Rough ER
The surface of rough endoplasmic reticulum is covered with ribosomes, giving it a bumpy appearance when viewed through the microscope. This type of endoplasmic reticulum is involved mainly with the production and processing of proteins that will be exported, or secreted, from the cell. The ribosomes assemble amino acids into protein units, which are transported into the rough endoplasmic reticulum for further processing. These proteins may be either transmembrane proteins, which become embedded in the membrane of the endoplasmic reticulum, or water-soluble proteins, which are able to pass completely through the membrane into the lumen. Those that reach the inside of the endoplasmic reticulum are folded into the correct three-dimensional conformation, as a flattened cardboard box might be opened up and folded into its proper shape in order to become a useful container. Chemicals, such as carbohydrates or sugars, are added, then the endoplasmic reticulum either transports the completed proteins to areas of the cell where they are needed, or they are sent to the Golgi apparatus for further processing and modification.
Protein folding unit
It is in the lumen of the rough ER that proteins are folded to produce the highly important biochemical architecture which will provide 'lock and key' and other recognition and linking sites.
Protein quality control section
It is also in the lumen that an amazing process of quality control checking is carried out. Proteins are subjected to a quality control check and any that are found to be incorrectly formed or incorrectly folded are rejected. These rejects are stored in the lumen or sent for recycling for eventual breakdown to amino acids. A type of emphysema (a lung problem) is caused by the ER quality control section continually rejecting an incorrectly folded protein. The protein is wrongly folded as a result of receiving an altered genetic message. The required protein is never exported from the lumen of rough ER. Research into protein structure failures relating to HIV are also focusing on reactions in the ER
Rigorous quality control plays a part in cystic fibrosis
A form of cystic fibrosis is caused by a missing single amino acid, phenylanaline, in a particular position in the protein construction. The protein might work well without the amino acid but the very exacting service provided by the quality control section spots the error and rejects the protein retaining it in the lumen of the rough ER. In this case the customer (the person with cystic fibrosis) loses out completely due to high standards when a slightly poorer product would have been better than no product at all.
From Rough ER to Golgi
In most cases proteins are transferred to the Golgi apparatus for 'finishing'. They are conveyed in vesicles or possibly directly between the ER and Golgi surfaces. After 'finishing' they are delivered to specific locations.