13.5 Gene Expression: Regulation, RNA & Protein Degradation

Gene Expression: From DNA to Degraded Protein

The PA-CAT Bulletin of Information, rev. 20240815 includes Gene Expression and its regulation in General Biology (Table 6). Gene expression is the full path from a DNA sequence to a functional protein product, and the cell controls that path at multiple checkpoints — transcription, RNA processing, translation, and protein degradation.

Transcription and Translation Recap

Transcription (in the nucleus, eukaryotes): RNA polymerase binds a promoter, unwinds DNA, and synthesizes mRNA 5' to 3' using one DNA strand as template. In eukaryotes the transcript is processed: a 5' 7-methylguanosine cap (stability and ribosome binding), a 3' poly-A tail (stability and export), and splicing that removes introns and joins exons via the spliceosome (snRNPs with small nuclear RNAs). The mature mRNA exits through a nuclear pore.

Translation (in the cytoplasm, on ribosomes): the mRNA is read 5' to 3' in triplets (codons). tRNA carries a specific amino acid and pairs its anticodon with the codon. Ribosomes (large + small subunit, rRNA + protein) catalyze peptide-bond formation. Translation has three stages: initiation (small subunit finds the start codon AUG, large subunit joins), elongation (peptide bonds form as the ribosome translocates), and termination (a stop codon recruits release factors and the polypeptide is released). The genetic code is degenerate (multiple codons per amino acid — 61 sense codons for 20 amino acids), unambiguous (one codon to one amino acid), and nearly universal (mitochondria have minor variations). AUG starts; UAA, UAG, UGA stop.

Regulatory Proteins and Prokaryotic Regulation

Gene expression is controlled by regulatory proteins that bind DNA:

• Activators increase transcription (e.g., CAP in the lac operon).
• Repressors block transcription (e.g., lac repressor when lactose is absent).
• Inducers disable repressors (allolactose induces the lac operon).

The lac operon is the classic prokaryotic model: when lactose is absent, a repressor binds the operator and transcription is off; when lactose is present, allolactose inactivates the repressor, and RNA polymerase transcribes the three lactose-metabolism genes (lacZ, lacY, lacA). CAP-cAMP also activates transcription when glucose is low, coupling sugar preference to gene expression. The trp operon is repressible — it is normally on but switches off when tryptophan is abundant (feedback repression), an efficient way to stop producing an amino acid the cell already has.

Eukaryotic Regulation: Enhancers and Transcription Factors

Eukaryotic regulation is more elaborate because of chromatin and nuclear compartmentalization:

• Transcription factors — proteins that bind specific DNA sequences (promoters or distant enhancers) and recruit or stabilize RNA polymerase. General transcription factors (TFIID, TFIIB, and others) assemble at the core promoter (TATA box); specific transcription factors tune which genes turn on in which cells.
• Enhancers — DNA sequences often thousands of base pairs away that loop back to contact the promoter via cohesin-mediated DNA looping, dramatically increasing transcription. A gene's expression pattern is shaped by its combination of enhancers.
• Silencers — enhancer-like elements that decrease transcription by binding repressors.
• Epigenetic regulation — DNA methylation at CpG islands (typically silences genes, e.g., imprinted genes, X-chromosome inactivation) and histone acetylation (loosens chromatin via neutralization of lysine charges, increasing transcription) alter accessibility without changing sequence. Histone deacetylation reverses the effect, condensing chromatin.

Post-transcriptional Regulation

Control does not end at transcription:

• Alternative splicing — one gene produces multiple mRNA isoforms by including or skipping exons, greatly expanding the proteome (humans have about 20,000 genes but more than 100,000 proteins). Errors in splicing cause disease (e.g., spinal muscular atrophy from SMN1/SMN2 splicing defects).
• RNA stability — the poly-A tail length and 3' UTR elements determine how long an mRNA survives; miRNAs bind 3' UTRs and trigger degradation or translational repression.
• RNA interference (RNAi) — small interfering RNAs (siRNAs) and microRNAs (miRNAs) load into the RISC complex, base-pair with target mRNAs, and either cleave them (siRNA, perfect match) or repress translation (miRNA, partial match). RNAi is both a research tool and a therapeutic approach (patisiran for hereditary transthyretin amyloidosis).

RNA's Many Roles

RNA is not just a messenger. Functional classes:

• mRNA — carries the coding sequence to the ribosome.
• tRNA — adapter matching codon to amino acid, charged by aminoacyl-tRNA synthetase.
• rRNA — structural and catalytic core of the ribosome (a ribozyme; the peptidyl transferase activity is rRNA, not protein).
• snRNA — spliceosome components that remove introns.
• miRNA / siRNA — gene silencing.
• lncRNA — long non-coding RNAs regulating chromatin and transcription (e.g., Xist silences the inactive X chromosome).

Protein Degradation: The Ubiquitin-Proteasome System

Proteins are not permanent; regulated destruction is essential for cell-cycle control, signaling, and quality control. The ubiquitin-proteasome pathway tags proteins for destruction: a cascade of E1 (activating), E2 (conjugating), and E3 (ligase) enzymes attaches a chain of ubiquitin molecules to a lysine on the target. The E3 ligase provides substrate specificity — it decides which protein is tagged. The 26S proteasome recognizes the polyubiquitin tag, unfolds the protein, and degrades it into peptides, recycling ubiquitin. Cyclin destruction at the end of mitosis is the textbook example — without cyclin degradation, the cell cycle stalls. Misfolded or damaged proteins that escape chaperone-assisted refolding are similarly removed; failure of this quality control contributes to neurodegenerative diseases such as Parkinson's, where alpha-synuclein aggregates overwhelm the proteasome.

Why This Matters for the PA-CAT

Test items may ask which RNA carries amino acids (tRNA), which machinery performs splicing (the spliceosome with snRNAs), how enhancers act at a distance (DNA looping), or what tags a protein for proteasomal degradation (ubiquitin). Linking each checkpoint — transcription to splicing to translation to degradation — to its molecular machinery lets you answer regulation items without memorizing disconnected facts.