Slide 1How Cells Decide as Seen Through Three Hall of Fame ``Model’’ OrganismsThe Central Dogma of Molecular Biology: How Genes Lead to ProteinsHow Are Genes Related to What an Organism Is Like?The Big MessageMeasuring the Diet of a BacteriumDeciding What to Eat: Giant Discoveries Often Arise From Seemingly Arcane TopicsThe Development of the Operon Concept: What Cells Eat and When They DieNot All DNA Codes for ProteinsRepressors: The CartoonActivators: The CartoonThe Single Molecule CensusWays to Measure Gene ExpressionCount the Messenger RNA MoleculesEnzymatic Assay or In-Situ HybridizationSlide 16Information Processing in Living Cells: Beyond First ApproximationsSimple Case of Turning a Gene “On”Slide 19Measuring mRNA & protein numbersSlide 21Transcriptional bursting in eukaryotesInput-Output Curves: An AnalogyYeast Care What They Eat Too - Galactose vs GlucoseChance Caught on a Wing: Decision Making and EvolutionSlide 26Slide 27Fun Case Studies: Changes in Body Plan in FishThe Ingredients of Evolution: Natural SelectionSlide 30Genes, Chromosomes and GenomesGenes, Chromosomes and GenomesAPh/BE161: Physical Biology of the CellWinter 2009“Lecture 6”Rob PhillipsHow Cells Decide as Seen Through How Cells Decide as Seen Through Three Hall of Fame ``Model’’ OrganismsThree Hall of Fame ``Model’’ Organisms(Berman et al.)E. coliyeast Fruit flyVarious organisms are accorded hall of fame status as ``model’’ organisms either because they are specialists at some particular process of interest or they are experimentally convenient (grow fast, easily accessible).Each of these organisms offers something extremely important on the question of how cells decide.The Central Dogma of Molecular The Central Dogma of Molecular Biology: How Genes Lead to ProteinsBiology: How Genes Lead to Proteins(Berman et al.)Crick and others mused over the ``two great polymer languages’’. Central dogma explains the chain of events relating them.The ribosome is the universal translating machine that speaks both languages.We have seen what genes are and how they serve as the informational memory of organisms. But we have NOT said how they are controlled.Now we have the background to tackle the question we started with: how do cells make decisions?How Are Genes Related to What an How Are Genes Related to What an Organism Is Like?Organism Is Like?(Berman et al.)How are the DNA and protein alphabets related?The sequence of A, T, G, C in the DNA is turned into a sequence of 20 amino acids strung together to make a protein.The Big MessageThe Big MessageThe Puzzle: All the cells in a given organism (almost) carry the samegenetic information. And yet, depending upon where they are withinthe organism, they turn out quite differently.The Insight: The genome (i.e. genetic material) is under exquisite control. Genes are turned on and off in response to environmental cues.This lecture: how we found out, some beautiful examples, where we stand now.Measuring the Diet of a BacteriumMeasuring the Diet of a BacteriumGrowth curves have served a central role in dissecting the physiology of cells of all types.In particular, we know much about how cells decide based upon watching them grow and seeing what they like to eat.Deciding What to Eat: Giant Discoveries Often Arise Deciding What to Eat: Giant Discoveries Often Arise From Seemingly Arcane TopicsFrom Seemingly Arcane Topics(Berman et al.)Fascinating twist of history of science: human curiosity leads to investigation of seemingly arcane topics (spectral lines of atoms, specific heats of solids, peculiarities in the orbits of Uranus or Mercury, etc.) from which emerge hugely important insights.An example: nutrition of single cells like yeast and bacteria.Yeast cells express preferences about which sugar to use.Interestingly, the proteins used to digest the less preferable sugars are only synthesized when those sugars are present and the more preferable sugars are absent.(Spiegelman et al., PNAS, 1944)The Development of the Operon Concept: What Cells The Development of the Operon Concept: What Cells Eat and When They DieEat and When They Die(Berman et al.)Studies of the cultures of bacterial cells sufficed to lead Jacob and Monod to formulate the operon concept - the revolutionary view that there are certain genes whose mission is to control other genes.This superseded the dictum of Beadle and Tatum which was ``one gene, one enzyme’’.The Mendelian revolution taken to the next stage.Bacterial growth curves(J. Monod)Not All DNA Codes for ProteinsNot All DNA Codes for Proteins(Berman et al.)The regulatory landscapeThe E. coli genome is a circle with roughly 4.7 million base pairs.How many genes? An estimate.The genes related to sugar usage have been one of the most important stories in the history of modern biology and biochemistry (and take us right back to the great debate on vitalism played out with Pasteur in the 1800s).“Promoter” region on DNA is subject to intervention by various molecular bouncers that govern the gene.Repressors: The CartoonRepressors: The CartoonRepressor molecules inhibit action of RNA polymerase.Repressors can be under the control of other molecules (i.e. inducers) that dictate when repressor is bound and not.Activators: The CartoonActivators: The CartoonActivator molecules enhance the action of RNA polymerase.Activators can be under the control of other molecules (i.e. inducers) that dictate when activator is bound and not.Activators “RECRUIT” the polymerase.Adhesive interaction between RNAPand activatorThe Single Molecule CensusThe Single Molecule Census(Beautiful work of David Goodsell)Ways to Measure Gene Ways to Measure Gene ExpressionExpressionBasic point: looking for “reporters” of the level of expression of gene of interest.Can ask the system to report on the level of gene expression at various steps in the processes linking DNA to active protein.Promoter occupancy, level of mRNA, level of active protein.This image shows a Drosophila embryo colored to show the expression patterns of early gene regulators. Each color represents the level of expression of one of three gene regulators, Knirps (green), Kruppel (blue), and Giant (red). Color intensity reflects a higher level of expression. The darker areas of the embryo are cells where none of these gene regulators are expressed, and the yellowish areas indicate that both Knirps and Giant are being
View Full Document
Unlocking...