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