RIBOSOMES: CHARACTERISTICS, TYPES, STRUCTURE, FUNCTIONS - BIOLOGY - 2024

The ribosomes are the most abundant cell organelles and are involved in protein synthesis. They are not surrounded by a membrane and are made up of two types of subunits: a large and a small, as a general rule the large subunit is almost twice the small.

The prokaryotic lineage possesses 70S ribosomes composed of a large 50S and a small 30S subunit. Likewise, ribosomes of the eukaryotic lineage are composed of a large 60S and a small 40S subunit.

The ribosome is analogous to a moving factory, capable of reading messenger RNA, translating it into amino acids, and linking them together by peptide bonds.

Ribosomes are equivalent to almost 10% of the total proteins of a bacterium and more than 80% of the total amount of RNA. In the case of eukaryotes, they are not as abundant with respect to other proteins but their number is higher.

In 1950, researcher George Palade first visualized ribosomes and this discovery was awarded the Nobel Prize in physiology or medicine.

General characteristics

Ribosomes are essential components of all cells and are related to protein synthesis. They are very small in size so they can only be visualized under the light of an electron microscope.

Ribosomes are found free in the cell's cytoplasm, anchored in the rough endoplasmic reticulum - ribosomes give it that "wrinkled" appearance - and in some organelles, such as mitochondria and chloroplasts.

Membrane-bound ribosomes are responsible for the synthesis of proteins that will be inserted into the plasma membrane or will be sent to the outside of the cell.

Free ribosomes, which are not coupled to any structure in the cytoplasm, synthesize proteins whose destination is inside the cell. Finally, the ribosomes of the mitochondria synthesize proteins for mitochondrial use.

In the same way, several ribosomes can join and form "polyribosomes", forming a chain coupled to a messenger RNA, synthesizing the same protein, multiple times and simultaneously

They are all composed of two subunits: one called large or larger and the other small or smaller.

Some authors consider ribosomes to be nonmembranous organelles, since they lack these lipid structures, although other researchers do not consider them as organelles themselves.

Structure

Ribosomes are small cellular structures (from 29 to 32 nm, depending on the group of organism), rounded and dense, composed of ribosomal RNA and protein molecules, which are associated with each other.

The most studied ribosomes are those of eubacteria, archaea and eukaryotes. In the first lineage the ribosomes are simpler and smaller. Eukaryotic ribosomes, for their part, are more complex and larger. In archaea, ribosomes are more similar to both groups in certain respects.

Vertebrate and angiosperm ribosomes (flowering plants) are particularly complex.

Each ribosomal subunit is made up primarily of ribosomal RNA and a wide variety of proteins. The large subunit can be made up of small RNA molecules in addition to ribosomal RNA.

Proteins are coupled to ribosomal RNA in specific regions, following an order. Within ribosomes, several active sites can be distinguished, such as catalytic zones.

Ribosomal RNA is of crucial importance to the cell and this can be seen in its sequence, which has been virtually unchanged during evolution, reflecting the high selective pressures against any change.

Ribosome functions

Ribosomes are responsible for mediating the protein synthesis process in the cells of all organisms, being a universal biological machinery.

Ribosomes - together with transfer RNA and messenger RNA - manage to decode the DNA message and interpret it into a sequence of amino acids that will form all the proteins in an organism, in a process called translation.

In the light of biology, the word translation refers to the change of "language" from nucleotide triplets to amino acids.

These structures are the central part of translation, where most of the reactions occur, such as the formation of peptide bonds and the release of the new protein.

Protein translation

The process of protein formation begins with the union between a messenger RNA and a ribosome. The messenger travels through this structure at a specific end called the "chain initiator codon."

As the messenger RNA passes through the ribosome, a protein molecule is formed, because the ribosome is capable of interpreting the message encoded in the messenger.

This message is encoded in nucleotide triplets, with every three bases indicating a particular amino acid. For example, if the messenger RNA carries the sequence: AUG AUU CUU UUG GCU, the peptide formed will consist of the amino acids: methionine, isoleucine, leucine, leucine, and alanine.

This example shows the “degeneracy” of the genetic code, since more than one codon - in this case CUU and UUG - is coding for the same type of amino acid. When the ribosome detects a stop codon in messenger RNA, translation ends.

The ribosome has an A site and a P site. The P site holds the peptidyl-tRNA and the aminoacyl-tRNA enters the A site.

Transfer RNA

Transfer RNAs are responsible for transporting the amino acids to the ribosome and have the sequence complementary to the triplet. There is a transfer RNA for each of the 20 amino acids that make up proteins.

Chemical steps of protein synthesis

The process begins with the activation of each amino acid with the binding of ATP in an adenosine monophosphate complex, releasing high-energy phosphates.

The previous step results in an amino acid with excess energy and binding occurs with its respective transfer RNA, to form an amino acid-tRNA complex. Here the release of adenosine monophosphate occurs.

In the ribosome, the transfer RNA meets the messenger RNA. At this stage the sequence of the transfer or anticodon RNA hybridizes with the codon or triplet of the messenger RNA. This leads to the alignment of the amino acid with its proper sequence.

The enzyme peptidyl transferase is responsible for catalyzing the formation of peptide bonds that bind amino acids. This process consumes large amounts of energy, as it requires the formation of four high-energy bonds for each amino acid that is attached to the chain.

The reaction removes a hydroxyl radical at the COOH end of the amino acid and removes a hydrogen at the NH ₂ end of the other amino acid. The reactive regions of the two amino acids come together and create the peptide bond.

Ribosomes and antibiotics

As protein synthesis is an essential event for bacteria, certain antibiotics target ribosomes and different stages of the translation process.

For example, streptomycin binds to the small subunit to interfere with the translation process, causing errors in the reading of messenger RNA.

Other antibiotics, such as neomycins and gentamicins, can also cause errors in translation, coupling to the small subunit.

Types of ribosomes

Ribosomes in prokaryotes

Bacteria, like E. coli, possess more than 15,000 ribosomes (in proportions this equates to almost a quarter of the dry weight of the bacterial cell).

Ribosomes in bacteria have a diameter of about 18 nm and are made up of 65% ribosomal RNA and only 35% proteins of various sizes, between 6,000 and 75,000 kDa.

The large subunit is called 50S and the small 30S, which combine to form a 70S structure with a molecular mass of 2.5 × 10 ⁶ kDa.

The 30S subunit is elongated in shape and not symmetrical, while the 50S is thicker and shorter.

The small subunit of E. coli is composed of 16S ribosomal RNAs (1542 bases) and 21 proteins, and the large subunit contains 23S ribosomal RNAs (2904 bases), 5S (1542 bases), and 31 proteins. The proteins that compose them are basic and the number varies according to the structure.

Ribosomal RNA molecules, along with proteins, are grouped together in a secondary structure similar to other types of RNA.

Ribosomes in eukaryotes

Ribosomes in eukaryotes (80S) are larger, with a higher content of RNA and protein. RNAs are longer and are called 18S and 28S. As in prokaryotes, the composition of ribosomes is dominated by ribosomal RNA.

In these organisms, the ribosome has a molecular mass of 4.2 × 10 ⁶ kDa and is decomposed into the 40S and 60S subunit.

The 40S subunit contains a single RNA molecule, 18S (1874 bases), and about 33 proteins. Similarly, the 60S subunit contains the RNAs 28S (4718 bases), 5.8S (160 bases) and 5S (120 bases). In addition, it is made up of basic proteins and acid proteins.

Ribosomes in archaea

Archaea are a group of microscopic organisms that resemble bacteria, but differ in so many characteristics that they constitute a separate domain. They live in diverse environments and are capable of colonizing extreme environments.

The types of ribosomes found in archaea are similar to the ribosomes of eukaryotic organisms, although they also have certain characteristics of bacterial ribosomes.

It has three types of ribosomal RNA molecules: 16S, 23S and 5S, coupled to 50 or 70 proteins, depending on the species of study. In terms of size, archaea ribosomes are closer to bacterial ones (70S with two subunits 30S and 50S) but in terms of their primary structure they are closer to eukaryotes.

As archaea tend to inhabit environments with high temperatures and high salt concentrations, their ribosomes are highly resistant.

Sedimentation coefficient

The S or Svedbergs, refers to the sedimentation coefficient of the particle. It expresses the relation between the constant speed of sedimentation and the applied acceleration. This measure has dimensions of time.

Note that Svedbergs are not additive, since they take into account the mass and shape of the particle. For this reason, in bacteria the ribosome composed of 50S and 30S subunits does not add up to 80S, likewise the 40S and 60S subunits do not form a 90S ribosome.

Ribosome synthesis

All the cellular machinery necessary for the synthesis of ribosomes is found in the nucleolus, a dense region of the nucleus that is not surrounded by membranous structures.

The nucleolus is a variable structure depending on the cell type: it is large and conspicuous in cells with high protein requirements and it is an almost imperceptible area in cells that synthesize little protein.

The processing of ribosomal RNA occurs in this area, where it couples with ribosomal proteins and gives rise to granular condensation products, which are the immature subunits that form functional ribosomes.

The subunits are transported outside the nucleus - through the nuclear pores - to the cytoplasm, where they are assembled into mature ribosomes that can begin protein synthesis.

Ribosomal RNA genes

In humans, the genes that code for ribosomal RNAs are found on five specific chromosome pairs: 13, 14, 15, 21 and 22. Since cells require large numbers of ribosomes, the genes are repeated several times on these chromosomes.

The nucleolus genes encode for 5.8S, 18S, and 28S ribosomal RNAs and are transcribed by RNA polymerase into a 45S precursor transcript. 5S ribosomal RNA is not synthesized in the nucleolus.

Origin and evolution

Modern ribosomes must have appeared in the time of LUCA, the last universal common ancestor, probably in the hypothetical world of RNA. It is proposed that transfer RNAs were fundamental for the evolution of ribosomes.

This structure could arise as a complex with self-replicating functions that later acquired functions for the synthesis of amino acids. One of the most outstanding characteristics of RNA is its ability to catalyze its own replication.

References

1. Berg JM, Tymoczko JL, Stryer L. (2002). Biochemistry. 5th edition. New York: WH Freeman. Section 29.3, A Ribosome Is a Ribonucleoprotein Particle (70S) Made of a Small (30S) and a Large (50S) Subunit. Available at: ncbi.nlm.nih.gov
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