Compartmentalisation makes the organisation of eukaryotic cells so much more complex than prokaryotic – the whole of a eukaryotic cell is subdivided up into membrane bound compartments and this is important for many reasons:
-Different processes require different environments e.g. hydrolytic enzymes in lysosomes have a lower optimum pH – the pH of a lysosome can be lowered by H+ ATPase pumps in the membrane pumping H+ in. Enclosing in chloroplasts allows a high concentration of the enzymes needed there to be maintained.
-Many fundamental processes take place at membranes and because eukaryotic cells are so much larger than prokaryotic cells eukaryotic cells need the additional membrane surface area inside the cell – e.g. in mitochondria synthesis of ATP by the f type ATPase takes place at the inner mitochondrial membrane – the ATPase is an integral membrane protein.
-Enclosing DNA in the nucleus protects it and allows post transcriptional modifications to the mRNA to occur before translation into a protein takes place in the cytosol.
-Translation of integral membrane which are very important in regulating what enters and exits the cell must be inserted into a membrane whilst they are translated – this happens at the endoplasmic reticulum.
However the disadvantage of all this is that there needs to be a complex system of ensuring that the right vesicles get to the right membranes etc. and this involves a lot of signals.

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