chemistry

and living systems

123.101
 an
introduction
to
chemistry
and...
...how
it relates
to
living
things
the study guide contains
all the information you need
my lectures contain
explanation
and 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 need
organic chemistry?
...because its fun??

why do we need
organic chemistry?
 why do we need
organic chemistry?
...it keeps me in a job?
Or...
if we wan t t o
understand
living systems...
we need to
understand the
individual organs...
...to understand
organs, we have to
understand cells...
...and still we have to
get smaller and
smaller...
...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
 ...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...
 simple chemical
principles control
biology
 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
 $
chemistry
and medicine
 penicillin G
antibacterial
H H
N S
Me
O N Me
O
CO2H

http://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
CO2H

http://staff.science.uva.nl/~dcslob/lesbrieven/maarten/Bacterien.html
 F

OH OH O

H N O Ca2+
N

O Me
Me
2

Liptor
cholesterol treatment
US$ 12.9 billion
the language
of chemistry...
 First we need to be
able to communicate
with each other...

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

the language
of chemistry...
 MACROSCOPIC
bulk
properties

MICROSCOPIC SYMBOLIC
atoms & chemical
molecules formulae
macroscopic
representation
physical
properities

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

©DC Comics
macroscopic
representation
physical
properities

but ignored in this

lecture...lets just
leave it for the lab...

©DC Comics
how do we represent
molecules?
microscopic
representation
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
 symbolic
representation
 symbolic
representation
quick and dirty ways
to represent
molecules
 C3H7
empirical
formula
 C3H7 just the ratio of
atoms...

empirical
formula
 C3H7 ...too many
possibilities!

C6H14C24H56C12H28
C H
C27H63C3H7C30H70
15 35
C 18 H 42 C21H49
formulaC33H77
empirical
C9H21
C6H14
molecular
formula
C6H14
exact number of
atoms...

molecular
formula
 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
CH3CH2CH2CH2CH2CH3

condensed
formula
CH3CH2CH2CH2CH2CH3
bonding sorted...

condensed
formula
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
 H H H H H H
C C C H
H 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 CH CH2
C C
HC C H C N CH2
N 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
 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
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
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
...key to this course
is understanding /
interpreting these
symbols

©Lucasfilms
understanding
skeletal (structural)
formulae
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
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
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
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
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
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
2
C H

O H

N H
ELECTRONS
2
we’ll explain why in a
C H
later lecture...

O H

N H
ELECTRONS
so how do we draw
skeletal 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 be
all 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 be
all 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 be
all and removed
example
one

H H H
C
C C
H C
H H
example
one
remove H

H H H
C C
C C C C
H C C
H H

–H
example
one

H H H
C C
C C C C
H C C
H H

–H –C
now remove C
example
two

H
H C H
C C
C C
H C H
H
example
two

H remove H

H C H C
C C C C
C C C C
H C H C

–H
H
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
example
three

H O
H
C H
H C
O
H N H
H
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
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
example
four
reverse

CO2H
HO
NH2
example
four
reverse add C to corners

CO2H C CO2H
HO HO C

+C
NH2 NH2
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
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
 CHO

NC CO2H

example
five
reverse
 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
 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
 4
what have
....we learnt?

or gan ic ch emist ry is
easy if we can count to...
 4
what have
....we learnt?

oh, and it’s really

important!

or gan ic ch emist ry is
easy if we can count to...
Acknowledgments
gareth
(Dr. GJ Rowlands)
wouldlike to
thank
Trevor Kitson
Massey University
& the 101 students
www.massey.ac.nz/~gjrowlan