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)

Protein kinases
(figure) Protein kinase B phosphorylates protein kinase C to prevent it from phosphorylating something else. Is this a good device? How can you fix it? Goal: can you describe a biological function that you can use without worrying about the details?
 * No. Signal is specific. PEpS not interchangeable. Need common signal carrier.

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
 * 2) *Reuse functions
 * 3) **Call function more than once
 * 4) *Nest functions
 * 5) Even with differences, we've been able to map to biology
 * 6) *We've made genetic devices that can respond to intermediate levels of an input signal

Sender/receiver
Band detectors: detect intermediate concentration
 * i.e., AHL low, PoPS low
 * AHL high, PoPs low
 * AHL juuuuuust right, PoPS high