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3.4: Ribosomes - Biology

3.4: Ribosomes - Biology



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Ribosomes are the protein-synthesizing machines of the cell. They translate the information encoded in messenger RNA (mRNA) into a polypeptide.

Shape, size and function

Ribosomes are roughly spherical with a diameter of ~20 nm, they can be seen only with the electron microscope. Figure (PageIndex{1}) is an electron micrograph showing clusters of ribosomes. These clusters, called polysomes, are held together by messenger RNA (mRNA). They can make up 25% of the dry weight of cells (e.g., pancreas cells) and specialize in protein synthesis. A single pancreas cell can synthesize 5 million molecules of protein per minute.

In eukaryotes, ribosomes that synthesize proteins for use within the cytosol (e.g., enzymes of glycolysis) are suspended in the cytosol. The specific ribosomes that synthesize proteins destined for secretion (by exocytosis), the plasma membrane (e.g., cell surface receptors), and lysosomes. These ribosomes are attached to the cytosolic face of the membranes of the endoplasmic reticulum. As the polypeptide is synthesized, it is extruded into the interior (lumen) of the endoplasmic reticulum. Then, before these proteins reach their final destinations, they undergo a series of processing steps in the Golgi apparatus.

Ribosomes that synthesize 13 of the proteins destined for the inner membrane of mitochondria are found within the mitochondrion itself and are quite different in structure from the others. The ribosomes of bacteria, eukaryotes, and mitochondria differ in many details of their structure (Table (PageIndex{1})). However, despite these differences, the basic operations of bacterial, eukaryotic, and mitochondrial ribosomes are very similar.

Bacterial (70S)Eukaryotic (80S)Mitochondrial (55S)
Table (PageIndex{1}): Comparison of Ribosome Structure in Bacteria, Eukaryotes, and Human Mitochondria
Large Subunit50S60S39S
rRNAs
(1 of each)
23S (2904 nts)28S (4700 nts)16S (1560 nts)
5S (120 nts)5S (120 nts)
5.8S (160 nts)
Proteins354750
Small Subunit30S40S28S
rRNA16S (1542 nts)18S (1900 nts)12S (950 nts)
Proteins203330
S values are the sedimentation coefficient: a measure of the rate at which the particles are spun down in the ultracentrifuge. S values are not additive. nts = nucleotides.

Ribosomal RNA

Ribosomal ribonucleic acid (rRNA) is a type of non-coding RNA which is the primary component of ribosomes, essential to all cells. rRNA is a ribozyme which carries out protein synthesis in ribosomes. Ribosomal RNA is transcribed from ribosomal DNA (rDNA) and then bound to ribosomal proteins to form small and large ribosome subunits. rRNA is the physical and mechanical factor of the ribosome that forces transfer RNA (tRNA) and messenger RNA (mRNA) to process and translate the latter into proteins. [1] Ribosomal RNA is the predominant form of RNA found in most cells it makes up about 80% of cellular RNA despite never being translated into proteins itself. Ribosomes are composed of approximately 60% rRNA and 40% ribosomal proteins by mass.


The ribosome challenge to the RNA world

An RNA World that predated the modern world of polypeptide and polynucleotide is one of the most widely accepted models in origin of life research. In this model, the translation system shepherded the RNA World into the extant biology of DNA, RNA, and protein. Here, we examine the RNA World Hypothesis in the context of increasingly detailed information available about the origins, evolution, functions, and mechanisms of the translation system. We conclude that the translation system presents critical challenges to RNA World Hypotheses. Firstly, a timeline of the RNA World is problematic when the ribosome is incorporated. The mechanism of peptidyl transfer of the ribosome appears distinct from evolved enzymes, signaling origins in a chemical rather than biological milieu. Secondly, we have no evidence that the basic biochemical toolset of life is subject to substantive change by Darwinian evolution, as required for the transition from the RNA world to extant biology. Thirdly, we do not see specific evidence for biological takeover of ribozyme function by protein enzymes. Finally, we can find no basis for preservation of the ribosome as ribozyme or the universality of translation, if it were the case that other information transducing ribozymes, such as ribozyme polymerases, were replaced by protein analogs and erased from the phylogenetic record. We suggest that an updated model of the RNA World should address the current state of knowledge of the translation system.


Overview

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. 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 mRNA pattern, and 2) a larger subunit which binds to the tRNA, the amino acids, and the smaller subunit. 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 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 mRNA 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 mitochondria. [5] [6]


Structure of the mammalian ribosome-Sec61 complex to 3.4 Å resolution

Cotranslational protein translocation is a universally conserved process for secretory and membrane protein biosynthesis. Nascent polypeptides emerging from a translating ribosome are either transported across or inserted into the membrane via the ribosome-bound Sec61 channel. Here, we report structures of a mammalian ribosome-Sec61 complex in both idle and translating states, determined to 3.4 and 3.9 Å resolution. The data sets permit building of a near-complete atomic model of the mammalian ribosome, visualization of A/P and P/E hybrid-state tRNAs, and analysis of a nascent polypeptide in the exit tunnel. Unprecedented chemical detail is observed for both the ribosome-Sec61 interaction and the conformational state of Sec61 upon ribosome binding. Comparison of the maps from idle and translating complexes suggests how conformational changes to the Sec61 channel could facilitate translocation of a secreted polypeptide. The high-resolution structure of the mammalian ribosome-Sec61 complex provides a valuable reference for future functional and structural studies.

Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

Figures

The Structure of a Mammalian…

The Structure of a Mammalian Ribosome-Translocon Complex (A) Model of the idle 80S…

Representative Density for the Ribosomal…

Representative Density for the Ribosomal Proteins and rRNA (A–D) Cryo-EM density for the…

An A/P Hybrid State tRNA (A) Overview of the hybrid A/P (purple) and…

Interaction of Sec61 with the…

Interaction of Sec61 with the Ribosome (A) Overview of the region of the…

Conformation of Ribosome-Bound Sec61α (A)…

Conformation of Ribosome-Bound Sec61α (A) Overview of the lateral gate of the ribosome-bound…

The Translating Ribosome-Sec61 Complex (A)…

The Translating Ribosome-Sec61 Complex (A) Cryo-EM density within the ribosomal exit tunnel for…

A Two-Step Model for Activation…

A Two-Step Model for Activation of Sec61 Displayed here is a cut-away view…

Biochemical Characterization of the Ribosome-Sec61…

Biochemical Characterization of the Ribosome-Sec61 Sample, Related to Experimental Procedures (A) Immunoblot using…

Refinement and 3D Classification Strategy,…

Refinement and 3D Classification Strategy, Related to Experimental Procedures Each class in the…

Map and Model Quality, Related…

Map and Model Quality, Related to Figure 1 (A) Gold-standard Fourier Shell Correlation…

Examples of Revised and Newly…

Examples of Revised and Newly Visible Ribosome Features, Related to Figure 2 (A)…

Density in Different Regions of…

Density in Different Regions of the idle Sec61 Structure, Related to Figure 4…

Density and Features of the…

Density and Features of the Sec61 Structure Bound to the Translating Ribosome, Related…


Evolution of the ribosome at atomic resolution

The origins and evolution of the ribosome, 3-4 billion years ago, remain imprinted in the biochemistry of extant life and in the structure of the ribosome. Processes of ribosomal RNA (rRNA) expansion can be "observed" by comparing 3D rRNA structures of bacteria (small), yeast (medium), and metazoans (large). rRNA size correlates well with species complexity. Differences in ribosomes across species reveal that rRNA expansion segments have been added to rRNAs without perturbing the preexisting core. Here we show that rRNA growth occurs by a limited number of processes that include inserting a branch helix onto a preexisting trunk helix and elongation of a helix. rRNA expansions can leave distinctive atomic resolution fingerprints, which we call "insertion fingerprints." Observation of insertion fingerprints in the ribosomal common core allows identification of probable ancestral expansion segments. Conceptually reversing these expansions allows extrapolation backward in time to generate models of primordial ribosomes. The approach presented here provides insight to the structure of pre-last universal common ancestor rRNAs and the subsequent expansions that shaped the peptidyl transferase center and the conserved core. We infer distinct phases of ribosomal evolution through which ribosomal particles evolve, acquiring coding and translocation, and extending and elaborating the exit tunnel.

Keywords: C value RNA evolution origin of life phylogeny translation.

Conflict of interest statement

The authors declare no conflict of interest.

Figures

Phylogram indicating the sizes of…

Phylogram indicating the sizes of LSU rRNAs and the sizes of genomes. Circle…

LSU rRNA secondary structures. (…

LSU rRNA secondary structures. ( A ) E. coli , ( B )…

The evolution of helix 25/ES…

The evolution of helix 25/ES 7 shows serial accretion of rRNA onto a…

rRNA expansion elements in two…

rRNA expansion elements in two and three dimensions. ( A ) Helix 52…

Origins and evolution of the…

Origins and evolution of the PTC. Trunk rRNA is shown before and after…

rRNA evolution mapped onto the…

rRNA evolution mapped onto the LSU rRNA secondary structure. The common core is…


Researchers design first artificial ribosome

Researchers at the University of Illinois at Chicago and Northwestern University have engineered a tethered ribosome that works nearly as well as the authentic cellular component, or organelle, that produces all the proteins and enzymes within the cell. The engineered ribosome may enable the production of new drugs and next-generation biomaterials and lead to a better understanding of how ribosomes function.

The artificial ribosome, called Ribo-T, was created in the laboratories of Alexander Mankin, director of the UIC College of Pharmacy's Center for Biomolecular Sciences, and Northwestern's Michael Jewett, assistant professor of chemical and biological engineering. The human-made ribosome may be able to be manipulated in the laboratory to do things natural ribosomes cannot do.

When the cell makes a protein, mRNA (messenger RNA) is copied from DNA. The ribosomes' two subunits, one large and one small, unite on mRNA to form the functional unit that assembles the protein in a process called translation. Once the protein molecule is complete, the ribosome subunits -- both of which are themselves made up of RNA and protein -- separate from each other.

In a new study in the journal Nature, the researchers describe the design and properties of Ribo-T, a ribosome with subunits that will not separate. Ribo-T may be able to be tuned to produce unique and functional polymers for exploring ribosome functions or producing designer therapeutics -- and perhaps one day even non-biological polymers.

No one has ever developed something of this nature.

"We felt like there was a small -- very small -- chance Ribo-T could work, but we did not really know," Mankin said.

Mankin, Jewett and their colleagues were frustrated in their investigations by the ribosomes' subunits falling apart and coming together in every cycle of protein synthesis. Could the subunits be permanently linked together? The researchers devised a novel designer ribosome with tethered subunits -- Ribo-T.

"What we were ultimately able to do was show that by creating an engineered ribosome where the ribosomal RNA is shared between the two subunits and linked by these small tethers, we could actually create a dual translation system," Jewett said.

"It was surprising that our hybrid chimeric RNA could support assembly of a functional ribosome in the cell. It was also surprising that this tethered ribosome could support growth in the absence of wild-type ribosomes," he said.

Ribo-T worked even better than Mankin and Jewett believed it could. Not only did Ribo-T make proteins in a test-tube, it was able to make enough protein in bacterial cells that lacked natural ribosomes to keep the bacteria alive.

Jewett and Mankin were surprised by this. Scientists had previously believed that the ability of the two ribosomal subunits to separate was required for protein synthesis.

"Obviously this assumption was incorrect," Jewett said.

"Our new protein-making factory holds promise to expand the genetic code in a unique and transformative way, providing exciting opportunities for synthetic biology and biomolecular engineering," Jewett said.

"This is an exciting tool to explore ribosomal functions by experimenting with the most critical parts of the protein synthesis machine, which previously were 'untouchable,'" Mankin added.


Ribosome

Quick look:
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)

This is an electron microscope image showing part of the rough endoplasmic reticulum in a plant root cell from maize. The dark spots are ribosomes.

(courtesy of Chris Hawes, The Research School of Biology & Molecular Sciences, Oxford Brookes University, Oxford, UK)

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)

Binding Site

mRNA strand entry site

Biological term

Main processes

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

Site E

Preparation of ‘uncharged’ tRNA for exit

The Three stages:

  1. 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)].
  1. 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.
  2. 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’.

An overview diagram of protein production, including a note about protein modification.


The regulating hand in ribosome formation

Ribosomes, which use a fixed genetic programme to manufacture cell proteins, also form according to a strict hierarchical plan. In an interdisciplinary approach, the research teams of Prof. Dr. Ed Hurt of the Heidelberg University Biochemistry Center (BZH) and Prof. Dr. André Hoelz of the California Institute of Technology (Caltech) in Pasadena (USA) have decoded the mechanism that regulates this process. They discovered a previously unknown protein that regulates the processes in the cell nucleus that permit the cell to incorporate ribosomal proteins into the developing pre-ribosome in the correct order. The results of their research were published online in "Molecular Cell."

Ribosomes are complexly structured cellular nanomachines consisting of four ribonucleic acids and approximately 80 different ribosomal proteins (r-proteins). They are responsible for synthesising protein chains. "Correct ribosomal formation is of elementary importance in cell division and propagation. Their structure is highly complicated because all ribosomal proteins are added to the developing pre-ribosome in a strict sequence, with approximately 200 helper proteins assisting in the process," says Ed Hurt.

In eukaryotes, new ribosomes are formed primarily in the cell nucleus. The r-proteins needed for their formation must travel from the cell plasma to the site in the nucleus where the ribosomes are manufactured, called the nucleolus. Until now, scientists knew only that r-proteins were built into the newly forming ribosome following a strict hierarchy -- r-protein B comes after r-protein A and so on. "But the question of how the strict sequence is ensured and who is responsible remained largely unanswered," explains Prof. Hurt.

The researchers have now been able to demonstrate that the newly discovered protein, called the assembly chaperone of L4 or Acl4, regulates the orderly integration of ribosomal protein L4 into the early pre-ribosome. "This employs a well-known everyday concept, like an usher holding a seat open until the correct occupant arrives," explains the researcher.

Using new investigative procedures, the two primary authors of the publication, Dr. Philipp Stelter of the BZH and Ferdinand Huber of Caltech, were able to decode the detection mechanism between the L4 r-protein and the developing ribosome. According to the researchers, the underlying basis is a eukaryote-specific extension of the L4 ribosomal protein that comes into contact with the surface of the ribosome and is released for assembly by the Acl4 helper protein. If these interactions are hindered by insufficient production of the r-protein or an error in the growing ribosome, the helper protein remains bound and prevents the development of a faulty ribosome.

The collaboration between the researchers of the Heidelberg University Biochemistry Center and the California Institute of Technology offered an opportunity to combine traditional and newly developed methods in cellular biology, biochemistry and biophysics. "This was pivotal for the detailed characterisation of the newly discovered mechanisms and the participating components," emphasises Ed Hurt.


Alert to biologists: Ribosomes can translate 'untranslated region' of messenger RNA

In what appears to be an unexpected challenge to a long-accepted fact of biology, Johns Hopkins researchers say they have found that ribosomes -- the molecular machines in all cells that build proteins -- can sometimes do so even within the so-called untranslated regions of the ribbons of genetic material known as messenger RNA (mRNA).

"This is an exciting find that generates a whole new set of questions for researchers," says Rachel Green, Ph.D., a Howard Hughes Medical Institute investigator and professor of molecular biology and genetics at the Johns Hopkins University School of Medicine. Chief among them, she adds, is whether the proteins made in this unusual way have useful or damaging functions and under what conditions, questions that have the potential to further our understanding of cancer cell growth and how cells respond to stress.

In a summary of the findings in yeast cells, to be published Aug. 13 in the journal Cell, Green and her team report that the atypical protein-making happens when ribosomes fail to get "recycled" when they reach the "stop" signal in the mRNA. For reasons not yet understood, Green says, "rogue" ribosomes restart without a "start" signal and make small proteins whose functions are unknown.

Ribosomes are made out of specialized RNA molecules (DNA's chemical cousin) that work together with proteins to read instruction-bearing mRNAs and "translate" their message to create proteins. Each mRNA begins with a "start" code, followed by the blueprint for a specific protein, followed by a "stop" code. And then there's a segment of code that has always been called the "untranslated region," because scientists never saw it translated into protein.

But no longer, according to Green and postdoctoral fellow Nicholas Guydosh, Ph.D., who, along with a team at the National Institute of Child Health and Human Development, began the project out of curiosity about a yeast protein called Rli1.

Previous studies had shown that Rli1 can split ribosomes into their two component parts once they encounter a stop code and are no longer needed. This "recycling" process, they say, disengages a ribosome from its current mRNA molecule so that it's available to translate another one. But it was unclear whether Rli1 behaved the same way in live cells.

To find out, the researchers deprived living yeast cells of Rli1, predicting that translation would slow down as ribosomes piled up at stop codes. To "see" where the ribosomes were, the team added an enzyme to the cells that would chew up any exposed RNA. The RNA bound by ribosomes would be protected and could then be isolated and identified. As predicted, the depletion of Rli1 increased the number of ribosomes sitting on stop codes. But they also saw evidence of ribosomes sitting in the untranslated region, which they called a surprise.

To find out if the ribosomes were actually reading from the untranslated region to create proteins, the team inserted genetic code in that region for a protein whose quantity they could easily measure. Cells with Rli1 didn't make the protein, but cells missing Rli1 did, proving that their ribosomes were indeed active in the untranslated region.

Further experiments showed that the ribosomes weren't just continuing translation past the stop code to create an extra-long protein. They first released the regularly coded protein as usual and then began translation again nearby.

"It seems like the ribosomes get tired of waiting to be disassembled and decide to get back to work," says Guydosh. "The protein-making work that appears right in front of them is in the untranslated region."

As noted, the purpose of these many small proteins is unknown, but Green says one possibility stems from the fact that ribosomes increase in the untranslated region when yeast are stressed by a lack of food. "It's possible that these small proteins actually help the yeast respond to starvation, but that's just a guess," she says.

Because ribosomes are essential to create new proteins and cell growth, Green notes, scientists believe the rate at which cells replicate is determined, at least in part, by how many ribosomes they have. Cells lacking Rli1 can't grow because their ribosomes are all occupied at stop codes and in untranslated regions. Thus cancer cells increase their levels of Rli1 in order to grow rapidly.

"We didn't understand previously how important ribosome recycling is for the proper translation of mRNA," says Green. "Without it, ribosomes are distracted from their usual work, which is crucial for normal cell maintenance and growth. This finding opens up questions we didn't even know to ask before."


Watch the video: Μικροσκοπική παρατήρηση Φυτικών-Ζωικών κυττάρων (August 2022).