Chemistry and living system
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Chemistry and living system Chemistry and living system Presentation Transcript

  • chemistryand living systems123.101
  • anintroduction tochemistry and...
  • ...howit relates to living things View slide
  • the study guide contains all the information you need View slide
  • my lectures containexplanationand examples
  • but as I’m not here... ! ...the Prof will have to do
  • my notes are available from:www.massey.ac.nz/~gjrowlan/teaching.html
  • Ready?
  • Unit One Part 1: introduction pic: Aquarium of the Pacific
  • Unit One Part 1: introduction these are not random pictures; the molecule is a potential painkiller called epibatidine which is isolated from poison dart frogs... pic: Aquarium of the Pacific
  • why do we needorganic chemistry?
  • ...because its fun?? why do we need organic chemistry?
  • why do we needorganic chemistry? ...it keeps me in a job? Or...
  • if we wan t t ounderstandliving systems...
  • we need tounderstand theindividual organs...
  • ...to understandorgans, we have tounderstand cells...
  • ...and still we have to get smaller and smaller...
  • ...and to do this we must understand themolecules that make up these systems Me N Me Me N Fe N HO2C(H2C)2 N HO2C(H2C)2 Me haem
  • ...lets stop with atoms & electrons! And none of this maths malarkey. but we dont needImage Credit: NIST/University of Colorado to get carried away...
  • simple chemicalprinciples control biology
  • Me Me Me 11 12 Me Me Rhodopsin H 11-cis-retinal N (aldehyde not imine) Opsin photon Me Me Me Meisomers and the Me N Hvisual cascade all trans-retinal starts VISUAL CASCADE Opsin
  • $chemistryand medicine
  • penicillin G antibacterial H H N S Me O N Me O CO2Hhttp://staff.science.uva.nl/~dcslob/lesbrieven/maarten/Bacterien.html
  • penicillin G Chemistry explains how penicillin blocks antibacterial bacterial cell wall synthesis. H H N S Me O N Me O CO2Hhttp://staff.science.uva.nl/~dcslob/lesbrieven/maarten/Bacterien.html
  • F OH OH OH N O Ca2+N O Me Me 2 Liptor cholesterol treatment US$ 12.9 billion
  • the languageof chemistry...
  • First we need to be able to communicate with each other...the languageof chemistry...
  • There are three ways of talking about chemicals...the languageof chemistry...
  • MACROSCOPIC bulk propertiesMICROSCOPIC SYMBOLIC atoms & chemical molecules formulae
  • macroscopicrepresentation physical properities©DC Comics
  • macroscopicrepresentation physical properities obviously important (if you happen to get dunked in a vat of the stuff)©DC Comics
  • macroscopicrepresentation physical properities but ignored in this lecture...lets just leave it for the lab...©DC Comics
  • how do we represent molecules?
  • microscopicrepresentation
  • how we represent the actual molecules themselves... microscopic representation
  • hexane molecular orbital representation
  • hexane electrons spread over entire molecule...true but not very useful! molecular orbital representation
  • hexane space filling representation
  • hexane shows us the atoms and their relative size...but bonds hard to see space filling representation
  • hexane ball and stick representation
  • hexane atoms, bonds, shape, it has it all. Time consuming to draw so... ball and stick representation
  • symbolicrepresentation
  • symbolic representationquick and dirty ways to represent molecules
  • C3H7empiricalformula
  • C3H7 just the ratio of atoms...empiricalformula
  • C3H7 ...too many possibilities!C6H14C24H56 12H28 C C15H35C30H70 C27H63 3H7 C18H42 C C21H49formula 33H77 9H21 C Cempirical
  • C6H14 molecular formula
  • C6H14exact number of atoms... molecular formula
  • C6H14 ...but not how they H H H H are connected H H H HH C C H H C H H H H C H H H C C C H C C H C C H C C H H HH C H H C C C H H H H H C H H H H H H H H H H H H H H H H H C C C C C C H molecular H H H H H H formula
  • CH3CH2CH2CH2CH2CH3condensedformula
  • CH3CH2CH2CH2CH2CH3 bonding sorted...condensedformula
  • CH3CH2CH2CH2CH2CH3 H H O Me H C H H H Me N N H C C C C H (CH3)2CHCH(CH3)CH3 O N N H H H C H H H ...but bulky...and Me some structurescondensed would be confusing!formula
  • H H H H H H C C C HH C C C H H H H H H structural formula
  • H H H H H H C C C H H C C C H H H H H H now we’re talking; atoms, bonding,shape. It has it all. But... structural formula
  • H H H H H H C C C H H C C C H H H H H H ...can be messy and time consuming... H C H2C CH OH OH H2C N H H2C C CH2 H C C N CH HC C H C 2N H N C C CH OMe HC C CH3 structural formula C O H
  • skeletal(structural) formula
  • Quick, easy and tells me everything...but do you understand what it means?skeletal(structural) formula
  • otherrepresentations H H C H O O H H C C CHO H C C H H H H H OH Et H CHO Et H H OH HO Ph CH3 H CH3 H CH3 Ph Fischer Newman Sawhorse projection projection projection
  • do not use thisrepresentation! H H H H H HH C C C C C C H H H H H H H
  • do not use thisrepresentation! H H H H H HH C C C C C C H H H H H H H
  • ...key to this course is understanding / interpreting these symbols ©Lucasfilms
  • understandingskeletal (structural)formulae
  • 4 H H C H H H H C C H H H C C HCARBON O H C H C O H H
  • 4 H H C H Hcarbon always has H H four bonds... C C H H H C C HCARBON O H C H C O H H
  • 1 H H C H HHYDROGEN H C C H H H O H C H C O H H H H O C C H H C O H N H H
  • 1 H H C H HHYDROGEN H C C H H H O H C H C O H Hhydrogen always has one bond... H H O C C H H C O H N H H
  • 2 H H C O H C H H H H H H H C C H C C H H O H H H O C C H H C OOXYGEN H N H H
  • 3 H H ONITROGEN H C C C O H H N H H H H C N H H C C H H H H C C N H
  • 2 C H O H N HELECTRONS
  • 2 we’ll explain why in a C H later lecture... O H N HELECTRONS
  • so how do we drawskeletal formulae?
  • HO HO OH O O O NH2 O Cl OH O O HO Cl OH O O O H H H O N N N N N N H H H HN O O O O HO NH2 OH HO OH C CH Vancomycin can beall and removed
  • HO HO OH O O O O assume each corner NH2 Cl OH O O is a carbon... HO Cl OH O O O H H H O N N N N N N H H H HN O O O O HO NH2 OH HO OH C CH Vancomycin can beall and removed
  • HO HO OH O O O NH2 O Cl OH O O HO Cl OH O O O H H H O N N N N N N H H H HN O O O O NH2 ...and it will always HO have four bonds. OH HO OH C CH Vancomycin can beall and removed
  • exampleone H H H C C CH C H H
  • exampleone remove H H H H C C C C C CH C C H H –H
  • exampleone H H H C C C C C CH C C H H –H –C now remove C
  • exampletwo HH C H C C C CH C H H
  • exampletwo H remove HH C H C C C C C C C C CH C H C –H H
  • exampletwo HH C H C C C C C C C C CH C H C –H –C H now remove C
  • examplethree H OH C HH C O H N H H
  • examplethree remove C–H BUT H O O leave all others!H C H C C HH C O C O H N H N H H H only remove CH
  • examplethree O H O O OHH C H C C H NH2H C O C O H N H N H CO2H H H NH2 only remove –C CH now remove C
  • examplefourreverse CO2HHO NH2
  • examplefourreverse add C to corners CO2H C CO2HHO HO C +C NH2 NH2
  • examplefourreverse H H CO2H C CO2HHO HO C C CO2H HO C +C +H NH2 NH2 H NH2 Add H to make all C have four bonds
  • examplefour remember C hasreverse four; O has two bonds and H has one H H CO2H C CO2HHO HO C C CO2H HO C +C +H NH2 NH2 H NH2 H H O H H O H H O H C C C C H C C HHO C O HO C O HO C O H NH2 H NH2 H NH2
  • CHONC CO2Hexamplefivereverse
  • H CHO H C CHO C C H H C C CNC CO2H NC C C CO2H H H H add C to corners and H to make four bondsexamplefivereverse
  • H CHO H C CHO C C H H C C CNC CO2H NC C C CO2H now get three bonds H H H to N; two bonds to O and one to H H O H C C C C H H H C C C Oexample N C C C C Hfive H H H Oreverse
  • 4what have....we learnt? or gan ic ch emist ry is easy if we can count to...
  • 4what have....we learnt? oh, and it’s really important! or gan ic ch emist ry is easy if we can count to...
  • Acknowledgmentsgareth(Dr. GJ Rowlands) would to like thank Trevor Kitson Massey University & the 101 students www.massey.ac.nz/~gjrowlan