Ribosomes

Ribosomes comprise a complex, found within all living , that serves as the site of (translation). Ribosomes link together in the order specified by  (mRNA) molecules. Ribosomes consist of two major components: the small ribosomal subunits, which read the, and the large subunits, which join amino acids to form a chain. Each subunit consists of one or more (rRNA) molecules and a variety of s (r-protein or rProtein). The ribosomes and associated molecules are also known as the translational apparatus.

Overview
The sequence of, which encodes the sequence of the amino acids in a protein, is copied into a messenger RNA chain. It may be copied many times into RNA chains. Ribosomes can bind to a messenger RNA chain and use its sequence for determining the correct sequence of amino acids for generating a given protein. Amino acids are selected, collected, and carried to the ribosome by (tRNA) molecules, which enter one part of the ribosome and bind to the messenger RNA chain. It is during this binding that the correct translation of nucleic acid sequence to amino acid sequence occurs. For each coding triplet in the messenger RNA there is a distinct transfer RNA that matches and which carries the correct amino acid for that coding triplet. The attached amino acids are then linked together by another part of the ribosome. Once the protein is produced, it can then to produce a specific functional three-dimensional structure although during synthesis some proteins start folding into their correct form.

A ribosome is made from of RNAs and proteins and is therefore a. Each ribosome is divided into two subunits: When a ribosome finishes reading an mRNA molecule, these two subunits split apart. Ribosomes are s, because the  activity that links amino acids together is performed by the ribosomal RNA. Ribosomes are often associated with the intracellular membranes that make up the.
 * 1) a smaller subunit which binds to a larger subunit and the mRNA pattern, and
 * 2) a larger subunit which binds to the tRNA, the amino acids, and the smaller subunit.

Ribosomes from, and s in the , resemble each other to a remarkable degree, evidence of a common origin. They differ in their size, sequence, structure, and the ratio of protein to RNA. The differences in structure allow some s to kill bacteria by inhibiting their ribosomes, while leaving human ribosomes unaffected. In bacteria and archaea, more than one ribosome may move along a single mRNA chain at one time, each "reading" its sequence and producing a corresponding protein molecule.

The s of eukaryotic cells, are produced from s, and functionally resemble many features of those in bacteria, reflecting the likely evolutionary origin of mitochondria.

Discovery
Ribosomes were first observed in the mid-1950s by cell biologist, using an , as dense particles or granules. The term "ribosome" was proposed by scientist Richard B. Roberts in the end of 1950s:

,, and were jointly awarded the , in 1974, for the discovery of the ribosome. The in  2009 was awarded to,  and  for determining the detailed structure and mechanism of the ribosome.

Structure
The ribosome is a highly complex cellular machine. It is largely made up of specialized RNA known as (rRNA) as well as dozens of distinct proteins (the exact number varies slightly between species). The ribosomal proteins and rRNAs are arranged into two distinct ribosomal pieces of different size, known generally as the large and small subunit of the ribosome. Ribosomes consist of two subunits that fit together (Figure 2) and work as one to translate the mRNA into a polypeptide chain during protein synthesis (Figure 1). Because they are formed from two subunits of non-equal size, they are slightly longer in the axis than in diameter.

Bacterial ribosomes
Prokaryotic ribosomes are around 20 (200 ) in diameter and are composed of 65% rRNA and 35% s. Eukaryotic ribosomes are between 25 and 30  (250–300 Å) in diameter with an rRNA-to-protein ratio that is close to 1. 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 do not directly participate in peptide bond formation catalysis, but rather that these proteins act as a scaffold that may enhance the ability of rRNA to synthesize protein (See: ).

The ribosomal subunits of and eukaryotes are quite similar.

The unit of measurement used to describe the ribosomal subunits and the rRNA fragments is the unit, a measure of the rate of  in  rather than size. This accounts for why fragment names do not add up: for example, bacterial 70S ribosomes are made of 50S and 30S subunits.

Bacteria have 70 ribosomes, each consisting of a small and a large  subunit. E. coli, for example, has a RNA subunit (consisting of 1540 nucleotides) that is bound to 21 proteins. The large subunit is composed of a RNA subunit (120 nucleotides), a 23S RNA subunit (2900 nucleotides) and 31 s.
 * {| class="wikitable float-right" style="text-align:center"

! width="25%"| ribosome ! width="25%"| subunit ! width="25%"| rRNAs ! width="25%"| r-proteins Affinity label for the tRNA binding sites on the E. coli ribosome 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. Additional research has demonstrated that the S1 and S21 proteins, in association with the 3′-end of 16S ribosomal RNA, are involved in the initiation of translation.
 * + Ribosome of E. coli (a bacterium)
 * rowspan="3" | 70S || rowspan="2" | 50S || 23S (2904 ) || rowspan="2" | 31
 * 5S (120 nt)
 * 30S || 16S (1542 nt) || 21
 * }
 * 30S || 16S (1542 nt) || 21
 * }
 * }

Eukaryotic ribosomes
Eukaryotes have 80S ribosomes located in their cytosol, each consisting of a and. Their 40S subunit has an (1900 nucleotides) and 33 proteins. The large subunit is composed of a (120 nucleotides),  (4700 nucleotides), a  (160 nucleotides) subunits and 46 proteins.
 * {| class="wikitable float-right" style="text-align:center"

! width="25%"| ribosome ! width="25%"| subunit ! width="25%"| rRNAs ! width="25%"| r-proteins During 1977, Czernilofsky published research that used ing to identify tRNA-binding sites on rat liver ribosomes. Several proteins, including L32/33, L36, L21, L23, L28/29 and L13 were implicated as being at or near the center.
 * + eukaryotic cytosolic ribosomes (R. norvegicus)
 * rowspan="4" | 80S || rowspan="3" | 60S || 28S (4718 nt) || rowspan="3" | 49
 * 5.8S (160 nt)
 * 5S (120 nt)
 * 40S || 18S (1874 nt) || 33
 * }
 * 5S (120 nt)
 * 40S || 18S (1874 nt) || 33
 * }
 * }

Plastoribosomes and mitoribosomes
In eukaryotes, ribosomes are present in (sometimes called ) and in s such as s (also called plastoribosomes). They also consist of large and small subunits bound together with s into one 70S particle. These ribosomes are similar to those of bacteria and these organelles are thought to have originated as  Of the two, chloroplastic ribosomes are closer to bacterial ones than mitochrondrial ones are. Many pieces of ribosomal RNA in the mitochrondria are shortened, and in the case of, replaced by other structures in animals and fungi. In particular,  has a minimalized set of mitochondrial rRNA.

The and  algae may contain a  that resembles a vestigial eukaryotic nucleus. Eukaryotic 80S ribosomes may be present in the compartment containing the nucleomorph.

Making use of the differences
The differences between the bacterial and eukaryotic ribosomes are exploited by to create s 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 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. The same cannot be said of chloroplasts, where antibiotic resistance in ribosomal proteins is a trait to be introduced as a marker in genetic engineering.

Common properties
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, for example s that exhibit. The extra 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 ; the proteins reside on the surface and seem to stabilize the structure.

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, of the order of a few s.

The first papers giving the structure of the ribosome at atomic resolution were published almost simultaneously in late 2000. The 50S (large prokaryotic) subunit was determined from the Haloarcula marismortui and the bacterium ', and the structure of the 30S subunit was determined from '. These structural studies were awarded the Nobel Prize in Chemistry in 2009. In May 2001 these coordinates were used to reconstruct the entire  70S particle at 5.5 resolution.

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

The first atomic structures of the ribosome complexed with and  molecules were solved by using X-ray crystallography by two groups independently, at 2.8  and at 3.7. These structures allow one to see the details of interactions of the  ribosome with and with s bound at classical ribosomal sites. Interactions of the ribosome with long mRNAs containing s were visualized soon after that at 4.5–5.5 resolution.

In 2011, the first complete atomic structure of the eukaryotic 80S ribosome from the yeast  was obtained by crystallography. The model reveals the architecture of eukaryote-specific elements and their interaction with the universally conserved core. At the same time, the complete model of a eukaryotic 40S ribosomal structure in  was published and described the structure of the, as well as much about the 40S subunit's interaction with during. Similarly, the eukaryotic structure was also determined from  in complex with.

Function
Ribosomes are minute particles consisting of RNA and associated proteins that function to synthesize proteins. Proteins are needed for many cellular functions such as repairing damage or directing chemical processes. Ribosomes can be found floating within the cytoplasm or attached to the. Basically, their main function is to convert genetic code into an amino acid sequence and to build protein polymers from amino acid monomers.

Ribosomes act as catalysts in two extremely important biological processes called peptidyl transfer and peptidyl hydrolysis. The "PT center is responsible for producing protein bonds during protein elongation".

Translation
Ribosomes are the workplaces of, the process of translating into. The mRNA comprises a series of s which are decoded by the ribosome so as to make the protein. Using the mRNA as a template, the ribosome traverses each codon (3 s) of the mRNA, pairing it with the appropriate amino acid provided by an. Aminoacyl-tRNA contains a complementary on one end and the appropriate amino acid on the other. For fast and accurate recognition of the appropriate tRNA, the ribosome utilizes large conformational changes . The small ribosomal subunit, typically bound to an aminoacyl-tRNA containing the first amino acid, binds to an AUG codon on the mRNA and recruits the large ribosomal subunit. The ribosome contains three RNA binding sites, designated A, P and E. The binds an aminoacyl-tRNA or termination release factors; the  binds a peptidyl-tRNA (a tRNA bound to the poly-peptide chain); and the  (exit) binds a free tRNA. Protein synthesis begins at a AUG near the 5' end of the mRNA. mRNA binds to the P site of the ribosome first. The ribosome recognizes the start codon by using the of the mRNA in prokaryotes and  in eukaryotes.

Although catalysis of the involves the C2  of RNA's P-site  in a proton shuttle mechanism, other steps in protein synthesis (such as translocation) are caused by changes in protein conformations. Since their is made of RNA, ribosomes are classified as "s," and it is thought that they might be remnants of the.

In Figure 5, both ribosomal subunits ( small and large ) assemble at the start codon (towards the 5' end of the ). The ribosome uses that matches the current codon (triplet) on the mRNA to append an  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 .

Cotranslational folding
The ribosome is known to actively participate in the. The structures obtained in this way are usually identical to the ones obtained during protein chemical refolding, however, the pathways leading to the final product may be different. In some cases, the ribosome is crucial in obtaining the functional protein form. For example, one of the possible mechanisms of folding of the deeply s relies on the ribosome pushing the chain through the attached loop.

Addition of translation-independent amino acids
Presence of a ribosome quality control protein Rqc2 is associated with mRNA-independent protein elongation. This elongation is a result of ribosomal addition (via tRNAs brought by Rqc2) of CAT tails: ribosomes extend the of a stalled protein with random, translation-independent sequences of  and.

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 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.

Ribosomes are sometimes referred to as s, 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".

Free ribosomes
Free ribosomes can move about anywhere in the, but are excluded from the 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 and is, therefore, a, proteins containing , which are formed from oxidized cysteine residues, cannot be produced within it.

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 undertaking and are then transported to their destinations, through the. Bound ribosomes usually produce proteins that are used within the plasma membrane or are expelled from the cell via .

Biogenesis
In bacterial cells, ribosomes are synthesized in the cytoplasm through the of multiple ribosome gene s. In eukaryotes, the process takes place both in the cell cytoplasm and in the, which is a region within the. 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.

Origin
The ribosome may have first originated in an, appearing as a self-replicating complex that only later evolved the ability to synthesize proteins when s began to appear. Studies suggest that ancient ribosomes constructed solely of could have developed the ability to synthesize s. In addition, evidence strongly points to ancient ribosomes as self-replicating complexes, where the rRNA in the ribosomes had informational, structural, and catalytic purposes because it could have coded for  and proteins needed for ribosomal self-replication. Hypothetical cellular organisms with self-replicating RNA but without DNA are called s (or ribocells).

As amino acids gradually appeared in the RNA world under prebiotic conditions, their interactions with catalytic RNA would increase both the range and efficiency of function of catalytic RNA molecules. Thus, the driving force for the evolution of the ribosome from an ancient self-replicating machine into its current form as a translational machine may have been the selective pressure to incorporate proteins into the ribosome’s self-replicating mechanisms, so as to increase its capacity for self-replication.

Specialized ribosome
Many textbooks suggest that there are only two kinds of ribosomes, namely prokaryotic and eukaryotic ribosomes. However, ribosomes are surprisingly heterogeneous with different compositions in different species. Heterogeneous ribosomes have different structures and thus different activities compared to typical ribosomes in major model organisms.

Heterogeneity in ribosome composition has been proposed to be involved in translational control of protein synthesis. Vincent Mauro and proposed the ribosome filter hypothesis to explain the regulatory functions of ribosomes. Emerging evidence has shown that specialized ribosomes specific to different cell populations can affect how genes are translated. Some ribosomal proteins exchange from the assembled complex with ic copies suggesting that the structure of the in vivo ribosome can be modified without synthesizing an entire new ribosome.

Ribosomal proteins
A group of highly acidic ribosomal proteins (RPs), also known as P proteins, are known to be present on the 60S subunit in multiple copies in the ribosomes stalk and P proteins mediate selective translation. These P proteins can be found in yeast and mammalian cells. If P proteins are not present in yeast this can cause the yeast to have a cold-sensitive phenotype. If P proteins are not present in human cells, this could cause autophagy induction.

Certain ribosomal proteins are absolutely critical while others are not. For instance, Rpl28 and Rpl5 mutant flies are alive but have abnormally large wings. Rpl38 also appears to be critical in mammals only under very specific conditions: in mice Rpl38 is required for the translation of a subset of Hox mRNA and a mutation of Rpl38 lead to a homeotic transformation with a short tail.

Other ways heterogeneity can arise from post-translational modifications to RPs include acetylation and methylation in species like yeast, Arabidopsis, and human cells. But there is no overall change in protein synthesis.

Modifications to core ribosomal proteins (RPs) can also give rise to the formation of heterogeneous ribosomes. For instance, in yeast, Rpl28 ubiquitination levels vary with the cell cycle. Ribosomes with the polyubiquitinated Rpl28 carry out protein synthesis at a higher rate in vitro compared with ribosomes with monoubiquitinated Rpl28.

Ribosome-associated factors
Heterogeneous ribosomes can also arise from other factors binding to the ribosome surface. For example, ribosome-associated factor (RACK1) is so tightly associated with the ribosome that its binding is resistant to high-salt washes in vitro. RACK1 is required for efficient translation of mRNA with short open reading frames.

rRNA heterogeneity
Viral IRES translations can also be mediated by specialized ribosomes. undefinedSpecifically, 40S ribosomal units without RPS25 in yeast and mammalian cells are unable to begin translation from two viral IRESes, namely the IRES and the  (CrPV) intergenic region. The CrPV only needs RPS25 to begin translation and mediate ribosome recruitment. Usually if RPS25 is not present in a certain IRES, initiation from these IRESes can be defective.

rRNA modifications
Heterogeneity of ribosomal RNA modifications plays an important role in structural maintenance and/or function, such as modulating translation and most mRNA modifications are found in highly conserved regions. The most common rRNA modifications are and 2’-O methylation of ribose.