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Related Concept Videos

Enzymes02:34

Enzymes

80.2K
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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Introduction to Enzyme Kinetics01:19

Introduction to Enzyme Kinetics

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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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Introduction to Enzymes01:22

Introduction to Enzymes

16.8K
The use of enzymes by humans dates to 7000 BCE. Humans first used enzymes to ferment sugars and produce alcohol without knowing that this was an enzyme-catalyzed reaction. Wilhelm Kuhne coined the term 'enzyme' in 1877 from the Greek words ‘en’ meaning ‘in’ or ‘within’ and ‘zyme’ meaning ‘yeast.’
Most enzymes are proteins that speed up biochemical reactions without being consumed. Enzymes contain one or more active sites that...
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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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Updated: May 12, 2025

Modeling an Enzyme Active Site using Molecular Visualization Freeware
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A Foundational Shift in Models for Enzyme Function.

Judith P Klinman, Susan M Miller1, Nigel G J Richards2,3

  • 1Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States.

Journal of the American Chemical Society
|April 25, 2025
PubMed
Summary
This summary is machine-generated.

Enzymes use protein reorganization and water molecule dynamics to cross energy barriers, enabling rapid catalytic reactions. This process involves rapid protein restructuring and efficient energy transfer for improved enzyme design.

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Area of Science:

  • Biochemistry
  • Physical Chemistry
  • Enzyme Kinetics

Background:

  • Enzymes facilitate biochemical reactions by stabilizing transition states.
  • The precise mechanism of enzyme-catalyzed barrier crossing remains a significant challenge in biochemistry.

Purpose of the Study:

  • To elucidate the mechanism by which enzymes transition from enzyme-substrate complexes to product formation.
  • To investigate the role of protein reorganization and solvent dynamics in enzymatic catalysis.

Main Methods:

  • Extension of Marcus theory to enzyme-catalyzed reactions.
  • Measurement of temperature dependence of hydrogen/deuterium exchange in backbone amides.
  • Measurement of time-dependent Stokes shifts in protein-appended chromophores.

Main Results:

  • Environmental reorganization of the protein scaffold and water molecules facilitates the intersection of potential energy surfaces.
  • Rapid (ns-ps timescale) and long-range collective protein restructuring is essential for catalysis.
  • Identification of specific pathways for thermal energy transfer from solvent to substrate bonds.

Conclusions:

  • A comprehensive model for enzyme-catalyzed barrier crossing is proposed, involving structural preorganization and conformational sampling.
  • Anisotropic energy distribution pathways connect the protein surface to the active site.
  • These findings offer new insights for de novo enzyme design.