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Chapter: Biochemistry: Nucleic Acids: How Structure Conveys Information

The Principal Kinds of RNA and Their Structures

Six kinds of RNA-transfer RNA (tRNA), ribosomal RNA (rRNA), messenger RNA (mRNA), small nuclear RNA (snRNA), micro RNA (miRNA), and small interfering RNA (siRNA)-play an important role in the life processes of cells.

The Principal Kinds of RNA and Their Structures

What kinds of RNA play a role in life processes?

Six kinds of RNA-transfer RNA (tRNA), ribosomal RNA (rRNA), messenger RNA (mRNA), small nuclear RNA (snRNA), micro RNA (miRNA), and small interfering RNA (siRNA)-play an important role in the life processes of cells. Figure 9.20 shows the process of information transfer. The various kinds of RNA participate in the synthesis of proteins in a series of reactions ultimately directed by the base sequence of the cell’s DNA. The base sequences of all types of RNA are determined by that ofDNA. The process by which the order of bases is passed from DNA to RNA is calledtranscription.

Ribosomes, in which rRNA is associated with proteins, are the sites for assembly of the growing polypeptide chain in protein synthesis. Amino acids are brought to the assembly site covalently bonded to tRNA, as aminoacyltRNAs. The order of bases in mRNA specifies the order of amino acids in the growing protein; this process is called translation of the genetic message. A sequence of three bases in mRNA directs the incorporation of a particular amino acid into the growing pro-tein chain. We are going to see that the details of the process differ in prokaryotes and in eukaryotes (Figure 9.21). In prokaryotes, there is no nuclear membrane, so mRNA can direct the synthesis of proteins while it is still being transcribed. Eukaryotic mRNA, on the other hand, undergoes considerable processing. One of the most important parts of the process is splicing out intervening sequences (introns), so that the parts of the mRNA that will be expressed (exons) are contiguous to each other.

Small nuclear RNAs are found only in the nucleus of eukaryotic cells, and they are distinct from the other RNA types. They are involved in processing of initial mRNA transcription products to a mature form suitable for export from the nucleus to the cytoplasm for translation. Micro RNAs and small interfering RNAs are the most recent discoveries. SiRNAs are the main players in RNAinterference (RNAi), a process that was first discovered in plants and later inmammals, including humans. RNAi causes the suppression of certain genes. It is also being used extensively by scientists who wish to eliminate the effect of a gene to help discover its function. Table 9.1 summarizes the types of RNA.

What is the role of transfer RNA in protein synthesis?

The smallest of the three important kinds of RNA is tRNA. Different types of tRNA molecules can be found in every living cell because at least one tRNA bonds specifically to each of the amino acids that commonly occur in proteins.

Frequently there are several tRNA molecules for each amino acid. A tRNA is a single-stranded polynucleotide chain, between 73 and 94 nucleotide residues long, that generally has a molecular mass of about 25,000 Da. (Note that bio-chemists tend to call the unit of atomic mass the dalton, abbreviated Da.)

Intrachain hydrogen bonding occurs in tRNA, forming A–U and G–C base pairs similar to those that occur in DNA except for the substitution of uracil for thymine. The duplexes thus formed have the A-helical form, rather than the B-helical form, which is the predominant form in DNA. The molecule can be drawn as a cloverleaf structure, which can be considered the secondary structure of tRNA because it shows the hydrogen bonding between certain bases (Figure 9.22). 

The hydrogen-bonded portions of the molecule are called stems, and the non-hydrogen-bonded portions are loops. Some of these loops contain modified bases (Figure 9.23). During protein synthesis, both tRNA and mRNA are bound to the ribosome in a definite spatial arrange-ment that ultimately ensures the correct order of the amino acids in the grow-ing polypeptide chain.

A particular tertiary structure is necessary for tRNA to interact with the enzyme that covalently attaches the amino acid to the 2' or 3' end. To produce this tertiary structure, the tRNA folds into an L-shaped conformation that has been determined by X-ray diffraction (Figure 9.24).

How does ribosomal RNA combine with proteins to form the site of protein synthesis?

In contrast with tRNA, rRNA molecules tend to be quite large, and only a few types of rRNA exist in a cell. Because of the intimate association between rRNA and proteins, a useful approach to understanding the structure of rRNA is to investigate ribosomes themselves.

The RNA portion of a ribosome accounts for 60%–65% of the total weight, and the protein portion constitutes the remaining 35%–40% of the weight. Dissociation of ribosomes into their components has proved to be a useful way of studying their structure and properties. A particularly important endeavor has been to determine both the number and the kind of RNA and protein mol-ecules that make up ribosomes. This approach has helped elucidate the role of ribosomes in protein synthesis. In both prokaryotes and eukaryotes, a ribosome consists of two subunits, one larger than the other. In turn, the smaller subunit consists of one large RNA molecule and about 20 different proteins; the larger subunit consists of two RNA molecules in prokaryotes (three in eukaryotes) and about 35 different proteins in prokaryotes (about 50 in eukaryotes). The subunits are easily dissociated from one another in the laboratory by lowering the Mg2+ concentration of the medium. Raising the Mg2+ concentration to its original level reverses the process, and active ribosomes can be reconstituted by this method.

A technique called analytical ultracentrifugation has proved very useful for monitoring the dissociation and reassociation of ribosomes. Figure 9.25 shows an analytical ultracentrifuge. We need not consider all the details of this tech-nique, as long as it is clear that its basic aim is the observation of the motion of ribosomes, RNA, or protein in a centrifuge. The motion of the particle is characterized by a sedimentation coefficient, expressed in Svedberg units (S), which are named after Theodor Svedberg, the Swedish scientist who invented the ultracentrifuge. The S value increases with the molecular weight of the sedi-menting particle, but it is not directly proportional to it because the particle’s shape also affects its sedimentation rate.

Ribosomes and ribosomal RNA have been studied extensively via sedimen-tation coefficients. Most research on prokaryotic systems has been done with the bacterium Escherichia coli, which we shall use as an example here. An E.coli ribosome typically has a sedimentation coefficient of 70S. When an intact70S bacterial ribosome dissociates, it produces a light 30S subunit and a heavy 50S subunit. Note that the values of sedimentation coefficients are not addi-tive, showing the dependence of the S value on the shape of the particle. The 30S subunit contains a 16S rRNA and 21 different proteins. The 50S subunit contains a 5S rRNA, a 23S rRNA, and 34 different proteins (Figure 9.26). For comparison, eukaryotic ribosomes have a sedimentation coefficient of 80S, and the small and large subunits are 40S and 60S, respectively. The small subunit of eukaryotes contains an 18S rRNA, and the large subunit contains three types of rRNA molecules: 5S, 5.8S, and 28S.

The 5S rRNA has been isolated from many different types of bacteria, and the nucleotide sequences have been determined. A typical 5S rRNA is about 120 nucleotide residues long and has a molecular mass of about 40,000 Da. Some sequences have also been determined for the 16S and 23S rRNA mol-ecules. These larger molecules are about 1500 and 2500 nucleotide residues long, respectively. The molecular mass of 16S rRNA is about 500,000 Da, and that of 23S rRNA is about one million Da. The degrees of secondary and ter-tiary structure in the larger RNA molecules appear to be substantial.

A secondary structure has been proposed for 16S rRNA (Figure 9.27), and suggestions have been made about the way in which the proteins associate with the RNA to form the 30S subunit.

The self-assembly of ribosomes takes place in the living cell, but the process can be duplicated in the laboratory. Elucidation of ribosomal structure is an active field of research. The binding of antibiotics to bacterial ribosomal subunits so as to prevent self-assembly of the ribosome is one focus of the investigation. The structure of ribosomes is also one of the points used to compare and contrast eukaryotes, eubacteria, and archaebacteria. The study of RNA became much more exciting in 1986, when Thomas Cech showed that certain RNA molecules exhibited catalytic activity. Equally exciting was the recent discovery that the ribosomal RNA, and not protein, is the part of a ribosome that catalyzes the formation of peptide bonds in bacteria.

How does messenger RNA direct protein synthesis?

The least abundant of the main types of RNA is mRNA. In most cells, it constitutes no more than 5%–10% of the total cellular RNA. The sequences of bases in mRNA specify the order of the amino acids in proteins. In rapidly growing cells, many different proteins are needed within a short time interval. Fast turnover in protein synthesis becomes essential. Consequently, it is logical that mRNA is formed when it is needed, directs the synthesis of proteins, and then is degraded so that the nucleotides can be recycled. Of the main types of RNA, mRNA is the one that usually turns over most rapidly in the cell. Both tRNA and rRNA (as well as ribosomes themselves) can be recycled intact for many rounds of protein synthesis.

The sequence of mRNA bases that directs the synthesis of a protein reflects the sequence of DNA bases in the gene that codes for that protein, although this mRNA sequence is often altered after it is produced from the DNA. Messenger RNA molecules are heterogeneous in size, as are the proteins whose sequences they specify. Less is known about possible intrachain folding in mRNA, with the exception of folding that occurs during termination of transcription. It is also likely that several ribosomes are associated with a single mRNA molecule at some time during the course of protein synthesis. In eukaryotes, mRNA is initially formed as a larger precursor molecule called heteroge-neous nuclear RNA (hnRNA). These contain lengthy portions of interveningsequences called introns that do not encode a protein. These introns are removed by posttranscriptional splicing. In addition, protective units called 5'-caps and - > ' poly(A) tails are added before the mRNA is complete.

How does small nuclear RNA help with the processing of RNA?

A recently discovered RNA molecule is the small nuclear RNA (snRNA), which is found, as the name implies, in the nucleus of eukaryotic cells. This type of RNA is small, about 100 to 200 nucleotides long, but it is not a tRNA molecule nor a small subunit of rRNA. 

In the cell, it is complexed with proteins forming smallnuclear ribonucleoprotein particles, usually abbreviated snRNPs (pronounced“snurps”). These particles have a sedimentation coefficient of 10S. Their function is to help with the processing of the initial mRNA transcribed from DNA into a mature form that is ready for export out of the nucleus. In eukaryotes, transcription occurs in the nucleus, but because most protein synthesis occurs in the cytosol, the mRNA must first be exported.

What is RNA interference, and why is it important?

The process called RNA interference was heralded as the breakthrough of the year in 2002 in Science magazine. Short stretches of RNA (20–30 nucleotides long) have been found to have an enormous control over gene expression.

This process has been found to be a protection mechanism in many species, with the siRNAs being used to eliminate expression of an undesirable gene, such as one that is causing uncontrolled cell growth or a gene that came from a virus. These small RNAs are also being used by scientists who wish to study gene expres-sion. In what has become an explosion of new biotechnology, many companies have been created to produce and to market designer siRNA to knock out hun-dreds of known genes. This technology also has medical applications: siRNA has been used to protect mouse liver from hepatitis and to help clear infected liver cells of the disease. For the moment, we can say that many new biotechnology companies have sprung up in recent years to exploit possible applications of RNA interference.


Four kinds of RNA-transfer RNA, ribosomal RNA, messenger RNA, and small nuclear RNA-are involved in protein synthesis.

Transfer RNA transports amino acids to the sites of protein synthesis on ribosomes, which consist of ribosomal RNAs and proteins.

Messenger RNA directs the amino acid sequence of proteins. Small nuclear RNA is used to help process eukaryotic mRNA to its final form.

RNA interference, which requires short stretches of siRNA, controls gene expression.


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