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Biochemistry and the Genomic Revolution 1.1
Dedication About the authors Preface Tools and Techniques Clinical Applications Molecular Evolution Supplements Supporting Biochemistry, Fifth Edition Acknowledgments I. The Molecular Design of Life 1. Prelude: Biochemistry and the Genomic Revolution 1.1. DNA Illustrates the Relation between Form and Function 1.2. Biochemical Unity Underlies Biological Diversity 1.3. Chemical Bonds in Biochemistry 1.4. Biochemistry and Human Biology Appendix: Depicting Molecular Structures 2. Biochemical Evolution 2.1. Key Organic Molecules Are Used by Living Systems 2.2. Evolution Requires Reproduction, Variation, and Selective Pressure 2.3. Energy Transformations Are Necessary to Sustain Living Systems 2.4. Cells Can Respond to Changes in Their Environments Summary Problems Selected Readings 3. Protein Structure and Function 3.1. Proteins Are Built from a Repertoire of 20 Amino Acids 3.2. Primary Structure: Amino Acids Are Linked by Peptide Bonds to Form Polypeptide Chains 3.3. Secondary Structure: Polypeptide Chains Can Fold Into Regular Structures Such as the Alpha Helix, the Beta Sheet, and Turns and Loops 3.4. Tertiary Structure: Water-Soluble Proteins Fold Into Compact Structures with Nonpolar Cores 3.5. Quaternary Structure: Polypeptide Chains Can Assemble Into Multisubunit Structures 3.6. The Amino Acid Sequence of a Protein Determines Its Three-Dimensional Structure Summary Appendix: Acid-Base Concepts Problems Selected Readings 4. Exploring Proteins 4.1. The Purification of Proteins Is an Essential First Step in Understanding Their Function 4.2. Amino Acid Sequences Can Be Determined by Automated Edman Degradation 4.3. Immunology Provides Important Techniques with Which to Investigate Proteins 4.4. Peptides Can Be Synthesized by Automated Solid-Phase Methods 4.5. -
The Lock-And-Key Analogy in 20Th Century Biochemistry
From: Rebecca Mertens The Construction of Analogy-Based Research Programs The Lock-and-Key Analogy in 20th Century Biochemistry April 2019, 224 p., pb., ill. 34,99 € (DE), 978-3-8376-4442-5 E-Book: PDF: 34,99 € (DE), ISBN 978-3-8394-4442-9 When the German chemist Emil Fischer presented his lock-and-key hypothesis in 1899, his analogy to describe the molecular relationship between enzymes and substrates quickly gained vast influence and provided future generations of scientists with a tool to investigate the relation between chemical structure and biological specificity. Rebecca Mertens explains the appeal of the lock-and-key analogy by its role in model building and in the construction of long-term, cross-generational research programs. She argues that a crucial feature of these research programs, namely ascertaining the continuity of core ideas and concepts, is provided by a certain way of analogy-based modelling. Rebecca Mertens (PhD), born in 1984, is a postdoctoral researcher in the history and philosophy of science at the University of Bielefeld, Germany. She works on the role of analogies, models and forms of comparison in the history of molecular genetics and is a member of the collaborative research program "Practices of ComparisonÚ Ordering and Changing the World". During her graduate and doctoral studies, she was a visiting scholar at the École Normale Supérieure in Paris and a visiting graduate fellow at the Minnesota Center for Philosophy of Science. For further information: www.transcript-verlag.de/en/978-3-8376-4442-5 © 2019 -
Biographical References for Nobel Laureates
Dr. John Andraos, http://www.careerchem.com/NAMED/Nobel-Biographies.pdf 1 BIOGRAPHICAL AND OBITUARY REFERENCES FOR NOBEL LAUREATES IN SCIENCE © Dr. John Andraos, 2004 - 2021 Department of Chemistry, York University 4700 Keele Street, Toronto, ONTARIO M3J 1P3, CANADA For suggestions, corrections, additional information, and comments please send e-mails to [email protected] http://www.chem.yorku.ca/NAMED/ CHEMISTRY NOBEL CHEMISTS Agre, Peter C. Alder, Kurt Günzl, M.; Günzl, W. Angew. Chem. 1960, 72, 219 Ihde, A.J. in Gillispie, Charles Coulston (ed.) Dictionary of Scientific Biography, Charles Scribner & Sons: New York 1981, Vol. 1, p. 105 Walters, L.R. in James, Laylin K. (ed.), Nobel Laureates in Chemistry 1901 - 1992, American Chemical Society: Washington, DC, 1993, p. 328 Sauer, J. Chem. Ber. 1970, 103, XI Altman, Sidney Lerman, L.S. in James, Laylin K. (ed.), Nobel Laureates in Chemistry 1901 - 1992, American Chemical Society: Washington, DC, 1993, p. 737 Anfinsen, Christian B. Husic, H.D. in James, Laylin K. (ed.), Nobel Laureates in Chemistry 1901 - 1992, American Chemical Society: Washington, DC, 1993, p. 532 Anfinsen, C.B. The Molecular Basis of Evolution, Wiley: New York, 1959 Arrhenius, Svante J.W. Proc. Roy. Soc. London 1928, 119A, ix-xix Farber, Eduard (ed.), Great Chemists, Interscience Publishers: New York, 1961 Riesenfeld, E.H., Chem. Ber. 1930, 63A, 1 Daintith, J.; Mitchell, S.; Tootill, E.; Gjersten, D., Biographical Encyclopedia of Scientists, Institute of Physics Publishing: Bristol, UK, 1994 Fleck, G. in James, Laylin K. (ed.), Nobel Laureates in Chemistry 1901 - 1992, American Chemical Society: Washington, DC, 1993, p. 15 Lorenz, R., Angew. -
CV Sir Arthur Harden
Curriculum Vitae Prof. Dr. Arthur Harden Name: Sir Arthur Harden Lebensdaten: 12. Oktober 1865 ‐ 17. Juni 1940 Arthur Harden war ein britischer Chemiker. Nach ihm sind die Harden‐Young‐Ester (Zuckerphospha‐ te) benannt. Für seine Forschungen über die Gärung von Zucker und dessen Gärungsenzyme wurde er im Jahr 1929 gemeinsam mit dem deutsch‐schwedischen Chemiker Hans von Euler‐Chelpin mit dem Nobelpreis für Chemie ausgezeichnet. Werdegang Arthur Harden studierte von 1882 bis 1885 Chemie am Owens College der University of Manchester. 1868 ging er mit einem Dalton Scholarship an die Universität Erlangen, um beim Chemiker Otto Fi‐ scher, einem Vetter von Emil Fischer (Nobelpreis für Chemie 1902), zu arbeiten. Dort wurde er 1888 promoviert. Im Anschluss arbeitete er als Dozent am Owens College. Ab 1897 war er am neu gegrün‐ deten British Jenner Institute of Preventive Medicine tätig. 1907 wurde er dort Leiter der Abteilung Biochemie. Außerdem erhielt er 1912 eine Professur für Biochemie an der University of London. Auch nach seiner Emeritierung im Jahr 1930 blieb Harden wissenschaftlich aktiv. So befasste er sich unter anderem mit dem Stoffwechsel von E.coli‐Bakterien sowie mit der Gärung. Gemeinsam mit dem deutsch‐schwedischen Wissenschaftler Hans von Euler‐Chelpin gelang es ihm, diesen Vorgang vollständig aufzuklären. Nobelpreis für Chemie 1929 Die Aufklärung der Gärung als eine der ältesten biologischen Technologien der Menschheit hatte bereits zuvor viele Wissenschaftler zu Forschungsarbeiten angeregt, unter ihnen Louis Pasteur und Justus Freiherr von Liebig. Arthur Harden wurde für seine Forschungen über die Gärung von Zucker und die daran beteiligten Gärungsenzyme im Jahr 1929 gemeinsam mit Hans von Euler‐Chelpin mit dem Nobelpreis für Chemie ausgezeichnet. -
A Nobel Synthesis
MILESTONES IN CHEMISTRY Ian Grayson A nobel synthesis IAN GRAYSON Evonik Degussa GmbH, Rodenbacher Chaussee 4, Hanau-Wolfgang, 63457, Germany he first Nobel Prize for chemistry was because it is a scientific challenge, as he awarded in 1901 (to Jacobus van’t Hoff). described in his Nobel lecture: “The synthesis T Up to 2010, the chemistry prize has been of brazilin would have no industrial value; awarded 102 times, to 160 laureates, of whom its biological importance is problematical, only four have been women (1). The most but it is worth while to attempt it for the prominent area for awarding the Nobel Prize sufficient reason that we have no idea how for chemistry has been in organic chemistry, in to accomplish the task” (4). which the Nobel committee includes natural Continuing the list of Nobel Laureates in products, synthesis, catalysis, and polymers. organic synthesis we arrive next at R. B. This amounts to 24 of the prizes. Reading the Woodward. Considered by many the greatest achievements of the earlier organic chemists organic chemist of the 20th century, he who were recipients of the prize, we see that devised syntheses of numerous natural they were drawn to synthesis by the structural Alfred Nobel, 1833-1896 products, including lysergic acid, quinine, analysis and characterisation of natural cortisone and strychnine (Figure 1). 6 compounds. In order to prove the structure conclusively, some In collaboration with Albert Eschenmoser, he achieved the synthesis, even if only a partial synthesis, had to be attempted. It is synthesis of vitamin B12, a mammoth task involving nearly 100 impressive to read of some of the structures which were deduced students and post-docs over many years. -
Timeline of Genomics (1901–1950)*
Research Resource Timeline of Genomics (1901{1950)* Year Event and Theoretical Implication/Extension Reference 1901 Hugo de Vries adopts the term MUTATION to de Vries, H. 1901. Die Mutationstheorie. describe sudden, spontaneous, drastic alterations in Veit, Leipzig, Germany. the hereditary material of Oenothera. Thomas Harrison Montgomery studies sper- 1. Montgomery, T.H. 1898. The spermato- matogenesis in various species of Hemiptera and ¯nds genesis in Pentatoma up to the formation that maternal chromosomes only pair with paternal of the spermatid. Zool. Jahrb. 12: 1-88. chromosomes during meiosis. 2. Montgomery, T.H. 1901. A study of the chromosomes of the germ cells of the Metazoa. Trans. Am. Phil. Soc. 20: 154-236. Clarence Ervin McClung postulates that the so- McClung, C.E. 1901. Notes on the acces- called accessory chromosome (now known as the \X" sory chromosome. Anat. Anz. 20: 220- chromosome) is male determining. 226. Hermann Emil Fischer(1902 Nobel Prize Laure- 1. Fischer, E. and Fourneau, E. 1901. UberÄ ate for Chemistry) and Ernest Fourneau report einige Derivate des Glykocolls. Ber. the synthesis of the ¯rst dipeptide, glycylglycine. In Dtsch. Chem. Ges. 34: 2868-2877. 1902 Fischer introduces the term PEPTIDES. 2. Fischer, E. 1907. Syntheses of polypep- tides. XVII. Ber. Dtsch. Chem. Ges. 40: 1754-1767. 1902 Theodor Boveri and Walter Stanborough Sut- 1. Boveri, T. 1902. UberÄ mehrpolige Mi- ton found the chromosome theory of heredity inde- tosen als Mittel zur Analyse des Zellkerns. pendently. Verh. Phys -med. Ges. WÄurzberg NF 35: 67-90. 2. Boveri, T. 1903. UberÄ die Konstitution der chromatischen Kernsubstanz. Verh. Zool. -
Institute News
Institute News The Celebration Begins: IYC 2011 Causes Reactions in Paris, Philadelphia he International Year of Chemistry heritage. For example, Zhigang Shuai, the discussion of the sense and sensibil- T(IYC 2011) is underway, following professor of physical chemistry at ity of smell. its official launch at two world-class Tsinghua Univ., Beijing, spoke about • On Feb. 3, professor and histori- events. the history of chemistry in China up cal recreator James Armstead came to The celebration began Jan. 27–28, to the 17th century. Thomas Tritton, Philadelphia in the character of Percy 2011, at the world headquarters of the president and CEO of CHF, proposed a Julian, the 20th century chemist who United Nations Educational, Scientific, top ten list of the “rock stars of chem- was the subject of the PBS documen- and Cultural Organization (UNESCO) istry” — Marie Curie, John Dalton, tary titled Forgotten Genius. Armstead in Paris, then moved to the U.S. for a Emil Fischer, Antoine Lavoisier, Justus spoke to students at Philadelphia’s week-long North American kick-off Liebig, Dmitri Mendeleev, Linus Paul- African-American Museum and at The at the Chemical Heritage Foundation ing, Joseph Priestley, Friedrich Wöhler, College of Physicians. (CHF) in Philadelphia, PA. AIChE and Robert B. Woodward. • On Feb. 4., “Elemental Matters,” collaborated with CHF, the American On Feb. 1, the CHF hosted more an exhibit of seven contemporary art- Chemical Society (ACS), the American than 200 visitors, including members ists responding to the periodic table of Chemistry Council (ACC), and other of AIChE’s Board of Directors, AIChE elements, opened at the CHF’s Hach organizations on the U.S. -
Subject Categories
Subject Categories Click on a Subject Category below: Anthropology Archaeology Astronomy and Astrophysics Atmospheric Sciences and Oceanography Biochemistry and Molecular Biology Business and Finance Cellular and Developmental Biology and Genetics Chemistry Communications, Journalism, Editing, and Publishing Computer Sciences and Technology Economics Educational, Scientific, Cultural, and Philanthropic Administration (Nongovernmental) Engineering and Technology Geology and Mineralogy Geophysics, Geography, and Other Earth Sciences History Law and Jurisprudence Literary Scholarship and Criticism and Language Literature (Creative Writing) Mathematics and Statistics Medicine and Health Microbiology and Immunology Natural History and Ecology; Evolutionary and Population Biology Neurosciences, Cognitive Sciences, and Behavioral Biology Performing Arts and Music – Criticism and Practice Philosophy Physics Physiology and Pharmacology Plant Sciences Political Science / International Relations Psychology / Education Public Affairs, Administration, and Policy (Governmental and Intergovernmental) Sociology / Demography Theology and Ministerial Practice Visual Arts, Art History, and Architecture Zoology Subject Categories of the American Academy of Arts & Sciences, 1780–2019 Das, Veena Gellner, Ernest Andre Leach, Edmund Ronald Anthropology Davis, Allison (William Gluckman, Max (Herman Leakey, Mary Douglas Allison) Max) Nicol Adams, Robert Descola, Philippe Goddard, Pliny Earle Leakey, Richard Erskine McCormick DeVore, Irven (Boyd Goodenough, Ward Hunt Frere Adler-Lomnitz, Larissa Irven) Goody, John Rankine Lee, Richard Borshay Appadurai, Arjun Dillehay, Tom D. Grayson, Donald K. LeVine, Robert Alan Bailey, Frederick George Dixon, Roland Burrage Greenberg, Joseph Levi-Strauss, Claude Barth, Fredrik Dodge, Ernest Stanley Harold Levy, Robert Isaac Bateson, Gregory Donnan, Christopher B. Greenhouse, Carol J. Levy, Thomas Evan Beall, Cynthia M. Douglas, Mary Margaret Grove, David C. Lewis, Oscar Benedict, Ruth Fulton Du Bois, Cora Alice Gumperz, John J. -
A Tribute to the Memory of Svante Arrhenius (1859-1927)
A TRIBUTE TO THE MEMORY OF SVANTE ArrHENIUS (1859–1927) A SCIENTIst AHEAD OF HIS TIME BY GUstAF A rrHENIUS, K ARIN CALDWELL AND SVANTE WOLD ROYAL SWEDISH ACADEMY OF ENGINEERING SCIENCES (IVA) A TRIBUTE TO THE MEMORY OF SVANTE ARRHENIUS (1859–1927) P RESENTED at THE 2008 A NNUA L MEETING OF THE ROYA L SWEDISH ACA DEM Y OF ENGINEERING SCIENCES BY GUSta F A RRHENIUS, K A RIN CA LDWELL A ND SVA NTE WOLD The Royal Swedish Academy of Engineering Sciences (IVA) is an independent, learned society that promotes the engineering and economic sciences and the development of industry for the benefit of Swedish society. In cooperation with the business and academic communities, the Academy initiates and proposes measures designed to strengthen Sweden’s industrial skills base and competitiveness. For further information, please visit IVA’s website at www.iva.se. Published by the Royal Swedish Academy of Engineering Sciences (IVA) and Gustaf Arrhenius, Scripps Institution of Oceanography, University of California, San Diego, Karin Caldwell, Surface Biotechnology, Uppsala University and Svante Wold, Umetrics AB and Institute of Chemistry, Umeå University. Cover picture: photography of original painting by Richard Bergh, 1910. Photos and illustrations provided by the authors and by courtesy of the archives at the Royal Swedish Academy of Sciences. The authors would like to express their gratitude to professor Henning Rodhe at Stockholm University for his comments and contributions on selected text. IVA, P.O. Box 5073, SE-102 42 Stockholm, Sweden Phone: +46 8 791 29 00 Fax: +46 8 611 56 23 E-mail: [email protected] Website: www.iva.se IVA-M 395 • ISSN 1102-8254 • ISBN 978-91-7082-779-2 Editor: Eva Stattin, IVA Layout and production: Hans Melcherson, Tryckfaktorn AB, Stockholm, Sweden Printed by OH-Tryck, Stockholm, Sweden, 2008 FOREWORD Every year, the Royal Academy of Engineering Sciences (IVA) produces a booklet com- memorating a person whose scientific, engineering, economic or industrial achieve- ments were of significant benefit to the society of his or her day. -
Hermann Emil Fischer: Life and Achievements
GENERAL ARTICLE Hermann Emil Fischer: Life and Achievements G Nagendrappa Emil Fischer, considered as one of the greatest chemists of all times, carried out much of the fundamental work on purines, sugars, proteins, stereochemistry and several other areas of chemistry during the late nineteenth and early twentieth century. Because most of these are biological molecules, he is known as the ‘Father of Biochemistry’. His achievements in G Nagendrappa was a Professor of Organic chemical synthesis and analytical skills were much ahead of Chemistry at Bangalore his times. He was the second to get the Nobel Prize in Chem- University, and Head of istry in 1902. the Department of Medicinal Chemistry, Sri Introduction Ramachandra (Medical) University, Chennai. He is Carbohydrates, proteins, fats, and nucleic acids are the four major currently in Jain Univer- sity, Bangalore. He chemical constituents of living organisms. These four classes of continues to teach and do organic compounds are the main players in the emergence and research. His work is in existence of life. Extensive pioneering contributions to the devel- the area of organosilicon opment of all these areas of organic chemistry and biochemistry chemistry, synthetic and mechanistic organic were made by Emil Fischer through his more than four decades of chemistry, and clay- brilliant research work starting from the early 1870s. His uncanny catalysed organic reactions skills in analytical and synthetic work, his extraordinary under- (Green Chemistry). standing of the enormous amount of experimental results and their correct interpretation laid a solid foundation for the chemis- try of these biologically important molecules. Though his work essentially constituted analytical and synthetic organic chemis- try, its reach extended to other areas, particularly stereochemis- try, biochemistry, physiology and medicine. -
President's Report 2018
VISION COUNTING UP TO 50 President's Report 2018 Chairman’s Message 4 President’s Message 5 Senior Administration 6 BGU by the Numbers 8 Building BGU 14 Innovation for the Startup Nation 16 New & Noteworthy 20 From BGU to the World 40 President's Report Alumni Community 42 2018 Campus Life 46 Community Outreach 52 Recognizing Our Friends 57 Honorary Degrees 88 Board of Governors 93 Associates Organizations 96 BGU Nation Celebrate BGU’s role in the Israeli miracle Nurturing the Negev 12 Forging the Hi-Tech Nation 18 A Passion for Research 24 Harnessing the Desert 30 Defending the Nation 36 The Beer-Sheva Spirit 44 Cultivating Israeli Society 50 Produced by the Department of Publications and Media Relations Osnat Eitan, Director In coordination with the Department of Donor and Associates Affairs Jill Ben-Dor, Director Editor Elana Chipman Editorial Staff Ehud Zion Waldoks, Jacqueline Watson-Alloun, Angie Zamir Production Noa Fisherman Photos Dani Machlis Concept and Design www.Image2u.co.il 4 President's Report 2018 Ben-Gurion University of the Negev - BGU Nation 5 From the From the Chairman President Israel’s first Prime Minister, David Ben–Gurion, said:“Only Apartments Program, it is worth noting that there are 73 This year we are celebrating Israel’s 70th anniversary and Program has been studied and reproduced around through a united effort by the State … by a people ready “Open Apartments” in Beer-Sheva’s neighborhoods, where acknowledging our contributions to the State of Israel, the the world and our students are an inspiration to their for a great voluntary effort, by a youth bold in spirit and students live and actively engage with the local community Negev, and the world, even as we count up to our own neighbors, encouraging them and helping them strive for a inspired by creative heroism, by scientists liberated from the through various cultural and educational activities. -
Thermodynamic and Extrathermodynamic Requirements of Enzyme Catalysis
Biophysical Chemistry 105 (2003) 559–572 Thermodynamic and extrathermodynamic requirements of enzyme catalysis Richard Wolfenden* Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599-7260, USA Received 24 October 2002; received in revised form 22 January 2003; accepted 22 January 2003 Abstract An enzyme’s affinity for the altered substrate in the transition state (symbolized here as S‡) matches the value of kcatyK m divided by the rate constant for the uncatalyzed reaction in water. The validity of this relationship is not affected by the detailed mechanism by which any particular enzyme may act, or on whether changes in enzyme conformation occur on the path to the transition state. It subsumes potential effects of substrate desolvation, H- bonding and other polar attractions, and the juxtaposition of several substrates in a configuration appropriate for reaction. The startling rate enhancements that some enzymes produce have only recently been recognized. Direct measurements of the binding affinities of stable transition-state analog inhibitors confirm the remarkable power of binding discrimination of enzymes. Several parts of the enzyme and substrate, that contribute to S‡ binding, exhibit extremely large connectivity effects, with effective relative concentrations in excess of 108 M. Exact structures of enzyme complexes with transition-state analogs also indicate a general tendency of enzyme active sites to close around S‡ in such a way as to maximize binding contacts. The role of solvent water in these binding equilibria, for which Walter Kauzmann provided a primer, is only beginning to be appreciated. ᮊ 2003 Elsevier Science B.V. All rights reserved.