Ribosomes
Ribosome Structure and Function
Ribosome Structure and Function

RIBOSOMES All living cells contain ribosomes, tiny organelles composed of approximately 60 percent ribosomal RNA (rRNA) and 40 percent protein. However, though they are generally described as organelles, it is important to note that ribosomes are not bound by a membrane and are much smaller than other organelles. Some cell types may hold a few million ribosomes, but several thousand is more typical. The organelles require the use of an electron microscope to be visually detected. Ribosomes are complexes of RNA and protein that are found in all cells. Ribosomes are the sites of protein synthesis, where RNA is translated into protein. Ribosomes make the protein for the cell. Ribosomes are responsible for assembling the proteins of the cell. Ribosomal subunits are synthesized by the nucleolus. Depending on the protein production level of a particular cell, ribosomes may number in the millions. Ribosomes are the protein builders or the protein synthesizers of the cell. They are like construction guys who connect one amino acid at a time and build long chains. Ribosomes are found in many places around the cell. You might find them floating in the cytoplasm (cytosol). Those floating ribosomes make proteins that will be used inside of the cell. Other ribosomes are found on the endoplasmic reticulm. Endoplasmic reticulum with attached ribosomes is called rough. It looks bumpy under a microscope. Those attached ribosomes make proteins that will be used inside the cell and proteins made for export out of the cell. A ribosome is not just one piece. There are two pieces or subunits. Scientists named them 60-S (large) and 40-S (small). When the cell needs to make protein, mRNA is created in the nucleus. The mRNA is then sent into the cell and the ribosomes. When it is time to make the protein, the two subunits come together and combine with the mRNA. The subunits lock onto the mRNA and start the protein synthesis. The 60-S/ 40-S model works fine for eukaryotic cells. Prokaryotic cells have ribosomes made of 50-S and 30-S subunits. It's a small difference, but one of many you will find in the two different types of cells. Scientists have used this difference in ribosome size to develop drugs that can kill prokaryotic microorganisms that cause disease. http://www.biology4kids.com/files/cell_ribos.htmlRibosomes are the sites where the cell assembles proteins according to genetic instructions. A bacterial cell may have a few thousand ribosomes, although a human cell has a few million. Cells that have high rates of protein synthesis have a particularly great number of ribosomes. Cells active in protein synthesis also have prominent nucleoli, which make the ribosomes. Ribosomes function in two cytoplasmic areas. Free ribosomes are spread throughout the cytosol, while bound ribosomes are attached to the outside of a membranous network, endoplasmic reticulum. Most of the proteins that are made by free ribosomes will function inside the cytosol. The proteins produced by bound ribosomes usually exported from the cell. Each ribosome is built from two subunits, each having its own mix of ribosomal RNA and proteins. Ribosomes are built with RNA from the nucleolus and are made in the nucleolus istself. These subunits join together to form a functional ribosome only when they attach to a messenger RNA molecule. The ribosomes present in eukaryotic cells are slightly larger than those found in prokaryotic cells. Ribosomes function in protein synthesis. As they move along messenger RNA, amino acids are joined in an order originally dictated by DNA. Several ribosomes can be moving along the same messenger RNA at once and the entire complex is called a polysome.
Ribosomes
Ribosomes
Ribosomes external image hr.jpg - Each cell contains thousands - Miniature 'protein factories' - Composes 25% of cell's mass - Stationary type: embedded in rough endoplasmic reticulum - Mobile type: injects proteins directly into cytoplasm **info^** The nucleolus is responsible for assembling ribosomes. Ribosomes are composed of proteins and ribosomal RNA. They are found in four areas of the plant cell: the cytoplasm, the surface of the endoplasmic reticulum, the mitochondria, and on chloroplasts.

There are two main types of ribosomes: free ribosomes and attached ribosomes.
Attached ribosomes are attached to the endoplasmic reticulum and serve as sites for protein synthesis. Proteins synthesized on these ribosomes will be exported from the cell, moved into other organelles of the endomembrane system, or incorporated into membranes.
Protein synthesis also occurs on free ribosomes.

Ribosomes make protiens for the cell.


Structure

external image 10_small_subunit.gif

Atomic structure of the 30S Subunit from Thermus thermophilus. Proteins are shown in blue and the single RNA strand in orange.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 accounts for why fragment names do not add up (70s is made of 50s and 30s - you would expect this to give 80s, but they do not as this is not a direct measurement of size).Prokaryotes have 70S ribosomes, each consisting of a small (30S) and a large (50S) subunit. Their large subunit is composed of a 5S RNA subunit (consisting of 120 nucleotides), a 23S RNA subunit (2900 nucleotides) and 34 proteins. The 30S subunit has a 1540 nucleotide RNA subunit (16S) bound to 21 proteins.Eukaryotes have 80S ribosomes, each consisting of a small (40S) and large (60S) subunit. Their large subunit is composed of a 5S RNA (120 nucleotides), a 28S RNA (4700 nucleotides), a 5.8S subunit (160 nucleotides) and ~49 proteins. The 40S subunit has a 1900 nucleotide (18S) RNA and ~33 proteins.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. 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. 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.


Atomic structure

external image 10_large_subunit.gif

Proteins are shown in blue and the two RNA strands 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, in the order of a few Ångströms.
The first papers giving the structure of the ribosome at atomic resolution were published in rapid succession in late 2000. First, the 50S (large bacteria) subunit from the archea, Haloarcula marismortui was published.Soon after the structure of the 30S subunit from Thermus thermophilus was published. Shortly thereafter a more detailed structure was published.Early the next year (May 2001) these coordinates were used to reconstruct the entire T. thermophilus 70S particle at 5.5 Ångström resolution.Two papers were published in November 2005 with structures of the Escherichia coli 70S ribosome. The structures of vacant ribosome were determined at 3.5 Ångström resolution using x-ray crystallography.Then, two weeks later, a structure based on cryo-electron microsopy was published, which depicts the ribosome at 11-15 Ångström resolution in the act of passing a newly synthesized protein strand into the protein-conducting channel.
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 Ångström and at 3.7 Ångström 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 Ångström resolution.http://en.wikipedia.org/wiki/Ribosomes

Ribosomes are mainly found bound to the endoplasmic reticulum and the nuclear envelope, as well as freely scattered throughout the cytoplasm, depending upon whether the cell is plant, animal, or bacteria. The organelles serve as the protein production machinery for the cell and are consequently most abundant in cells that are active in protein synthesis, such as pancreas and brain cells. Some of the proteins synthesized by ribosomes are for the cell's own internal use, especially those that are produced by free ribosomes. Many of the proteins produced by bound ribosomes, however, are transported outside of the cell.
In eukaryotes, the rRNA in ribosomes is organized into four strands, and in prokaryotes, three strands. Eukaryote ribosomes are produced and assembled in the nucleolus. Ribosomal proteins enter the nucleolus and combine with the four rRNA strands to create the two ribosomal subunits (one small and one large) that will make up the completed ribosome (see Figure 1). The ribosome units leave the nucleus through the nuclear pores and unite once in the cytoplasm for the purpose of protein synthesis. When protein production is not being carried out, the two subunits of a ribosome are separated.
In 2000, the complete three-dimensional structure of the large and small subunits of a ribosome was established. Evidence based on this structure suggests, as had long been assumed, that it is the rRNA that provides the ribosome with its basic formation and functionality, not proteins. Apparently the proteins in a ribosome help fill in structural gaps and enhance protein synthesis, although the process can take place in their absence, albeit at a much slower rate.
The units of a ribosome are often described by their Svedberg (s) values, which are based upon their rate of sedimentation in a centrifuge. The ribosomes in a eukaryotic cell generally have a Svedberg value of 80S and are comprised of 40s and 60s subunits. Prokaryotic cells, on the other hand, contain 70S ribosomes, each of which consists of a 30s and a 50s subunit. As demonstrated by these values, Svedberg units are not additive, so the values of the two subunits of a ribosome do not add up to the Svedberg value of the entire organelle. This is because the rate of sedimentation of a molecule depends upon its size and shape, rather than simply its molecular weight.
Protein synthesis requires the assistance of two other kinds of RNA molecules in addition to rRNA. Messenger RNA (mRNA) provides the template of instructions from the cellular DNA for building a specific protein. Transfer RNA (tRNA) brings the protein building blocks, amino acids, to the ribosome. There are three adjacent tRNA binding sites on a ribosome: the aminoacyl binding site for a tRNA molecule attached to the next amino acid in the protein (as illustrated in Figure 1), the peptidyl binding site for the central tRNA molecule containing the growing peptide chain, and an exit binding site to discharge used tRNA molecules from the ribosome.
Once the protein backbone amino acids are polymerized, the ribosome releases the protein and it is transported to the cytoplasm in prokaryotes or to the Golgi apparatus in eukaryotes. There, the proteins are completed and released inside or outside the cell. Ribosomes are very efficient organelles. A single ribosome in a eukaryotic cell can add 2 amino acids to a protein chain every second. In prokaryotes, ribosomes can work even faster, adding about 20 amino acids to a polypeptide every second.
In addition to the most familiar cellular locations of ribosomes, the organelles can also be found inside mitochondria and the chloroplasts of plants. These ribosomes notably differ in size and makeup than other ribosomes found in eukaryotic cells, and are more akin to those present in bacteria and blue-green algae cells. The similarity of mitochondrial and chloroplast ribosomes to prokaryotic ribosomes is generally considered strong supportive evidence that mitochondria and chloroplasts evolved from ancestral prokaryotes.

external image ribosome1.jpg

Ribosomes (from ribonucleic acid and "Greek: soma (meaning body)") are complexes of RNA and protein that are found in all cells. Ribosomes from bacteria, archaea and eukaryotes, the three domains of life, have significantly different structure and RNA. Interestingly, the ribosomes in the mitochondrion of eukaryotic cells resemble those in bacteria, reflecting the evolutionary origin of this organelle.[1[[http://en.wikipedia.org/wiki/Ribosome#cite_note-0|]]]
The ribosome functions in the expression of the genetic code from nucleic acid into protein, in a process called translation. Ribosomes do this by catalyzing the assembly of individual amino acids into polypeptide chains; this involves binding a messenger RNA and then using this as a template to join together the correct sequence of amino acids. This reaction uses adapters called transfer RNA molecules, which read the sequence of the messenger RNA and are attached to the amino acids.

Ribosomes are organelles that consist of RNA an proteins. They are responsible for assembling the proteins of the cell. Depending on the protein production level of a particular cell, ribosomes may number in the millions.

Ribosomes are typically composed of two subunits: a large subunit and a small subunit. Ribosomal subunits are synthesized by the nucleolus. These two units join together when the ribosome attaches to messenger RNA to produce a protein in the cytoplasm.

There are two places that ribosomes usually exist in the cell: suspended in the cytosol and bound to the endoplasmic reticulum. These ribosomes are called free ribosomes and bound ribosomes respectively. In both cases, the ribosomes usually form aggregates called polysomes.

Free ribosomes usually make proteins that will function in the cytosol, while bound ribosomes usually make proteins that are exported or included in the cell's membranes. Interestingly enough, free ribosomes and bound ribosomes are interchangeable and the cell can change their numbers according to metabolic needs.

The Ribosome http://rna.ucsc.edu/rnacenter/ribosome.html

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DNA-RNA.jpg (25692 bytes)
DNA-RNA.jpg (25692 bytes)
Before cell division, the DNA in our chromosomes replicates so each daughter cell has an identical set of chromosome. In addition, the DNA is responsible for coding for all proteins. Each amino acid is designated by one or more set of triplet nucleotides. The code is produced from one strand of the DNA by a process called "transcription". This produces mRNA which then is sent out of the nucleus where the message is translated into proteins. This can be done in the cytoplasm on clusters of ribosomes, called "polyribosomes". Or it can be done on the membranes of the rough endoplasmic reticulum. The cartoon to the left shows the basic sequence of transcription and translational events. ||

What happens at the site of the ribosome?

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tRNA.jpg (51285 bytes)
tRNA.jpg (51285 bytes)
The code is actually translated on structures that are also made in the nucleus, called Ribosomes. These ribosomes provide the structural site where the mRNA sits. The amino acids for the proteins are carried to the site by "transfer RNAs,". In the cartoon to the left, these are shown as blue molecules. Each transfer RNA (tRNA) has a nucleotide triplet which binds to the complementary sequence on the mRNA (see the three letters at the bottom of each molecule). The tRNA carries the amino acid at its opposite end. One can trace and detect binding of a particular tRNA-amino acid complex to the mRNA by labeling that amino acid. It will bind to its tRNA. In the case to the left, Phenylalanine is bound to the tRNA which carries the complementary base code AAA (adenine-adenine-adenine). This triplet code would bind to the complementary sequence on mRNA UUU (uracil X3). The mRNA is shown as a green arrow. This cartoon shows the selective binding site on the mRNA which is attached in the ribosome. It also shows the tRNA carrying the Phenylalanine bound at the site In this particular assay which uses a polyuracil mRNA, only phenylalanine-bearing tRNA is bound and detected on the filter.

Initiation
ribosome1.jpg (37988 bytes)
ribosome1.jpg (37988 bytes)

The cartoon shows the initiation of this process. It begins with the small subunit of the ribosome bound to the mRNA. An initiator tRNA is attracted to the region (carrying a methionine. It binds to the triplet code AUG.
This then attracts the large ribosomal subunit which will bind to the small subunit. Note that it has an A site and a P site. These are different binding sites for the tRNAs. The cartoon below describes the next phase in the process.

http://www.cytochemistry.net/Cell-biology/ribosome.htm Role of the Ribosome

The route from the DNA code to the protein.

DNA-RNA.jpg (25692 bytes)
DNA-RNA.jpg (25692 bytes)
Before cell division, the DNA in our chromosomes replicates so each daughter cell has an identical set of chromosome. In addition, the DNA is responsible for coding for all proteins. Each amino acid is designated by one or more set of triplet nucleotides. The code is produced from one strand of the DNA by a process called "transcription". This produces mRNA which then is sent out of the nucleus where the message is translated into proteins. This can be done in the cytoplasm on clusters of ribosomes, called "polyribosomes". Or it can be done on the membranes of the rough endoplasmic reticulum. The cartoon to the left shows the basic sequence of transcription and translational events.

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http://cellbio.utmb.edu/CELLBIO/ribosome.htm

Ribosomes are composed of proteins and ribosomal RNA.
They are found in four areas of the plant cell: the cytoplasm, the surface of the endoplasmic reticulum, the mitochondria, and on chloroplasts.
There are two main types of ribosomes: free ribosomes and attached ribosomes.
Attached ribosomes are attached to the endoplasmic reticulum and serve as sites for protein synthesis. Proteins synthesized on these ribosomes will be exported from the cell, moved into other organelles of the endomembrane system, or incorporated into membranes.
Protein synthesis also occurs on free ribosomes.