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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. -
Springer A++ Viewer
PublisherInfo PublisherName : BioMed Central PublisherLocation : London PublisherImprintName : BioMed Central Ubiquitin researchers win Nobel ArticleInfo ArticleID : 5007 ArticleDOI : 10.1186/gb-spotlight-20041007-02 ArticleCitationID : spotlight-20041007-02 ArticleSequenceNumber : 70 ArticleCategory : Research news ArticleFirstPage : 1 ArticleLastPage : 3 RegistrationDate : 2004–10–7 ArticleHistory : OnlineDate : 2004–10–7 ArticleCopyright : BioMed Central Ltd2004 ArticleGrants : ArticleContext : 130595511 Stephen Pincock Email: [email protected] Three researchers who made fundamental breakthroughs in understanding ubiquitin-mediated proteolysis have been awarded the 2004 Nobel Prize in Chemistry, the Royal Swedish Academy of Sciences said on Wednesday (October 6). Aaron Ciechanover and Avram Hershko, from the Israel Institute of Technology, Haifa, and Irwin Rose, of the University of California, Irvine, will share the prize for their discoveries in the 1970s and 1980s that began to reveal the central role of the tiny 76-amino acid protein in numerous cellular processes. "Thanks to the work of the three laureates, it is now possible to understand at a molecular level how the cell controls a number of central processes by breaking down certain proteins and not others," the academy said. "Without doubt they deserve this prize," John Mayer, professor of molecular cell biology at the University of Nottingham, told us. "Protein modification by ubiquitylation is just as important as protein phosphorylation for what goes on in the cell." Ubiquitin-mediated protein degradation governs processes as varied as cell division, DNA repair, quality control of newly produced proteins, and parts of the immune system. Problems with the ubiquitin–proteosome system are implicated in human diseases including cervical cancer and cystic fibrosis. "The reason they've got this Nobel Prize is because ubiquitin is attached to proteins in different ways not only for degradation, but also to make other things happen in the cell," Mayer added. -
Ubiquitin-Mediated Proteolysis the Nobel Prize in Chemistry for 2004 Is
Advanced information on the Nobel Prize in Chemistry, 6 October 2004 Information Department, P.O. Box 50005, SE-104 05 Stockholm, Sweden Phone: +46 8 673 95 00, Fax: +46 8 15 56 70, E-mail: [email protected], Website: www.kva.se Ubiquitin-mediated proteolysis The Nobel Prize in Chemistry for 2004 is shared between three scientists who have made fundamental discoveries concerning how cells regulate the breakdown of intracellular proteins with extreme specificity as to target, time and space. Aaron Ciechanover, Avram Hershko and Irwin Rose together discovered ubiquitin- mediated proteolysis, a process where an enzyme system tags unwanted proteins with many molecules of the 76-amino acid residue protein ubiquitin. The tagged proteins are then transported to the proteasome, a large multisubunit protease complex, where they are degraded. Numerous cellular processes regulated by ubiquitin-mediated proteolysis include the cell cycle, DNA repair and transcription, protein quality control and the immune response. Defects in this proteolysis have a causal role in many human diseases, including a variety of cancers. Fig. 1 Ubiquitin-mediated proteolysis and its many biological functions 2 Introduction Eukaryotic cells, from yeast to human, contain some 6000 to 30000 protein-encoding genes and at least as many proteins. While much attention and research had been devoted to how proteins are synthesized, the reverse process, i.e. how proteins are degraded, long received little attention. A pioneer in this field was Schoenheimer, who in 1942 published results from isotope tracer techniques indicating that proteins in animals are continuously synthesized and degraded and therefore are in a dynamic state (Schoenheimer, 1942). -
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. -
Antibodies with Some Bite Antibodies Have Yet to Be Determined, It Is Reasonable to Suppose That the Ester Or David E
-~-------------------------------------N8NSANDVIEWS----------------_N_A_TU_R_E_V-O_L_._32_5_22_J_A_N_U_A_RY__ 19~87 Enzyme catalysis kinetics and is subject to competitive inhibition. Although the detailed chemical mechanisms of these catalytic Antibodies with some bite antibodies have yet to be determined, it is reasonable to suppose that the ester or David E. Hansen carbamate is strained towards a tetra hedral geometry on binding, thus facilitat THE spectacular specificities and rate William Jencks', more directly, stated in ing the attack of the hydroxide ion. Fur enhancements of enzymes are without 1969 thermore, the Scripps group has already equal among all known catalysts. It is no If complementarity between active site and found that their antibody can act via both wonder then that the design of new en transition state contributes significantly to nucleophilic and general base catalysis, zymes has long been a goal of biochemists. enzyme catalysis, it should be possible to syn depending on the substrate used. Now two independent groups, one led by thesize an enzyme by constructing a binding The fact that this approach succeeded at Alfonso Tramontano and Richard Lerner site. One way to do this is to prepare an anti all gives great hope to those attempting to of the Scripps Clinic and Research Foun body to a haptenic group which resembles the isolate even more efficient antibody cat dation', and the other by Peter Schultz of transition state of a given reaction. The com alysts by this and by other strategies. In the University of California at Berkeley\ bining sites of such antibodies should be com addition, it may be possible to modify have taken steps towards this goal by plementary to the transition state and should cause an acceleration by forcing bound sub existing catalytic antibodies. -
Proteasome Inhibitors in Cancer Therapy: Death by Indigestion
Cell Death and Differentiation (2005) 12, 1255–1257 & 2005 Nature Publishing Group All rights reserved 1350-9047/05 $30.00 www.nature.com/cdd Book Review Proteasome inhibitors in cancer therapy: death by indigestion M Rossi1, A Oberst2, A Emre Sayan1 and P Salomoni*,1 1 MRC, Toxicology Unit, Leicester, UK; 2 IDI-IRCCS Biochemistry Lab, c/o University of Rome Tor Vergata, Rome, Italy * Corresponding author. P Salomoni. E-mail: [email protected] Cell Death and Differentiation (2005) 12, 1255–1257. doi:10.1038/sj.cdd.4401701 Proteasome Inhibitors in Cancer Therapy. Cancer Drug Discovery and Development. By J Adams. Humana Press, Totowa, New Jersey: 2004. pp 312. ISBN: 1-58829-250-9 As Eugene Garfield said, while it is easy to recognize a good same issue containing manuscripts from scientists that have paper, it could be more difficult to recognize a bad paper. In originated in this field.7–10 fact, the results could be weak, but the conclusion could still For those of us engaged in basic research in the field be right, even though not fully supported by the data shown. of cancer and apoptosis, the hope that our work might, in Preliminary reports could also fall in this category. After some small way and at some future juncture, contribute to all, it was not a Cell but a BBRC paper – only a little BBRC of the clinical treatment of human cancers is a major motivator. three impact factor – describing a novel experimental model Proteasome Inhibitors in Cancer Therapy, edited by Julian in which to study ATP-dependent proteolysis.1 In a lysate Adams, which is part of the ‘Cancer Drug Discovery and from rabbit reticulocytes, where the proteolytic activity was not Development’ series from Humana Press, tells the happy tale due to lysosomes (pH optimum of 7.8), they separated two of one drug’s journey from concept, through development, fractions in a DEAE cellulose column, each one individually to FDA approval, and application. -
Steven J. Cohen, Md
STEVEN J. COHEN, MD Background Oncology Cornell University Director, Rosenfeld Cancer Center and Cancer Service Line Ithaca, NY Chief, Medical Oncology and Hematology Division (BA, Psychology, 1988-1992) Vice-Chair, Department of Medical Oncology Professor of Medical Oncology, Thomas Jefferson University, Stony Brook University School of Medicine Sidney Kimmel Cancer Center Stony Brook, NY (MD, 1992-1996) Steven J. Cohen, MD earned his Bachelor’s degree in Psychology Temple University Hospital in 1992 from Cornell Philadelphia, PA University. In 1996, he earned (Resident, Internal Medicine, 1996-1999) his medical degree from the State University of New York at Fox Chase Cancer Center Stony Brook. Dr. Cohen Temple University Hospital completed his residency in Philadelphia, PA Internal Medicine at Temple (Fellow, Medical Oncology and Hematology, 1999-2001) University Hospital in 1999. He (Chief Fellow, Medical Oncology and Hematology, 2001- completed his fellowship in 2002) Medical Oncology and (Program Director, Hematology/Oncology Fellowship, Hematology in 2002 at Fox 2009-2016) Chase Cancer Center, and also served as Chief Fellow from 2001 to 2002. Fox Chase Cancer Center Philadelphia, PA Dr. Cohen specializes in the care and treatment of GI cancers. He is a member of the American Society of Clinical (Assistant Member, Division of Medical Science, 2002- Oncology, where he has served on the Scientific Program 2004) Committee for Colorectal Cancer and chaired the Test (Attending Physician, Department of Medical Oncology, Development Committee. He is an active member of the GI 2002-2004) Committee of the Eastern Cooperative Oncology Group (Assistant Professor, Divisions of Medical and Population where he has chaired the Colorectal Cancer Subcommittee. -
The Ubiquitin System for Protein Degradation and Some of Its Roles in the Control of the Cell Division Cycle*
Cell Death and Differentiation (2005) 12, 1191–1197 & 2005 Nature Publishing Group All rights reserved 1350-9047/05 $30.00 www.nature.com/cdd Review: Nobel Lecture The ubiquitin system for protein degradation and some of its roles in the control of the cell division cycle* A Hershko*,1 further molecular mechanisms that regulate the expression of specific genes. Owing to the intensive research activity on 1 The B. Rappaport Faculty of Medicine and the Rappaport Institute for protein synthesis, little attention was paid at that time to the Research in the Medical Sciences, Technion-Israel Institute of Technology, fact that many proteins are rapidly degraded to amino acids. Haifa, Israel This dynamic turnover of cellular proteins had been previously * Corresponding author: A Hershko, Unit of Biochemistry, the B. Rappaport known by the pioneering work of Schoenheimer and co- Faculty of Medicine and the Rappaport Institute for Research in the Medical Sciences, Technion-Israel Institute of Technology, 1 Efron Street, P.O. Box workers, who were among the first to introduce the use of 9649, Haifa 31096, Israel. Fax: 9724 853 5773; isotopically labeled compounds to biological studies. They 15 E-mail: [email protected] administered N-labeled L-leucine to adult rats, and the distribution of the isotope in body tissues and in excreta was Received 18.5.05; accepted 18.5.05 examined. It was observed that less than one-third of the Edited by G Melino isotope was excreted in the urine, and most of it was incorporated into tissue proteins.1 Since the weight of the Abstract animals did not change during the experiment, it could be assumed that the mass and composition of body proteins also Owing to the intensive research activity on protein synthesis, did not change. -
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. -
Early Work on the Ubiquitin Proteasome System, an Interview with Irwin Rose
Cell Death and Differentiation (2005) 12, 1162–1166 & 2005 Nature Publishing Group All rights reserved 1350-9047/05 $30.00 www.nature.com/cdd Interview Early work on the ubiquitin proteasome system, an interview with Irwin Rose I Rose*,1 Irwin Rose was one of the first scientists working on UPS mechanisms. In particular, his early work was dedicated to the 1 Department of Physiology and Biophysics, College of Medicine, University of biochemistry and the role of nonlysosomal protein degra- California, Irvine, CA 92697, USA dation. But how did it all begin? What triggered his scientific * Corresponding author: I Rose, Department of Physiology and Biophysics, interest in this field from his previous work? Now a large College of Medicine, University of California, Irvine, CA 92697, USA. family of related proteins exist, with interesting therapeutical E-mail: [email protected] potential. Here, Cell Death and Differentiation asks Irwin Cell Death and Differentiation (2005) 12, 1162–1166. Rose about the early work on enzymology. This interview doi:10.1038/sj.cdd.4401700 was obtained, thanks to the kind help of the Nobel Foundation in Stockholm, http://nobelprize.org (rThe Nobel Founda- tion 2004). CDD: How did you Move from your Early Family Life into your Scientific Interest? We left my birthplace, Brooklyn, New York in 1939 when I was 13. I enjoyed the ethnic variety and the interesting students in my public school, P.S. 134. The kids in my neighborhood were only competitive in games although unfriendly gangs tended to define the limits of our neighborhood. The major extracurricular activities that I can remember were a Victory Garden on school grounds, our contribution to the war effort, and a favorite sport, handball, played between the walls of our apartment house. -
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.