User:Yeem/BE.180 notes/Semester review

Programming in BE

Abstract concepts

• Abstraction hierarchy: high to low
• Decouling: breaking a complex system down

Comparison of Python and Biology

Python

• Functions
• Classes
• Inheritance
  • Instances
  • Passing data

Biology

• DNA
  • TAATA, etc.
• Parts
  • Basic biological function encoded in DNA
• Devices
  • One or more parts that encode a human-defined function
• Systems
• One or more devices that perform a human-defined function

Recall that for an example of a genetic device, we spent a bunch of time making genetically encoded inverters, where one protein controls the operator of another protein. (see figure)

PoPS-based inverter

Protein kinases

Kinase cascade

(figure) Protein kinase B phosphorylates protein kinase C to prevent it from phosphorylating something else. Is this a good device?

• No. Signal is specific. PEpS not interchangeable. Need common signal carrier.

How can you fix it?

• ???

Goal: can you describe a biological function that you can use without worrying about the details?

Redundancy

DNA to RNA to Protein

• ATCG to AUCG (one to one mapping for DNA to RNA)
• Mapping via a triplet code (RNA to protein)
• Looking at a piece of DNA, since there's 20 amino acids and 64 possible combinations of 3 nucleotides, there's redundancy
• Redundancy means flexibility in the specific DNA sequence

If you had the coding region of a particular open reading frame, and you found that there was a restriction site in the middle of it, you could remove it by specifying the same amino acid with a different nucleotide sequence.

Programming in time & space

See other notes for more info

Explored two examples of early languages

• Growing point language ("GPL") developed by Coore
• "Crop circle language" language

1. With "structured computer programming", you can
   • Reuse functions
     • Call function more than once
   • Nest functions
2. Even with differences, we've been able to map to biology
   • We've made genetic devices that can respond to intermediate levels of an input signal

Sender/receiver

sender-receiver diagram

Band detectors: detect intermediate concentration

• i.e., AHL low, PoPS low
• AHL high, PoPs low
• AHL juuuuuust right, PoPS high