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from my knowledge, it all comes down to the structure of the protein. if there is no complimentary shape for the protein then no binding will occur and therefore no reaction. furthermore there can be proteins or molecules that can bind to the protein and change its shape (i.e. goes through a conformational change) and therefore can stop other proteins binding to it and causing a reaction. in terms of enzymes and substrates, the substrate can ether bind in the active site of the enzyme, in which case it is classed as a competitive inhibitor or it can bind to an allosteric site (sites other than the active site of an enzyme) in which case it is classed as non competitive inhibitor. both these forms of inhibitory action can stop a reaction taking place.

Ive never done much chemistry so i may be wrong but from a chemistry point of view these non reaction can be explained by electron sharing, losing and gaining. atoms are more likely to share or give an electron depending on the number of electrons found on its most outer layer. in pure basic terms the first layer/shell/energy level likes to have two electrons and the second layer/shell/energy level has eight electrons. it is also important to note the first shall has to be full before it can move onto the second shell. so for example if we consider oxygen it has 8 electrons. the first layer will be filled with 2 electrons and the second with 6. oxygen by itself can be referred to as radicals and they are very unstable and can be toxic to the cells in the body. however when oxygen binds with another oxygen to form an oxygen molecule the structure becomes stable and will get a reaction. this is because oxygen will start to share two electron from its outer most layer which will conquer with the rule of having 2 or 8 electrons on its outer most layer. I've only talked about the first and second layer but there can be many more layers/shells/energy levels and the number of electrons on the outer most layer can change to a higher number.

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