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BIOL 200 Lecture Notes - Eif6, Tetrahymena, Transfer Rna

Biology (Sci)
Course Code
BIOL 200
Mathieu Roy

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Eukaryotes have 80S ribosomes, 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 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.
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 (large prokaryotic) subunit was determined from
the archaeons Haloarcula marismortui andDeinococcus 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 (May 2001) 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 1115 Å 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.
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