Ribosome

Ribosomes are macromolecular complexes of proteins and ribonucleic acids ( RNA), which occur in the mitochondria and the chloroplasts, in the cytoplasm. Proteins are produced by them, corresponding to the base sequence of DNA comprising the information of the amino acid sequence of the proteins. Here the individual amino acids are assembled in exactly the order prescribed by the respective gene to a chain molecule. The information on the amino acid sequence in the DNA is mediated by the messenger RNA (mRNA). The conversion of the stored information in mRNA into a sequence of linked amino acids is referred to as translation (Latin for translation ). The translation of the mRNA to the ribosome is a central component of protein biosynthesis and is present in all living things.

Structure and species

Ribosomes are granular particles having a diameter of about 20-25 nm, and they are made to approximately two-thirds of RNA (rRNA) and one third of ribosomal proteins. You put in all organisms composed of two differently sized and functionally distinct subunits. The mass of the ribosome is characterized by their sedimentation behavior, which is given in Svedberg units (S). During translation they assemble into a functional complex, wherein the large subunit in the linked protein, the amino acids to the chain ( peptidyl ) and the small subunit is responsible for mRNA detection. Both subunits are composed of proteins and rRNA, where the proteins are responsible for the cohesion and proper positioning, the actual reactions, however, are made by the rRNAs. Both subunits are made in eukaryotes in the nucleoli inside the cell nuclei, and then passed through the nuclear pore to the cytoplasm.

Prokaryotic ribosomes

The number of ribosomes per cell is prokaryote is of the order of 10,000, for example, has a single E. coli bacterium 20,000 ribosomes. The ribosomes have a sedimentation coefficient of 70S and a molar mass of about 2.5 MDa. At magnesium concentrations below 1 mmol / l, the 70S ribosome is divided into a 50S and a smaller 30S subunit. The 30S subunit ( 0.9 MDa ) composed of 21 different ribosomal proteins and 16S ribosomal RNA ( 16S rRNA). In the 50S subunit (1.6 MDa ), there are 31 different proteins and two rRNAs ( 23S and 5S rRNA).

The proteins of the small subunit are indicated by " S" (English small, small ' ) that the large subunit with "L" ( engl. large, big' marked). Their amino acid sequences have no special similarities, but are rich in positively charged amino acids such as L- lysine or L- arginine. This allows a better interaction with the negatively charged rRNAs. The largest bacterial, ribosomal protein S1 is 61.2 kDa and 557 amino acids, the smallest is L34 with 5.4 kDa and 34 amino acids.

Eukaryotic ribosomes

In eukaryotic cells ribosomes are not only in the cytoplasm but also in the mitochondria or - in plants - in addition to the chloroplasts. It is estimated that cytosolic ribosomes per cell to between 105 and 107, which eukaryotic cells more than prokaryotic ribosomes possess. The number is dependent on cell type, from the rate of protein synthesis of the cell. Thus, the number of ribosomes in liver cells is particularly high. In addition, eukaryotic ribosomes of the cytosol are also larger, they have a diameter of about 25 nm These have a molar mass of about 4.2 MDa, the sedimentation coefficient of 80S. When it is large subunit 60S (2.8 MDa ), and in its case small subunit 40S (1.4 MDa ). The small subunit consists of 33 proteins in mammals and rRNA ( 18S rRNA), the large subunit of 49 proteins and three rRNAs ( 28S, 5.8S and 5S). Cytosolic ribosomes of higher eukaryotes are more complex than the lower eukaryotes. Thus, the 28S rRNA is 3,392 nucleotides long in baker's yeast, in mammals such as the rat, however, 4,718 nucleotides. The 18S rRNA is smaller in yeast than in the rat (1799 compared to 1874 nucleotides).

The actual catalytic function has the rRNA, whereas the proteins rather sit on the edge of the ribosome. In eukaryotes, there are except the free cytoplasmic ribosomes and membrane-bound ribosomes attached to the membrane of the rough endoplasmic reticulum (ER ) ( see below). The formation of ribosomal subunits takes place in the nucleolus. Therefore, cells with a high rate of protein synthesis have particularly well-developed nucleoli. Free and membrane-bound ribosomes have the same structure and can switch between functions.

The ribosomes from mitochondria and chloroplasts are the prokaryotic ribosomes similar to what the Endosymbiontenhypothese supported.

The spelling of eukaryotic ribosomal proteins is not entirely uniform. In yeast proteins of the large subunit with " Rpl " that the small are designated by " ps ". In the corresponding proteins of mammals are also used capitalization RPL and RPS.

Free and membrane-bound ribosomes

Ribosomes can be distinguished in eukaryotic cells according to the site of synthesis activity. Free ribosomes are scattered in the cytoplasm and produce proteins, which usually also play their role in the cytoplasm. Membrane-bound ribosomes associated with the membrane of the endoplasmic reticulum. The synthesized proteins are directed there by the co-translational protein transport into the lumen of the endoplasmic reticulum. Membrane-bound ribosomes are found in clusters in secretion- forming cells such as in the pancreas.

Operation

The operation of the ribosome during translation can be characterized by the three- site model. Accordingly, the ribosome has two tRNA binding sites, the A - ( aminoacyl ) - P ( peptidyl ) and E - ( exit ) point. During the elongation cycle, the ribosome oscillates between two states, the pre-and the post-translational state, two of the three tRNA - binding sites are occupied by a tRNA. In pretranslational state, the A- and P-site occupied, with the P-site tRNA carries the polypeptide chain and the A site is occupied by the newly added aminoacyl- tRNA. In the ribosome, the polypeptide chain is now transferred to the A- site tRNA by peptidyl transferase of the P-site tRNA. The ribosome then switches to the post-translational state and travels to three bases on the mRNA further, eliminating the previous A-site tRNA to the P- site tRNA and the now empty former P- site tRNA on the E site ( exit ) is funneled out of the ribosome. Here, a translocase (EF -G) is involved.

The two main states of the ribosome (pre-and post-translationally ) are separated by a high activation energy barrier. The central role of the two elongation factors is to reduce this energy barrier and thus to enable the ribosome in the other state.

Often several prokaryotic ribosomes form on the same mRNA molecule like pearls on a polysome.

Once a peptide has been linked in the ribosome, it wanders through a ribosomal tunnel. This consists largely of rRNA and emerges from the large ribosomal subunit. It has a length of about 100 Å (10 nm) and an average diameter of 15 Å (1.5 nm). At its narrowest point of the channel is bounded by two conserved ribosomal proteins, L4e and L22.

Ribophagy

The reduction of the ribosome is not yet fully understood. It is usually initiated under nutrient deficiency. Bacteria such as E. coli has been suggested that intact 70S ribosomes initially divided into two sub-units. Under Mangelbedindungen the translation is shut down in the cell, so that many ribosomes are inactive. The two subunits are much more sensitive to ribonucleases ( RNases ) as an intact ribosome, as they offer a larger attack surface. Then also exonucleases could degrade the RNA ribosmale on.

For yeast, a eukaryote, one with " ribophagy " designated Autophagieweg was proposed. This rejects the terms Mitophagie to ( degradation of mitochondria), Pexophagie ( degradation of peroxisomes ) and Reticulophagie ( degradation of the endoplasmic reticulum ). Under nutrient deficiency builds yeast ribosomes onto a path that starts like in prokaryotes. First, the two subunits to be separated. A ubiquitin ligase in the ubiquitin then removed 60S subunit, which is then transported in a vesicle to the vacuole. This seems paradoxical, since ubiquitin is a common degradation signal for most proteins. From the authors has been proposed that a ubiquitin ligase, the 60S subunit first marked for degradation pathway, but the process can only take place through the final Ubiquitinprotease.

Structure elucidation

Ribosomes were discovered by the researcher Albert Claude middle of the 20th century. In 1940 he was identified with the aid of dark field microscopy RNA -containing granules from the cytosol of animal cells that were smaller than mitochondria. He described them as " microsomes ", later analysis showed that they were complexes of phospholipids and Ribonukleinproteinen. Nowadays fragments of the ERs are referred to as microsomes. Recent advances in electron microscopy succeeded in 1955 George Emil Palade, to identify those " microsomes " clearly as components of a cell and not merely as artifacts of cell debris. There were more and more indications that this Ribonukleinproteinpartikel had something to do with the translation. 1959, and the evidence in E. coli has been furnished that ribosomes are necessary for the biosynthesis of polypeptides.

1958 attacked Richard B. Roberts in a symposium on the proposal, the name " microsome " or " micro- some particles " on the better -sounding and simple name - to change the " ribosome " - says Roberts. This abbreviation refers to the type of particles, complexes of RNA and proteins ( Ribonukleopartikel ). The term " ribosome " was able to prevail and is used in language use.

Because of their size high-resolution structures of ribosomes could be obtained only recently, although the gross molecular structure has been known since the 1970s. Some details of ribosomal proteins could be elucidated by means of affinity labeling and chemical cross-linking ( cross-linking). The end of 2000 was elucidated for the first time the 50S subunit of the archaeon Haloarcula marismortui at a resolution of 2.4 Å. In this resolution can resolve individual molecules. At the same time, the structures of the small ribosomal subunit from Thermus thermophilus was published in an atomic resolution of 3 Å. At this time, data of the entire structure were no ribosome, the existing data is used to reconstruct the prokaryotic ribosome.

In 2005, the crystallographic structure data of an intact ribosome from E. coli were presented at a resolution of 3.5 Å .. almost the same time was able to present a structure of another research group, which was obtained by means of cryo-electron microscopy for the first time. The resolution was relatively low at about 10 Å, but showed a snapshot of the translation at the translocon.

Later, more and more structural data of ( prokaryotic ) ribosomes were released who had just bound mRNAs or tRNAs, and it confers a better insight on the processes of translation.

For the eukaryotic ribosome ( 80S ), there are no comparable data structure. A three-dimensional reconstruction is, however, possible from the collected data of cryo-electron microscopy, X-ray crystallography of individual ribosomal components and homology comparisons with prokaryotic ribosomes.

Thomas A. Steitz, Ada Yonath and Venkatraman Ramakrishnan won the Nobel Prize in Chemistry for their work on the structure elucidation 2009.