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Related Concept Videos

Introduction to Enzyme Kinetics01:19

Introduction to Enzyme Kinetics

35.7K
Enzyme kinetics studies the rates of biochemical reactions. Scientists monitor the reaction rates for a particular enzymatic reaction at various substrate concentrations. Additional trials with inhibitors or other molecules that affect the reaction rate may also be performed.
The experimenter can then plot the initial reaction rate or velocity (Vo) of a given trial against the substrate concentration ([S]) to obtain a graph of the reaction properties. For many enzymatic reactions involving a...
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Enzymes02:34

Enzymes

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Inside living organisms, enzymes act as catalysts for many biochemical reactions involved in cellular metabolism. The role of enzymes is to reduce the activation energies of biochemical reactions by forming complexes with its substrates. The lowering of activation energies favor an increase in the rates of biochemical reactions.
Enzyme deficiencies can often translate into life-threatening diseases. For example, a genetic abnormality resulting in the deficiency of the enzyme G6PD...
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Introduction to Mechanisms of Enzyme Catalysis01:13

Introduction to Mechanisms of Enzyme Catalysis

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For many years, scientists thought that enzyme-substrate binding took place in a simple "lock-and-key" fashion. This model stated that the enzyme and substrate fit together perfectly in one instantaneous step. However, current research supports a more refined view scientists call induced fit. The induced-fit model expands upon the lock-and-key model by describing a more dynamic interaction between enzyme and substrate. As the enzyme and substrate come together, their interaction causes...
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Induced-fit Model01:13

Induced-fit Model

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Most chemical reactions in cells require enzymes—biological catalysts that speed up the reaction without being consumed or permanently changed. They reduce the activation energy needed to convert the reactants into products. Enzymes are proteins, that usually work by binding to a substrate—a reactant molecule that they act upon.
Enzymes exhibit substrate specificity, meaning that they can only bind to certain substrates. This is mainly determined by the shape and chemical...
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Enzyme Kinetics01:19

Enzyme Kinetics

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Enzymes speed up reactions by lowering the activation energy of the reactants. The speed at which the enzyme turns reactants into products is called the rate of reaction. Several factors impact the rate of reaction, including the number of available reactants. Enzyme kinetics is the study of how an enzyme changes the rate of a reaction.
Scientists typically study enzyme kinetics with a fixed amount of enzyme in the controlled environment of a test tube. When more reactant, or substrate, is...
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Modeling an Enzyme Active Site using Molecular Visualization Freeware
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A Networks Approach to Modeling Enzymatic Reactions.

P Imhof1

  • 1Institute of Theoretical Physics, Free University Berlin, Berlin, Germany.

Methods in Enzymology
|August 7, 2016
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Summary
This summary is machine-generated.

Modeling complex enzymatic reactions requires understanding multiple pathways. Transition networks map these pathways, revealing the most favorable routes and alternatives for comprehensive analysis.

Keywords:
Energy landscapeHydrolysisPath samplingQM/MMTransition network

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Area of Science:

  • Biochemistry
  • Computational Chemistry
  • Chemical Kinetics

Background:

  • Enzymatic reactions are complex, involving numerous degrees of freedom and intricate chemical/conformational changes.
  • A single reaction pathway is insufficient to fully describe enzymatic processes, necessitating exploration of multiple routes.

Purpose of the Study:

  • To develop a method for comprehensively visualizing and analyzing enzymatic reaction pathways.
  • To identify energetically favorable and alternative reaction mechanisms in enzymatic systems.

Main Methods:

  • Construction of transition networks by combining intermediate states and chemical transition steps.
  • Discretization of the potential energy landscape into a network of interconnected pathways.
  • Utilizing graph structures for pathway analysis.

Main Results:

  • Transition networks provide a discretized representation of the potential energy landscape.
  • The graph structure facilitates identification of the most favorable reaction pathways.
  • Alternative reaction routes and competing mechanisms can be readily discerned.

Conclusions:

  • Transition networks offer a powerful tool for understanding the complexity of enzymatic reactions.
  • This approach enables a comprehensive overview of possible reaction paths and mechanisms.
  • Facilitates the identification of optimal and alternative enzymatic reaction pathways.