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The ribosome (/ˈraɪbəˌsoʊm, -boʊ-/[1]) is a complex molecular machine, found within all living cells, that serves as the site of biological protein synthesis (translation). Ribosomes link amino acids together in the order specified by messenger RNA
RNA
(mRNA) molecules. Ribosomes consist of two major components: the small ribosomal subunits, which reads the RNA, and the large subunits, which joins amino acids to form a polypeptide chain. Each subunit is composed of one or more ribosomal RNA
RNA
(rRNA) molecules and a variety of ribosomal proteins (r-protein or rProtein[2][3][4]). The ribosomes and associated molecules are also known as the translational apparatus.

Contents

1 Overview 2 Discovery 3 Structure

3.1 High-resolution structure

4 Function

4.1 Translation 4.2 Addition of translation-independent amino acids

5 Ribosome
Ribosome
locations

5.1 Free ribosomes 5.2 Membrane-bound ribosomes

6 Biogenesis 7 Origin 8 Specialized ribosomes 9 See also 10 References 11 External links

Overview[edit] The sequence of DNA, which encodes the sequence of the amino acids in a protein, is copied into a messenger RNA
RNA
chain. It may be copied many times into RNA
RNA
chains. Ribosomes can bind to a messenger RNA
RNA
chain and use its sequence for determining the correct sequence of amino acids. Amino acids
Amino acids
are selected, collected, and carried to the ribosome by transfer RNA
RNA
(tRNA) molecules, which enter one part of the ribosome and bind to the messenger RNA
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
RNA
there is a distinct transfer RNA
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 fold to produce a specific functional three-dimensional structure although during synthesis some proteins start folding into their correct form. A ribosome is made from complexes of RNAs and proteins and is therefore a ribonucleoprotein. Each ribosome is divided into two subunits:

a smaller subunit which binds to a larger subunit and the mRNA pattern, and a larger subunit which binds to the tRNA, the amino acids, and the smaller subunit.

When a ribosome finishes reading an m RNA
RNA
molecule, these two subunits split apart. Ribosomes are ribozymes, because the catalytic peptidyl transferase activity that links amino acids together is performed by the ribosomal RNA. Ribosomes are often associated with the intracellular membranes that make up the rough endoplasmic reticulum. Ribosomes from bacteria, archaea and eukaryotes in the three-domain system, 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 antibiotics 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 m RNA
RNA
chain at one time, each "reading" its sequence and producing a corresponding protein molecule. The mitochondrial ribosomes of eukaryotic cells, are produced from mitochondrial genes, and functionally resemble many features of those in bacteria, reflecting the likely evolutionary origin of mitochondria.[5][6] Discovery[edit] Ribosomes were first observed in the mid-1950s by Romanian-American cell biologist George Emil Palade, using an electron microscope, as dense particles or granules.[7] The term "ribosome" was proposed by scientist Richard B. Roberts in the end of 1950s:

During the course of the symposium a semantic difficulty became apparent. To some of the participants, "microsomes" mean the ribonucleoprotein particles of the microsome fraction contaminated by other protein and lipid material; to others, the microsomes consist of protein and lipid contaminated by particles. The phrase "microsomal particles" does not seem adequate, and "ribonucleoprotein particles of the microsome fraction" is much too awkward. During the meeting, the word "ribosome" was suggested, which has a very satisfactory name and a pleasant sound. The present confusion would be eliminated if "ribosome" were adopted to designate ribonucleoprotein particles in sizes ranging from 35 to 100S. — Albert, Microsomal Particles and Protein
Protein
Synthesis[8]

Albert Claude, Christian de Duve, and George Emil Palade
George Emil Palade
were jointly awarded the Nobel Prize
Nobel Prize
in Physiology or Medicine, in 1974, for the discovery of the ribosome.[9] The Nobel Prize
Nobel Prize
in Chemistry
Chemistry
2009 was awarded to Venkatraman Ramakrishnan, Thomas A. Steitz
Thomas A. Steitz
and Ada E. Yonath for determining the detailed structure and mechanism of the ribosome.[10] Structure[edit]

Figure 2 : Large (red) and small (blue) subunit fit together.

The ribosome is a highly complex cellular machine. It is largely made up of specialized RNA
RNA
known as ribosomal RNA
RNA
(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 m RNA
RNA
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. Prokaryotic ribosomes are around 20 nm (200 Å) in diameter and are composed of 65% r RNA
RNA
and 35% ribosomal proteins.[11] Eukaryotic ribosomes are between 25 and 30 nm (250–300 Å) in diameter with an rRNA-to-protein ratio that is close to 1.[12] Crystallographic work [13] 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 r RNA
RNA
to synthesize protein (See: Ribozyme).

Figure 3 : Atomic structure of the 30S subunit from Thermus thermophilus.[14] Proteins are shown in blue and the single RNA
RNA
chain in orange.

The ribosomal subunits of prokaryotes and eukaryotes are quite similar.[15] The unit of measurement used to describe the ribosomal subunits and the r RNA
RNA
fragments is the Svedberg
Svedberg
unit, a measure of the rate of sedimentation in centrifugation rather than size. This accounts for why fragment names do not add up: for example, prokaryotic 70S ribosomes are made of 50S
50S
and 30S subunits. Prokaryotes have 70S ribosomes, each consisting of a small (30S) and a large (50S) subunit. Their small subunit has a 16S RNA
RNA
subunit (consisting of 1540 nucleotides) bound to 21 proteins. The large subunit is composed of a 5S RNA
RNA
subunit (120 nucleotides), a 23S RNA subunit (2900 nucleotides) and 31 proteins.[15]

prokaryotic ribosomes (E. coli)[16]

ribosome subunit rRNAs r-proteins

70S 50S 23S (2904 nt) 31

5S (120 nt)

30S 16S (1542 nt) 21

Affinity label for the t RNA
RNA
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.[17][18] 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.[19] Eukaryotes have 80S ribosomes, each consisting of a small (40S) and large (60S) subunit. Their 40S
40S
subunit has an 18S RNA
RNA
(1900 nucleotides) and 33 proteins.[20][21] The large subunit is composed of a 5S RNA
RNA
(120 nucleotides), 28S RNA
RNA
(4700 nucleotides), a 5.8S RNA (160 nucleotides) subunits and 46 proteins.[15][20][22]

eukaryotic cytosolic ribosomes (R. norvegicus)[23]

ribosome subunit rRNAs r-proteins

80S 60S 28S (4718 nt) 49

5.8S (160 nt)

5S (120 nt)

40S 18S (1874 nt) 33

During 1977, Czernilofsky published research that used affinity labeling 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 peptidyl transferase center.[24] The ribosomes found in chloroplasts and mitochondria of eukaryotes also consist of large and small subunits bound together with proteins into one 70S particle.[15] These organelles are believed to be descendants of bacteria (see Endosymbiotic theory) and, as such, their ribosomes are similar to those of bacteria.[15] The various ribosomes share a core structure, which is quite similar despite the large differences in size. Much of the RNA
RNA
is highly organized into various tertiary structural motifs, for example pseudoknots that exhibit coaxial stacking. The extra RNA
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.[15] 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.[15] 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.[25] 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.[26] High-resolution structure[edit]

Figure 4 : Atomic structure of the 50S
50S
subunit from Haloarcula marismortui. Proteins are shown in blue and the two RNA
RNA
chains in orange and yellow.[27] The small patch of green in the center of the subunit is the active site.

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 ångström (Å). 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 archaeon Haloarcula marismortui[27] and the bacterium Deinococcus radiodurans,[28] and the structure of the 30S subunit was determined from Thermus thermophilus.[14] These structural studies were awarded the Nobel Prize
Nobel Prize
in Chemistry
Chemistry
in 2009. In May 2001 these coordinates were used to reconstruct the entire T. thermophilus 70S particle at 5.5 Å resolution.[29] Two papers were published in November 2005 with structures of the Escherichia coli
Escherichia coli
70S ribosome. The structures of a vacant ribosome were determined at 3.5-Å resolution using x-ray crystallography.[30] Then, two weeks later, a structure based on cryo-electron microscopy was published,[31] which depicts the ribosome at 11–15Å 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 t RNA
RNA
and m RNA
RNA
molecules were solved by using X-ray crystallography
X-ray crystallography
by two groups independently, at 2.8 Å[32] and at 3.7 Å.[33] These structures allow one to see the details of interactions of the Thermus thermophilus ribosome with m RNA
RNA
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-Å resolution.[34] In 2011, the first complete atomic structure of the eukaryotic 80S ribosome from the yeast Saccharomyces cerevisiae
Saccharomyces cerevisiae
was obtained by crystallography.[20] 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
40S
ribosomal structure in Tetrahymena thermophila
Tetrahymena thermophila
was published and described the structure of the 40S
40S
subunit, as well as much about the 40S
40S
subunit's interaction with eIF1 during translation initiation.[21] Similarly, the eukaryotic 60S
60S
subunit structure was also determined from Tetrahymena thermophila
Tetrahymena thermophila
in complex with eIF6.[22] Function[edit] Ribosomes are organelles that 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 endoplasmic reticulum. Translation[edit] Main article: Translation (genetics) Ribosomes are the workplaces of protein biosynthesis, the process of translating m RNA
RNA
into protein. The m RNA
RNA
comprises a series of codons that dictate to the ribosome the sequence of the amino acids needed to make the protein. Using the m RNA
RNA
as a template, the ribosome traverses each codon (3 nucleotides) of the mRNA, pairing it with the appropriate amino acid provided by an aminoacyl-tRNA. Aminoacyl-tRNA contains a complementary anticodon 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 (conformational proofreading) .[35] The small ribosomal subunit, typically bound to an aminoacyl-t RNA
RNA
containing the amino acid methionine, binds to an AUG codon on the m RNA
RNA
and recruits the large ribosomal subunit. The ribosome contains three RNA
RNA
binding sites, designated A, P and E. The A-site binds an aminoacyl-tRNA;[36] the P-site binds a peptidyl-t RNA
RNA
(a t RNA
RNA
bound to the peptide being synthesized); and the E-site (exit) binds a free t RNA
RNA
before it exits the ribosome. Protein
Protein
synthesis begins at a start codon AUG near the 5' end of the mRNA. m RNA
RNA
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 m RNA
RNA
in prokaryotes and Kozak box in eukaryotes. Although catalysis of the peptide bond involves the C2 hydroxyl of RNA's P-site adenosine in a proton shuttle mechanism, other steps in protein synthesis (such as translocation) are caused by changes in protein conformations. Since their catalytic core is made of RNA, ribosomes are classified as "ribozymes,"[37] and it is thought that they might be remnants of the RNA
RNA
world.[38]

Figure 5 : Translation of m RNA
RNA
(1) by a ribosome (2)(shown as small and large subunits) into a polypeptide chain (3). The ribosome begins at the start codon of RNA
RNA
(AUG) and ends at the stop codon (UAG).

In Figure 5, both ribosomal subunits (small and large) assemble at the start codon (towards the 5' end of the RNA). The ribosome uses RNA that matches the current codon (triplet) on the m RNA
RNA
to append an amino acid to the polypeptide chain. This is done for each triplet on the RNA, while the ribosome moves towards the 3' end of the mRNA. Usually in bacterial cells, several ribosomes are working parallel on a single RNA, forming what is called a polyribosome or polysome. Addition of translation-independent amino acids[edit] Presence of a ribosome quality control protein Rqc2 is associated with mRNA-independent protein elongation.[39][40] This elongation is a result of ribosomal addition (via tRNAs brought by Rqc2) of CAT tails: ribosomes extend the C-terminus
C-terminus
of a stalled protein with random, translation-independent sequences of alanines and threonines.[41][42] Würzburg University
Würzburg University
and Max Planck Institute researches, the results of which were published in Cell Reports and The EMBO magazines in September 2016, have shown that ribosomes have the role of being "a quality control point". Professor Utz Fischer from the University of Würzburg has been researching the assembly of proteins called "macromolecular machines" in the cell for years. He describes this assembly process as LEGO blocks: "Think of it as LEGO bricks at the molecular level: One brick is attached to the next until the product is finished. If only one defective or wrong brick is used, the entire building may be compromised as a result."[43][44][45] Ribosome
Ribosome
locations[edit] Ribosomes are classified as being either "free" or "membrane-bound".

Figure 6 : A ribosome translating a protein that is secreted into the endoplasmic reticulum.

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. 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". Free ribosomes[edit] 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 within it. Membrane-bound ribosomes[edit] 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 vectorial synthesis 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.[46] Biogenesis[edit] Main article: Ribosome
Ribosome
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. Origin[edit] The ribosome may have first originated in an RNA
RNA
world, appearing as a self-replicating complex that only later evolved the ability to synthesize proteins when amino acids began to appear.[47] Studies suggest that ancient ribosomes constructed solely of r RNA
RNA
could have developed the ability to synthesize peptide bonds.[48][49][50] In addition, evidence strongly points to ancient ribosomes as self-replicating complexes, where the r RNA
RNA
in the ribosomes had informational, structural, and catalytic purposes because it could have coded for tRNAs and proteins needed for ribosomal self-replication.[51] Hypothetical cellular organisms with self-replicating RNA
RNA
but without DNA
DNA
are called ribocytes (or ribocells).[52][53] As amino acids gradually appeared in the RNA
RNA
world under prebiotic conditions,[54][55] their interactions with catalytic RNA
RNA
would increase both the range and efficiency of function of catalytic RNA molecules.[47] 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.[51] Specialized ribosomes[edit] Heterogeneity in ribosome composition has been proposed to be involved in translational control of protein synthesis.[56] Vincent Mauro and Gerald Edelman
Gerald Edelman
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.[57] Some ribosomal proteins exchange from the assembled complex with cytosolic copies [58] suggesting that the structure of the in vivo ribosome can be modified without synthesizing an entire new ribosome. See also[edit]

Aminoglycosides Biological machines Eukaryotic translation Posttranslational modification Prokaryotic translation Protein
Protein
dynamics RNA
RNA
tertiary structure Translation (genetics) Wobble base pair

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External links[edit]

Wikimedia Commons has media related to Ribosomes.

Lab computer simulates ribosome in motion Role of the Ribosome, Gwen V. Childs, copied here Ribosome
Ribosome
in Proteopedia - The free, collaborative 3D encyclopedia of proteins & other molecules Ribosomal proteins families in ExPASy Molecule of the Month © RCSB Protein
Protein
Data Bank:

Ribosome Elongation Factors Palade

3D electron microscopy structures of ribosomes at the EM Data Bank(EMDB)

v t e

Structures of the cell / organelles

Endomembrane system

Cell membrane Nucleus Endoplasmic reticulum Golgi apparatus Parenthesome Autophagosome Vesicles

Exosome Lysosome Endosome Phagosome Vacuole Acrosome

Cytoplasmic
Cytoplasmic
granules

Melanosome Microbody Glyoxysome Peroxisome Weibel–Palade body

Cytoskeleton

Microfilaments Intermediate filaments Microtubules Prokaryotic cytoskeleton MTOCs

Centrosome Centriole Basal body Spindle pole body

Myofibril

Endosymbionts

Mitochondrion Plastids

Chloroplast Chromoplast Gerontoplast Leucoplast Amyloplast Elaioplast Proteinoplast Tannosome

Other internal

Nucleolus RNA

Ribosome Spliceosome Vault

Cytoplasm

Cytosol Inclusions

Proteasome

External

Undulipodium

Cilium Flagellum Axoneme Radial spoke

Extracellular matrix

Cell wall

v t e

Protein
Protein
biosynthesis: translation (bacterial, archaeal, eukaryotic)

Proteins

Initiation factor

Bacterial

PIF-1 PIF-2 PIF-3

Archaeal

aIF1 aIF2 aIF5 aIF6

Eukaryotic

eIF1

eIF1 EIF1AX AY 1B

eIF2

EIF2S1 EIF2S2 EIF2S3 EIF2B1 EIF2B2 EIF2B3 EIF2B4 EIF2B5 EIF-2 kinase eIF2A eIF2D

eIF3

EIF3A B C D E F G H I J K L M

eIF4

EIF4A2 A3 B E1 E2 E3 G1 G2 G3 H

eIF5

EIF5 EIF5A A2 5B

eIF6

EIF6

Elongation factor

Bacterial

EF-Tu EF-Ts EF-G

Archaeal

aEF-1 aEF-2

Eukaryotic

EEF-1

EEF1A1 EEF1A2 EEF1A3 EEF1B1 EEF1B2 EEF1B3 EEF1B4 EEF1D EEF1E1 EEF1G

EEF2

Release factor

Bacterial Archaeal Eukaryotic (ETF1)

Ribosomal Proteins

Cytoplasmic

60S
60S
subunit

RPL3 RPL4 RPL5 RPL6 RPL7 RPL7A RPL8 RPL9 RPL10 RPL10A RPL10-like RPL11 RPL12 RPL13 RPL13A RPL14 RPL15 RPL17 RPL18 RPL18A RPL19 RPL21 RPL22 RPL23 RPL23A RPL24 RPL26 RPL27 RPL27A RPL28 RPL29 RPL30 RPL31 RPL32 RPL34 RPL35 RPL35A RPL36 RPL36A RPL37 RPL37A RPL38 RPL39 RPL40 RPL41 RPLP0 RPLP1 RPLP2 RRP15-like RSL24D1

40S
40S
subunit

RPSA RPS2 RPS3 RPS3A RPS4 (RPS4X, RPS4Y1, RPS4Y2) RPS5 RPS6 RPS7 RPS8 RPS9 RPS10 RPS11 RPS12 RPS13 RPS14 RPS15 RPS15A RPS16 RPS17 RPS18 RPS19 RPS20 RPS21 RPS23 RPS24 RPS25 RPS26 RPS27 RPS27A RPS28 RPS29 RPS30 RACK1

Mitochondrial

39S subunit

MRPL1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42

28S subunit

MRPS1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35

Other concepts

Aminoacyl t RNA
RNA
synthetase Reading frame Start codon Stop codon Shine-Dalgarno sequence/Kozak consensus sequence

v t e

Ribosomal RNA
Ribosomal RNA
/ ribosome subunits

Archaea

Large:

Small:

Bacteria
Bacteria
(70S)

Large: 50S 5S 23S

Small: 30S 16S

Eukaryotes (80S)

Cytoplasmic

Large: 60S 5S 5.8S 28S

Small: 40S 18S

Mitochondrial

Large: MT-RNR2, 16S

Small: MT-RNR1, 12S

Chloroplast

Large chloroplast subunit

Small chloroplast subunit

 This article incorporates public domain material from the NCBI document "Science Primer".

Authority control

GND: 41277

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