The ER is organized into many branching tubules and flattened sacs extending throughout the cytosol. Its membrane usually constitutes more than 1/2 of the total membrane of an average animal cell. The ER membrane encloses a single internal space called the ER lumen.

In contrast to the import of proteins into mitochondria, nuclei and peroxisomes, import into the ER is a co-translational process in that import begins before the polypeptide chain is completely synthesized. Since one end of the protein is typically translocated into the ER as the rest of the polypeptide chain is being made, the protein is never released into the cytosol. The ribosome that is synthesizing the protein is directly attached to the ER membrane in regions called rough ER. This protection from the cytosol means that proteins bound for the ER do not need chaperone proteins to keep the protein unfolded. Only those mRNA molecules that encode proteins with an ER signal sequence bind to rough ER. Other mRNAs without the sequence remain free in the cytosol. Individual ribosomal subunits are thought to move randomly between these 2 populations of mRNA molecules. 

Rough ER can easily be separated from ER which do not have ribosomes bound (called “smooth ER”) because the rough ER have a higher density and thus float nearer to the bottom of a tube after centrifugation. The main cell type in the liver, the hepatocyte has abundant smooth ER which is the principal site of production of lipoprotein particles which carry lipids via the bloodstream to the body. The enzymes that synthesize these lipoproteins are in the membrane of the smooth ER. In addition, there are enzymes such as the cytochrome P450 family that catalyze a series of reactions which detoxify harmful substances. When the drug phenobarbital is given, the smooth ER doubles in surface area within a few days due to the synthesis of detoxification enzymes.

An ER signal sequence (which varies greatly in amino acid sequence) which emerges from the ribosome is bound by a signal recognition particle (SRP) that has a large hydrophobic pocket that can accommodate many different hydrophobic signal sequences. This binding by the SRP causes a pause in protein synthesis which gives the ribosome time to bind to the ER membrane. The SRP-ribosome complex binds to a SRP receptor which is on the cytosolic surface of the rough ER membrane. The SRP and SRP receptor are then released and the growing polypeptide chain is transferred across the membrane through a protein translocator having a water filled pore called the Sec61 complex. It is thought that a lumenal ER protein serves as a plug when no ribosome is bound to the complex.

Translocation of proteins which are not translated by ribosomes bound to the ER is similar to that described above except that a hsp70 like chaperone protein called BiP (for “binding protein”) on the lumenal side of the ER membrane binds the polypeptide chain as it emerges from the pore into the ER lumen. Unidirectional translocation is driven by cycles of BiP binding and release as described for the hsp70 proteins that use a ratchet like mechanism in import of proteins to mitochondria.

As with mitochondria, the ER signal sequence is cleaved once the protein crosses the membrane by a signal peptidase on the lumenal side. A separate adjacent cleavage site to the N terminal ER signal sequence signals cleavage. 

The translocation process for proteins that are to remain in the ER membrane is similar to what has been said above except for some modifications. For a transmembrane protein which will end up having its C terminus facing the cytosol and its amino terminus facing the lumen, an additional hydrophobic segment called a stop-transfer signal in the polypeptide chain stops the transfer process and anchors the protein in the membrane. In other mechanisms of integration of a single pass membrane what is important is not a stop transfer signal but rather the location of the ER signal sequence. This sequence is not at the N-terminal side of the protein but is rather found at an internal site. Internal start transfer sequences can bind to the translocation apparatus in either of 2 orientations depending on whether more positively charged amino acids proceed or follow the start sequence. In one orientation, the C terminus will end up facing the lumen side and in the other orientation it will end up facing the cytosolic side of the ER membrane. In multipass transmembrane proteins, the polypeptide chain passes back and forth repeatedly across the lipid bilayer. It is thought that an internal signal sequence serves as a start transfer signal in these proteins to initiate translocation, which continues until a stop transfer sequence is reached. In more complex multi pass membranes a second start signal reinitiates translocation until the next sop transfer is found. 

Some proteins such as the BiP protein discussed above contain an ER retention signal (a KDEL sequence in this case for Lys-Asp-Glu-Leu ) on their C terminus that is responsible for retaining the protein. Many other proteins in the lumen of the ER are destined for other organelles. 

Modification of Proteins in the ER: A single species of asparagine N linked oligosaccharid is attached to many proteins in the ER and then trimmed.

N-linked glycosylation of proteins in the lumen is necessary for the proper folding of these proteins. An ER chaperone protein called calnexin binds to incompletely folded proteins containing one terminal glucose on N-linked oligosaccharides which traps the protein in the ER. Removal of the glucose by a glucosidasereleases the protein from calnexin. An enzyme called glucosyl transferase then determines whether the protein is folded properly. If it is still incompletely folded, the enzyme adds a new glucose to the N-linked oligosaccharide which starts the cycle with calnexin again. This occurs until the protein is property folded whereupon it exits from the ER. If a protein simply can not fold properly it is exported back into the cytosol where it will be ubiquitylated. The chaperone protein BiP (discussed above) also may retain misfolded proteins. 

An accumulation of misfolded proteins in the ER triggers an unfolded protein response which includes an increased transcription of genes encoding ER chaperones and enzymes involved in ER protein degradation. This pathway is quite remarkable in that a transmembrane protein kinase in the ER is activated by misfolded proteins which causes autophosphrylation and activation of an endoribonuclease domain that cleaves a cytosolic RNA molecule excising an intron. These exons are joined by an RNA ligase which is then translated on ribosomes to produce a gene regulatory protein that migrates to the nucleus and activates transcription of genes.

The retention of unfolded proteins can be extensive. In the case of newly synthesized subunits of the T cell receptor, for example, more than 90% of the proteins are retained. Sometimes the process goes ary causing disease. For example, cystic fibrosis is due to an active protein that is discarded rather than because a mutation inactivates the protein.

Rough ER:

Proteins synthesized on teh surface of the rough EF (RER) are destinged to be exported form teh cell, sent to lysosomes or vauoles or embedded in the plasma membrane. These proteins enter the cisternal space as a first step in the pathway that will sort proteins to their eventual destinations. 

Smooth ER:

Regions of the ER with relatively few bound ribosomes are refered to as smooth ER (SER). The sturcture of the SER ranges form a network of tubules, to flattened sacs, to higher order tubular arrays. The membranes of the SER contain many embedded enzymes, involved in the synthesis of a vareity of carbohydrates and lipids. Seroid hormones are also synthesized in the SER. The majority of membrane lipids are assembled in the SER and then sent to whatever parts of the cell need membrane components. 

Functions: 

Intracellular Ca2+ storage: An important function of the SER is to store intracellular Ca2+. This keeps the cytoplasmic level low, allowing Ca2+ to be used as a signaling molecule. In muscle cells, for example, Ca2+, is used to trigger muscle contraction. In other cells, Ca2+ release from SER stores is involved in diverse signaling pathway. 

Modify substances to make them less toxic: Another role of the SER is to modify foreign substances to make them less toxic. In the liver, enzymes in the SER carry out this detoxificaiton. This can remove substances that we have taken for a therapetic reason, for enstance, penicillin. Thus, relatively high doses of some drugs are presribed to offset our body’s efforts to remove them. Liver cells have extnsive SER with enzymes that can process a vareity of substances by chemically modifying them.