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Related Concept Videos

Introduction to Chemical Reactions01:23

Introduction to Chemical Reactions

All chemical reactions begin with a reactant, the general term for one or more substances entering the reaction. Sodium and chloride ions, for example, are the reactants in the production of table salt. One or more substances produced by a chemical reaction are called the product. Chemical reactions follow the law of conservation of mass, which means that matter cannot be created nor destroyed in a chemical reaction. The components of the reactants—the number of atoms and the elements—are all...
Coupled Reactions01:17

Coupled Reactions

Cellular processes such as building and breaking down complex molecules occur through stepwise chemical reactions. Some of these chemical reactions are spontaneous and release energy, whereas others require energy to proceed. Cells often couple the energy-releasing reaction with the energy-requiring one to carry out important cell functions. 
Energy in adenosine triphosphate or ATP molecules is easily accessible to do work. ATP powers the majority of energy-requiring cellular reactions. Cells...
The Reaction Gibbs Energy01:29

The Reaction Gibbs Energy

The reaction Gibbs energy (ΔrG) is a crucial parameter that determines whether a reaction will occur spontaneously or not. It can be used to categorize reactions into two types: exergonic and endergonic.Exergonic reactions are those in which ΔrG is less than zero. This implies that these reactions can occur spontaneously without an external input of energy. In biological systems, a typical example of an exergonic reaction is the oxidation of carbohydrates. This reaction produces simple...
Consecutive Reactions01:22

Consecutive Reactions

Consecutive reactions involve a sequence where the product of a preceding reaction becomes the reactant for the subsequent one. In a simple scheme, A transforms into B, which further reacts to form C, with rate constants k1 and k2, respectively. This concept is evident in the radioactive decay series. Assuming an initial state with only A present, the conservation of matter leads to three coupled differential equations, determining the concentrations of A, B, and C over time.The rate of change...
Reaction Mechanisms03:06

Reaction Mechanisms

Chemical reactions often occur in a stepwise fashion, involving two or more distinct reactions taking place in a sequence. A balanced equation indicates the reacting species and the product species, but it reveals no details about how the reaction occurs at the molecular level. The reaction mechanism (or reaction path) provides details regarding the precise, step-by-step process by which a reaction occurs.
For instance, the decomposition of ozone appears to follow a mechanism with two steps:
Multi-Step Reactions02:31

Multi-Step Reactions

Chemical reactions often occur in a stepwise fashion involving two or more distinct reactions taking place in a sequence. A balanced equation indicates the reacting species and the product species, but it reveals no details about how the reaction occurs at the molecular level. The reaction mechanism (or reaction path) provides details regarding the precise, step-by-step process by which a reaction occurs. Each of the steps in a reaction mechanism is called an elementary reaction. These...

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Updated: May 30, 2026

A Web Tool for Generating High Quality Machine-readable Biological Pathways
08:01

A Web Tool for Generating High Quality Machine-readable Biological Pathways

Published on: February 8, 2017

BKM-react, an integrated biochemical reaction database.

Maren Lang1, Michael Stelzer, Dietmar Schomburg

  • 1Department of Bioinformatics and Biochemistry, Institute for Biochemistry and Biotechnology, Technische Universität Braunschweig, Langer Kamp 19 B, 38106 Braunschweig, Germany.

BMC Biochemistry
|August 10, 2011
PubMed
Summary
This summary is machine-generated.

Researchers created a comprehensive, non-redundant reaction database by integrating data from BRENDA, KEGG, and MetaCyc. This valuable resource accelerates the accurate reconstruction of metabolic pathways and genome-scale models.

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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

Area of Science:

  • Systems Biology
  • Biochemistry
  • Bioinformatics

Background:

  • Reconstructing genome-scale metabolic networks is challenging due to the need for complete biochemical reaction knowledge.
  • Existing biological databases vary in reaction content and annotation, highlighting the need for an integrated resource.

Purpose of the Study:

  • To develop a unified, non-redundant database of biochemical reactions.
  • To facilitate the accurate and efficient construction of metabolic models.

Main Methods:

  • Integrated biochemical reactions from BRENDA, KEGG, and MetaCyc databases.
  • Matched and aligned reactions based on substrates and products using structural (InChI) and name comparisons.
  • Included all unique biochemical reactions present in at least one source database.

Main Results:

  • Developed a comprehensive, non-redundant reaction database containing 18,172 unique enzyme-catalyzed and spontaneous reactions.
  • Successfully integrated reaction data from multiple established biochemical databases.
  • Created a valuable resource for systems biology research.

Conclusions:

  • An integrated, non-redundant reaction database has been successfully developed and made available.
  • This database significantly aids in accelerating the creation of accurate biochemical and metabolic models.