site for a repressor protein that blocks transcription), and structural genes that code for proteins in the same metabolic pathway. There are two main types of operons:
- **Inducible operons**: Default state is off, activated by an inducer molecule when the target substrate is available. Example: *lac* operon for lactose metabolism.
- **Repressible operons**: Default state is on, repressed by a corepressor molecule when the end product of the pathway is abundant. Example: *trp* operon for tryptophan synthesis.
Exam tip: Examiners frequently test all four combinations of glucose/lactose presence for the *lac* operon, so memorize how each condition affects transcription.
4. Eukaryotic Gene Regulation ★★★★☆ ⏱ 4 min
Eukaryotes have complex multi-level gene regulation that enables cell-specific gene expression and cell differentiation, even though all somatic cells have identical genomic DNA. Regulation can occur at five main stages:
- **Epigenetic regulation**: Heritable chemical modifications to DNA or histones that alter chromatin structure without changing DNA sequence. DNA methylation represses transcription, while histone acetylation activates transcription.
- **Transcriptional regulation**: Cell-specific transcription factors (activators/repressors) bind to distant enhancer or silencer sequences to alter transcription levels.
- **Post-transcriptional regulation**: Includes alternative splicing and mRNA degradation by microRNAs (miRNAs).
- **Translational regulation**: Controls ribosome binding to mRNA to adjust protein synthesis rates.
- **Post-translational regulation**: Modifies protein activity or lifespan via folding, cleavage, phosphorylation, or ubiquitination (tagging for degradation).
5. Mutation Types and Phenotypic Effects ★★★☆☆ ⏱ 3 min
Mutations are grouped by their size and effect on the protein sequence:
- **Point mutations**: Single nucleotide pair changes: 1) Silent: no change to amino acid sequence due to genetic code redundancy, 2) Missense: changes one amino acid (effect varies), 3) Nonsense: creates a premature stop codon, almost always produces nonfunctional protein.
- **Frameshift mutations**: Insertion or deletion of 1 or 2 nucleotides, shifting the entire reading frame downstream, almost always producing nonfunctional protein. Insertions/deletions of multiples of 3 nucleotides do not cause frameshifts.
- **Chromosomal mutations**: Large-scale changes to chromosome structure (deletions, duplications, inversions, translocations), typically with severe phenotypic effects.
Common Pitfalls
Why: Students forget core directionality rules for nucleic acid polymerases.
Why: Students mix up which strand matches the mRNA sequence.
Why: Students incorrectly generalize prokaryotic regulatory mechanisms to eukaryotes.
Why: Students assume all insertions/deletions cause frameshifts.
Why: Students confuse the function of each operon type.