Week 7: Genetic Circuits Part II
Context
Continuing from Week 6, we’ll deepen genetic circuit thinking and connect it to post-transcriptional and post-translational control.
Lecture (03/18)
- Slides: will be posted here.
- Class recording: https://mit.zoom.us/rec/play/hCZLhF5JpHgb7bIFG1lD92tNqSjYpdl6Io1-nqizSGxdHYvQPa5XGIvUS773z07T31VyspiRXhfSN9Cj.nmStNBmlzpp8uh06?accessLevel=meeting&canPlayFromShare=true&componentName=rec-play&continueMode=true&from=share_recording_detail&originRequestUrl=https%3A%2F%2Fmit.zoom.us%2Frec%2Fshare%2FDmkau4LZ9dibv5Y6PIThYjeS89-eIh4CSNzwYl-RoiVtciDLP-BT2Ewx_yhc5iyL.uk5XQn8Fzv_r5OQy
Recitation (03/19)
- Slides: will be posted here.
- Recitation recording: https://mit.zoom.us/rec/share/sEMhXPRvwp2JcHcfcHR_erjWeTj_8XA_PdWbgXbGSId_aJv9h6xMJZJm_a9bolhe.XikoakMZF4RuyKfE
Homework
This homework builds on the Week 7 lab and is a good moment to refine your final project plan and protocols.
Key link
- Week 7 Lab — Neuromorphic Circuits (Google Doc):
https://docs.google.com/document/d/1DwQ7I2By4BIKbnY48m6iQ_081TFI-C4xmoVOrPgcNVQ/edit?tab=t.0
Questions 1–3 (mandatory)
Q1. How do endoribonucleases (ERNs) decrease protein levels?
Name two differences between how ERNs work and how proteases work.
Tip
Helpful context for Q1 (read-only references):
- Endoribonucleases cleave RNA internally (phosphodiester bond) and are central to mRNA decay (e.g., RNase E).
- Proteases cleave peptide bonds in proteins; many cellular machines (e.g., ClpXP, Lon, proteasome) are ATP-dependent unfoldase–peptidase complexes.
Use these distinctions (substrate, chemistry, machinery/energy, cellular fate) to frame your answer.
Suggested explorations (optional, aligns with Part II theme)
- Bistability & oscillations: revisit classic circuits (toggle switch; repressilator) and note what parameters control switching/period.
- Layering control: combine transcriptional logic with RNA-level decay or proteolysis tags to sharpen responses.
- Model quick-checks: use iBioSim/Cello or your preferred simulator to sanity-check qualitative behavior.
What to submit
- Answers to Q1–Q3 (Q1 prompt above; Q2–Q3 per lab/recitation).
- 1–2 screenshots/figures that support your reasoning (e.g., model sketch, truth table, design diagram).
- One short paragraph on how this informs your final project plan.
References & reading
- mRNA decay / endoribonucleases: RNase E review (Nature Reviews Microbiology); roles in RNA metabolism (Microbiology Spectrum).
- ATP-dependent proteases: overview of bacterial energy-dependent proteases (Trends in Biochemical Sciences).
- Circuit classics: genetic toggle switch; repressilator (Nature, 2000).
- Tools: iBioSim (model/analysis), Cello (design automation).