RNA

Examples of RNA in the following topics:

• Processing of tRNAs and rRNAs

  • The tRNAs and rRNAs are structural molecules that have roles in protein synthesis; however, these RNAs are not themselves translated.
  • One contains just the pre-rRNA that will be processed into the 5S rRNA; the other spans the 28S, 5.8S, and 18S rRNAs.
  • The 60S subunit is composed of the 28S rRNA, 5.8S rRNA, 5S rRNA, and 50 proteins.
  • In bacteria, multiple tRNAs are often transcribed as a single RNA.
  • Describe how pre-rRNAs and pre-tRNAs are processed into mature rRNAs and tRNAs.

• RNA Regulation and Antisense RNA

  • Antisense RNAs are single-stranded RNA molecules that can bind and inhibit specific mRNA translation to protein.
  • There are specific types of RNA molecules that can be utilized to control gene regulation, including messenger RNAs (mRNAs), small RNAs such as microRNAs and lastly, antisense RNAs.
  • The following is a brief overview of antisense RNAs and their role in RNA regulation.
  • Antisense RNAs are single-stranded RNA molecules that exhibit a complementary relationship to specific mRNAs.
  • The antisense RNA can physically pair and bind to the complementary mRNA, thus inhibiting the ability of the mRNA to be processed in the translation machinery.

• Small Regulatory RNAs

  • Small regulatory RNAs encompass a specific class of RNAs that affect gene regulation.
  • Antisense RNAs are used to bind to complementary mRNAs and inhibit protein translation.
  • The antisense RNAs are categorized as small regulatory RNAs due to their small size.
  • Small regulatory RNAs encompass many RNAs involved in house-keeping processes as well.
  • The antisense RNA can bind to the mRNA and inhibit translation.

• The Central Dogma: DNA Encodes RNA; RNA Encodes Protein

• The Protein Synthesis Machinery

  • Protein synthesis, or translation of mRNA into protein, occurs with the help of ribosomes, tRNAs, and aminoacyl tRNA synthetases.
  • The tRNA molecules are transcribed by RNA polymerase III.
  • The transfer RNAs (tRNAs) are structural RNA molecules.
  • In eukaryotes, tRNA mole are transcribed from tRNA genes by RNA polymerase III.
  • The opposite end of the folded tRNA has the anticodon loop where the tRNA will basepair to the mRNA codon.

• Viral Replication and Gene Expression

  • Viruses that replicate via RNA intermediates need an RNA-dependent RNA-polymerase to replicate their RNA, but animal cells do not seem to possess a suitable enzyme.
  • Therefore, this type of animal RNA virus needs to code for an RNA-dependent RNA polymerase.
  • No viral proteins can be made until viral messenger RNA is available; thus, the nature of the RNA in the virion affects the strategy of the virus: In plus-stranded RNA viruses, the virion (genomic) RNA is the same sense as mRNA and so functions as mRNA.
  • One of these includes RNA-dependent RNA polymerase (RNA replicase), which copies the viral RNA to form a double-stranded replicative form, in turn this directs the formation of new virions.
  • The positive-sense RNA serves as template for complementary negative-strand synthesis, thereby producing a double-stranded RNA (replicative form, RF) (5).

• Cancer and Post-Transcriptional Control

  • Recently, several groups of researchers have shown that specific cancers have altered expression of microRNAs (miRNAs) . miRNAs bind to the 3' UTR or 5' UTR of RNA molecules to degrade them.
  • Overexpression of these miRNAs could be detrimental to normal cellular activity.
  • An increase in many miRNAs could dramatically decrease the RNA population leading to a decrease in protein expression.
  • Overexpression of miRNAs could be detrimental to normal cellular activity because miRNAs bind to the 3' UTR of RNA molecules to degrade them.
  • Specific types of miRNAs are only found in cancer cells.

• Unsticking Stuck Ribosomes

  • As a result it cannot eject the mRNA.
  • The proteins which freed the ribosome remain with the mRNA which targets the nonstop mRNA for recognition by RNA degradation pathway.
  • Trans-translation is a recently discovered pathway in E. coli, although it is not completely understood, it involves Transfer-messenger RNA (abbreviated tmRNA) which is a bacterial RNA molecule with dual tRNA-like and messenger RNA-like properties.
  • Subsequently, the ribosome moves from the 3' end of the truncated messenger RNA onto the tmRNA where it translates the codons of the tmRNA until the tmRNA stop codon is encountered.
  • A ribosome with its RNA binding sites, designated E, P, and A, is stuck near the 3' end of a broken mRNA.

• Positive-Strand RNA Viruses of Animals

  • Positive strand RNA viruses are the single largest group of RNA viruses with 30 families.
  • Single stranded RNA viruses can be classified according to the sense or polarity of their RNA into negative-sense and positive-sense, or ambisense RNA viruses.
  • Positive-sense viral RNA is similar to mRNA and thus can be immediately translated by the host cell.
  • Negative-sense viral RNA is complementary to mRNA and thus must be converted to positive-sense RNA by an RNA polymerase before translation.
  • Purified RNA of a negative-sense virus is not infectious by itself as it needs to be transcribed into positive-sense RNA; each virion can be transcribed to several positive-sense RNAs.

• Elongation and Termination in Eukaryotes

  • RNA Polymerase II will continue to elongate the newly-synthesized RNA until transcription terminates.
  • The protein-encoding, structural RNA, and regulatory RNA genes transcribed by RNA Polymerse II lack any specific signals or sequences that direct RNA Polymerase II to terminate at specific locations.
  • The tRNA, 5S rRNA, and structural RNAs genes transcribed by RNA Polymerase III have a not-entirely-understood termination signal.
  • The RNAs transcribed by RNA Polymerase III have a short stretch of four to seven U's at their 3' end.
  • This somehow triggers RNA Polymerase III to both release the nascent RNA and disengage from the template DNA strand.