Scribe.Lecture 17.docx

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Cell and Systems Biology
William Navarre

Lecture 17: 2 1. bacteria are not passive players in their own biology 2. bacteria adapt to their envmt 3. and only in rare cases, the case of endosymbionts like mitochorndria for example do we ever see this ability to adapt lost 4. any free living bacteria or host associated bacteria will be capable of responding to its envmt 5. how well it does so depends on its fitness in its niche 6. bacteria may have to respond to multiple signals 3 7. various ways, we will learn about a few 8. direct sensing of molecues…. 1. either by binding to a ligand or temperature responsis (TF that fold differently under one temp than another) 4 9. there are a number of varied envmts that bacteria have to routinely respond to 1. presence/absence of oxygen 2. change in pH 5 10. lac operon of e coli is an example of response to nutrient availability 11. e coli grows in gut 12. e coli has the ability to break down lactase 13. e coli thought o have coevolved w mammals 14. mammals produce lactase that the bacteria can take advantage of 15. in th absence of lactose, there is a repressor called lacI which is encoded in the lac operon structure (upstream) 16. lacI binds to DNA seq just upstream of the promoter so RNAP cant bind 17. binding site’s called operators (operators are DNA sequences hwere DNA can bind) 18. no lactose around, lacI binds there and shuts off the system 19. sometimes the lacI falls off and RNAP transcribes lactose permeans and beta-galactocidase (Small amounts, low concentrations) 6 20. when lactose is in the envmt, lacI has the capability of bidinding lactose 21. lactose is a disaccharide (2 sugars) 22. lacI falls off of its operator 23. and the promoter for RNAP to bind and the downstream operons are transcribed 24. beta-galactosidase is an enzyme that breaks down lactose into monosacharides 25. plenty of lactose in the envmt 26. lacy, the permease also gets expressed at high levels 27. cell sgoes from only having a few permeases in its membrane to havin g many 1. more avid vacuum cleansers of lactose 28. beta galactocidase is in high amounts too, so the cell has converted its metabolism to a lactose- degradation machinery – ingesting lactose and breaking it down 29. eventually, as lactose is used up, and is chewed through w very little in the envmt, lacI loses its affinity for lactose at this very low conc and binds back on the operator 30. cell goes back to its original state 9 31. adaptive response is reversible 32. different thana mutational change (where bacteria mutate DNA and one of the clones is lucky and survives the condition better) 33. understress, bacteria exhibit cross-protection: where pretreatment w one stress allows the bacteria to become able to survive a lot of other stresses 1. …. 10 34. polymyxin B is an antimicrobial peptide produced by… 35. it is a cyclic peptide 36. it has the ability to poke holes in the OM of gram –ve bacteria 37. and can penetrate inside 38. very potent antibiotic 39. in eyedrops, polysporin ointments 40. pertub gram –ve membrane network 11 41. salmonella is a gram negative rod that is sensitive to poymyxin 42. if you take salmonella and you grow it in culture, it grows to 100% 43. if you suddenly give high dose of polymyxin, cell is not prepared and majority wil be killed (100 to 0 percent survival) 44. if pretreat w sublethal dose (not at lethal threshold) – polymyxin is not lethal unless at certain conc – and then high dose of polymyxin, 40% cells urvive 45. cross protection – don’t have to pretreat w low dose of polymyxin, can pretreat cells w low magnesium (low mg stresses out the OM) 46. same thing w acid 47. mg and acid can perturb OM of bacteria 12 48. cell turn on adaptive response (DNA damage) 49. cell responsds to radiation by turning on DNA repair enymes 50. and since those enzymes are already made and rpeexisting in the cell, if hit them w chemical mutagens that would normally cause DNA damage, already have dna damage enzymes made and cells are ready, therefore much more able to repair damage caused by the chemical mutagens 13 51. two component systems are a typical bacterial signalling cell 1. 2 proteins 52. most common way…. 53. type of regulatory system 54. …endosymbiont may only have a few 1. only if it lives out in soil does it have to respond to all diff things and fend off many diff things 55. …can swap back and forth diff modules in diff systems 14 56. classical version of a two-component system 57. in the CM, the sensor kinase (histidine kinase) 1. uses ATP to phosphorylate an aspartic acid on a RR 58. often times, RR are DNA binding proteins, once phosphorylated they either increase or decrease their affinity for a specific sequenc of DNA 15 59. e coli has many two component regulatory systems 16 60. periplasmic domain of the hk is sensing the signal 1. triggers a conformational change 17 61. sensor kinase autophospohoarylates and transfers a phosphate onto its own histdine residue 18 62. sensor kinase recognizes its own response regulator and transfers that P onto the aspartic acid 19 63. RR goes to DNA and binds promoter to activate/repress transcription 64. in many cases, it will bind to multiple promoters and some promoters, it can bind the alpha c terminal domain and can act as an activator, in other cases, the same RR can bind bw -10 and -5 sequences and block transcription 20 65. HK can stop acting as a a kinase ans sometimes can act as a phosphatise and cleave offthe P it added earlyier and shut the system down 21 66. phosphates are the common way in which signals are transduced for prokaryotic and eukaryotic cells from outside to inside 67. in eukaryotic cells, phorphorylations on alcohol groups (OH groups) of serine threonine and tyrosine 1. this type of bond is very stable 68. bacterial bonds are not stable, will naturally come off (aspartic acid, histidine)- much harder to study these 22 69. there are many extensions of the basic two component system motif 70. there are more complex phosphorelay systems 71. bounce of P bw HK and RR allows other inputs to feed in to the phosphorelay, and alolows them to P multiple response regulators 72. sometimes they are found in separate domains or all coennected together 23 73. not all sensor or histidine kinases sit in the membrane, som are cytoplasmic, at least the big portion that does the sensing is cytoplasmic, sometimes they sense signals in the inner membrane, and some sense in the periplasmic membrane (most common) 74. periplasmic sensors are imp for molecules that are not permeable to the cell 24 75. specific example 76. ArcAB system is a two component regulatory system imp for e coli 77. tells whether there is oxygen in the envmt this tells e coli whether it will behave as an anaerobe or aerobe 78. completely alters its metabolism away form fermentation for its oxidative phosphorylation or vice versa 79. it a phosphotrelay type two component system 80. once ArcA is phosphorylated, you can get repression enxymes involved in aerobic metabolism 1. active state of ArcB is when there is no oxygen around so represses enzymes involved in aerobic metabolism 2. and activates several metabolic enzymes involved in anaerobic metabolism 25 81. doesn’t actually sens oxygen at all 82. it is sensing the electron carriers (quinones) that are lipids int eh membrane 83. when there is no oxygen to transfer electrosn to, there is a buildup of reduced quinones( carrying electrons) 84. disulfide bonds are a way for proteins to sense the oxidative state 85. when there is oxygen around, there are a lot of oxidized quinones, and disulfide bridges are formed 86. if oxygen goes away,
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