Bi23 Syllabus

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Introduction and Background: biochemistry, molecular biology, and biotechnology

  • Engineering across scales – molecules to organisms
  • Nucleic acid structure and chemistry.
  • Basic molecular biology techniques

Self-replicating molecules and the RNA world

  • The prebiotic world and some ideas for the first self replicator
  • What the RNA world might have looked like
  • The tragedy of the molecular commons - or, the origin of the cell
  • The twilight of the RNA empire and the rise of proteins

Evolving molecules in the lab

  • Function from random libraries - aptamer selections
  • Evolving catalysis - ribozymes
  • Evolving catalysis - proteins

Biosensors and detectors

  • Diagnostic and forensic PCR, RFLP, microarrays, molecular beacons
  • ELISAs and other antibody-based technologies
  • Aptamer and ribozyme-based detection
  • Interfacing the biomolecular and electronic worlds

Nanomaterials, nanodevices, and biomolecular computation

  • DNA as a programmable material
  • DNA as a nanomechanical device
  • DNA as a computer

Controlling gene expression: natural and engineered systems

  • Functional RNA in biology: catalysis, riboswitch, miRNA, RNAi
  • siRNA as a research tool and therapeutic
  • Programmable gene regulation

Synthetic biology – genetic circuits and control

  • Control circuits in biology
  • Forward engineering of genetic circuits
  • Modeling and standardization of biological parts

Systems biology – biology of complex networks

  • Network-scale biology: data, modeling, and theory
  • Systems-level properties: information processing, robustness, evolvability

Risk and responsibility in engineering the living world

  • Ownership of biological material and knowledge – the intellectual property landscape
  • Engineering biology and security issues
  • Engineering biology and access to innovation
  • Engineering challenges in the future