Module: Roebe::KnowledgeBase

Defined in:
lib/roebe/knowledge_base/knowledge_base.rb

Overview

Foo::KnowledgeBase

Instance Method Summary collapse

Instance Method Details

#how_does_alpha_amanitin_work ⇒ Object

#

how_does_alpha_amanitin_work

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# File 'lib/roebe/knowledge_base/knowledge_base.rb', line 17

def how_does_alpha_amanitin_work
  fancy2 'Alpha-Amanitin'
  p_default_le {
    e 'Alpha-Amanitin is a potent inhibitor of RNA polymerase II. It binds
    to RNA polymerase and jams the moving parts of the enzyme, thus
    interfering with its ability to move along the DNA template.'
  }
end

#show_tRNA ⇒ Object

#

show_tRNA

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# File 'lib/roebe/knowledge_base/knowledge_base.rb', line 40

def show_tRNA
  # ======================================================================= #
  # === tRNA                                                     (tRNA tag)
  # ======================================================================= #
  fancy2 'tRNA'
  p_default_le {
    e "The <b>enzyme</b> <b>RNase P</b> (an <b>endonuclease</b>) removes
    the 5' leader sequence of the tRNA precursor."
    br
    e "The 3' trailer of a primary tRNA transcript is
    cleaved off by the <two>RNase Z</two>."
    br
    e 'This is important, because <b>all tRNAs must conform to the same
    structure (in 3D)</b>. In fact: tRNAs were among the first RNA
    molecules that have been structurally analysed by X-ray
    crystallography.'
    br
    e '<b>tRNAs</b> contain various modified nucleotides. For instance,
    <b>pseudourudine</b> or <b>dihydrouridine</b>. <b>Dihydrouridine</b>
    is the reason why the D arm of the tRNA is named that way, which
    explains the name given to the <b>D arm</b>.'
    br
    e 'The two most important functions of the tRNA are that
    they it must carry the cognate amino acid to the ribosome, 
    for protein synthesis, and that the the RNA must decode
    the genetic code.'
    br
    e 'tRNA-Synthetases provide a docking platform for
    aminoacids and their cognate tRNAs.'
    br
    e 'In prokaryotes, tRNA genes are frequently integrated into ribosomal
    DNA repeats, generating transcriptional units that allow for the
    coordinated transcription of different factors required for protein
    synthesis.'
    br
    e 'In eukaryotes, <b>mature tRNAs</b> interact with the <b>export
    receptor exportin-t</b>, which will interact with Ran-GTP, in order
    to export the mature tRNA into the cytosol.'
    br
    e 'Many tRNA genes found in yeast, are found to be associated
    with nucleoli.'
    br
    e 'tRNAs may be <b>methylated</b>. Methylation of the sugar backbone 
    of tRNAs tends to stabilize the tRNA molecule, protecting it against
    hydrolysis by ribonucleases.'
    br
    e 'In bacteria, tRNA introns are self-splicing and thus do not
    require help from other enzymes.'
    br
    e 'In eukaryotes, tRNA introns are typically 14-60 nucleotides
    in length and interrupt the anticodon loop.'
    br
    e 'Die verfügbare Anzahl an tRNAs in einer Zelle mag sich
    auf die Geschwindigkeit der Translation auswirken. Wenn bestimmte
    tRNAs nur selten vorkommen, dann wird das Ribosom bei
    der Translation nicht zügig voranschreiten können.'
  }
end

#what_is_a_silencer ⇒ Object

#

what_is_a_silencer

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# File 'lib/roebe/knowledge_base/knowledge_base.rb', line 29

def what_is_a_silencer
  fancy2 'Silencer'
  p_default_le {
    e 'A regulatory site that binds more negative regulators than positive
    regulators to control transcription is called a <b>silencer</b>.'
  }
end