Toward “Wet” Implementation of Genetic Algorithm for Protein EngineeringK. Sakamoto, M. Yamamura, H. Someya
Summarized by Ha-Young Jang
What Do the Following 3 Things
Have in Common? Genetic Algorithms (GAs)GAs design jet engines.
GAs draw criminals.
GAs program computers. A Potpourri of ApplicationsGeneral Electric’s Engineous (generalized engineering optimization).
Face space (criminology).
Genetic programming (machine learning). Gas Turbine DesignJet engine design at General Electric (Powell, Tong, & Skolkick, 1989)
Coarse optimization - 100 design variables.
Hybrid GA + numerical optimization + expert system.
Found 2% increase in efficiency.
Spending $250K to test in laboratory.
Boeing 777 design based on these results. ...
or Frankenfood?Scientists transferred daffodil genes into rice
Rice with beta-carotene may help prevent vitamin A deficiencies
Opponents fear unforeseen consequences of creating genetically modified organisms Genetic ChangesHumans have changed the genetics of other species for thousands of years
Artificial selection of plants and animals
Natural processes also at work
Mutation, crossing over Genetic EngineeringGenes are isolated, modified, and inserted into an organism
Made possible by recombinant DNA technology
Cut up DNA and recombine pieces
Amplify modified pieces Discovery of Restriction EnzymesHamilton Smith studied how bacterium Haemophilus influenzae cut invading viral DNA
Discovered that bacteria have an enzyme that chops up viral DNA Specific CutsRestriction enzymes cut DNA at a specific nucleotide sequence
Cuts leave “sticky ends” on DNA fragments that pair with matching cuts Making Recombinant DNA5’3’GC T T A AA A T T CGGA A T T CC T T A AG3’5’one DNA fragmentanother DNA fragment3’5’ Making Recombinant DNAnick5’3’3’5’GA A T T CC T T A AGnickGA A T T CC T T A AGDNA ligase action ...
7. Protein Synthesis and the Genetic Code a). Overview of translation
i). Requirements for protein synthesis
ii). messenger RNA
iii). Ribosomes and polysomes
iv). Polarity of protein synthesis
b). Transfer RNA
i). tRNA as an adaptor
ii). Amino acid activation
iii). Aminoacyl tRNA synthetases
iv). “Charged” tRNA
c). The genetic code
i). Codon-anticodon interactions
ii). Initiation codon in prokaryotes vs. eukaryotes
iii). Reading frame
d). Mutations affecting translation
i). Frameshift mutations
ii). Missense and nonsense mutations Overview of translation
last step in the flow of genetic information
definition of translation
requirements for protein synthesis
elongation and termination factors
aminoacyl tRNA synthetases
ATP Messenger RNA (mRNA) m7GpppCap5’5’ untranslated regionAUGinitiation
codontranslated (coding) region(AAAA)npoly(A) tail3’ untranslated regionUGAtermination
eukaryotic ribosome Polysomes
direction of translation is 5’ to 3’ along the mRNA
direction of protein synthesis is N terminus to C terminusUGA5’large ribosomal subunitsmall ribosomal subunitAUGpolysome nascent
polypeptideNNsubunits dissociate Transfer RNA
tRNA is the “adaptor” molecule in protein synthesis
CCA-3’ terminus to which amino acid is coupled
carries amino acid on terminal adenosine
anticodon stem and anticodon loop ...