Lecture 6

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  • endosymbiotic event
  • mitochondria and chloroplasts
    • mitochondria actually look like golgi, globular, only look like beans after you've centrifuged them.
  • proteins that are "co-associated" with mitochondria
  • what about proteins that are sent to the mitochondria
  • a lot of question marks related to
  • associations, not necessarily causal, did the disease bring the bacteria, or bacteria bring disease?
  • same ranscription machinery, same translation machinery
  • 1995 - 1st free living org sequenced, shocking how similar genes are
  • COGs - clusters of orthologous genes ("groups") - same gene dift organisms

prokaryotic

  • leading strand lagging strand
  • codon usage, some codons are more optimal than others.
  • no redundancy for methionine, tryptophan
  • 9 aa's have 2 synonyms
  • 1 aa has 3 synonyms
  • 4 aa's has 4
  • 6 aa's
  • codon usage table changes, mitochondia ribisomes code for different things
  • "put gene in highly expressed operon"
  • can predict highly expressed proteins by looking at codon usage table, graph all genes
  • CAI - per gene phenomenon
  • transcription, intron splicing, leaves nucleus, gets translated - but prokaryotes don't have that.
  • prophage - low level expression cause it doesn't want to kill the host

project 2

  • take homo sapiens gene and put into e.coli
  • three outcomes
    • low (no), mean for e. coli, high
  • select favorite human gene, use cDNA (mRNA change u's to Gs)
  • take intron out
  • optimize codon usage of gene
  • OPTIMIZER
  • useful to reduce, -- creating concentration gradient makes transcription more efficient -- ergo, reduce number of codons!
  • repeats bad cause it can confuse the tRNAs - filter out repeats, nothing more than 4 of anything in a row
  • even ribosomal doesn't have CAI of 1, is possible to be too optimal! can use up all the food, too much protein, tie up the tRNAs, can't make things
  • don't super optimize protien, not more highly expressed than any gene, step back.
    • guided random walk, pick a synonym that's less efficient,
  • so now bacteria can make protein and can still survive.
  • mRNA protein vs genomic
  • transposase uses ribosomal slippage on purpose, always slips in the same place,
  • polya tail on 3prime, cap on 5prime ... mRNA is unstable - polya tail says don't kill me yet. ubiquitination. code, then 3' lag area, then polya tail.
  • severe combined immuno deficiency - caused frame shift mutation - leukemia
  • random insert vs target insertion
  • put in plasmid - use two anti bacterial, those that survived took up the sequence