The RIBOSOME (/ˈraɪbəˌsoʊm, -boʊ-/ ) 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 (mRNA) molecules.
Ribosomes consist of two major components: the small ribosomal
subunit, which reads the
RNA , and the large subunit, which joins
amino acids to form a polypeptide chain. Each subunit is composed of
one or more ribosomal
RNA (rRNA) molecules and a variety of ribosomal
proteins (r-protein or r
Protein ). The ribosomes and associated
molecules are also known as the translational apparatus.
* 1 Overview
* 2 Discovery
* 3 Structure
* 3.1 High-resolution structure
* 4 Function
* 4.1 Translation
* 4.2 Addition of translation-independent amino acids
* 5.1 Free Ribosomes
* 5.2 Membrane-bound ribosomes
* 6 Biogenesis
* 7 Origin
* 8 Specialized ribosomes
* 9 See also
* 10 References
* 11 External links
The sequence of
DNA , 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 are selected, collected, and carried to the
ribosome by transfer
RNA (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 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: 1; a smaller subunit which binds to a larger subunit and the
RNA pattern, and 2; a larger subunit which binds to the tRNA, the
amino acids, and the smaller subunit. When a ribosome finishes reading
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 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
Ribosomes were first observed in the mid-1950s by Romanian cell
George Emil Palade , using an electron microscope , as dense
particles or granules. 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
Albert Claude ,
Christian de Duve
Christian de Duve , and
George Emil Palade were
jointly awarded the
Nobel Prize in Physiology or Medicine
Nobel Prize in Physiology or Medicine , in 1974,
for the discovery of the ribosome. The
Nobel Prize in
was awarded to
Venkatraman Ramakrishnan ,
Thomas A. Steitz and Ada E.
Yonath for determining the detailed structure and mechanism of the
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 known as ribosomal
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
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 and 35% ribosomal proteins . 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 work has
shown that there are no ribosomal proteins close to the reaction site
for polypeptide synthesis. This proves that the protein components of
ribosomes do not directly participate in peptide bond formation
catalysis, but rather suggests that these proteins act as a scaffold
that may enhance the ability of r
RNA to synthesize protein (See:
Ribozyme ). FIGURE 3 : Atomic structure of the
30S Subunit from
Thermus thermophilus . Proteins are shown in blue and the single RNA
chain in orange.
The ribosomal subunits of prokaryotes and eukaryotes are quite
The unit of measurement used to describe the ribosomal subunits and
RNA fragments is the
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
Prokaryotes have 70S ribosomes, each consisting of a small (
30S ) and
a large (
50S ) subunit. Their small subunit has a 16S
(consisting of 1540 nucleotides) bound to 21 proteins. The large
subunit is composed of a 5S
RNA subunit (120 nucleotides), a 23S RNA
subunit (2900 nucleotides) and 31 proteins .
prokaryotic ribosomes (E. coli)
23S (2904 nt )
5S (120 nt)
16S (1542 nt)
Affinity label for the t
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. 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
Eukaryotes have 80S ribosomes, each consisting of a small (
40S ) and
60S ) subunit. Their
40S subunit has an 18S
nucleotides) and 33 proteins. The large subunit is composed of a 5S
RNA (120 nucleotides), 28S
RNA (4700 nucleotides), a 5.8S
nucleotides) subunits and 46 proteins.
eukaryotic cytosolic ribosomes (R. norvegicus)
28S (4718 nt)
5,8S (160 nt)
5S (120 nt)
18S (1874 nt)
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.
The ribosomes found in chloroplasts and mitochondria of eukaryotes
also consist of large and small subunits bound together with proteins
into one 70S particle. These organelles are believed to be
descendants of bacteria (see
Endosymbiotic theory ) and, as such,
their ribosomes are similar to those of bacteria.
The various ribosomes share a core structure, which is quite similar
despite the large differences in size. Much of the
RNA is highly
organized into various tertiary structural motifs , for example
pseudoknots that exhibit coaxial stacking. The extra
RNA in the larger
ribosomes is in several long continuous insertions, such that they
form loops out of the core structure without disrupting or changing
it. All of the catalytic activity of the ribosome is carried out by
RNA ; the proteins reside on the surface and seem to stabilize the
The differences between the bacterial and eukaryotic ribosomes are
exploited by pharmaceutical chemists to create antibiotics that can
destroy a bacterial infection without harming the cells of the
infected person. Due to the differences in their structures, the
bacterial 70S ribosomes are vulnerable to these antibiotics while the
eukaryotic 80S ribosomes are not. Even though mitochondria possess
ribosomes similar to the bacterial ones, mitochondria are not affected
by these antibiotics because they are surrounded by a double membrane
that does not easily admit these antibiotics into the organelle .
FIGURE 4 : Atomic structure of the
50S Subunit from Haloarcula
marismortui . Proteins are shown in blue and the two
RNA chains in
orange and yellow. 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 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 and the bacterium Deinococcus radiodurans,
and the structure of the
30S subunit was determined from Thermus
thermophilus . These structural studies were awarded the Nobel Prize
Chemistry in 2009. In May 2001 these coordinates were used to
reconstruct the entire T. thermophilus 70S particle at 5.5 Å
Two papers were published in November 2005 with structures of the
Escherichia coli 70S ribosome. The structures of a vacant ribosome
were determined at 3.5-Å resolution using x-ray crystallography .
Then, two weeks later, a structure based on cryo-electron microscopy
was published, which depicts the ribosome at 11–15Å resolution in
the act of passing a newly synthesized protein strand into the
The first atomic structures of the ribosome complexed with t
RNA molecules were solved by using
X-ray crystallography by two
groups independently, at 2.8 Å and at 3.7 Å . These structures
allow one to see the details of interactions of the Thermus
thermophilus ribosome with m
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.
In 2011, the first complete atomic structure of the eukaryotic 80S
ribosome from the yeast
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 was published and
described the structure of the
40S subunit , as well as much about the
40S subunit's interaction with eIF1 during translation initiation .
Similarly, the eukaryotic
60S subunit structure was also determined
Tetrahymena thermophila in complex with eIF6 .
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 .
Ribosomes are the workplaces of protein biosynthesis , the process of
RNA into protein . The m
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 as a template, the ribosome traverses
each codon (3 nucleotides) of the mRNA, pairing it with the
appropriate amino acid provided by an aminoacyl-t
RNA . 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 ) . The small ribosomal subunit,
typically bound to an aminoacyl-t
RNA containing the amino acid
methionine , binds to an AUG codon on the m
RNA and recruits the large
ribosomal subunit. The ribosome contains three
RNA binding sites,
designated A, P and E. The A site binds an aminoacyl-tRNA; the P site
binds a peptidyl-t
RNA (a t
RNA bound to the peptide being synthesized);
and the E site binds a free t
RNA before it exits the ribosome. Protein
synthesis begins at a start codon AUG near the 5' end of the mRNA.
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
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 ," and it is thought that they
might be remnants of the
RNA world . FIGURE 5 : Translation of mRNA
(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
(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 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
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
C-terminus of a stalled protein with random,
translation-independent sequences of Alanines and Threonines .
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 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.
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 .
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.
The ribosome may have first originated in an
RNA world , appearing as
a self-replicating complex that only later evolved the ability to
synthesize proteins when amino acids began to appear. Studies suggest
that ancient ribosomes constructed solely of r
RNA could have developed
the ability to synthesize peptide bonds . In addition, evidence
strongly points to ancient ribosomes as self-replicating complexes,
where the r
RNA in the ribosomes had informational, structural, and
catalytic purposes because it could have coded for tRNAs 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
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.
Heterogeneity in ribosome composition has been proposed to be
involved in translational control of protein synthesis. Vincent Mauro
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. Some ribosomal proteins exchange
from the assembled complex with cytosolic copies suggesting that the
structure of the in vivo ribosome can be modified without synthesizing
an entire new ribosome.
* Biological machines
RNA tertiary structure
Wobble base pair
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