The ribosome is a large and complex molecular machine, found within all living cells, that
serves as the primary site of biological protein synthesis. Ribosomes link amino acids together
in the order specified by messenger RNA 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 molecules and a variety of proteins. The ribosomes and associated molecules are also
known as the translational apparatus. The sequence of DNA encoding for a protein
may be copied many times into messenger RNA chains of a similar sequence. Ribosomes can
bind to an mRNA chain and use it as a template for determining the correct sequence of amino
acids in a particular protein. Amino acids are selected, collected and carried to the
ribosome by transfer RNA, which enter one part of the ribosome and bind to the messenger
RNA chain. 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. 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 the mRNA pattern, and a larger subunit which binds
to the tRNA and the amino acids. When a ribosome finishes reading an mRNA 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 from bacteria, archaea and eukaryotes 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 mRNA chain at one time, each
"reading" its sequence and producing a corresponding protein molecule. The ribosomes in the mitochondria
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 cell biologist George Emil Palade using an electron microscope as dense particles
or granules for which, in 1974, he would win a Nobel Prize. The term "ribosome" was proposed
by scientist Richard B. Roberts in 1958:
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.
— Roberts, R. B., Microsomal Particles and Protein Synthesis
Albert Claude, Christian de Duve, and George Emil Palade were jointly awarded the Nobel
Prize in Physiology or Medicine, in 1974, for the discovery of the ribosomes. The Nobel
Prize in Chemistry 2009 was awarded to Venkatraman Ramakrishnan, Thomas A. Steitz and Ada E.
Yonath for determining the detailed structure and mechanism of the ribosome.
Structure
The ribosome is responsible for the synthesis of proteins in cells and is found in all organisms.
It serves to convert the instructions found in messenger RNA into the chains of amino-acids
that make up proteins. The ribosome is a cellular machine which is
highly complex. It is made up of dozens of distinct proteins as well as a few specialized
RNA molecules known as ribosomal RNA. Note – these rRNAs do not carry instructions
to make specific proteins like mRNAs. 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 and work
as one to translate the mRNA into a polypeptide chain during protein synthesis. 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 in diameter and are composed
of 65% ribosomal RNA and 35% ribosomal proteins. Eukaryotic ribosomes are between 25 and 30
nm in diameter with an rRNA to protein ratio that is close to 1. Bacterial ribosomes are
composed of one or two rRNA strands. Eukaryotic ribosomes contain one or three very large
rRNA molecules and multiple smaller protein molecules. 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 rRNA to synthesize protein.
The ribosomal subunits of prokaryotes and eukaryotes are quite similar.
The unit of measurement is the Svedberg unit, a measure of the rate of sedimentation in
centrifugation rather than size, and this accounts for why fragment names do not add
up. Prokaryotes have 70S ribosomes, each consisting
of a small and a large subunit. Their small subunit has a 16S RNA subunit bound to 21
proteins. The large subunit is composed of a 5S RNA subunit, a 23S RNA subunit and 31
proteins. Affinity label for the tRNA binding sites on the E. coli ribosome allowed the
identification of A and P site proteins most likely associated with the peptidyltransferase
activity; labelled proteins are L27, L14, L15, L16, L2; at least L27 is located at the
donor site, as shown by E. Collatz and A.P. Czernilofsky. Additional research has demonstrated
that the S1 and S21 proteins, in association with the 3'-end of 16S ribosomal RNA, are
involved in the initiation of translation. Eukaryotes have 80S ribosomes, each consisting
of a small and large subunit. Their 40S subunit has an 18S RNA and 33 proteins. The large
subunit is composed of a 5S RNA, 28S RNA, a 5.8S RNA 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 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 and as such their ribosomes are similar to those of bacteria.
The various ribosomes share a core structure, which is quite similar despite the large differences
in size. Much of the RNA is highly organized into various tertiary structural motifs, for
example pseudoknots that exhibit coaxial stacking. The extra RNA in the larger ribosomes is in
several long continuous insertions, such that they form loops out of the core structure
without disrupting or changing it. All of the catalytic activity of the ribosome is
carried out by the RNA; the proteins reside on the surface and seem to stabilize the structure.
The differences between the bacterial and eukaryotic ribosomes are exploited by pharmaceutical
chemists to create antibiotics that can destroy a bacterial infection without harming the
cells of the infected person. Due to the differences in their structures, the bacterial 70S ribosomes
are vulnerable to these antibiotics while the eukaryotic 80S ribosomes are not. Even
though mitochondria possess ribosomes similar to the bacterial ones, mitochondria are not
affected by these antibiotics because they are surrounded by a double membrane that does
not easily admit these antibiotics into the organelle.
High-resolution structure
The general molecular structure of the ribosome has been known since the early 1970s. In the
early 2000s the structure has been achieved at high resolutions, on the order of a few
Å. The first papers giving the structure of the
ribosome at atomic resolution were published almost simultaneously in late 2000. The 50S
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 in Chemistry in 2009. Early the
next year these coordinates were used to reconstruct the entire T. thermophilus 70S particle at
5.5 Å resolution. Two papers were published in November 2005
with structures of the Escherichia coli 70S ribosome. The structures of a vacant ribosome
were determined at 3.5-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
protein-conducting channel. The first atomic structures of the ribosome
complexed with tRNA and mRNA molecules were solved by using X-ray crystallography by two
groups independently, at 2.8 Å and at 3.7 Å. These structures allow one to see the
details of interactions of the Thermus thermophilus ribosome with mRNA and with tRNAs bound at
classical ribosomal sites. Interactions of the ribosome with long mRNAs containing Shine-Dalgarno
sequences were visualized soon after that at 4.5- to 5.5-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 from Tetrahymena thermophila in complex with eIF6.
Function
Ribosomes are the workhorses of protein biosynthesis, the process of translating mRNA into protein.
The mRNA comprises a series of codons that dictate to the ribosome the sequence of the
amino acids needed to make the protein. Using the mRNA as a template, the ribosome traverses
each codon 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 . The small ribosomal subunit, typically bound to an aminoacyl-tRNA
containing the amino acid 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 binds an aminoacyl- RNA; the P site binds a peptidyl-tRNA; and the E site
binds a free tRNA before it exits the ribosome. Protein synthesis begins at a start codon
AUG near the 5' end of the mRNA. mRNA binds to the P site of the ribosome first. The ribosome
is able to identify the start codon by use of the Shine-Dalgarno sequence of the mRNA
in prokaryotes and Kozak box in eukaryotes. Although catalysis of the peptide bond involves
the C2 hydroxyl of RNA's P-site adenosine in a protein shuttle mechanism, other steps
in protein synthesis 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.
In Figure 5, both ribosomal subunits assemble at the start codon. The ribosome uses RNA
that matches the current codon on the mRNA 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.
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 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 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
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 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. 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.
See also
References
External links Lab computer simulates ribosome in motion
Role of the Ribosome, Gwen V. Childs, copied here
Ribosome in Proteopedia - The free, collaborative 3D encyclopedia of proteins & other molecules
Ribosomal proteins families in ExPASy Molecule of the Month © RCSB Protein Data
Bank: Ribosome
Elongation Factors Palade
3D electron microscopy structures of ribosomes at the EM Data Bank(EMDB)
This article incorporates public domain material from the NCBI document "Science Primer".