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Chemistryand living systems123.101Gareth Rowlands
anintroduction    tochemistry        and...
...howit relates    to living    things
the study guide contains     all the information you need
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
my notes are available from:http://www.slideshare.net/gjr2323
Slideshare is an awesome resourcefor learning about presentations
read each chapter in advance         I will give different         examples. Do not         expect me to read it         t...
Ready?
Unit One Part 1: introduction  pic: Aquarium  of the Pacific
Unit One Part 1: introduction                    these are not random                  pictures; the molecule is          ...
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 w e want tounderstandliving 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                      ...
...lets stop with                                                 atoms & electrons!                                      ...
simple chemicalprinciples control           biology
Me     Me         Me                                          11                                               12         ...
$chemistryand medicine
penicillin G                                                                        antibacterial                         ...
penicillin G                                            Chemistry explains                                           how p...
F                      OH   OH   OH            N                      O   Ca2+N    O            Me        Me              ...
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  m...
macroscopicrepresentation    physical     properities©DC Comics
macroscopicrepresentation    physical     properities             obviously important              (if you happen to      ...
macroscopicrepresentation    physical     properities              but ignored in this               lecture...lets just  ...
how do we represent           molecules?
microscopicrepresentation
how we represent the  actual molecules    themselves...                       microscopic                       representa...
hexane         molecular orbital            representation
hexane    electrons spread over    entire molecule...true     but not very useful!                             molecular o...
hexane          space filling         representation
hexane          shows us the atoms           and their relative         size...but bonds hard                 to see      ...
hexane         ball and stick         representation
hexane    atoms, bonds, shape,      it has it all. Time     consuming to draw              so...                          ...
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  ...
C6H14   molecular   formula
C6H14exact number of    atoms...                  molecular                  formula
C6H14       ...but not how they   H H H H          are connected                           H H                            ...
CH3CH2CH2CH2CH2CH3condensedformula
CH3CH2CH2CH2CH2CH3    bonding sorted...condensedformula
CH3CH2CH2CH2CH2CH3   H H                                                O    Me  H C H H H                                ...
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,...
H H H H H H               C   C   C   H             H   C   C   C                H H H H H H                              ...
skeletal(structural) formula
Quick, easy and                            tells me                       everything...but do                        you u...
otherrepresentations         H    H        C H O              O   H H C   C                                 CHO  H C    C ...
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 ...
4                             H                        H C H                         Hcarbon always has       H         H ...
why? a good                      question & one we                      will partially answer                             ...
1                     H                H C H                 HHYDROGEN        H                    C C                    ...
1                                H                           H C H                            HHYDROGEN                   ...
2           H H            C   O          H   C   H             H H              H   H          H           H             ...
3            H H ONITROGEN   H             C               C                 C                   O                     H  ...
so how do we drawskeletal formulae?
HO                      HO                                      OH                                  O                  O  ...
HO                      HO                                      OH                                  O                  O  ...
HO                      HO                                      OH                                  O                  O  ...
exampleone H H      H        C  C   CH   C   H H
exampleone                                   remove H H H      H        C                      C  C   C            C      ...
exampleone H H      H        C                      C  C   C            C       CH   C                  C   H H           ...
exampletwo        HH       C       H    C       C    C       CH       C       H        H
exampletwo        H                            remove HH       C       H            C    C       C            C       C   ...
exampletwo        HH       C       H             C    C       C             C       C    C       C             C       CH ...
examplethree    H       OH    C           HH       C        O    H N H     H
examplethree                                             remove C–H                                                 BUT   ...
examplethree                                This is key. We                                  can only remove C–H          ...
examplethree                                                   O    H       O                    O                      OH...
example       very im                      p   ortantfourreverse       CO2HHO     NH2
examplefourreverse                        add C to corners       CO2H          C       CO2HHO              HO       C     ...
examplefourreverse                                                H H       CO2H                   C       CO2HHO         ...
examplefour                           remember C hasreverse                         four; O has two                       ...
2examplefourreverse           H H                         O                   H            C   C         HO   C    O      ...
2examplefourreverse     H H                          O      C   C    H   HO   C    O          O still does not have       ...
4examplefourreverse     H H                       O      C     C   H   HO    C    O       CARBON       H NH2       C still...
Functional Groups   pages 16-29         learn them ©"lapolab"@Flickr
CHONC              CO2Hexamplefivereverse
H          CHO                        H      C                                            CHO                             ...
H                CHO             H       C                                        CHO                                  C  ...
OH   O                         OH      OOHC                         OHC       C       C                       +C          ...
4what have....we learnt?        o r ga n i c c h e m i s try is        easy if we can count to...
4what have....we learnt?                       oh, and it’s really                          important!        o r ga n i c...
before next lecture...readUnit 1 Part 2            ©Noukka Signe@Flickr
Acknowledgmentsgareth(Dr. GJ Rowlands)         would to             like              thank               Trevor Kitson   ...
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Chemistry Living and Systems: 123.101 Lecture 1

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123.101 Chemistry & Living Systems: Unit 1 Lecture 1 from Gareth Rowlands Section - Any comments would be greatly appreciated.

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Chemistry Living and Systems: 123.101 Lecture 1

  1. Chemistryand living systems123.101Gareth Rowlands
  2. anintroduction tochemistry and...
  3. ...howit relates to living things
  4. the study guide contains all the information you need
  5. my lectures containexplanationand examples
  6. but as I’m not here... ! ...the Prof will have to do
  7. my notes are available from:www.massey.ac.nz/~gjrowlan/teaching.html
  8. my notes are available from:http://www.slideshare.net/gjr2323
  9. Slideshare is an awesome resourcefor learning about presentations
  10. read each chapter in advance I will give different examples. Do not expect me to read it to you... ©Noukka Signe@Flickr
  11. Ready?
  12. Unit One Part 1: introduction pic: Aquarium of the Pacific
  13. 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
  14. why do we needorganic chemistry?
  15. ...because its fun?? why do we need organic chemistry?
  16. why do we needorganic chemistry? ...it keeps me in a job? Or...
  17. if w e want tounderstandliving systems...
  18. we need tounderstand theindividual organs...
  19. ...to understandorgans, we have tounderstand cells...
  20. ...and still we have to get smaller and smaller...
  21. ...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
  22. ...lets stop with atoms & electrons! And none of this maths malarkey. but we dont needImage Credit: NIST/University of Colorado to get carried away...
  23. simple chemicalprinciples control biology
  24. 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
  25. $chemistryand medicine
  26. penicillin G antibacterial H H N S Me O N Me O CO2Hhttp://staff.science.uva.nl/~dcslob/lesbrieven/maarten/Bacterien.html
  27. penicillin G Chemistry explains how penicillin blocks antibacterial bacterial cell wall synthesis. H H N S Me O N Me O CO2Hhttp://staff.science.uva.nl/~dcslob/lesbrieven/maarten/Bacterien.html
  28. F OH OH OH N O Ca2+N O Me Me 2 Liptor cholesterol treatment US$ 12.9 billion
  29. the languageof chemistry...
  30. First we need to be able to communicate with each other...the languageof chemistry...
  31. There are three ways of talking about chemicals...the languageof chemistry...
  32. MACROSCOPIC bulk propertiesMICROSCOPIC SYMBOLIC atoms & chemical molecules formulae
  33. macroscopicrepresentation physical properities©DC Comics
  34. macroscopicrepresentation physical properities obviously important (if you happen to get dunked in a vat of the stuff)©DC Comics
  35. macroscopicrepresentation physical properities but ignored in this lecture...lets just leave it for the lab...©DC Comics
  36. how do we represent molecules?
  37. microscopicrepresentation
  38. how we represent the actual molecules themselves... microscopic representation
  39. hexane molecular orbital representation
  40. hexane electrons spread over entire molecule...true but not very useful! molecular orbital representation
  41. hexane space filling representation
  42. hexane shows us the atoms and their relative size...but bonds hard to see space filling representation
  43. hexane ball and stick representation
  44. hexane atoms, bonds, shape, it has it all. Time consuming to draw so... ball and stick representation
  45. symbolicrepresentation
  46. symbolic representationquick and dirty ways to represent molecules
  47. C3H7empiricalformula
  48. C3H7 just the ratio of atoms...empiricalformula
  49. C3H7 ...too many possibilities!C6H14C24H56 12H28 C C15H35C30H70 C27H63 3H7 C18H42 C C21H49formula 33H77 9H21 C Cempirical
  50. C6H14 molecular formula
  51. C6H14exact number of atoms... molecular formula
  52. 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
  53. CH3CH2CH2CH2CH2CH3condensedformula
  54. CH3CH2CH2CH2CH2CH3 bonding sorted...condensedformula
  55. 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
  56. H H H H H H C C C HH C C C H H H H H H structural formula
  57. 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
  58. 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
  59. skeletal(structural) formula
  60. Quick, easy and tells me everything...but do you understand what it means?skeletal(structural) formula
  61. 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
  62. do not use thisrepresentation! H H H H H HH C C C C C C H H H H H H H
  63. do not use thisrepresentation! H H H H H HH C C C C C C H H H H H H H
  64. ...key to this course is understanding / interpreting these symbols ©Lucasfilms
  65. understandingskeletal (structural)formulae
  66. 4 H H C H H H H C C H H H C C HCARBON O H C H C O H H
  67. 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
  68. why? a good question & one we will partially answer later©ultraBobban@Flickr
  69. 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
  70. 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
  71. 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
  72. 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
  73. so how do we drawskeletal formulae?
  74. 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
  75. 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
  76. 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
  77. exampleone H H H C C CH C H H
  78. exampleone remove H H H H C C C C C CH C C H H –H
  79. exampleone H H H C C C C C CH C C H H –H –C now remove C
  80. exampletwo HH C H C C C CH C H H
  81. exampletwo H remove HH C H C C C C C C C C CH C H C –H H
  82. exampletwo HH C H C C C C C C C C CH C H C –H –C H now remove C
  83. examplethree H OH C HH C O H N H H
  84. 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
  85. examplethree This is key. We can only remove C–H bonds. We must leave all others... H O OH C H C C HH C O C O H N H N H H H only remove CH
  86. 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
  87. example very im p ortantfourreverse CO2HHO NH2
  88. examplefourreverse add C to corners CO2H C CO2HHO HO C +C NH2 NH2
  89. 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
  90. 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
  91. 2examplefourreverse H H O H C C HO C O H NH2 neither of the O has OXYGEN two bonds
  92. 2examplefourreverse H H O C C H HO C O O still does not have two bonds. This structure is wrong H NH2 OXYGEN
  93. 4examplefourreverse H H O C C H HO C O CARBON H NH2 C still does not have four bonds. This structure is wrong
  94. Functional Groups pages 16-29 learn them ©"lapolab"@Flickr
  95. CHONC CO2Hexamplefivereverse
  96. 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
  97. 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
  98. OH O OH OOHC OHC C C +C CO2H C C CO2H OH OH OH OH +H O H OH O H OH O C C C O OHC C CH C C C H C C CO2H HO H H OH O HO H H OHexamplesix
  99. 4what have....we learnt? o r ga n i c c h e m i s try is easy if we can count to...
  100. 4what have....we learnt? oh, and it’s really important! o r ga n i c c h e m i s try is easy if we can count to...
  101. before next lecture...readUnit 1 Part 2 ©Noukka Signe@Flickr
  102. Acknowledgmentsgareth(Dr. GJ Rowlands) would to like thank Trevor Kitson Massey University & the 101 students www.massey.ac.nz/~gjrowlan

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