BE/APh161 – Physical Biology of the Cell!Rob Phillips Applied Physics and Bioengineering California Institute of TechnologyFirst topic!Gnome management: a feeling for the numbers!! Politicians and generals can make some information “classified” and it can be circumvented by cleverness. ! Taylor made simplifying assumptions such as “spherical” blast. ! This is a segue into our main topic: genomes and their use. Estimates on genome management. ! Same idea could be used to estimate genome length. ! The concept: figure out the length of the genome using a single picture and pure thought! (G. Stent)! Use the simplest nunchuk physics of random walks to estimate the genome size. ! What makes DNA different from some other polymer? The persistence length! ! The radius of gyration scales as N1/2, which allows us to estimate the number of such Kuhn segments and hence back out the genome length. ! Note: This also tells us that work needs to be done to squish genomes into their hosts. (G. Stent) (R. Kavenoff)Putting Genomes to work: The Central Dogma!! Francis Crick referred to nucleic acids and proteins as “the two great polymer languages”. ! One of the great stories of modern biology is the working out of the mechanisms behind the way information read out in one polymer language (nucleic acids) is converted into information in the second polymer language (proteins). ! A beautiful and key insight: the genetic code.Thinking Up the Number of Genes: “What is true for E. coli is true for the elephant”!(Berman et al.) The bet: genesweep pool- Science 6 June 2003: Vol. 300. no. 5625, p. 1484 A Low Number Wins the GeneSweep Pool Elizabeth Pennisi COLD SPRING HARBOR, NEW YORK--The human genome has been sequenced, but calculating the number of genes it contains is taking more time. DNA experts have nonetheless decided they know who made the best prediction. ! A betting pool (Las Vegas for estimates) was set up on the number of genes in the human genome and responses varied from 25,000 to 150,000. ! A winner was declared, but the issue remains unsettled. ! Simplest logic: use “typical” protein size of 300 amino acids, which requires roughly 1000 nucleotides to code for them. This naïve estimate says: € Ngenes≈ Nbp/1000! Works great for E. coli, fails miserably for humans (and elephants).The Problem With Eukaryotes!(Berman et al.) ! Conundrums and surprises are a great way to learn things. The failure of the simplest estimate for eukaryotes reveals the important concept of “split genes”, referring to the fact that the coding regions are riddled with “introns”. ! The failure of our estimate also reflects the existence of endogenous retroviruses and all sorts of other interesting genomic stories. (P. Chambon, Scientific American, 1981) (Mattick, 2004)Second topic!How fast do biological processes occur!The rates of things in biology: A feeling for the numbers!• Bio structures exist over a wide range of spatial scales… …and bio processes take place over time scales from < ns to the age of the Earth. • A standard stopwatch: the cell cycle of E.coli • Cells strategy: ! manage time by stringing together processes in succession; ! manipulate time (e.g., using enzymes) to alter the intrinsic rates of processes • To some extent, coupling btw temporal and spatial scales (small things tend to operate at faster rates…)The standard stopwatch!• Cell cycle = set of processes whereby a single cell becomes 2 daughter cells, through the process of cell division (courtesy of Linda Song)Growth Curves Reveal Cells Care What’s For Dinner!(Berman et al.) ! The fundamental mystery of life: Take 5 mL of solution with some salt and sugar, add a single cell, and 12 hours later you will have 1010 cells! ! These growth curves tell the story of how genes are turned on and off in response to environmental cues. Bacterial growth curvesThe hierarchy of temporal scales!Molecular motion of biochem. species as they interact and change identity Unfolding of the lives of individual cells Trajectories of entire speciesTo build a fly!Biological time scales in powers of 10: 10 days!• Drosophila melanogaster: a workhorse of developmental biology • ~ 10 days btw fertilization of the egg and the emergence of a fully functioning adult flyBiological time scales in powers of 10: 10 hours!• Development of the fly embryo: ~10 hrs • a single cell → 1000s of cells with particular spatial positions and functions • a dramatic part of embryonic development: the process of gastrulation (a series of folding events in the embryo → formation of the future gut)Time scales in embryonic development!Development in a box! Doubling time = 8min How are these spatial patterns of gene expression established? Patterns of gene expression in the fly embryo!Cell Division in the Fly Embryo!Biological time scales in powers of 10: 10s of seconds!• a swimming E.coli: episodes of directed motion, punctuated by rapid directional changes (courtesy of Howard Berg)Biological time scales in powers of 10: deciseconds!• AAs incorporation during protein synthesis • process which any cell must undertake to make a new cell• synthesis of mRNA molecules as faithful copies of the nucleotide sequence in the DNA • polymerization process catalyzed by enzyme RNA polymerase • the incorporation by RNA polymerase of nucleotides onto the mRNA during transcription happens a few times faster than AA incorporation by ribosomes during protein synthesis Biological time scales in powers of 10: deciseconds!How Fast Is the Information Read Out?!(Berman et al.) ! Amazing microscopy images of transcription “Christmas trees” at various times after treatment with an antibiotic. ! Rifampin stops transcription initiation, but not elongation. ! This was used to estimate the rate at which RNA polymerase produces the messenger RNA molecule. (L. S. Gotta et al, J. Bacteriol., 1991)Biological time scales in powers of 10: !milliseconds!• many proteins are able to operate at time scales much faster than the machinery carrying out the central dogma operations • E.g., many bio processes are dictated by the passage of ions across ion channels (scale of msec)Biological time scales in powers of 10: !µseconds!• Enzyme kinetics (µsec and faster) • Note: these time scales
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