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Lecture Lecture Presentation Transcript

  • Central Dogma Information storage in molecules DNA RNA Protein transcription translation replication
  • Proteins Carbon-Nitrogen backbone amino acid side chains
  • The twenty amino acids
  • Translation: RNA Proteins How do we get from bases to amino acids? 1nt => 1aa can code for 4 aa 2nt => 1aa can code for (4x4)= 16 aa 3nt => 1aa can code for (4X4x4)= 64 aa G CAC CCG CGA AG His Pro Arg The code consists of continuous Nonoverlapping triplets GCA CCC GCG AAG Ala Pro Ala Lys
  • Degenerate-- most amino acids have more than one code word often these redundant codes share the same first two bases The genetic code is:
  • The genetic code: another view Codons in the same color encode identical amino acids What are the likely effects of a mutation at the first vs. third codon position?
  • The Genetic code is universal (mostly) some exceptions- eg-Mycoplasma TGA=Trp (instead of stop) Candida cylindrica CTG= Ser (instead of Leu) mitochondrial DNA—several different exceptions depending on organism NCBI site covering alternative genetic codes: http://www3.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wprintgc?mode=c The Codon Usage Database http://www.kazusa.or.jp/codon/
  •  
  • Leading vs lagging strand synthesis
  • %G+C content plotted as difference from genomic mean GC skew = (G-C)/(G+C) Theoretical range from -1 to 1 An indication of origin of replication
  • Prochlorococcus MED4 Genome %G+C=31% Prochlorococcus MIT9313 Genome %G+C=51%
  • Genetic code 61 possible codons (64-3 stop) BUT, not all are used with equal frequency
  • Measures of codon usage
    • Measures based on a set of highly expressed genes (presumed optimal CU)
      • CAI (codon adaptation index)
      • Fop (Frequency of optimal codons)
      • CBI (codon bias index)
    • Measures independent of presumed optimal codon set
      • Nc (effective number of codons)
      • RFSCU (Relative frequency of synonymous codon usage)
    • Read more about these at
      • http://www.molbiol.ox.ac.uk/cu/Indices.html
  • Role of tRNA complement in translation efficiency 1 tRNA recognizes a particular codon BUT, most genomes do not have 61 tRNA genes……
  • Getting Artemis
    • Go to Sanger center web site
      • Software/Informatics/artemis
    • Download Artemis V8
      • Save in Ocean 539D folder
    • Make a shortcut to the .jar file on the desktop
      • Edit the properties of the shortcut and add "java -mx250m -jar " to the start of the Target: field.
  •