Suggested Guidelines for Starting an Undergraduate Biophysics Program
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Glossary - Cellbiology
1 Glossary - Cellbiology Blotting: (Blot Analysis) Widely used biochemical technique for detecting the presence of specific macromolecules (proteins, mRNAs, or DNA sequences) in a mixture. A sample first is separated on an agarose or polyacrylamide gel usually under denaturing conditions; the separated components are transferred (blotting) to a nitrocellulose sheet, which is exposed to a radiolabeled molecule that specifically binds to the macromolecule of interest, and then subjected to autoradiography. Northern B.: mRNAs are detected with a complementary DNA; Southern B.: DNA restriction fragments are detected with complementary nucleotide sequences; Western B.: Proteins are detected by specific antibodies. Cell: The fundamental unit of living organisms. Cells are bounded by a lipid-containing plasma membrane, containing the central nucleus, and the cytoplasm. Cells are generally capable of independent reproduction. More complex cells like Eukaryotes have various compartments (organelles) where special tasks essential for the survival of the cell take place. Cytoplasm: Viscous contents of a cell that are contained within the plasma membrane but, in eukaryotic cells, outside the nucleus. The part of the cytoplasm not contained in any organelle is called the Cytosol. Cytoskeleton: (Gk. ) Three dimensional network of fibrous elements, allowing precisely regulated movements of cell parts, transport organelles, and help to maintain a cell’s shape. • Actin filament: (Microfilaments) Ubiquitous eukaryotic cytoskeletal proteins (one end is attached to the cell-cortex) of two “twisted“ actin monomers; are important in the structural support and movement of cells. Each actin filament (F-actin) consists of two strands of globular subunits (G-Actin) wrapped around each other to form a polarized unit (high ionic cytoplasm lead to the formation of AF, whereas low ion-concentration disassembles AF). -
Chemistry with Biophysical Chemistry Chemistry & Chemical Sciences (CCS)
Chemistry with Biophysical Chemistry Chemistry & Chemical Sciences (CCS) Sample pathway for a degree in Chemistry with Biophysical Chemistry* YEAR 1 ENGAGE WITH THE PRINCIPLES CHEMISTRY MATHEMATICS BIOLOGY Modules include: Modules include: Modules include: 4One Elective 4 4 4 The Basis of Organic and Mathematics for the Cell Biology & Genetics module Biological Chemistry Biological & Chemical 4One 4 The Basis of Physical Sciences Small- Chemistry Group 4 The Molecular World Project YEAR 2 CHOOSE YOUR SUBJECTS A nanoparticle with encapsulated active ingredient is penetrating a cell The subject combinations listed below are illustrative of what a student who graduates in Chemistry with Biophysical Chemistry could choose in Year 2. Further subject combinations are possible depending on the choices in Year 1. Further information is available on page 23. membrane. Image and copyright of Nanobotmodels Company CHEMISTRY WITH BIOPHYSICAL CHEMISTRY ([email protected]). CHEMISTRY Modules include: Modules include: 4Biophysical Chemistry 4Students who choose Chemistry with 4Two n Develop theoretical and 4Physical Chemistry Biophysical Chemistry as their main subject Elective 4Inorganic Chemistry for second year also cover the requirements modules practical skills in exploiting 4 Organic Chemistry for Chemistry. the physical and chemical YEAR principles of the FOCUS ON YOUR CHOSEN SUBJECT 3 biomolecular world in CHEMISTRY WITH BIOPHYSICAL CHEMISTRY – Modules include: modern industrial and 4Instrumental Analysis 4Organometallic & Solid State Chemistry -
Quantum Biology: an Update and Perspective
quantum reports Review Quantum Biology: An Update and Perspective Youngchan Kim 1,2,3 , Federico Bertagna 1,4, Edeline M. D’Souza 1,2, Derren J. Heyes 5 , Linus O. Johannissen 5 , Eveliny T. Nery 1,2 , Antonio Pantelias 1,2 , Alejandro Sanchez-Pedreño Jimenez 1,2 , Louie Slocombe 1,6 , Michael G. Spencer 1,3 , Jim Al-Khalili 1,6 , Gregory S. Engel 7 , Sam Hay 5 , Suzanne M. Hingley-Wilson 2, Kamalan Jeevaratnam 4, Alex R. Jones 8 , Daniel R. Kattnig 9 , Rebecca Lewis 4 , Marco Sacchi 10 , Nigel S. Scrutton 5 , S. Ravi P. Silva 3 and Johnjoe McFadden 1,2,* 1 Leverhulme Quantum Biology Doctoral Training Centre, University of Surrey, Guildford GU2 7XH, UK; [email protected] (Y.K.); [email protected] (F.B.); e.d’[email protected] (E.M.D.); [email protected] (E.T.N.); [email protected] (A.P.); [email protected] (A.S.-P.J.); [email protected] (L.S.); [email protected] (M.G.S.); [email protected] (J.A.-K.) 2 Department of Microbial and Cellular Sciences, School of Bioscience and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK; [email protected] 3 Advanced Technology Institute, University of Surrey, Guildford GU2 7XH, UK; [email protected] 4 School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK; [email protected] (K.J.); [email protected] (R.L.) 5 Manchester Institute of Biotechnology, Department of Chemistry, The University of Manchester, -
Chemistry Courses 2005-2006
Chemistry Courses 2005-2006 Autumn 2005 Chem 11101 General Chemistry I, Variant A Lee Chem 11102 General Chemistry I, Variant B Norris Chem 12200 Honors General Chemistry I Levy Chem 22000 Organic Chemistry I Yu Chem 22300 Intermediate Organic Chemistry Mrksich Chem 26100 Quantum Mechanics Mazziotti Chem 30100 Advanced Inorganic Chemistry Hopkins Chem 30900 Bioinorganic Chemistry He Chem 32100 Physical Organic Chemistry I Ismagilov Chem 32200 Organic Synthesis and Structure Rawal Chem 32600 Protein Fundamentals Piccirilli Chem 36100 Wave Mechanics & Spectroscopy Butler Chem 36400 Chemical Thermodynamics Dinner Winter 2006 Chem 11201 General Chemistry II, Variant A Scherer Chem 11202 General Chemistry II, Variant B Butler Chem 12300 Honors General Chemistry II Dinner Chem 20100 Inorganic Chemistry I Hillhouse Chem 22100 Organic Chemistry II Rawal Chem 23100 Honors Organic Chemistry II Kozmin Chem 26200 Thermodynamics Norris Chem 26700 Experimental Physical Chemistry Levy Chem 30200 Synthesis & Physical Methods in Inorganic Chemistry Jordan Chem 30400 Organometallic Chemistry Bosnich Chem 32300 Tactics of Organic Synthesis Yamamoto Chem 32400 Physical Organic Chemistry II Mrksich Chem 36200 Quantum Mechanics Freed Chem 36300 Statistical Mechanics Mazziotti Chem 38700 Biophysical Chemistry Lee Spring 2006 Chem 11301 General Chemistry III, Variant A Kozmin Chem 11302 General Chemistry III, Variant B Guyot-Sionnest Chem 20200 Inorganic Chemistry II Jordan Chem 22200 Organic Chemistry III Kent Chem 23200 Honors Organic Chemistry III Yamamoto Chem 22700 Advanced Organic / Inorganic Laboratory (8 students) He Chem 26300 Chemical Kinetics and Dynamics Sibner Chem 26800 Computational Chemistry & Biology Freed Chem 30600 Chemistry of the Elements Hillhouse Chem 31100 Supramolecular Chemistry Bosnich Chem 32500 Bioorganic Chemistry Piccirilli Chem 32900 Polymer Chemistry Yu Chem 33000 Complex Systems Ismagilov Chem 36500 Chemical Dynamics Scherer Chem 36800 Advanced Computational Chemistry & Biology Freed . -
Quantum Mechanics and Biology
QUANTUM MECHANICS AND BIOLOGY H. C. LONGUET-HIGGINS From the University of Cambridge, England I should like to begin by saying that I feel very diffident about speaking on the subject which the organizers of this Conference invited me to discuss with you. What I have to say will inevitably be limited by the extreme superficiality of my acquaintance with modem biochemistry and biophysics. The only apology which I can offer for being here at all is that I feel, in common with most scientists, that it is a good thing for workers in quite different fields to meet occasionally and compare notes so as to discover whether the methods of one discipline can usefully be applied to the problems of another. It will soon become apparent to you that my opinions on the usefulness of quantum mechanics to biologists are decidedly con- servative; but if these opinions are not generally shared, perhaps at least they will provoke discussion. The thesis which I want to develop in the next few minutes will seem to many of you to be rather pedestrian. Briefly I want to suggest that for many years to come the student of living matter will have much more need for an understanding of physical chemistry than for a knowledge of quantum mechanics. However much one may marvel at the variety and versatility of living things, it cannot be denied that all organisms are in one sense physico-chemical machines. Ingenious and baffling as their structure and function may seem to be, it is therefore proper, in attempting to understand them, to compare their component parts with those in- animate systems which the physical chemist now understands more or less thor- oughly. -
Biophysics 1
Biophysics 1 on interactions between proteins involved in Notch signaling using BIOPHYSICS modern biophysical methods. Thermodynamics of association and allosteric effects are determined by spectroscopic, ultracentrifugation, http://biophysics.jhu.edu/ and calorimetric methods. Atomic structure information is being obtained by NMR spectroscopy. The ultimate goal is to determine the The Department of Biophysics offers programs leading to the B.A., M.A., thermodynamic partition function for a signal transduction system and and Ph.D. degrees. Biophysics is appropriate for students who wish interpret it in terms of atomic structure. to develop and integrate their interests in the physical and biological sciences. NMR Spectroscopy (Dr. Lecomte) Research interests in the Department cover experimental and Many proteins require stable association with an organic compound computational, molecular and cellular structure, function, and biology, for proper functioning. One example of such “cofactor” is the heme membrane biology, and biomolecular energetics. The teaching and group, a versatile iron-containing molecule capable of catalyzing a research activities of the faculty bring its students in contact with broad range of chemical reactions. The reactivity of the heme group biophysical scientists throughout the university. Regardless of their choice is precisely controlled by interactions with contacting amino acids. of research area, students are exposed to a wide range of problems of Structural fluctuations within the protein are also essential to the fine- biological interest. For more information, and for the most up-to-date list tuning of the chemistry. We are studying how the primary structure of of course offerings and requirements, consult the department web page at cytochromes and hemoglobins codes for heme binding and the motions biophysics.jhu.edu (http://biophysics.jhu.edu/). -
Change the Description of CHEM 323, Foundations of Biochemistry; Change Title and Description of CHEM 437, Modern Biochemistry
APC Document RRR (CHEM): Change the description of CHEM 323, Foundations of Biochemistry; Change title and description of CHEM 437, Modern Biochemistry 1. Delete: On page 99, the description for CHEM 323, Foundations of Biochemistry: Designed to approach the fundamentals of biochemistry from a chemical perspective, this course examines the structure and function of biological systems such as proteins, carbohydrates, and lipids; develops an understanding of the kinetics of biological reactions including metabolism and enzyme catalysis. It expands the study of biological equilibria and thermodynamics through the discussion of the properties of aqueous solutions, thermodynamics of enzyme binding and recognition, and oxidation and reduction processes. Prerequisites: CHEM 232, 233. Fall. Add: On page 99, in place of deleted entry: Designed to approach the fundamentals of biochemistry from a chemical perspective, this course examines the structure and function of biological molecules such as nucleic acids, proteins, carbohydrates, and lipids. It introduces the principles of molecular recognition, enzyme catalysis, enzyme kinetics, and metabolism and develops an understanding of biological equilibria, redox, and energy transduction through the discussion of core metabolic pathways and oxidative phosphorylation. Prerequisites: CHEM 232, 233. Fall. Impact: None anticipated. Rationale: The changes are editorial to better reflect the course content. 2. Delete: On page 101, the entry for CHEM 437, Modern Biochemistry: 437 Modern Biochemistry (3) An in depth exploration of reaction kinetics and catalytic mechanisms of enzymes; metabolism; the expression and transmission of genetic information; and biological structural analysis with an emphasis on current research in the field. Prerequisites: CHEM 323, 331. Spring. Add: On page 101, in place of deleted entry: 437 Biophysical Chemistry (3) Takes a deeper look into the dynamic structures and myriad functions of proteins, nucleic acids, and lipids from a quantitative, physical perspective. -
Graduate Group in Biochemistry and Molecular Biophysics General Information for Incoming Students
Graduate Group in Biochemistry and Molecular Biophysics General Information for Incoming Students Student mailboxes are located on the left as you enter the Mail Room (257 Anatomy-Chemistry Building) of the Dept. of Biochemistry and Biophysics. Use the following address to have mail sent to you at this location: Department of Biochemistry and Biophysics, 257 Anatomy-Chemistry Bldg., Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104- 6059. The Student Room is located in 250 Anatomy-Chemistry Building. Keys to this room have been placed in your mailbox. The room has two computers (1 MAC, 1 PC) and a printer. Please make sure the door is locked and securely closed when you leave the room. Lockers: Please contact Kelli McKenna if you would like a locker. They are located in the hallway outside of Rm 234 Anatomy- Chemistry. Advising: You will be meeting individually with the Advising Committee to select your fall courses and for guidance on your rotations. Course registration forms should be returned to Kelli McKenna as soon as possible after your meeting. Any changes in your fall schedule should be made within two weeks of the start of the semester and need to be approved by one of the members of the Advising Committee. Lab Rotation Approval forms are to be completed by Friday, September 13, 2021. You can find the forms for course registration and lab rotation on the BMB webpage: www.med.upenn.edu/bmbgrad under the resources page. Seminars which you are expected to attend: · Raiziss Rounds: Thursdays at noon (Austrian Auditorium, Clinical Research Building). -
MOLECULAR BIOPHYSICS and BIOCHEMISTRY* by William C. Summers
MOLECULAR BIOPHYSICS AND BIOCHEMISTRY* by William C. Summers (Professor of Therapeutic Radiology, Molecular Biophysics and Biochemistry, and History of Medicine, and Lecturer in History) MOLECULAR BIOPHYSICS During World War II many university physicists undertook new research programs aimed at wartime goals. Notable among these goals were the Manhattan Project to investigate and exploit nuclear energy for military purposes and the project, based at the MIT Radiation Laboratory, to develop radar as a military surveillance tool. Yale nuclear physicist Ernest Pollard, a student of Chadwick and Rutherford, was recruited for the Radiation Lab (known informally as the “Rad Lab”) by Ernest Lawrence. Prior to the war, Pollard had been carrying on a modest program of teaching and research in nuclear physics at Yale in the Department of Physics, then chaired by William Watson. In Pollard’s view, wartime physics research fundamentally changed the style and form of physics in America. Nuclear physics had become big science, requiring expensive equipment and teams of scientists, not an activity for a university professor with a small research group and major teaching obligations. In addition, having spent the war years working on microwave research, Pollard and other members of the Rad Lab had lost out on the excitement and new advances, many of them still classified, in nuclear physics coming out of the Manhattan Project. When Pollard and his small group of students, including Franklin Hutchinson, returned to Yale after the war, he considered two new directions for his research, cosmology and biology. In Pollard’s view, he was not temperamentally suited to be a cosmologist, and he thought it might be hard to start up in that field at Yale at that time. -
BIOPHYSICAL CHEMISTRY an International Journal Devoted to the Physics and Chemistry of Biological Phenomena
BIOPHYSICAL CHEMISTRY An International Journal devoted to the Physics and Chemistry of Biological Phenomena AUTHOR INFORMATION PACK TABLE OF CONTENTS XXX . • Description p.1 • Audience p.1 • Impact Factor p.2 • Abstracting and Indexing p.2 • Editorial Board p.2 • Guide for Authors p.5 ISSN: 0301-4622 DESCRIPTION . Biophysical Chemistry publishes original work and reviews in the areas of chemistry and physics directly impacting biological phenomena. Quantitative analysis of the properties of biological macromolecules, biologically active molecules, macromolecular assemblies and cell components in terms of kinetics, thermodynamics, spatio-temporal organization, NMR and X-ray structural biology, as well as single-molecule detection represent a major focus of the journal. Theoretical and computational treatments of biomacromolecular systems, macromolecular interactions, regulatory control and systems biology are also of interest to the journal. The journal publishes Regular Articles, Reviews, Short Communications (maximum of 4 printed pages) and Feature Articles. Feature Articles are normally by Editor's invitation only, but interested authors can contact the Editors before submission. Author(s) will be asked to focus on her/his recent research contributions, thereby adding a personal perspective to their field of research. These short reviews will include the authors' photo and a brief bio/CV and will have a page limit of 5 printed pages in print. Manuscripts that fall outside the scopes and interests of the journal are returned to the Authors without in-depth review. Relevant manuscripts are reviewed expeditiously with decisions generally made within 3 weeks from receipt. Short Communications are 6 printed pages maximum, reporting results of unusual timeliness and significance. -
BS in Biophysics (285720) MAP Sheet Life Sciences, Cell Biology and Physiology for Students Entering the Degree Program During the 2021-2022 Curricular Year
BS in Biophysics (285720) MAP Sheet Life Sciences, Cell Biology and Physiology For students entering the degree program during the 2021-2022 curricular year. University Core and Graduation Requirements Suggested Sequence of Courses University Core Requirements: FRESHMAN YEAR JUNIOR YEAR Requirements #Classes Hours Classes 1st Semester 5th Semester First-Year Writing or American Heritage 3.0 CELL 360 3.0 Religion Cornerstones CELL 120 (Biological Science) 3.0 CHEM 481 3.0 Teachings and Doctrine of The Book of 1 2.0 REL A 275 CHEM 105 4.0 PHSCS 220 3.0 Mormon MATH 112 (Languages of Learning & Quantitative Reasoning) 4.0 PHSCS 225 2.0 Religion Cornerstone Course 2.0 Religion Elective 2.0 Jesus Christ and the Everlasting Gospel 1 2.0 REL A 250 Total Hours 16.0 Mentored Lab Experience (CELL 495R) 1-2.0 Foundations of the Restoration 1 2.0 REL C 225 2nd Semester Total Hours 14-15.0 The Eternal Family 1 2.0 REL C 200 First-Year Writing or American Heritage 3.0 6th Semester The Individual and Society BIO 250 2.0 CELL 362 3.0 American Heritage 1-2 3-6.0 from approved list CHEM 106 3.0 CELL 363 1.0 CHEM 107 1.0 CHEM 468 3.0 Global and Cultural Awareness 1 3.0 from approved list MATH 113 4.0 Advanced Writing (WRTG 316 recommended) 3.0 Skills Religion Cornerstone Course 2.0 Global & Cultural Awareness Elective 3.0 First Year Writing 1 3.0 from approved list Total Hours 15.0 Religion Elective 2.0 Total Hours 15.0 Advanced Written and Oral Communications 1 3.0 WRTG 316 SOPHOMORE YEAR recommended 3rd Semester SENIOR YEAR MMBIO 240 3.0 7th Semester Quantitative -
Department of Biochemistry and Molecular Biophysics (09/25/21)
Bulletin 2021-22 Department of Biochemistry and Molecular Biophysics (09/25/21) Department of Eric A. Galburt, PhD McDonnell Sciences Building, 2nd Floor Biochemistry and Phone: 314-362-5201 Biophysical studies of transcription initiation in eukaryotes and Molecular Biophysics mycobacterial tuberculosis Website: http://biochem.wustl.edu Roberto Galletto, PhD Research Electives McDonnell Sciences Building, 2nd Floor Phone: 314-362-4368 Biochemistry and Molecular Biophysics Mechanistic studies of DNA motor proteins Research Electives During the fourth year, opportunities exist for many varieties of Michael Greenberg, PhD advanced clinical or research experiences. McDonnell Sciences Building, 2nd Floor Phone: 314-362-8670 Wayne M. Barnes, PhD Our lab is focused on cytoskeletal molecular motors in health McDonnell Sciences Building, 2nd Floor and disease. We are currently studying the effects of mutations Phone: 314-362-3351 that cause heart disease. Inventing a new way to sequence DNA; PCR at one temp; RT- enabled Taq pol Kathleen Hall, PhD South Building, 2nd Floor Phone: 314-362-4196 Greg Bowman, PhD South Building, 2nd Floor We study RNA folding and RNA binding to proteins. Phone: 314-362-7433 The Bowman lab seeks to understand how protein dynamics Alex Holehouse, PhD gives rise to functional processes like allosteric communication McDonnell Sciences Building, 2nd Floor between distant sites and to exploit our insight into this shape- Phone: 314-273-8371 shifting to design new drugs and proteins. Understand how function is encoded into