Module 2 Expression Engineering 20 109 Lecture 1 October 11th 2007 Cite as Natalie Kuldell Course materials for 20 109 Laboratory Fundamentals in Biological Engineering Fall 2007 MIT OpenCourseWare http ocw mit edu Massachusetts Institute of Technology Downloaded on DD Month YYYY Scientific Endeavors Images of butterfly collection and evolving hominid skulls removed due to copyright restrictions Is a butterfly collection a science experiment Cite as Natalie Kuldell Course materials for 20 109 Laboratory Fundamentals in Biological Engineering Fall 2007 MIT OpenCourseWare http ocw mit edu Massachusetts Institute of Technology Downloaded on DD Month YYYY Charles Darwin was once asked if he thought that natural historians should collect data without the prejudice of a preformed hypothesis or whether they should be observing nature with a particular theory in mind In a stinging reply to friend the economist Henry Fawcett Darwin wrote that they may as well go into a gravel pit and count the pebbles and describe the colors From Erren T C et al Comparing Neanderthal and Human Genomes Science 315 no 5819 3 March 2007 1664 Cite as Natalie Kuldell Course materials for 20 109 Laboratory Fundamentals in Biological Engineering Fall 2007 MIT OpenCourseWare http ocw mit edu Massachusetts Institute of Technology Downloaded on DD Month YYYY The dynamic proteome not the static genome determines an organism s phenotype For instance the caterpillar and tadpole share genomes with the butterfly and the frog but their very different proteomes create very different organisms Images removed due to copyright restrictions Cite as Natalie Kuldell Course materials for 20 109 Laboratory Fundamentals in Biological Engineering Fall 2007 MIT OpenCourseWare http ocw mit edu Massachusetts Institute of Technology Downloaded on DD Month YYYY Eukaryotic Gene Expression Obstacles to expression Transcription Courtesy of Arkitek Studios Used with permission Source RNAi Interface animation for nature com http www nature com focus rnai animations index html Cite as Natalie Kuldell Course materials for 20 109 Laboratory Fundamentals in Biological Engineering Fall 2007 MIT OpenCourseWare http ocw mit edu Massachusetts Institute of Technology Downloaded on DD Month YYYY Eukaryotic Gene Expression mRNA processing Export Translation Courtesy of Arkitek Studios Used with permission Source RNAi Interface animation for nature com http www nature com focus rnai animations index html Cite as Natalie Kuldell Course materials for 20 109 Laboratory Fundamentals in Biological Engineering Fall 2007 MIT OpenCourseWare http ocw mit edu Massachusetts Institute of Technology Downloaded on DD Month YYYY DNA RNA Protein Movie source http www exploratorium edu imaging station gal media stemcells mouse embryonic 1 mouse embryonic 1 mov Credit Kristina Yu Courtesy of The Exploratorium The Exploratorium http www exploratorium edu This movie was taken over a 12 hour period 1 To cell s behavior genome engineering too slow 2 To understand cell s behavior we need a way to study them Cite as Natalie Kuldell Course materials for 20 109 Laboratory Fundamentals in Biological Engineering Fall 2007 MIT OpenCourseWare http ocw mit edu Massachusetts Institute of Technology Downloaded on DD Month YYYY Expression Engineering Pressure Points Figure courtesy of National Academy of Sciences U S A Used with permission Source Belle A et al Quantification of protein half lives in the budding yeast proteome PNAS 103 no 35 2006 13004 9 DOI 10 1073 pnas 0605420103 Copyright 2006 National Academy of Sciences U S A Cite as Natalie Kuldell Course materials for 20 109 Laboratory Fundamentals in Biological Engineering Fall 2007 MIT OpenCourseWare http ocw mit edu Massachusetts Institute of Technology Downloaded on DD Month YYYY Expression Engineering Pressure Points 1 txn processing export degradation Figure courtesy of National Academy of Sciences U S A Used with permission Source Belle A et al Quantification of protein half lives in the budding yeast proteome PNAS 103 no 35 2006 13004 9 DOI 10 1073 pnas 0605420103 Copyright 2006 National Academy of Sciences U S A Cite as Natalie Kuldell Course materials for 20 109 Laboratory Fundamentals in Biological Engineering Fall 2007 MIT OpenCourseWare http ocw mit edu Massachusetts Institute of Technology Downloaded on DD Month YYYY Expression Engineering Pressure Points 1 2 transcription translation processing folding export modification degradation localization Figure courtesy of National Academy of Sciences U S A Used with permission Source Belle A et al Quantification of protein half lives in the budding yeast proteome PNAS 103 no 35 2006 13004 9 DOI 10 1073 pnas 0605420103 Copyright 2006 National Academy of Sciences U S A Cite as Natalie Kuldell Course materials for 20 109 Laboratory Fundamentals in Biological Engineering Fall 2007 MIT OpenCourseWare http ocw mit edu Massachusetts Institute of Technology Downloaded on DD Month YYYY Expression Engineering Pressure Points 1 transcription 2 microRNA translation processing folding export modification degradation siRNA localization Figure courtesy of National Academy of Sciences U S A Used with permission Source Belle A et al Quantification of protein half lives in the budding yeast proteome PNAS 103 no 35 2006 13004 9 DOI 10 1073 pnas 0605420103 Copyright 2006 National Academy of Sciences U S A Cite as Natalie Kuldell Course materials for 20 109 Laboratory Fundamentals in Biological Engineering Fall 2007 MIT OpenCourseWare http ocw mit edu Massachusetts Institute of Technology Downloaded on DD Month YYYY Why care about gene expression Why work on a module called expression engineering 1 Disease from mis expression 2 Expression is part of cellular reactions to environment 3 Knowledge is good 4 Make things that are useful from gene expression regulation 5 Silencing timing of gene expression regulate growth and development Cite as Natalie Kuldell Course materials for 20 109 Laboratory Fundamentals in Biological Engineering Fall 2007 MIT OpenCourseWare http ocw mit edu Massachusetts Institute of Technology Downloaded on DD Month YYYY DNA RNA Protein Movie source http www exploratorium edu imaging station gal media stemcells mouse embryonic 1 mouse embryonic 1 mov Credit Kristina Yu Courtesy of The Exploratorium The Exploratorium http www exploratorium edu This movie was taken over a 12 hour period 1 To cell s behavior genome engineering too slow 2 To understand cell s behavior we