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

1. Chemistry
and living systems
123.101
Gareth Rowlands

2. an
introduction
to
chemistry
and...

3. ...how
it relates
to
living
things

4. the study guide contains
all the information you need

5. my lectures contain
explanation
and 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 resource
for 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 need
organic chemistry?

15. ...because its fun??
why do we need
organic chemistry?

16. why do we need
organic chemistry?
...it keeps me in a job?
Or...

17. if w e want to
understand
living systems...

18. we need to
understand the
individual organs...

19. ...to understand
organs, we have to
understand cells...

20. ...and still we have to
get smaller and
smaller...

21. ...and to do this we must understand the
molecules 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 don't need
Image Credit: NIST/University of Colorado
to get carried away...

23. simple chemical
principles control
biology

24. Me Me Me
11
12
Me Me
Rhodopsin H
11-cis-retinal N
(aldehyde not imine) Opsin
photon
Me Me Me Me
isomers and the Me N
H
visual cascade all trans-retinal
starts VISUAL CASCADE
Opsin

25. $
chemistry
and medicine

26. penicillin G
antibacterial
H H
N S
Me
O N Me
O
CO2H
http://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
CO2H
http://staff.science.uva.nl/~dcslob/lesbrieven/maarten/Bacterien.html

28. F
OH OH O
H N O Ca2+
N
O Me
Me
2
Liptor
cholesterol treatment
US$ 12.9 billion

29. the language
of chemistry...

30. First we need to be
able to communicate
with each other...
the language
of chemistry...

31. There are three ways
of talking about
chemicals...
the language
of chemistry...

32. MACROSCOPIC
bulk
properties
MICROSCOPIC SYMBOLIC
atoms & chemical
molecules formulae

33. macroscopic
representation
physical
properities
©DC Comics

34. macroscopic
representation
physical
properities
obviously important
(if you happen to
get dunked in a vat
of the stuff)
©DC Comics

35. macroscopic
representation
physical
properities
but ignored in this
lecture...lets just
leave it for the lab...
©DC Comics

36. how do we represent
molecules?

37. microscopic
representation

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. symbolic
representation

46. symbolic
representation
quick and dirty ways
to represent
molecules

47. C3H7
empirical
formula

48. C3H7 just the ratio of
atoms...
empirical
formula

49. C3H7 ...too many
possibilities!
C6H14C24H56 12H28
C
C15H35C30H70
C27H63 3H7
C18H42 C C21H49
formula 33H77 9H21
C C
empirical

50. C6H14
molecular
formula

51. C6H14
exact number of
atoms...
molecular
formula

52. C6H14
...but not how they
H H H H
are connected
H H
H H
H 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. CH3CH2CH2CH2CH2CH3
condensed
formula

54. CH3CH2CH2CH2CH2CH3
bonding sorted...
condensed
formula

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 structures
condensed would be confusing!
formula

56. H H H H H H
C C C H
H 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 2
N 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. other
representations
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 this
representation!
H H H H H H
H C C C C C C H
H H H H H H

63. do not use this
representation!
H H H H H H
H 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. understanding
skeletal (structural)
formulae

66. 4
H
H C H
H
H H
C C
H H
H C C H
CARBON
O
H C H
C O
H H

67. 4
H
H C H
H
carbon always has H H
four bonds...
C C
H H
H C C H
CARBON
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
H
HYDROGEN 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
H
HYDROGEN H
C C
H
H H
O
H C H
C O
H H
hydrogen 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 O
OXYGEN H N H
H

72. 3
H H O
NITROGEN 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 draw
skeletal 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 be
all 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 be
all 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 be
all and removed

77. example
one
H H H
C
C C
H C
H H

78. example
one
remove H
H H H
C C
C C C C
H C C
H H
–H

79. example
one
H H H
C C
C C C C
H C C
H H
–H –C
now remove C

80. example
two
H
H C H
C C
C C
H C H
H

81. example
two
H remove H
H C H C
C C C C
C C C C
H C H C
–H
H

82. example
two
H
H C H C
C C C C
C C C C
H C H C
–H –C
H
now remove C

83. example
three
H O
H
C H
H C
O
H N H
H

84. example
three
remove C–H
BUT
H O O leave all others!
H
C H C C H
H C
O C O
H N H N H
H H
only
remove
CH

85. example
three This is key. We
can only remove C–H
bonds. We must leave
all others...
H O O
H
C H C C H
H C
O C O
H N H N H
H H
only
remove
CH

86. example
three
O
H O O OH
H
C H C C H NH2
H 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 ortant
four
reverse
CO2H
HO
NH2

88. example
four
reverse add C to corners
CO2H C CO2H
HO HO C
+C
NH2 NH2

89. example
four
reverse
H H
CO2H C CO2H
HO HO C C CO2H
HO C
+C +H
NH2 NH2
H NH2
Add H to make all C
have four bonds

90. example
four remember C has
reverse four; O has two
bonds and H has
one
H H
CO2H C CO2H
HO 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 H
HO C O HO C O HO C O
H NH2 H NH2 H NH2

91. 2
example
four
reverse
H H O
H
C C
HO C O
H NH2
neither of the O has
OXYGEN
two bonds

92. 2
example
four
reverse
H H O
C C H
HO C O
O still does not have
two bonds. This
structure is wrong
H NH2
OXYGEN

93. 4
example
four
reverse
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. CHO
NC CO2H
example
five
reverse

96. H
CHO H C
CHO
C C H H
C C C
NC CO2H NC C C CO2H
H H H
add C to corners
and H to make four
bonds
example
five
reverse

97. H
CHO H C
CHO
C C H H
C C C
NC 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 O
example N
C C C C H
five H H H O
reverse

98. OH O OH O
OHC 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 C
H C C C H C C CO2H
HO H H OH O HO H H OH
example
six

99. 4
what have
....we learnt?
o r ga n i c c h e m i s try is
easy if we can count to...

100. 4
what 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...
read
Unit 1 Part 2 ©Noukka Signe@Flickr

102. Acknowledgments
gareth
(Dr. GJ Rowlands)
would to
like
thank
Trevor Kitson
Massey University
& the 101 students
www.massey.ac.nz/~gjrowlan