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Related Concept Videos

Measuring Reaction Rates03:09

Measuring Reaction Rates

Polarimetry finds application in chemical kinetics to measure the concentration and reaction kinetics of optically active substances during a chemical reaction. Optically active substances have the capability of rotating the plane of polarization of linearly polarized light passing through them—a feature called optical rotation. Optical activity is attributed to the molecular structure of substances. Normal monochromatic light is unpolarized and possesses oscillations of the electrical field in...
Reaction Mechanisms: Rate-limiting Step Approximation01:29

Reaction Mechanisms: Rate-limiting Step Approximation

The rate-determining step, or RDS, in a chemical reaction is the slowest step that determines the overall reaction rate. It is identified by using the observed rate law and typically involves approximation methods like the RDS approximation or the steady-state approximation.In the RDS approximation, also known as the rate-limiting-step or equilibrium approximation, the reaction mechanism consists of one or more reversible reactions near equilibrium, followed by a slower RDS, and then one or...
Reaction Mechanisms: The Steady-State Approximation01:26

Reaction Mechanisms: The Steady-State Approximation

The steady-state approximation, also referred to as the quasi-steady-state approximation to differentiate it from a true steady state, is a widely used method for simplifying calculations in complex reaction mechanisms. This approach is particularly useful when dealing with multi-step reactions that involve reverse reactions or several steps, which can significantly increase mathematical complexity and make the reactions nearly unsolvable analytically.The steady-state approximation operates on...
Enzyme Kinetics01:19

Enzyme Kinetics

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...
Introduction to Enzyme Kinetics01:19

Introduction to Enzyme Kinetics

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...
Induced-fit Model01:13

Induced-fit Model

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 characteristics of...

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Modelling reaction kinetics inside cells.

Ramon Grima1, Santiago Schnell

  • 1Institute for Mathematical Sciences, Imperial College, London, U.K.

Essays in Biochemistry
|September 17, 2008
PubMed
Summary
This summary is machine-generated.

Understanding intracellular reaction kinetics requires choosing the right theoretical framework. Stochastic and spatial models offer qualitatively different physiological predictions compared to classical deterministic approaches, revealing the impact of noise and space.

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Area of Science:

  • Molecular Biology
  • Biochemistry
  • Computational Biology

Background:

  • Recent advances in molecular biology, including single molecule imaging, provide insights into cellular biochemical activities.
  • Intracellular reaction kinetics are complex and require appropriate theoretical frameworks for accurate modeling.

Purpose of the Study:

  • To review four distinct theoretical and simulation frameworks for modeling intracellular reaction kinetics: non-spatial deterministic, spatial deterministic, non-spatial stochastic, and spatial stochastic.
  • To discuss the differences in predictions between these modeling methodologies.
  • To highlight how incorporating noise and space can lead to qualitatively different physiological predictions.

Main Methods:

  • Review of four theoretical and simulation frameworks.
  • Estimation of fundamental length scales to guide model selection.
  • Comparative analysis of predictions from deterministic and stochastic, spatial and non-spatial models.

Main Results:

  • Each of the four frameworks (non-spatial/spatial, deterministic/stochastic) is suited for modeling intracellular reaction kinetics.
  • Fundamental length scales can guide the selection of the most appropriate model for a given reaction pathway.
  • Considering noise and space can yield qualitatively different physiological predictions beyond quantitative accuracy.

Conclusions:

  • The choice of theoretical framework significantly impacts the understanding of intracellular reaction kinetics.
  • Stochastic and spatial modeling approaches offer unique insights not captured by classical deterministic models.
  • Accurate modeling of cellular processes necessitates consideration of both spatial and stochastic elements.