Biochemistry

CHEM 181 (CHEMENG 181, CHEMENG 182) - Fall 2016 - Instructor: Cegelski, L.

Structure and function of major classes of biomolecules, including proteins, carbohydrates and lipids. Mechanistic analysis of properties of proteins including catalysis, signal transduction and membrane transport. Students will also learn to critically analyze data from the primary biochemical literature.

Course reserves books

Please ask for items by first author at the Swain Library's reserve desk.

Physical Chemistry for the Life Sciences
2nd ed. Oxford ; New York : Oxford University Press, c2011.
Science Library (Li and Ma) » Stacks » QP517 .P49 A86 2011
Physical chemistry lies at the heart of the behaviour of those macromolecules and molecular assemblies that have vital roles in all living organisms. Physical principles determine the stability of proteins and nucleic acids, the rate at which biochemical reactions proceed, the transport of molecules across biological molecules; they allow us to describe structure and reactivity in complex biological systems, and make sense of how these systems operate. Physical Chemistry for the Life Sciences provides a balanced presentation of the concepts of physical chemistry, and their extensive applications to biology and biochemistry.
Biochemistry by Berg
Eighth edition.
Science Library (Li and Ma) » Ask at circulation desk » QP514.2 .S66 2015
For four decades, this extraordinary textbook played an pivotal role in the way biochemistry is taught, offering exceptionally clear writing, innovative graphics, coverage of the latest research techniques and advances, and a signature emphasis on physiological and medical relevance. Those defining features are at the heart of this edition.
Proteins Structures and Properties
2nd ed. New York : W.H. Freeman, c1993.
Marine Biology Library (Miller) » Stacks » QP551 .C737 1993
Creighton's landmark textbook offers an expert introduction to all aspects of proteins--biosynthesis, evolution, structures, dynamics, ligand binding, and catalysis.  It works equally well as a reference or as a classroom text.
Biochemistry: a short course
Third edition, first printing.
Science Library (Li and Ma) » Stacks » QP514.2 .T96 2015
" Biochemistry: A Short Course" focuses on the major topics taught in a one-semester biochemistry course. With its short chapters and relevant examples, it s uniquely effective in helping students see the connections between the biochemistry they re studying and their own lives. This new edition takes into account recent discoveries and advances that have changed how we think about the fundamental concepts in biochemistry and human health.
Biochemistry by Voet
4th ed. Hoboken, NJ : John Wiley & Sons, c2011.
Science Library (Li and Ma) » Stacks » QP514.2 .V64 2011
The "Gold Standard" in Biochemistry text books, Biochemistry 4e, is a modern classic that has been thoroughly revised. Don and Judy Voet explain biochemical concepts while offering a unified presentation of life and its variation through evolution. Incorporates both classical and current research to illustrate the historical source of much of our biochemical knowledge.

Databases: 3D structures, sequences, & pathways

RCSB Protein Data Bank
[La Jolla, CA] : [University of California, San Diego Supercomputer Center]
Stanford University Libraries » Online resource » eResource
The Protein Data Bank (PDB) archive is the single worldwide repository of information about the 3D structures of large biological molecules, including proteins and nucleic acids.  Simple and advanced searching for macromolecules and ligands, tabular reports, specialized visualization tools, sequence-structure comparisons, RCSB PDB Mobile, Molecule of the Month and other educational resources at PDB-101, and more..
PDBe - Protein Data Bank of Europe
Stanford University Libraries » Online resource » eResource
Rich information about all PDB entries, multiple search and browse facilities, advanced services including PDBePISA, PDBeFold and PDBeMotif, advanced visualisation and validation of NMR and EM structures, tools for bioinformaticians.
Stanford University Libraries » Online resource » eResource
CSD-Enterprise includes everything in the CSD-System, CSD-Discovery and CSD-Materials, software and application data for the Cambridge Structural Database (CSD), the world’s only comprehensive, up-to-date, and fully-curated knowledge base of small molecule crystal structures.  Stanford also has a license to the web version of CSD which is updated weekly. (Structure Searching)

Sequences

BLAST: Basic Local Alignment Search Tool
[Bethesda, MD] : [National Center for Biotechnology Information], [1990]-
Stanford University Libraries » Online resource » eResource
BLAST finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance.

Biochemical pathways

BioPath database
Stanford University Libraries » Online resource » eResource
BioPath is a database of biochemical pathways that provides access to metabolic transformations and cellular regulations derived from the "Biochemical Pathways" wall chart and additional literature harvesting. With its emphasis on chemical structure and reaction information BioPath offers a variety of novel applications for drug target identification and the modeling of biological systems. All structure and reaction information in BioPath is stored on an atomic level allowing for direct access to all atoms and bonds of all metabolites and to the bonds broken and made during an enzymatic reaction. See flyer for more details.
Reactome Pathway Database
<2003>-
Medical Library (Lane) » Check Lane Library catalog for status » (no call number)
Reactome is a free, open-source, curated and peer reviewed pathway database. Our goal is to provide intuitive bioinformatics tools for the visualization, interpretation and analysis of pathway knowledge to support basic research, genome analysis, modeling, systems biology and education. Reactome Team is a multi-disciplinary group of curators and software developers, located at the Ontario Institute for Cancer Research (OICR), New York University Medical Centre (NYUMC) and the European Bioinformatics Institute (EBI).

Encyclopedias & handbooks

Encyclopedias

[S.l.] : Wiley, c1999-
Stanford University Libraries » Online resource » eResource
Spanning the entire spectrum of the life sciences, ELS is a monthly-updating reference work containing over 4,500 specially commissioned and peer-reviewed articles written by leaders in the field. ELS has articles on these subject areas: Biochemistry, Cell Biology, Developmental Biology, Ecology, Evolution and Diversity of Life, Genetics and Disease, Genetics and Molecular Biology, Immunology, Microbiology, Neuroscience, Plant Science, Science and Society, Structural Biology, and Virology.
Weinheim [Germany] : Wiley-VCH, c2008.
Science Library (Li and Ma) » Reference » QP620 .N797 2008
"Concise but complete, this mini-encyclopedia contains over 1,500 entries covering all important concepts, compounds, techniques and acronyms for quick and easy reference.  Guiding readers through the ever-increasing jungle of nucleic acid science and technology, the book distills the key information out of the large body of primary literature and presents it in a single volume. A first-stop resource for everyone, from students to established researchers, as both a desktop and library reference."
[New York] : Wiley, c2008-
Stanford University Libraries » Online resource » eResource
Protein Science Encyclopedia , the single most comprehensive knowledge source for protein scientists covers: structure of proteins, function of proteins, analytical methods of proteins, engineering of proteins, and medical aspects of proteins.  This encyclopedia contains some 160 articles (corresponding to approx. 4500 printed pages) on fundamental and current topics in 14 subject fields: Transcription and Translation, Technical and Recombinant Synthesis, Modification and Regulation, Damage and Degradation, Structure and Folding, Protein-Ligand Interaction, Protein-Protein Interaction, Enzymatic Function, Engineering and Design, Biotechnology and Bioengineering, Misfolding and Disease, Model Proteins, Structural Analysis, and Functional Analysis."
Protopedia
[S.l.] : BioMed Central.
Stanford University Libraries » Online resource » eResource
Proteopedia is an interactive wiki-style web resource that presents 3D structural and functional information in a user-friendly manner and allows real-time community annotation.
Hoboken, N.J. : John Wiley & Sons, c2009.
Science Library (Li and Ma) » Reference » QP512 .W48 2009 V.1
"This encyclopedia illuminates the crucial role of chemistry and chemical techniques in the life sciences. WECB is an evolving online database of information, combining the most useful features of traditional reference works and review journals in a compelling format designed to exploit the full potential of the online medium. Includes extensive linking to the primary literature and to other online resources." (publisher's description)

Handbooks

Biochemical Pathways examines the biochemistry of bacteria, plants, and animals. It offers a quick overview of the metabolic sequences in biochemical pathways, the chemistry and enzymology of conversions, the regulation of turnover, the expression of genes, the immunological interactions, and the metabolic background of health disorders. A standard set of conventions is used in all illustrations, enabling readers to easily gather information and compare the key elements of different biochemical pathways.
A repository for data from NMR spectroscopy on proteins, peptides, nucleic acids, and other biomolecules.  Collects NMR data from any experiment and captures assigned chemical shifts, coupling constants, and peak lists for a variety of macromolecules; contains derived annotations such as hydrogen exchange rates, pKa values, and relaxation parameters.
Color Atlas of Biochemstry 3rd edition
3rd ed., rev. and updated. Stuttgart ; New York : Thieme, c2013.
Medical Library (Lane) » Check Lane Library catalog for status » THIEME BOOK
Providing a powerful visual overview of the entire spectrum of human biochemistry, the third edition of the popular Color Atlas of Biochemistry is an ideal reference and study aid. It utilizes the signature Flexibook format, consisting of double-page spreads with clear explanatory text on the left-hand page and exquisitely detailed full-color graphics on the right. These bite-sized learning capsules ensure that your review of any given topic is quick, efficient, and comprehensive, allowing you to target the exact information you need for classroom and exam success.
Web version. Boca Raton, FL : Chapman & Hall/CRC
Stanford University Libraries » Online resource » eResource
Includes descriptive and numerical data on the chemical, physical and biological properties of compounds; systematic and common names of compounds; literature references; structure diagrams and their associated connection tables. CCD online includes: organic compounds (269,000 records); natural products (178,000 records); inorganic and organometallic compounds (103,000 records); drugs (44,000 records); analytical reagents (14,000 records); and carbohydrates (24,000). (Structure searching)
Handbook of Biochemistry and Molecular Biology
4th ed. Boca Raton : CRC Press, c2010.
Science Library (Li and Ma) » Reference » QH345 .H347 2010
Offering a molecular perspective not available 20 years ago, it provides physical and chemical data on proteins, nucleic acids, lipids, and carbohydrates. Presented in an organized, concise, and simple-to-use format, this popular reference allows quick access to the most frequently used data. Covering a wide range of topics, from classical biochemistry to proteomics and genomics, it also details the properties of commonly used biochemicals, laboratory solvents, and reagents.
Physical Chemistry for the Biological Sciences
Second edition /
Stanford University Libraries » Online resource » eResource
This book provides an introduction to physical chemistry that is directed toward applications to the biological sciences. Advanced mathematics is not required. This book can be used for either a one semester or two semester course, and as a reference volume by students and faculty in the biological sciences. This book was pubished in 2015 and is volume 55 in the series Methods of Biochemical Analysis.

Software

PyMOL
[S.l.] : Schrodinger
Stanford University Libraries » Online resource » eResource
PyMOL is molecular visualization software that is available in Mac, PC, and Linux. Stanford has a campus-wide site license that allows users to download the latest version of the software as well as documentation on how to use PyMOL. For more information, please see the PyMOL wiki and the PyMOL website

For instructors

Biochemistry education journal

For more chemistry education resources, please see Chemical Information Sources, Chapter 19: Teaching and Studying Chemistry.

The aim of BAMBED is to enhance teacher preparation and student learning in Biochemistry, Molecular Biology, and related sciences such as Biophysics and Cell Biology, by promoting the world-wide dissemination of educational materials.