If earlier the opinion about the secondary role of RNA prevailed, now it is clear that it is a necessary and most important element of cell vital activity. The mechanisms of many...

By Masterweb

09.04.2018 14:00

Various types of DNA and RNA - nucleic acids - is one of the objects of study of molecular biology. One of the most promising and rapidly developing areas in this science in recent years has been the study of RNA.

Briefly about the structure of RNA

So, RNA, ribonucleic acid, is a biopolymer whose molecule is a chain formed by four types of nucleotides. Each nucleotide, in turn, consists of a nitrogenous base (adenine A, guanine G, uracil U or cytosine C) in combination with a ribose sugar and a phosphoric acid residue. Phosphate residues, connecting with the riboses of neighboring nucleotides, "sew" the constituent blocks of RNA into a macromolecule - a polynucleotide. This is how the primary structure of RNA is formed.

The secondary structure - the formation of a double chain - is formed in some parts of the molecule in accordance with the principle of complementarity of nitrogenous bases: adenine forms a pair with uracil through a double, and guanine with cytosine - a triple hydrogen bond.

In the working form, the RNA molecule also forms a tertiary structure - a special spatial structure, conformation.

RNA synthesis

All types of RNA are synthesized using the enzyme RNA polymerase. It can be DNA- and RNA-dependent, that is, it can catalyze synthesis on both DNA and RNA templates.

The synthesis is based on the complementarity of the bases and the antiparallelism of the reading direction of the genetic code and proceeds in several stages.

First, RNA polymerase is recognized and bound to a special nucleotide sequence on DNA - the promoter, after which the DNA double helix unwinds in a small area and the assembly of the RNA molecule begins over one of the chains, called the template (the other DNA chain is called coding - it is its copy that is synthesized RNA). The asymmetry of the promoter determines which of the DNA strands will serve as a template, and thus allows RNA polymerase to initiate synthesis in the correct direction.

The next step is called elongation. The transcription complex, which includes RNA polymerase and an untwisted region with a DNA-RNA hybrid, begins to move. As this movement proceeds, the growing RNA strand gradually separates, and the DNA double helix unwinds in front of the complex and reassembles behind it.

The final stage of synthesis occurs when RNA polymerase reaches a specific region of the matrix called the terminator. Termination (end) of the process can be achieved in various ways.

The main types of RNA and their functions in the cell

They are the following:

• Matrix or informational (mRNA). Through it, transcription is carried out - the transfer of genetic information from DNA.
• Ribosomal (rRNA), which provides the process of translation - protein synthesis on the mRNA template.
• Transport (tRNA). Produces recognition and transport of amino acids to the ribosome, where protein synthesis occurs, and also takes part in translation.
• Small RNAs are an extensive class of small molecules that perform various functions during the processes of transcription, RNA maturation, and translation.
• RNA genomes are coding sequences that contain genetic information in some viruses and viroids.

In the 1980s, the catalytic activity of RNA was discovered. Molecules with this property are called ribozymes. There are not so many natural ribozymes yet known, their catalytic ability is lower than that of proteins, but in the cell they perform extremely important functions. Currently, successful work is underway on the synthesis of ribozymes, which, among other things, have applied significance.

Let us dwell in more detail on the different types of RNA molecules.

Matrix (information) RNA

This molecule is synthesized over the untwisted section of DNA, thus copying the gene encoding a particular protein.

RNA of eukaryotic cells, before becoming, in turn, a matrix for protein synthesis, must mature, that is, go through a complex of various modifications - processing.

First of all, even at the stage of transcription, the molecule undergoes capping: a special structure of one or more modified nucleotides, the cap, is attached to its end. It plays an important role in many downstream processes and enhances mRNA stability. The so-called poly(A) tail, a sequence of adenine nucleotides, is attached to the other end of the primary transcript.

The pre-mRNA is then spliced. This is the removal of non-coding regions from the molecule - introns, which are abundant in eukaryotic DNA. Next, the mRNA editing procedure occurs, in which its composition is chemically modified, as well as methylation, after which the mature mRNA leaves the cell nucleus.

Ribosomal RNA

The basis of the ribosome, a complex that provides protein synthesis, is made up of two long rRNAs that form subparticles of the ribosome. They are synthesized together as a single pre-rRNA, which is then separated during processing. The large subunit also includes low molecular weight rRNA synthesized from a separate gene. Ribosomal RNAs have a densely packed tertiary structure that serves as a scaffold for proteins that are present in the ribosome and perform auxiliary functions.

In the non-working phase, the ribosome subunits are separated; at the initiation of the translational process, the rRNA of the small subunit combines with messenger RNA, after which the elements of the ribosome are completely combined. When the RNA of the small subunit interacts with the mRNA, the latter, as it were, stretches through the ribosome (which is equivalent to the movement of the ribosome along the mRNA). The ribosomal RNA of the large subunit is a ribozyme, that is, it has enzymatic properties. It catalyses the formation of peptide bonds between amino acids during protein synthesis.

It should be noted that the largest part of all RNA in the cell is ribosomal - 70-80%. DNA has a large number of genes encoding rRNA, which ensures its very intensive transcription.

Transfer RNA

This molecule is recognized by a certain amino acid with the help of a special enzyme and, connecting with it, transports the amino acid to the ribosome, where it serves as an intermediary in the process of translation - protein synthesis. The transfer is carried out by diffusion in the cytoplasm of the cell.

The newly synthesized tRNA molecules, like other types of RNA, are processed. Mature tRNA in its active form has a conformation resembling a cloverleaf. On the "petiole" of the leaf - the acceptor site - there is a CCA sequence with a hydroxyl group that binds to the amino acid. At the opposite end of the "leaf" is an anticodon loop that connects to a complementary codon on the mRNA. The D-loop serves to bind the transfer RNA to the enzyme when interacting with the amino acid, and the T-loop is used to bind to the large subunit of the ribosome.

Small RNA

These types of RNA play an important role in cellular processes and are now being actively studied.

For example, small nuclear RNAs in eukaryotic cells are involved in mRNA splicing and possibly have catalytic properties along with spliceosome proteins. Small nucleolar RNAs are involved in the processing of ribosomal and transfer RNA.

Small interfering and microRNAs are the most important elements of the gene expression regulation system, which is necessary for the cell to control its own structure and vital activity. This system is an important part of the cell's immune antiviral response.

There is also a class of small RNAs that function in complex with Piwi proteins. These complexes play a huge role in the development of germline cells, in spermatogenesis, and in the suppression of transposable genetic elements.

RNA genome

The RNA molecule can be used as the genome by most viruses. Viral genomes are different - single- and double-stranded, circular or linear. Also, RNA genomes of viruses are often segmented and generally shorter than DNA-containing genomes.

There is a family of viruses whose genetic information, encoded in RNA, after infection of the cell by reverse transcription, is rewritten to DNA, which is then introduced into the genome of the victim cell. These are the so-called retroviruses. These include, in particular, the human immunodeficiency virus.

Significance of RNA research in modern science

If earlier the opinion about the secondary role of RNA prevailed, now it is clear that it is a necessary and most important element of intracellular life activity. Many processes of paramount importance cannot do without the active participation of RNA. The mechanisms of such processes remained unknown for a long time, but thanks to the study of various types of RNA and their functions, many details are gradually becoming clear.

It is possible that RNA played a decisive role in the emergence and development of life at the dawn of the Earth's history. The results of recent studies speak in favor of this hypothesis, testifying to the extraordinary antiquity of many mechanisms of cell functioning with the participation of certain types of RNA. For example, the recently discovered riboswitches as part of mRNA (a system of protein-free regulation of gene activity at the transcription stage), according to many researchers, are echoes of an era when primitive life was built on the basis of RNA, without the participation of DNA and proteins. MicroRNAs are also considered to be a very ancient component of the regulatory system. The structural features of the catalytically active rRNA indicate its gradual evolution by adding new fragments to the ancient protoribosome.

A thorough study of which types of RNA and how are involved in certain processes is also extremely important for theoretical and applied fields of medicine.

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Transfer RNA, tRNA-ribonucleic acid, the function of which is to transport AA to the site of protein synthesis. It has a typical length of 73 to 93 nucleotides and a size of about 5 nm. tRNAs are also directly involved in the growth of the polypeptide chain, joining - being in a complex with an amino acid - to the mRNA codon and providing the conformation of the complex necessary for the formation of a new peptide bond. Each amino acid has its own tRNA. tRNA is a single-stranded RNA, but in its functional form it has a cloverleaf conformation. AA covalently attaches to the 3 "end of the molecule using the enzyme aminoacyl-tRNA synthetase, specific for each type of tRNA. At site C, there is an anticodon corresponding to AA-te. tRNAs are synthesized by ordinary RNA polymerase in the case of prokaryotes and by RNA polymerase III in the case of eukaryotes Transcripts of tRNA genes undergo multistage processing, which leads to the formation of a spatial structure typical of tRNA.

tRNA processing involves 5 key steps:

removal of the 5" leader nucleotide sequence;

removal of the 3'-terminal sequence;

adding a CCA sequence at the 3" end;

excision of introns (in eukaryotes and archaea);

modifications of individual nucleotides.

Transport of tRNA is carried out along a Ran-dependent pathway with the participation of the transport factor exportin t, which recognizes the characteristic secondary and tertiary str-ru of mature tRNA: short double-stranded sections and correctly processed 5 "- and 3" ends. This mechanism ensures that only mature tRNAs are exported from the nucleus.

62. Translation - mRNA codon recognition
Translation is a protein synthesis carried out by ribosomes from amino acids on an mRNA (or and RNA) template. The constituent elements of the translation process: amino acids, tRNA, ribosomes, mRNA, enzymes for aminoacylation of tRNA, protein translation factors (protein factors of initiation, elongation, termination - specific extraribosomal proteins necessary for translation processes), ATP and GTP energy sources, magnesium ions (stabilize ribosome structure). 20 amino acids are involved in protein synthesis. In order for an amino acid to “recognize” its place in the future polypeptide chain, it must bind to a transfer RNA (tRNA) that performs an adapter function. The tRNA that binds to the amino acid then recognizes the corresponding codon on the mRNA. mRNA codon recognition:

The codon-anticodon interaction is based on the principles of complementarity and antiparallelism:

3'----C - G-A*------5' tRNA anticodon

5'-----G-C-Y*------3' mRNA codon

The wobble hypothesis was proposed by F. Crick:

The 3'-base of the mRNA codon has a non-strict pairing with the 5'-base of the tRNA anticodon: for example, Y (mRNA) can interact with A and G (tRNA)

Some tRNAs can pair with more than one codon.

63. Characteristics of the constituent elements of the translation process. Translation (translatio-translation) is the process of protein synthesis from amino acids on the matrix of informational (matrix) RNA (mRNA, mRNA) carried out by the ribosome.

Protein synthesis is the basis of cell life. To carry out this process in the cells of all organisms there are special organelles - ribosomes- ribonucleoprotein complexes built from 2 subunits: large and small. The function of ribosomes is to recognize three-letter (three-nucleotide) codons mRNA, comparing them with the corresponding tRNA anticodons carrying amino acids, and the addition of these amino acids to the growing protein chain. Moving along the mRNA molecule, the ribosome synthesizes a protein in accordance with the information contained in the mRNA molecule.

For recognition of AK-t in the cell, there are special "adapters", transfer RNA molecules(tRNA). These cloverleaf-shaped molecules have a site (anticodon) complementary to an mRNA codon, as well as another site to which the amino acid corresponding to that codon is attached. The attachment of amino acids to tRNA is carried out in an energy-dependent reaction by enzymes aminoacyl-tRNA synthetases, and the resulting molecule is called aminoacyl-tRNA. Thus, the specificity of translation is determined by the interaction between the mRNA codon and the tRNA anticodon, as well as the specificity of aminoacyl-tRNA synthetases that attach amino acids strictly to their corresponding tRNAs (for example, the GGU codon will correspond to a tRNA containing the CCA anticodon, and only AK glycine).

prokaryotic ribosome

5S and 23S rRNA 16S rRNA

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Prokaryotic ribosomes have a sedimentation constant of 70S, which is why they are called 70S particles. They are built from two different subunits: 30S and 50S subunits. Each subunit is a complex of rRNA and ribosomal proteins.

The 30S particle contains one 16S rRNA molecule and in most cases one protein molecule from more than 20 species (21) . The 50S subunit consists of two rRNA molecules (23S and 5S). It consists of more than 30 different proteins (34), also represented, as a rule, by one copy. Most of the ribosomal proteins perform a structural function.

eukaryotic ribosome

5S; 5,8S and 28S rRNA 18S rRNA

at least 50 proteins at least 33 proteins

The ribosome consists of large and small subunits. The basis of the structure of each subunit is a complexly folded rRNA. Ribosome proteins were attached to the rRNA scaffold.

The sedimentation coefficient of a complete eukaryotic ribosome is about 80 Svedberg units (80S), and the sedimentation coefficient of its subparticles is 40S and 60S.

The smaller 40S subunit consists of one 18S rRNA molecule and 30-40 protein molecules. The large 60S subunit contains three types of rRNA with sedimentation coefficients of 5S, 5.8S, and 28S and 40-50 proteins (for example, rat hepatocyte ribosomes include 49 proteins).

Functional regions of ribosomes

P - peptidyl site for peptidyl tRNA

A - aminoacyl site for aminoacyl tRNA

E - site for the release of tRNA from the ribosome

The ribosome contains 2 functional sites for interaction with tRNA: aminoacyl (acceptor) and peptidyl (donor). Aminoacyl-tRNA enters the acceptor site of the ribosome and interacts to form hydrogen bonds between codon and anticodon triplets. After the formation of hydrogen bonds, the system advances 1 codon and ends up in the donor site. At the same time, a new codon appears in the vacated acceptor site, and the corresponding aminoacyl-t-RNA is attached to it.

Ribosomes: structure, function

Ribosomes are the cytoplasmic centers of protein biosynthesis. They consist of large and small subunits, differing in sedimentation coefficients (sedimentation rate during centrifugation), expressed in units of Svedberg - S.

Ribosomes are present in both eukaryotic and prokaryotic cells, as they perform an important function in protein biosynthesis. Each cell contains tens, hundreds of thousands (up to several million) of these small rounded organelles. It is a rounded ribonucleoprotein particle. Its diameter is 20-30 nm. The ribosome consists of large and small subunits, differing in sedimentation coefficients (sedimentation rate during centrifugation), expressed in Svedberg units - S. These subunits are combined in the presence of a strand of m-RNA (matrix, or informational, RNA). A complex of a group of ribosomes united by a single mRNA molecule like a string of beads is called polysome. These structures are either freely located in the cytoplasm or attached to the membranes of the granular ER (in both cases, protein synthesis actively proceeds on them).

Polysomes of granular ER form proteins that are excreted from the cell and used for the needs of the whole organism (for example, digestive enzymes, proteins of human breast milk). In addition, ribosomes are present on the inner surface of mitochondrial membranes, where they also take an active part in the synthesis of protein molecules.

The cytoplasm of cells contains three main functional types of RNA:

• messenger RNA (mRNA) that act as templates for protein synthesis;
• ribosomal RNA (rRNA), which act as structural components of ribosomes;
• transfer RNAs (tRNAs) involved in the translation (translation) of mRNA information into the amino acid sequence of a protein molecule.

In the nucleus of cells, nuclear RNA is found, constituting from 4 to 10% of the total cellular RNA. The bulk of nuclear RNA is represented by high-molecular precursors of ribosomal and transfer RNA. Precursors of high molecular weight rRNAs (28 S, 18 S and 5 S RNA) are mainly localized in the nucleolus.

RNA is main genetic material in some viruses of animals and plants (genomic RNA). Most RNA viruses are characterized by reverse transcription of their RNA genome, directed by reverse transcriptase.

All ribonucleic acids are ribonucleotide polymers, connected, as in a DNA molecule, by 3",5"-phosphorodiester bonds. Unlike DNA, which has a double-stranded structure, RNA is single-stranded linear polymer molecules.

mRNA structure. mRNA is the most heterogeneous class of RNA in terms of size and stability. The content of mRNA in cells is 2-6% of the total amount of RNA. mRNAs consist of sections - cistrons, which determine the sequence of amino acids in the proteins they encode.

tRNA structure . Transfer RNAs act as mediators (adapters) in the course of mRNA translation. They account for approximately 15% of total cellular RNA. Each of the 20 proteinogenic amino acids has its own tRNA. For some amino acids encoded by two or more codons, there are multiple tRNAs. tRNAs are relatively small single-stranded molecules consisting of 70-93 nucleotides. Their molecular weight is (2.4-3.1) .104 kDa.

Secondary structure of tRNA is formed due to the formation of the maximum number of hydrogen bonds between intramolecular complementary pairs of nitrogenous bases. As a result of the formation of these bonds, the tRNA polynucleotide chain twists with the formation of spiralized branches ending in loops of unpaired nucleotides. The spatial image of the secondary structures of all tRNAs has the form clover leaf.

In the "cloverleaf" distinguish four required branches, longer tRNAs also contain short fifth (additional) branch. The adapter function of tRNA is provided by an acceptor branch, to the 3 "end of which an amino acid residue is attached by an ether bond, and an anticodon branch opposite the acceptor branch, at the top of which there is a loop containing an anticodon. An anticodon is a specific triplet of nucleotides that is complementary in the antiparallel direction to the mRNA codon, encoding the corresponding amino acid.

The T-branch carrying the pseudouridine loop (TyC-loop) ensures the interaction of tRNA with ribosomes.

The D-branch, carrying the dehydrouridine loop, ensures the interaction of tRNA with the corresponding aminoacyl-tRNA synthetase.

Secondary structure of tRNA

The functions of the fifth additional branch are still poorly understood; most likely, it equalizes the length of different tRNA molecules.

Tertiary structure of tRNA very compact and is formed by bringing together individual branches of a clover leaf due to additional hydrogen bonds to form an L-shaped structure "elbow bend". In this case, the acceptor arm that binds the amino acid is located at one end of the molecule, and the anticodon is at the other.

Tertiary structure of tRNA (according to A.S. Spirin)

The structure of rRNA and ribosomes . Ribosomal RNAs form the scaffold to which specific proteins bind to form ribosomes. Ribosomes are nucleoprotein organelles that provide protein synthesis from mRNA. The number of ribosomes in a cell is very large: from 104 in prokaryotes to 106 in eukaryotes. Ribosomes are localized mainly in the cytoplasm, in eukaryotes, in addition, in the nucleolus, in the matrix of mitochondria and in the stroma of chloroplasts. Ribosomes are made up of two subunits: large and small. By size and molecular weight, all studied ribosomes are divided into 3 groups - 70S ribosomes of prokaryotes (S-sedimentation coefficient), consisting of small 30S and large 50S subparticles; 80S eukaryotic ribosomes, consisting of 40S small and 60S large subunits.

Small subparticle The 80S ribosome is made up of one rRNA molecule (18S) and 33 molecules of various proteins. Large subparticle formed by three rRNA molecules (5S, 5.8S and 28S) and about 50 proteins.

Secondary structure of rRNA is formed due to short double-stranded sections of the molecule - hairpins (about 2/3 of rRNA), 1/3 - is represented single strand sections rich in purine nucleotides.

Nucleic acids are macromolecular substances consisting of mononucleotides, which are connected to each other in a polymer chain using 3",5" - phosphodiester bonds and packed in cells in a certain way.

Nucleic acids are biopolymers of two varieties: ribonucleic acid (RNA) and deoxyribonucleic acid (DNA). Each biopolymer consists of nucleotides that differ in carbohydrate residue (ribose, deoxyribose) and one of the nitrogenous bases (uracil, thymine). Accordingly, nucleic acids got their name.

Structure of ribonucleic acid

Primary structure of RNA

RNA molecule are linear (i.e., unbranched) polynucleotides with a similar organization principle to DNA. RNA monomers are nucleotides consisting of phosphoric acid, a carbohydrate (ribose), and a nitrogenous base connected by 3", 5" phosphodiester bonds. The polynucleotide chains of the RNA molecule are polar, i.e. have distinguishable 5'- and 3"-ends. At the same time, unlike DNA, RNA is a single-stranded molecule. The reason for this difference is three features of the primary structure:

1. RNA, unlike DNA, contains ribose instead of deoxyribose, which has an additional hydroxyl group. The hydroxy group makes the double strand structure less compact
2. Among the four main, or major, nitrogenous bases (A, G, C and U), instead of thymine, uracil is contained, which differs from thymine only in the absence of a methyl group in the 5th position. Due to this, the strength of the hydrophobic interaction in the complementary A-U pair decreases, which also reduces the likelihood of the formation of stable double-stranded molecules.
3. Finally, RNA (especially tRNA) has a high content of so-called. minor bases and nucleosides. Among them are dihydrouridine (there is no single double bond in uracil), pseudouridine (uracil is bound to ribose differently than usual), dimethyladenine and dimethylguanine (two additional methyl groups in nitrogenous bases) and many others. Almost all of these bases cannot participate in complementary interactions. Thus, the methyl groups in dimethyladenine (unlike thymine and 5-methylcytosine) are located at an atom that forms a hydrogen bond in the A-U pair; therefore, now this connection cannot be closed. This also prevents the formation of double-stranded molecules.

Thus, the well-known differences in the composition of RNA from DNA are of great biological significance: after all, RNA molecules can perform their function only in a single-stranded state, which is most obvious for mRNA: it is difficult to imagine how a double-stranded molecule could be translated on ribosomes.

At the same time, remaining single, in some areas the RNA chain can form loops, protrusions or "hairpins", with a double-stranded structure (Fig. 1.). This structure is stabilized by the interaction of bases in pairs A::U and G:::C. However, "incorrect" pairs can also be formed (for example, GU), and in some places there are "hairpins" and no interaction occurs at all. Such loops can contain (especially in tRNA and rRNA) up to 50% of all nucleotides. The total content of nucleotides in RNA varies from 75 units to many thousands. But even the largest RNAs are several orders of magnitude shorter than chromosomal DNAs.

The primary structure of mRNA was copied from a DNA region containing information about the primary structure of the polypeptide chain. The primary structure of the remaining types of RNA (tRNA, rRNA, rare RNA) is the final copy of the genetic program of the corresponding DNA genes.

Secondary and tertiary structures of RNA

Ribonucleic acids (RNA) are single-stranded molecules, therefore, unlike DNA, their secondary and tertiary structures are irregular. These structures, defined as the spatial conformation of a polynucleotide chain, are formed mainly by hydrogen bonds and hydrophobic interactions between nitrogenous bases. If a stable helix is ​​characteristic of a native DNA molecule, then the structure of RNA is more diverse and labile. X-ray diffraction analysis showed that individual sections of the RNA polynucleotide chain, bending over, wind on themselves with the formation of intrahelical structures. Stabilization of structures is achieved through complementary pairings of nitrogenous bases of antiparallel sections of the chain; the specific pairs here are A-U, G-C, and, more rarely, G-U. Due to this, both short and extended coiled sections belonging to the same chain appear in the RNA molecule; these areas are called hairpins. The model of the secondary structure of RNA with hairpin elements was developed in the late 1950s and early 1960s. 20th century in the laboratories of A. S. Spirin (Russia) and P. Doty (USA).

Some types of RNA
Types of RNA	Size in nucleotides	Function
gRNA - genomic RNA	10000-100000
mRNA - informational (matrix) RNA	100-100000	transfers information about the structure of a protein from a DNA molecule
tRNA - transfer RNA	70-90	transports amino acids to the site of protein synthesis
rRNA - ribosomal RNA	several discrete classes from 100 to 500,000	contained in ribosomes, participates in maintaining the structure of the ribosome
sn-RNA - small nuclear RNA	100	removes introns and enzymatically joins exons into mRNA
sno-RNA - small nucleolar RNA		involved in directing or carrying out base modifications in rRNA and small nuclear RNA, such as, for example, methylation and pseudouridinization. Most small nucleolar RNAs are found in the introns of other genes.
srp-RNA - signal recognition RNA		recognizes the signal sequence of proteins intended for expression and participates in their transfer across the cytoplasmic membrane
mi-RNA - micro-RNA	22	control the translation of structural genes by complementary binding to the 3' ends of untranslated mRNA regions

The formation of helical structures is accompanied by a hypochromic effect - a decrease in the optical density of RNA samples at 260 nm. The destruction of these structures occurs when the ionic strength of the RNA solution decreases or when it is heated to 60-70 °C; it is also called melting and is explained by the structural transition helix - chaotic coil, which is accompanied by an increase in the optical density of the nucleic acid solution.

There are several types of RNA in cells:

1. information (or template) RNA (mRNA or mRNA) and its predecessor - heterogeneous nuclear RNA (g-n-RNA)
2. transfer RNA (t-RNA) and its precursor
3. ribosomal (r-RNA) and its predecessor
4. small nuclear RNA (sn-RNA)
5. small nucleolar RNA (sno-RNA)
6. signal recognition RNA (srp-RNA)
7. miRNA (mi-RNA)
8. mitochondrial RNA (t+ RNA).

Heterogeneous nuclear and informational (matrix) RNA

Heterogeneous nuclear RNA is unique to eukaryotes. It is the precursor of messenger RNA (i-RNA), which carries genetic information from nuclear DNA to the cytoplasm. Heterogeneous nuclear RNA (pre-mRNA) was discovered by the Soviet biochemist G. P. Georgiev. The number of types of g-RNA is equal to the number of genes, since it serves as a direct copy of the coding sequences of the genome, due to which it has copies of DNA palindromes, therefore its secondary structure contains hairpins and linear sections. The enzyme RNA polymerase II plays a key role in the transcription of RNA from DNA.

Messenger RNA is formed as a result of processing (maturation) of rn-RNA, during which hairpins are cut off, non-coding regions (introns) are excised, and coding exons are glued together.

Messenger RNA (i-RNA) is a copy of a certain section of DNA and acts as a carrier of genetic information from DNA to the site of protein synthesis (ribosome) and is directly involved in the assembly of its molecules.

Mature messenger RNA has several regions with different functional roles (Fig.)

• at the 5 "end is the so-called "cap" or cap - a section of one to four modified nucleotides. This structure protects the 5" end of the mRNA from endonucleases
• behind the "cap" is a 5 "untranslated region - a sequence of several tens of nucleotides. It is complementary to one of the sections of the rRNA that is part of the small subunit of the ribosome. Due to this, it serves for the primary binding of mRNA to the ribosome, but itself not broadcast
• initiating codon - AUG encoding methionine. All mRNAs have the same start codon. The translation (reading) of mRNA begins with it. If methionine is not needed after the synthesis of the peptide chain, then, as a rule, it is cleaved off from its N-terminus.
• The start codon is followed by the coding part, which contains information about the sequence of amino acids in the protein. In eukaryotes, mature mRNAs are monocistronic; each of them carries information about the structure of only one polypeptide chain.

  Another thing is that sometimes the peptide chain shortly after formation on the ribosome is cut into several smaller chains. This happens, for example, in the synthesis of insulin and a number of oligopeptide hormones.

  The coding part of the mature eukaryotic mRNA is devoid of introns - any intercalated non-coding sequences. In other words, there is a continuous sequence of sense codons that must be read in the 5" -> 3" direction.

• At the end of this sequence, there is a termination codon - one of three "meaningless" codons: UAA, UAG or UGA (see the table of the genetic code below).
• This codon may be followed by another 3'-untranslated region, which is much longer than the 5'-untranslated region.
• Finally, almost all mature eukaryotic mRNAs (except histone mRNAs) contain a poly(A) fragment of 150–200 adenyl nucleotides at the 3' end.

The 3'-untranslated region and the poly(A)-fragment are related to the regulation of mRNA lifespan, since the destruction of mRNA is carried out by 3'-exonucleases. After the completion of mRNA translation, 10–15 nucleotides are cleaved from the poly(A) fragment. When this fragment is exhausted, a significant part of the mRNA begins to degrade (if the 3'-untranslated region is missing).

The total number of nucleotides in mRNA usually varies within a few thousand. In this case, the coding part can sometimes account for only 60-70% of nucleotides.

In cells, mRNA molecules are almost always associated with proteins. The latter probably stabilize the linear structure of mRNA, i.e., prevent the formation of "hairpins" in the coding part. In addition, proteins can protect mRNA from premature degradation. Such complexes of mRNA with proteins are sometimes called informosomes.

Transfer RNA in the cell cytoplasm carries amino acids in an activated form to ribosomes, where they are combined into peptide chains in a specific sequence, which is set by the RNA template (mRNA). At present, data on the nucleotide sequence of more than 1700 types of tRNA from prokaryotic and eukaryotic organisms are known. All of them have common features both in their primary structure and in the way the polynucleotide chain is folded into a secondary structure due to the complementary interaction of the nucleotides included in their structure.

Transfer RNA in its composition contains no more than 100 nucleotides, among which there is a high content of minor, or modified, nucleotides. The first fully decoded transfer RNA was alanine RNA isolated from yeast. The analysis showed that alanine RNA consists of 77 nucleotides arranged in a strictly defined sequence; they include the so-called minor nucleotides, represented by atypical nucleosides dihydrouridine (dgU) and pseudouridine (Ψ); inosine (I): compared to adenosine, the amino group is replaced by a keto group; methylinosine (mI), methyl- and dimethylguanosine (mG and m 2 G); methyluridine (mU): same as ribothymidine. Alanine tRNA contains 9 unusual bases with one or more methyl groups, which are enzymatically attached to them after the formation of phosphodiester bonds between nucleotides. These bases are incapable of forming ordinary pairs; perhaps they serve to prevent base pairing in certain parts of the molecule and thus expose specific chemical groups that form secondary bonds with the messenger RNA, the ribosome, or perhaps with the enzyme necessary to attach a particular amino acid to the corresponding transfer RNA. The known sequence of nucleotides in tRNA essentially means that its sequence in the genes on which this tRNA is synthesized is also known. This sequence can be derived based on the specific base pairing rules established by Watson and Crick. In 1970, a complete double-stranded DNA molecule with the corresponding sequence of 77 nucleotides was synthesized, and it turned out that it could serve as a template for constructing alanine transfer RNA. It was the first artificially synthesized gene.

tRNA transcription

Transcription of tRNA molecules occurs from DNA encoding sequences with the participation of the enzyme RNA polymerase III. During transcription, the primary structure of tRNA is formed in the form of a linear molecule. Formation begins with the compilation of a nucleotide sequence by RNA polymerase in accordance with the gene containing information about this transfer RNA. This sequence is a linear polynucleotide chain in which nucleotides follow each other. A linear polynucleotide chain is a primary RNA, a precursor of tRNA, which includes introns - non-informative excesses of nucleotides. At this level of organization, pre-tRNA is not functional. Formed in different places in the DNA of chromosomes, pre-tRNA contains an excess of about 40 nucleotides compared to mature tRNA.

In the second step, the newly synthesized tRNA precursor undergoes post-transcriptional maturation or processing. During processing, non-informative excesses in pre-RNA are removed and mature, functional RNA molecules are formed.

pre-tRNA processing

Processing begins with the formation of intramolecular hydrogen bonds in the transcript and the tRNA molecule takes the form of a cloverleaf. This is the secondary level of tRNA organization, at which the tRNA molecule is not yet functional. Next, non-informative regions are excised from pre-RNA, informative regions of "broken genes" are spliced ​​- splicing and modification of the 5'- and 3'-terminal regions of RNA.

Excision of non-informative regions of pre-RNA is carried out with the help of ribonucleases (exo- and endonucleases). After removal of excess nucleotides, methylation of tRNA bases occurs. The reaction is carried out by methyltransferases. S-adenosylmethionine acts as a methyl group donor. Methylation prevents the destruction of tRNA by nucleases. The finally mature tRNA is formed by attaching a specific trio of nucleotides (acceptor end) - CCA, which is carried out by a special RNA polymerase.

Upon completion of processing, additional hydrogen bonds are again formed in the secondary structure, due to which tRNA passes to the tertiary level of organization and takes the form of the so-called L-form. In this form, tRNA goes into the hyaloplasm.

tRNA structure

The structure of transfer RNA is based on a chain of nucleotides. However, due to the fact that any chain of nucleotides has positively and negatively charged parts, it cannot be in the cell in an unfolded state. These charged parts, being attracted to each other, easily form hydrogen bonds with each other according to the principle of complementarity. Hydrogen bonds bizarrely twist the tRNA strand and hold it in that position. As a result, the secondary structure of t-RNA has the form of a "clover leaf" (Fig.), containing 4 double-stranded regions in its structure. A high content of minor or modified nucleotides noted in the tRNA chain and incapable of complementary interactions forms 5 single-stranded regions.

That. the secondary structure of tRNA is formed as a result of intrastrand pairing of complementary nucleotides of individual sections of tRNA. The regions of tRNA not involved in the formation of hydrogen bonds between nucleotides form loops or linear links. The following structural regions are distinguished in tRNA:

1. Acceptor site (end), consisting of four linearly arranged nucleotides, three of which have the same sequence in all types of tRNA - CCA. The hydroxyl 3 "-OH of adenosine is free. An amino acid is attached to it with a carboxyl group, hence the name of this section of tRNA is acceptor. The tRNA amino acid bound to the 3"-hydroxyl group of adenosine delivers the amino acid to the ribosomes, where protein synthesis occurs.
2. Anticodon loop, usually formed by seven nucleotides. It contains a triplet of nucleotides specific to each tRNA, called an anticodon. The tRNA anticodon pairs with the mRNA codon according to the principle of complementarity. The codon-anticodon interaction determines the order in which amino acids are arranged in the polypeptide chain during its assembly in ribosomes.
3. Pseudouridyl loop (or TΨC loop), consisting of seven nucleotides and necessarily containing a pseudouridylic acid residue. It is assumed that the pseudouridyl loop is involved in the binding of tRNA to the ribosome.
4. Dihydrouridine, or D-loop, usually consisting of 8-12 nucleotide residues, among which there are necessarily several dihydrouridine residues. It is believed that the D-loop is necessary for binding to the aminoacyl-tRNA synthetase, which is involved in the recognition of its tRNA by an amino acid (see "Protein biosynthesis"),
5. Additional loop, which varies in size and composition of nucleotides in different tRNAs.

The tertiary structure of tRNA no longer has the shape of a cloverleaf. Due to the formation of hydrogen bonds between nucleotides from different parts of the "clover leaf", its petals wrap around the body of the molecule and are additionally held in this position by van der Waals bonds, resembling the shape of the letter G or L. The presence of a stable tertiary structure is another feature of t -RNA, in contrast to the long linear mRNA polynucleotides. You can understand exactly how different parts of the t-RNA secondary structure are bent during the formation of the tertiary structure by comparing the colors of the diagram of the secondary and tertiary structure of t-RNA.

Transfer RNAs (tRNAs) carry amino acids from the cytoplasm to the ribosomes during protein synthesis. From the table with the genetic code, it can be seen that each amino acid is encoded by several nucleotide sequences, therefore, each amino acid has its own transfer RNA. As a result, there is a wide variety of tRNAs, from one to six species for each of the 20 amino acids. Types of tRNA that can bind the same amino acid are called isoacceptor (for example, alanine can be attached to tRNA, the anticodon of which will be complementary to the codons GCU, GCC, GCA, GCG). The specificity of a tRNA is indicated by a superscript, for example: tRNA Ala.

For the process of protein synthesis, the main functional parts of t-RNA are: anticodon - a sequence of nucleotides located on the anticodon loop, complementary to the codon of informational RNA (i-RNA) and the acceptor part - the end of t-RNA opposite to the anticodon, to which the amino acid is attached. The base sequence in the anticodon directly depends on the type of amino acid attached to the 3"-terminus. For example, tRNA, the anticodon of which has the sequence 5"-CCA-3", can only carry the amino acid tryptophan. It should be noted that this dependence lies at the heart of the transfer of genetic information, the carrier of which is t-RNA.

In the process of protein synthesis, the tRNA anticodon recognizes the three-letter sequence of the genetic code (codon) of the i-RNA, matching it with the only corresponding amino acid fixed at the other end of the tRNA. Only if the anticodon is complementary to the mRNA region can the transfer RNA join it and donate the transferred amino acid for the formation of a protein chain. The interaction between t-RNA and i-RNA occurs in the ribosome, which is also an active participant in translation.

Recognition of tRNA of its amino acid and codon of i-RNA occurs in a certain way:

• The binding of "own" amino acid to tRNA occurs with the help of an enzyme - a specific aminoacyl-tRNA synthetase

  There is a wide variety of aminoacyl-tRNA synthetases, according to the number of tRNAs used by the amino acids. They are called ARSases for short. Aminoacyl-tRNA synthetases are large molecules (molecular weight 100,000 - 240,000) with a quaternary structure. They specifically recognize tRNA and amino acids and catalyze their combination. This process requires ATP, the energy of which is used to activate the amino acid from the carboxyl end and attach it to the hydroxyl (3 "-OH) of the adenosine acceptor end (CCA) of tRNA. It is believed that in the molecule of each aminoacyl-tRNA synthetase there are binding centers at least at least three binding centers: for amino acids, isoacceptor tRNAs and ATP.At the binding centers, a covalent bond is formed when the amino acid of the tRNA matches, and such a bond is hydrolyzed in case of their mismatch (attachment to the tRNA of the "wrong" amino acid).

  ARSases have the ability to selectively use an assortment of tRNAs for each amino acid upon recognition, i.e. the leading link in recognition is the amino acid, and its own tRNA is adjusted to it. Further, tRNA, by simple diffusion, transfers the amino acid attached to it to the ribosomes, where the protein is assembled from amino acids supplied in the form of different aminoacyl-tRNAs.

  

  Binding of an amino acid to tRNA

  The binding of tRNA and amino acid occurs as follows (Fig.): an amino acid and an ATP molecule are attached to aminoacyl-tRNA synthetase. For subsequent aminoacetylation, the ATP molecule releases energy by splitting off two phosphate groups. The remaining AMP (adenosine monophosphate) attaches to the amino acid, preparing it for connection with the acceptor site of tRNA - the acceptor hairpin. After that, the synthetase attaches the related tRNA to the corresponding amino acid. At this stage, the compliance of tRNA with synthetase is checked. In the case of matching, tRNA tightly attaches to the synthetase, changing its structure, which leads to the launch of the process of aminoacylation - the attachment of an amino acid to tRNA.

  Aminoacylation occurs when an AMP molecule attached to an amino acid is replaced by a tRNA molecule. After this replacement, AMP leaves the synthetase and tRNA is held up for one last amino acid check.

  Checking the correspondence of tRNA to the attached amino acid

  The synthetase model for checking the correspondence of tRNA to the attached amino acid assumes the presence of two active centers: synthetic and corrective. In the synthetic center, tRNA is attached to an amino acid. The acceptor site of the tRNA captured by the synthetase first contacts the synthetic center, which already contains the amino acid bound to AMP. This contact of the tRNA acceptor site gives it an unnatural twist until the amino acid is attached. After the amino acid is attached to the acceptor site of tRNA, the need for this site to be in the synthetic center disappears, the tRNA straightens and moves the amino acid attached to it to the correction center. If the size of the amino acid molecule attached to the tRNA and the size of the correction center do not match, the amino acid is recognized as incorrect and detached from the tRNA. Synthetase is ready for the next cycle. When the size of the amino acid molecule attached to the tRNA and the size of the correction center match, the amino acid-charged tRNA is released: it is ready to play its role in protein translation. And the synthetase is ready to attach new amino acids and tRNAs, and start the cycle again.

  The connection of an inappropriate amino acid with a synthetase occurs on average in 1 case out of 50 thousand, and with an erroneous tRNA only once per 100 thousand attachments.

• The interaction of mRNA codon and tRNA anticodon occurs according to the principle of complementarity and antiparallelism

  The interaction of tRNA with the mRNA codon according to the principle of complementarity and antiparallelism means: since the meaning of the mRNA codon is read in the direction 5 "-> 3", then the anticodon in tRNA should be read in the direction 3 "-> 5". In this case, the first two bases of the codon and anticodon are paired strictly complementary, that is, only pairs A U and G C are formed. The pairing of third bases may deviate from this principle. Valid pairs are defined by the scheme:

  The following follows from the scheme.

  • A tRNA molecule binds only to type 1 codon if the third nucleotide in its anticodon is C or A
  • tRNA binds to 2 types of codons if the anticodon ends in U or G.
  • And finally, tRNA binds to 3 types of codons if the anticodon ends in I (inosine nucleotide); such a situation, in particular, in alanine tRNA.

    From this, in turn, it follows that recognition of 61 sense codons requires, in principle, not the same, but a smaller number of different tRNAs.

  Ribosomal RNA

  

  Ribosomal RNAs are the basis for the formation of ribosome subunits. Ribosomes provide the spatial arrangement of mRNA and tRNA during protein synthesis.

  Each ribosome consists of a large and a small subunit. Subunits include a large number of proteins and ribosomal RNAs that do not undergo translation. Ribosomes, like ribosomal RNA, differ in the coefficient of sedimentation (sedimentation), measured in Svedberg units (S). This coefficient depends on the rate of sedimentation of subunits during centrifugation in a saturated aqueous medium.

  Each eukaryotic ribosome has a sedimentation coefficient of 80S and is commonly referred to as an 80S particle. It includes

  • a small subunit (40S) containing ribosomal RNA with a sedimentation coefficient of 18S rRNA and 30 molecules of various proteins,
  • a large subunit (60S), which includes 3 different rRNA molecules (one long and two short - 5S, 5.8S and 28S), as well as 45 protein molecules.

    The subunits form the "skeleton" of the ribosome, each surrounded by its own proteins. The sedimentation coefficient of a complete ribosome does not coincide with the sum of the coefficients of its two subunits, which is associated with the spatial configuration of the molecule.

  The structure of ribosomes in prokaryotes and eukaryotes is approximately the same. They differ only in molecular weight. The bacterial ribosome has a sedimentation coefficient of 70S and is designated as a 70S particle, indicating a lower sedimentation rate; contains

  • small (30S) subunit - 16S rRNA + proteins
  • large subunit (50S) - 23S rRNA + 5S rRNA + proteins of the large subunit (Fig.)

  In rRNA, among the nitrogenous bases, the content of guanine and cytosine is higher than usual. Minor nucleosides are also found, but not as often as in tRNA: approximately 1%. These are mainly ribose-methylated nucleosides. The secondary structure of rRNA has many double-stranded regions and loops (Fig.). Such is the structure of RNA molecules formed in two successive processes - DNA transcription and maturation (processing) of RNA.

  Transcription of rRNA from DNA and processing of rRNA

  Pre-rRNA is produced in the nucleolus, where the rRNA transcriptons are located. Transcription of rRNA from DNA occurs with the help of two additional RNA polymerases. RNA polymerase I transcribes 5S, 5.8S, and 28S as one long 45S transcript, which is then split into the required parts. This ensures an equal number of molecules. In the human body, each haploid genome contains approximately 250 copies of the DNA sequence encoding the 45S transcript. They are located in five clustered tandem repeats (i.e., in pairs one behind the other) on the short arms of chromosomes 13, 14, 15, 21, and 22. These regions are known as nucleolar organizers, since their transcription and subsequent processing of the 45S transcript occur inside nucleolus.

  There are 2000 copies of the 5S-pRNA gene in at least three clusters of chromosome 1. Their transcription proceeds in the presence of RNA polymerase III outside the nucleolus.

  During processing, slightly more than half of the pre-rRNA remains and mature rRNA is released. Part of the rRNA nucleotides undergoes modification, which consists in base methylation. The reaction is carried out by methyltransferases. S-adenosylmethionine acts as a methyl group donor. Mature rRNAs combine in the nucleus with proteins of ribosomes that come here from the cytoplasm and form small and large ribosomal subunits. Mature rRNAs are transported from the nucleus to the cytoplasm in a complex with a protein, which additionally protects them from destruction and facilitates their transfer.

  Ribosome centers

  Ribosomes differ significantly from other cell organelles. In the cytoplasm, they occur in two states: inactive, when the large and small subunits are separated from each other, and in active - during the performance of their function - protein synthesis, when the subunits are connected to each other.

  The process of joining ribosome subunits or assembly of an active ribosome is referred to as translation initiation. This assembly occurs in a strictly ordered manner, which is provided by the functional centers of the ribosomes. All these centers are located on the contact surfaces of both subunits of the ribosome. These include:

  1. mRNA binding center (M center). It is formed by the 18S rRNA region, which is complementary for 5-9 nucleotides to the 5'-untranslated mRNA fragment.
  2. Peptidyl center (P-center). At the beginning of the translation process, the initiating aa-tRNA binds to it. In eukaryotes, the initiating codon of all mRNAs always codes for methionine, so the initiating aa-tRNA is one of the two methionine aa-tRNAs, marked with the subscript i: Met-tRNA i Met . At the subsequent stages of translation, the peptidyl-tRNA containing the already synthesized part of the peptide chain is located in the P-center.

     Sometimes they also talk about the E-center (from "exit" - exit), where the tRNA that has lost its connection with the peptidyl moves before leaving the ribosome. However, this center can be considered as an integral part of the P-center.

  3. Amino acid center (A-center) - the site of binding of the next aa-tRNA.
  4. Peptidyl transferase center (PTF center) - it catalyzes the transfer of peptidyl from the composition of peptidyl-tRNA to the next aa-tRNA that has entered the A center. In this case, another peptide bond is formed and the peptidyl is extended by one amino acid.

  Both in the amino acid center and in the peptidyl center, the anticodon loop of the corresponding tRNA (aa-tRNA or peptidyl-tRNA) obviously faces the M-center - the binding center of messenger RNA (interacting with mRNA), and the acceptor loop with aminoacyl or peptidyl PTF center.

  Distribution of centers between subunits

  The distribution of centers between subunits of the ribosome occurs as follows:

  • Small subunit. Since it is this subunit that contains 18S-rRNA, with the site of which mRNA binds, the M-center is located on this subunit. In addition, the main part of the A-center and a small part of the P-center are also located here.
  • Large subunit. The remaining parts of the P- and A-centers are located on its contacting surface. In the case of the P-center, this is its main part, and in the case of the A-center, the binding site of the α-tRNA acceptor loop with the amino acid radical (aminoacyl); the rest and most of the aa-tRNA binds to the small subunit. The PTF center also belongs to the large subunit.
  All these circumstances determine the order of assembly of the ribosome at the stage of translation initiation.

  Ribosome initiation (preparation of the ribosome for protein synthesis)

  Protein synthesis, or translation itself, is usually divided into three phases: initiation (beginning), elongation (elongation of the polypeptide chain) and termination (end). In the initiation phase, the ribosome is prepared for work: the connection of its subunits. In bacterial and eukaryotic ribosomes, the connection of subunits and the beginning of translation proceed in different ways.

  Starting a broadcast is the slowest process. In addition to the subunits of the ribosome, mRNA and tRNA, GTP and three protein initiation factors (IF-1, IF-2 and IF-3), which are not integral components of the ribosome, take part in it. Initiation factors facilitate the binding of mRNA to the small subunit and GTP. GTP, through hydrolysis, provides energy for the closure of ribosome subunits.

  

  1. Initiation begins when the small subunit (40S) binds to initiation factor IF-3, resulting in an obstacle to premature binding of the large subunit and the possibility of mRNA attachment to it.
  2. Further, mRNA (with its 5'-untranslated region) joins the "small subunit (40S) + IF-3" complex. In this case, the initiating codon (AUG) is located at the level of the peptidyl center of the future ribosome.
  3. Further, two more initiation factors join the "small subunit + IF-3 + mRNA" complex: IF-1 and IF-2, while the latter carries with it a special transfer RNA, which is called the initiating aa-tRNA. The complex also includes GTP.

     The small subunit binds to the mRNA and presents two codons for reading. At the first stage, the IF-2 protein anchors the initiator aa-tRNA. The second codon closes the IF-1 protein, which blocks it and does not allow the next tRNA to join until the ribosome is fully assembled.

  4. After binding of the initiating aa-tRNA, i.e., Met-tRNA i Met, due to complementary interaction with mRNA (initiating codon AUG) and setting it in its place in the P-center, the binding of ribosome subunits occurs. GTP is hydrolyzed to GDP and inorganic phosphate, and the energy released when this high-energy bond is broken creates a thermodynamic stimulus for the process to proceed in the right direction. Simultaneously, initiation factors leave the ribosome.

  Thus, a kind of "sandwich" of four main components is formed. At the same time, the initiating mRNA codon (AUG) and the initiating aa-tRNA associated with it are located in the P-center of the assembled ribosome. The latter, in the formation of the first peptide bond, plays the role of peptidyl-tRNA.

  

  RNA transcripts synthesized by RNA polymerase usually undergo further enzymatic transformations, called post-transcriptional processing, and only after that do they acquire their functional activity. Transcripts of immature messenger RNA are called heterogeneous nuclear RNA (hnRNA). They consist of a mixture of very long RNA molecules containing introns and exons. The maturation (processing) of hnRNA in eukaryotes includes several stages, one of which is the removal of introns - non-translated insertion sequences and the fusion of exons. The process proceeds in such a way that successive exons, i.e., coding mRNA fragments, never physically separate. Exons are very precisely connected to each other by molecules called small nuclear RNAs (snRNAs). The function of these short nuclear RNAs, consisting of approximately one hundred nucleotides, remained unclear for a long time. It was established after it was found that their nucleotide sequence is complementary to the sequences at the ends of each of the introns. As a result of pairing of bases contained in snRNA and at the ends of the looped intron, the sequences of two exons approach each other in such a way that it becomes possible to remove the intron separating them and enzymatic connection (splicing) of coding fragments (exons). Thus, snRNA molecules play the role of temporary templates that keep the ends of two exons close to each other in order for splicing to occur in the correct place (Fig.).

  The conversion of hnRNA to mRNA by removing introns takes place in a nuclear RNA-protein complex called the splicesome. Each spliceome has a nucleus, consisting of three small (low molecular weight) nuclear ribonucleoproteins, or snurps. Each snurp contains at least one small nuclear RNA and several proteins. There are several hundred different small nuclear RNAs transcribed primarily by RNA polymerase II. It is believed that their main function is the recognition of specific ribonucleic sequences through base pairing according to the RNA-RNA type. Ul, U2, U4/U6 and U5 are most important for hnRNA processing.

  Mitochondrial RNA

  Mitochondrial DNA is a continuous loop and encodes 13 polypeptides, 22 tRNAs and 2 rRNAs (16S and 23S). Most of the genes are located on the same (heavy) chain, but some of them are also located on the complementary light chain. In this case, both chains are transcribed as continuous transcripts using mitochondria-specific RNA polymerase. This enzyme is encoded by the nuclear gene. Long RNA molecules are then cleaved into 37 separate species, and mRNA, rRNA and tRNA together translate 13 mRNA. A large number of additional proteins that enter the mitochondria from the cytoplasm are translated from nuclear genes. Patients with systemic lupus erythematosus have antibodies to their own body snurp proteins. In addition, it is believed that a certain set of small nuclear RNA genes of chromosome 15q plays an important role in the pathogenesis of Prader-Willi syndrome (a hereditary combination of mental retardation, short stature, obesity, muscle hypotension).

  
  

The interaction and structure of IRNA, tRNA, RRNA - the three main nucleic acids, is considered by such a science as cytology. It will help to find out what is the role of transport (tRNA) in cells. This very small, but at the same time undeniably important molecule takes part in the process of combining the proteins that make up the body.

What is the structure of tRNA? It is very interesting to consider this substance "from the inside", to find out its biochemistry and biological role. And also, how are the structure of tRNA and its role in protein synthesis interrelated?

What is TRNA, how is it arranged?

Transport ribonucleic acid is involved in the construction of new proteins. Almost 10% of all ribonucleic acids are transport. To make it clear what chemical elements a molecule is formed from, we will describe the structure of the secondary structure of tRNA. The secondary structure considers all the major chemical bonds between the elements.

Consisting of a polynucleotide chain. Nitrogenous bases in it are connected by hydrogen bonds. Like DNA, RNA has 4 nitrogenous bases: adenine, cytosine, guanine, and uracil. In these compounds, adenine is always associated with uracil, and guanine, as usual, with cytosine.

Why does a nucleotide have the prefix ribo-? Simply, all linear polymers that have a ribose instead of a pentose at the base of the nucleotide are called ribonucleic. And transfer RNA is one of 3 types of just such a ribonucleic polymer.

The structure of tRNA: biochemistry

Let's look into the deepest layers of the structure of the molecule. These nucleotides have 3 components:

1. Sucrose, ribose is involved in all types of RNA.
2. Phosphoric acid.
3. nitrogenous and pyrimidines.

Nitrogenous bases are linked together by strong bonds. It is customary to divide bases into purine and pyrimidine.

Purines are adenine and guanine. Adenine corresponds to an adenyl nucleotide of 2 interconnected rings. And guanine corresponds to the same “single-ring” guanine nucleotide.

Pyramidines are cytosine and uracil. Pyrimidines have a single ring structure. There is no thymine in RNA, since it is replaced by an element such as uracil. This is important to understand before looking at other structural features of tRNA.

Types of RNA

As you can see, the structure of tRNA cannot be briefly described. You need to delve into biochemistry to understand the purpose of the molecule and its true structure. What other ribosomal nucleotides are known? There are also matrix or informational and ribosomal nucleic acids. Abbreviated as RNA and RNA. All 3 molecules work closely with each other in the cell so that the body receives correctly structured protein globules.

It is impossible to imagine the work of one polymer without the help of 2 others. Structural features of tRNAs become more understandable when considered in conjunction with functions that are directly related to the work of ribosomes.

The structure of RNA, tRNA, rRNA is similar in many ways. All have a ribose base. However, their structure and functions are different.

Discovery of nucleic acids

The Swiss Johann Miescher found macromolecules in the cell nucleus in 1868, later called nucleins. The name "nucleins" comes from the word (nucleus) - the nucleus. Although a little later it was found that in unicellular creatures that do not have a nucleus, these substances are also present. In the middle of the 20th century, the Nobel Prize was received for the discovery of the synthesis of nucleic acids.

in protein synthesis

The name itself - transfer RNA - indicates the main function of the molecule. This nucleic acid "brings" with it the essential amino acid required by the ribosomal RNA to make a particular protein.

The tRNA molecule has few functions. The first is the recognition of the IRNA codon, the second function is the delivery of building blocks - amino acids for protein synthesis. Some more experts distinguish the acceptor function. That is, the addition of amino acids according to the covalent principle. It helps to “attach” this amino acid to an enzyme such as aminocil-tRNA synthatase.

How is the structure of tRNA related to its functions? This special ribonucleic acid is designed in such a way that on one side of it there are nitrogenous bases, which are always connected in pairs. These are the elements known to us - A, U, C, G. Exactly 3 "letters" or nitrogenous bases make up the anticodon - a reverse set of elements that interacts with the codon according to the principle of complementarity.

This important structural feature of tRNA ensures that there will be no errors in decoding the template nucleic acid. After all, it depends on the exact sequence of amino acids whether the protein that the body needs at the present time is synthesized correctly.

Structural features

What are the structural features of tRNA and its biological role? This is a very ancient structure. Its size is somewhere around 73 - 93 nucleotides. The molecular weight of the substance is 25,000-30,000.

The structure of the secondary structure of tRNA can be disassembled by examining the 5 main elements of the molecule. So, this nucleic acid consists of the following elements:

• loop for contact with the enzyme;
• loop for contact with the ribosome;
• anticodon loop;
• acceptor stem;
• the anticodon itself.

And also allocate a small variable loop in the secondary structure. One arm in all types of tRNA is the same - a stem of two cytosine and one adenosine residues. It is in this place that the connection with 1 of the 20 available amino acids occurs. For each amino acid, a separate enzyme is intended - its own aminoacyl-tRNA.

All the information that encrypts the structure of all is contained in the DNA itself. The structure of tRNA in all living creatures on the planet is almost identical. It will look like a leaf when viewed in 2-D.

However, if you look in volume, the molecule resembles an L-shaped geometric structure. This is considered the tertiary structure of tRNA. But for the convenience of studying it is customary to visually “untwist”. The tertiary structure is formed as a result of the interaction of the elements of the secondary structure, those parts that are mutually complementary.

The tRNA arms or rings play an important role. One arm, for example, is required for chemical bonding with a particular enzyme.

A characteristic feature of a nucleotide is the presence of a huge number of nucleosides. There are more than 60 types of these minor nucleosides.

tRNA structure and amino acid coding

We know that the tRNA anticodon is 3 molecules long. Each anticodon corresponds to a specific, "personal" amino acid. This amino acid is connected to the tRNA molecule using a special enzyme. As soon as the 2 amino acids come together, the bonds to the tRNA are broken. All chemical compounds and enzymes are needed until the required time. This is how the structure and functions of tRNA are interconnected.

In total, there are 61 types of such molecules in the cell. There can be 64 mathematical variations. However, 3 types of tRNA are absent due to the fact that exactly this number of stop codons in IRNA does not have anticodons.

Interaction between RNA and tRNA

Let us consider the interaction of a substance with RNA and RRNA, as well as structural features of tRNA. The structure and purpose of a macromolecule are interrelated.

The structure of the IRNA copies information from a separate section of DNA. DNA itself is too large a connection of molecules, and it never leaves the nucleus. Therefore, an intermediary RNA is needed - informational.

Based on the sequence of molecules copied by the RNA, the ribosome builds a protein. The ribosome is a separate polynucleotide structure, the structure of which needs to be explained.

Ribosomal tRNA: interaction

Ribosomal RNA is a huge organelle. Its molecular weight is 1,000,000 - 1,500,000. Almost 80% of the total amount of RNA is ribosomal nucleotides.

It seems to capture the IRNA chain and wait for anticodons that will bring tRNA molecules with them. Ribosomal RNA consists of 2 subunits: small and large.

The ribosome is called the "factory", because in this organelle all the synthesis of the substances necessary for everyday life takes place. It is also a very ancient cell structure.

How does protein synthesis occur in the ribosome?

The structure of tRNA and its role in protein synthesis are interrelated. The anticodon located on one of the sides of the ribonucleic acid is suitable in its form for the main function - the delivery of amino acids to the ribosome, where the phased alignment of the protein takes place. Essentially, the TRNA acts as an intermediary. Its task is only to bring the necessary amino acid.

When information is read from one part of the RNA, the ribosome moves further along the chain. The template is needed only to convey encoded information about the configuration and function of a single protein. Next, another tRNA approaches the ribosome with its nitrogenous bases. It also decodes the next part of the MRNA.

Decoding proceeds as follows. Nitrogenous bases combine according to the principle of complementarity in the same way as in DNA itself. Accordingly, TRNA sees where it needs to "moor" and to which "hangar" to send the amino acid.

Then, in the ribosome, the amino acids selected in this way are chemically bound, step by step a new linear macromolecule is formed, which, after the end of synthesis, twists into a globule (ball). Used tRNA and RNA, having fulfilled their function, are removed from the protein "factory".

When the first part of the codon joins with the anticodon, the reading frame is determined. Subsequently, if for some reason a frame shift occurs, then some sign of the protein will be rejected. The ribosome cannot intervene in this process and solve the problem. Only after the process is completed, the 2 rRNA subunits are combined again. On average, for every 10 4 amino acids, there is 1 error. For every 25 proteins already assembled, at least 1 replication error is sure to occur.

tRNA as relic molecules

Since tRNA may have existed at the time of the birth of life on earth, it is called a relic molecule. It is believed that RNA is the first structure that existed before DNA and then evolved. The RNA World Hypothesis - formulated in 1986 by laureate Walter Gilbert. However, it is still difficult to prove this. The theory is defended by obvious facts - tRNA molecules are able to store blocks of information and somehow implement this information, that is, perform work.

But opponents of the theory argue that a short period of the life of a substance cannot guarantee that tRNA is a good carrier of any biological information. These nucleotides are rapidly degraded. The lifetime of tRNA in human cells ranges from several minutes to several hours. Some species can last up to a day. And if we talk about the same nucleotides in bacteria, then the terms are much shorter - up to several hours. In addition, the structure and functions of tRNA are too complex for a molecule to become the primary element of the Earth's biosphere.