A ribosome is a structure composed of RNA and protein that constructs proteins based on the instructions provided by DNA. They may be either floating freely in the cytoplasm or attached to the endoplasmic reticulum (ER), a cellular organelle that forms a network for manufacturing cellular materials such as proteins. Ribosomes are the sites of translation during protein synthesis. Ribosomes are not amino acid-specific; rather, they can bind to any strand of mRNA and any tRNA. They are also recyclable, able to be used over and over again. Ribosomes are made of two separate subunits that come together when it is time to synthesize proteins. These subunits are different in size, with the large subunit composed of three different molecules of RNA (rRNA) and 49 unique proteins. The small subunit is comprised of one rRNA molecule and 33 proteins.
The large subunit of the ribosome has three places where a tRNA molecule can attach:
- A site: where tRNA binds to the mRNA, making sure it is aligned correctly to the right amino acid
- P site: where the ribosome catalyzes the peptide bond between adjacent amino acids
- E site: the exit site, where the tRNA releases from the ribosome
Each site has fail-safe mechanisms in place to make sure the correct amino acids are being assembled based on the code in the mRNA.
Like transcription, translation occurs in three main steps. The first is called initiation. Here, an initiation complex is formed, made of tRNA and the small subunit of the ribosome, when both are attached to the mRNA. The 5′ cap of the mRNA that was attached back in the nucleus binds to the small subunit of the rRNA, which then moves along the mRNA until it reaches the start codon. This happens every time mRNA gets translated, so the first amino acid on every polypeptide chain will be AUG, or methionine. Once this happens, the large subunit of the ribosome joins the complex to form a large molecule, aligning the A site of the ribosome with the second mRNA codon.
The second step of translation is called elongation. Here, the tRNA moves to the P site, where the bond between the tRNA and its amino acid is broken and the amino is attached to the amino acid from the previous tRNA that occupied the P site, making the polypeptide chain longer. Sequences of rRNA act as the catalyst for this assembly. Once the tRNA has released its amino acid, it moves to the E site of the ribosome and is released to bind another amino acid. The mRNA moves through the ribosome as each amino acid is added to the growing polypeptide chain in repeating elongation cycles.The final step of translation is called termination. The three-nucleotide sequence in the mRNA that signals termination to occur is the stop codon. When the A site of the ribosome reaches the stop codon (UAA, UAG, or UGA), a protein called a release factor binds to the stop codon. The release factor disconnects the polypeptide from the tRNA in the P site. The ribosomal subunits and mRNA then separate.
Protein Modification and Folding
Proteins are needed all over the body. They are used for building muscle, hair, claws and fingernails, and many other purposes. All metabolic processes involve proteins in the form of enzymes. Many times, the proteins are built in areas far away from where they are actually needed. They are also often modified to suit a particular purpose. Polypeptide chains formed by the ribosome undergo folding into a three-dimensional shape based in intramolecular attractions. Some proteins will be immediately used by the cell after production. Other proteins contain a signal sequence, an amino acid sequence that determines the destination of a protein. If this signal is not present, the protein stays within the cell where it was created. If the signal is present, then the ribosome will bind to the endoplasmic reticulum and the growing polypeptide chain will either become embedded in the membrane or released into the interior of the endoplasmic reticulum, depending on the signal sequences present.
There are several ways in which a protein can be modified before it has full functionality and moves to where it is needed. The first is called proteolysis. Here, the protein is cut through the actions of enzymes called proteases. It is possible at this time that the sequence of amino acids that creates the signals that determine where the protein will go are cut off. If this happens, the protein would move back into the cytoplasm. The second way of modifying proteins is called glycosylation. This involves the addition of sugars to the new proteins to form compounds called glycoproteins. These special proteins are needed on the cell's surface for cell communication and cell-to-cell interaction. The third type of modification is called phosphorylation. In this case, phosphate groups are added to the new proteins. If the protein is an enzyme, this changes the way it looks and exposes the active site, the region of the enzyme where the substrate binds.Proteins have four levels of structure and each influence the function of the protein. A protein's primary structure is its amino acid sequence. This structure is encoded by DNA. Its secondary structure is the three-dimensional shape the amino acids make as they bond together in space. These come in two varieties: alpha-helix and beta-sheet (sometimes called beta-strand). The alpha-helix is helical in shape, while the beta-sheet is long and flat. The beta-sheets appear as a folded piece of paper. The protein's tertiary structure refers to the larger shape made up by the interactions between portions of the secondary structure. The alpha-helices and beta-sheets of the secondary structure fold into specific forms based on interactions of the molecules that make them up, such as hydrogen bonds between amino acids. Finally, the quaternary structure is the aggregate of all portions of the protein, which often consists of multiple subunits (tertiary structures) held together in a particular arrangement.
Protein Synthesis in Prokaryotes
The movement of mRNA out of the nucleus and its translation on the ribosome describes protein synthesis in eukaryotic cells, which contain a nucleus. This nucleus presents an obstacle, which is why transcription is somewhat complicated. In organisms that do not possess nuclei, the same events of transcription and translation occur, but with slight modifications. Since these cells lack membrane-bound organelles, the entire process takes place in the cytoplasm. It also happens faster because translation can begin before the entire mRNA molecule is transcribed. This is called transcription-translation coupling. Processing of mRNA is not necessary in prokaryotes as there are no intron sequences to be spliced out and no nuclear membrane to traverse.Because prokaryotic mRNA lack the 5′ end cap and poly-A tail, a different method of initiation of translation is needed. Prokaryotes use a special nucleotide sequence before the AUG start codon to begin transcription. Prokaryotes also have only three initiating factors, while more than 10 have been identified in eukaryotes. The ribosomes in prokaryotes are smaller than those in eukaryotes and contain different RNA sequences. This has proven to be beneficial as certain antibiotics (drugs that kill bacteria) target the ribosomes of bacteria specifically, which means the infection can be destroyed without hurting the cells of the person who is ill.