mRNA Processing and Ribosomal RNA part 5

Ribosomal RNA Genes

  • Multiple copies (e.g., 200) of genes for ribosomal RNA (rRNA) exist.
  • These genes transcribe ribosomal RNA, which is then processed.
  • Processing involves cutting pieces from the RNA transcript to produce different rRNA molecules.
  • 18S rRNA: Incorporated into the small ribosomal subunit. "S" refers to the rate of sedimentation; larger sedimentation rate means a larger RNA piece.
  • 5. 8S, 28S, and 5S rRNAs (5S coded by another rRNA gene): Form part of the large ribosomal subunit.
  • Ribosomes are composed of rRNA transcripts and proteins.

Final Gene Product and Amplification

  • rRNAs are the final product; they are not translated into polypeptides.
  • Actively dividing cells need millions of ribosomes, necessitating millions of rRNA transcripts.
  • Multiple rRNA genes are spread over five different chromosomes.
  • Unlike mRNA, where multiple polypeptides can be made from a single transcript (amplification step), rRNA amplification occurs in the number of genes.

Abundance of rRNA

  • 80% of the total RNA in the cell is rRNA.
  • Ribosomes, containing rRNA, synthesize polypeptides.
  • Proteins carry out cell functions.
  • mRNA accounts for only 3-5% of total RNA, despite the focus on its processing.

RNA Processing: Primary Transcript

  • RNA polymerase II transcribes the primary transcript.
  • Processing begins even before the transcript fully separates from the RNA polymerase.
  • The five prime end receives a modified nucleotide cap.
    • The cap includes a methylated guanine.
    • This "special end" is recognized by proteins, marking it as mRNA.
    • The cap helps the cell distinguish mRNA from other RNA types.
  • Regions are cut out and spliced together.
  • Not all of the primary transcript codes for the polypeptide.

Poly-A Tail

  • A specific sequence in the RNA allows enzymes to add a poly-A tail to the three prime end.
  • The poly-A tail consists of about 200 adenine nucleotides.
  • It is added by poly-A polymerase (PAP), which does not require a template.
  • The poly-A tail is also not translated.
  • Function: It helps to determine how long the mRNA transcript remains active, that is, how many times it is translated.

Functions of Cap and Tail

  • The five prime cap and poly-A tail are recognized by proteins.
  • They protect mRNA from degradation by hydrolytic enzymes.
  • They help ribosomes recognize the five prime end to initiate translation.
  • They facilitate mRNA's exit from the nucleus.

Untranslated Regions (UTRs)

  • Five prime and three prime UTRs are part of the mRNA that is exported but do not code for amino acids.
  • Five prime UTR is at the five prime end, and three prime UTR is at the three prime end.

Exons and Introns

  • Exons: Expressed sequences that code for the polypeptide and exit the nucleus.
  • Introns: Intervening sequences that do not code for the protein and remain in the nucleus to be degraded.

Splicing

  • Splicing: Cutting out introns and connecting exons to form the processed transcript (not yet mRNA).
  • mRNA is shorter than the primary transcript due to the removal of introns.
  • Most protein-coding genes contain introns.

Spliceosome

  • Splicing is performed by a complex of RNA molecules and proteins called the spliceosome.
  • The spliceosome recognizes the boundaries of introns and exons.
  • RNA within the spliceosome base pairs with the RNA of the transcript.
  • Introns are cut out in a lariat form and then degraded.
  • Exons are joined together to make the final mRNA.
  • Splicing can happen concurrently with transcription.

Alternative RNA Splicing

  • Alternative RNA splicing allows a primary transcript to be processed in different ways.
  • This increases the coding potential of the eukaryotic genome.
  • Different processing can occur at different developmental stages or in different cells.
  • Example: The troponin gene involved in muscle contraction can produce different mRNAs (A and B) through alternative splicing.
  • To make these RNAs, the cell selects different combinations of exons, resulting in the exclusion of specific regions as intronic regions.
  • Alternative splicing allows the production of multiple different poly peptides from the same gene at one time.

mRNA Export and Recognition

  • The pre-mRNA, which still contains introns, is not yet a full mRNA.
  • After the introns are cut out, exon one, containing nucleotides up to a certain point, is directly connected to exon two, beginning with the subsequent nucleotide.
  • The final mRNA is recognized by various proteins for export.
  • Cap-binding complex recognizes the five prime cap.
  • Some proteins are restricted to the nucleus.
  • Others travel and help mRNA through the nuclear pore into the cytoplasm where translation can begin.

Final Notes on mRNA Processing

  • Modifications facilitate mRNA export into the cytoplasm and mark it for translation.
  • A five prime cap and a three prime cap bound by proteins indicate that this is an intact mRNA transcript.
  • These modifications further protect this transcript and signal to the cell that it's meant to be translated.