A ribosome functions as a micro-machine for making proteins. Ribosomes are composed of special proteins and nucleic acids. The TRANSLATION of information and the Linking of AMINO ACIDS are at the heart of the protein production process.A ribosome, formed from two subunits locking together, functions to: (1) Translate encoded information from the cell nucleus provided by messenger ribonucleic acid (mRNA), (2) Link together amino acids selected and collected from the cytoplasm by transfer ribonucleic acid (tRNA). (The order in which the amino acids are linked together is determined by the mRNA) and, (3) Export the polypeptide produced to the cytoplasm where it will form a functional protein.
Ribosomes are found ‘free’ in the cytoplasm or bound to the endoplasmic reticulum (ER) to form rough ER. In a mammalian cell there can be as many as 10 million ribosomes. Several ribosomes can be attached to the same mRNA strand, this structure is called a polysome. Ribosomes have only a temporary existence. When they have synthesised a polypeptide the two sub-units separate and are either re-used or broken up.
Ribosomes can join up amino acids at a rate of 200 per minute. Small proteins can therefore be made fairly quickly but two to three hours are needed for larger proteins such as the massive 30,000 amino acid muscle protein titin.
Ribosomes in prokaryotes use a slightly different process to produce proteins than do ribosomes in eukaryotes. Fortunately this difference presents a window of molecular opportunity for attack by antibiotic drugs such as streptomycin. Unfortunately some bacterial toxins and the polio virus also use it to enable them to attack the translation mechanism.
For an overview diagram of protein production click here.
(The diagram will open in a separate window)
A LONGER LOOK at Ribosomes:
Ribosomes are macro-molecular production units. They are composed of ribosomal proteins (riboproteins) and ribonucleic acids (ribonucleoproteins). The word ribosome is made from taking ‘ribo’ from ribonucleic acid and adding it to ‘soma’, the Latin word for body. Ribosomes can be bound by a membrane(s) but they are not membranous.
Ribosome: a micro-machine for manufacturing proteins
A ribosome is basically a very complicated but elegant micro-‘machine’ for producing proteins. Each complete ribosome is constructed from two sub-units. A eukaryotic ribosome is composed of nucleic acids and about 80 proteins and has a molecular mass of about 4,200,000 Da. About two-thirds of this mass is composed of ribosomal RNA and one third of about 50+ different ribosomal proteins.
Ribosomes are found in prokaryotic and eukaryotic cells; in mitochondria, chloroplasts and bacteria. Those found in prokaryotes are generally smaller than those in eukaryotes. Ribosomes in mitochondria and chloroplasts are similar in size to those in bacteria. There are about 10 billion protein molecules in a mammalian cell and ribosomes produce most of them. A rapidly growing mammalian cell can contain about 10 million ribosomes. [A single cell of E. Coli contains about 20,000 ribosomes and this accounts for about 25% of the total cell mass].
The proteins and nucleic acids that form the ribosome sub-units are made in the nucleolus and exported through nuclear pores into the cytoplasm. The two sub-units are unequal in size and exist in this state until required for use. The larger sub-unit is about twice as large as the smaller one.
The larger sub-unit has mainly a catalytic function; the smaller sub-unit mainly a decoding one. In the large sub-unit ribosomal RNA performs the function of an enzyme and is termed a ribozyme. The smaller unit links up with mRNA and then locks-on to a larger sub-unit. Once formed ribosomes are not static units. When production of a specific protein has finished the two sub-units separate and are then usually broken down. Ribosomes have only a temporary existence.
Sometimes ribosome sub-units admit mRNA as soon as the mRNA emerges from the nucleus. When many ribosomes do this the structure is called a polysome. Ribosomes can function in a ‘free’ state in the cytoplasm but they can also ‘settle’ on the endoplasmic reticulum to form ‘rough endoplasmic reticulum’. Where there is rough endoplasmic reticulum the association between ribosome and endoplasmic reticulum (ER) facilitates the further processing and checking of newly made proteins by the ER.
The Protein Factory: site and services.
All factories need services such as gas, water, drainage and communications. For these to be provided there must a location or site.
Protein production also needs service requirements. A site requiring the provision of services is produced in a small ribosome sub-unit when a strand of mRNA enters through one selective cleft, and a strand of initiator tRNA through another. This action triggers the small sub-unit to lock-on to a ribosome large sub-unit to form a complete and active ribosome. The amazing process of protein production can now begin.
For translation and protein synthesis to take place many initiator and release chemicals are involved, and many reactions using enzymes take place. There are however general requirements and these have to be satisfied. The list below shows the main requirements and how they are provided:
- Requirement: A safe (contamination free) and suitable facility for the protein production process to take place.
- Provision: this facility is provided by the two ribosomal sub-units. When the two sub-units lock together to form the complete ribosome, molecules entering and exiting can only do so through selective clefts or tunnels in the molecular structure.
- Requirement: A supply of information in a form that the ribosome can translate with a high degree of accuracy. The translation must be accurate in order that the correct proteins are produced.
- Provision: Information is supplied by the nucleus and delivered to the ribosome in the form of a strand of mRNA. When mRNA is formed in the nucleus introns (non-coding sections) are cut out, and exons (coding sections) are joined together by a process called splicing.
- Requirement: A supply of amino acids from which the ribosomal mechanism can obtain the specific amino acids needed.
- Provision: Amino acids, mainly supplied from food, are normally freely available in the cytoplasm.
- Requirement: A system that can select and lock-on to an amino acid in the cytoplasm and deliver it to the translation and synthesis site in the ribosome.
- Provision: Short strands of transfer ribonucleic acid (tRNA) made in the nucleus and available in the cytoplasm act as ‘adaptor tools’. When a strand of tRNA has locked on to an amino acid the tRNA is said to be ‘charged’. tRNA diffuses into the smaller ribosome sub-unit and each short tRNA strand will deliver ONE amino acid.
- Requirement: A means of releasing into the cytoplasm: (a) a newly formed polypeptide, (b) mRNA that has been used in the translating process, and (c) tRNA that has delivered the amino acid it was carrying and is now ‘uncharged’.
- Provision: (a) when a newly formed peptide chain is produced deep inside the ribosome large sub-unit, it is directed out to the cytoplasm along a tunnel or cleft. (b) ‘Used’ mRNA leaves the smaller ribosome sub-unit through a tunnel on the side opposite to its point of entry. Movement through the ribosome is brought about by a one-way only, intermittent movement of the ribosome along, and in the direction of, the incoming mRNA strand. (c) tRNA in the ‘uncharged’ state leaves via a tunnel in the molecular architecture of the ribosome large sub-unit.
The Protein Factory: What happens on the inside?
– A look at the protein production line that can join up amino acids at a rate of 200 per minute!
Now we have considered the requirements and provisions needed for the protein production machine to operate, we can look at the inner workings.
As mentioned earlier many detailed biochemical reactions take place in the ribosome and only a brief outline is given here to illustrate the concept.
(Please also see ‘schematic of ribosome’ at end of section)
In the ribosome there are THREE STAGES and THREE operational SITES involved in the protein production line.
The three STAGES are (1) Initiation, (2) Elongation and (3) Termination.
The three operational or binding SITES are A, P and E reading from the mRNA entry site (conventionally the right hand side).
Sites A and P span both the ribosome sub-units with a larger part residing in the ribosome large sub-unit, and a smaller part in the smaller sub-unit. Site E, the exit site, resides in the large ribosome sub-unit.
Table of binding sites, positions and functions in a ribosome
(please also see schematic of ribosome at end of section)
mRNA strand entry site
Admission of codon of mRNA & ‘charged’ strand of tRNA. Checking and decoding and start of ‘handing over’ one amino acid molecule
Peptide synthesis, consolidation, elongation and transfer of peptide chain to site A
Preparation of ‘uncharged’ tRNA for exit
The Three stages:
- Initiation. During this stage a small ribosome sub-unit links onto the ‘start end’ of an mRNA strand. ‘Initiator tRNA’ also enters the small sub-unit. This complex then joins onto a ribosome large sub-unit. At the beginning of the mRNA strand there is a ‘start translating’ message and a strand of tRNA ‘charged’ with one specific amino acid, enters site A of the ribosome. Production of a polypeptide has now been initiated.For the tRNA not to be rejected the three letter code group it carries (called an anti-codon) must match up with the three letter code group (called a codon) on the strand of mRNA already in the ribosome. This is a very important part of the translation process and it is surprising how few ‘errors of translation’ occur. [In general the particular amino acid it carries is determined by the three letter anticodon it bears, e.g. if the three letter code is CAG (Cytosine, Adenine, Guanine) then it will select and transport the amino acid Glutamine (Gln)].
- Elongation.This term covers the period between initiation and termination and it is during this time that the main part of the designated protein is made. The process consists of a series of cycles, the total number of which is determined by the mRNA. One of the main events during elongation is translocation. This is when the ribosome moves along the mRNA by one codon notch and a new cycle starts.During the ‘start-up’ process the ‘initiation tRNA’ will have moved to site P (see schematic of ribosome at end of section) and the ribosome will have admitted into site A, a new tRNA ‘charged’ with one amino acid.The ‘charged’ tRNA resides in site A until it has been checked and accepted (or rejected) and until the growing peptide chain attached to the tRNA in site P, has been transferred across by enzymes, to the ‘charged’ tRNA in site A. Here one new amino acid is donated by the tRNA and added to the peptide chain. By this process the peptide chain is increased in length by increments of one amino acid. [The peptide bond formation between the growing peptide chain and the newly admitted amino acid is assisted by peptidyl transferase and takes place in the large ribosome sub-unit. The reaction occurs between tRNA that carries the nascent peptide chain, peptidyl-tRNA and the tRNA that carries the incoming amino acid, the aminoacyl-tRNA]. When this has taken place the tRNA in site P, having transferred its peptide chain, and now without any attachments, is moved to site E the exit site.Next, the tRNA in site A, complete with a peptide chain increased in length by one amino acid, moves to site P. In site P riboproteins act to consolidate the bonding of the peptide chain to the newly added amino acid. If the peptide chain is long the oldest part will be moved out into the cytoplasm to be followed by the rest of the chain as it is produced.The next cycle
With site A now empty translocation takes place. The ribosome moves on by a distance of one (three letter) codon notch along the mRNA to bring a new codon into the processing area. tRNA ‘charged’ with an attached amino acid now enters site A, and provided a satisfactory match of the mRNA codon and tRNA anti-codon is made, the cycle starts again. This process continues until a termination stage is reached.
- Termination. When the ribosome reaches the end of the mRNA strand, a terminal or ‘end of protein code’ message is flagged up. This registers the end of production for the particular protein coded for by this strand of mRNA. ‘Release factor’ chemicals prevent any more amino acid additions, and the new protein (polypeptide) is completely moved out into the cytoplasm through a cleft in the large sub-unit. The two ribosome sub-units disengage, separate and are re-used or broken down.
- Nearly all the proteins required by cells are synthesised by ribosomes. Ribosomes are found ‘free’ in the cell cytoplasm and also attached to rough endoplasmic reticulum.
- Ribosomes receive information from the cell nucleus and construction materials from the cytoplasm.
- Ribosomes translate information encoded in messenger ribonucleic acid (mRNA).
- They link together specific amino acids to form polypeptides and they export these to the cytoplasm.
- A mammalian cell may contain as many as 10 million ribosomes, but each ribosome has only a temporary existence.
- Ribosomes can link up amino acids at a rate of 200 per minute.
- Ribosomes are formed from the locking of a small sub-unit on to a large sub-unit. The sub-units are normally available in the cytoplasm, the larger one being about twice the size of the smaller one.
- Each ribosome is a complex of ribonucleoproteins with two-thirds of its mass is composed of ribosomal RNA and about one-third ribosomal protein.
- Protein production takes place in three stages: (1) initiation, (2) elongation, and (3) termination.
- During peptide production the ribosome moves along the mRNA in an intermittent process called translocation.
- Antibiotic drugs such as streptomycin can be used to attack the translation mechanism in prokaryotes. This is very useful. Unfortunately some bacterial toxins and viruses can also do this.
- After they leave the ribosome most proteins are folded or modified in some way. This is called ‘post translational modification’.