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Lectures on biological energy conversion (Biophysics 354)
Introduces and explores the major mechanisms of energy conversion in biology, with particular emphasis on respiratory and photosynthetic bioenergetics, and the physic-chemical tools required to describe these processes.

bc1 complex site  
This site contains information, links, pictures, and down-loadable materials based on research on the bc1 complex. This group of electron transfer enzymes,- generally known as bc1 complexes in mitochondria, bacterial respiratory chains and photosynthetic bacteria, or b6f complexes in the photosynthetic chains of oxygenic photosynthesis,- carries the main flux of energy through the biosphere

The Thermosynthesis Home Page
Thermosynthesis is a physical theory for the stepwise emergence during evolution of the contemporary biological energy conversion machinery. The basic tenet of the thermosynthesis (TS) theory is that thermal cycling is a major agent in the origin and evolution of life.

Bioenergetics, respiratory chain, microbiology.

 The Prosthetic groups and Metal Ions in Protein Active Sites Database

Biophysics Textbook On-Line
A number of book chapters and Biophysical Journal teaching articles presently available in PDF or html format (about 20). Sponsored by the Biophysical Society.

Glactone is a three year project funded by the Chancellor of the University System of Georgia. The goal of this project to provide computer based resources for chemistry and biochemistry students and faculty in the State of Georgia. There are currently 9 colleges and universities making up Glactone, with Georgia State University being the lead institution.

Introduction to Macromolecular Simulation
The purpose of this tutorial is to introduce several popular numerical techniques used to simulate the structure and dynamics of biomolecules. The discussion is confined to simulation methods that apply classical mechanics to biological systems, although some quantum theory is presented to quantify some shortcomings of classical approximations. Molecular dynamics (MD) simulation, Langevin dynamics (LD) simulation, Monte Carlo (MC) simulation, and normal mode analysis are among the methods surveyed here.

Molecular biology Hypertextbook
This hypertextbook is designed to supplement the course materials of 7.01 (MIT Introductory Biology) and give you additional tools to learn introductory molecular biology. The 7.01 hypertextbook is organized in a very straightforward manner and contains a variety of components designed to be used independently or together to facilitate your understanding of introductory molecular biology

The Metabolic Control Analysis Web
These web pages contain a brief electronic review of metabolic control analysis (MCA) by P. Mendes.

Guide to metabolic control analysis. Fundamentals of Enzyme Kinetics
These pages are based closely on Chapter 10 of Fundamentals of Enzyme Kinetics (Athel Cornish-Bowden, 1995, Portland Press, London).

Metabolic control analysis FAQ
This page is intended as an elementary introduction to metabolic control analysis for people who have heard of metabolic control analysis but have very little idea of what it is.

Amino Acid Information
Some information about various properties of Amino Acids

The information provided on this site is a service of the Hardy Research Group, Department of Chemistry, The University of Akron. Site contains educational information on general-, organic- and biochemistry.  Introduction to General, Organic and Biochemistry I and II page is included in Virtual Classroom on this site.

THCME Medical Biochemistry Course
Medical Biochemistry Course Guide Indiana University School of Medicine Terre Haute Center for Medical Education

NetBiochem is intended to be a complete Medical Biochemistry center which can be accessed over a computer network. The distinction of this course is a lot of information in Tables.

- Comprehensive Recommendations on Biochemical & Organic Nomenclature, Symbols & Terminology etc.

- Comprehensive Recommendations on Organic Chemistry Nomenclature, Symbols & Terminology etc.

Biochemical Pathways Map
Giant  detailed searchable scheme of biochemical reactions in a cell.

Metabolic Pathways of Biochemistry,
the online reference of metabolism for students, scientists, and the world. This site is designed to graphically represent (with schemes and 3D models) all major metabolic pathways, primarily those important to human biochemistry.

Oxidative Phosphorylation Home Page
These pages describe how mitochondria use the energy from substrate oxidation to drive the synthesis of ATP from ADP and inorganic phosphate. The system also powers many cellular transport processes.

Biochemistry (Moscow) On-Line,
World Wide Web version of the international edition of Russian leading scientific journal in the fields of biochemistry and biochemical aspects of molecular biology, bioorganic chemistry, microbiology, immunology, physiology, and biomedical sciences. Some articles available in full text (in HTML)

Mitochondria Studies
The experiments on mitochondria, described here, were designed to augment the student's understanding of how mitochondria function, while providing a hands-on experience. The recommended studies have been carried out successfully on preparations from rat liver.

Physics of biological processes
This is a physics hypertext book: it is intended as a vehicle for students in the biological and chemical sciences, enabling them to understand the physical underpinnings of their later studies. As often as possible, the systems under investigation will relate to human physiology, for there is no substitute for relevance to motivate the study of a subject.

Encyclopedia of Analytical Instrumentation (Science  Hypermedia, Inc.)
Books, Journals, Software, and other Resources / Data Acquisition and Electronics / Data Handling / Diffraction / Electrochemistry / Gravimetry / Imaging / Mass Spectrometry / Materials & Surface Analysis / Optics / Sensors / Separations / Spectroscopy / Standards / Thermal Methods / Titration

Complex I Home Page
The purpose of this site is to provide general information regarding complex I (NADH quinone oxidoreductase) to researchers in the field of bioenergetics as well as to those who are simply curious about what this enzyme complex does.

M.Yagi Lab's Home Page
Oxidative phosphorylation, Complex I

Y. Hatefi Lab Homepage
Bioenergetics in Mitochondria and Bacteria, CYTOCHROME c OXIDOREDUCTASE

The second law of thermodynamics
This site shows that some ancient questions about "things going wrong" in our lives have surprisingly simple answers in modern basic chemistry (even things happening to us which cause that painful cry of "Why me?")

Brdiczka Laboratory
University of Konstanz, Faculty of Biology, Brdiczka Laboratory. Scientific work concentrates on: Energy transfer and signal transduction between mitochondria and cytosol. On this site you can find some great  related educational software.

The 1996 Albany Conference: Frontiers of Mitochondrial Research
September 19-22, 1996 Rensselaerville, New York

The 1997 Albany Conference: Biomolecular Motors and Nanomachines
September 4-7, 1997 Rensselaerville, New York

Frontiers of Mitochondrial Research
2nd Albany Conference, September 24-27, 1998 Rensselaerville, NY

3D model gallery
You can find here Rat Liver Mitochondrion 3D model and several other interesting models

A Forum for Disseminating Recent Information on this Enzyme

Graham Palmer homepage
Laboratory is involved in the characterization of two of these enzymes, the ubiquinol cytochrome c oxidoreductase (Complex III) and cytochrome oxidase (Complex IV). The experimental approach depends on the application of spectroscopic and other physical methods, in conjunction with transient state kinetic experiments, to define the structures and dynamics of the species which function in the electron transport, and to a lesser extent, the proton translocation reactions.

The bc1 complex of Rhodobacter sphaeroides
site with a number of related links (pictures are not downloaded)

Peter Nicholls Homepage
Oxidative enzymes and the bioenergetics of membrane systems, studying catalase and cytochrome c oxidase

XIth International Congress on Photosynthesis
 August 17-22, Budapest, Hungary

Chang-An Yu homepage
Structure/function of membrane proteins; biocatalysis, Q-cycle

The Department of Bacteriology. University of Wisconsin-Madison.
There are several very detailed courses and textbooks on Bacteriology  (including materials on Thermophillic bacteria)

Prof. Dr. G. Hauska Homepage
Principles of Energy Conservation in the Electron Transport Chains of Photosynthesis and Respiration

Molecular Biology and Cellular Regulation course
1999. Instructor: Dr. Frank Pugh

MICROBIOLOGY 401. Microbial Physiology course.
(Fall, 1996). Detailed information.

BIOCHEMISTRY AND GENETICS OF RESPIRATION We are investigating several aspects of the mitochondrial cytochrome bc1 complex, including identifying electron transfer pathways within individual proteins by site directed mutagenesis combined with kinetics measurements on a msec time scale of mutated enzymes.

JD Lab page
Our lab at UT Southwestern. We study the three-dimensional structures of biological macromolecules with the methods of X-ray crystallography. Among the techniques we use are heterologous expression, purification, crystallization, and mutagenesis of proteins, X-ray diffraction, computational crystallography, and structure analysis. Our interests focus on the following main areas: Proteins involved in energy transfer and electron transfer, proteins using light energy, membrane proteins, membrane associating proteins, chaperonins and proteins with repeating sequence motifs.

Prof. Dr. Ulrich Brandt
Complex I

Theoretical Biophysics group
Light Harvesting in Bacterial Photosynthesis

Cytochrome bc1 project
site with research information on this topic

Biochemistry and Biophysics department of University of Pennsylvania

Mitochondrial Disease Information
The United Mitochondrial Disease Foundation. Glossary of Terms. Literature Reviews. Mitochondria and Disease. Mitochondrial Disease Descriptions. Mitochondrial Disease Publications by UMDF. UMDF Medical Article Database and Library.

Biochemistry 623. ADVANCED GENERAL BIOCHEMISTRY. Spring 1999
Detailed course.

Andrew Rodgers Home Page
Andrew Rodgers studies the FoF1-ATPase, the enzyme complex catalyzing the terminal step in oxidative phosphorylation and photophosphorylation.

studying energy coupling and ATPases

George Oster. University of California Department of Molecular and Cellular Biology 
Mathematical modeling of ATP synthase. Bibliography with full-text articles. Software description.

Hongyun Wang's Home Page (Works with G. Oster)
Mathematical modeling of ATP synthase. Bibliography with full-text articles. Links to ATPase work movies - more than 20!!! (in MPEG and AVI format).

Metabolic Control Analysis Research Group (Headed by D. Fell)
The group. News. Introduction. Projects. Publications (New items 18 Feb. 1999). Software. Group members. Links to other control analysis research.

Pedro Mendes Homepage
computer simulation of biochemical processes, protein-protein interactions especially metabolic channeling, enzymology, nonlinear dynamics, metabolic control analysis, gene expression.

Prof. Reinhart Heinrich Homepage
The Regulation of Cellular Systems, Mathematical modeling

Roderick A. Capaldi Lab Homepage
Research focuses on enzymes of oxidative phosphorylation. With high resolution structures already determined for complex III, cytochrome c oxidase and the F1 part of the ATP synthase, it is now possible for the first time to explore the mechanism of oxidative phosphorylation at a detailed molecular level. Primary emphasis has been to understand the workings of the ATP synthase, also called the F1F0-ATPase.

Ortholog Group of ATP Synthase
Gene map with Amino Acids sequences and brief subunits description for different types of F- and V- ATP(synth)ases

 An invited position paper for discussion among the participants of the NATO ARW on Technological and Medical Implications of Metabolic Control Analysis, Visegrad 10-16 April 1999

Workshop on theoretical biophysics Hiddensee, April 1 - 4 1998
Programme and Abstracts

Hiddensee Workshop of the Graduiertenkolleg "Dynamics and evolution of cellular and macromolecular processes" March, 17-19, 1999
Programme only

3rd Berlin Workshop on Theoretical Biophysics (1996)
Programme and abstracts.
The main topics are: Nonlinear dynamics (calcium oscillations and waves, synchronization of cellular oscillations, minimal models of oscillations), evolutionary optimization of enzymatic systems, metabolic control analysis and kinetic modelling, flux modes in chemical reaction networks, Molecular dynamics of proteins, DNA sequences, membrane dynamics, Evolutionary game theory, modelling of signal transduction in the visual cascade.

GEPASI (developed by Pedro Mendes)
a user- friendly MS- Windows computer program to simulate the dynamics of biochemical systems, with an emphasis on the steady- state properties of pathways containing enzymes that interact by transferring their intermediate metabolite directly (metabolic channelling).

Whilst there is much current interest in the genome-wide analysis of cells at the level of transcription (to define the 'transcriptome') and translation (to define the 'proteome'), the third level of analysis, that of the 'metabolome', has been curiously unexplored to date. The term 'metabolome' refers to the entire complement of all the small molecular weight metabolites inside a cell suspension (or other sample) of interest. It is likely that measurement of the metabolome in different physiological states will in fact be much more discriminating for the purposes of functional genomics.

Computers for Biochemists & Molecular Biologists. Course of lectures
This course is being developed by B. Tracy Nixon ( Two prior versions were offered in the Fall of 1995, 1996 and 1997. It is being offered again in the Fall of 1998 in two sections.

MCA 99 NATO Advanced Research Workshop on Technological and Medical Implications of Metabolic Control Analysis
This page contains information about the NATO Advanced Research Workshop in April 1999 at Visegrad, Hungary. Programme, abstracts, poster texts, detailed information about participants.

What is Controlling Life? 50 years after Erwin Schrödinger's What is Life? Modern Trends in BioThermoKinetics Volume 3 Series edited by the International BioThermoKinetics Study Group (1994).
Scope: Modern Trends in BioThermoKinetics deals with developments in biological thermodynamics, kinetics, metabolic regulation and control. It is aimed at promoting the understanding and application of bioenergetics, including theory, models, computation, instrumentation, experiment and generalized concepts. Applications of bioenergetics are discussed in relation to physiology, medicine, ecology and biotechnology. Interdisciplinary integration and international cooperation visibly characterize the contributions published in this series which thus conveys the spirit of an ongoing process of scientific enterprise rather than the static picture of closed chapters in science.

Simulation of metabolic systems (by Pedro Mendes)
Work in the following areas: 1. Construction of a biochemical kinetics simulation program (GEPASI). 2. Usage of simulation to study protein-protein interactions, more specifically metabolite channelling 3. simulation of heterogeneous spatio-temporal biochemical models. Another area actively involved is Metabolic Control Analysis. MCA can be used both to analyze experimental results and to characterize results from simulations.

Metatool is a program for studying structural properties of metabolic networks by using methods of linear and convex algebra. The theoretical background of the program and examples are given under publications and literature, for details of the algorithms and a description of the program follow the metatool description link.

Biotechnology Areas
Brief description of various Biotechnology areas (with links to some companies): Biotechnology (General), Molecular Biology, Sequence Search and Analysis, Software, Tutorials, Biochemistry, Protein Purification, Tutorials, Software, Biophysics, Photosynthesis, Scientific Analysis/Modeling, Molecular Modeling, Software, Bioinformatics, Sequence Search and Analysis, Structure Search and Analysis

Microelectrode Techniques
The full text of this vital textbook - 450 pages of practical and theoretical discussion and teaching materials on the latest developments in electrophysiology. The first Plymouth 'Microelectrode Techniques' workshop was held in April 1984. Interest in this subject area was very high and the workshop was greatly oversubscribed. The workshop has been updated and repeated many times since, and this handbook arose out of the need to further disseminate the knowledge assembled by the leading experts in this field. This year's course (1999) is being held in September, and you can find full details here.

Atlas of Side-Chain and Main-Chain Hydrogen Bonding by Ian McDonald and Janet M Thornton
WWW Edition December 1994, original edition April 1993 Awarded 4/4 by the Magellan survey. This document is a graphical summary of hydrogen bonding in a dataset of high-resolution protein structures. It shows the distributions of the frequencies and geometries of hydrogen bonds formed by main-chain and side-chain donors and acceptors. It is hoped that it will serve as a record of the hydrogen bonding patterns of the standard hydrogen bonding groups for molecular modellers and crystallographers who would like to know whether the hydrogen bonding in their model is normative.

ExPASy - ENZYME - Enzyme nomenclature database
ENZYME is a repository of information relative to the nomenclature of enzymes. It is primarily based on the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (IUBMB) and it describes each type of characterized enzyme for which an EC (Enzyme Commission) number has been provided. Release 24.0, January 1999, and updates up to 05-Feb-1999 (3704 entries)

ExPASy - PROSITE Database of protein families and domains
PROSITE is a database of protein families and domains. It consists of biologically significant sites, patterns and profiles that help to reliably identify to which known protein family (if any) a new sequence belongs. Release 15, July 1998 and updates up to 05-Feb-1999 (contains 1025 documentation entries that describe 1361 different patterns, rules and profiles/matrices).

The objective of the glossary is to provide in a single document a consistent terminology and concise definitions of terms covering the various aspects of medicinal chemistry. This was felt necessary with regard to the rapid changes occurring in medicinal chemistry and also by the need to establish international definition standards. Effectively the possibility exists that in different countries certain terms may not have the same meaning, in such a case the creation of an internationally accepted definition is particularly justified.

Recommendations for nomenclature and tables in biochemical thermodynamics (1994)
IUBMB-IUPAC JOINT COMMISSION ON BIOCHEMICAL NOMENCLATURE (JCBN). The recommendations in this version are identical to those in the published document prepared by Robert A. Alberty (Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA), see Eur. J. Biochem., 1996, 240, 1-14; 242, 433; Pure Appl. Chem. 1994, 66, 1641-1666 [Copyright IUBMB and IUPAC].