History of the Membrane (Pump) Theory of the Living Cell from Its
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Single Molecule Enzymology À La Michaelis-Menten
Single molecule enzymology à la Michaelis-Menten Ramon Grima1, Nils G. Walter2 and Santiago Schnell3* 1 School of Biological Sciences and SynthSys, University of Edinburgh, Edinburgh, UK 2 Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA 3 Department of Molecular & Integrative Physiology, Department of Computational Medicine & Bioinformatics, and Brehm Center for Diabetes Research, University of Michigan Medical School, Ann Arbor, Michigan, USA * To whom the correspondence should be addressed. E-mail: [email protected] Review article accepted for publication to FEBS Journal special issue on Enzyme Kinetics and Allosteric Regulation 1 Abstract In the past one hundred years, deterministic rate equations have been successfully used to infer enzyme-catalysed reaction mechanisms and to estimate rate constants from reaction kinetics experiments conducted in vitro. In recent years, sophisticated experimental techniques have been developed that allow the measurement of enzyme- catalysed and other biopolymer-mediated reactions inside single cells at the single molecule level. Time course data obtained by these methods are considerably noisy because molecule numbers within cells are typically quite small. As a consequence, the interpretation and analysis of single cell data requires stochastic methods, rather than deterministic rate equations. Here we concisely review both experimental and theoretical techniques which enable single molecule analysis with particular emphasis on the major developments in the field of theoretical stochastic enzyme kinetics, from its inception in the mid-twentieth century to its modern day status. We discuss the differences between stochastic and deterministic rate equation models, how these depend on enzyme molecule numbers and substrate inflow into the reaction compartment and how estimation of rate constants from single cell data is possible using recently developed stochastic approaches. -
Introduction to the Cell Cell History Cell Structures and Functions
Introduction to the cell cell history cell structures and functions CK-12 Foundation December 16, 2009 CK-12 Foundation is a non-profit organization with a mission to reduce the cost of textbook materials for the K-12 market both in the U.S. and worldwide. Using an open-content, web-based collaborative model termed the “FlexBook,” CK-12 intends to pioneer the generation and distribution of high quality educational content that will serve both as core text as well as provide an adaptive environment for learning. Copyright ©2009 CK-12 Foundation This work is licensed under the Creative Commons Attribution-Share Alike 3.0 United States License. To view a copy of this license, visit http://creativecommons.org/licenses/by-sa/3.0/us/ or send a letter to Creative Commons, 171 Second Street, Suite 300, San Francisco, California, 94105, USA. Contents 1 Cell structure and function dec 16 5 1.1 Lesson 3.1: Introduction to Cells .................................. 5 3 www.ck12.org www.ck12.org 4 Chapter 1 Cell structure and function dec 16 1.1 Lesson 3.1: Introduction to Cells Lesson Objectives • Identify the scientists that first observed cells. • Outline the importance of microscopes in the discovery of cells. • Summarize what the cell theory proposes. • Identify the limitations on cell size. • Identify the four parts common to all cells. • Compare prokaryotic and eukaryotic cells. Introduction Knowing the make up of cells and how cells work is necessary to all of the biological sciences. Learning about the similarities and differences between cell types is particularly important to the fields of cell biology and molecular biology. -
Anti-Duhring
Friedrich Engels Herr Eugen Dühring’s Revolution in Science Written: September 1876 - June 1878; Published: in Vorwärts, Jan 3 1877-July 7 1878; Published: as a book, Leipzig 1878; Translated: by Emile Burns from 1894 edition; Source: Frederick Engels, Anti-Dühring. Herr Eugen Dühring’s Revolution in Science, Progress Publishers, 1947; Transcribed: [email protected], August 1996; Proofed and corrected: Mark Harris 2010. Formerly known as Herr Eugen Dühring's Revolution in Science, Engels’ Anti-Dühring is a popular and enduring work which, as Engels wrote to Marx, was an attempt “to produce an encyclopaedic survey of our conception of the philosophical, natural-science and historical problems.” Marx and Engels first became aware of Professor Dühring with his December 1867 review of Capital, published in Ergänzungsblätter. They exchanged a series of letters about him from January-March 1868. He was largely forgotten until the mid-1870s, at which time Dühring entered Germany's political foreground. German Social-Democrats were influenced by both his Kritische Geschichte der Nationalökonomie und des Sozialismus and Cursus der Philosophie als streng wissenschaftlicher Weltanschauung und Lebensgestaltung. Among his readers were included Johann Most, Friedrich Wilhelm Fritzsche, Eduard Bernstein – and even August Bebel for a brief period. In March 1874, the Social-Democratic Workers’ Party paper Volksstaat ran an anonymous article (actually penned by Bebel) favorably reviewing one of Dühring's books. On both February 1 and April 21, 1875, Liebknecht encouraged Engels to take Dühring head-on in the pages of the Volksstaat. In February 1876, Engels fired an opening salvo with his Volksstaat article “Prussian Vodka in the German Reichstag”. -
Covalent Modification of Reduced Flavin Mononucleotide in Type-2 Isopentenyl Diphosphate Isomerase by Active-Site-Directed Inhibitors
Covalent modification of reduced flavin mononucleotide in type-2 isopentenyl diphosphate isomerase by active-site-directed inhibitors Takuya Nagaia,1, Hideaki Unnob,1, Matthew Walter Janczakc,1, Tohru Yoshimuraa, C. Dale Poulterc,2, and Hisashi Hemmia,2 aDepartment of Applied Molecular Bioscience, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan; bDivision of Chemistry and Materials Science, Graduate School of Engineering, Nagasaki University, Bunkyo-machi, Nagasaki, Nagasaki 852-8521, Japan; and cDepartment of Chemistry, University of Utah, 315 South 1400 East RM2020, Salt Lake City, UT 84112 Contributed by C. Dale Poulter, October 11, 2011 (sent for review July 9, 2011) Evidence for an unusual catalysis of protonation/deprotonation by not detect signals for putative radical intermediates (9). Attempts a reduced flavin mononucleotide cofactor is presented for type-2 to inhibit the enzyme by incubation with a cyclopropyl analogue isopentenyl diphosphate isomerase (IDI-2), which catalyzes isomer- of IPP, designed to rearrange to a homoallylic structure by a ization of the two fundamental building blocks of isoprenoid bio- radical clock mechanism, were unsuccessful (12, 13). Instead, the synthesis, isopentenyl diphosphate and dimethylallyl diphosphate. analogue was an alternate substrate that isomerized to the cor- The covalent adducts formed between irreversible mechanism- responding DMAPP derivative without a cyclopropylcarbinyl- based inhibitors, 3-methylene-4-penten-1-yl diphosphate or 3-oxi- homoallyl radical rearrangement. ranyl-3-buten-1-yl diphosphate, and the flavin cofactor were inves- Mechanism-based inhibitors of IDI-1, which are activated by tigated by X-ray crystallography and UV-visible spectroscopy. Both protonation of epoxide and diene moieties in these compounds, the crystal structures of IDI-2 binding the flavin-inhibitor adduct – and the UV-visible spectra of the adducts indicate that the covalent also inactivate IDI-2 (12 15). -
The Cell-Theory: a Restatement, History, and Critique Part III
*57 The Cell-theory: A Restatement, History, and Critique Part III. The Cell as a Morphological Unit By JOHN R. BAKER (From the Department of Zoology and Comparative Anatomy, Oxford) SUMMARY A long time elapsed after the discovery of cells before they came to be generally regarded as morphological units. As a first step it was necessary to show that the cell-walls of plants were double and that cells could therefore be separated. The earliest advances in this direction were made by Treviranus (1805) and Link (1807). The idea of a cell was very imperfect, however, so long as attention was con- centrated on its wall. The first person who stated clearly that the cell-wall is not a necessary constituent was Leydig (1857). Subsequently the cell came to be regarded as a naked mass of protoplasm with a nucleus, and to this unit the name of protoplast was given. The true nature of the limiting membrane of the protoplast was discovered by Overton (1895). The plasmodesmata or connective strands that sometimes connect cells were prob- ably first seen by Hartig, in sieve-plates (1837). They are best regarded from the point of view of their functions in particular cases. They do not provide evidence for the view that the whole of a multicellular organism is basically a protoplasmic unit. Two or more nuclei in a continuous mass of protoplasm appear to have been seen for the first time in 1802, by Bauer. That an organism may consist wholly of a syn- cytium was discovered in i860, in the Mycetozoa. -
Maud Menten, a Physician and Biochemist
Maud Menten Canadian medical researcher Maud Menten (1879-1960) has been called the "grandmother of biochemistry," a "radical feminist 1920s flapper," and a "petite dynamo." Not only was she an author of Michaelis-Menten equation for enzyme kinetics (like the plot in indigo in my portrait), she invented the azo-dye coupling for alkaline phosphatase, the first example of enzyme histochemistry, still used in histochemistry imaging of tissues today (which inspired the histology background of the portrait), and she also performed the first electrophoretic separation of blood haemoglobin in 1944! Born in Port Lambton, Ontario, she studied at the University of Toronto, earning her bachelor's in 1904, and then graduated from medical school (M.B., bachelor's of medicine) in 1907. She published her first paper with Archibald Macallum, the Professor of Physiology at U of T (who went on to set up the National Research Council of Canada), on the distribution of chloride ions in nerve cells in 1906. She worked a year at the Rockefeller Institute in New York, where along with Simon Flexner, first director of the Institute, she co-authored a book on radium bromide and cancer, the first publication produced by the Institute - barely 10 years after Marie Curie had discovered radium. She completed the first of two fellowships at Western Reserve University (now Case Western Reserve University), then she earned a doctorate in medical research in 1911 at U of T. She was one of the first Canadian women to earn such an advanced medical degree. She then moved to Berlin (travelling by boat, unfazed by the recent sinking of the Titanic) to work with Leonor Michaelis. -
The Population Problem Inherited Evolutio
2000 Earthlearningidea - http://www.earthlearningidea.com/ top edge of Sorting out the evolution of evolution headlines page Lay out your own timeline of how the theory of evolution developed Cut off the left hand edge of these four Earthlearningidea sheets and stick them together to form a timeline. Then stick it down on a bench or table. The ‘Evolution of evolution’ timeline Cut out the milestone boxes in the evolution of evolutionary theory below into strips. Leave the dates attached for less able pupils, but remove them for the more able. Then invite the pupils to sort out the headlines 1975 and place them in the correct places on the timeline – to show how evolutionary theory Photo: Chris King evolved. Species static This image is in the public The early part of the bible is interpreted to show that domain because species are static and there is no evolution. The date of its copyright has expired. 1650 creation of all species is calculated by Archbishop Ussher as 4004BC. Archbishop Ussher Evolution – but how? This image is in the public Early evolutionary ideas are presented by natural domain because 1740 philosophers, Pierre Maupertuis and Erasmus Darwin. its copyright has - expired. 1796 1950 Pierre Maupertuis The population problem This image is in the public Thomas Malthus publishes his idea that populations domain because increase geometrically (2,4,16) whilst food production its copyright has 1798 only increases arithmetically (2,3,4) so there must be expired. population crashes. Thomas Malthus Inherited evolution Permission is granted to copy, Jean-Baptiste Lamarck develops his evolutionary theory distribute and/or – that evolution occurs because offspring change in modify this document under 1800 response to the environment, and these changes are the terms of the inherited from their parents (later shown to be 1925 GNU Free incorrect). -
Unifying Principles of Biology - Advanced
Unifying Principles of Biology - Advanced Douglas Wilkin, Ph.D. Niamh Gray-Wilson Say Thanks to the Authors Click http://www.ck12.org/saythanks (No sign in required) AUTHORS Douglas Wilkin, Ph.D. To access a customizable version of this book, as well as other Niamh Gray-Wilson interactive content, visit www.ck12.org CK-12 Foundation is a non-profit organization with a mission to reduce the cost of textbook materials for the K-12 market both in the U.S. and worldwide. Using an open-source, collaborative, and web-based compilation model, CK-12 pioneers and promotes the creation and distribution of high-quality, adaptive online textbooks that can be mixed, modified and printed (i.e., the FlexBook® textbooks). Copyright © 2016 CK-12 Foundation, www.ck12.org The names “CK-12” and “CK12” and associated logos and the terms “FlexBook®” and “FlexBook Platform®” (collectively “CK-12 Marks”) are trademarks and service marks of CK-12 Foundation and are protected by federal, state, and international laws. Any form of reproduction of this book in any format or medium, in whole or in sections must include the referral attribution link http://www.ck12.org/saythanks (placed in a visible location) in addition to the following terms. Except as otherwise noted, all CK-12 Content (including CK-12 Curriculum Material) is made available to Users in accordance with the Creative Commons Attribution-Non-Commercial 3.0 Unported (CC BY-NC 3.0) License (http://creativecommons.org/ licenses/by-nc/3.0/), as amended and updated by Creative Com- mons from time to time (the “CC License”), which is incorporated herein by this reference. -
Biology (BIOL) 1
Biology (BIOL) 1 Biology (BIOL) Courses BIOL 0848. DNA: Friend or Foe. 3 Credit Hours. This course is typically offered in Fall. Through the study of basic biological concepts, think critically about modern biotechnology. Consider questions like: What are the ethical and legal implications involving the gathering and analysis of DNA samples for forensic analysis and DNA fingerprinting? Are there potential discriminatory implications that might result from the human genome project? What are embryonic stem cells, and why has this topic become an important social and political issue? Will advances in medicine allow humans to live considerably longer, and how will a longer human life span affect life on earth? We will learn through lectures, lecture demonstrations, problem solving in small groups and classroom discussion, and make vivid use of technology, including short videos from internet sources such as YouTube, electronic quizzes, imaging and video microscopy. NOTE: This course fulfills a Science & Technology (GS) requirement for students under GenEd and the Science & Technology Second Level (SB) requirement for students under Core. Students cannot receive credit for this course if they have successfully completed Biology 0948. Course Attributes: GS Repeatability: This course may not be repeated for additional credits. BIOL 0948. Honors DNA: Friend or Foe. 3 Credit Hours. This course is not offered every year. Through the study of basic biological concepts, think critically about modern biotechnology. Consider questions like: What are -
Table of Contents Upcoming AAHM Meetings
Table of contents • General Information • Participant Guide (Alphabetical List) • CME Information • Acknowledgements • Book Publishers’ Advertisements • Program Overview • AAHM Officers, Council, LAC and Program Committee • Sigerist Circle Program • AAHM Detailed Meeting Program • Abstracts Listed by Session • Information and Accommodations for Persons with Disabilities • Directions to Meeting Venues • Corrections and Modifications to Program Upcoming AAHM Meetings 2016 Minneapolis, 28 April – 1 May 2017 Nashville, 4 - 6 May Alphabetical List of Participants and Sessions PC = Program Committee; OP = Opening Plenary; GL = Garrison Lecture; FL = Friday Lunch; SL = Saturday Lunch; RW = Research Workshop; SS = Special Session; SC = Sigerist Circle; DF = Documentary Film Åhren, Eva – I1 De Borros, Juanitia – E1 Heitman, Kristin – FL1 Anderson, Warwick – OP, E1 DeMio , Michelle – F1 Herzberg, David – G3 Andrews, Bridie – D2 Dodman, Thomas – G2 Higby, Greg – B4 Apple, Rima – A5 Dong, Lorraine – I5 Hildebrandt, Sabine - C3 Downey, Dennis – E4 Hoffman, Beatrix – SC, I3 Baker, Jeffrey – A3 Downs, James – F2 Hogan, Andrew – C2 Barnes, Nicole – B5, C1, PC Dubois, Marc-Jacques –C4 Hogarth, Rana – H4 Barr, Justin – D4, E5 Duffin, Jacalyn – G1 Howell, Joel – I4 Barry, Samuel – A2 Dufour, Monique – A5 Huisman, Frank – F2 Bhattacharya, Nandini–D2 Dwyer, Ellen – E2 Humphreys, Margaret - OP,GL Bian, He – D2 Dwyer, Erica - A1 Birn, Anne-Emanuelle –H3 Dwyer, Michael – E2 Imada, Adria - C5 Bivins, Roberta – F5 Inrig, Stephen – PC, D1 Blibo, Frank – C4 Eaton, Nicole – A4 Bonnell-Freidin, Anne - B2 Eder, Sandra - C2 Johnson, Russell- RW Borsch, Stuart – E3 Edington, Claire – E1 Jones, David – C4 Boster, Dea – I4 Engelmann, Lukas – A1 Jones, Kelly – B4 Braslow, Joel – E4 Espinosa, Mariola – FL2, H4 Jones, Lori – E3 Braswell, Harold – C5 Evans, Bonnie – A2 Brown, Theodore M. -
Genome As a Multipurpose Structure Built by Evolution Michel Morange
1 Genome as a multipurpose structure built by evolution Michel Morange, Centre Cavaillès, République des savoirs USR 3608, Ecole normale supérieure, 29 rue d’Ulm, 75230 Paris Cedex05, France Email: [email protected] Abstract The publication in 2012 of the results of the ENCODE program generated an acrimonious debate about the role of junk DNA. This debate is a symptom of the difficulties of dovetailing functional and evolutionary descriptions of genomes. My argument is that extant genomes are the result of a progressive evolutionary construction. To the basic function – to give rise to RNA and proteins – have been successively added other functions – regulation by microRNA and epigenetic marks, for instance. This process of complexification was not a regular one, but the result of a complex evolutionary history, different for the different genomes. Better knowledge of the evolutionary history of genomes would help to understand these structures and their functions. Historians and philosophers of biology have amply discussed the difficulty, even the impossibility, of providing a precise definition of a gene (Beurton et al. 2000). The genome no longer appears as a collection of similar genes, but as a multitasking structure formed of different types of genetic elements (Gingeras 2006). Participants in these debates nonetheless often agree on one issue, that the genome is (and has to be) something well defined: a collection of genes, a 2 reservoir of junk DNA, or a structure filled with regulatory sequences. My point of view will be different: the genome is what evolution has progressively made of it. This vision has three important consequences. -
Spontaneous Generation & Origin of Life Concepts from Antiquity to The
SIMB News News magazine of the Society for Industrial Microbiology and Biotechnology April/May/June 2019 V.69 N.2 • www.simbhq.org Spontaneous Generation & Origin of Life Concepts from Antiquity to the Present :ŽƵƌŶĂůŽĨ/ŶĚƵƐƚƌŝĂůDŝĐƌŽďŝŽůŽŐLJΘŝŽƚĞĐŚŶŽůŽŐLJ Impact Factor 3.103 The Journal of Industrial Microbiology and Biotechnology is an international journal which publishes papers in metabolic engineering & synthetic biology; biocatalysis; fermentation & cell culture; natural products discovery & biosynthesis; bioenergy/biofuels/biochemicals; environmental microbiology; biotechnology methods; applied genomics & systems biotechnology; and food biotechnology & probiotics Editor-in-Chief Ramon Gonzalez, University of South Florida, Tampa FL, USA Editors Special Issue ^LJŶƚŚĞƚŝĐŝŽůŽŐLJ; July 2018 S. Bagley, Michigan Tech, Houghton, MI, USA R. H. Baltz, CognoGen Biotech. Consult., Sarasota, FL, USA Impact Factor 3.500 T. W. Jeffries, University of Wisconsin, Madison, WI, USA 3.000 T. D. Leathers, USDA ARS, Peoria, IL, USA 2.500 M. J. López López, University of Almeria, Almeria, Spain C. D. Maranas, Pennsylvania State Univ., Univ. Park, PA, USA 2.000 2.505 2.439 2.745 2.810 3.103 S. Park, UNIST, Ulsan, Korea 1.500 J. L. Revuelta, University of Salamanca, Salamanca, Spain 1.000 B. Shen, Scripps Research Institute, Jupiter, FL, USA 500 D. K. Solaiman, USDA ARS, Wyndmoor, PA, USA Y. Tang, University of California, Los Angeles, CA, USA E. J. Vandamme, Ghent University, Ghent, Belgium H. Zhao, University of Illinois, Urbana, IL, USA 10 Most Cited Articles Published in 2016 (Data from Web of Science: October 15, 2018) Senior Author(s) Title Citations L. Katz, R. Baltz Natural product discovery: past, present, and future 103 Genetic manipulation of secondary metabolite biosynthesis for improved production in Streptomyces and R.