A functional protein is not necessarily the same as the polypeptide chain that is released from the ribosome. Especially in eukaryotic cells, the polypeptide may need to be moved far from the site of synthesis in the cytoplasm, moved into an organelle, or even secreted from the cell. In addition, the polypeptide is often modified by the addition of new chemical groups that have functional significance. In this section, we examine these two posttranslational aspects of protein synthesis.
Chemical signals in proteins direct them to their cellular destinations
As a polypeptide chain emerges from the ribosome, it folds into its three-dimensional shape. This conformation is determined by the sequence of the amino acids that make up the protein, as well as by factors such as the polarity and charge of their R groups. Ultimately, the conformation of the polypeptide allows it to interact with other molecules in the cell, such as a substrate or another polypeptide. In addition to this structural information, the amino acid sequence contains an “address label” indicating where in the cell the polypeptide belongs. All protein synthesis begins on free ribosomes in the cytoplasm. As a polypeptide chain is made, the information contained in its amino acid sequence gives it one of two sets of instructions:
- “Finish translation and be released to the cytoplasm.” Such proteins are sent to the nucleus, mitochondria, plastids, or peroxisomes, depending on the address in their instructions; or, lacking such specific instructions, they remain in the cytosol . “Stop translation, go to the endoplasmic reticulum (ER), and finish synthesis there.” After protein synthesis is completed, such proteins may be retained in the ER or sent to lysosomes via the Golgi apparatus. Alternatively, they may be sent to the plasma membrane, or, lacking such specific instructions, they are secreted from the cell via vesicles that emanate from the plasma membrane.
DESTINATION: CYTOPLASM.After translation, some folded polypeptides have a short exposed sequence of amino acids that acts like a postal “zip code” directing them to an organelle. These signal sequencesare either at the N terminus or in the interior of the amino acid chain. For example, the following sequence directs a protein to the nucleus:
This amino acid sequence occurs, for example, in the histone proteins associated with nuclear DNA but not in citric acid cycle enzymes, which are addressed to the mitochondria. The signal sequences have a conformation that allows them to bind to specific receptor proteins, appropriately called docking proteins, on the outer membrane of the appropriate organelle.Once the protein has bound to it, the receptor forms achannel in the membrane, allowing the protein to pass throughto its organelle destination. (In this process, the protein is usuallyunfolded by a chaperonin so that it can pass through thechannel, then refolds into its normal conformation.).
Destination: endoplasmic reticulum
If a specific hydrophobic sequence of about 25 amino acids occurs at the beginning of a polypeptide chain, the finished product is sent initially to the ER, and then to the lysosomes, the plasma membrane, or out of the cell. In the cytoplasm, before translation is finished, the signal sequence binds to a signal recognition particlecomposed of protein and RNA. This binding blocks further protein synthesis until the ribosome can become attached to a specific receptor protein in the membrane of the rough ER. Once again, the receptor protein is converted into a channel, through which the growing polypeptide passes. The elongating polypeptide may be retained in the ER membrane itself, or it may enter the interior space-the lumen-of the ER. In either case, an enzyme in the lumen of the ER removes the signal sequence from the polypeptide chain. At this point, protein synthesis resumes, and the chain grows longer until its sequence is completed. If the finished protein enters the ER lumen, it can be transported to its appropriate location - to other cellular compartments or to the outside of the cell - without mixing with other molecules in the cytoplasm. Additional signals are needed for sorting the protein further (remember that the signal sequence that sent it to the ER has been removed). These signals are of two kinds:
- Some are sequences of amino acids that allow the protein’s retention within the ER.
- Others are sugars added in the Golgi apparatus, to which the protein is transferred in vesicles from the ER.
The resulting glycoproteins end up either at the plasma membrane or in a lysosome (or plant vacuole), depending on which sugars are added. Proteins with no additional signals pass from the ER through the Golgi apparatus and are secreted from the cell. It is important to emphasize that the addressing of a protein to its destination is a property of its amino acid sequence, and so is genetically determined. An example of what can go wrong if a gene for protein targeting is mutated is mucoplidosis II, or I-cell disease. People with this disease lack an essential enzyme for the formation of the lysosomal targeting signal. Consequently, proteins destined for their lysosomes never get there, but instead either stay in the Golgi (where they form I or inclusion, bodies) or are secreted from the cell. The lack of normal lysosome functions in a person’s cells leads to progressive illness and death in childhood.
Many proteins are modified after translation
Most finished proteins are not identical to the polypeptide chains translated from mRNA on the ribosomes. Instead, most polypeptides are modified after translation, and these modifications are essential to the final functioning of the protein.
Proteolysisis the cutting of a polypeptide chain. Cleavage of the signal sequence from the growing polypeptide chain in the ER is an example of proteolysis; the protein might move back out of the ER through the membrane channel if the signal sequence were not cut off. Also, some proteins are actually made from polyproteins (long polypeptides) that are cut into final products by enzymes called proteases. Proteases are essential to some viruses, including HIV, because the large viral polyprotein cannot fold properly unless it is cut. Certain drugs used to treat AIDS work by inhibiting the HIV protease, thereby preventing the formation of proteins needed for viral reproduction.
Glycosylationinvolves the addition of sugars to proteins, as described above. In both the ER and the Golgi apparatus, resident enzymes catalyze the addition of various sugar residues or short sugar chains to certain amino acid R groups on proteins as they pass through. One such type of “sugar coating” is essential for addressing proteins to lysosomes discussed in the preceding section. Other types are important in the conformation and the recognition functions of proteins at the cell surface. Still other attached sugar residues help in stabilizing proteins stored in storage vacuoles in plant seeds.
Phosphorylation, the addition of phosphate groups to proteins, is catalyzed by protein kinases. The charged phosphate groups change the conformation of targeted proteins, often exposing an active site of an enzyme or a binding site for another protein. All of the processes we have just described result in a functional protein only if the amino acid sequence of that protein is correct. If the sequence is not correct, cellular dysfunction and disease may result. Changes in the DNA -mutations - are a major source of errors in amino acid sequences.