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Ribosomes ( ), also called Palade granules, are macromolecular machines, found within all
cells Cell most often refers to: * Cell (biology), the functional basic unit of life Cell may also refer to: Closed spaces * Monastic cell, a small room, hut, or cave in which a monk or religious recluse lives * Prison cell, a room used to hold peopl ...
, that perform
biological protein synthesis
biological protein synthesis
(mRNA translation). Ribosomes link
amino acids Amino acids are organic compound In , organic compounds are generally any s that contain - . Due to carbon's ability to (form chains with other carbon s), millions of organic compounds are known. The study of the properties, reactions, a ...

amino acids
together in the order specified by the
codon The genetic code is the set of rules used by living cells Cell most often refers to: * Cell (biology), the functional basic unit of life Cell may also refer to: Closed spaces * Monastic cell, a small room, hut, or cave in which a monk or rel ...

codon
s of
messenger RNA In molecular biology, messenger ribonucleic acid (mRNA) is a single-stranded molecule of RNA that corresponds to the genetic sequence of a gene, and is read by a ribosome in the process of Protein biosynthesis, synthesizing a protein. mRNA i ...
(mRNA) molecules to form
polypeptide Peptides (from Greek language Greek ( el, label=Modern Greek Modern Greek (, , or , ''Kiní Neoellinikí Glóssa''), generally referred to by speakers simply as Greek (, ), refers collectively to the dialects of the Greek language spoken ...
chains. Ribosomes consist of two major components: the small and large ribosomal subunits. Each subunit consists of one or more ribosomal RNA (rRNA) molecules and many
ribosomal protein A ribosomal protein (r-protein or rProtein) is any of the proteins that, in conjunction with Ribosomal RNA, rRNA, make up the Ribosome, ribosomal subunits involved in the cellular process of translation (genetics), translation. ''E. coli'', other ...
s (RPs or r-proteins). The ribosomes and associated molecules are also known as the ''translational apparatus''.


Overview

The sequence of
DNA Deoxyribonucleic acid (; DNA) is a molecule A scanning tunneling microscopy image of pentacene molecules, which consist of linear chains of five carbon rings. A molecule is an electrically Electricity is the set of physical ...

DNA
that encodes the sequence of the amino acids in a protein is transcribed into a messenger RNA chain. Ribosomes bind to messenger RNAs and use their sequences for determining the correct sequence of amino acids to generate a given protein. Amino acids are selected and carried to the ribosome by transfer RNA (tRNA) molecules, which enter the ribosome and bind to the messenger RNA chain via an anti-codon stem loop. For each coding triplet (
codon The genetic code is the set of rules used by living cells Cell most often refers to: * Cell (biology), the functional basic unit of life Cell may also refer to: Closed spaces * Monastic cell, a small room, hut, or cave in which a monk or rel ...

codon
) in the messenger RNA, there is a unique transfer RNA that must have the exact anti-codon match, and carries the correct amino acid for incorporating into a growing
polypeptide Peptides (from Greek language Greek ( el, label=Modern Greek Modern Greek (, , or , ''Kiní Neoellinikí Glóssa''), generally referred to by speakers simply as Greek (, ), refers collectively to the dialects of the Greek language spoken ...
chain. Once the protein is produced, it can then
fold Fold or folding may refer to: Arts, entertainment, and media *Fold (album), ''Fold'' (album), the debut release by Australian rock band Epicure *Fold (poker), in the game of poker, to discard one's hand and forfeit interest in the current pot *Ab ...

fold
to produce a functional three-dimensional structure. A ribosome is made from complexes of RNAs and proteins and is therefore a ribonucleoprotein complex. Each ribosome is composed of small (30 S) and large (50 S) components, called subunits, which are bound to each other: # (30S) has mainly a decoding function and is also bound to the mRNA # (50S) has mainly a catalytic function and is also bound to the aminoacylated tRNAs. The synthesis of proteins from their building blocks takes place in four phases: initiation, elongation, termination, and recycling. The start codon in all mRNA molecules has the sequence AUG. The stop codon is one of UAA, UAG, or UGA; since there are no tRNA molecules that recognize these codons, the ribosome recognizes that translation is complete. When a ribosome finishes reading an mRNA molecule, the two subunits separate and are usually broken up but can be re-used. Ribosomes are
ribozyme Ribozymes (ribonucleic acid enzymes) are RNA Ribonucleic acid (RNA) is a polymer A polymer (; Greek ''wikt:poly-, poly-'', "many" + ''wikt:-mer, -mer'', "part") is a Chemical substance, substance or material consisting of very large m ...

ribozyme
s, because the
catalytic that utilizes a low-temperature oxidation catalyst to convert carbon monoxide to less toxic carbon dioxide Carbon dioxide (chemical formula ) is a colorless gas with a density about 53% higher than that of dry air. Carbon dioxide molecules ...

catalytic
peptidyl transferase The peptidyl transferase is an aminoacyltransferase () as well as the primary enzymatic Enzymes () are protein Proteins are large biomolecules or macromolecules that are comprised of one or more long chains of amino acid residue (biochem ...
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 The endoplasmic reticulum (ER) is, in essence, the transportation system of the eukaryotic cell, and has many other important functions such as protein folding. It is a type of organelle In cell biology Cell biology (also cellular biology o ...
. Ribosomes from
bacteria Bacteria (; common noun bacteria, singular bacterium) are ubiquitous, mostly free-living organisms often consisting of one Cell (biology), biological cell. They constitute a large domain (biology), domain of prokaryotic microorganisms. Typ ...

bacteria
,
archaea Archaea ( ; singular archaeon ) constitute a domain Domain may refer to: Mathematics *Domain of a function, the set of input values for which the (total) function is defined **Domain of definition of a partial function **Natural domain of a pa ...

archaea
and
eukaryote Eukaryotes () are organism In biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular interact ...

eukaryote
s in the
three-domain system The three-domain system is a biological classification In biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, ...
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
antibiotic An antibiotic is a type of antimicrobial An antimicrobial is an agent that kills microorganism A microorganism, or microbe,, ''mikros'', "small") and ''organism In biology, an organism () is any organic, life, living system t ...
s to kill bacteria by inhibiting their ribosomes, while leaving human ribosomes unaffected. In all species, more than one ribosome may move along a single mRNA chain at one time (as a
polysome A polyribosome (or polysome or ergosome) is a group of ribosomes bound to an mRNA molecule like “beads” on a “thread”. It consists of a complex of an mRNA molecule and two or more ribosome Ribosomes ( ), also called Palade granules, are ...
), each "reading" a specific sequence and producing a corresponding protein molecule. The
mitochondrial ribosome The mitochondrial ribosome, or mitoribosome, is a protein complex A protein complex or multiprotein complex is a group of two or more associated polypeptide chain Peptides (from Greek language Greek (modern , romanized: ''Elliniká'', Anci ...
s of eukaryotic cells 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
Romanian-American Romanian Americans are Americans who have Romanians, Romanian ancestry. According to the 2017 American Community Survey, 478,278 Americans indicated Romanian as their first or second ancestry. Other sources provide higher estimates for the numbe ...
cell biologist
George Emil Palade George Emil Palade (; November 19, 1912 – October 7, 2008) was a Romanian-United States, American cell biology, cell biologist. Described as "the most influential cell biologist ever",electron microscope An electron microscope is a microscope that uses a beam of accelerated electrons as a source of illumination. As the wavelength of an electron can be up to 100,000 times shorter than that of visible light photons, electron microscopes have a high ...

electron microscope
, as dense particles or granules. The term "ribosome" was proposed by scientist Haguenau in the end of 1958:
Albert Claude Albert Claude (24 August 1899 – 22 May 1983) was a Belgian Belgian may refer to: * Something of, or related to, Belgium Belgium, ; french: Belgique ; german: Belgien officially the Kingdom of Belgium, is a country in Western Europe ...
,
Christian de Duve Christian René Marie Joseph, Viscount de Duve (2 October 1917 – 4 May 2013) was a Nobel Prize-winning Belgian cytologist Cell biology (also cellular biology or cytology) is a branch of biology studying the Structural biology, structure an ...
, and
George Emil Palade George Emil Palade (; November 19, 1912 – October 7, 2008) was a Romanian-United States, American cell biology, cell biologist. Described as "the most influential cell biologist ever",Nobel Prize in Physiology or Medicine The Nobel Prize in Physiology or Medicine is awarded yearly by the Nobel Assembly , native_name_lang = , image = Nobel Assembly at Karolinska Institutet.jpeg , size = , motto = , formation = 190113 March 1978(as a forma ...
, in 1974, for the discovery of the ribosome. The
Nobel Prize The Nobel Prizes ( ; sv, Nobelpriset ; no, Nobelprisen ) are five separate prizes that, according to Alfred Nobel Alfred Bernhard Nobel ( , ; 21 October 1833 – 10 December 1896) was a Swedish chemist, engineer, inventor, busines ...
in
Chemistry Chemistry is the scientific Science () is a systematic enterprise that builds and organizes knowledge Knowledge is a familiarity or awareness, of someone or something, such as facts A fact is an occurrence in the real world. T ...

Chemistry
2009 was awarded to
Venkatraman Ramakrishnan Venkatraman Ramakrishnan (born 1952) is an India India, officially the Republic of India (Hindi Hindi (Devanagari: , हिंदी, ISO 15919, ISO: ), or more precisely Modern Standard Hindi (Devanagari: , ISO 15919, ISO: ), ...
,
Thomas A. Steitz
Thomas A. Steitz
and
Ada E. Yonath
Ada E. Yonath
for determining the detailed structure and mechanism of the ribosome.


Structure

The ribosome is a complex cellular machine. It is largely made up of specialized RNA known as
ribosomal RNA Ribosomal ribonucleic acid (rRNA) is a type of non-coding RNA A non-coding RNA (ncRNA) is an RNA Ribonucleic acid (RNA) is a polymer A polymer (; Greek '' poly-'', "many" + '' -mer'', "part") is a substance or material consis ...
(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 sizes, 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

Bacterial ribosomes are around 20  nm (200 
Å
Å
) in diameter and are composed of 65% rRNA and 35%
ribosomal protein A ribosomal protein (r-protein or rProtein) is any of the proteins that, in conjunction with Ribosomal RNA, rRNA, make up the Ribosome, ribosomal subunits involved in the cellular process of translation (genetics), translation. ''E. coli'', other ...
s. Eukaryotic ribosomes are between 25 and 30 nm (250–300 Å) in diameter with an rRNA-to-protein ratio that is close to 1.
Crystallographic Crystallography is the experimental science of determining the arrangement of atoms in crystalline solids (see crystal structure). The word "crystallography" is derived from the Greek words ''crystallon'' "cold drop, frozen drop", with its mean ...

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 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:
Ribozyme Ribozymes (ribonucleic acid enzymes) are RNA Ribonucleic acid (RNA) is a polymer A polymer (; Greek ''wikt:poly-, poly-'', "many" + ''wikt:-mer, -mer'', "part") is a Chemical substance, substance or material consisting of very large m ...

Ribozyme
). The ribosomal subunits of
bacteria Bacteria (; common noun bacteria, singular bacterium) are ubiquitous, mostly free-living organisms often consisting of one Cell (biology), biological cell. They constitute a large domain (biology), domain of prokaryotic microorganisms. Typ ...

bacteria
and eukaryotes are quite similar. The unit of measurement used to describe the ribosomal subunits and the rRNA fragments is the
Svedberg A Svedberg unit (symbol S, sometimes Sv) is a non- SI metric unit for sedimentation coefficientThe sedimentation coefficient ''(s)'' of a particle characterizes its sedimentation during centrifugation. It is defined as the ratio of a particle's s ...
unit, a measure of the rate of
sedimentation Sedimentation is the deposition of sediments Sediment is a naturally occurring material that is broken down by processes of weathering Weathering is the deterioration of rocks In geology Geology (from the Ancient Greek γ ...
in
centrifugation Centrifugation is a mechanical process which involves the use of the centrifugal force In Newtonian mechanics, the centrifugal force is an inertial force (also called a "fictitious" or "pseudo" force) that appears to act on all objects when v ...
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 S ribosomes, each consisting of a small (
30S The prokaryotic small ribosomal subunit, or 30 S subunit, is the smaller subunit of the 70S ribosome Ribosomes ( ), also called Palade granules, are macromolecular machines, found within all cells Cell most often refers to: * Cell (biol ...
) and a large (
50S 50 S is the larger subunit of the 70S Significant people * Titus Flavius Vespasianus, Roman Emperor The Roman emperor was the ruler of the Roman Empire during the imperial period (starting in 27 BC). The emperors used a variety of d ...
) subunit. ''E. coli'', for example, has a 16S RNA subunit (consisting of 1540 nucleotides) that is bound to 21 proteins. The large subunit is composed of a 5S RNA subunit (120 nucleotides), a 23S RNA subunit (2900 nucleotides) and 31
protein Proteins are large biomolecule , showing alpha helices, represented by ribbons. This poten was the first to have its suckture solved by X-ray crystallography by Max Perutz and Sir John Cowdery Kendrew in 1958, for which they received a No ...

protein
s. : 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.


Archaeal ribosomes

Archaeal ribosomes share the same general dimensions of bacteria ones, being a 70S ribosome made up from a 50S large subunit, a 30S small subunit, and containing three rRNA chains. However, on the sequence level, they are much closer to eukaryotic ones than to bacterial ones. Every extra ribosomal protein archaea have compared to bacteria has a eukaryotic counterpart, while no such relation applies between archaea and bacteria.


Eukaryotic ribosomes

Eukaryotes have 80S ribosomes located in their cytosol, each consisting of a small (40S) and large (60S) subunit. Their 40S subunit has an 18S RNA (1900 nucleotides) and 33 proteins. The large subunit is composed of a 5S RNA (120 nucleotides), 28S RNA (4700 nucleotides), a 5.8S RNA (160 nucleotides) subunits and 46 proteins. : 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 The peptidyl transferase is an aminoacyltransferase () as well as the primary enzymatic Enzymes () are protein Proteins are large biomolecules or macromolecules that are comprised of one or more long chains of amino acid residue (biochem ...
center.


Plastoribosomes and mitoribosomes

In eukaryotes, ribosomes are present in
mitochondria A mitochondrion (; ) is a double-membrane A membrane is a selective barrier; it allows some things to pass through but stops others. Such things may be molecules, ions, or other small particles. Biological membranes include cell membranes ...

mitochondria
(sometimes called mitoribosomes) and in
plastid The plastid (Greek: πλαστός; plastós: formed, molded – plural plastids) is a membrane-bound organelle In cell biology, an organelle is a specialized subunit, usually within a cell (biology), cell, that has a specific function. The name ' ...
s such as
chloroplast A chloroplast is a type of membrane-bound organelle In cell biology, an organelle is a specialized subunit, usually within a cell (biology), cell, that has a specific function. The name ''organelle'' comes from the idea that these structure ...

chloroplast
s (also called plastoribosomes). They also consist of large and small subunits bound together with
protein Proteins are large biomolecule , showing alpha helices, represented by ribbons. This poten was the first to have its suckture solved by X-ray crystallography by Max Perutz and Sir John Cowdery Kendrew in 1958, for which they received a No ...

protein
s into one 70S particle. These ribosomes are similar to those of bacteria and these organelles are thought to have originated as
symbiotic Symbiosis (from Ancient Greek, Greek , , "living together", from , , "together", and , bíōsis, "living") is any type of a close and long-term biological interaction between two different Organism, biological organisms, be it Mutualism (biolog ...

symbiotic
bacteria Bacteria (; common noun bacteria, singular bacterium) are ubiquitous, mostly free-living organisms often consisting of one Cell (biology), biological cell. They constitute a large domain (biology), domain of prokaryotic microorganisms. Typ ...

bacteria
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 5S rRNA, replaced by other structures in animals and fungi. In particular, ''
Leishmania ''Leishmania'' is a genus Genus /ˈdʒiː.nəs/ (plural genera /ˈdʒen.ər.ə/) is a taxonomic rank used in the biological classification of extant taxon, living and fossil organisms as well as Virus classification#ICTV classification, viru ...
tarentolae'' has a minimalized set of mitochondrial rRNA. In contrast, plant mitoribosomes have both extended rRNA and additional proteins as compared to bacteria, in particular, many pentatricopetide repeat proteins. The
cryptomonad The cryptomonads (or cryptophytes) are a group of algae, most of which have plastids. They are common in freshwater, and also occur in marine and brackish habitats. Each cell is around 10–50 μm in size and flattened in shape, with an anterio ...
and
chlorarachniophyte The chlorarachniophytes are a small group of exclusively marine alga Algae (; singular alga ) is an informal term for a large and diverse group of photosynthesis, photosynthetic eukaryotic organisms. It is a polyphyletic grouping that includes ...
algae may contain a
nucleomorph Nucleomorphs are small, vestigial eukaryotic nuclei found between the inner and outer pairs of membranes in certain plastid The plastid (Greek: πλαστός; plastós: formed, molded – plural plastids) is a membrane-bound organelle found in th ...
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 pharmaceutical chemists to create
antibiotic An antibiotic is a type of antimicrobial An antimicrobial is an agent that kills microorganism A microorganism, or microbe,, ''mikros'', "small") and ''organism In biology, an organism () is any organic, life, living system t ...
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
mitochondria A mitochondrion (; ) is a double-membrane A membrane is a selective barrier; it allows some things to pass through but stops others. Such things may be molecules, ions, or other small particles. Biological membranes include cell membranes ...

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 In cell biology Cell biology (also cellular biology or cytology) is a branch of biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, ...
. A noteworthy counterexample, however, includes the antineoplastic antibiotic
chloramphenicol Chloramphenicol is an antibiotic An antibiotic is a type of antimicrobial substance active against bacteria. It is the most important type of antibacterial agent for fighting pathogenic bacteria, bacterial infections, and antibiotic medicat ...

chloramphenicol
, which successfully inhibits bacterial 50S and eukaryotic mitochondrial 50S ribosomes. The same of mitochondria 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 tertiary structural motifs, for example
pseudoknot __NOTOC__ A pseudoknot is a nucleic acid secondary structure containing at least two stem-loop structures in which half of one stem is intercalated between the two halves of another stem. The pseudoknot was first recognized in the Turnip yellow m ...

pseudoknot
s that exhibit coaxial stacking. The extra
RNA Ribonucleic acid (RNA) is a polymer A polymer (; Greek ''wikt:poly-, poly-'', "many" + ''wikt:-mer, -mer'', "part") is a Chemical substance, substance or material consisting of very large molecules, or macromolecules, composed of many Re ...

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 Ribonucleic acid (RNA) is a polymer A polymer (; Greek ''wikt:poly-, poly-'', "many" + ''wikt:-mer, -mer'', "part") is a Chemical substance, substance or material consisting of very large molecules, or macromolecules, composed of many Re ...

RNA
; 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
ångström The angstromEntry "angstrom" in the Oxford online dictionary. Retrieved on 2019-03-02 from https://en.oxforddictionaries.com/definition/angstrom.Entry "angstrom" in the Merriam-Webster online dictionary. Retrieved on 2019-03-02 from https://www.me ...

ångström
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
archaeon Archaea ( ; singular archaeon ) constitute a domain Domain may refer to: Mathematics *Domain of a function, the set of input values for which the (total) function is defined **Domain of definition of a partial function **Natural domain of a pa ...

archaeon
''Haloarcula marismortui'' and the bacterium ''
Deinococcus radiodurans ''Deinococcus radiodurans'' is an extremophilic bacterium Bacteria (; common noun bacteria, singular bacterium) are a type of Cell (biology), biological cell. They constitute a large domain (biology), domain of prokaryotic microorganisms ...

Deinococcus radiodurans
'', and the structure of the 30S subunit was determined from '' Thermus thermophilus''. These structural studies were awarded the Nobel Prize in Chemistry in 2009. In May 2001 these coordinates were used to reconstruct the entire '' T. thermophilus'' 70S particle at 5.5  resolution. Two papers were published in November 2005 with structures of the ''
Escherichia coli ''Escherichia coli'' (),Wells, J. C. (2000) Longman Pronunciation Dictionary. Harlow ngland Pearson Education Ltd. also known as ''E. coli'' (), is a Gram-negative bacteria, Gram-negative, Facultative anaerobic organism, facultative anaer ...

Escherichia coli
'' 70S ribosome. The structures of a vacant ribosome were determined at 3.5  resolution using
X-ray crystallography X-ray crystallography is the experimental science determining the atomic and molecular structure of a crystal, in which the crystalline structure causes a beam of incident X-rays to Diffraction, diffract into many specific directions. By measurin ...

X-ray crystallography
. Then, two weeks later, a structure based on cryo-
electron microscopy An electron microscope is a microscope that uses a beam of accelerated electrons as a source of illumination. As the wavelength of an electron can be up to 100,000 times shorter than that of visible light photons, electron microscopes have a hig ...

electron microscopy
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
tRNA Transfer RNA (abbreviated tRNA and formerly referred to as sRNA, for soluble RNA) is an adaptor molecule A scanning tunneling microscopy image of pentacene molecules, which consist of linear chains of five carbon rings. A molecule is an e ...

tRNA
and
mRNA In molecular biology, messenger ribonucleic acid (mRNA) is a single-stranded molecule of RNA that corresponds to the genetic sequence of a gene, and is read by a ribosome in the process of Protein biosynthesis, synthesizing a protein. mRNA i ...

mRNA
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 '' Thermus thermophilus'' ribosome with
mRNA In molecular biology, messenger ribonucleic acid (mRNA) is a single-stranded molecule of RNA that corresponds to the genetic sequence of a gene, and is read by a ribosome in the process of Protein biosynthesis, synthesizing a protein. mRNA i ...

mRNA
and with
tRNA Transfer RNA (abbreviated tRNA and formerly referred to as sRNA, for soluble RNA) is an adaptor molecule A scanning tunneling microscopy image of pentacene molecules, which consist of linear chains of five carbon rings. A molecule is an e ...

tRNA
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 ''
Saccharomyces cerevisiae ''Saccharomyces cerevisiae'' () is a species of yeast Yeasts are eukaryotic Eukaryotes () are organism In biology, an organism () is any organic, life, living system that functions as an individual entity. All organisms are ...

Saccharomyces cerevisiae
'' 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 ''
Tetrahymena thermophila ''Tetrahymena'', a unicellular A unicellular organism, also known as a single-celled organism, is an organism In biology, an organism (from Ancient Greek, Greek: ὀργανισμός, ''organismos'') is any individual contiguous system t ...

Tetrahymena thermophila
'' was published and described the structure of the 40S subunit, as well as much about the 40S subunit's interaction with
eIF1 Eukaryotic translation initiation factor 1 (eIF1) is a protein Proteins are large biomolecule , showing alpha helices, represented by ribbons. This poten was the first to have its suckture solved by X-ray crystallography by Max Perutz and ...
during . Similarly, the eukaryotic 60S subunit structure was also determined from ''
Tetrahymena thermophila ''Tetrahymena'', a unicellular A unicellular organism, also known as a single-celled organism, is an organism In biology, an organism (from Ancient Greek, Greek: ὀργανισμός, ''organismos'') is any individual contiguous system t ...

Tetrahymena thermophila
'' in complex with
eIF6 Eukaryotic translation initiation factor 6 (EIF6), also known as Integrin beta 4 binding protein (ITGB4BP), is a human gene In biology, a gene (from ''genos'' "...Wilhelm Johannsen coined the word gene to describe the Mendelian_inheritance# ...
.


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
endoplasmic reticulum The endoplasmic reticulum (ER) is, in essence, the transportation system of the eukaryotic cell, and has many other important functions such as protein folding. It is a type of organelle made up of two subunits – rough endoplasmic reticulum ( ...
. 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
protein biosynthesis Protein biosynthesis (or protein synthesis) is a core biological process, occurring inside cells Cell most often refers to: * Cell (biology), the functional basic unit of life Cell may also refer to: Closed spaces * Monastic cell, a small ro ...
, the process of translating
mRNA In molecular biology, messenger ribonucleic acid (mRNA) is a single-stranded molecule of RNA that corresponds to the genetic sequence of a gene, and is read by a ribosome in the process of Protein biosynthesis, synthesizing a protein. mRNA i ...

mRNA
into
protein Proteins are large biomolecule , showing alpha helices, represented by ribbons. This poten was the first to have its suckture solved by X-ray crystallography by Max Perutz and Sir John Cowdery Kendrew in 1958, for which they received a No ...

protein
. The mRNA comprises a series of
codon The genetic code is the set of rules used by living cells Cell most often refers to: * Cell (biology), the functional basic unit of life Cell may also refer to: Closed spaces * Monastic cell, a small room, hut, or cave in which a monk or rel ...

codon
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
nucleotide Nucleotides are organic molecules , CH4; is among the simplest organic compounds. In chemistry, organic compounds are generally any chemical compounds that contain carbon-hydrogen chemical bond, bonds. Due to carbon's ability to Catenation, ...

nucleotide
s) of the mRNA, pairing it with the appropriate amino acid provided by an
aminoacyl-tRNA Aminoacyl-tRNA (also aa-tRNA or charged tRNA) is tRNA Transfer RNA (abbreviated tRNA and formerly referred to as sRNA, for soluble RNA) is an adaptor molecule A scanning tunneling microscopy image of pentacene molecules, which consist of ...

aminoacyl-tRNA
. Aminoacyl-tRNA contains a complementary
anticodon Transfer RNA (abbreviated tRNA and formerly referred to as sRNA, for soluble RNA) is an adaptor molecule A molecule is an electrically Electricity is the set of physical phenomena associated with the presence and motion Image:Le ...
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 proofreadingConformational proofreading or conformational selection is a general mechanism of molecular recognition systems in which introducing a structural mismatch between a molecular recognizer and its target, or an energetic barrier, enhances the recogniti ...
). The small ribosomal subunit, typically bound to an aminoacyl-tRNA containing the first amino acid
methionine Methionine (symbol Met or M) () is an essential amino acid An essential amino acid, or indispensable amino acid, is an amino acid that cannot be synthesized from scratch by the organism fast enough to supply its demand, and must therefore come ...

methionine
, 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
A-site The A-site (A for aminoacyl) of a ribosome Ribosomes ( ), also called Palade granules, are macromolecular machines, found within all cells Cell most often refers to: * Cell (biology), the functional basic unit of life Cell may also refer t ...
binds an aminoacyl-tRNA or termination release factors; the
P-site The P-site (for peptidyl) is the second binding site Binding may refer to: Computing * Binding, associating a network socket with a local port number and IP address * Data binding, the technique of connecting two data elements together ** UI dat ...
binds a peptidyl-tRNA (a tRNA bound to the poly-peptide chain); and the
E-site The E-site is the third and final binding site Binding may refer to: Computing * Binding, associating a network socket with a local port number and IP address * Data binding, the technique of connecting two data elements together ** UI data bindin ...
(exit) binds a free tRNA. Protein synthesis begins at a
start codon The start codon is the first codon The genetic code is the set of rules used by living cells Cell most often refers to: * Cell (biology), the functional basic unit of life Cell may also refer to: Closed spaces * Monastic cell, a small room, ...
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
peptide bond In organic chemistry Organic chemistry is a branch of chemistry Chemistry is the study of the properties and behavior of . It is a that covers the that make up matter to the composed of s, s and s: their composition, structure, pro ...

peptide bond
involves the C2
hydroxyl A hydroxy or hydroxyl group is a functional group with the chemical formula -OH and composed of one oxygen Oxygen is the chemical element Image:Simple Periodic Table Chart-blocks.svg, 400px, Periodic table, The periodic table of the ...

hydroxyl
of RNA's P-site
adenosine Adenosine is an organic compound , CH4; is among the simplest organic compounds. In chemistry, organic compounds are generally any chemical compounds that contain carbon-hydrogen chemical bond, bonds. Due to carbon's ability to Catenation, cate ...

adenosine
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 "
ribozyme Ribozymes (ribonucleic acid enzymes) are RNA Ribonucleic acid (RNA) is a polymer A polymer (; Greek ''wikt:poly-, poly-'', "many" + ''wikt:-mer, -mer'', "part") is a Chemical substance, substance or material consisting of very large m ...

ribozyme
s," and it is thought that they might be remnants of the
RNA world The RNA world is a hypothetical stage in the evolutionary history of life The history of life on Earth Earth is the third planet from the Sun and the only astronomical object known to harbour and support life. 29.2% of Earth's surfa ...
. In Figure 5, both ribosomal subunits (small and large) assemble at the start codon (towards the 5' end of the
mRNA In molecular biology, messenger ribonucleic acid (mRNA) is a single-stranded molecule of RNA that corresponds to the genetic sequence of a gene, and is read by a ribosome in the process of Protein biosynthesis, synthesizing a protein. mRNA i ...
). The ribosome uses
tRNA Transfer RNA (abbreviated tRNA and formerly referred to as sRNA, for soluble RNA) is an adaptor molecule A scanning tunneling microscopy image of pentacene molecules, which consist of linear chains of five carbon rings. A molecule is an e ...
that matches the current codon (triplet) on the mRNA to append an
amino acid Amino acids are organic compound In , organic compounds are generally any s that contain - . Due to carbon's ability to (form chains with other carbon s), millions of organic compounds are known. The study of the properties, reactions, a ...

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 A polyribosome (or polysome or ergosome) is a group of ribosomes bound to an mRNA molecule like “beads” on a “thread”. It consists of a complex of an mRNA molecule and two or more ribosome Ribosomes ( ), also called Palade granules, are ...
''.


Cotranslational folding

The ribosome is known to actively participate in the
protein folding Protein folding is the physical process Physical changes are changes affecting the form of a chemical substance A chemical substance is a form of matter In classical physics and general chemistry, matter is any substance that has mass ...

protein folding
. 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 knotted proteins 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 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
organelle In cell biology Cell biology (also cellular biology or cytology) is a branch of biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, ...
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
cytosol The cytosol, also known as cytoplasmic matrix or groundplasm, is one of the liquids found inside cells Cell most often refers to: * Cell (biology), the functional basic unit of life Cell may also refer to: Closed spaces * Monastic cell, a s ...
, but are excluded from the
cell nucleus In cell biology, the nucleus (pl. ''nuclei''; from Latin or , meaning ''kernel'' or ''seed'') is a biological membrane#Function, membrane-bound organelle found in eukaryote, eukaryotic cell (biology), cells. Eukaryotes usually have a single n ...

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 Glutathione (GSH) is an antioxidant Antioxidants are that inhibit , a that can produce and s that may damage the of organisms. Antioxidants such as s or (vitamin C) may act to inhibit these reactions. To balance , plants and animals ma ...

glutathione
and is, therefore, a , proteins containing
disulfide bonds In chemistry Chemistry is the scientific discipline involved with Chemical element, elements and chemical compound, compounds composed of atoms, molecules and ions: their composition, structure, properties, behavior and the changes they underg ...

disulfide bonds
, 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 vectorial synthesis and are then transported to their destinations, through the
secretory pathway Secretion is the movement of material from one point to another, such as a secreted chemical substance A chemical substance is a form of matter In classical physics and general chemistry, matter is any substance that has mass and takes up sp ...
. Bound ribosomes usually produce proteins that are used within the plasma membrane or are expelled from the cell via ''
exocytosis Exocytosis () is a form of active transport In cellular biology Cell biology (also cellular biology or cytology) is a branch of biology Biology is the natural science that studies life and living organisms, including their anatomy, phys ...
''.


Biogenesis

In bacterial cells, ribosomes are synthesized in the cytoplasm through the transcription of multiple ribosome gene
operon In genetics Genetics is a branch of biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular interactions ...

operon
s. In eukaryotes, the process takes place both in the cell cytoplasm and in the
nucleolus The nucleolus (, plural: nucleoli ) is the largest structure in the nucleus ''Nucleus'' (plural nuclei) is a Latin word for the seed inside a fruit. It most often refers to: *Atomic nucleus, the very dense central region of an atom *Cell nuc ...

nucleolus
, which is a region within the
cell nucleus In cell biology, the nucleus (pl. ''nuclei''; from Latin or , meaning ''kernel'' or ''seed'') is a biological membrane#Function, membrane-bound organelle found in eukaryote, eukaryotic cell (biology), cells. Eukaryotes usually have a single n ...

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

The ribosome may have first originated in an
RNA world The RNA world is a hypothetical stage in the evolutionary history of life The history of life on Earth Earth is the third planet from the Sun and the only astronomical object known to harbour and support life. 29.2% of Earth's surfa ...
, appearing as a self-replicating complex that only later evolved the ability to synthesize proteins when
amino acid Amino acids are organic compound In , organic compounds are generally any s that contain - . Due to carbon's ability to (form chains with other carbon s), millions of organic compounds are known. The study of the properties, reactions, a ...

amino acid
s began to appear. Studies suggest that ancient ribosomes constructed solely of
rRNA Ribosomal ribonucleic acid (rRNA) is a type of non-coding RNA A non-coding RNA (ncRNA) is an RNA Ribonucleic acid (RNA) is a polymer A polymer (; Greek '' poly-'', "many" + '' -mer'', "part") is a substance or material consis ...
could have developed the ability to synthesize
peptide bond In organic chemistry Organic chemistry is a branch of chemistry Chemistry is the study of the properties and behavior of . It is a that covers the that make up matter to the composed of s, s and s: their composition, structure, pro ...

peptide bond
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
tRNAs A transfer RNA (abbreviated tRNA and formerly referred to as sRNA, for soluble RNA) is an adaptor molecule composed of RNA, typically 76 to 90 nucleotides in length (in eukaryotes), that serves as the physical link between the Messenger RNA, mRNA ...
and proteins needed for ribosomal self-replication. Hypothetical cellular organisms with self-replicating RNA but without DNA are called ribocytes (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 A self-replicating machine is a type of autonomous robot An autonomous robot, also known as simply an autorobot or autobot, is a robot A robot is a machine—especially one programmable by a computer A computer is a machine that can ...

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.


Heterogeneous ribosomes

Ribosomes are compositionally heterogeneous between species and even within the same cell, as evidenced by the existence of cytoplasmic and mitochondria ribosomes within the same eukaryotic cells. Certain researchers have suggested that heterogeneity in the composition of ribosomal proteins in mammals is important for gene regulation, ''i.e.'', the specialized ribosome hypothesis. However, this hypothesis is controversial and the topic of ongoing research. Heterogeneity in ribosome composition was first proposed to be involved in translational control of protein synthesis by Vince Mauro and
Gerald Edelman Gerald Maurice Edelman (; July 1, 1929 – May 17, 2014) was an American biologist who shared the 1972 Nobel Prize in Physiology or Medicine for work with Rodney Robert Porter on the immune system. Edelman's Nobel Prize-winning research concerne ...
. They proposed the ribosome filter hypothesis to explain the regulatory functions of ribosomes. Evidence has suggested that specialized ribosomes specific to different cell populations may affect how genes are translated. Some ribosomal proteins exchange from the assembled complex with
cytosol The cytosol, also known as cytoplasmic matrix or groundplasm, is one of the liquids found inside cells Cell most often refers to: * Cell (biology), the functional basic unit of life Cell may also refer to: Closed spaces * Monastic cell, a s ...
ic copies suggesting that the structure of the ''in vivo'' ribosome can be modified without synthesizing an entire new ribosome. Certain ribosomal proteins are absolutely critical for cellular life while others are not. In
budding yeast ''Saccharomyces cerevisiae'' () is a species of yeast Yeasts are eukaryotic Eukaryotes () are organism In biology, an organism () is any organic, life, living system that functions as an individual entity. All organisms are ...

budding yeast
, 14/78 ribosomal proteins are non-essential for growth, while in humans this depends on the cell of study. Other forms of heterogeneity include post-translational modifications to ribosomal proteins such as acetylation, methylation, and phosphorylation. ''Arabidopsis'', Viral internal ribosome entry sites (IRESs) may mediate translations by compositionally distinct ribosomes. For example, 40S ribosomal units without in yeast and mammalian cells are unable to recruit the CrPV IGR IRES. Heterogeneity of ribosomal RNA modifications plays an important role in structural maintenance and/or function and most mRNA modifications are found in highly conserved regions. The most common rRNA modifications are Pseudouridine, pseudouridylation and 2'-O-methylation, 2’-O methylation of ribose.


See also

* Aminoglycosides * Molecular machine#Biological, Biological machines * Posttranslational modification * Protein dynamics * RNA tertiary structure * Translation (genetics) * Wobble base pair * Ada Yonath—Israeli crystallographer known for her pioneering work on the structure of the ribosome, for which she won the
Nobel Prize The Nobel Prizes ( ; sv, Nobelpriset ; no, Nobelprisen ) are five separate prizes that, according to Alfred Nobel Alfred Bernhard Nobel ( , ; 21 October 1833 – 10 December 1896) was a Swedish chemist, engineer, inventor, busines ...
.


References


External links


Lab computer simulates ribosome in motion


Gwen V. Childs, copie


Ribosome
i
''Proteopedia''
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Ribosomal proteins families in ExPASy

© RCSB Protein Data Bank
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3D electron microscopy structures of ribosomes at the EM Data Bank (EMDB)
* {{Authority control Ribosome, Ribozymes Protein biosynthesis