Ribosome

A ribosome is a component of cells that assembles the twenty specific amino acid molecules to form the particular protein molecule determined by the nucleotide sequence of an RNA molecule.

One of the central tenets of biology, often referred to as the central dogma of molecular biology, is that DNA is used to make RNA, which is used to make proteins. The DNA sequence in genes is copied into a messenger RNA (mRNA). Ribosomes then read the information in this mRNA and use it to create proteins. This process is known as translation; the ribosome translates the genetic information from the RNA into proteins. Ribosomes do this by binding to an mRNA and using it as a template for determining the correct sequence of amino acids in a particular protein. The amino acids are attached to transfer RNA (tRNA) molecules, which enter one part of the ribosome and bind to the messenger RNA sequence. The attached amino acids are then joined together by another part of the ribosome. The ribosome moves along the mRNA, "reading" its sequence and producing a corresponding chain of amino acids.

Ribosomes are made from complexes of RNAs and proteins called ribonucleoproteins. Ribosomes are divided into two subunits. The smaller subunit binds to the mRNA, while the larger subunit binds to the tRNA and the amino acids. When a ribosome finishes reading a mRNA, these two subunits split apart. Ribosomes have been classified as ribozymes, because the ribosomal RNA seems to be most important for the peptidyl transferase activity that links amino acids together.

Ribosomes from bacteria, archaea and eukaryotes (the three domains of life on Earth), have significantly different structures and RNA sequences. These differences in structure allow some antibiotics to kill bacteria by inhibiting their ribosomes, while leaving human ribosomes unaffected. The ribosomes in the mitochondria of eukaryotic cells functionally resemble in many features those in bacteria, reflecting the likely evolutionary origin of mitochondria. The word ribosome comes from ribonucleic acid and the Greek: soma (meaning body).

Description
Archaeal, eubacterial and eukaryotic ribosomes differ in their size, composition and the ratio of protein to RNA. Because they are formed from two subunits of non-equal size, they are slightly longer in the axis than in diameter. Prokaryotic ribosomes are around 20 nm (200 ångströms) in diameter and are composed of 65% ribosomal RNA and 35% ribosomal proteins. Eukaryotic ribosomes are between 25 and 30 nm (250-300 angstroms) in diameter and the ratio of rRNA to protein is close to 1. Ribosomes translate messenger RNA (mRNA) and build polypeptide chains (e.g., proteins) using amino acids delivered by transfer RNA (tRNA). Their active sites are made of RNA, so ribosomes are now classified as "ribozymes".

Ribosomes build proteins from the genetic instructions held within messenger RNA. Free ribosomes are suspended in the cytosol (the semi-fluid portion of the cytoplasm); others are bound to the rough endoplasmic reticulum, giving it the appearance of roughness and thus its name, or to the nuclear envelope. As ribozymes are partly constituted from RNA, it is thought that they might be remnants of the RNA world. Although catalysis of the peptide bond involves the C2 hydroxyl of RNA's P-site (see Function section below) adenosine in a protein shuttle mechanism, other steps in protein synthesis (such as translocation) are caused by changes in protein conformations.

Ribosomes are sometimes referred to as organelles, but the use of the term organelle is often restricted to describing sub-cellular components that include a phospholipid membrane, which ribosomes, being entirely particulate, do not. For this reason, ribosomes may sometimes be described as "non-membranous organelles".

Ribosomes were first observed in the mid-1950s by Romanian cell biologist George Palade using an electron microscope as dense particles or granules for which he would win the Nobel Prize. The term "ribosome" was proposed by scientist Richard B. Roberts in 1958:

The structure and function of the ribosomes and associated molecules, known as the translational apparatus, has been of research interest since the mid-twentieth century and is a very active field of study today.

Ribosomes consist of two subunits (Figure 1) that fit together (Figure 2) and work as one to translate the mRNA into a polypeptide chain during protein synthesis (Figure 3). Bacterial subunits consist of one or two and eukaryotic of one or three very large RNA molecules (known as ribosomal RNA or rRNA) and multiple smaller protein molecules. Crystallographic work has shown that there are no ribosomal proteins close to the reaction site for polypeptide synthesis. This suggests that the protein components of ribosomes act as a scaffold that may enhance the ability of rRNA to synthesize protein rather than directly participating in catalysis (See: Ribozyme).

Biogenesis
In bacterial cells, ribosomes are synthesized in the cytoplasm through the transcription of multiple ribosome gene operons. In eukaryotes, the process takes place both in the cell cytoplasm and in the nucleolus, which is a region within the cell nucleus. The assembly process involves the coordinated function of over 200 proteins in the synthesis and processing of the four rRNAs, as well as assembly of those rRNAs with the ribosomal proteins.

Ribosome locations
Ribosomes are classified as being either "free" or "membrane-bound".

Free and membrane-bound ribosomes differ only in their spatial distribution; they are identical in structure. Whether the ribosome exists in a free or membrane-bound state depends on the presence of an ER-targeting signal sequence on the protein being synthesized, so an individual ribosome might be membrane-bound when it is making one protein, but free in the cytosol when it makes another protein.

Free ribosomes
Free ribosomes can move about anywhere in the cytosol, but are excluded from the cell nucleus and other organelles. Proteins that are formed from free ribosomes are released into the cytosol and used within the cell. Since the cytosol contains high concentrations of glutathione and is, therefore, a reducing environment, proteins containing disulfide bonds, which are formed from oxidized cysteine residues, cannot be produced in this compartment.

Membrane-bound ribosomes
When a ribosome begins to synthesize proteins that are needed in some organelles, the ribosome making this protein can become "membrane-bound". In eukaryotic cells this happens in a region of the endoplasmic reticulum (ER) called the "rough ER". The newly produced polypeptide chains are inserted directly into the ER by the ribosome and are then transported to their destinations, through the secretory pathway. Bound ribosomes usually produce proteins that are used within the plasma membrane or are expelled from the cell via exocytosis.

Structure
The ribosomal subunits of prokaryotes and eukaryotes are quite similar.

The unit of measurement is the Svedberg unit, a measure of the rate of sedimentation in centrifugation rather than size and accounts for why fragment names do not add up (70S is made of 50S and 30S).

Prokaryotes have 70S ribosomes, each consisting of a small (30S) and a large (50S) subunit. Their large subunit is composed of a 5S RNA subunit (consisting of 120 nucleotides), a 23S RNA subunit (2900 nucleotides) and 34 proteins. The 30S subunit has a 1540 nucleotide RNA subunit (16S) bound to 21 proteins. . Affinity label for the tRNA binding sites on the E. coli ribosme allowed the identification of A and P site proteins most likely associated with the peptidyltransferase activity; labelled proteins are L27, L14, L15, L16, L2; at least L27 is located at the donor site as shown by E. Collatz and A.P. Czernilofsky et al. (FEBS Letters, 63 pp 283-286, 1976, Proc. Natl. Sci., USA, 71, pp230-234, 1974. Proteins involved in the initiation of translation, S1 and S21 are associated with the 3'-end of 16S ribosomal RNA, as determined by A.P. Czernilofsky et al. by RNA-protein crosslinking (FEBS Leter, 58, pp281-284, 1975) Shine-Dalgarno_sequence.

Eukaryotes have 80S ribosomes, each consisting of a small (40S) and large (60S) subunit. Their large subunit is composed of a 5S RNA (120 nucleotides), a 28S RNA (4700 nucleotides), a 5.8S subunit (160 nucleotides) and ~49 proteins. The 40S subunit has a 1900 nucleotide (18S) RNA and ~33 proteins. .The identification of the tRNA-Bibding Sites on Rat Liver Ribosomes by Affinity Labeling was performed by A.P. Czernilofsky et al. 1977, several proteins including L32/33, L36, L21, L23, L28/29 and L13 (Molec. Gen. Genet. 153, pp231-235, 1977).

The ribosomes found in chloroplasts and mitochondria of eukaryotes also consist of large and small subunits bound together with proteins into one 70S particle. These organelles are believed to be descendants of bacteria (see Endosymbiotic theory) and as such their ribosomes are similar to those of bacteria.

The various ribosomes share a core structure, which is quite similar despite the large differences in size. Much of the RNA is highly organized into various tertiary structural motifs, for example pseudoknots that exhibit coaxial stacking. The extra RNA in the larger ribosomes is in several long continuous insertions, such that they form loops out of the core structure without disrupting or changing it. All of the catalytic activity of the ribosome is carried out by the RNA; the proteins reside on the surface and seem to stabilize the structure.

The differences between the bacterial and eukaryotic ribosomes are exploited by pharmaceutical chemists to create antibiotics that can destroy a bacterial infection without harming the cells of the infected person. Due to the differences in their structures, the bacterial 70S ribosomes are vulnerable to these antibiotics while the eukaryotic 80S ribosomes are not. Even though mitochondria possess ribosomes similar to the bacterial ones, mitochondria are not affected by these antibiotics because they are surrounded by a double membrane that does not easily admit these antibiotics into the organelle.

High-resolution structure
The general molecular structure of the ribosome has been known since the early 1970s. In the early 2000s the structure has been achieved at high resolutions, on the order of a few ångströms.

The first papers giving the structure of the ribosome at atomic resolution were published in rapid succession in late 2000. First, the 50S (large prokaryotic) subunit from the archaeon Haloarcula marismortui was published. Soon after, the structure of the 30S subunit from Thermus thermophilus was published. Shortly thereafter, a more detailed structure was published. These structural studies were awarded the Nobel Prize in Chemistry in 2009. Early the next year (May 2001) these coordinates were used to reconstruct the entire T. thermophilus 70S particle at 5.5 ångström resolution.

Two papers were published in November 2005 with structures of the Escherichia coli 70S ribosome. The structures of a vacant ribosome were determined at 3.5-ångström resolution using x-ray crystallography. Then, two weeks later, a structure based on cryo-electron microscopy was published, which depicts the ribosome at 11-15 ångström resolution in the act of passing a newly synthesized protein strand into the protein-conducting channel.

First atomic structures of the ribosome complexed with tRNA and mRNA molecules were solved by using X-ray crystallography by two groups independently, at 2.8 ångström and at 3.7 ångström. These structures allow one to see the details of interactions of the Thermus thermophilus ribosome with mRNA and with tRNAs bound at classical ribosomal sites. Interactions of the ribosome with long mRNAs containing Shine-Dalgarno sequences were visualized soon after that at 4.5- to 5.5-ångström resolution.

Function
Ribosomes are the workhorses of protein biosynthesis, the process of translating mRNA into protein. The mRNA comprises a series of codons that dictate to the ribosome the sequence of the amino acids needed to make the protein. Using the mRNA as a template, the ribosome traverses each codon (3 nucleotides) of the mRNA, pairing it with the appropriate amino acid provided by a tRNA. Molecules of transfer RNA (tRNA) contain a complementary anticodon on one end and the appropriate amino acid on the other. The small ribosomal subunit, typically bound to a tRNA containing the amino acid methionine, binds to an AUG codon on the mRNA and recruits the large ribosomal subunit. The ribosome then contains three RNA binding sites, designated A, P and E. The A site binds an aminoacyl-tRNA (a tRNA bound to an amino acid); the P site binds a peptidyl-tRNA (a tRNA bound to the peptide being synthesized); and the E site binds a free tRNA before it exits the ribosome. Protein synthesis begins at a start codon AUG near the 5' end of the mRNA. mRNA binds to the P site of the ribosome first. The ribosome is able to identify the start codon by use of the Shine-Dalgarno sequence of the mRNA in prokaryotes and Kozak box in eukaryotes.



In Figure 3, both ribosomal subunits (small and large ) assemble at the start codon (towards the 5' end of the mRNA). The ribosome uses tRNA that matches the current codon (triplet) on the mRNA to append an amino acid to the polypeptide chain. This is done for each triplet on the mRNA, while the ribosome moves towards the 3' end of the mRNA. Usually in bacterial cells, several ribosomes are working parallel on a single mRNA, forming what is called a polyribosome or polysome.

Nobel Prize
Together with Albert Claude and Christian de Duve, George Emil Palade was awarded the Nobel Prize in Physiology or Medicine, in 1974, for the discovery of the ribosomes. The Nobel Prize in Chemistry 2009 was awarded to Drs Venkatraman Ramakrishnan, Thomas A. Steitz and Ada E. Yonath "for studies of the structure and function of the ribosome"