on biological energy conversion (Biophysics 354)
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.
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
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.
RICHARD CROFTS homepage
Bioenergetics, respiratory chain, microbiology.
Prosthetic groups and Metal Ions in Protein Active Sites Database
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
to Macromolecular Simulation
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.
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
Metabolic Control Analysis Web
These web pages contain a brief electronic review
of metabolic control analysis (MCA) by P. Mendes.
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,
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.
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
to General, Organic and Biochemistry I and II page is included in Virtual
Classroom on this site.
Medical Biochemistry Course
Medical Biochemistry Course
Guide Indiana University School of Medicine Terre Haute Center for Medical
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.
UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY
- Comprehensive Recommendations on Biochemical & Organic
Nomenclature, Symbols & Terminology etc.
UNION OF PURE AND APPLIED CHEMISTRY
- Comprehensive Recommendations
on Organic Chemistry Nomenclature, Symbols & Terminology etc.
Giant detailed searchable scheme of biochemical reactions in
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.
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
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)
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.
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.
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
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.
Lab's Home Page|
phosphorylation, Complex I
Hatefi Lab Homepage
Bioenergetics in Mitochondria
and Bacteria, CYTOCHROME c OXIDOREDUCTASE
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?")
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.
1996 Albany Conference: Frontiers of Mitochondrial Research
September 19-22, 1996 Rensselaerville, New York
1997 Albany Conference: Biomolecular Motors and Nanomachines
September 4-7, 1997 Rensselaerville, New York
of Mitochondrial Research
2nd Albany Conference, September 24-27, 1998
You can find here Rat Liver Mitochondrion 3D model and
several other interesting models
OXIDASE HOME PAGE
A Forum for Disseminating Recent Information on this
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.
bc1 complex of Rhodobacter sphaeroides
site with a number of related links (pictures are not
Oxidative enzymes and the bioenergetics of membrane
systems, studying catalase and cytochrome c oxidase
International Congress on Photosynthesis
August 17-22, Budapest, Hungary
Structure/function of membrane proteins; biocatalysis,
Department of Bacteriology. University of Wisconsin-Madison.
There are several very detailed courses and
textbooks on Bacteriology
(including materials on Thermophillic
Dr. G. Hauska Homepage
Principles of Energy Conservation in the Electron
Transport Chains of Photosynthesis and Respiration
Biology and Cellular Regulation course
1999. Instructor: Dr. Frank Pugh
401. Microbial Physiology course.
(Fall, 1996). Detailed information.
L. TRUMPOWER, PROFESSOR OF BIOCHEMISTRY
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.
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.
Dr. Ulrich Brandt
Light Harvesting in Bacterial Photosynthesis
site with research information on this topic
and Biophysics department of University of Pennsylvania
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.
623. ADVANCED GENERAL BIOCHEMISTRY. Spring 1999
Andrew Rodgers Home Page
Andrew Rodgers studies the FoF1-ATPase, the enzyme
complex catalyzing the terminal step in oxidative phosphorylation and
OF MEDICAL BIOCHEMISTRY of THE OHIO STATE UNIVERSITY COLLEGE OF MEDICINE
studying energy coupling and ATPases
Oster. University of California Department of Molecular and Cellular Biology
Mathematical modeling of ATP synthase. Bibliography
with full-text articles. Software description.
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).
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
computer simulation of biochemical processes,
protein-protein interactions especially metabolic channeling, enzymology,
nonlinear dynamics, metabolic control analysis, gene expression.
Reinhart Heinrich Homepage
The Regulation of Cellular Systems, Mathematical
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.
Group of ATP Synthase
Gene map with Amino Acids sequences and brief subunits
description for different types of F- and V- ATP(synth)ases
OF SYSTEMS -METABOLIC CONTROL ANALYSIS AND BIOTECHNOLOGY IN THE POST-GENOMIC
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
on theoretical biophysics Hiddensee, April 1 - 4 1998
Programme and Abstracts
Workshop of the Graduiertenkolleg "Dynamics and evolution of cellular
and macromolecular processes" March, 17-19, 1999
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.
(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
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.
for Biochemists & Molecular Biologists. Course of lectures
This course is being developed by B. Tracy Nixon (firstname.lastname@example.org).
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.
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.
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.
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
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.
of Side-Chain and Main-Chain Hydrogen Bonding by Ian McDonald and Janet M
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
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
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
GLOSSARY OF TERMS USED IN MEDICINAL
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.
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].