chemistry and living systems

123.101

chemistry and...

an introduction to

...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

Me N HO2C(H2C)2

N Fe N N

Me

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 N H

Rhodopsin 11-cis-retinal (aldehyde not imine) photon Me

Opsin

Me

Me

Me

isomers and the

visual cascade

Me N all trans-retinal Opsin starts VISUAL CASCADE

H

chemistry
and medicine

$

penicillin G
antibacterial
H N O O H S N Me Me CO2H

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

Chemistry explains how penicillin blocks bacterial cell wall synthesis.

penicillin G
antibacterial
H N O O H S N Me Me CO2H

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

F

OH H N O Me N Me

OH

O O Ca2+

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 atoms & molecules

SYMBOLIC chemical 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

representation

symbolic

representation
quick and dirty ways to represent molecules

symbolic

C3H7
empirical formula

C3H7
just the ratio of atoms...

empirical formula

C6H14C24H56 12H28 C C15H35C30H70 C27H63 3H7 C C21H49 C18H42 empirical C C formula 33H77 9H21

C3H7
...too many possibilities!

C6H14
molecular formula

C6H14
exact number of atoms...

molecular formula

C6H14
...but not how they are connected

H H H H H C C H C C C H HH C H H H H H

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

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

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

molecular formula

CH3CH2CH2CH2CH2CH3

condensed formula

CH3CH2CH2CH2CH2CH3
bonding sorted...

condensed formula

CH3CH2CH2CH2CH2CH3
H H H C H H H H C C C C H H H H C H H H O Me Me N N Me N

(CH3)2CHCH(CH3)CH3
O
...but bulky...and some structures would be confusing!

N

condensed 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...

OH N N OMe

H2C

H C

CH

OH H2C H H2C C CH2 H C C N CH HC C H C 2 H N C C CH HC C H C O CH3

structural formula

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 CHO H H C C C H H C H H H CHO H OH CH3 Fischer projection H CH3 Ph Newman projection OH Et H

Et HO H Ph

H

CH3

Sawhorse 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
CARBON

H H C H H

H C C H

H H

H C C H

O H C C O H

H H

4
carbon always has four bonds...

H H C H H

H C C H

H H

CARBON

H C C H

O H C C O H

H H

1
HYDROGEN

H H C H H H C C H O H C C O H H H

H H

H H O C C H H C O H N H H

1
HYDROGEN
hydrogen always has one bond...

H H C H H H C C H O H C C O H H H

H H

H H O C C H H C O H N H H

2
OXYGEN

H H C O H C H H H

H

H

H

C C

H

H C C H O H H

H H O C C H H C O H N H H

3
NITROGEN

H H O C C H O H C H N H H

H H C N H H C C H H

H H C C N H

2
ELECTRONS

C H
O H

N H

2
we’ll explain why in a later lecture...

C H
O H

ELECTRONS

N H

so how do we draw skeletal formulae?

HO HO OH O NH2 OH HO O O HN O HO HO OH OH N H O O Cl H N O O N H O NH2 H N O O O O OH O N H Cl

H N

all

C CH
Vancomycin

and

can be
removed

HO HO OH O NH2 OH HO O O HN O HO HO OH OH N H O O Cl H N O O N H O NH2 H N O O O O Cl

assume each corner is a carbon...
OH O N H

H N

all

C CH
Vancomycin

and

can be
removed

HO HO OH O NH2 OH HO O O HN O HO HO OH OH N H O O Cl H N O O N H O NH2 H N O O O O OH O N H Cl

H N

...and it will always have four bonds.

all

C CH
Vancomycin

and

can be
removed

example

one

H H H C C C H C H H

example

one

remove H

H H H C C C H C H H

C

C

C

C

–H

example

one

H H H C C C H C H H

C

C

C

C

–H
now remove C

–C

example

two

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

example

two

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

remove H

–H

example

two

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

–H
now remove C

–C

example

three
H H H C C O

O H N H H

H

example

three
H H H C C O

O H C C H O N H C H

remove C–H BUT leave all others!

O H N H H

only remove

CH

example

three
H H H C C O

O O H C C H O N H C H NH2 CO2H NH2 OH

O H N H H

only remove

CH

–C
now remove C

example

four
HO

reverse
CO2H NH2

example

four
HO

reverse
CO2H NH2 HO C C

add C to corners

CO2H

+C

NH2

example

four
HO

reverse
CO2H NH2 HO C C CO2H H H C CO2H HO C H NH2

Add H to make all C have four bonds

+C

NH2

+H

example

four
HO

reverse
CO2H NH2 HO C C

remember C has four; O has two bonds and H has one

CO2H

+C

NH2

+H

H H C CO2H HO C H NH2

H H O H C C HO C O H NH2

H H O C C H HO C O H NH2

H H O C C H HO C O H NH2

CHO NC CO2H

example

five

reverse

H CHO NC CO2H CHO C C H H C C C NC C C CO2H H H H
add C to corners and H to make four bonds

H

C

example

five

reverse

H CHO NC
now get three bonds to N; two bonds to O and one to H

CO2H

CHO C C H H C C C NC C C CO2H H H H

H

C

H H C C C

O C H

example

five

reverse

H H C C C O C C C C H N H H H O

what have ....we learnt?

4
or gan ic ch emist ry is easy if we can count to...

what have ....we learnt?

4
oh, and it’s really important!

or gan ic ch emist ry is easy if we can count to...

Acknowledgments

gareth

(Dr. GJ Rowlands)

would to like

Trevor Kitson Massey University & the 101 students
www.massey.ac.nz/~gjrowlan

thank

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