- Related Topics:
- RNA
- DNA
- nucleotide
- base pair
- nucleoside
Ribosomal RNA (rRNA) molecules are the structural components of the ribosome. The rRNAs form extensive secondary structures and play an active role in recognizing conserved portions of mRNAs and tRNAs. They also assist with the catalysis of protein synthesis. In the prokaryote E. coli, there are anywhere from one to 15 copies of the rRNA operon (an operon is a group of protein-coding structural genes in bacteria); the model E. coli organism has seven rRNA operons. These operons synthesize about 15,000 ribosomes per cell for slow-growing E. coli and as many as 70,000 ribosomes per cell for fast-growing E. coli.
In eukaryotes the numbers are much larger. Anywhere from 50 to 5,000 sets of rRNA genes and as many as 10 million ribosomes may be present in a single cell. In eukaryotes these rRNA genes are looped out of the main chromosomal fibres and coalesce in the presence of proteins to form an organelle called the nucleolus. The nucleolus is where the rRNA genes are transcribed and the early assembly of ribosomes takes place.
Transfer RNA (tRNA)
Transfer RNA (tRNA) carries individual amino acids into the ribosome for assembly into the growing polypeptide chain. The tRNA molecules contain 70 to 80 nucleotides and fold into a characteristic cloverleaf structure. Specialized tRNAs exist for each of the 20 amino acids needed for protein synthesis, and in many cases more than one tRNA for each amino acid is present. The nucleotide sequence is converted into a protein sequence by translating each three-base sequence (called a codon) with a specific protein. The 61 codons used to code amino acids can be read by many fewer than 61 distinct tRNAs.
In E. coli a total of 40 different tRNAs are used to translate the 61 codons. The amino acids are loaded onto the tRNAs by specialized enzymes called aminoacyl tRNA synthetases, usually with one synthetase for each amino acid. However, in some organisms, less than the full complement of 20 synthetases are required because some amino acids, such as glutamine and asparagine, can be synthesized on their respective tRNAs. All tRNAs adopt similar structures because they all have to interact with the same sites on the ribosome.
Ribozymes
Not all catalysis within the cell is carried out exclusively by proteins. Thomas Cech and Sidney Altman, jointly awarded a Nobel Prize in 1989, discovered that certain RNAs, now known as ribozymes, showed enzymatic activity. Cech showed that a noncoding sequence (intron) in the small subunit rRNA of protozoans, which had to be removed before the rRNA was functional, can excise itself from a much longer precursor RNA molecule and rejoin the two ends in an autocatalytic reaction. Altman showed that the RNA component of an RNA protein complex called ribonuclease P can cleave a precursor tRNA to generate a mature tRNA. In addition to self-splicing RNAs similar to the one discovered by Cech, artificial RNAs have been made that show a variety of catalytic reactions. It is now widely held that there was a stage during evolution when only RNA catalyzed and stored genetic information. This period, sometimes referred to as the RNA world, is hypothesized to have preceded the function of DNA as genetic material.

Antisense RNAs
Most antisense RNAs are synthetically modified derivatives of RNA or DNA with potential therapeutic value. In nature, antisense RNAs contain sequences that are the complement of the normal coding sequences found in mRNAs (also called sense RNAs). Like mRNAs, antisense RNAs are single-stranded, but they cannot be translated into protein. They can inactivate their complementary mRNA by forming a double-stranded structure that blocks the translation of the base sequence. Artificially introducing antisense RNAs into cells selectively inactivates genes by interfering with normal RNA metabolism.
Viral genomes
Many viruses use RNA for their genetic material. This is most prevalent among eukaryotic viruses, but a few prokaryotic RNA viruses are also known. Some common examples include polio, HIV, and influenza A H1N1, all of which affect humans, and tobacco mosaic virus, which infects plants. In some viruses the entire genetic material is encoded in a single RNA molecule, while in the segmented RNA viruses several RNA molecules may be present. Many RNA viruses such as HIV use a specialized enzyme called reverse transcriptase that permits replication of the virus through a DNA intermediate. In some cases this DNA intermediate becomes integrated into the host chromosome during infection; the virus then exists in a dormant state and effectively evades the host immune system.
Other RNAs
Many other small RNA molecules with specialized functions are present in cells. For example, small nuclear RNAs (snRNAs) are involved in RNA splicing, and other small RNAs that form part of the enzymes telomerase or ribonuclease P are part of ribonucleoprotein particles. The RNA component of telomerase contains a short sequence that serves as a template for the addition of small strings of oligonucleotides at the ends of eukaryotic chromosomes. Other RNA molecules serve as guide RNAs for editing, or they are complementary to small sections of rRNA and either direct the positions at which methyl groups need to be added or mark U residues for conversion to the isomer pseudouridine.
RNA processing
Cleavage
Following synthesis by transcription, most RNA molecules are processed before reaching their final form. Many rRNA molecules are cleaved from much larger transcripts and may also be methylated or enzymatically modified. In addition, tRNAs are usually formed as longer precursor molecules that are cleaved by ribonuclease P to generate the mature 5′ end and often have extra residues added to their 3′ end to form the sequence CCA. The hydroxyl group on the ribose ring of the terminal A of the 3′-CCA sequence acts as the amino acid acceptor necessary for the function of RNA in protein building.
Splicing
In prokaryotes the protein coding sequence occupies one continuous linear segment of DNA. However, in eukaryotic genes the coding sequences are frequently “split” in the genome—a discovery reached independently in the 1970s by Richard J. Roberts and Phillip A. Sharp, whose work won them a Nobel Prize in 1993. The segments of DNA or RNA coding for protein are called exons, and the noncoding regions separating the exons are called introns. Following transcription, these coding sequences must be joined together before the mRNAs can function. The process of removal of the introns and subsequent rejoining of the exons is called RNA splicing. Each intron is removed in a separate series of reactions by a complicated piece of enzymatic machinery called a spliceosome. This machinery consists of a number of small nuclear ribonucleoprotein particles (snRNPs) that contain snRNAs.
RNA editing
Some RNA molecules, particularly those in protozoan mitochondria, undergo extensive editing following their initial synthesis. During this editing process, residues are added or deleted by a posttranscriptional mechanism under the influence of guide RNAs. In some cases as much as 40 percent of the final RNA molecule may be derived by this editing process, rather than being coded directly in the genome. Some examples of editing have also been found in mRNA molecules, but these appear much more limited in scope.
Nucleic acid metabolism
DNA metabolism
Replication, repair, and recombination—the three main processes of DNA metabolism—are carried out by specialized machinery within the cell. DNA must be replicated accurately in order to ensure the integrity of the genetic code. Errors that creep in during replication or because of damage after replication must be repaired. Finally, recombination between genomes is an important mechanism to provide variation within a species and to assist the repair of damaged DNA. The details of each process have been worked out in prokaryotes, where the machinery is more streamlined, simpler, and more amenable to study. Many of the basic principles appear to be similar in eukaryotes.
Replication
Basic mechanisms
DNA replication is a semiconservative process in which the two strands are separated and new complementary strands are generated independently, resulting in two exact copies of the original DNA molecule. Each copy thus contains one strand that is derived from the parent and one newly synthesized strand. Replication begins at a specific point on a chromosome called an origin, proceeds in both directions along the strand, and ends at a precise point. In the case of circular chromosomes, the end is reached automatically when the two extending chains meet, at which point specific proteins join the strands. DNA polymerases cannot initiate replication at the end of a DNA strand; they can only extend preexisting oligonucleotide fragments called primers. Therefore, in linear chromosomes, special mechanisms initiate and terminate DNA synthesis to avoid loss of information. The initiation of DNA synthesis is usually preceded by synthesis of a short RNA primer by a specialized RNA polymerase called primase. Following DNA replication, the initiating primer RNAs are degraded.
The two DNA strands are replicated in different fashions dictated by the direction of the phosphodiester bond. The leading strand is replicated continuously by adding individual nucleotides to the 3′ end of the chain. The lagging strand is synthesized in a discontinuous manner by laying down short RNA primers and then filling the gaps by DNA polymerase, such that the bases are always added in the 5′ to 3′ direction. The short RNA fragments made during the copying of the lagging strand are degraded when no longer needed. The two newly synthesized DNA segments are joined by an enzyme called DNA ligase. In this way, replication can proceed in both directions, with two leading strands and two lagging strands proceeding outward from the origin.
Enzymes of replication
DNA polymerase adds single nucleotides to the 3′ end of either an RNA or a DNA molecule. In the prokaryote E. coli, there are three DNA polymerases; one is responsible for chromosome replication, and the other two are involved in the resynthesis of DNA during damage repair. DNA polymerases of eukaryotes are even more complicated. In human cells, for instance, more than five different DNA polymerases have been characterized. Separate polymerases catalyze the synthesis of the leading and lagging strands in human cells, and a separate polymerase is responsible for replication of mitochondrial DNA. The other polymerases are involved in the repair of DNA damage.
A number of other proteins are also essential for replication. Proteins called DNA helicases help to separate the two strands of DNA, and single-stranded DNA binding proteins stabilize them during opening prior to being copied. The opening of the DNA helix introduces considerable strain in the form of supercoiling, a movement that is subsequently relaxed by enzymes called topoisomerases (see above Supercoiling). A special RNA polymerase called primase synthesizes the primers needed at the origin to begin transcription, and DNA ligase seals the nicks formed between individual fragments.
The ends of linear eukaryotic chromosomes are marked by special sequences called telomeres that are synthesized by the DNA polymerase known as telomerase. This enzyme contains an RNA component that serves as a template for the exact sequence found at the ends of chromosomes. Multiple copies of a short sequence within the telomerase-associated RNA are made and added to the telomere ends. This has the effect of preventing shortening of the DNA chain that would otherwise occur during replication.
Single-stranded viral genomes and mitochondrial genomes are replicated in specialized ways. Several viruses such as adenovirus use a nucleotide covalently bound to a protein as a primer, and the protein remains covalently bound to the DNA after replication. Many single-stranded viruses use a rolling circle mechanism of replication whereby a double-stranded copy of the virus is first made. The replicating machinery then copies the nonviral strand in a continuous fashion, generating long single-stranded DNA from which full-length viral DNA strands are excised by specialized nucleases.