Chap. 1 "Introduction to Biochemistry" Reading Assignment: Pp. 3-25
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The Architecture of the Protein Domain Universe
The architecture of the protein domain universe Nikolay V. Dokholyan Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, School of Medicine, Chapel Hill, NC 27599 ABSTRACT Understanding the design of the universe of protein structures may provide insights into protein evolution. We study the architecture of the protein domain universe, which has been found to poses peculiar scale-free properties (Dokholyan et al., Proc. Natl. Acad. Sci. USA 99: 14132-14136 (2002)). We examine the origin of these scale-free properties of the graph of protein domain structures (PDUG) and determine that that the PDUG is not modular, i.e. it does not consist of modules with uniform properties. Instead, we find the PDUG to be self-similar at all scales. We further characterize the PDUG architecture by studying the properties of the hub nodes that are responsible for the scale-free connectivity of the PDUG. We introduce a measure of the betweenness centrality of protein domains in the PDUG and find a power-law distribution of the betweenness centrality values. The scale-free distribution of hubs in the protein universe suggests that a set of specific statistical mechanics models, such as the self-organized criticality model, can potentially identify the principal driving forces of molecular evolution. We also find a gatekeeper protein domain, removal of which partitions the largest cluster into two large sub- clusters. We suggest that the loss of such gatekeeper protein domains in the course of evolution is responsible for the creation of new fold families. INTRODUCTION The principles of molecular evolution remain elusive despite fundamental breakthroughs on the theoretical front 1-5 and a growing amount of genomic and proteomic data, over 23,000 solved protein structures 6 and protein functional annotations 7-9. -
Cmse 520 Biomolecular Structure, Function And
CMSE 520 BIOMOLECULAR STRUCTURE, FUNCTION AND DYNAMICS (Computational Structural Biology) OUTLINE Review: Molecular biology Proteins: structure, conformation and function(5 lectures) Generalized coordinates, Phi, psi angles, DNA/RNA: structure and function (3 lectures) Structural and functional databases (PDB, SCOP, CATH, Functional domain database, gene ontology) Use scripting languages (e.g. python) to cross refernce between these databases: starting from sequence to find the function Relationship between sequence, structure and function Molecular Modeling, homology modeling Conservation, CONSURF Relationship between function and dynamics Confromational changes in proteins (structural changes due to ligation, hinge motions, allosteric changes in proteins and consecutive function change) Molecular Dynamics Monte Carlo Protein-protein interaction: recognition, structural matching, docking PPI databases: DIP, BIND, MINT, etc... References: CURRENT PROTOCOLS IN BIOINFORMATICS (e-book) (http://www.mrw.interscience.wiley.com/cp/cpbi/articles/bi0101/frame.html) Andreas D. Baxevanis, Daniel B. Davison, Roderic D.M. Page, Gregory A. Petsko, Lincoln D. Stein, and Gary D. Stormo (eds.) 2003 John Wiley & Sons, Inc. INTRODUCTION TO PROTEIN STRUCTURE Branden C & Tooze, 2nd ed. 1999, Garland Publishing COMPUTER SIMULATION OF BIOMOLECULAR SYSTEMS Van Gusteren, Weiner, Wilkinson Internet sources Ref: Department of Energy Rapid growth in experimental technologies Human Genome Projects Two major goals 1. DNA mapping 2. DNA sequencing Rapid growth in experimental technologies z Microrarray technologies – serial gene expression patterns and mutations z Time-resolved optical, rapid mixing techniques - folding & function mechanisms (Æ ns) z Techniques for probing single molecule mechanics (AFM, STM) (Æ pN) Æ more accurate models/data for computer-aided studies Weiss, S. (1999). Fluorescence spectroscopy of single molecules. -
Physiology, Biochemistry, and Pharmacology of Transporters for Organic Cations
International Journal of Molecular Sciences Editorial Physiology, Biochemistry, and Pharmacology of Transporters for Organic Cations Giuliano Ciarimboli Experimental Nephrology, Department of Internal Medicine D, University Hospital Münster, 48149 Münster, Germany; [email protected] This editorial summarizes the 13 scientific papers published in the Special Issue “Physiology, Biochemistry, and Pharmacology of Transporters for Organic Cations” of the International Journal of Molecular Sciences. In this Special Issue, the readers will find integrative information on transporters for organic cations. Besides reviews on physi- ology, pharmacology, and toxicology of these transporters [1–3], which offer a concise overview of the field, the readers will find original research work focusing on specific transporter aspects. Specifically, the review “Organic Cation Transporters in Human Physiology, Phar- macology, and Toxicology” by Samodelov et al. [1] summarizes well the general as- pects of physiology, pharmacology, and toxicology of transporter for organic cations. The other review “Organic Cation Transporters in the Lung—Current and Emerging (Patho)Physiological and Pharmacological Concepts” by Ali Selo et al. [2] focuses on these aspects of transporters for organic cations in the lung, an important but often ne- glected field. In the paper “Systems Biology Analysis Reveals Eight SLC22 Transporter Subgroups, Including OATs, OCTs, and OCTNs”, by performing a system biology analysis of SLC22 transporters, Engelhart et al. [4] suggest the existence of a transporter–metabolite network. They propose that, in this network, mono-, oligo-, and multi-specific SLC22 transporters Citation: Ciarimboli, G. Physiology, interact to regulate concentrations and fluxes of many metabolites and signaling molecules. Biochemistry, and Pharmacology of In particular, the organic cation transporters (OCT) subgroup seems to be associated with Transporters for Organic Cations. -
BIOCHEMISTRY MAJOR the Biochemistry Major Is Offered Through the Department of Chemistry
BIOCHEMISTRY MAJOR The Biochemistry major is offered through the Department of Chemistry. This sequence is recommended for students planning entry into graduate school in Biochemistry, Pharmacology, or related subjects. It is also strongly recommend for those desiring to pursue medical or dental school. NOTE: This course sequence may be modified to include a Senior Capstone Experience. FIRST YEAR Fall Semester Credits Spring Semester Credits General Chemistry I for Majors (CHE111) 3 General Chemistry II for Majors (CHE112) 3 General Chemistry I Lab for Majors (CHE111L) 1 General Chemistry II Lab for Majors (CHE112L) 1 General Chemistry I Récitation (CHE111R) 0 General Chemistry II Récitation (CHE112R) 0 Precalculus (MAT116 or MAT120) 3-4 Calculus I (MAT231) 4 First Year Composition (ENG103) 4 Foreign Language (FL201) 4 African Diaspora/World I (ADW111) 4 African Diaspora/World II (ADW112) 4 First Year Experience (FYE 101-Chemistry) 1 First Year Experience (FYE 102-Chemistry) 1 First Year Seminar in Chemistry (CHE101) 0 Big Questions Colloquia (BQC) 1 TOTAL HOURS 16-17 TOTAL HOURS 18 SOPHOMORE YEAR Fall Semester Credits Spring Semester Credits Organic Chemistry I for Majors (CHE231) 4 Organic Chemistry II for Majors (CHE232) 4 Organic Chemistry I Lab (CHE233L) 1 Organic Chemistry II Lab (CHE234L) 1 Organic Chemistry I Récitation (CHE233R) 0 Organic Chemistry II Récitation (CHE234R) 0 Biology of the Cell (BIO120) 4 Organismal Form and Function(BIO115) 4 Calculus II (MAT 232) 4 Physics I: Mechanics & Lab (PHY151) 4 Foreign Language (FL202) -
Biochemistry and Molecular Biology
School of Life Sciences / Department of Biochemistry and Biophysics BIOCHEMISTRY AND MOLECULAR BIOLOGY Revealing how life works Department of Biochemistry and Biophysics Oregon State University 2011 Agriculture and Life Sciences Building Corvallis, OR 97331 OSUBB 541-737-4511 biochem.oregonstate.edu College of Science Oregon State University 128 Kidder Hall Corvallis, OR 97331 541-737-4811 science.oregonstate.edu This publication will be made available in an accessible alternative format upon request. Please contact the College COLLEGE OF SCIENCE of Science at 541-737-4811 or [email protected]. ACADEMIC BROCHURE / 2020 Highlights • Solve problems at the What will you discover? intersection of biological and physical sciences with our The Department of Biochemistry and Biophysics offers nationally accredited program world-class faculty, a tradition of interdisciplinary in biochemistry, molecular and research, teaching excellence and extraordinary cellular biology, chemistry, laboratories to facilitate undergraduate learning. molecular genetics, physics and statistics. The department ranks high nationally and internationally in many research areas, including signal transduction, gene • Tailor your education to expression, epigenetics, metabolic regulation, structural specific career goals with three biology, and genetic code expansion technology. different options. The department offers two Bachelor of Science degrees, • Thrive in a smaller, supportive both accredited by the American Society for Biochemistry department within a world-class and Molecular Biology (ASBMB): research university. • Biochemistry and Molecular Biology (BMB) with • Pursue interdisciplinary research options in Advanced Molecular Biology, Computational projects with faculty across OSU. Molecular Biology, and Pre-medicine; • Participate in the Biochemistry • Biochemistry and Biophysics (BB) with options in Club for community, leadership Advanced Biophysics, Neuroscience, and Pre-medicine. -
And Even-Length, Medium-Chain Fatty Acids in Plants (Amino Adds/Elongtin) ANTOANETA B
Proc. Nadl. Acad. Sci. USA Vol. 91, pp. 11437-11441, November 1994 Biochemistry A pathway for the biosynthesis of straight and branched, odd- and even-length, medium-chain fatty acids in plants (amino adds/elongtin) ANTOANETA B. KROUMOVA, ZHIYI XIE, AND GEORGE J. WAGNER* Plant Physiology/Biochemistry/Molecular Biology Program, Agronomy Department, University of Kentucky, Lexington, KY 40546-0091 Communicated by Martin Gibbs, July 25, 1994 ABSTRACT Pathways and enzymes offatty acid synthase- and even-length scFAs are synthesized via modified mediated, long-even-chain (generally C16-C20) fatty add syn- branched-chain amino acid (bcAA) metabolism in tobacco thesis are well studied, and general metabolism involved in trichome glands (6, 7). It is possible that at least branched and short-chain (Cs-C7) fatty acid biosynthesis is also understood. odd-length mcFAs are formed in this tissue similarly. Alter- In contrast, mechanism of medinm-chain (C#-C14) fatty acid natively, primers derived from bcAA metabolism may be synthesis are unclear. Recent work suggests involvement of elongated by fatty acid synthase (FAS), as suggested for chain-elongation-terminating thloesterases in medium-chain tomato trichomes (8) and tobacco epidermis (9). fatty acid formation in oilseeds and animals. We have shown The classical pathway for bcAA (Val, Leu, Ileu) biosyn- that iso- and anteiso-branched and straigbt, odd- and even- thesis in microorganisms (and largely by inference in plants, length, short-chain fatty adds esterifled in plant-trichome- ref. 10) is shown in the shaded areas of Fig. 1. Key activities gland-produced sucrose esters are synthesized by using carbon involved in branched-chain formation (reactions 1, 1A, and 2) skeletons provided by modified branched-chain amino acid are those catalyzing leucine biosynthesis in all organisms and metabolism/catablis. -
Biochemistry Major University of Michigan - Department of Chemistry Effective 9/2017 ______
Biochemistry Major University of Michigan - Department of Chemistry Effective 9/2017 _____________________________________________________________________________________________ Biochemistry is, literally the chemistry of life. Biochemists seek to understand the chemical principles that underpin all living organisms. Biochemistry is central to medical science as almost all diseases and drugs act to change the body’s chemistry. Advances in biochemistry directly impact the fields of biotechnology, pharmaceutical science, agriculture and environmental science, among many others. The B.S. major in Biochemistry is for those are interested in learning about life from a chemical perspective. Students will be well equipped for graduate studies in biochemistry, chemical biology, and many other fields of inquiry in the life sciences. The degree will also provide excellent preparation for students intending to pursue professional careers in industry and medicine. Prerequisites Course # Course Description Term Term Credits Completed Typically Offered CHEM 210 Structure and Reactivity I F, W, Sp 4 CHEM 211 Investigations in Chemistry: Laboratory F, W, Sp 1 CHEM 215 Structure and Reactivity II F, W, Sp 3 BIO 171 Introductory Biology: Ecology and Evolution F, W, Sp, Su 4 BIO 172 Introductory Biology: Molecular Cellular and Developmental F, W, Sp 4 MATH 115 Calculus I F, W, Sp, Su 4 MATH 116 Calculus II F, W, Sp, Su 4 One of the Following: CHEM 262 Mathematical Methods for Chemists F, W 4 OR MATH 215 Calculus III F, W, Sp, Su 4 One of the Following -
Action of Multiple Rice -Glucosidases on Abscisic Acid Glucose Ester
International Journal of Molecular Sciences Article Action of Multiple Rice β-Glucosidases on Abscisic Acid Glucose Ester Manatchanok Kongdin 1, Bancha Mahong 2, Sang-Kyu Lee 2, Su-Hyeon Shim 2, Jong-Seong Jeon 2,* and James R. Ketudat Cairns 1,* 1 School of Chemistry, Institute of Science, Center for Biomolecular Structure, Function and Application, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand; [email protected] 2 Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin 17104, Korea; [email protected] (B.M.); [email protected] (S.-K.L.); [email protected] (S.-H.S.) * Correspondence: [email protected] (J.-S.J.); [email protected] (J.R.K.C.); Tel.: +82-31-2012025 (J.-S.J.); +66-44-224304 (J.R.K.C.); Fax: +66-44-224185 (J.R.K.C.) Abstract: Conjugation of phytohormones with glucose is a means of modulating their activities, which can be rapidly reversed by the action of β-glucosidases. Evaluation of previously characterized recombinant rice β-glucosidases found that nearly all could hydrolyze abscisic acid glucose ester (ABA-GE). Os4BGlu12 and Os4BGlu13, which are known to act on other phytohormones, had the highest activity. We expressed Os4BGlu12, Os4BGlu13 and other members of a highly similar rice chromosome 4 gene cluster (Os4BGlu9, Os4BGlu10 and Os4BGlu11) in transgenic Arabidopsis. Extracts of transgenic lines expressing each of the five genes had higher β-glucosidase activities on ABA-GE and gibberellin A4 glucose ester (GA4-GE). The β-glucosidase expression lines exhibited longer root and shoot lengths than control plants in response to salt and drought stress. -
Biochemistry and Molecular Biology (BMB) 1
Biochemistry and Molecular Biology (BMB) 1 BMB 372. Advanced Molecular Biology. (3 h) BIOCHEMISTRY AND Presents molecular mechanisms by which stored genetic information is expressed including the mechanisms for and regulation of gene MOLECULAR BIOLOGY (BMB) expression, protein synthesis, and genome editing. Emphasizes analysis and interpretation of experimental data from the primary literature. Also Interdisciplinary Major listed as BIO 372. P-BIO 213 and 214 and BIO 370/BMB 370/CHM 370 or BIO 265 and BIO 370/BMB 370/CHM 370. This interdisciplinary Bachelor of Science major, jointly offered by the Departments of Biology and Chemistry, provides a strong foundation BMB 372L. Advanced Molecular Biology Laboratory. (1.5 h) in biological chemistry and molecular biology, and related topics at Introduces modern methods of molecular biology to analyze and the interface of these two disciplines. The major is designed to build manipulate expression of genes and function of gene products. Also conceptual understanding and practical and critical thinking skills to listed as BIO 372L. P or C-BIO 372/CHM 372 or BMB 373/CHM 373. address current biological, biochemical, and biomedical challenges. A BMB 373. Biochemistry II. (3 h) required research experience spanning multiple semesters, culminating Examines the structure, function, and synthesis of proteins and nucleic in a senior project, will give students strong experimental skills and acids and includes advanced topics in biochemistry including catalytic provide insight into biochemical and molecular biological experimental mechanisms of enzymes and ribozymes, use of sequence and structure approaches and results that demonstrate the function of biological databases, and molecular basis of disease and drug action. -
Evolution of Biomolecular Structure Class II Trna-Synthetases and Trna
University of Illinois at Urbana-Champaign Luthey-Schulten Group Theoretical and Computational Biophysics Group Evolution of Biomolecular Structure Class II tRNA-Synthetases and tRNA MultiSeq Developers: Prof. Zan Luthey-Schulten Elijah Roberts Patrick O’Donoghue John Eargle Anurag Sethi Dan Wright Brijeet Dhaliwal March 2006. A current version of this tutorial is available at http://www.ks.uiuc.edu/Training/Tutorials/ CONTENTS 2 Contents 1 Introduction 4 1.1 The MultiSeq Bioinformatic Analysis Environment . 4 1.2 Aminoacyl-tRNA Synthetases: Role in translation . 4 1.3 Getting Started . 7 1.3.1 Requirements . 7 1.3.2 Copying the tutorial files . 7 1.3.3 Configuring MultiSeq . 8 1.3.4 Configuring BLAST for MultiSeq . 10 1.4 The Aspartyl-tRNA Synthetase/tRNA Complex . 12 1.4.1 Loading the structure into MultiSeq . 12 1.4.2 Selecting and highlighting residues . 13 1.4.3 Domain organization of the synthetase . 14 1.4.4 Nearest neighbor contacts . 14 2 Evolutionary Analysis of AARS Structures 17 2.1 Loading Molecules . 17 2.2 Multiple Structure Alignments . 18 2.3 Structural Conservation Measure: Qres . 19 2.4 Structure Based Phylogenetic Analysis . 21 2.4.1 Limitations of sequence data . 21 2.4.2 Structural metrics look further back in time . 23 3 Complete Evolutionary Profile of AspRS 26 3.1 BLASTing Sequence Databases . 26 3.1.1 Importing the archaeal sequences . 26 3.1.2 Now the other domains of life . 27 3.2 Organizing Your Data . 28 3.3 Finding a Structural Domain in a Sequence . 29 3.4 Aligning to a Structural Profile using ClustalW . -
Biochemistry Metabolism
Biochemistry Metabolism 07.11.2017 – 27.11.2017 Photosynthesis Gerhild van Echten-Deckert Tel. 73 2703 E-mail: [email protected] www.limes-institut-bonn.de Photosynthesis Light reaction: - Light absorption, generation of a high energy electron and oxidation of water - Electron transport from water to NADPH and generation of a proton-motive force -Synthesis of ATP Berg, Tymoczko, Stryer: Biochemistry “Dark reaction”: - CO2 conversion into carbohydrates consuming ATP and NADPH (Calvin Cycle) Photosynthesis is localized to the thylakoid membranes Lodish et al. Molecular Cell Biology Comparison of photosynthesis and oxidative phosphorylation Berg, Tymoczko, Stryer: Biochemistry Chlorophyll a is the main pigment capturing energy of light Lodish et al. Molecular Cell Biology Energy diagram indicating the electronic states of chlorophyll and their most important modes of interconversion Other light-absorbing pigments, such as carotenoids, extend the range of light that can be absorbed and used for photosynthesis The action spectrum of photosynthesis matches the absorption spectra of chlorophyll a and b and of -carotene The absorption of photons from two distinct photosystems (PSI and PSII + is required for complete electron flow from H2O to NADP Berg, Tymoczko, Stryer: Biochemistry Light absorption by reaction-centre chlorophylls causes a charge separation across the thylakoid membrane The energy of the absorbed light is used to strip an electron from a chlorophyll molecule of the reaction centre to a primary electron acceptor thereby acquiring a positive charge (generation of a strong oxidizing- and a strong reducing agent) Lodish et al. Molecular Cell Biology Subsequent electron flow and coupled proton movement Lodish et al. -
Bsc in Biochemistry and Cell Biology
School of Science - BSc in Biochemistry and Cell Biology (For students admitted in 2019-20 under the 4-year degree) BSc in Biochemistry and Cell Biology In addition to the requirements of their major programs, students are required to complete the University and School requirements for graduation. For details please refer to the respective sections on this website. Some courses used to fulfill Major and/or School Requirements can also fulfill University Common Core Requirements. Students may reuse a maximum of 9 credits of these courses to count towards Common Core Requirements. Students may use no more than 6 credits earned from courses offered in pure online delivery mode to satisfy the graduation requirements of a degree program. This 6-credit limit does not apply to credits obtained through the credit transfer procedures of the University. For students graduating with an additional major, they must take all the requirements specified for that major, within which they must complete at least 20 single-counted credits. These 20 credits cannot be used to fulfill any other requirements for graduation except for the 120-credit degree requirement. Major Requirements Students MUST take the following courses prior to enrollment into the major Major Pre-requisite course(s) Credit(s) attained LIFS Note: Students with level 3 or above in HKDSE 1x Biology 0-3 are exempted from taking LIFS 1901 LIFS 1901 General Biology I 3 LIFS 1902 General Biology II 3 Required Course(s) Credit(s) attained LIFS Note: Students with level 3 or above in HKDSE 1x