"
Team:Leicester/Modeling
From 2012.igem.org
Ladybird136 (Talk | contribs) |
Ladybird136 (Talk | contribs) |
||
| Line 45: | Line 45: | ||
<h2>Enzyme Kenetics</h2> | <h2>Enzyme Kenetics</h2> | ||
<p>Enzyme Kinetics is the processes by which chemical reactions are catalysed by enzymes. When we say that we aim to "genetically modify a bacteria that can degrade expanded polystyrene" what we really mean is that we aim to "create a chemical reaction catalysed by enzymes that can break down polystyrene polymer chains". The polymer chains in expanded polystyrene can be broken into monomers by industrial processes, however this involves the use of nasty chemicals. </p> | <p>Enzyme Kinetics is the processes by which chemical reactions are catalysed by enzymes. When we say that we aim to "genetically modify a bacteria that can degrade expanded polystyrene" what we really mean is that we aim to "create a chemical reaction catalysed by enzymes that can break down polystyrene polymer chains". The polymer chains in expanded polystyrene can be broken into monomers by industrial processes, however this involves the use of nasty chemicals. </p> | ||
| - | <p>The method adopted by bacteria to modify their environment, in order to obtain useful products, is the use of enzymes. Enzymes are biological molecules that have the ability to act as a | + | <p>The method adopted by bacteria to modify their environment, in order to obtain useful products, is the use of enzymes. Enzymes are biological molecules that have the ability to act as a catalyst in chemical reactions, in other words increase the rate of reaction. Enzymes have an active site that fits the substrate, like a "lock and key", once connected the enzyme performs the reaction. The <em>Psuedmonas</em> bacteria in our project secrete enzymes that break the polystyrene polymer in order to extract the carbon. </p> |
<div align="center"><img src="https://static.igem.org/mediawiki/2012/8/88/ModelingGraphic2.gif" width="471" height="163"/></div> | <div align="center"><img src="https://static.igem.org/mediawiki/2012/8/88/ModelingGraphic2.gif" width="471" height="163"/></div> | ||
<p>Above is a diagram illustrating an example of a substrate can be manipulated by the enzyme. The substrate collides with the active site of the enzyme to form a complex, the products are later released by the enzyme.</p> | <p>Above is a diagram illustrating an example of a substrate can be manipulated by the enzyme. The substrate collides with the active site of the enzyme to form a complex, the products are later released by the enzyme.</p> | ||
Revision as of 14:57, 24 August 2012
Modeling
What are we modeling?
The aim of our project is to genetically modify a bacteria that can break down the polymer chains in expanded polystyrene (EPS). The result is a solution of monomer chains that can be extracted and used in the synthetic production of other useful chemicals, for instance Lactic Acid (C3H6O3). The computational model is going to be used to aid calculations predicting how much substrate (polymer chains) will be needed, how much product will be required to sustain the bacteria colony and how much product will be left over for other uses.
Why are we modeling?
By creating a computational model of a biological system, theoretical and experimental biologists are able to predict the outcomes and behaviour of a system for a set of input parameters. The results of the simulation can provide guidance to the success of the experiment for the tested input parameters before undertaking physically in the lab. The model built in our project will help determine the next steps in the project, for example to attempt to change the number of enzymes produced by the bacteria or modify how the enzyme behaves. The major advantages of developing and using a model in the project are that it can save time exploring an idea that had a high probability of failure and simultaneously save resources.
Enzyme Kenetics
Enzyme Kinetics is the processes by which chemical reactions are catalysed by enzymes. When we say that we aim to "genetically modify a bacteria that can degrade expanded polystyrene" what we really mean is that we aim to "create a chemical reaction catalysed by enzymes that can break down polystyrene polymer chains". The polymer chains in expanded polystyrene can be broken into monomers by industrial processes, however this involves the use of nasty chemicals.
The method adopted by bacteria to modify their environment, in order to obtain useful products, is the use of enzymes. Enzymes are biological molecules that have the ability to act as a catalyst in chemical reactions, in other words increase the rate of reaction. Enzymes have an active site that fits the substrate, like a "lock and key", once connected the enzyme performs the reaction. The Psuedmonas bacteria in our project secrete enzymes that break the polystyrene polymer in order to extract the carbon.
Above is a diagram illustrating an example of a substrate can be manipulated by the enzyme. The substrate collides with the active site of the enzyme to form a complex, the products are later released by the enzyme.
The formation of substrate to product via the use of enzymes can be described in the following expression:
Where:
E is the number of enzymes
S is the substrate concentration
ES is the enzyme-substrate complex
P is the product
k1 is the forward rate constant for enzyme-substrate formation
k-1 is the reverse rate constant for enzyme-substrate formation (the enzyme "drops" the substrate)
k2 is the forward rate constant for production formation from the enzyme-substrate complex and is assumed irreversible
